Modeling the structure of amorphous MoS3: a neutron diffraction and reverse Monte Carlo study

A model for the structure of amorphous molybdenum trisulfide, a-MoS3, has been created using reverse Monte Carlo methods. This model, which consists of chains Of MoS6 units sharing three sulfurs with each of its two neighbors and forming alternate long, nonbonded, and short, bonded, Mo-Mo separations, is a good fit to the neutron diffraction data and is chemically and physically realistic. The paper identifies the limitations of previous models based on Mo-3 triangular clusters in accounting for the available experimental data.

The local adsorption geometry and electronic structure of alanine on Cu{110}

The adsorption of alanine on Cu {110} was studied by a combination of near edge X-ray absorption fine structure (NEXAFS) spectroscopy, X-ray photoelectron spectroscopy (XPS) and density functional theory (DFT). Large chemical shifts in the C 1s, N 1s, and O 1s XP spectra were found between the alanine multilayer and the chemisorbed and pseudo-(3 x 2) alaninate layers. From C, N, and O K-shell NEXAFS spectra the tilt angles of the carboxylate group (approximate to 26 degrees in plane with respect to [1 (1) over bar0] and approximate to 45 degrees out of plane) and the C-N bond angle with respect to [1 (1) over bar0] could be determined for the pseudo-(3 x 2) overlayer. Using this information three adsorption geometries could be eliminated from five p(3 x 2) structures which lead to almost identical heats of adsorption in the DFT calculations between 1.40 and 1.47 eV/molecule. Due to the small energy difference between the remaining two structures it is not unlikely that these coexist on the surface at room temperature. (c) 2006 Elsevier B.V. All rights reserved.

Vibrations in the B-4 rhombic structure

A double minimum six-dimensional Potential energy surface (PES) is determined in symmetry coordinates for the most stable rhombic (D-2h) B-4 isomer in its (1)A(g) electronic ground state by fitting to energies calculated ab initio. The PES exhibits a barrier to the D-4h square structure of 255 cm(-1). The vibrational levels (J=0) are calculated variationally using an approach which involves the Watson kinetic energy operator expressed in normal coordinates. The pattern of about 65 vibrational levels up to 1600 cm-1 for all stable isotopomers is analyzed. Analogous to the inversion in ammonia-like molecules, the rhombus rearrangements lead to splittings of the vibrational levels. In B-4 it is the B-1g (D-4h mode which distorts the square molecule to its planar rhombic form. The anharmonic fundamental vibrational transitions of B-11(4) are calculated to be (splittings in parentheses): G(O) = 2352(22) cm(-1), v(1)(A(1g)) - 1136(24) cm(-1,) v(2)(B-1g)=209(144) cm(-1) v(3)(B-2g)=1198(19)cm(-1), v(4)(B-2u) = 271(24) cm(-1), and v(5) (E-u) = 1030( 166) cm(-1) (D-4h notation). Their variations in all stable isotoporners were investigated. Due to the presence of strong anharmonic resonances between the B-1g in-plane distortion and the B-2u, out-of-plane bending modes. the hiaher overtones and combination levels are difficult to assign unequivocally. (C) 2005 American Institute of Physics.

Synthesis, crystal structure and thermal studies of catena(L-glutamato)-aqua copper(II) monohydrate

The synthesis. crystal structure and thermal study of the blue catena-(L-glutamato)-aqua copper(II) monohydrate have been reported. The compound crystallizes in P2(1)2(1)2(1) space group and consists of a polymeric three-dimensional network of copper(II) which is coordinated with the amino nitrogen and the carboxylate oxygen Of L-glutamate, the side chain carboxylate oxygen of a neighbouring L-glutamate and the oxygen of a water molecule in the equatorial position. Weak coordination of two additional glutamate oxygen atoms to both the axial positions Completes a distorted octahedron. The crystal structure shows that the lattice water is stabilized by the formation of strong H-bonding network with the coordinated water molecule. Removal and reabsorption of the water molecule have been studied by thermal analysis.

Mono, di and polynuclear Cu(II)-azido complexes incorporating N,N,N reduced Schiff base: syntheses, structure and magnetic behavior

