Self-assembly of hybrid organic–inorganic polyoxovanadates: functionalised mixed-valent clusters and molecular cages’

Herein we report the intra- and inter-molecular assembly of a {V5O9} subunit. This mixed-valent structural motif can be stabilised as [V5O9(L1–3)4]5−/9− (1–3) by a range of organoarsonate ligands (L1–L3) whose secondary functionalities influence its packing arrangement within the crystal structures. Variation of the reaction conditions results in the dodecanuclear cage structure [V12O14(OH)4(L1)10]4− (4) where two modified convex building units are linked via two dimeric {O4VIV(OH)2VIVO4} moieties. Bi-functional phosphonate ligands, L4–L6 allow the intramolecular connectivity of the {V5O9} subunit to give hybrid capsules [V10O18(L4–6)4]10− (5–7). The dimensions of the electrophilic cavities of the capsular entities are determined by the incorporated ligand type. Mass spectrometry experiments confirm the stability of the complexes in solution. We investigate and model the temperature-dependent magnetic properties of representative complexes 1, 4, 6 and 7 and provide preliminary cell-viability studies of three different cancer cell lines with respect to Na8H2[6]·36H2O and Na8H2[7]·2DMF·29H2O.

Hybrid Organic–Inorganic Polyoxometalates: Functionalization of VIV/ VV Nanosized Clusters to Produce Molecular Capsules

Functionalization of polyoxovanadate clusters using phosphonate and arsonate ligands results in molecular capsules (see structure; green V, purple P, red O, black C). Through the use of extended homologous ligands, these hybrid organic-inorganic capsules can be successively elongated into tubular molecules.

Computational challenges in atomic, molecular and optical physics

Six challenges are discussed. These are the laser-driven helium atom; the laser-driven hydrogen molecule and hydrogen molecular ion: electron scattering (with ionization) from one-electron atoms; the vibrational and rotational structure of molecules such as H-3(+) and water at their dissociation limits; laser- heated clusters; and quantum degeneracy and Bose-Einstein condensation. The first four concern fundamental few-body systems where use of high-performance computing (HPC) is currently making possible accurate modelling from first principles. This leads to reliable predictions and support for laboratory experiment as well as true understanding of the dynamics. Important aspects of these challenges addressable only via a terascale facility are set out. Such a facility makes the last two challenges in the above list meaningfully accessible for the first time, and the scientific interest together with the prospective role for HPC in these is emphasized.

Hydrogen bonding and collective proton modes in clusters and periodic layers of squaric acid: A density functional study

Hydrogen bonding in clusters and extended layers of squaric acid molecules has been investigated by density functional computations. Equilibrium geometries, harmonic vibrational frequencies, and energy barriers for proton transfer along hydrogen bonds have been determined using the Car-Parrinello method. The results provide crucial parameters for a first principles modeling of the potential energy surface, and highlight the role of collective modes in the low-energy proton dynamics. The importance of quantum effects in condensed squaric acid systems has been investigated, and shown to be negligible for the lowest-energy collective proton modes. This information provides a quantitative basis for improved atomistic models of the order-disorder and displacive transitions undergone by squaric acid crystals as a function of temperature and pressure. (C) 2001 American Institute of Physics.

An isothermal-isobaric Langevin thermostat for simulating nanoparticles under pressure: Application to Au clusters

We present a method for simulating clusters or, molecules subjected to an external pressure, which is exerted by a pressure-transmitting medium. It is based on the canoninical Langevin thermostat, but extended in such a way that the Brownian forces are allowed to operate only from the region exterior to the cluster. We show that the frictional force of the Langevin thermostat is linked to the pressure of the reservoir in a unique way, and that this property manifests itself when the particle it acts upon is not pointlike but has finite dimensions. By choosing appropriately the strength of the random forces and the friction coefficient, both temperature and pressure can be controlled independently. We illustrate the capabilities of this new method by calculating the compressibility of small gold clusters under pressure.

The basis for the formation of stable metal clusters on an electrode surface

Metal nanoclusters can be produced cheaply and precisely in an electrochemical environment. Experimentally this method works in some systems, but not in others, and the unusual stability of the clusters has remained a mystery. We have simulated the deposition of the clusters using classical molecular dynamics and studied their stability by grand-canonical Monte Carlo simulations. We find that electrochemically stable clusters occur only in those cases where the two metals involved form stable alloys.

