Rearrangement Of Clusters Research Articles

Ion Size Influence on the Ar Solvation Shells of M+–C6F6 Clusters (M = Na, K, Rb, Cs)

The size-specific influence of alkali metal ions in the gradual transition from cluster rearrangement to solvation dynamics is investigated by means of molecular dynamics simulations for alkali metal cation-hexafluorobenzene systems, M(+)-C(6)F(6) (M = Na, K, Rb and Cs), surrounded by Ar atoms. To analyze such transition, different small aggregates of the M(+)-C(6)F(6)-Ar(n) (n = 1, ..., 30) type and M(+)-C(6)F(6) clusters solvated by about 500 Ar atoms are considered. The Ar-C(6)F(6) interaction contribution has been described using two different formalisms, based on the interaction decomposition in atom-bond and in atom-effective atom terms, which have been applied to study the small aggregates and to investigate the Ar solvated M(+)-C(6)F(6) clusters, respectively. The selectivity of the promoted phenomena from the M(+) ion size and their dependence from the number of Ar atoms is characterized.

Investigation on the atomic structural evolution of as-prepared and annealed ZrCuAl metallic glasses

Abstract

Surface-enhanced absorption by self-organized silver films with aciniform-like nanoaggregates at elevated temperatures

Morphological evolution of silver nanocomposite films prepared by the wet colloidal route and surface-enhanced phenomena on aggregate nanostructures evolved during annealing were investigated. Dramatic changes in morphologies of particles and pores incurred by rearragement, coarsening, premelting, and dewetting of the silver clusters at different concentrations (i.e., mass thicknesses). At a higher mass thickness, the morphological transitions from self-organized nanoaggregates with aciniform pattern at 300 °C to elongated and coarsened particles with circular holes at 400 °C to island clusters at 500 °C occurred in the films. The peculiar absorption with a much redder and broader surface plasmon feature, which gone far beyond the theoretical prediction, induced by the formation of aciniform nanoaggregates embedded in the porous polymer matrix at a critical mass thickness of 9.6 nm during partial degradation of the PVP polymer and rearrangement of silver clusters at 300 °C. The surface-enhanced absorption was dramatically reduced by the elemination of the aggregate nanostructures and the spontaneous formation of the silver nanoisland film at the dewetting temperature of 500 °C.

Ar Solvation Shells in K+–HFBz: From Cluster Rearrangement to Solvation Dynamics

The effect of some leading intermolecular interaction components on specific features of weakly bound clusters involving an aromatic molecule, a closed shell ion, and Ar atoms is analyzed by performing molecular dynamics simulations on potential energy surfaces properly formulated in a consistent way. In particular, our investigation focuses on the three-dimensional Ar distributions around the K(+)-hexafluorobenzene (K(+)-HFBz) dimer, in K(+)-HFBz-Ar(n) aggregates (n ≤ 15), and on the gradual evolution from cluster rearrangement to solvation dynamics when ensembles of 50, 100, 200, and 500 Ar atoms are taken into account. Results indicate that the Ar atoms compete to be placed in such a way to favor an attractive interaction with both K(+) and HFBz, occupying positions above and below the aromatic plane but close to the cation. When these positions are already occupied, the Ar atoms tend to be placed behind the cation, at larger distances from the center of mass of HFBz. Accordingly, three different groups of Ar atoms are observed when increasing n, with two of them surrounding K(+), thus, disrupting the K(+)-HFBz equilibrium geometry and favoring the dissociation of the solvated cation when the temperature increases. The selective role of the leading intermolecular interaction components directly depending on the ion size repulsion is discussed in detail by analyzing similarities and differences on the behavior of the Ar-solvated K(+)-HFBz and Cl(-)-Bz aggregates.

