Metastable Clusters Research Articles

Multimerization and Retention of the Scavenger Receptor SR-B1 in the Plasma Membrane

Scavenger receptor B1 (SR-B1), the main receptor for high-density lipoprotein (HDL), is key in preventing atherosclerosis. It removes cholesterol from HDL, returning the lipid-poor lipoprotein to the circulation. To study the mechanisms controlling SR-B1 dynamics at the plasma membrane and its internalization rate, we developed a single-chain variable fragment (ScFv) antibody to image the receptor in live cells and track the behavior of single SR-B1 molecules. Unlike transferrin receptors, cholera-toxin-binding gangliosides, and bulk membrane markers, SR-B1 was internalized only marginally over hours. Plasmalemmal retention was not attributable to its C-terminal PDZ-binding domain or to attachment to the cortical cytoskeleton. Instead, SR-B1 undergoes multimerization into large metastable clusters that, despite being mobile in the membrane, fail to enter endocytic pathways. SR-B1 multimerization was impaired by mutating its C-terminal leucine zipper and by disrupting actin polymerization, causing rapid receptor internalization. Multimerization and plasmalemmal retention are critical for SR-B1 function.

Metastability of Quantum Droplet Clusters.

We show that metastable ring-shaped clusters can be constructed from two-dimensional quantum droplets in systems described by the Gross-Pitaevskii equations augmented with Lee-Huang-Yang quantum corrections. The clusters exhibit dynamical behavior ranging from contraction to rotation with simultaneous periodic pulsations, or expansion, depending on the initial radius of the necklace pattern and phase shift between adjacent quantum droplets. We show that, using an energy-minimization analysis, one can predict equilibrium values of the cluster radius that correspond to rotation without radial pulsations. In such a regime, the clusters evolve as metastable states, withstanding abrupt variations in the underlying scattering lengths and keeping their azimuthal symmetry in the course of evolution, even in the presence of considerable perturbations.

Electric Potentials of Metastable Salt Clusters

Electric potentials and fields experienced by the ions in small metastable NaCl clusters and cubic crystals in vacuum and aqueous electrolyte solutions are used to characterize features underlying condensed-phase nucleation. The range of electrostatic potentials and fields experienced by NaCl nanocrystals and metastable clusters is analyzed using point charges and quantified as a function of particle size and charge state. We show how the potentials and fields of these crystals can be classified into various subgroups corresponding to corners, edges, faces, and interior sites. The differences between the interior and face potentials are correlated with the interfacial surface energy. This, in turn, influences cluster free energies and their corresponding populations in solution. As a result, the nucleation rate is correlated to these potentials through the formalism of classical nucleation theory. Additionally, we consider the importance of representation of the charge density, comparing point charge and ...

Identity ordering and metastable clusters in fluids with random interactions.

We use Langevin dynamics simulations to study dense two-dimensional systems of particles where all binary interactions are different in the sense that each interaction parameter is characterized by a randomly chosen number. We compare two systems that differ by the probability distributions from which the interaction parameters are drawn: uniform (U) and exponential (E). Both systems undergo neighborhood identity ordering and form metastable clusters in the fluid phase near the liquid-solid transition, but the effects are much stronger in E than in U systems. Possible implications of our results for the control of the structure of multicomponent alloys are discussed.

Nonequilibrium steady states, coexistence, and criticality in driven quasi-two-dimensional granular matter.

Nonequilibrium steady states of vibrated inelastic frictionless spheres are investigated in quasi-two-dimensional confinement via molecular dynamics simulations. The phase diagram in the density-amplitude plane exhibits a fluidlike disordered and an ordered phase with threefold symmetry, as well as phase coexistence between the two. A dynamical mechanism exists that brings about metastable traveling clusters and at the same time stable clusters with anisotropic shapes at low vibration amplitude. Moreover, there is a square bilayer state which is connected to the fluid by BKTHNY-type two-step melting with an intermediate tetratic phase. The critical behavior of the two continuous transitions is studied in detail. For the fluid-tetratic transition, critical exponents of γ[over ̃]=1.73,η_{4}≈1/4, and z=2.05 are obtained.

