Electronic structure calculations of small AI_n (n = 2 - 8) clusters

The electronic states of small AI_n (n = 2 - 8) clusters have been calculated with a relativistic ab-initio MOLCAO Dirac-Fock-Slater method using numerical atomic DFS wave-functions. The excitation energies were obtained from a ground state calculation of neutral clusters, and in addition from negative clusters charged by half an electron in order to account for part of the relaxation. These energies are compared with experimental photoelectron spectra.

Electron-Nuclear Correlation in Laser-Driven Diatomic Molecules

The interaction of short intense laser pulses with atoms/molecules produces a multitude of highly nonlinear processes requiring a non-perturbative treatment. Detailed study of these highly nonlinear processes by numerically solving the time-dependent Schrodinger equation becomes a daunting task when the number of degrees of freedom is large. Also the coupling between the electronic and nuclear degrees of freedom further aggravates the computational problems. In the present work we show that the time-dependent Hartree (TDH) approximation, which neglects the correlation effects, gives unreliable description of the system dynamics both in the absence and presence of an external field. A theoretical framework is required that treats the electrons and nuclei on equal footing and fully quantum mechanically. To address this issue we discuss two approaches, namely the multicomponent density functional theory (MCDFT) and the multiconfiguration time-dependent Hartree (MCTDH) method, that go beyond the TDH approximation and describe the correlated electron-nuclear dynamics accurately. In the MCDFT framework, where the time-dependent electronic and nuclear densities are the basic variables, we discuss an algorithm to calculate the exact Kohn-Sham (KS) potentials for small model systems. By simulating the photodissociation process in a model hydrogen molecular ion, we show that the exact KS potentials contain all the many-body effects and give an insight into the system dynamics. In the MCTDH approach, the wave function is expanded as a sum of products of single-particle functions (SPFs). The MCTDH method is able to describe the electron-nuclear correlation effects as the SPFs and the expansion coefficients evolve in time and give an accurate description of the system dynamics. We show that the MCTDH method is suitable to study a variety of processes such as the fragmentation of molecules, high-order harmonic generation, the two-center interference effect, and the lochfrass effect. We discuss these phenomena in a model hydrogen molecular ion and a model hydrogen molecule. Inclusion of absorbing boundaries in the mean-field approximation and its consequences are discussed using the model hydrogen molecular ion. To this end, two types of calculations are considered: (i) a variational approach with a complex absorbing potential included in the full many-particle Hamiltonian and (ii) an approach in the spirit of time-dependent density functional theory (TDDFT), including complex absorbing potentials in the single-particle equations. It is elucidated that for small grids the TDDFT approach is superior to the variational approach.

X-ray crystallographic study of DNA duplex cross-linking: simultaneous binding to two d(CGTACG)(2) molecules by a bis(9-aminoacridine-4-carboxamide) derivative

Acridine-4-carboxamides form a class of known DNA mono-intercalating agents that exhibit cytotoxic activity against tumour cell lines due to their ability to inhibit topoisomerases. Previous studies of bis-acridine derivatives have yielded equivocal results regarding the minimum length of linker necessary between the two acridine chromophores to allow bis-intercalation of duplex DNA. We report here the 1.7 angstrom resolution X-ray crystal structure of a six-carbon-linked bis(acridine-4-carboxamide) ligand bound to d(CGTACG)(2) molecules by non-covalent duplex cross-linking. The asymmetric unit consists of one DNA duplex containing an intercalated acridine-4-carboxamide chromophore at each of the two CG steps. The other half of each ligand is bound to another DNA molecule in a symmetry-related manner, with the alkyl linker threading through the minor grooves. The two crystallographically independent ligand molecules adopt distinct side chain interactions, forming hydrogen bonds to either O6 or N7 on the major groove face of guanine, in contrast to the semi-disordered state of mono-intercalators bound to the same DNA molecule. The complex described here provides the first structural evidence for the non-covalent cross-linking of DNA by a small molecule ligand and suggests a possible explanation for the inconsistent behaviour of six-carbon linked bis-acridines in previous assays of DNA bis-intercalation.

