Thallium pi-cation complexation by calix[4]tubes: Tl-205 NMR and X-ray evidence

Thallium cation complexation by calix[4]tubes has been investigated by a combination of (TI)-T-205, H-1 NMR and ES MS demonstrating the solution formation of a dithallium complex in which the cations are held in the calix[4]arene cavities. In addition, the structure of the complex has been determined in the solid state revealing the cations to be held exclusively by pi-cation interactions. Furthermore, this crystal structure has been used as the basis for molecular dynamics simulations to confirm that binding of the smaller K+ cation in the calix[4]tube cryptand like array occurs via the axial route featuring a g-cation intermediate.

Ocean acoustic models for low frequency propagation in 2D and 3D environments

In this paper we are mainly concerned with the development of efficient computer models capable of accurately predicting the propagation of low-to-middle frequency sound in the sea, in axially symmetric (2D) and in fully 3D environments. The major physical features of the problem, i.e. a variable bottom topography, elastic properties of the subbottom structure, volume attenuation and other range inhomogeneities are efficiently treated. The computer models presented are based on normal mode solutions of the Helmholtz equation on the one hand, and on various types of numerical schemes for parabolic approximations of the Helmholtz equation on the other. A new coupled mode code is introduced to model sound propagation in range-dependent ocean environments with variable bottom topography, where the effects of an elastic bottom, of volume attenuation, surface and bottom roughness are taken into account. New computer models based on finite difference and finite element techniques for the numerical solution of parabolic approximations are also presented. They include an efficient modeling of the bottom influence via impedance boundary conditions, they cover wide angle propagation, elastic bottom effects, variable bottom topography and reverberation effects. All the models are validated on several benchmark problems and versus experimental data. Results thus obtained were compared with analogous results from standard codes in the literature.

Influence of the solvent on the self-assembly of a modified amyloid beta peptide fragment. II. NMR and computer simulation investigation

The conformation of a model peptide AAKLVFF based on a fragment of the amyloid beta peptide A beta 16-20, KLVFF, is investigated in methanol and water via solution NMR experiments and Molecular dynamics computer simulations. In previous work, we have shown that AAKLVFF forms peptide nanotubes in methanol and twisted fibrils in water. Chemical shift measurements were used to investigate the solubility of the peptide as a function of concentration in methanol and water. This enabled the determination of critical aggregation concentrations, The Solubility was lower in water. In dilute solution, diffusion coefficients revealed the presence of intermediate aggregates in concentrated solution, coexisting with NMR-silent larger aggregates, presumed to be beta-sheets. In water, diffusion coefficients did not change appreciably with concentration, indicating the presence mainly of monomers, coexisting with larger aggregates in more concentrated solution. Concentration-dependent chemical shift measurements indicated a folded conformation for the monomers/intermediate aggregates in dilute methanol, with unfolding at higher concentration. In water, an antiparallel arrangement of strands was indicated by certain ROESY peak correlations. The temperature-dependent solubility of AAKLVFF in methanol was well described by a van't Hoff analysis, providing a solubilization enthalpy and entropy. This pointed to the importance of solvophobic interactions in the self-assembly process. Molecular dynamics Simulations constrained by NOE values from NMR suggested disordered reverse turn structures for the monomer, with an antiparallel twisted conformation for dimers. To model the beta-sheet structures formed at higher concentration, possible model arrangements of strands into beta-sheets with parallel and antiparallel configurations and different stacking sequences were used as the basis for MD simulations; two particular arrangements of antiparallel beta-sheets were found to be stable, one being linear and twisted and the other twisted in two directions. These structures Were used to simulate Circular dichroism spectra. The roles of aromatic stacking interactions and charge transfer effects were also examined. Simulated spectra were found to be similar to those observed experimentally.(in water or methanol) which show a maximum at 215 or 218 nm due to pi-pi* interactions, when allowance is made for a 15-18 nm red-shift that may be due to light scattering effects.

Characterising the variability and extremes of the stratospheric polar vortices using 2D moment analysis

