Direct visualisation of lipid bilayer cubic phases using Atomic Force Microscopy

Inverse bicontinuous cubic (Q(II)) phases are nanostructured materials formed by lipid self-assembly. We have successfully imaged thin films of hydrated Q(II) phases from two different systems using AFM. The images show periodic arrays of water channels with spacing and symmetry consistent with published SAXS data on the bulk materials.

Non-stoichiometric oxide and metal interfaces and reactions

We have employed a combination of experimental surface science techniques and density functional calculations to study the reduction of TiO2(110) surfaces through the doping with submonolayer transition metals. We concentrate on the role of Ti adatoms in self doping of rutile and contrast the behaviour to that of Cr. DFT+U calculations enable identification of probable adsorption structures and their spectroscopic characteristics. Adsorption of both metals leads to a broken symmetry and an asymmetric charge transfer localised around the defect site of a mixed localised/delocalised character. Charge transfer creates defect states with Ti 3d character in the band gap at similar to 1-eV binding energy. Cr adsorption, however, leads to a very large shift in the valence-band edge to higher binding energy and the creation of Cr 3d states at 2.8-eV binding energy. Low-temperature oxidation lifts the Ti-derived band-gap states and modifies the intensity of the Cr features, indicative of a change of oxidation state from Cr3+ to Cr4+. Higher temperature processing leads to a loss of Cr from the surface region, indicative of its substitution into the bulk.

Structure of adsorbed organometallic rhodium: model single atom catalysts

We have determined the structure of a complex rhodium carbonyl chloride [Rh(CO)(2)Cl] molecule adsorbed on the TiO2 (110) surface by the normal incidence x-ray standing wave technique. The data show that the technique is applicable to reducible oxide systems and that the dominant adsorbed species is undissociated with Rh binding atop bridging oxygen and to the Cl found close to the fivefold coordinated Ti ions in the surface. A minority geminal dicarboryl species, where Rh-Cl bond scission has occurred, is found bridging the bridging oxygen ions forming a high-symmetry site.

A geometric approach to generalized Stokes conjectures

We consider the Stokes conjecture concerning the shape of extreme two-dimensional water waves. By new geometric methods including a nonlinear frequency formula, we prove the Stokes conjecture in the original variables. Our results do not rely on structural assumptions needed in previous results such as isolated singularities, symmetry and monotonicity. Part of our results extends to the mathematical problem in higher dimensions.

Guanine specific binding at a DNA junction formed by d[CG(5-BrU)ACG]2 with a topoisomerase poison in the presence of Co2+Ions†,‡

The structure of the duplex d[CG(5-BrU)ACG]2 bound to 9-bromophenazine-4-carboxamide has been solved through MAD phasing at 2.0 Å resolution. It shows an unexpected and previously unreported intercalation cavity stabilized by the drug and novel binding modes of Co2+ ions at certain guanine N7 sites. For the intercalation cavity the terminal cytosine is rotated to pair with the guanine of a symmetry-related duplex to create a pseudo-Holliday junction geometry, with two such cavities linked through the minor groove interactions of the N2/N3 guanine sites at an angle of 40°, creating a quadruplex-like structure. The mode of binding of the drug is shown to be disordered, with the major conformations showing the side chain bound to the N7 position of adjacent guanines. The other end of the duplex exhibits a terminal base fraying in the presence of Co2+ ions linking symmetry-related guanines, causing the helices to intertwine through the minor groove. The stabilization of the structure by the intercalating drug shows that this class of compound may bind to DNA junctions as well as duplex DNA or to strand-nicked DNA (‘hemi-intercalated'), as in the cleavable complex. This suggests a structural basis for the dual poisoning of topoisomerase I and II enzymes by this family of drugs.

The anions [(ZrOH(CO3)3)2]6− and [(ZrOH(C2O4)3)2]6−: single crystal X-ray diffraction studies of the complexes guanidinium zirconium carbonate [(C(NH2)3)3ZrOH(CO3)3·H2O]2 and sodium zirconium oxalate Na6(ZrOH(C2O4)3)2·7H2O

The complex [(C(NH2)3)3ZrOH(CO3)3·H2O]2 (A) has been shown by means of a single crystal X-ray diffraction study to contain [C(NH2)3]+ cations and dimeric anions of formulation [(ZrOH(CO3)3)2]6−. The anion is centrosymmetric with each metal being bonded to two bridging OH groups and three chelating CO2−3 ions. The Zr atoms are thus eight coordinate with a dodecahedral environments. The ZrO distances formed by the bridgng OH groups are shorter than those formed through zirconiu carbonate interactions. The non-bonded Zr…Zr distance is 3.47(2) Å. An infrared spectroscopic investigation of A provides data which support the findings of the crystallographic study. Likewise the complex Na6(ZrOH(CO2O4)3)2·7H2O (B) contains the anion [(ZrOH(C2O4)3)2]6−. This anion is structurally related to the anion in A as each Zr atom has an eight-coordinate dodecahedral environment being bonded to two bridging OH groups and three chelating oxalate ligands, but has no imposed crysallographic symmetry. The Zr…Zr non-bonded distance is 3.50(1) Å. The OZrO bridge angles are 69.7(4)° and A and 67.4(3)° in B.