Neutral and Charged 1-Butyl-3-methylimidazolium Triflate Clusters: Equilibrium Concentration in the Vapor Phase and Thermal Properties of Nanometric Droplets

Ground state energy, structure, and harmonic vibrational modes of 1-butyl-3-methylimidazolium triflate ([bmim][Tf]) clusters have been computed using an all-atom empirical potential model. Neutral and charged species have been considered up to a size (30 [bmim][Tf] pairs) well into the nanometric range. Free energy computations and thermodynamic modeling have been used to predict the equilibrium composition of the vapor phase as a function of temperature and density. The results point to a nonnegligible concentration of very small charged species at pressures (P ~ 0.01 Pa) and temperatures (T 600 K) at the boundary of the stability range of [bmim][Tf]. Thermal properties of nanometric neutral droplets have been investigated in the 0 T 700 K range. A near-continuous transition between a liquidlike phase at high T and a solidlike phase at low T takes place at T ~ 190 K in close correspondence with the bulk glass point Tg ~ 200 K. Solidification is accompanied by a transition in the dielectric properties of the droplet, giving rise to a small permanent dipole embedded into the solid cluster. The simulation results highlight the molecular precursors of several macroscopic properties and phenomena and point to the close competition of Coulomb and dispersion forces as their common origin.

Molecular analysis of endothelial progenitor cell (EPC) subtypes reveals two distinct cell populations with different identities

BACKGROUND: The term endothelial progenitor cells (EPCs) is currently used to refer to cell populations which are quite dissimilar in terms of biological properties. This study provides a detailed molecular fingerprint for two EPC subtypes: early EPCs (eEPCs) and outgrowth endothelial cells (OECs). METHODS: Human blood-derived eEPCs and OECs were characterised by using genome-wide transcriptional profiling, 2D protein electrophoresis, and electron microscopy. Comparative analysis at the transcript and protein level included monocytes and mature endothelial cells as reference cell types. RESULTS: Our data show that eEPCs and OECs have strikingly different gene expression signatures. Many highly expressed transcripts in eEPCs are haematopoietic specific (RUNX1, WAS, LYN) with links to immunity and inflammation (TLRs, CD14, HLAs), whereas many transcripts involved in vascular development and angiogenesis-related signalling pathways (Tie2, eNOS, Ephrins) are highly expressed in OECs. Comparative analysis with monocytes and mature endothelial cells clusters eEPCs with monocytes, while OECs segment with endothelial cells. Similarly, proteomic analysis revealed that 90% of spots identified by 2-D gel analysis are common between OECs and endothelial cells while eEPCs share 77% with monocytes. In line with the expression pattern of caveolins and cadherins identified by microarray analysis, ultrastructural evaluation highlighted the presence of caveolae and adherens junctions only in OECs. CONCLUSIONS: This study provides evidence that eEPCs are haematopoietic cells with a molecular phenotype linked to monocytes; whereas OECs exhibit commitment to the endothelial lineage. These findings indicate that OECs might be an attractive cell candidate for inducing therapeutic angiogenesis, while eEPC should be used with caution because of their monocytic nature.

Molecular line emission from a protoplanetary disk irradiated externally by a nearby massive star

Star formation often occurs within or nearby stellar clusters. Irradiation by nearby massive stars can photoevaporate protoplanetary disks around young stars (so-called proplyds) which raises questions regarding the ability of planet formation to take place in these environments. We investigate the two-dimensional physical and chemical structure of a protoplanetary disk surrounding a low-mass (T Tauri) star which is irradiated by a nearby massive O-type star to determine the survivability and observability of molecules in proplyds. Compared with an isolated star-disk system, the gas temperature ranges from a factor of a few (in the disk midplane) to around two orders of magnitude (in the disk surface) higher in the irradiated disk. Although the UV flux in the outer disk, in particular, is several orders of magnitude higher, the surface density of the disk is sufficient for effective shielding of the disk midplane so that the disk remains predominantly molecular in nature. We also find that non-volatile molecules, such as HCN and H2O, are able to freeze out onto dust grains in the disk midplane so that the formation of icy planetesimals, e.g., comets, may also be possible in proplyds. We have calculated the molecular line emission from the disk assuming LTE and determined that multiple transitions of atomic carbon, CO (and isotopologues, 13CO and C18O), HCO+, CN, and HCN may be observable with ALMA, allowing characterization of the gas column density, temperature, and optical depth in proplyds at the distance of Orion (˜400 pc).

