An adaptive finite element water column model using the Mellor-Yamada level 2.5 turbulence closure scheme

A one-dimensional water column model using the Mellor and Yamada level 2.5 parameterization of vertical turbulent fluxes is presented. The model equations are discretized with a mixed finite element scheme. Details of the finite element discrete equations are given and adaptive mesh refinement strategies are presented. The refinement criterion is an "a posteriori" error estimator based on stratification, shear and distance to surface. The model performances are assessed by studying the stress driven penetration of a turbulent layer into a stratified fluid. This example illustrates the ability of the presented model to follow some internal structures of the flow and paves the way for truly generalized vertical coordinates. (c) 2005 Elsevier Ltd. All rights reserved.

Probing the large-scale topology of the heliospheric magnetic field using Jovian electrons

Jupiter’s magnetosphere acts as a point source of near-relativistic electrons within the heliosphere. In this study, three solar cycles of Jovian electron data in near-Earth space are examined. Jovian electron intensity is found to peak for an ideal Parker spiral connection, but with considerable spread about this point. Assuming the peak in Jovian electron counts indicates the best magnetic connection to Jupiter, we find a clear trend for fast and slow solar wind to be over- and under-wound with respect to the ideal Parker spiral, respectively. This is shown to be well explained in terms of solar wind stream interactions. Thus, modulation of Jovian electrons by corotating interaction regions (CIRs) may primarily be the result of changing magnetic connection, rather than CIRs acting as barriers to cross-field diffusion. By using Jovian electrons to remote sensing magnetic connectivity with Jupiter’s magnetosphere, we suggest that they provide a means to validate solar wind models between 1 and 5 AU, even when suitable in situ solar wind observations are not available. Furthermore, using Jovian electron observations as probes of heliospheric magnetic topology could provide insight into heliospheric magnetic field braiding and turbulence, as well as any systematic under-winding of the heliospheric magnetic field relative to the Parker spiral from footpoint motion of the magnetic field.

The two-dimensional anharmonic oscillator II: the microwave spectrum of silyl isocyanate, SiH3NCO

The J + 1 ← J transitions (J = 2, 3, 4, 5, and 6) in the microwave spectrum of SiH3NCO have been assigned for the vibrational ground state and for the vibrational states v10 = 1, 2, and 3. The results for v10 = 0 confirm earlier work. The vibration-rotation constants show a remarkable variation with v10 and l10. To a large extent the anomalous behavior of these constants has been explained in terms of a strongly anharmonic potential function for the ν10 vibrational mode.

The two-dimensional anharmonic oscillator III: the CCC bending mode of C3O2

Newly observed data on the rotational constants of carbon suboxide in excited vibrational states of the low-wavenumber bending vibration ν7 have been successfully interpreted in terms of the two-dimensional anharmonic oscillator wavefunctions associated with this vibration. By combining these results with published infrared and Raman spectra the vibrational assignment has been extended and a refined bending potential for ν7 has been derived: this has a minimum at a bending angle of about 24° at the central C atom, with an energy maximum at the linear configuration some 23 cm−1 above the minimum. From similar data on the combination and hot bands of ν7 with ν4 (1587 cm−1) and ν2 (786 cm−1) the effective ν7 bending potential has also been determined in the one-quantum excited states of ν4 and ν2. The effective ν7 potential shows significant changes from the ground vibrational state; the central hump in the ν7 potential surface is increased to about 50 cm−1 in the v4 = 1 state, and decreased to about 1 cm−1 in the v2 = 1 state. In the light of these results vibrational assignments are suggested for most of the observed bands in the infrared and Raman spectra of C3O2.

