The effect of electrode material on the electrochemical formation of porous copper surfaces using hydrogen bubble templating

The electrodeposition of copper onto copper, gold, palladium and glassy carbon (GC) electrodes via a hydrogen bubble templating method is reported. It is found that the composition of the underlying electrode material significantly influences the morphology of the copper electrodeposit. Highly ordered porous structures are achieved with Cu and Au electrodes, however on Pd this order is disrupted and a rough randomly oriented surface is formed whereas on GC a bubble templating effect is not observed. Chronopotentiograms recorded during the electrodeposition process allows bubble formation and detachment from the surface to be monitored where distinctly different potential versus time profiles are observed at the different electrodes. The porous Cu surfaces are characterised with scanning electron microscopy, X-ray diffraction and cyclic voltammetric measurements recorded under alkaline conditions. The latter demonstrates that there are active sites present on electrodeposited copper whose coverage and reactivity depend on the underlying electrode material. The most active Cu surface is achieved at a Pd substrate for both the hydrogen evolution reaction and the catalytic reduction of ferricyanide ions with thiosulphate ions. This demonstrates that the highly ordered porous structure on the micron scale which typifies the morphology that can be achieved with the hydrogen bubbling template method is not required in producing the most effective material.

Ozonolysis of phospholipid double bonds during electrospray ionization : A new tool for structure determination

Phospholipids are the key structural component of cell membranes, and recent advances in electrospray ionization mass spectrometry provide for the fast and efficient analysis of these compounds in biological extracts.1-3 The application of electrospray ionization tandem mass spectrometry (ESI-MS/MS) to phospholipid analysis has demonstrated several key advantages over the more traditional chromatographic methods, including speed and greater structural information.4 For example, the ESI-MS/MS spectrum of a typical phospholipidsparticularly in negative ion modesreadily identifies the carbon chain length and the degree of unsaturation of each of the fatty acids esterified to the parent molecule.5 A critical limitation of conventional ESI-MS/MS analysis, however, is the inability to uniquely identify the position of double bonds within the fatty acid chains. This is especially problematic given the importance of double bond position in determining the biological function of lipid classes.6 Previous attempts to identify double bond position in intact phospholipids using mass spectrometry employ either MS3 or offline chemical derivatization.7-11 The former method requires specialized instrumentation and is rarely applied, while the latter methods suffer from complications inherent in sample handling prior to analysis. In this communication we outline a novel on-line approach for the identification of double bond position in intact phospholipids. In our method, the double bond(s) present in unsaturated phospholipids are cleaved by ozonolysis within the ion source of a conventional ESI mass spectrometer to give two chemically induced fragment ions that may be used to unambiguously assign the position of the double bond. This is achieved by using oxygen as the electrospray nebulizing gas in combination with high electrospray voltages to initiate the formation of an ozoneproducing.

Formation of neutral molecules of potential stellar interest by neutralisation of negative ions in a mass spectrometer - The application of experiment and molecular modelling in concert

This paper is a modified version of a lecture which describes the synthesis, structure and reactivity of some neutral molecules of stellar significance. The neutrals are formed in the collision cell of a mass spectrometer following vertical Franck-Condon one electron oxidation of anions of known bond connectivity. Neutrals are characterised by conversion to positive ions and by extensive theoretical studies at the CCSD(T)/aug-cc-pVDZ//B3LYP/6-31G(d) level of theory. Four systems are considered in detail, viz (i) the formation of linear C-4 and its conversion to the rhombus C-4, (ii) linear C-5 and the atom scrambling of this system when energised, (iii) the stable cumulene oxide CCCCCO, and (iv) the elusive species O2C-CO. This paper is not intended to be a review of interstellar chemistry: examples are selected from our own work in this area. (C) 2002 Elsevier Science Inc. All rights reserved.