The mean state, variability and extreme variability of the stratospheric polar vortices, with an emphasis on the Northern Hemisphere vortex, are examined using 2-dimensional moment analysis and Extreme Value Theory (EVT). The use of moments as an analysis to ol gives rise to information about the vortex area, centroid latitude, aspect ratio and kurtosis. The application of EVT to these moment derived quantaties allows the extreme variability of the vortex to be assessed. The data used for this study is ECMWF ERA-40 potential vorticity fields on interpolated isentropic surfaces that range from 450K-1450K. Analyses show that the most extreme vortex variability occurs most commonly in late January and early February, consistent with when most planetary wave driving from the troposphere is observed. Composites around sudden stratospheric warming (SSW) events reveal that the moment diagnostics evolve in statistically different ways between vortex splitting events and vortex displacement events, in contrast to the traditional diagnostics. Histograms of the vortex diagnostics on the 850K (∼10hPa) surface over the 1958-2001 period are fitted with parametric distributions, and show that SSW events comprise the majority of data in the tails of the distributions. The distribution of each diagnostic is computed on various surfaces throughout the depth of the stratosphere, and shows that in general the vortex becomes more circular with higher filamentation at the upper levels. The Northern Hemisphere (NH) and Southern Hemisphere (SH) vortices are also compared through the analysis of their respective vortex diagnostics, and confirm that the SH vortex is less variable and lacks extreme events compared to the NH vortex. Finally extreme value theory is used to statistically mo del the vortex diagnostics and make inferences about the underlying dynamics of the polar vortices.

NMR studies of the conformational effect of single and double 3'-S-phosphorothiolate substitutions within deoxythymidine trinucleotides

NMR spectroscopy has been used to investigate the conformational effects of single and two consecutive 3′-S-phosphorothiolate modifications within a deoxythymidine trinucleotide. The presence of a single 3′-phosphorothioate modification shifts the conformation of the sugar ring it is attached to, from a mainly south to north pucker; this effect is also transmitted to the 3′-neighbour deoxyribose. This transmission is thought to be caused by favourable stacking of the heterocyclic bases. Similar observations have been made previously by this group. When two adjacent modifications are present, the conformations of the attached deoxyribose rings are again shifted almost completely to the north, however, there is no transmission to the 3′ deoxyribose ring. Base proton chemical shift analysis and molecular modelling have been used to aid elucidation of the origin of this feature. The observation for the dimodified sequence is consistent with our previously reported results for a related system in which spaced modifications are more thermodynamically stable than consecutive ones.

The power of NMR.: in two and three dimensions

Soon after its discovery in the 1950s, NMR had become an indispensable tool fr chemists. In the 1970s and 1980s, the power of the technique was extended from one dimension to two and even three dimensions, opening up exciting applkications in both chemistry and biochemistry. the success of one dimensional. high-resolution NMR stems from the unique insights that it can provide about molecular structure. The chemical shift of a nucleus gives invaluable information abut the chemical environment in which that nucleus is located, Coupling interactions between hydorgen nuclei, as revealed by characteristic splitting patterns inthe 1H-NMR spectrum, provide informaton about the loaction of one group of hydorgen atoms relative to others inthe molecule. And the nuclearf Overhauser effect (nOe) can shed light on molecular stereochemistry.

Self-assembled molecular complexes and coordination polymers of CdII, hexamine, and monocarboxylates: structural analysis and theoretical studies of supramolecular interactions

Four new cadmium(II) complexes [Cd-2(bz)(4)(H2O)(4)(mu 2-hmt)]center dot Hbz center dot H2O (1), [Cd-3(bz)(6)(H2O)(6)(mu 2-hmt)(2)]center dot 6H(2)O (2), [Cd(pa)(2)(H2O)(mu(2)-hmt)](n) (3), and {[Cd-3(ac)(6)(H2O)(3)(mu(3)-hmt)(2)]center dot 6H(2)O}(n) (4) with hexamine (hmt) and monocarboxylate ions, benzoate (bz), phenylacetate (pa), or acetate (ac) have been synthesized and characterized structurally. Structure determinations reveal that 1 is dinuclear, 2 is trinuclear, 3 is a one-dimensional (1D) infinite chain, and 4 is a two-dimensional (2D) polymer with fused hexagonal rings consisting of Cd-II and hmt. All the Cd-II atoms in the four complexes (except one CdII in 2) possess seven-coordinate pentagonal bipyramidal geometry with the various chelating bidentate carboxylate groups in equatorial sites. One of the CdII ions in 2, a complex that contains two monodentate carboxylates is in a distorted octahedral environment. The bridging mode of hmt is mu 2- in complexes 1-3 but is mu 3- in complex 4. In all complexes, there are significant numbers of H-bonds, C-H/pi, and pi-pi interactions which play crucial roles in forming the supramolecular networks. The importance of the noncovalent interactions in terms of energies and geometries has been analyzed using high level ab initio calculations. The effect of the cadmium coordinated to hmt on the energetic features of the C-H/pi interaction is analyzed. Finally, the interplay between C-H/pi and pi-pi interactions observed in the crystal structure of 3 is also studied.