The two-dimensional anharmonic oscillator I: vibration-rotation constants of fulminic acid, HCNO

The lowest-wavenumber vibration of HCNO and DCNO, ν5, is known to involve a largeamplitude low-frequency anharmonic bending of the CH bond against the CNO frame. In this paper the anomalous vibrational dependence of the observed rotational constants B(v5, l5), and of the observed l-doubling interactions, is interpreted according to a simple effective vibration-rotation Hamiltonian in which the appropriate vibrational operators are averaged in an anharmonic potential surface over the normal coordinates (Q5x, Q5y). All of the data on both isotopes are interpreted according to a single potential surface having a minimum energy at a slightly bent configuration of the HCN angle ( 170°) with a maximum at the linear configuration about 2 cm−1 higher. The other coefficients in the Hamiltonian are also interpreted in terms of the structure and the harmonic and anharmonic force fields; the substitution structure at the “hypothetical linear configuration” determined in this way gives a CH bond length of 1.060 Å, in contrast to the value 1.027 Å determined from the ground-state rotational constants. We also discuss the difficulties in rationalizing our effective Hamiltonian in terms of more fundamental theory, as well as the success and limitations of its use in practice.

Proteomic analysis of redox- and ErbB2-dependent changes in mammary luminal epithelial cells using cysteine- and lysine-labelling two-dimensional difference gel electrophoresis

Differential protein expression analysis based on modification of selected amino acids with labelling reagents has become the major method of choice for quantitative proteomics. One such methodology, two-dimensional difference gel electrophoresis (2-D DIGE), uses a matched set of fluorescent N-hydroxysuccinimidyl (NHS) ester cyanine dyes to label lysine residues in different samples which can be run simultaneously on the same gels. Here we report the use of iodoacetylated cyanine (ICy) dyes (for labelling of cysteine thiols, for 2-D DIGE-based redox proteomics. Characterisation of ICy dye labelling in relation to its stoichiometry, sensitivity and specificity is described, as well as comparison of ICy dye with NHS-Cy dye labelling and several protein staining methods. We have optimised conditions for labelling of nonreduced, denatured samples and report increased sensitivity for a subset of thiol-containing proteins, allowing accurate monitoring of redox-dependent thiol modifications and expression changes. Cysteine labelling was then combined with lysine labelling in a multiplex 2-D DIGE proteomic study of redox-dependent and ErbB2-dependent changes in epithelial cells exposed to oxidative stress. This study identifies differentially modified proteins involved in cellular redox regulation, protein folding, proliferative suppression, glycolysis and cytoskeletal organisation, revealing the complexity of the response to oxidative stress and the impact that overexpression of ErbB2 has on this response.

Anion-directed synthesis of metal-organic frameworks based on 2-picolinate Cu(II) complexes: a ferromagnetic alternating chain and two unprecedented ferromagnetic fish backbone chains

Three new polynuclear copper(II) complexes of 2-picolinic acid (Hpic), {[Cu-2(pic)(3)(H2O)]ClO4}(n) (1), {[Cu-2(pic)(3)(H2O)]BF4}(n) (2), and [Cu-2(pic)3(H2O)(2)(NO3)](n) (3), have been synthesized by reaction of the "metalloligand" [Cu-(pic)(2)] with the corresponding copper(II) salts. The compounds are characterized by single-crystal X-ray diffraction analyses and variable-temperature magnetic measurements. Compounds 1 and 2 are isomorphous and crystallize in the triclinic system with space group P (1) over bar, while 3 crystallizes in the monoclinic system with space group P2(1)/n. The structural analyses reveal that complexes 1 and 2 are constructed by "fish backbone" chains through syn-anti (equatorial-equatorial) carboxylate bridges, which are linked to one another by syn-anti (equatorial-axial) carboxylate bridges, giving rise to a rectangular grid-like two-dimensional net. Complex 3 is formed by alternating chains of syn-anti carboxylate-bridged copper(II) atoms, which are linked together by strong H bonds involving coordinated nitrate ions and water molecules and uncoordinated oxygen atoms from carboxylate groups. The different coordination ability of the anions along with their involvement in the H-bonding network seems to be responsible for the difference in the final polymeric structures. Variable-temperature (2-300 K) magnetic susceptibility measurement shows the presence of weak ferromagnetic coupling for all three complexes that have been fitted with a fish backbone model developed for 1 and 2 (J = 1.74 and 0.99 cm(-1); J' = 0.19 and 0.25 cm(-1), respectively) and an alternating chain model for 3 (J = 1.19 cm(-1) and J' = 1.19 cm(-1)).

