Thermodynamical description of the interaction between holographic dark energy and dark matter

We present a thermodynamical description of the interaction between holographic dark energy and dark matter. If holographic dark energy and dark matter evolve separately, each of them remains in thermodynamic equilibrium. A small interaction between them may be viewed as a stable thermal fluctuation that brings a logarithmic correction to the equilibrium entropy. From this correction we obtain a physical expression for the interaction which is consistent with phenomenological descriptions and passes reasonably well the observational tests: (c) 2008 Elsevier B.V. All rights reserved.

Furan interaction with the Si(001)-(2 x 2) surface: structural, energetics, and vibrational spectra from first-principles

In this work we employ the state of the art pseudopotential method, within a generalized gradient approximation to the density functional theory, to investigate the adsorption process of furan on the silicon (001) surface. A direct comparison of different adsorption structures with x-ray photoelectron spectroscopy (XPS), ultra-violet photoelectron spectroscopy (UPS), high resolution electron energy loss spectroscopy (HREELS), near edge x-ray absorption fine structure (NEXAFS), and high resolution spectroscopy experimental data allows us to identify the [4 + 2] cycloaddition reaction as the most probable adsorbate. In addition, theoretical scanning tunnelling microscopy (STM) images are presented, with a view to contributing to further experimental investigations.

Structural and magnetic properties and hyperfine interaction in La(3.5)Ru(4)O(13) compound

Structural, magnetic and hyperfine interaction measurements have been carried out on the novel compound La(3.5)Ru(4)O(13) prepared under two different atmospheres (air and oxygen flow). This compound is formed in the orthorhombic structure (space group Pmmm, # 47). The coexistence of the triple-layered perovskite-type planes (quasi-2D structure) and the rutile-like slabs (1D structure) leads to interesting magnetic and electronic properties in this compound. The magnetic susceptibility of this system shows a peak at T similar to 47 K associated with antiferromagnetic interactions. The Curie-Weiss behaviour of the susceptibility provides an effective magnetic moment consistent with Ru ions in low-spin state. Perturbed angular correlation measurements carried out with (111)Cd probe in the temperature range 10-60 K reveal only quadrupole interactions and indicate the occurrence of structural distortions for T<40K. (C) 2009 Elsevier B.V. All rights reserved.

Structure and optical properties of [Ba(1-x)Y(2x/3)](Zr(0.25)Ti(0.75))O(3) powders

[Ba(1-x)Y(2x/3)](Zr(0.25)Ti(0.75))O(3) powders with different yttrium concentrations (x = 0, 0.025 and 0.05) were prepared by solid state reaction. These powders were analyzed by X-ray diffraction (XRD). Fourier transform Raman scattering (FT-RS), Fourier transform infrared (FT-IR) and X-ray absorption near-edge (XANES) spectroscopies. The optical properties were investigated by means of ultraviolet-visible (UV-vis) absorption spectroscopy and photoluminescence (PL) measurements. Even with the addition of yttrium, the XRD patterns revealed that all powders crystallize in a perovskite-type cubic structure. FT-RS and FT-IR spectra indicated that the presence of [YO(6)] clusters is able to change the interaction forces between the O-Ti-O and O-Zr-O bonds. XANES spectra were used to obtain information on the off-center Ti displacements or distortion effects on the [TiO(6)] clusters. The different optical band gap values estimated from UV-vis spectra suggested the existence of intermediary energy levels (shallow or deep holes) within the band gap. The PL measurements carried out with a 350 nm wavelength at room temperature showed that all powders present typical broad band emissions in the blue region. (C) 2010 Elsevier Masson SAS. All rights reserved.