Three kinds of copper(II) azide complexes have been synthesised in excellent yields by reacting Cu(ClO4)(2) . 6H(2)O with N,N-bis(2-pyridylmethyl)amine (L-1); N-(2-pyridylmethyl)-N',N'-dimethylethylenediamine (L-2); and N-(2-pyridylmethyl)-N',N'-diethylethylenediamine (L-3), respectively, in the presence of slight excess of sodium azide. They are the monomeric Cu(L-1)(N-3)(ClO4) (1), the end-to-end diazido-bridged Cu-2(L-2)(2)(mu-1,3-N-3)(2)(ClO4)(2) (2) and the single azido-bridged (mu-1,3-) 1D chain [Cu(L-3)(mu-1,3-N-3)](n)(ClO4)(n) (3). The crystal and molecular structures of these complexes have been solved. The variable temperature magnetic moments of type 2 and type 3 complexes were studied. Temperature dependent susceptibility for 2 was fitted using the Bleaney-Bowers expression which led to the parameters J = -3.43 cm(-1) and R = 1 X 10(-5). The magnetic data for 3 were fitted to Baker's expression for S = 1/2 and the parameters obtained were J = 1.6 cm(-1) and R = 3.2 x 10(-4). Crystal data are as follows. Cu(L-1)(N-3)(ClO4): Chemical formula, C12H13ClN6O4Cu; crystal system, monoclinic; space group, P2(1)/c; a = 8.788(12), b = 13.045(15), c = 14.213(15) Angstrom; beta = 102.960(10)degrees; Z = 4. Cu(L-2)(mu-N-3)(ClO4): Chemical formula. C10H17ClN6O4Cu: crystal system, monoclinic; space group, P2(1)/c; a = 10.790(12), b = 8.568(9), c = 16.651(17) Angstrom; beta = 102.360(10)degrees; Z = 4. [Cu(L-3)(mu-N-3)](ClO4): Chemical formula, C12H21ClN6O4Cu; crystal system, monoclinic; space group, P2(1)/c; a = 12.331(14), b = 7.804(9), c = 18.64(2) Angstrom; beta = 103.405(10)degrees; Z = 4. (C) 2004 Elsevier B.V. All rights reserved.

Synthesis, crystal structure and reactivity of copper(II) complexes of tetradentate N2S2 donor ligands

Two new hexa-coordinated mononuclear copper(II) complexes of two ligands L-1 and L-2 containing NSSN donor sets formulated as [Cu(L)(H2O)(2)](NO3)(2) [1a, L = 1,2-bis(2-pyridylmethylthio)ethane (L-1), 1b L = 1,3-bis(2-pyridyl-methylthio)propane (L-2)] were synthesized and characterized by physico-chemical and spectroscopic methods. In 1a the single crystal X-ray crystallography analysis showed a distorted octahedral geometry about copper(II) ion. The crystal packing evidences pairs of complexes arranged about a center of symmetry and connected through a H-bond occurring between aquo ligands and nitrate anions. On reaction with chloride and pseudohalides (N-3(-) and SCN-), in acetonitrile at ambient temperature. complexes 1 changed to monocationic penta-coordinated mononuclear copper(H) species formulated as [Cu(L)(Cl)]NO3 (2), [Cu(L)(N-3)]NO3 (3). and [Cu(L)(SCN)]NO3 (4). These copper(II) complexes have been isolated in pure form from the reaction mixtures and characterized by physico-chemical and spectroscopic tools. The solid-state structure of 2a, established by X-ray crystallography, shows a trigonal bipyramidal geometry about the metal ion with a trigonality index (tau) of 0.561. (C) 2009 Elsevier B.V. All rights reserved.

Chemical composition and reactivity of water on hexagonal Pt-group metal surfaces

The dissociation behaviour and valence-electronic structure of water adsorbed on clean and oxygen-covered Ru{0001}, Rh{111}, Pd{111}, Ir{111} and Pt{111} surfaces has been studied by high-resolution X-ray photoelectron spectroscopy with the aim of identifying similarities and trends within the Pt-group metals. On average, we find higher reactivity for the 4d metals (Ru, Rh, Pd) as compared to 5d (Ir, Pt), which is correlated with characteristic shifts in the 1b(1) and 3a(1) molecular orbitals of water. Small amounts of oxygen (<0.2 ML) induce dissociation of water on all five surfaces, for higher coverages (>0.25 ML) only intact water is observed. Under UHV conditions these higher coverages can only be reached on the 4d metals, the 5d metals are, therefore, not passivated.

X-ray scattering study of the effect of hydration on the cross-beta structure of amyloid fibrils

We have investigated the effect of sample hydration on the wide-angle X-ray scattering patterns of amyloid fibrils from two different sources, hen egg white lysozyme (HEWL) and an 11-residue peptide taken from the sequence of transthyretin (TTR105-115). Both samples show an inter-strand reflection at 4.7 Å and an inter-sheet reflection which occurs at 8.8 and 10 Å for TTR105-115 and HEWL fibrils, respectively. The positions, widths, and relative intensities of these reflections are conserved in patterns obtained from dried stalks and hydrated samples over a range of fibril concentrations. In 2D scattering patterns obtained from flow-aligned hydrated samples, the inter-strand and inter-sheet reflections showed, respectively, axial and equatorial alignment relative to the fibril axis, characteristic of the cross-β structure. Our results show that the cross-β structure of the fibrils is not a product of the dehydrating conditions typically employed to produce aligned samples, but is conserved in individual fibrils in hydrated samples under dilute conditions comparable to those associated with other biophysical and spectroscopic techniques. This suggests a structure consisting of a stack of two or more sheets whose interfaces are inaccessible to bulk water.

[Co(en)(3)][Sb12S19]: a new antimony sulfide with a zeolite-like structure containing one-dimensional channels

Solvothermal synthesis affords access to the first truly three-dimensional anti mony-sufide framework which contains one-dimensional circular channels.