A Systematic Study on Bond Activation Energies of NO, N2, and O2 on Hexamers of Eight Transition Metals

AbstractCatalytic bond activation pathways of diatomic molecules on small metal clusters have been studied by density functional theory calculations. The focus of this study is dissociation of NO, N2, and O2 on hexamers of eight transition metals (Ni, Cu, Rh, Pd, Ag, Ir, Pt, and Au). For all the 24 cases, the lowest energy structures at the molecular‐adsorption state, bond dissociation transition state (TS), and dissociative‐adsorption state were identified by a systematic procedure. At TS of 20 cases, the transition metal hexamer moiety took a different shape from bare transition metal hexamers. The results support the importance of metastable cluster structures in catalytic activity, recently proposed in several catalytic systems. Furthermore, using the obtained dataset, a simple linear regression analysis was made to explore the applicability of the Brønsted‐Evans‐Polanyi principle to flexible metal cluster catalysts.

Discrete Sequential Information Coding: Heteroclinic Cognitive Dynamics.

Discrete sequential information coding is a key mechanism that transforms complex cognitive brain activity into a low-dimensional dynamical process based on the sequential switching among finite numbers of patterns. The storage size of the corresponding process is large because of the permutation capacity as a function of control signals in ensembles of these patterns. Extracting low-dimensional functional dynamics from multiple large-scale neural populations is a central problem both in neuro- and cognitive- sciences. Experimental results in the last decade represent a solid base for the creation of low-dimensional models of different cognitive functions and allow moving toward a dynamical theory of consciousness. We discuss here a methodology to build simple kinetic equations that can be the mathematical skeleton of this theory. Models of the corresponding discrete information processing can be designed using the following dynamical principles: (i) clusterization of the neural activity in space and time and formation of information patterns; (ii) robustness of the sequential dynamics based on heteroclinic chains of metastable clusters; and (iii) sensitivity of such sequential dynamics to intrinsic and external informational signals. We analyze sequential discrete coding based on winnerless competition low-frequency dynamics. Under such dynamics, entrainment, and heteroclinic coordination leads to a large variety of coding regimes that are invariant in time.

On the Binding Free Energy and Molecular Origin of Sickle Cell Hemoglobin Aggregation.

Protein aggregation is associated with various diseases, including Alzheimer and Parkinson as well as sickle cell disease (SCD). From a molecular point of view, protein aggregation depends on a complex balance of electrostatic and hydrophobic interactions mediated by water. An impressive manifestation of the importance of this balance concerns the human hemoglobin (HbA) mutant, HbS (sickle cell Hb), where a single substitution at the 6th position of HbA β-chains, from glutamic acid to valine, causes the polymerization of deoxygenated HbS (deoxy-HbS), responsible for SCD. HbS polymerization is believed to occur via a double nucleation mechanism initiated by the formation of HbS fibers (homogeneous nucleation), followed by fiber growth. Furthermore, it was proposed that homogeneous nucleation proceeds through a two-step mechanism, where metastable dense clusters play the role of nucleation precursors. Thus, hindering or delaying the formation of such precursors could represent a potential SCD therapeutic route. Here, we study, through molecular dynamics, the binding free energy and protein-protein contacts involved in the deoxy-HbS dimer aggregation and stabilization process. A binding free energy of ∼-14.0 ± 1 kcal/mol is estimated from a one-dimensional potential of mean force. Analysis of protein-protein interactions shows that both electrostatic and van der Waals interactions play an important role on the aggregation of HbS. With respect to the former, our results indicate that aggregation is largely favored by the formation of salt bridges (SB), mostly, Lys-Glu, Lys-Asp, and Heme-Lys SB, which outweigh electrostatic repulsions involving similar residues. Thus, our results suggest that a potential antisickling drug could be one with the ability to weaken or hinder the formation of a few SB between carboxylate and ammonium groups.