A DFT and crystallographic reinvestigation of the [L 2RuC 2B 7H 9] and [L 3RuC 2B 7H 9] ‘ hypercloso’ and closo systems

A reinvestigation of the [L 2RuC 2B 7H 9] ‘ hypercloso’ 10-vertex cluster compounds, where L = PPh 3, PEt 3, which were first reported some 30 years ago, has been carried out. At that time no single-crystal X-ray diffraction structural analysis was obtained for the compounds and their description as featuring a ‘ hypercloso’ cluster constitution, where the descriptor hypercloso is defined as being a closed polyhedral structure possessing n skeletal bonding electron pairs, where n is the number of vertices, was largely based on a combination of chemical and NMR spectroscopic evidence, together with the application of Polyhedral Skeletal Electron Pair Theory as it was then understood. Reported here is a single-crystal X-ray diffraction study of the PPh 3 ligated ruthenacarborane allied with density functional calculations (DFT). The cluster structure is shown to be of isocloso geometry, albeit with considerable distortion towards isonido. Addition of excess PMe 3 leads to the formation of an [(PMe 3) 3RuC 2B 7H 9] species of conventional 10-vertex closo geometry but it undergoes a cluster rearrangement, resulting in a different isomer to that originally proposed.

Construction of tissue micro array from prostate needle biopsies using the vertical clustering re‐arrangement technique

Tissue microarray (TMA) allows for simultaneous rapid expression analysis of multiple molecular targets in many tissue specimens. TMA's are specifically in demand for the screening for diagnostic and prognostic markers in prostate cancer (PC). Consequently, TMAs from prostate needle biopsy (PNB) material taken at diagnosis before any treatment commenced are in demand. However, since PNB contain only limited amount of tumor arranged within a very thin tissue core, TMA construction from PNB is problematic. Archival PNB from 30 PC patients with variable Gleason scores (6-10) and % of cores involvement (30-90%) were used. Following selection of representative cores, the paraffin blocks were melted. Each core was sectioned into equal parts of 3-4 mm in length. For each case, a group of fragments was then re-embedded in a vertical orientation. Using Manual TMA Apparatus, 2 mm cores from each of the vertically rearranged fragments were harvested. Sections (4 µm) were stained with H&E and with high-molecular weight cytokeratin (HMWCK), PIN-cocktail (p63 + p504S), and PSA immunohistochemical stains. A TMA from PNB with a capacity of 80 serial 4 µm sections was constructed. In all cases, identical tumor and neighboring tissue morphology (atrophic changes and high-grade prostatic intra-epithelial neoplasia) with no loss of tissue was evident. The vertical clustering re-arrangement (VCR) technique is suitable for large scale construction of TMA blocks from PNB maintaining the morphological and immunohistochemical characteristics of the original samples. This method is promising both in terms of archival tissue preservation and biomarkers research.

Chromothripsis is a common mechanism driving genomic rearrangements in primary and metastatic colorectal cancer

BackgroundStructural rearrangements form a major class of somatic variation in cancer genomes. Local chromosome shattering, termed chromothripsis, is a mechanism proposed to be the cause of clustered chromosomal rearrangements and was recently described to occur in a small percentage of tumors. The significance of these clusters for tumor development or metastatic spread is largely unclear.ResultsWe used genome-wide long mate-pair sequencing and SNP array profiling to reveal that chromothripsis is a widespread phenomenon in primary colorectal cancer and metastases. We find large and small chromothripsis events in nearly every colorectal tumor sample and show that several breakpoints of chromothripsis clusters and isolated rearrangements affect cancer genes, including NOTCH2, EXO1 and MLL3. We complemented the structural variation studies by sequencing the coding regions of a cancer exome in all colorectal tumor samples and found somatic mutations in 24 genes, including APC, KRAS, SMAD4 and PIK3CA. A pairwise comparison of somatic variations in primary and metastatic samples indicated that many chromothripsis clusters, isolated rearrangements and point mutations are exclusively present in either the primary tumor or the metastasis and may affect cancer genes in a lesion-specific manner.ConclusionsWe conclude that chromothripsis is a prevalent mechanism driving structural rearrangements in colorectal cancer and show that a complex interplay between point mutations, simple copy number changes and chromothripsis events drive colorectal tumor development and metastasis.