Structural and thermodynamic analysis of thrombin:suramin interaction in solution and crystal phases

Suramin is a hexasulfonated naphthylurea which has been recently characterized as a non-competitive inhibitor of human alpha-thrombin activity over fibrinogen, although its binding site and mode of interaction with the enzyme remain elusive. Here, we determined two X-ray structure of the thrombin: suramin complex, refined at 2.4 angstrom resolution. While a single thrombin: suramin complex was found in the asymmetric unit cell of the crystal, some of the crystallographic contacts with symmetrically related molecules are mediated by both the enzyme and the ligand. Molecular dynamics simulations with the 1:1 complex demonstrate a large rearrangement of suramin in the complex, but with the protein scaffold and the more extensive protein-ligand regions keep unchanged. Small-angle X-ray scattering measurements at high micromolar concentration demonstrate a suramin-induced dimerization of the enzyme. These data indicating a dissimilar binding mode in the monomeric and oligomeric states, with a monomeric, 1:1 complex to be more likely to exist at the thrombin physiological, nanomolar concentration range. Collectively, close understanding on the structural basis for interaction is given which might establish a basis for design of suramin analogues targeting thrombin. Crown Copyright (C) 2009 Published by Elsevier B.V. All rights reserved.

Structure-Based Approach for the Study of Estrogen Receptor Binding Affinity and Subtype Selectivity

Estrogens exert important physiological effects through the modulation of two human estrogen receptor (hER) subtypes, alpa (hER alpha) and beta (hER beta). Because the levels and relative proportion of hER alpha and hER beta differ significantly in different target cells, selective hER ligands could target specific tissues or pathways regulated by one receptor subtype without affecting the other. To understand the structural and chemical basis by which small molecule modulators are able to discriminate between the two subtypes, we have applied three-dimensional target-based approaches employing a series of potent hER-ligands. Comparative molecular field analysis (CoMFA) studies were applied to a data set of 81 hER modulators, for which binding affinity values were collected for both hER alpha and hER beta. Significant statistical coefficients were obtained (hER alpha, q(2) = 0.76; hER beta, q(2) = 0.70), indicating the internal consistency of the models. The generated models were validated using external test sets, and the predicted values were in good agreement with the experimental results. Five hER crystal structures were used in GRID/PCA investigations to generate molecular interaction fields (MIF) maps. hER alpha and hER beta were separated using one factor. The resulting 3D information was integrated with the aim of revealing the most relevant structural features involved in hER subtype selectivity. The final QSAR and GRID/PCA models and the information gathered from 3D contour maps should be useful for the design or novel hER modulators with improved selectivity.

Resilience of protein-protein interaction networks as determined by their large-scale topological features

The relationship between the structure and function of biological networks constitutes a fundamental issue in systems biology. Particularly, the structure of protein-protein interaction networks is related to important biological functions. In this work, we investigated how such a resilience is determined by the large scale features of the respective networks. Four species are taken into account, namely yeast Saccharomyces cerevisiae, worm Caenorhabditis elegans, fly Drosophila melanogaster and Homo sapiens. We adopted two entropy-related measurements (degree entropy and dynamic entropy) in order to quantify the overall degree of robustness of these networks. We verified that while they exhibit similar structural variations under random node removal, they differ significantly when subjected to intentional attacks (hub removal). As a matter of fact, more complex species tended to exhibit more robust networks. More specifically, we quantified how six important measurements of the networks topology (namely clustering coefficient, average degree of neighbors, average shortest path length, diameter, assortativity coefficient, and slope of the power law degree distribution) correlated with the two entropy measurements. Our results revealed that the fraction of hubs and the average neighbor degree contribute significantly for the resilience of networks. In addition, the topological analysis of the removed hubs indicated that the presence of alternative paths between the proteins connected to hubs tend to reinforce resilience. The performed analysis helps to understand how resilience is underlain in networks and can be applied to the development of protein network models.