Site-Specific Doping of Mn2+ in a CdS-Based Molecular Cluster

The synthesis and characterization of a CdS-based molecular cluster, [Cd10S4(SPh)16]4– (Cd10), with site-specific substitution of Cd2+ with Mn2+ impurities are reported. The formation of the Cd10 cluster from the smaller [Cd4(SPh)10]2– (Cd4) cluster involves a metastable intermediate cluster, [Cd8S(SPh)16]2– (Cd8), that is detected by electrospray ionization mass spectrometry (ESI-MS). To account for this unexpected intermediate, we propose a complex equilibrium between Cd4, Cd8, and Cd10 exists that we exploit to introduce Mn2+ impurities at both core and surface cation sites of the Cd10 lattice. We demonstrate through two synthetic procedures that differ only in the sequence in which Mn2+ is introduced to the reaction dictates its speciation in the cluster. Introducing dopants at an early stage of the synthesis prevents full conversion of Cd8 to Cd10; however, it yields core doped Cd10 clusters. Addition of Mn2+ ions after the preparation of Cd10 yields only surface doped clusters. The composition of th...

Revisiting building block ordering of long-period stacking ordered structures in Mg–Y–Al alloys

Long-period stacking-ordered (LPSO) structures in Mg alloys have received considerable attention in the past decade due to their unique crystallographic features, but their precise structures are still not fully established. In this work, the 18R LPSO structure in two Mg–Y–Al alloys, in both cast and homogenized conditions, is systematically investigated using atomic-scale high-angle annular dark-field scanning transmission electron microscopy and density functional theory. Our observations reveal that there exist at least four types of building clusters—three of them being metastable and hitherto unreported—in the 18R structure in the as-cast condition. Each of the four types of building clusters comprises three Al–Y cubes that are connected by one Mg–Y cube. After annealing at 530–550 °C for 47–48 h, the three metastable building clusters transform to a stable configuration that is characterized by the Al6Y8 L12-type building cluster. These transformations are validated by first-principles calculations. Based on the experimental observations and computational results, the evolution of the building clusters in the 18R structure is elaborated.

Computational Design of Clusters for Catalysis.

When small clusters are studied in chemical physics or physical chemistry, one perhaps thinks of the fundamental aspects of cluster electronic structure, or precision spectroscopy in ultracold molecular beams. However, small clusters are also of interest in catalysis, where the cold ground state or an isolated cluster may not even be the right starting point. Instead, the big question is: What happens to cluster-based catalysts under real conditions of catalysis, such as high temperature and coverage with reagents? Myriads of metastable cluster states become accessible, the entire system is dynamic, and catalysis may be driven by rare sites present only under those conditions. Activity, selectivity, and stability are highly dependent on size, composition, shape, support, and environment. To probe and master cluster catalysis, sophisticated tools are being developed for precision synthesis, operando measurements, and multiscale modeling. This review intends to tell the messy story of clusters in catalysis.

Structural Polymorphism as the Result of Kinetically Controlled Self-Assembly.

Traditionally, the goal of self-assembly and supramolecular chemistry is to engineer an equilibrium structure with a desired geometry and functionality; this is achieved through careful choice of molecular monomers, growth conditions, and substrate. Supramolecular assemblies produced under nonequilibrium conditions, in contrast, can form metastable structures with conformations quite different from those accessible in equilibrium self-assembly. The study of nonequilibrium growth of clusters potentially impacts the study of nucleation in atmospheric aerosols, nucleation in organic crystallization, and mesoscale organization for systems ranging from biological molecules to molecular electronics. In our experiments, we prepare surface monolayers of small organic and organometallic molecules through direct injection of a solution onto a substrate in high vacuum. During this process, the rapid evaporation of small solution droplets in high vacuum can lead to nonequilibrium growth conditions. The resulting structures are then characterized by scanning tunneling microscopy. Among the features observed in these experiments are cyclic, hydrogen-bonded pentamers. For carboxylic acids, the two-molecule ring dimer is the common binding motif. Large, cyclic hydrogen-bonded systems are uncommon, especially so for rings with five members. Despite this, pentagonal clusters appear to be a general phenomenon for systems containing adjacent strong and weak hydrogen-bonding elements on five-member aromatic rings. Regular pentamers have been observed as metastable structures for ferrocenecarboxylic acid, indole-2-carboxylic acid, and isatin (1-H-indole-2,3-dione). Electronic structure calculations confirm the relative stability of these structures with respect to the dimer or catemer conformations which are observed in the solid-state crystal structures. For ferrocenecarboxylic acid, cyclic pentamers undergo further self-assembly, resulting in long-range order in conjunction with local 5-fold rotational symmetry. This system is the first reported self-assembled molecular quasicrystal, and it remains the only example of a hydrogen-bonded quasicrystal. This supramolecular structure forms as a result of the cocrystallization of hydrogen-bonded cyclic pentamers with intercalated molecular dimers. The shared bonding to a single dimer is responsible for locking the adjacent pentamers in specific distances and orientations, which produces the quasicrystal. Careful analysis of experimental data provides evidence that, in some cases, metastable clusters are formed in solution and then subsequently adsorb on the surface. This is a unusual mechanism for supramolecular assembly, and it has important implications for understanding questions in crystal growth, namely: what the initial stages of crystal growth are as molecules are first precipitating from solution; what role the solvent plays in determining crystal structure; and whether solvent-mediated clustering is important in the broader phenomenon of solid-state polymorphism.