Fulvalene titanium and zirconium complexes: synthesis and NMR study of phosphanido-, alkyl-, and alkynyl-derivatives. X-ray crystal structures of [{Ti(η5−C5H5)(μ−PPH2)}2{μ−(η5−C5H4−η5−C5H4)}] and [{Zr(η5−C5H5)(μ−C≡CSiMe3)}2{μ−(η5−C5H4−η5−C5H4)}]

Reaction of with one or two equivalents of LiPPh2 afforded the new phosphanidometal(III) complexes . Reaction of 2 with LiC≡CSiMe3 led to the diamagnetic zirconium(III) alkynyl derivative [{Zr(C5H5)(μ−C≡CSiMe3)}2(μ−η5−C5H4−η5−C5H4], 7. Alkylation of 6 with LiCH2CMe2Ph gave [{Zr(η5−C5H5)(CH2CMe2Ph)2}2{μ−(η5−C5H4)}], 8. A detailed NMR study of complexes 3 and 4 allowed the observation of the spectral behaviour of the eight different fulvalene protons through their coupling to the 31P nucleus. The fluxional behaviour of complex 7 was studied by dynamic DNMR, and kinetic parameters for the σ-π-conversion of the alkynyl ligand were determined. The molecular structures of complexes 3 and 7 were determined by X-ray diffraction methods.

Combined transcriptomic-(1)H NMR metabonomic study reveals yhat monoethylhexyl phthalate stimulates adipogenesis and glyceroneogenesis in human adipocytes

Adipose tissue is a major storage site for lipophilic environmental contaminants. The environmental metabolic disruptor hypothesis postulates that some pollutants can promote obesity or metabolic disorders by activating nuclear receptors involved in the control of energetic homeostasis. In this context, monoethylhexyl phthalate (MEHP) is of particular concern since it was shown to activate the peroxisome proliferator-activated receptor γ (PPARγ) in 3T3-L1 murine preadipocytes. In the present work, we used an untargeted, combined transcriptomic-(1)H NMR-based metabonomic approach to describe the overall effect of MEHP on primary cultures of human subcutaneous adipocytes differentiated in vitro. MEHP stimulated rapidly and selectively the expression of genes involved in glyceroneogenesis, enhanced the expression of the cytosolic phosphoenolpyruvate carboxykinase, and reduced fatty acid release. These results demonstrate that MEHP increased glyceroneogenesis and fatty acid reesterification in human adipocytes. A longer treatment with MEHP induced the expression of genes involved in triglycerides uptake, synthesis, and storage; decreased intracellular lactate, glutamine, and other amino acids; increased aspartate and NAD, and resulted in a global increase in triglycerides. Altogether, these results indicate that MEHP promoted the differentiation of human preadipocytes to adipocytes. These mechanisms might contribute to the suspected obesogenic effect of MEHP.

Data assimilation for state and parameter estimation: application to morphodynamic modelling

Data assimilation is predominantly used for state estimation; combining observational data with model predictions to produce an updated model state that most accurately approximates the true system state whilst keeping the model parameters fixed. This updated model state is then used to initiate the next model forecast. Even with perfect initial data, inaccurate model parameters will lead to the growth of prediction errors. To generate reliable forecasts we need good estimates of both the current system state and the model parameters. This paper presents research into data assimilation methods for morphodynamic model state and parameter estimation. First, we focus on state estimation and describe implementation of a three dimensional variational(3D-Var) data assimilation scheme in a simple 2D morphodynamic model of Morecambe Bay, UK. The assimilation of observations of bathymetry derived from SAR satellite imagery and a ship-borne survey is shown to significantly improve the predictive capability of the model over a 2 year run. Here, the model parameters are set by manual calibration; this is laborious and is found to produce different parameter values depending on the type and coverage of the validation dataset. The second part of this paper considers the problem of model parameter estimation in more detail. We explain how, by employing the technique of state augmentation, it is possible to use data assimilation to estimate uncertain model parameters concurrently with the model state. This approach removes inefficiencies associated with manual calibration and enables more effective use of observational data. We outline the development of a novel hybrid sequential 3D-Var data assimilation algorithm for joint state-parameter estimation and demonstrate its efficacy using an idealised 1D sediment transport model. The results of this study are extremely positive and suggest that there is great potential for the use of data assimilation-based state-parameter estimation in coastal morphodynamic modelling.

