Lifetime and strength of adhesive molecular bond clusters between elastic media

With a long-term objective toward a quantitative understanding of cell adhesion, we consider an idealized theoretical model of a cluster of molecular bonds between two dissimilar elastic media subjected to an applied tensile load. In this model, the distribution of interfacial traction is assumed to obey classical elastic equations whereas the rupture and rebinding of individual molecular bonds are governed by stochastic equations. Monte Carlo simulations that combine the elastic and stochastic equations are conducted to investigate the lifetime of the bond cluster as a function of the applied load. We show that the interfacial traction is generally nonuniform and for a given adhesion size the average cluster lifetime asymptotically approaches infinity as the applied load is reduced to below a critical value, defined as the strength of the cluster. The effects of elastic moduli, adhesion size, and rebinding rate on the cluster lifetime and strength are studied under strongly nonuniform distributions of interfacial traction. Although overly simplified in a number of aspects, our model seems to give predictions that are consistent with relevant experimental observations on focal adhesion dynamics.     

RP-Bridged Metal Carbonyl Clusters: Synthesis,Properties, and Reactions

Metal carbonyl clusters possess a complicated chemistry that is only beginning to be understood. One of the main current goals in this area is thus an understanding of their reactivity. This article describes the syntheses and reactions of clusters that contain metal carbonyl fragments bridged by a main-group element. But what is the sense of making such clusters still more complicated by the incorporation of main-group elements? The example of μ₃-bridged carbonyl clusters will serve to show that the main-group element plays an important role in the study of reaction paths; it holds the metal carbonyl fragments together even when the bonds between them are broken in the course of a reaction. Trinuclear μ₃-bridged clusters prove to be small enough to allow the analysis of typical cluster reactions (such as the reversible breaking of metal-metal bonds) in terms of single reaction steps. They are also large enough to provide surprises by their multifaceted reactivity. It will be shown that a detailed study of trinuclear RX-bridged metal carbonyl clusters (X ? N, P, As, Sb, Bi)—a very small part of carbonyl cluster chemistry—can lead to a better understanding of the general reaction principles involved.     

R-P Bridged Clusters: A Study of Metal-Metal Bond Reactivity

Abstract

RP groups are useful cluster constituents: They warrant a detailed analysis of cluster reactions even in those cases where metal-metal bonds break and where, without these linking groups, the clusters would desintegrate.     

Description of collective effects in computer models of water

The dynamics of a system containing 3456 water molecules in a cubic cell with periodic boundary conditions at 297 K was simulated. The time dependence of distances between oxygen atoms was examined for many pairs of molecules. These distances often oscillate around a certain average value over long periods of time (10 ps and longer). These average values can be about 2.8 Å (hydrogen bond) or much larger, up to 12–13 Å and more. This suggests that big groups of molecules are involved in a concerted motion. Lists of hydrogen bonds in 50 configurations divided by an interval of about 1 ps are compared. The average lifetime of a hydrogen bond is about 7 ps. The network of hydrogen bonds is colored according to their lifetimes for one of the configurations. The bonds that live longer than 7 ps form an infinite cluster. The bonds that live longer than 8 ps join to form a great number of finite clusters including several hundreds of nodes (molecules). These clusters contain few closed cycles. Even the bonds that live longer than 20 ps are united into clusters each containing two or three nodes (molecules). The self-diffusion coefficient for molecules involved in long-lived bonds is likely to be slightly smaller than that for molecules which do not participate in these bonds.     

Proton mobility in water clusters

Proton mobility in water occurs quickly according to the so-called Grotthuss mechanism. This process and its elementary reaction steps can be studied in great detail by applying suitable mass spectrometric methods to ionic water clusters. Careful choice of suitable core ions in combination with analysis of cluster size trends in hydrogen/deuterium isotope exchange rates allows for detailed insights into fascinating dynamical systems. Analysis of the experiments has been promoted by extensive and systematic quantum chemical model calculations. Detailed low-energy mechanistic pathways for efficient water rearrangement and proton transfer steps, in particular cases along short preformed "wires" of hydrogen bonds, have been identified in consistency with experimental findings.     