A 3D-analysis of cluster formation and dynamics of the X−-benzene (X = F, Cl, Br, I) ionic dimer solvated by Ar atoms

The specific influence of X(-) ions (X = F,Cl, Br, I) in the solvation process of halide-benzene (X(-)-Bz) ionic heterodimers by Ar atoms is investigated by means of molecular dynamic (MD) simulations. The gradual evolution from cluster rearrangement to solvation dynamics is discussed by considering ensembles of n (n = 1-15 and n = 30) Ar atoms around the X(-)-Bz stable ionic dimers. The potential energy surfaces employed are based on an atom/ion-atom and atom/ion-bond decomposition, which has been developed previously by some of the authors. The outcome of the dynamics is analyzed by employing radial distribution functions (RDF) and tridimensional (3D) probability densities.

Application of MLPA assay to characterize unsolved α-globin gene rearrangements

α-thalassemia belongs to those inherited diseases in which large genomic deletions/duplications represent a significant proportion of causative mutations. Until recently, large α-globin gene cluster rearrangements have been mainly detected by gap-PCR and Southern blotting, methods that have significant drawbacks. We tested the recently developed multiplex ligation-dependent probe amplification (MLPA) assay for deletional screening of the α-globin gene cluster in a cohort of 25 individuals suspected of having α-globin alteration(s), in which no or doubtful mutations had been found using conventional methods. In 13 out of 18 α-thalassemia carriers and in all 5 patients with HbH we found the causative α-globin defects. In 2 thalassemia intermedia patients, carriers of heterozygous β-globin mutations, the co-inheritance of homozygous α-genes triplication was detected. MLPA results were subsequently confirmed by real-time PCR. This study shows that MLPA can effectively identify different and unknown types of α-globin gene rearrangements, to allow characterizing previously unsolved α-thalassemia genotypes.

Irreversible atomic rearrangements in elastically deformed metallic glasses

The atomistic behaviour of elastically deformed Ni 50Zr 50 metallic glasses obtained at different quenching rates was studied by molecular dynamics. Deformation induces the irreversible rearrangement of atomic clusters of various chemical composition. The relative amount of Ni and Zr atoms participating in irreversible rearrangements depends on the quenching rate. The rearrangements are related to the potential energy difference between initial and final cluster configurations, connected in turn with volume effects. The role of local structures was investigated by focusing the attention on icosahedral coordination. The numerical findings indicate that icosahedral clusters become involved in rearrangements only after the average strain has overcome a certain value. Therefore, at small elastic strain only small atomic clusters with spatial organization different from the icosahedral one rearrange. The different involvement in rearrangements of different local structures is tentatively related to apparent local strain.

A 3D-analysis of the Cl−–benzene dimer solvation by Ar atoms

The solvation of the Cl−–benzene (Cl−–Bz) aggregate by Ar atoms has been investigated employing molecular dynamics (MD) simulations. The gradual evolution from cluster rearrangement to solvation dynamics is discussed by considering ensembles of n (n = 1,...,30) Ar atoms around the Cl−–Bz clusters. The energetic of the solvated cluster is decomposed as a sum of pairs (including both the Ar–Ar and the Cl−–Ar terms), Cl−–Bz and Ar–Bz interactions and their relative contributions are analyzed as a function of the cluster size. The geometrical distribution of Ar atoms around Cl−–Bz is investigated in terms of radial distribution functions (RDF), bidimensional (2D) angular distributions and tridimensional (3D) probability densities. The variation on the spatial distribution of the Ar atoms around Cl−–Bz when the Ar number increases is investigated from a novel prospective, employing spherical coordinates of the solvent atoms within an inertial reference frame. Isomerization processes are also studied.

ChemInform Abstract: Substituted Monocarbon Carboranes Involving Thiol, Disulfide or Dimethyl Sulfide Ligands.

New sulfur-substituted derivatives of closo- and nido-monocarbon carboranes have been synthesised for their potential application in 10B neutron capture therapy of tumours. The compounds 7-Me3N-4(6)-HS-nido-7-CB10H11 and 4,4′-, 6,6′- and 4,6′-S2(7-Me3N-nido-7-CB10H11)2 were obtained by Friedel-Crafts substitution of 7-Me3N-nido-7-CB10H12 with S2Cl2; high-temperature boron insertion and methylation of the products gave 1-Me2N-2-Me2S-closo-1-CB11H10 as a result of a cluster rearrangement process. Its structure has been confirmed by X-ray crystallography.