Metastable clusters and channels formed by active particles with aligning interactions

We introduce a novel model for active particles with short-range position-dependent aligning interactions and study their behaviour in crowded environments using numerical simulations. When only active particles are present, we observe a transition from a gaseous state to the emergence of metastable clusters as the level of orientational noise is reduced. When passive particles are also present, we observe the emergence of a network of metastable channels.

Reversible Self-Assembly of Glutathione-Coated Gold Nanoparticle Clusters via pH-Tunable Interactions.

Nanoparticle (NP) clusters with diameters ranging from 20 to 100 nm are reversibly assembled from 5 nm gold (Au) primary particles coated with glutathione (GSH) in aqueous solution as a function of pH in the range of 5.4 to 3.8. As the pH is lowered, the GSH surface ligands become partially zwitterionic and form interparticle hydrogen bonds that drive the self-limited assembly of metastable clusters in <1 min. Whereas clusters up to 20 nm in size are stable against cluster-cluster aggregation for up to 1 day, clusters up to 80 nm in size can be stabilized over this period via the addition of citrate to the solution in equal molarity with GSH molecules. The cluster diameter may be cycled reversibly by tuning pH to manipulate the colloidal interactions; however, modest background cluster-cluster aggregation occurs during cycling. Cluster sizes can be stabilized for at least 1 month via the addition of PEG-thiol as a grafted steric stabilizer, where PEG-grafted clusters dissociate back to starting primary NPs at pH 7 in fewer than 3 days. Whereas the presence of excess citrate has little effect on the initial size of the metastable clusters, it is necessary for both the cycling and dissociation to mediate the GSH-GSH hydrogen bonds. In summary, these metastable clusters exhibit significant characteristics of equilibrium self-limited assembly between primary particles and clusters on time scales where cluster-cluster aggregation is not present.

Non-intuitive clustering of 9,10-phenanthrenequinone on Au(111).

The direct injection of a 9,10-phenanthrenequinone in tetrahydrofuran solution on a Au(111) substrate in high vacuum results in the formation of metastable clusters with a non-intuitive structure. Metastable, rectangular tetramers of this molecule form in which the net molecular dipoles all orient toward the center of the cluster. This structure does not allow for additional hydrogen bonding and thus the origin of its metastability is not clear. We compare this feature to other structures observed on this surface, as well as those formed during the deposition of 9-fluorenone, which does not exhibit this anomalous clustering behavior.

Effect of Ligand Attachment on the C–I Bond Dissociation Process on Aluminum Nanoclusters: A DFT Investigation

The influence of the ligand attachment on the activation process of carbon halogen bond on small sized aluminum nanoclusters are investigated using density functional theory. Attaching suitable ligand to metal clusters is among the widely popular techniques often used by experimentalists in order to stabilize metastable clusters. In depth theoretical investigations have shown that based on the jellium configuration of the cluster, attaching an electron withdrawing ligand can either make a cluster more reactive toward the C–I dissociation or may convert the cluster relatively inert. The alteration of the activation barriers and other associated parameters due to ligand attachment are included in this paper along with additional calculations and explanations. The study also shows that even the reaction parameters of specific magic clusters can be significantly altered via ligand attachment. The activation process of small molecules on metal clusters are of crucial importance for the development of material ...