Phosphorus-based functional groups as hydrogen bonding templates for rotaxane formation

We report on the use of the hydrogen bond acceptor properties of some phosphorus-containing functional groups for the assembly of a series of [2]rotaxanes. Phosphinamides, and the homologous thio– and selenophosphinamides, act as hydrogen bond acceptors that, in conjunction with an appropriately positioned amide group on the thread, direct the assembly of amide-based macrocycles around the axle to form rotaxanes in up to 60% yields. Employing solely phosphorus-based functional groups as the hydrogen bond accepting groups on the thread, a bis(phosphinamide) template and a phosphine oxide-phosphinamide template afforded the corresponding rotaxanes in 18 and 15 % yields, respectively. X-Ray crystallography of the rotaxanes shows the presence of up to four intercomponent hydrogen bonds between the amide groups of the macrocycle and various hydrogen bond accepting groups on the thread, including rare examples of amide-to-phosphonamide, -thiophosphinamide and -selenophosphinamide groups. With a phosphine oxide-phosphinamide thread, the solid state structure of the rotaxane is remarkable, featuring no direct intercomponent hydrogen bonds but rather a hydrogen bond network involving water molecules that bridge the H-bonding groups of the macrocycle and thread through bifurcated hydrogen bonds. The incorporation of phosphorus-based functional groups into rotaxanes may prove useful for the development of molecular shuttles in which the macrocycle can be used to hinder or expose binding ligating sites for metal-based catalysts.

Formation of blood clot on biomaterial implants influences bone healing

The first step in bone healing is forming a blood clot at injured bones. During bone implantation, biomaterials unavoidably come into direct contact with blood, leading to a blood clot formation on its surface prior to bone regeneration. Despite both situations being similar in forming a blood clot at the defect site, most research in bone tissue engineering virtually ignores the important role of a blood clot in supporting healing. Dental implantology has long demonstrated that the fibrin structure and cellular content of a peri-implant clot can greatly affect osteoconduction and de novo bone formation on implant surfaces. This paper reviews the formation of a blood clot during bone healing in related to the use of platelet-rich plasma (PRP) gels. It is implicated that PRP gels are dramatically altered from a normal clot in healing, resulting conflicting effect on bone regeneration. These results indicate that the effect of clots on bone regeneration depends on how the clots are formed. Factors that influence blood clot structure and properties in related to bone healing are also highlighted. Such knowledge is essential for developing strategies to optimally control blood clot formation, which ultimately alter the healing microenvironment of bone. Of particular interest are modification of surface chemistry of biomaterials, which displays functional groups at varied composition for the purpose of tailoring blood coagulation activation, resultant clot fibrin architecture, rigidity, susceptibility to lysis, and growth factor release. This opens new scope of in situ blood clot modification as a promising approach in accelerating and controlling bone regeneration.

Formation and electron field emission of graphene films grown by hot filament chemical vapor deposition

Graphene films with different structures were catalytically grown on the silicon substrate pre-deposited with a gold film by hot filament chemical vapor deposition under different conditions, where methane, hydrogen and nitrogen were used as the reactive gases. The morphological and compositional properties of graphene films were studied using advanced instruments including field emission scanning electron microscopy, micro-Raman spectroscopy and X-ray photoelectron spectroscopy. The results indicate that the structure and composition of graphene films are changed with the variation of the growth conditions. According to the theory related to thermodynamics, the formation of graphene films was theoretically analyzed and the results indicate that the formation of graphene films is related to the fast incorporation and precipitation of carbon. The electron field emission (EFE) properties of graphene films were studied in a high vacuum system of ∼10-6 Pa and the EFE results show that the turn-on field is in a range of 5.2-5.64 V μm-1 and the maximum current density is about 63 μ A cm-2 at the field of 7.7 V μm-1. These results are important to control the structure of graphene films and have the potential applications of graphene in various nanodevices.

Kinetics of low-pressure, low-temperature graphene growth : toward single-layer, single-crystalline structure

Graphene grown on metal catalysts with low carbon solubility is a highly competitive alternative to exfoliated and other forms of graphene, yet a single-layer, single-crystal structure remains a challenge because of the large number of randomly oriented nuclei that form grain boundaries when stitched together. A kinetic model of graphene nucleation and growth is developed to elucidate the effective controls of the graphene island density and surface coverage from the onset of nucleation to the full monolayer formation in low-pressure, low-temperature CVD. The model unprecedentedly involves the complete cycle of the elementary gas-phase and surface processes and shows a precise quantitative agreement with the recent low-energy electron diffraction measurements and also explains numerous parameter trends from a host of experimental reports. These agreements are demonstrated for a broad pressure range as well as different combinations of precursor gases and supporting catalysts. The critical role of hydrogen in controlling the graphene nucleation and monolayer formation is revealed and quantified. The model is generic and can be extended to even broader ranges of catalysts and precursor gases/pressures to enable the as yet elusive effective control of the crystalline structure and number of layers of graphene using the minimum amounts of matter and energy.