Modelling small angle neutron scattering data from electrospun fibres

Electrospinning is a technique employed to produce nanoscale to microscale sized fibres by the application of a high voltage to a spinneret containing a polymer solution. Here we examine how small angle neutron scattering data can be modelled to analyse the polymer chain conformation. We prepared 1:1 blends of deuterated and hydrogenated atactic-polystyrene fibres from solutions in N, N-Dimethylformamide and Methyl Ethyl Ketone. The fibres themselves often contain pores or voiding within the internal structure on the length scales that can interfere with scattering experiments. A model to fit the scattering data in order to obtain values for the radius of gyration of the polymer molecules within the fibres has been developed, that includes in the scattering from the voids. Using this model we find that the radius of gyration is 20% larger than in the bulk state and the chains are slightly extended parallel to the fibre axis.

Adsorption of organic molecules at the TiO2(110) surface: the effect of van der Waals interactions

Understanding the interaction of organic molecules with TiO2 surfaces is important for a wide range of technological applications. While density functional theory (DFT) calculations can provide valuable insight about these interactions, traditional DFT approaches with local exchange-correlation functionals suffer from a poor description of non-bonding van der Waals (vdW) interactions. We examine here the contribution of vdW forces to the interaction of small organic molecules (methane, methanol, formic acid and glycine) with the TiO2 (110) surface, based on DFT calculations with the optB88-vdW functional. The adsorption geometries and energies at different configurations were also obtained in the standard generalized gradient approximation (GGA-PBE) for comparison. We find that the optB88-vdW consistently gives shorter surface adsorbate-to-surface distances and slightly stronger interactions than PBE for the weak (physisorbed) modes of adsorption. In the case of strongly adsorbed (chemisorbed) molecules both functionals give similar results for the adsorption geometries, and also similar values of the relative energies between different chemisorption modes for each molecule. In particular both functionals predict that dissociative adsorption is more favourable than molecular adsorption for methanol, formic acid and glycine, in general agreement with experiment. The dissociation energies obtained from both functionals are also very similar, indicating that vdW interactions do not affect the thermodynamics of surface deprotonation. However, the optB88-vdW always predicts stronger adsorption than PBE. The comparison of the methanol adsorption energies with values obtained from a Redhead analysis of temperature programmed desorption data suggests that optB88-vdW significantly overestimates the adsorption strength, although we warn about the uncertainties involved in such comparisons.

The Estrous Cycle Modulates Small Leucine-Rich Proteoglycans Expression in Mouse Uterine Tissues

In the pregnant mouse uterus, small leucine-rich proteoglycans (SLRPs) are drastically remodeled within a few hours after fertilization, suggesting that ovarian hormone levels modulate their synthesis and degradation. In this study, we followed by immunoperoxidase approach, the presence of four members of the SLRP family (decorin, lumican, biglycan, and fibromodulin) in the uterine tissues along the estrous cycle of the mouse. All molecules except fibromodulin, which predominates in the myometrium, showed a striking modulation in their distribution in the endometrial stroma, following the rise in the level of estrogen. Moreover, notable differences in the distribution of SLRPs were observed between superficial and deep stroma, as well as between the internal and external layers of the myometrium. Only biglycan and fibromodulin were expressed in the luminal and glandular epithelia. All four SLRPs were found in cytoplasmic granules of mononucleated cells. The pattern of distribution of the immunoreaction for these molecules in the uterine tissues was found to be estrous cycle-stage dependent, suggesting that these molecules undergo ovarian hormonal control and probably participate in the preparation of the uterus for decidualization and embryo implantation. In addition, this and previous results from our laboratory suggest the existence of two subpopulations of endometrial fibroblasts that may be related to the centrifugal development of the decidua. Anat Rec, 292:138-153, 2009. (c) 2008 Wiley-Liss, Inc.