Charge separation in water molecule clusters under thermal fluctuations: 1. Intermolecular interactions

A detailed model of intermolecular interactions in water molecule clusters is developed that makes it possible to describe their disintegration to ions under conditions of finite temperatures by the stochastic simulation methods. In this model, the Hamiltonian in explicit form includes Coulomb, dispersion, exchange, and polarization interactions; many-particle covalent interactions and hydrogen bonds; the interaction of induced dipoles; charge transfers from ions to molecules; and the recombination of counterion charges, as well as the effect of an ion field on the unpaired interactions of molecules. The model is consistent with experimental data on the free energy and entropy of ion hydration in water vapors and the free energy of the hydration of a recombined ion pair.     

Origin of the size-dependence of the polarizability per atom in heterogeneous clusters: The case of AlP clusters

An analysis of the atomic polarizabilities α in stoichiometric aluminum phosphide clusters, computed at the MP2 and density functional theory (DFT) levels, the latter using the B3LYP functional, and partitioned using the classic and iterative versions of the Hirshfeld method, is presented. Two sets of clusters are examined: the ground-state Al(n)P(n) clusters (n=2-9) and the prolate clusters (Al(2)P(2))(N) and (Al(3)P(3))(N) (N≤6). In the ground-state clusters, the mean polarizability per atom, i.e., α/2n, decreases with the cluster size but shows peaks at n=5 and at n=7. We demonstrate that these peaks can be explained by a large polarizability of the Al atoms and by a low polarizability of the P atoms in Al(5)P(5) and Al(7)P(7) due to the presence of homopolar bonds in these clusters. We show indeed that the polarizability of an atom within an Al(n)P(n) cluster depends on the cluster size and the heteropolarity of the bonds it forms within the cluster, i.e., on the charges of the atoms. The polarizabilities of the fragments Al(2)P(2) and Al(3)P(3) in the prolate clusters were found to depend mainly on their location within the cluster. Finally, we show that the iterative Hirshfeld method is more suitable than the classic Hirshfeld method for describing the atomic polarizabilities and the atomic charges in clusters with heteropolar bonds, although both versions of the Hirshfeld method lead to similar conclusions.     

Microscopic simulations of molecular cluster decay: Does the carrier gas affect evaporation?

We develop a kinetic theory of cluster decay by considering the stochastic motion of molecules within an effective potential of mean force (PMF) due to the cluster. We perform molecular dynamics simulations on a 50-atom argon cluster to determine the mean radial force on a component atom and hence the confining potential of mean force. Comparisons between isolated clusters and clusters thermostatted through the presence of a 100-atom helium carrier gas show that the heat bath has only a slight effect upon the PMF. This confirms the validity of calculations of cluster properties using isolated cluster simulations. The PMF is used to calculate the atomic evaporation rate from these clusters, and results are compared with the predictions of the capillarity approximation together with detailed balance, both components of the classical theory of aerosol nucleation.     

Treatment of dilute clusters of methanol and water by ab initio quantum mechanical calculations