Simultaneous bridge-localized and mixed-valence character in diruthenium radical cations featuring diethynylaromatic bridging ligands

A series of bimetallic ruthenium complexes [{Ru(dppe)Cp*}2(μ-C≡CArC≡C)] featuring diethynylaromatic bridging ligands (Ar = 1,4-phenylene, 1,4-naphthylene, 9,10-anthrylene) have been prepared and some representative molecular structures determined. A combination of UV–vis–NIR and IR spectroelectrochemical methods and density functional theory (DFT) have been used to demonstrate that one-electron oxidation of compounds [{Ru(dppe)Cp*}2(μ-C≡CArC≡C)](HC≡CArC≡CH = 1,4-diethynylbenzene; 1,4-diethynyl-2,5-dimethoxybenzene; 1,4-diethynylnaphthalene; 9,10-diethynylanthracene) yields solutions containing radical cations that exhibit characteristics of both oxidation of the diethynylaromatic portion of the bridge, and a mixed-valence state. The simultaneous population of bridge-oxidized and mixed-valence states is likely related to a number of factors, including orientation of the plane of the aromatic portion of the bridging ligand with respect to the metal d-orbitals of appropriate π-symmetry.

Coverage-dependent molecular tilt of carbon monoxide chemisorbed on Pt{110}: A combined LEED and DFT structural analysis

The adsorption of carbon monoxide on the Pt{110} surface at coverages of 0.5 ML and 1.0 ML was investigated using quantitative low-energy electron diffraction (LEED IV) and density-functional theory (DFT). At 0.5 ML CO lifts the reconstruction of the clean surface but does not form an ordered overlayer. At the saturation coverage, 1.0 ML, a well-ordered p(2×1) superstructure with glide line symmetry is formed. It was confirmed that the CO molecules adsorb on top of the Pt atoms in the top-most substrate layer with the molecular axes tilted by ±22° with respect to the surface normal in alternating directions away from the close packed rows of Pt atoms. This is accompanied by significant lateral shifts of 0.55 Å away from the atop sites in the same direction as the tilt. The top-most substrate layer relaxes inwards by −4% with respect to the bulk-terminated atom positions, while the consecutive layers only show minor relaxations. Despite the lack of long-range order in the 0.5 ML CO layer it was possible to determine key structural parameters by LEED IV using only the intensities of the integer-order spots. At this coverage CO also adsorbs on atop sites with the molecular axis closer to the surface normal (b10°). The average substrate relaxations in each layer are similar for both coverages and consistent with DFT calculations performed for a variety of ordered structures with coverages of 1.0 ML and 0.5 ML.

Eliminating the small-angle component of the scattering calculated for models

A straightforward procedure (assuming spherical symmetry) is described, which enables the unwanted small-angle component of the scattering for a finite model to be calculated. The method may be applied to models of any shape or size. It is illustrated by means of a single polymer chain.

Complete Experimental Structure Determination of the p(3x2)pg Phase of Glycine on Cu{110}

We present a quantitative low energy electron diffraction (LEED) surface-crystallograpic study of the complete adsorption geometry of glycine adsorbed on Cu{110} in the ordered p(3×2) phase. The glycine molecules form bonds to the surface through the N atoms of the amino group and the two O atoms of the de-protonated carboxylate group, each with separate Cu atoms such that every Cu atom in the first layer is involved in a bond. Laterally, N atoms are nearest to the atop site (displacement 0.41 Å). The O atoms are asymmetrically displaced from the atop site by 0.54 Å and 1.18 Å with two very different O-Cu bond lengths of 1.93 Å and 2.18 Å. The atom positions of the upper-most Cu layers show small relaxations within 0.07 Å of the bulk-truncated surface geometry. The unit cell of the adsorbate layer consists of two glycine molecules, which are related by a glide-line symmetry operation. This study clearly shows that a significant coverage of adsorbate structures without this glide-line symmetry must be rejected, both on the grounds of the energy dependence of the spot intensities (LEED-IV curves) and of systematic absences in the LEED pattern.