Experimental structure determination of the chemisorbed overlayers of chlorine and iodine on Au{111}

We have performed an experimental structure determination of the ordered p(sqrt[3] x sqrt[3])R30 degrees structures of chlorine and iodine on Au{111} using low-energy electron diffraction (LEED). Despite great similarities in the structure of the underlying substrate, which shows only minor deviations from the bulk positions in both cases, chlorine and iodine are found to adsorb in different adsorption sites, fcc and hcp hollow sites, respectively. The experimental Au-Cl and Au-I bond lengths of 2.56 and 2.84 A are close to the sums of the covalent radii, supporting the view that the bond is essentially covalent in nature; however, they are significantly shorter than predicted theoretically.

Hydrogelation and self-assembly of Fmoc-tripeptides: unexpected influence of sequence on self-assembled fibril structure, and hydrogel modulus and anisotropy

The self-assembly and hydrogelation properties of two Fmoc-tripeptides [Fmoc = N-(fluorenyl-9-methoxycarbonyl)] are investigated, in borate buffer and other basic solutions. A remarkable difference in self-assembly properties is observed comparing Fmoc-VLK(Boc) with Fmoc-K(Boc)LV, both containing K protected by N(epsilon)-tert-butyloxycarbonate (Boc). In borate buffer, the former peptide forms highly anisotropic fibrils which show local alignment, and the hydrogels show flow-aligning properties. In contrast, Fmoc-K(Boc)LV forms highly branched fibrils that produce isotropic hydrogels with a much higher modulus (G' > 10(4) Pa), and lower concentration for hydrogel formation. The distinct self-assembled structures are ascribed to conformational differences, as revealed by secondary structure probes (CD, FTIR, Raman spectroscopy) and X-ray diffraction. Fmoc-VLK(Boc) forms well-defined beta-sheets with a cross-beta X-ray diffraction pattern, whereas Fmoc-KLV(Boc) forms unoriented assemblies with multiple stacked sheets. Interchange of the K and V residues when inverting the tripeptide sequence thus leads to substantial differences in self-assembled structures, suggesting a promising approach to control hydrogel properties.

Structure of single-wall peptide nanotubes: in situ flow aligning X-ray diffraction

The structure of single wall peptide nanotubes is presented for the model surfactant-like peptide A6K. Capillary flow alignment of a sample in the nematic phase at high concentration in water leads to oriented X-ray diffraction patterns. Analysis of these, accompanied by molecular dynamics simulations, suggests the favourable self-assembly of antiparallel peptide dimers into beta-sheet ribbons that wrap helically to form the nanotube wall.

Synthesis, x-ray structure and anion binding properties of a cryptand-like hybrid calixpyrrole

The novel cryptand in/out-3, containing two tripyrrolemethane units briged by three 1,3- diisopropylidenbenzene arms was readily synthesized by a convergent three-step synthesis. It binds fluoride by inclusion with excellent selectivity with respect to a number of other tested anions. The structure of the free receptor and that of its fluoride complex were investigated in solution by NMR spectroscopy. The solid state X-ray structure of the free cryptand 3 was also determined.

The Structure of the chiral Pt{531} surface: a combined LEED and DFT study

The structure of the chiral kinked Pt{531} surface has been determined by low-energy electron diffraction intensity-versus-energy (LEED-IV) analysis and density functional theory (DFT). Large contractions and expansions of the vertical interlayer distances with respect to the bulk-terminated surface geometry were found for the first six layers (LEED: d(12) = 0.44 angstrom, d(23) = 0.69 angstrom, d(34) = 0.49 angstrom, d(45) = 0.95 angstrom, d(56) = 0.56 angstrom; DFT: d(12) = 0.51 angstrom, d(23) = 0.55 angstrom, d(34) = 0.74 angstrom, d(45) = 0.78 angstrom, d(56) = 0.63 angstrom; d(bulk) = 0.66 angstrom). Energy-dependent cancellations of LEED spots over unusually large energy ranges, up to 100 eV, can be explained by surface roughness and reproduced by applying a model involving 0.25 ML of vacancies and adatoms in the scattering calculations. The agreement between the results from LEED and DFT is not as good as in other cases, which could be due to this roughness of the real surface.

The structure of the mixed OH+H2O overlayer on Pt{111}

The structure of the mixed p(3x3)-(3OH+3H(2)O) phase on Pt{111} has been investigated by low-energy electron diffraction-IV structure analysis. The OH+H2O overlayer consists of hexagonal rings of coplanar oxygen atoms interlinked by hydrogen bonds. Lateral shifts of the O atoms away from atop sites result in different O-O separations and hexagons with only large separations (2.81 and 3.02 angstrom) linked by hexagons with alternating separations of 2.49 and 2.81/3.02 A. This unusual pattern is consistent with a hydrogen-bonded network in which water is adsorbed in cyclic rings separated by OH in a p(3x3) structure. The topmost two layers of the Pt atoms relax inwards with respect to the clean surface and both show vertical buckling of up to 0.06 angstrom. In addition, significant shifts away from the lateral bulk positions have been found for the second layer of Pt atoms. (C) 2005 American Institute of Physics.