Large molecular clusters can be considered as intermediate states between gas and condensed phases, and information about them can help us understand condensed phases. In this paper, ab initio quantum mechanical methods have been used to examine clusters formed of methanol and water molecules. The main goal was to obtain information about the intermolecular interactions and the structure of methanol/water clusters at the molecular level. The large clusters (CH(4)O...(H(2)O)(12) and H(2)O...(CH(4)O)(10)) containing one molecule of one component (methanol or water) and many (12, 10) molecules of the other component were considered. M?ller-Plesset perturbation theory (MP2) was used in the calculations. Several representative cluster geometries were optimized, and nearest-neighbor interaction energies were calculated for the geometries obtained in the first step. The results of the calculations were compared to the available experimental information regarding the liquid methanol/water mixtures and to the molecular dynamics and Monte Carlo simulations, and good agreement was found. For the CH(4)O...(H(2)O)(12) cluster, it was shown that the molecules of water can be subdivided into two classes: (i) H bonded to the central methanol molecule and (ii) not H bonded to the central methanol molecule. As expected, these two classes exhibited striking energy differences. Although they are located almost the same distance from the carbon atom of the central methanol molecule, they possess very different intermolecular interaction energies with the central molecule. The H bonding constitutes a dominant factor in the hydration of methanol in dilute aqueous solutions. For the H(2)O...(CH(4)O)(10) cluster, it was shown that the central molecule of water has almost three H bonds with the methanol molecules; this result differs from those in the literature that concluded that the average number of H bonds between a central water molecule and methanol molecules in dilute solutions of water in methanol is about two, with the water molecules being incorporated into the chains of methanol. In contrast, the present predictions revealed that the central water molecule is not incorporated into a chain of methanol molecules, but it can be the center of several (2-3) chains of methanol molecules. The molecules of methanol, which are not H bonded to the central water molecule, have characteristics similar to those of the methane molecules around a central water molecule in the H(2)O...(CH(4))(10) cluster. The ab initio quantum mechanical methods employed in this paper have provided detailed information about the H bonds in the clusters investigated. In particular, they provided full information about two types of H bonds between water and methanol molecules (in which the water or the methanol molecule is the proton donor), including information about their energies and lengths. The average numbers of the two types of H bonds in the CH(4)O...(H(2)O)(12) and H(2)O...(CH(4)O)(10) clusters have been calculated. Such information could hardly be obtained with the simulation methods.     

Two-photon absorption of hydrogen-bonded octupolar molecule clusters

Charge-transfer octupolar molecules can form clusters in solution through intermolecular hydrogen bonds. In the present work we explore the role of such clustering on two-photon absorption (TPA) spectra assuming 1,3,5-triamino-2,4,6-trinitrobenzene (TATB) as a model system. Using density functional quadratic response theory we examine different cluster structures of TATB dimers, trimers, and tetramers taken from snapshots of molecular dynamics simulations. In comparison with the TPA spectrum of a monomer, significant red shifts of charge-transfer states are predicted for all chosen clusters, which mainly is the result of the distortion of the structures induced by the aggregation. The TPA spectra for dimers and trimers show strong conformation dependence, whereas they turn out to be more stable for tetramers. Enhancements of TPA absorption have also been found for clusters containing less distorted molecules connected by hydrogen bonds.     

Controlling the stability and reversibility of micropillar assembly by surface chemistry

For many natural and synthetic self-assembled materials, adaptive behavior is central to their function, yet the design of such systems has mainly focused on the static form rather than the dynamic potential of the final structure. Here we show that, following the initial evaporation-induced assembly of micropillars determined by the balance between capillarity and elasticity, the stability and reversibility of the produced clusters are highly sensitive to the adhesion between the pillars, as determined by their surface chemistry and further regulated by added solvents. When the native surface of the epoxy pillars is masked by a thin gold layer and modified with monolayers terminated with various chemical functional groups, the resulting effect is a graded influence on the stability of cluster formation, ranging from fully disassembled clusters to an entire array of stable clusters. The observed assembly stabilization effect parallels the order of the strengths of the chemical bonds expected to form by the respective monolayer end groups: NH(2) ≈ OH < COOH < SH. For each functional group, the stability of the clusters can be further modified by varying the carbon chain length of the monolayer molecules and by introducing solvents into the clustered samples, allowing even finer tuning as well as temporal control of disassembly. Using these features together with microcontact printing, we demonstrate straightforward patterning of the microstructured surfaces with clusters that can be erased and regenerated at will by the addition of appropriate solvents. Subtle modifications to surface and solvent chemistry provide a simple way to tune the balance between adhesion and elasticity in real time, enabling structures to be designed for dynamic, responsive behavior.     

吡啶团簇的飞秒光电离和从头计算研究

用飞秒激光电离飞行时间质谱研究了吡啶分子团簇在400 nm波长下的多光子光电离,实验观测到一系列的质子化和非质子化团簇离子.结果表明,质子转移也能发生在弱氢键结合的分子间.通过分析离子峰宽和离子信号强度随气源压力的变化,得到质子化团簇离子来源于大团簇离子的碎裂,而非质子化团簇离子是中性团簇直接电离的结果.从头计算结果表明,吡啶团簇是通过弱氢键C-H…N 结合在一起的,并且团簇离子离解倾向于生成质子化产物.     