A simple analysis of thermodynamic properties for classical plasmas: I. theory

By eliminating the short range negative divergence of the Debye–Hückel pair distribution function, but retaining the exponential charge screening known to operate at large interparticle separation, the thermodynamic properties of one-component plasmas of point ions or charged hard spheres can be well represented even in the strong coupling regime. Predicted electrostatic free energies agree within 5% of simulation data for typical Coulomb interactions up to a factor of 10 times the average kinetic energy. Here, this idea is extended to the general case of a uniform ionic mixture, comprising an arbitrary number of components, embedded in a rigid neutralizing background. The new theory is implemented in two ways: (i) by an unambiguous iterative algorithm that requires numerical methods and breaks the symmetry of cross correlation functions; and (ii) by invoking generalized matrix inverses that maintain symmetry and yield completely analytic solutions, but which are not uniquely determined. The extreme computational simplicity of the theory is attractive when considering applications to complex inhomogeneous fluids of charged particles.

The Stokes conjecture for waves with vorticity

We study stagnation points of two-dimensional steady gravity free-surface water waves with vorticity. We obtain for example that, in the case where the free surface is an injective curve, the asymptotics at any stagnation point is given either by the “Stokes corner flow” where the free surface has a corner of 120°, or the free surface ends in a horizontal cusp, or the free surface is horizontally flat at the stagnation point. The cusp case is a new feature in the case with vorticity, and it is not possible in the absence of vorticity. In a second main result we exclude horizontally flat singularities in the case that the vorticity is 0 on the free surface. Here the vorticity may have infinitely many sign changes accumulating at the free surface, which makes this case particularly difficult and explains why it has been almost untouched by research so far. Our results are based on calculations in the original variables and do not rely on structural assumptions needed in previous results such as isolated singularities, symmetry and monotonicity.

Facile production of ordered 3D platinum nanowire networks with “single diamond” bicontinuous cubic morphology

Direct electrochemical templating is carried out using a thin layer of a self-assembled diamond phase (QIID) of phytantriol to create a platinum film with a novel nanostructure. Small-angle X-ray scattering shows that the nanostructured platinum films are asymmetrically templated and exhibit “single diamond” morphology with Fd3m symmetry.

Describing seasonal variability in the distribution of daily effective temperatures for 1985-2009 compared to 1904-1984 for De Bilt, Holland

This paper proposes a method for describing the distribution of observed temperatures on any day of the year such that the distribution and summary statistics of interest derived from the distribution vary smoothly through the year. The method removes the noise inherent in calculating summary statistics directly from the data thus easing comparisons of distributions and summary statistics between different periods. The method is demonstrated using daily effective temperatures (DET) derived from observations of temperature and wind speed at De Bilt, Holland. Distributions and summary statistics are obtained from 1985 to 2009 and compared to the period 1904–1984. A two-stage process first obtains parameters of a theoretical probability distribution, in this case the generalized extreme value (GEV) distribution, which describes the distribution of DET on any day of the year. Second, linear models describe seasonal variation in the parameters. Model predictions provide parameters of the GEV distribution, and therefore summary statistics, that vary smoothly through the year. There is evidence of an increasing mean temperature, a decrease in the variability in temperatures mainly in the winter and more positive skew, more warm days, in the summer. In the winter, the 2% point, the value below which 2% of observations are expected to fall, has risen by 1.2 °C, in the summer the 98% point has risen by 0.8 °C. Medians have risen by 1.1 and 0.9 °C in winter and summer, respectively. The method can be used to describe distributions of future climate projections and other climate variables. Further extensions to the methodology are suggested.

Wave-activity conservation laws for the three-dimensional anelastic and Boussinesq equations with a horizontally homogeneous background flow

Wave-activity conservation laws are key to understanding wave propagation in inhomogeneous environments. Their most general formulation follows from the Hamiltonian structure of geophysical fluid dynamics. For large-scale atmospheric dynamics, the Eliassen–Palm wave activity is a well-known example and is central to theoretical analysis. On the mesoscale, while such conservation laws have been worked out in two dimensions, their application to a horizontally homogeneous background flow in three dimensions fails because of a degeneracy created by the absence of a background potential vorticity gradient. Earlier three-dimensional results based on linear WKB theory considered only Doppler-shifted gravity waves, not waves in a stratified shear flow. Consideration of a background flow depending only on altitude is motivated by the parameterization of subgrid-scales in climate models where there is an imposed separation of horizontal length and time scales, but vertical coupling within each column. Here we show how this degeneracy can be overcome and wave-activity conservation laws derived for three-dimensional disturbances to a horizontally homogeneous background flow. Explicit expressions for pseudoenergy and pseudomomentum in the anelastic and Boussinesq models are derived, and it is shown how the previously derived relations for the two-dimensional problem can be treated as a limiting case of the three-dimensional problem. The results also generalize earlier three-dimensional results in that there is no slowly varying WKB-type requirement on the background flow, and the results are extendable to finite amplitude. The relationship A E =cA P between pseudoenergy A E and pseudomomentum A P, where c is the horizontal phase speed in the direction of symmetry associated with A P, has important applications to gravity-wave parameterization and provides a generalized statement of the first Eliassen–Palm theorem.