Proteomic analysis of redox- and ErbB2-dependent changes in mammary luminal epithelial cells using cysteine- and lysine-labelling two-dimensional difference gel electrophoresis

Differential protein expression analysis based on modification of selected amino acids with labelling reagents has become the major method of choice for quantitative proteomics. One such methodology, two-dimensional difference gel electrophoresis (2-D DIGE), uses a matched set of fluorescent N-hydroxysuccinimidyl (NHS) ester cyanine dyes to label lysine residues in different samples which can be run simultaneously on the same gels. Here we report the use of iodoacetylated cyanine (ICy) dyes (for labelling of cysteine thiols, for 2-D DIGE-based redox proteomics. Characterisation of ICy dye labelling in relation to its stoichiometry, sensitivity and specificity is described, as well as comparison of ICy dye with NHS-Cy dye labelling and several protein staining methods. We have optimised conditions for labelling of nonreduced, denatured samples and report increased sensitivity for a subset of thiol-containing proteins, allowing accurate monitoring of redox-dependent thiol modifications and expression changes, Cysteine labelling was then combined with lysine labelling in a multiplex 2-D DIGE proteomic study of redox-dependent and ErbB2-dependent changes in epithelial cells exposed to oxidative stress. This study identifies differentially modified proteins involved in cellular redox regulation, protein folding, proliferative suppression, glycolysis and cytoskeletal organisation, revealing the complexity of the response to oxidative stress and the impact that overexpression of ErbB2 has on this response.

The first metamagnetic thiocyanato-bridged one-dimensional nickel(II) complex

A novel single thiocyanato- bridged one- dimensional polymer, [NiL(NCS)(mu-NCS)](n) (L = N-1-(1-pyridin-2-yl-ethylidine)propane-1,3-diamine) has been synthesized and characterized by X-ray crystallography and a variable temperature magnetic study; the compound is a metamagnet with a Neel temperature (T-N) of 3.5 K.

Helices, chirality and interpenetration: the versatility and remarkable interconversion of silver-copper cyanide frameworks

The structural transformations between cesium silver-copper cyanides under modest conditions, both in solution and in the solid state, are described. Three new cesium silver(I) copper(I) cyanides with three-dimensional (3-D) framework structures were prepared as single crystals from a one-pot reaction initially heated under hydrothermal conditions. The first product to appear, Cs3Ag2Cu3(CN)(8) (I), when left in contact with the supernatant produced CsAgCu(CN)(3) (II) and CsAgCu(CN)(3)center dot 1/3H(2)O (III) over a few months via a series of thermodynamically controlled cascade reactions. Crystals of the hydrate (III) can be dehydrated to polycrystalline CsAgCu(CN)(3) (II) on heating at 100 degrees C in a remarkable solid-state transformation involving substantial breaking and reconnection of metal-cyanide linkages. Astonishingly, the conversion between the two known polymorphs of CsAg2Cu(CN)(4), which also involves a major change in connectivity and topology, occurs at 180 degrees C as a single-crystal to single-crystal transformation. Structural features of note in these materials include the presence of helical copper-cyanide chains in (I) and (II), which in the latter compound produce a chiral material. In (II) and (III), the silver-copper cyanide networks are both self- and interpenetrating, features also seen in the known polymorphs of CsAg2Cu(CN)(4).