Cluster analysis of single particle mass spectra measured at Flushing, NY

ART-2a and a density based cluster method, density based spatial clustering of application with noise (DBSCAN), have been used for classification of the single particle mass spectra measured at New York City. Using too large of a vigilance factor in ART-2a leads to many similar clusters with overlap, and thus a low vigilance factor was used in this study. The DBSCAN method can identify clusters with complex shapes and various sizes, and representative spectra are chosen to identify different particle types within each cluster. The cluster structure of the single particle mass spectra were examined by DBSCAN. Both methods found that the major clusters were sea salt and anthropogenic combustion emissions. The continua in sulfate, potassium and OC particles were found by DBSCAN and a large cluster was formed, while ART-2a broke it into several small clusters without finding this continuum. A detailed discussion of the cluster analysis results including representative mass spectra, size distributions and temporal behavior will be provided.     

GeneMCL in microarray analysis

Accurately and reliably identifying the actual number of clusters present with a dataset of gene expression profiles, when no additional information on cluster structure is available, is a problem addressed by few algorithms. GeneMCL transforms microarray analysis data into a graph consisting of nodes connected by edges, where the nodes represent genes, and the edges represent the similarity in expression of those genes, as given by a proximity measurement. This measurement is taken to be the Pearson correlation coefficient combined with a local non-linear rescaling step. The resulting graph is input to the Markov Cluster (MCL) algorithm, which is an elegant, deterministic, non-specific and scalable method, which models stochastic flow through the graph. The algorithm is inherently affected by any cluster structure present, and rapidly decomposes a graph into cohesive clusters. The potential of the GeneMCL algorithm is demonstrated with a 5,730 gene subset (IGS) of the Van't Veer breast cancer database, for which the clusterings are shown to reflect underlying biological mechanisms.     

Monitoring the dissolution process of metals in the gas phase: reactions of nanoscale Al and Ga metal atom clusters and their relationship to similar metalloid clusters

Formation and dissolution of metals are two of the oldest technical chemical processes. On the atomic scale, these processes are based on the formation and cleavage of metal-metal bonds. During the past 15 years we have studied intensively the intermediates during the formation process of metals, i.e. the formation of compounds containing many metal-metal bonds between naked metal atoms in the center and ligand-bearing metal atoms at the surface. We have called the clusters metalloid or, more generally, elementoid clusters. Via a retrosynthetic route, the many different Al and Ga metalloid clusters which have been structurally characterized allow us to understand also the dissolution process; i.e. the cleavage of metal-metal (M-M) bonds. However, this process can be detected much more directly by the reaction of single metal atom clusters in the gas phase under high vacuum conditions. A suitable tool to monitor the dissolution process of a metal cluster in the gas phase is FT-ICR (Fourier transform ion cyclotron resonance) mass spectrometry. Snapshots during these cleavage processes are possible because only every 1-10 s is there a contact between a cluster molecule and an oxidizing molecule (e.g. Cl2). This period is long, i.e. the formation of the primary product (a smaller metal atom cluster) is finished before the next collision happens. We have studied three different types of reaction:(1) Step-by-step fragmentation of a structurally known metalloid cluster allows us to understand the bonding principle of these clusters because in every step only the weakest bond is broken.(2) There are three oxidation reactions of an Al13(-) cluster molecule with Cl2, HCl and O2 central to this review. These three reactions represent three different reaction types, (a) an exothermic reaction (Cl2), (b) an endothermic reaction (HCl), and (c) a kinetically limited reaction based on spin conservation rules (O2).(3) Finally, we present the reaction of a metalloid cluster with Cl2 in order to show that in this cluster only the central naked metal atoms are oxidized, and a smaller metalloid cluster results containing the entire protecting shell as the primary cluster.All the experimental results, supported by quantum chemical calculations, give a rough idea about the complex reaction cascades which occur during the dissolution and formation of metals. Furthermore, these results cast a critical light on many simplifying and generalizing rules in order to understand the bonding and structure of metal clusters. Finally, the experiments and some recent results provided by physical measurements on a crystalline Ga(84) compound build a bridge to nanoscience; i.e. they may be a challenge for chemistry in the next decades, since it has been shown that only with a perfect orientation of nanoscale metal clusters, e.g. in a crystal, can novel, unexpected properties (e.g. superconducting nanoscale materials) be obtained.     