Synthesis, Infrared Spectroscopy and Crystal Structure Determination of a New Decavanadate

Synthesis, infrared spectroscopy and crystal structure of a new potassium decavanadate decahydrate, K(6)[V(10)O(28)] 10H(2)O, has been reported The infrared spectrum is dominated by decavanadate polyanion and water bands The X-ray crystallography analysis found the compound crystallizes in a triclinic system with the parameters a = 10 5334 (4) angstrom, b = 10 6600 (4) angstrom, c = 17 7351 (5) angstrom, alpha = 76 940 (2)degrees, beta = 75 836 (2)degrees, gamma = 64 776 (2)degrees, V = 1,729 86 (11) A(3), Z = 2, space group P (1) over bar The polyanion consists of ten [VO(6)] octahedra sharing edges, in which the V-O distances are in good agreement with those reported for other decavanadates The crystal structure is stabilized by potassium cations and water molecules forming a complex pattern of hydrogen bonding and short contact ionic interactions

Quartz recrystallization regimes, c-axis texture transitions and fluid inclusion reequilibration in a prograde greenschist to amphibolite facies mylonite zone (Ribeira Shear Zone, SE Brazil)

The crystal-plastic behavior of quartz mylonites from the Ribeira Shear Zone (SE Brazil), a major strike-slip structure that was active during a prograde metamorphic phase related to the Neoproterozoic Brasiliano-Pan African Orogeny, was investigated using a multi-method approach. Geothermobarometry results indicate deformational conditions ranging from similar to 300 to similar to 630 degrees C and 500-700 MPa. A strong correlation between mapped metamorphic zones and a dominance of different dynamic recrystallization mechanisms of quartz occurs within the mylonite zone. Bulging recrystallization (BLG) dominates within the chlorite zone between 300 and 410 degrees C, subgrain rotation recrystallization (SGR) operates within the biotite zone from 410 to 520 degrees C, and grain boundary migration recrystallization (GBM) dominates in the garnet zone above 520 degrees C. The development of quartz c-axis textures is mainly governed by temperature and dynamic recrystallization mechanisms. Textures from BLG zone mylonites are characterized by maxima around Z; SGR zone mylonites display single girdles or asymmetric type I crossed girdles; and GBM zone mylonites comprise maxima around Y and intermediate between X and Z. The scarcity or absence of water-bearing fluid inclusions in quartz mylonites from the SGR and GBM zones, which are dominated by carbonic inclusions, suggests water-deficient conditions, whereas BLG zone mylonites are dominated by water-bearing inclusions. This evidence indicates that water was available in the protoliths but has been eliminated with increasing deformation and deformation temperature. No effect of the water content variation on the quartz microstructural and recrystallized grain size evolution was detected, and little influence on c-axis texture development was observed. Most of the fluid inclusion densities were reequilibrated during the shear zone exhumation history, recording a decompression in the range of 300-500 MPa, while microstructural reequilibration effects related to the prograde metamorphism are largely preserved. Fluid inclusion microstructures and densities from two SGR zone samples preserved evidence for a near isothermal compression within the interior of the Ribeira Shear Zone during the prograde metamorphism. (C) 2009 Elsevier B.V. All rights reserved.

Interaction of cationic bilayer fragments with a model oligonucleotide

The interaction between cationic bilayer fragments and a model oligonucleotide was investigated by differential scanning calorimetry, turbidimetry, determination of excimer to monomer ratio of 2-(10-(1-pyrene)-decanoyl)-phosphatidyl-choline in bilayer fragment dispersions and dynamic light scattering for sizing and zeta-potential analysis. Salt (Na(2)HPO(4)), mononucleotide (2`-deoxyadenosine-5`-monophosphate) or poly (dA) oligonucleotide (3`-AAA AAA AAA A-5`) affected structure and stability of dioctadecyldimethylammonium bromide bilayer fragments. Oligonucleotide and salt increased bilayer packing due to bilayer fragment fusion. Mononucleotide did not reduce colloid stability or did not cause bilayer fragment fusion. Charge neutralization of bilayer fragments by poly (dA) at 1:10 poly (dA):dioctadecyldimethylammonium bromide molar ratio caused extensive aggregation, maximal size and zero of zeta-potential for the assemblies. Above charge neutralization, assemblies recovered colloid stability due to charge overcompensation. For bilayer fragments/poly (dA), the nonmonotonic behavior of colloid stability as a function of poly (dA) concentration was unique for the oligonucleotide and was not observed for Na(2)HPO(4) or 2`-deoxyadenosine-5`-monophosphate. For the first time, such interactions between cationic bilayer fragments and mono- or oligonucleotide were described in the literature. Bilayer fragments/oligonucleotide assemblies may find interesting applications in drug delivery. (c) 2010 Elsevier B.V. All rights reserved.