Control of core-shell structure and elemental composition of binary quantum dots

The possibility of initial stage control of the elemental composition and core/shell structure of binary SiC quantum dots by optimizing temporal variation of Si and C incoming fluxes and surface temperatures is shown via hybrid numerical simulations. Higher temperatures and influxes encourage the formation of a stoichiometric outer shell over a small carbon-enriched core, whereas lower temperatures result in a larger carbon-enriched core, Si-enriched undershell, and then a stoichiometric SiC outer shell. This approach is generic and is applicable to a broad range of semiconductor materials and nanofabrication techniques. © 2007 American Institute of Physics.

Structure, bonding state and in-vitro study of Ca–P–Ti film deposited on Ti6Al4V by RF magnetron sputtering

Experimental investigation of functionally graded calcium phosphate-based bio-active films on Ti-6A1-4V orthopaedic alloy prepared in an RF magnetron sputtering plasma reactor is reported. The technique involves concurrent sputtering of Hydroxyapatite (HA) and Ti targets, which results in remarkably enhanced adhesion of the film to the substrate and stability of the interface. The films have been characterized using X-ray diffraction (XRD) and X-ray photoelectron spectroscopy (XPS). The XPS data show that the films are composed of O, Ca, P and Ti, and reveal the formation of O=P groups and hybridization of O-Ca-P. The XRD pattern shows that the Ca-P thin films are of crystalline calcium oxide phosphate (4CaO·P2O5) with preferred orientation varying with processing parameters. High-resolution optical emission spectra show that the emission of CaO is dominant. The CaO, PO and CaPO species are strongly influenced by deposition conditions. The introduction of Ti element during deposition provides a stable interface between bio-inert substrates Ti-6A1-4V and bioactive HA coating. In-vitro cell culturing tests suggest excellent biocompatibility of the Ca-P-Ti films.

Structure and assembly of immature HIV

The major structural components of HIV are synthesized as a 55-kDa polyprotein, Gag. Particle formation is driven by the self-assembly of Gag into a curved hexameric lattice, the structure of which is poorly understood. We used cryoelectron tomography and contrast-transfer-function corrected subtomogram averaging to study the structure of the assembled immature Gag lattice to approximate to 17-angstrom resolution. Gag is arranged in the immature virus as a single, continuous, but incomplete hexameric lattice whose curvature is mediated without a requirement for pentameric defects. The resolution of the structure allows positioning of individual protein domains. High-resolution crystal structures were fitted into the reconstruction to locate protein-protein interfaces involved in Gag assembly, and to identify the structural transformations associated with virus maturation. The results of this study suggest a concept for the formation of nonsymmetrical enveloped viruses of variable sizes.

The antigen 43 structure reveals a molecular velcro-like mechanism of autotransporter-mediated bacterial clumping

Aggregation and biofilm formation are critical mechanisms for bacterial resistance to host immune factors and antibiotics. Autotransporter (AT) proteins, which represent the largest group of outer-membrane and secreted proteins in Gram-negative bacteria, contribute significantly to these phenotypes. Despite their abundance and role in bacterial pathogenesis, most AT proteins have not been structurally characterized, and there is a paucity of detailed information with regard to their mode of action. Here we report the structure–function relationships of Antigen 43 (Ag43a), a prototypic self-associating AT protein from uropathogenic Escherichia coli. The functional domain of Ag43a displays a twisted L-shaped β-helical structure firmly stabilized by a 3D hydrogen-bonded scaffold. Notably, the distinctive Ag43a L shape facilitates self-association and cell aggregation. Combining all our data, we define a molecular “Velcro-like” mechanism of AT-mediated bacterial clumping, which can be tailored to fit different bacterial lifestyles such as the formation of biofilms.