Glucose interaction with Au,Ag, and Cu clusters: Theoretical investigation

Interactions of α‐D ‐glucose with gold, silver, and copper metal clusters are studied theoretically at the density functional theory (CAM‐B3LYP) and MP2 levels of theory, using trimer clusters as simple catalytic models for metal particles as well as investigating the effect of cluster charge by studying the interactions of cationic and anionic gold clusters with glucose. The bonding between α‐D ‐glucose and metal clusters occurs by two major bonding factors; the anchoring of M atoms (M = Cu, Ag, and Au) to the O atoms, and the unconventional M…H? O hydrogen bond. Depending on the charge of metal clusters, each of these bonds contributes significantly to the complexation. Binding energy calculations indicate that the silver cluster has the lowest and gold cluster has the highest affinity to interact with glucose. Natural bond orbital analysis is performed to calculate natural population analysis and charge transfers in the complexes. Quantum theory of atoms in molecules was also applied to interpret the nature of bonds. © 2012 Wiley Periodicals, Inc.     

Continuum percolation of long lifespan clusters in a simple fluid

We present results on the percolation loci for chemical clusters and physical clusters of long lifespan. Chemical clusters are defined as sets of particles connected through particle-particle bonds that last for a given time tau. Physical clusters are sets of particles that remain close together at every instant for a given period of time tau. By using molecular dynamics simulations of a Lennard-Jones system we obtain the percolation loci at different values of tau as the lines in the temperature-density plane at which the system presents a spanning cluster in 50% of the configurations. We find that the percolation loci for chemical clusters shifts rapidly toward high densities as tau is increased. For moderate values of tau this line converges to the low-density branch of the liquid-solid coexistence curve. This implies that no stable chemical clusters can be found in the fluid phase. In contrast, the percolation loci for physical clusters tend to a limiting line, as tau tends to infinity, which is far from the liquid-solid transition line.     

Structural evolution in polyoxometalates: a DFT study of dimerization processes in Lindqvist and Keggin cluster anions

Density functional theory (DFT) calculations are used to investigate dimerization, by acid condensation, between Lindvist and Keggin cluster anions. When specific addendum atoms are present (notably, Ti, V, Nb, and Cr), these clusters dimerize in the presence of acid via the formation of mu-O linkages. These processes may be viewed as molecular models for the formation of metal-oxygen bonds in the active sites of metalloenzymes, or in materials chemistry, and we here provide detailed information concerning these reactions. For this, DFT calculations are used to provide insight into the mechanism(s) associated with dimerization of Lindqvist clusters, W5MO19(n-) (M = W, Mo, V, Nb, and Ti) in acidic media. In full accord with experimental data, our calculations show that dimerization of Nb and Ti derivatives is thermodynamically favored and that this is not the case for dimerization between Mo, V, and W addendum atoms. In addition, dimerization of PW11TiO40(5-) and SiW11NbO40(5-) to give the corresponding dimers was also calculated to be exothermic. Two possible mechanisms, involved in two competing pathways, are evaluated and discussed. Conclusions are presented concerning the role played by the nature of the metal atoms taking part in M-mu-O-M bond formation. A correlation is established between the relative strengths of specific terminal M=O bonds in monomeric precursors and the tendency of these to form M-mu-O-M bonds.     

The Surface Chemical Bond

Adsorbed particles can be bound chemically to the surface of a solid (chemisorption). Modern variants of electron diffraction and electron spectroscopy now enable us to gain an insight into the nature of such surface chemical bonds, which play a key role in heterogenous catalysis and many other technically important phenomena such as adhesion, lubrication etc. Predominantly localized surface bonds can be compared to the covalent bonds in cluster compounds.