Identification of lift-off mechanism failure for salt drill-in drilling fluid containing polymer filter cake through adsorption/desorption studies

Drilling fluid`s contact with the productive zone of horizontal or complex wells can reduce well productivity by fluid invasion in the borehole wall. Salted drilling drill-in fluid containing polymers has often been applied in horizontal or complex petroleum wells in the poorly consolidated sandstone reservoirs of the Campos basin, Rio de Janeiro, Brazil. This fluid usually consists of natural polymers such as starch and xanthan gum, which are deposited as a filter cake on the wellbore wall during the drilling. Therefore, the identification of a lift-off mechanism failure, which can be detachment or blistering and pinholing, will enable formulation improvements. increasing the chances of success during filter cake removal in open hole operations. Likewise, knowledge of drill-in drilling fluid adsorption/desorption onto sand can help understand the filter cake-rock adhesion mechanism and consequently filter cake lift-off mechanism failures. The present study aimed to identify the lift-off failure mechanism for this type of fluid filter cake studying adsorption/desorption onto SiO(2) using solutions of natural polymers, lubricants, besides the fluid itself. Ellipsometry was employed to measure this process. The adsorption/desorption studies showed that the adsorbed layer of drilling fluid onto the walls of the rock pores is made up of clusters of polymers, linked by hydrogen bonds, which results in a force of lower cohesion compared to the electrostatic interaction between silica and polymers. Consequently, it was found that the most probable filter cake failure mechanism is rupture (blistering and pinholing), which results in the formation of ducts within the filter cake. (C) 2009 Elsevier B.V. All rights reserved.

Electronic structure and spectra of a new molecular species: SI. A theoretical contribution

A high level theoretical approach is used to characterize for the first time a manifold of doublet and quartet A + S and Omega states correlating with the first two dissociation channels of an as yet experimentally unknown molecular species, SI, sulfur monoidide. A set of spectroscopic constants is determined, including vibrationally averaged spin-orbit coupling constants, vibrationally averaged dipole moments, and dissociation energies. The transition dipole moment function for the spin-forbidden transition a (4)Sigma -X (2)Pi, and the associated radiative lifetimes were also evaluated. Two possibilities to detect transitions experimentally and to derive spectroscopic constants are suggested. (C) 2011 Elsevier B. V. All rights reserved.

Conformational and electronic interaction studies of some p-substituted alpha-methylsulfonyl-alpha-diethoxyphosphorylacetophenones

The analysis of the IR carbonyl band of the alpha-methylsulfonyl-alpha-diethoxyphosphoryl p-substituted acetophenones p-Y-Ph-C(O)CH(SO(2)Me)[P(O)(OEt)(2)] (Y = OMe 1, H 2, F 3, Cl 4, Br 5 and NO(2) 6) supported by HF/6-31G(d,p) ab initio calculations of the alpha-methylsulfonyl-alpha-diethoxyphosphoryl acetophenone 2, indicated the existence of a single stable cl conformer in gas phase and in solvents of increasing polarity, along with the presence of second less stable conformation in gas phase. The cl conformer present the (SO(2)Me) group and the [P(O)(OEt(2))] groups in a syn-clinal (gauche) geometry and is stabilised through of the 0(`60)... P(%), 01NO(owl Crco), ONO)... C(,C*.), 060)... S(`S`02.,) and 0(`S-02) q o) electronic interactions 08along with H(8S*o2M,). 0(660). HU(5C_H2)lP0Erl- 0(8so2m), H(6 +Ph)- - - (co) and H(8o+`-Ph). 0( `Po) intramolecular hydrogen bonds. The almost co nstant negative carbonyl frequency shifts (Av) for the title compounds 1-6 with respect to the parent acetophenones 7-14 corroborates the prevalence of the electronic interactions over the -l(y inductive effect of the ot-substituents for the title compounds and gives strong support for the existence of the crossed 0`(`C-O)... S`(1S+02m,) and 0(""S-02) C(`C+O) (charge transfer and electrostatic); 08-) (co P(`i o) and 01`M-OFt)l C(` o), (electrostatic) interactions. 0 2008 Elsevier B.V. All rights reserved.