The molecular characteristics and genetic background of VanB phenotype-van A genotype vancomycin resistant Enterococcus

Objective To investigate the structure of Tn1546 like elements,the molecular features and genetic background of VanB phenotype-vanA genotype VREs and to explain the difference between phenotype and genotype. Methods Twenty-one VREs were collected in Beijing Hospital from March 2008 to January 2009. Etest was used to determin MICs of ten antibiotics. PCR product sequencing, PFGE and MLST were performed to study the molecular features and genetic background of the 21 VREs. Results All VREs were vanA genotype, but 3 of them( 14. 3% ) exhibited the VanB phenotype. Based on PFGE analysis, 21 VREs belonged to 9 different patterns. Six STs were identified by MLST analysis. The analysis of the structure of Tn1546 like elements showed the deletion of vanY, vanZ and the insertion of ISEfa4 in orf2-vanR intergenic region may be related to the formation of VanB phenotype-wanA genotype. Conclutions VanB phenotype-vanA genotype VREs were rarely found in China. The results of vanA cluster rearrangements could partly explain the causes of difference between phenotype and genotype. Key words: Vancomycin resistance; Enterococcus; Genotype; Electrophoresis,gel,pulsed-field; Bacterial typing techniques

Atomic structure in Al-doped multicomponent bulk metallic glass

The atomic structure of Zr 48 Cu 45 Al 7 bulk metallic glass is investigated by Monte Carlo simulation upon synchrotron radiation data. Strong bonding and dense cluster packing caused by the minor addition of Al are two key local structural features that may retard the rearrangement of atoms and clusters during quench, facilitating glass formation. Based on this work, we present a strategy to reveal the relationship between local structure and glass-forming ability by focusing on the structural features caused by doping atoms from the atomic and cluster scales.

Dielectric relaxation processes in stoichiometric Ge:Sb:Te amorphous films

The aim of this work is to investigate the relaxation processes of amorphous thin films by dielectric spectroscopy in films with stoichiometric compositions Ge 1Sb 4Te 7, Ge 1Sb 2Te 4 and Ge 2Sb 2Te 5. Experimental results fit well to an empiric Havriliak–Negami model. Two relaxation processes have been observed in all materials: an alpha relaxation in the low frequency range (0.1–10 kHz) and a secondary beta relaxation in the high frequency range (100 kHz–10 MHz). The temperature dependence of the relaxation time for the alpha relaxations is described by the Vogel–Fulcher–Tammann relation with Vogel temperature increasing from 280 K for Ge 1Sb 4Te 7 to 291 K for Ge 2Sb 2Te 5. The secondary beta or Johari–Goldstein relaxation observed in the high frequency range has an Arrhenius-type dependence and approximately the same activation energy 0.422 ± 0.009 eV for all studied Ge:Sb:Te films. A plausible explanation for relaxation processes observed in Ge:Sb:Te films can be related to cooperative and local rearrangements of molecules or clusters of GeTe and/or Sb 2Te 3.

Direct Visualization of Two-State Dynamics on Metallic Glass Surfaces Well Below Tg

Direct atomically resolved observation of dynamics deep in the glassy regime has proved elusive for atomic and molecular glasses. Studies below the glass transition temperature Tg are especially rare due to long waiting times required to observe dynamics. Here, we directly visualize surface glass dynamics deep in the glassy regime. We analyze scanning tunneling microscopy movies of the surface of metallic glasses with time resolution as fast as 1 min and extending up to 1000 min. Rearrangements of surface clusters occur almost exclusively by two-state hopping (P3-state ≈ 0.06). All clusters are compact structures with a width of 2−8 atomic spacings along the surface plane. The two-state dynamics is both spatially and temporally heterogeneous. We estimate an average activation free energy of 14 kBT for surface clusters.