A self-learning algorithm for biased molecular dynamics

A new self-learning algorithm for accelerated dynamics, reconnaissance metadynamics, is proposed that is able to work with a very large number of collective coordinates. Acceleration of the dynamics is achieved by constructing a bias potential in terms of a patchwork of one-dimensional, locally valid collective coordinates. These collective coordinates are obtained from trajectory analyses so that they adapt to any new features encountered during the simulation. We show how this methodology can be used to enhance sampling in real chemical systems citing examples both from the physics of clusters and from the biological sciences.

A Molecular Dynamics Study of the Early Stages of Calcium Carbonate Growth

The precipitation of calcium carbonate in water has been examined using a combination of molecular dynamics and umbrella sampling. During 20 ns molecular dynamics trajectories at elevated calcium carbonate concentrations, amorphous particles are observed to form and appear to be composed of misaligned domains of vaterite and aragonite. The addition of further calcium ions to these clusters is found to be energetically favorable and virtually barrierless. By contrast, there is a large barrier to the addition of calcium to small calcite crystals. Thus, even though calcite nanocrystals are stable in solution, at high supersaturations, particles of amorphous material form because this material grows much faster than ordered calcite nanocrystals.

Simulations of Biased Agonists in the β2 Adrenergic Receptor with Accelerated Molecular Dynamics

The biased agonism of the G protein-coupled receptors (GPCRs), where in addition to a traditional G protein-signalling pathway a GPCR promotes intracellular signals though ß-arrestin, is a novel paradigm in pharmacology. Biochemical and biophysical studies have suggested that a GPCR forms a distinct ensemble of conformations signalling through the G protein and ß-arrestin. Here we report on the dynamics of the ß2 adrenergic receptor bound to the ß-arrestin and G protein biased agonists and the empty receptor to further characterize the receptor conformational changes caused by biased agonists. We use conventional and accelerated molecular dynamics (aMD) simulations to explore the conformational transitions of the GPCR from the active state to the inactive state. We found that aMD simulations enable monitoring the transition within the nanosecond timescale while capturing the known microscopic characteristics of the inactive states, such as the ionic lock, the inward position of F6.44, and water clusters. Distinct conformational states are shown to be stabilized by each biased agonist. In particular, in simulations of the receptor with the ß-arrestin biased agonist, N-cyclopentylbutanepherine we observe a different pattern of motions in helix 7 when compared to simulations with the G protein biased agonist, Salbutamol that involves perturbations of the network of interactions within the NPxxY motif. Understanding the network of interactions induced by biased ligands and the subsequent receptor conformational shifts will lead to development of more efficient drugs. © 2013 American Chemical Society

Molecular characterisation of Alternaria linicola and its detection in linseed

Nucleotide sequences of the ribosomal DNA (rDNA) internal transcribed spacers (ITS) 1 and 2 and a 1068 bp section of the beta-tubulin gene divided seven designated species of Alternaria into five taxa. Stemphylium botryosum formed a sixth closely related taxon. Isolates of A. linicola possessed an identical ITS sequence to one group of A. solani isolates, and two clusters of A. linicola isolates, revealed from beta-tubulin gene data to show minor variation, were as genetically similar to isolates of A. solani as they were to each other. We suggest, therefore, that A. linicola falls within the species A. solani. Similar results suggest that A. lini falls within the species A. alternata. RAPD analysis of the total genomic DNA from the Alternaria spp. concurred with the nucleotide sequence analyses. An oligonucleotide primer (ALP) was selected from the rDNA ITS1 region of A. linicola/A. solani. PCR with primers ALP and ITS4 (from a conserved region of the rDNA) amplified a c. 536 bp fragment from isolates of A. linicola and A. solani but not from other Alternaria spp. nor from other fungi which may be associated with linseed. These primers amplified an identical fragment, confirmed by Southern hybridization, from DNA released from infected linseed seed and leaf tissues. These primers have the potential to be used also for the detection of A. solani in host tissues.