Potassium nickel(II) gallium phosphate hydrate, K[NiGa2(PO4)(3)(H2O)(2)]

The title compound, potassium nickel(II) digallium tris-( phosphate) dihydrate, K[NiGa2(PO4)(3)(H2O)(2)], was synthesized hydrothermally. The structure is constructed from distorted trans-NiO4(H2O)2 octahedra linked through vertices and edges to GaO5 trigonal bipyramids and PO4 tetrahedra, forming a three-dimensional framework of formula [NiGa2(PO4)(3)(H2O)(2)](-). The K, Ni and one P atom lie on special positions (Wyckoff position 4e, site symmetry 2). There are two sets of channels within the framework, one running parallel to the [10 (1) over bar] direction and the other parallel to [001]. These intersect, forming a three-dimensional pore network in which the water molecules coordinated to the Ni atoms and the K+ ions required to charge balance the framework reside. The K+ ions lie in a highly distorted environment surrounded by ten O atoms, six of which are closer than 3.1 angstrom. The coordinated water molecules are within hydrogen-bonding distance to O atoms of bridging Ga-O-P groups.

Zinc(II) mediated synthesis of an N-substituted 2-(2-pyridyl)imidazole from a 1,2-diketone and 2-(aminomethyl)pyridine and its ligational behaviour

Reaction of anhydrous ZnCl2 with the 1:2 condensate (L) of benzil and 2-(aminomethyl)pyridine in methanol gives monomeric ZnL'Cl-2 (1) where L' is 2-[(4,5-diphenyl-2-pyridin-2-yl-1H-imidazol-1-yl)-methyl]pyridine. In the X-ray crystal structure, 1 is found to contain tetrahedral zinc with an N2Cl2 coordination sphere and the N-substituent methylpyridine fragment hanging as a free arm. A tentative mechanism is proposed for the zinc mediated conversion of L-->L'. Demetallation of 1 by the action of aqueous NaOH yields L' in the free state. When L' is reacted with Zn(ClO4)(2).6H(2)O in a 1:2 molar proportion, [Zn(L')(2)](n)(ClO4)(2n).(H2O)(n/2).(CH2Cl2)(n/2) (2) is obtained. The zinc atom in 2, as revealed by X-ray crystallography, has a trigonal bipyramidal N-5 coordination sphere. There are two independent ligands in the asymmetric unit of 2. One of them bonds only to one zinc atom in a bidentate mode with the N-substituent methylpyridine hanging free while the other ligand binds to two different zinc atoms in a tridentate fashion, employing the N-substituent methylpyridine nitrogen atom to form the polymeric one-dimensional chain cation.

A novel cation induced polymeric chain in Na-8[{Cu(gly)(2)}(2)]{H-2(H2W12O42)}] center dot 24H(2)O: hydrothermal synthesis, spectroscopic characterization and X-ray structure analysis

A novel bis(glycinato) copper(II) paradodecatungstate Na-8[{Cu(gly)(2)}(2)]-{H-2(H2W12O42)}] center dot 24H(2)O (1) has been synthesized under hydrothermal conditions. The crystal structure of 1 reveals an infinite one-dimensional chain along the [100] direction and is built from paradodecatungstate (H2W12O42)(10-) clusters joined through [Cu(gly)(2)] moieties. Parallel chains are interlinked by NaO6 octahedra to generate a two-dimensional network.

Novel charge transfer supramolecular assemblies with Keggin anions and 2-amino-5-nitropyridine

Several novel compounds with the non-linear optical chromophore 2-amino-5-nitropyridine (2A5NP) and Keggin polyoxoanions (alpha-isomers), having the general formula (2A5NP)(m)H-n[XM12O40]center dot xH(2)O, M = Mo, W, were synthesised. Compounds were obtained with X = P, n = 3, m = 3 and 4 and X = Si, n = m = 4 ( x = 2 - 6). Thus, for each of the anions [PMo12O40](3-) and [PW12O40](3-) two different compounds were obtained, with the same anion and organic counterpart but with a different stoichiometric ratio. These presented different charge transfer properties and thermal stability. All compounds were characterised by spectroscopic and analytical techniques. The single crystal X-ray diffraction structure of (2A5NP)(4)H-3[PMo12O40]center dot 2.5H(2)O center dot 0.5C(2)H(5)OH showed that the water solvent molecules and the organic chromophores are assembled via infinite one-dimensional chains of hydrogen bonds with formation of open channels, which accommodate [ PMo12O40] 3- and ethanol solvent molecules.