Observational tracking of the 2D structure of coronal mass ejections between the sun and 1 AU

The Solar TErrestrial RElations Observatory (STEREO) provides high cadence and high resolution images of the structure and morphology of coronal mass ejections (CMEs) in the inner heliosphere. CME directions and propagation speeds have often been estimated through the use of time-elongation maps obtained from the STEREO Heliospheric Imager (HI) data. Many of these CMEs have been identified by citizen scientists working within the SolarStormWatch project ( www.solarstormwatch.com ) as they work towards providing robust real-time identification of Earth-directed CMEs. The wide field of view of HI allows scientists to directly observe the two-dimensional (2D) structures, while the relative simplicity of time-elongation analysis means that it can be easily applied to many such events, thereby enabling a much deeper understanding of how CMEs evolve between the Sun and the Earth. For events with certain orientations, both the rear and front edges of the CME can be monitored at varying heliocentric distances (R) between the Sun and 1 AU. Here we take four example events with measurable position angle widths and identified by the citizen scientists. These events were chosen for the clarity of their structure within the HI cameras and their long track lengths in the time-elongation maps. We show a linear dependency with R for the growth of the radial width (W) and the 2D aspect ratio (χ) of these CMEs, which are measured out to ≈ 0.7 AU. We estimated the radial width from a linear best fit for the average of the four CMEs. We obtained the relationships W=0.14R+0.04 for the width and χ=2.5R+0.86 for the aspect ratio (W and R in units of AU).

Structural variations in self-assembled coordination complexes of Zn(II) with hexamethylenetetramine and isomeric 2-, 3- and 4-nitrobenzoates

Three new zinc(II)-hexamethylenetetramine (hmt) complexes [Zn-2(4-nbz)(4)(mu(2)-hmt)(OH2)(hmt)] (1). [Zn-2(2-nbz)(4)(mu(2)-hmt)(2)](n) (2) and [Zn-3(3-nbz)(4)(mu(2)-hmt)(mu(2)-OH)(mu(3)-OH)](n) (3) with three isomeric nitrobenzoate, [4-nbz = 4-nitrobenzoate, 2-nbz = 2-nitrobenzoate and 3-nbz = 3-nitrobenzoate] have been synthesized and structurally characterized by X-ray crystallography. Their identities have also been established by elemental analysis: IR, NMR, UV-Vis and mass spectral studies. 1 is a dinuclear complex formed by bridging hmt with mu(2) coordinating mode. The geometry around the Zn centers in 1 is distorted tetrahedral. Paddle-wheel centrosymmetric Zn-2(2-nbz)(4) units of complex 2 are interconnected by mu(2)-hmt forming a one-dimensional chain with square-pyramidal geometries around the Zn centers. Compound 3 contains a mu(2)/mu(3)-hydroxido and mu(2)-hmt bridged 1D chain. In this complex, varied geometries around the Zn centers are observed viz, tetrahedral, square pyramidal and trigonal bipyramidal. Various weak forces, i.e. lone pair-pi, pi-pi and CH-pi interactions, play a key role in stabilizing the observed structures for complexes 1,2 and 3. This series of complexes demonstrates that although the nitro group does not coordinate to the metal center, its presence at the 2-, 3- or 4-position of the phenyl ring has a striking effect on the dimensionality as well as the structure of the resulted coordination polymers, probably due to the participation of the nitro group in 1.p.center dot center dot center dot pi and/or C-H center dot center dot center dot pi interactions.

An unusual axial–axial combination of alternating cyclic rings in the chair conformations of hexameric water and chlorine-water clusters

An alternating hexameric water (H2O)(6) cluster and a chlorine-water cluster [Cl-2(H2O)(4)](2-) in the chair forms combine axially to each other to form a 1D chain [{Cl-2(H2O)(6)}(2-)](n) in complex [FeL2]Cl center dot(H2O)(3) (L=2-[(2-methylaminoethylimino)-methyl]-phenol)]. The water molecules display extensive H-bonding interactions with monomeric iron-organic units to form a hydrogen-bonded 2D supramolecular assembly.

A depth-integrated 2D coastal and estuarine model with conformal boundary-fitted mesh generation

Details are given of the development and application of a 2D depth-integrated, conformal boundary-fitted, curvilinear model for predicting the depth-mean velocity field and the spatial concentration distribution in estuarine and coastal waters. A numerical method for conformal mesh generation, based on a boundary integral equation formulation, has been developed. By this method a general polygonal region with curved edges can be mapped onto a regular polygonal region with the same number of horizontal and vertical straight edges and a multiply connected region can be mapped onto a regular region with the same connectivity. A stretching transformation on the conformally generated mesh has also been used to provide greater detail where it is needed close to the coast, with larger mesh sizes further offshore, thereby minimizing the computing effort whilst maximizing accuracy. The curvilinear hydrodynamic and solute model has been developed based on a robust rectilinear model. The hydrodynamic equations are approximated using the ADI finite difference scheme with a staggered grid and the solute transport equation is approximated using a modified QUICK scheme. Three numerical examples have been chosen to test the curvilinear model, with an emphasis placed on complex practical applications