A dielectric study of the structure of propylene glycol

The dielectric spectra of propylene glycol over the frequency and temperature ranges 10 mHz–75 GHz and 175–423 K, respectively, were analyzed using the Dissado-Hill cluster model. A correlation between relaxation processes of breaking and formation of intermolecular H-bonds in clusters was obtained. A correlation of fluctuation processes of synchronous exchange of molecules between neighboring clusters corresponded to the redistribution of H-bonds between them. The Dissado-Hill theory was used to determine the integral relaxation times, n DH and m DH parameters and calculate the mean dipole moments of propylene glycol clusters and the energy characteristics of processes of their rearrangement. The mean dipole moments of clusters (23617–18.65 D) were compared with those of molecules in the liquid phase (3.67–3.03 D). The apparent activation enthalpy of processes of cluster rearrangements decreased from 141.8 to 25.2 kJ/mol, the activation energy decreased from 46.03 to 18.47 kJ/mol, and the energy of orientation dipole-dipole interactions, from 3.78 to 3.45 kJ/mol as the temperature increased.

GC Content-Based Pan-Pox Universal PCR Assays for Poxvirus Detection

Chordopoxviruses of the subfamily Chordopoxvirinae, family Poxviridae, infect vertebrates and consist of at least eight genera with broad host ranges. For most chordopoxviruses, the number of viral genes and their relative order are highly conserved in the central region. The GC content of chordopoxvirus genomes, however, evolved into two distinct types: those with genome GC content of more than 60% and those with a content of less than 40% GC. Two standard PCR assays were developed to identify chordopoxviruses based on whether the target virus has a low or high GC content. In design of the assays, the genus Avipoxvirus, which encodes major rearrangements of gene clusters, was excluded. These pan-pox assays amplify DNA from more than 150 different isolates and strains, including from primary clinical materials, from all seven targeted genera of chordopoxviruses and four unclassified new poxvirus species. The pan-pox assays represent an important advance for the screening and diagnosis of human and animal poxvirus infections, and the technology used is accessible to many laboratories worldwide.

Characterization of Protein Aggregation via Intrinsic Fluorescence Lifetime

Aggregation plays an integral role in multivalent protein-carbohydrate interactions, Alzheimer's and other amyloid-related diseases, and infection response. Efforts to apply controlled aggregation in toxin sensors have been made. We have developed a label-free intrinsic fluorescence lifetime assay that uniquely can monitor aggregation processes in real time without interference from precipitation. Fluorescence decay curves were measured with high precision at 1 s time intervals following addition of a glycodendrimer to a lectin-containing solution. Changes in the fluorescence intensity and lifetime signified formation of complexes. However, these changes were not associated with the initial lectin-sugar binding events. Rather, they appeared to be caused by clustering and subsequent conformational rearrangement of the lectins. Studies were conducted with mannose-functionalized polyamidoamine (PAMAM) dendrimers of the second through sixth generations and Concanavalin A. The apparent rate constant, when expressed on a per-mannose basis, increased with dendrimer generation, particularly in going from the fourth to the sixth generation. However, the identical fluorescence decay waveforms for saturating amounts of dendrimer suggested that all of the glycodendrimer generations studied reach a comparable state of aggregation. Although self-quenching of tryptophan resonances that was induced by clustering was monitored in this study, the reported method is not limited to such and is viable for numerous binding studies.

A Bimetallic Iron–Nickel Cluster from the Reaction of Nickelocene with a Pentairon Carbonyl Carbide Cluster Complex

The new bimetallic Fe–Ni carbide containing cluster complex, Fe4Ni(Cp)2(CO)10(μ5-C), 4 was afforded by metal–metal exchange and metal cluster rearrangement processes in the reaction of Fe5(μ5-C)(CO)15, 1, with NiCp2 at 80 °C. A minor product Fe5(Cp)2(CO)10(μ5-C), 5, was also obtained from this reaction which contains no nickel and is a di-Cp substituted derivative of 1. Both compounds were characterized by a combination of IR, 1H NMR, mass spectrometry, elemental and single crystal X-ray diffraction analyses. Compound 4 consists of an open Fe4Ni(μ5-C) cluster framework with a carbide ligand where one iron atom bridges a butterfly arrangement of one nickel and three iron atoms.