Electronic Structure and Chemical Bonding in the Ground and Low-Lying Electronic States of Ta(2)

The electronic structure and chemical bonding of the ground and low-lying Lambda - S and Omega states of Ta(2) were investigated at the multiconfiguration second-order perturbation theory (CASSCF//CASPT2) level. The ground state of Ta(2) is computed to be a X(3)Sigma(-)(g) state (R(e) = 2.120 angstrom, omega(e) = 323 cm(-1), and D(e) = 4.65 eV), with two low-lying singlet states close to it (a(1) Sigma(+)(g) : T(e) = 409 cm(-1), R(e) = 2.131 angstrom, and omega(e) = 313 cm(-1); b(1) Gamma(g): T(e) = 1, 038 cm(-1), R(e) = 2.127 angstrom, and omega(e) = 316 cm(-1)). These electronic states are derived from the same electronic configuration: vertical bar 13 sigma(2)(g)14 sigma(2)(g)7 delta(2)(g)13 pi(4)(u)>. The effective bond order of the X(3) Sigma(-)(g) state is 4.52, which indicates that the Ta atoms are bound by a quintuple chemical bond. The a(1) Sigma(+)(g) state interacts strongly with the X(3)Sigma(-)(g) g ground state by a second-order spin-orbit interaction, giving rise to the (1)0(g)(+) (ground state) (dominated by the X(3)Sigma(-)(g) Lambda - S ground state) and (9)0(g)(+) (dominated by the a(1) Sigma(+)(g) Lambda - S state) Omega states. These results are in line with those reported for the group 5B homonuclear transition metal diatomics. (C) 2010 Wiley Periodicals, Inc. Int J Quantum Chem 111: 1306-1315, 2011

Stereochemical and electronic interaction studies of some N-methoxy-N-methyl-2-[(4 `-substituted)phenylsulfinyl]propanamides

The (1)H NMR spectra of N-methoxy-N-methyl-2-[(4`-substituted)phenylsulfinyl]-propanamides [Y-Ph-S(O)CH(Me)C(O)N(OMe)Me; Y = OMe 1, Me 2, H 3. Cl 4, NO(2) 5] along with the X-ray diffraction analysis of the nitro-derivative (5). have shown the existence of two pairs of diastereomers (racemic mixture) [C(R)S(S)/C(S)S(R) (diast(1)) and C(R)S(R)/C(S)S(S) (diast(2))] in the ratio of ca. 7:3. respectively. The v(CO) IR analysis of the title compounds supported by HF and B3LYP/6-31G** calculations of 3 and of the parent N-methoxy-N-methyl-propanamide (6) by HF, have shown that diast(1) exists in an equilibrium between the two more polar and more stable quasi-cis (q-c(1) and q-c(2)) conformers and the gauche(g) conformer. The population of the g conformer in the equilibrium increases with the increase in the solvent polarity, which is attributed to a larger solvation effect on the carbonyl and sulfinyl groups. Diast(2) of compound 3 occurs in the gas phase as an equilibrium between the most stable quasi-gauche (q-g) conformer and the quasi-cis (q-c) conformer, both presenting very similar dipole moments. The former is stabilized by electrostatic and charge transfer interactions, which results in a less solvated spatial arrangement. Moreover, all conformers of both diastereomers are stabilized by several intramolecular hydrogen bonds. X-ray single crystal analysis performed for diast(1) and for diast(2) of 5 indicates that both stereoisomers assume, in the solid state, the anti-clinal (gauche) conformation. For the crystal packing, diast(1) of 5 is made up of three molecules joined through two centro-symmetric H center dot center dot center dot O hydrogen bonds. (C) 2008 Elsevier B.V. All rights reserved.