The nucleation of protein crystals as a race against time with on- and off-pathways

High supersaturation levels are a necessary but insufficient condition for the crystallization of purified proteins. Unlike most small molecules, proteins can take diverse aggregation pathways that make the outcome of crystallization assays quite unpredictable. Here, dynamic light scattering and optical microscopy were used to show that the nucleation of lysozyme crystals is preceded by an initial step of protein oligomerization and by the progressive formation of metastable clusters. Because these steps deplete the concentration of soluble monomers, the probability of obtaining protein crystals decreases as time progresses. Stochastic variations of the induction time are thus amplified to a point where fast crystallization can coexist with unyielding regimes in the same conditions. With an initial hydrodynamic radius of ∼100 nm, the metastable clusters also promote the formation of protein crystals through a mechanism of heterogeneous nucleation. Crystal growth (on-pathway) takes place in parallel with cluster growth (off-pathway). The Janus-faced influence of the mesoscopic clusters is beneficial when it accelerates the formation of the first precrystalline nuclei and is detrimental as it depletes the solution of protein ready to crystallize. Choosing the right balance between the two effects is critical for determining the success of protein crystallization trials. The results presented here suggest that a mild oligomerization degree promotes the formation of a small number of metastable clusters which then catalyze the nucleation of well differentiated crystals.

Effect of Neutron Irradiation on SiC Etching in KOH Melt

The effect of reactor neutron irradiation on the SiC crystals etching rate in KOH melt has been investigated. It is shown that at high doses of irradiation (1019 - 1021 neutrons/cm2) the SiC etching rate sharply increases, especially in the [0001] Si direction, leading to essential reduction of orientation anisotropy of polar {0001} faces etching. The increased rate of irradiated crystals etching remains after high-temperature annealing, up to the temperatures of 1400 – 1600 °C. The results are explained by the presence of meta-stable clusters of radiation defects which are the centers of increased chemical activity in the irradiated crystals.

Nucleation and thermal stability of an icosahedral nanophase during the early crystallization stage in Zr-Co-Cu-Al metallic glasses

The early stage of crystallization in amorphous phases is a key step in the overall microstructural evolution. In a Zr-based amorphous alloy the formation of metastable nanophase was observed at the earliest crystallization stage, with an ultra-high nucleation density of 6.5 × 1024 m−3 and a size of ∼1–2 nm. The nanophase has an icosahedral structure and exhibits an extremely high thermal stability up to 150 K above the crystallization onset. The chemical and structural heterogeneity in the early stage of the glass crystallization were observed using high-resolution high-angle annular dark-field (HAADF) scanning transmission electron microscopy (STEM), which can be applied to study materials with atomic resolution. A nucleation kinetics analysis of the nanophase formation accounts for the high product number density and indicates a low interface energy value between the metastable clusters and the amorphous matrix, σa,i of 14 mJ/m2. The thermal stability and resistance to size change by growth or coarsening are attributed to a stalled growth due to solute depletion and the low σa,i value. With the high nucleation rate and the low barrier, it is remarkable that the kinetics follow conventional nucleation theory.

Recombination of ions of a dense ion plasma in a fluorine atmosphere

A new effect leading to the slowing of recombination in a weakly nonideal ion plasma is considered. The solvation of ions is included in the explanation of the results from studying a gas discharge afterglow in a fluorine atmosphere. It is shown that recombination in such a system is slowed in comparison to the standard relationships for ideal plasma. The formation and composition of cluster ions in such a medium are considered. The relationship between the variation in the kinetics of recombination and the course of the process according to a complicated mechanism with the intermediate formation of metastable cluster pairs is established. A quantitative model is built and a formula allowing us to describe the recombination rate over a wide range of parameters of the medium is obtained. It is shown that the proposed model is in good agreement with the experimental data.