UpaH Is a newly identified autotransporter protein That contributes to biofilm formation and bladder colonization by Uropathogenic Escherichia coli CFT073

Escherichia coli is the primary cause of urinary tract infection (UTI) in the developed world. The major factors associated with virulence of uropathogenic E. coli (UPEC) are fimbrial adhesins, which mediate specific attachment to host receptors and trigger innate host responses. Another group of adhesins is represented by the autotransporter (AT) subgroup of proteins. In this study, we identified a new AT-encoding gene, termed upaH, present in a 6.5-kb unannotated intergenic region in the genome of the prototypic UPEC strain CFT073. Cloning and sequencing of the upaH gene from CFT073 revealed an intact 8.535-kb coding region, contrary to the published genome sequence. The upaH gene was widely distributed among a large collection of UPEC isolates as well as the E. coli Reference (ECOR) strain collection. Bioinformatic analyses suggest β-helix as the predominant structure in the large N-terminal passenger (α) domain and a 12-strand β-barrel for the C-terminal β-domain of UpaH. We demonstrated that UpaH is expressed at the cell surface of CFT073 and promotes biofilm formation. In the mouse UTI model, deletion of the upaH gene in CFT073 and in two other UPEC strains did not significantly affect colonization of the bladder in single-challenge experiments. However, in competitive colonization experiments, CFT073 significantly outcompeted its upaH isogenic mutant strain in urine and the bladder.

Mathematical modelling of intramembranous bone formation during fracture healing

During fracture healing, many complex and cryptic interactions occur between cells and bio-chemical molecules to bring about repair of damaged bone. In this thesis two mathematical models were developed, concerning the cellular differentiation of osteoblasts (bone forming cells) and the mineralisation of new bone tissue, allowing new insights into these processes. These models were mathematically analysed and simulated numerically, yielding results consistent with experimental data and highlighting the underlying pattern formation structure in these aspects of fracture healing.

Structure analysis on the nanoscale : closed WS2 nanoboxes through a cascade of topo- and epitactic processes

Closed WS2 nanoboxes were formed by topotactic sulfidization of a WO3/WO3 center dot 1/3H(2)O intergrowth precursor. Automated diffraction tomography was used to elucidate the growth mechanism of these unconventional hollow structures. By partial conversion and structural analysis of the products, each of them representing a snapshot of the reaction at a given point in time, the overall reaction can be broken down into a cascade of individual steps and each of them identified with a basic mechanism. During the initial step of sulfidization WO3 center dot 1/3H(2)O transforms into hexagonal WO3 whose surface allows for the epitaxial induction of WS2. The initially formed platelets of WS2 exhibit a preferred orientation with respect to the nanorod surface. In the final step individual layers of WS2 coalesce to form closed shells. In essence, a cascade of several topotactic reactions leads to epitactic induction and formation of closed rectangular hollow boxes made up from hexagonal layers.

Influences of molecular structure on co-crystallization of polypyridyl metal complexes.

Heteroleptic complexes of the type \[RuL2L′](PF6)2 (L, L′ = combinations of 1,10-phenanthroline (phen) and 2,2′-bipyridine (bipy)) were found to cocrystallize with \[Ni(phen)3](PF6)2 to produce cocrystals of \[Ni(phen)3]x\[RuL2L′]1–x(PF6)2. In this report we show that the ability of the complexes to cocrystallize is influenced by the number of common ligands between complexes in solution. Supramolecular selection is a phenomenon caused by molecular recognition through which cocrystals can grow from the same solution but contain different ratios of the molecular components. It was found that systems where L = phen displayed less supramolecular selection than systems where L = bipy. With increasing supramolecular selection, the composition of cocrystals was found to vary significantly from the initial relative concentration in the cocrystallizing solution, and therefore it was increasingly difficult to control the final composition of the resultant cocrystals. Consequently, modulation of concentration-dependent properties such as phase was also found to be less predictable with increasing supramolecular selection. Notwithstanding the complication afforded by the presence of supramolecular selection, our results reaffirm the robustness of the \[M(phen)3](PF6)2 structure because it was maintained even when ca. 90% of the complexes in the cocrystals were \[Ru(phen)(bipy)2](PF6)2, which in its pure form is not isomorphous with \[M(phen)3](PF6)2. Experiments between complexes without common ligands, i.e., \[Ru(bipy)3](PF6)2 cocrystallized with \[Ni(phen)3](PF6)2, were found to approach the limit to which molecular recognition processes can be confused into cocrystallizing different molecules to form single cocrystals. For these systems the result was the formation of block-shaped crystals skewered by a needle-shaped crystals.