Self-assembling of phenothiazine compounds investigated by small-angle X-ray scattering and electron paramagnetic resonance spectroscopy

Small-angle X-ray scattering (SAXS) and electron paramagnetic resonance (EPR) have been carried out to investigate the structure of the self-aggregates of two phenothiazine drugs, chlorpromazine (CPZ) and trifluoperazine (TFP), in aqueous solution. In the SAXS studies, drug solutions of 20 and 60 mM, at pH 4.0 and 7.0, were investigated and the best data fittings were achieved assuming several different particle form factors with a homogeneous electron density distribution in respect to the water environment. Because of the limitation of scattering intensity in the q range above 0.15 angstrom(-1), precise determination of the aggregate shape was not possible and all of the tested models for ellipsoids, cylinders, or parallelepipeds fitted the experimental data equally well. The SAXS data allows inferring, however, that CPZ molecules might self-assemble in a basis set of an orthorhombic cell, remaining as nanocrystallites in solution. Such nanocrystals are composed of a small number of unit cells (up to 10, in c-direction), with CPZ aggregation numbers of 60-80. EPR spectra of 5- and 16-doxyl stearic acids bound to the aggregates were analyzed through simulation, and the dynamic and magnetic parameters were obtained. The phenothiazine concentration in EPR experiments was in the range of 5-60 mM. Critical aggregation concentration of TFP is lower than that for CPZ, consistent with a higher hydrophobicity of TFP. At acidic pH 4.0 a significant residual motion of the nitroxide relative to the aggregate is observed, and the EPR spectra and corresponding parameters are similar to those reported for aqueous surfactant micelles. However, at pH 6.5 a significant motional restriction is observed, and the nitroxide rotational correlation times correlate very well with those estimated for the whole aggregated particle from SAXS data. This implies that the aggregate is densely packed at this pH and that the nitroxide is tightly bound to it producing a strongly immobilized EPR spectrum. Besides that, at pH 6.5 the differences in motional restriction observed between 5- and 16-DSA are small, which is different from that observed for aqueous surfactant micelles.

Quantum spin tunneling of magnetization in small ferromagnetic particles

An approach is presented that can also account for the description of small ferromagnetic particle magnetization tunneling. An estimate of the saturation value of an external applied magnetic field along the easy axis is obtained. An analytic expression for the tunneling factor in the absence of an external magnetic field is deduced from the present approach that also allows one to obtain the crossover temperature characterizing the regime where tunneling is dominated by quantum effects. (C) 2009 Published by Elsevier B.V.

Empirical analysis of the Lieb-Oxford bound in ions and molecules

Universal properties of the Coulomb interaction energy apply to all many-electron systems. Bounds on the exchange-correlation energy, in particular, are important for the construction of improved density functionals. Here we investigate one such universal property-the Lieb-Oxford lower bound-for ionic and molecular systems. In recent work [J Chem Phys 127, 054106 (2007)], we observed that for atoms and electron liquids this bound may be substantially tightened. Calculations for a few ions and molecules suggested the same tendency, but were not conclusive due to the small number of systems considered. Here we extend that analysis to many different families of ions and molecules, and find that for these, too, the bound can be empirically tightened by a similar margin as for atoms and electron liquids. Tightening the Lieb-Oxford bound will have consequences for the performance of various approximate exchange-correlation functionals. (C) 2008 Wiley Periodicals Inc.

Enhanced stabilization of aerosol-OT surfactant monolayer upon interaction with small amounts of bovine serum albumin at the air-water interface

An investigation is made of the influence from small amounts of the protein bovine serum albumin (BSA) on the lateral organization of low molecular weight surfactant sodium bis-2-ethylhexyl sulfosuccinate (AOT) at the air-water interface. Surface pressure (pi - A), surface potential (DeltaV - A) and Brewster angle microscopy (BAM) experiments were carried out, with particular emphasis on the monolayer stability under successive compression-expansion cycles. AOT monolayer is not stable at the air-water interface, which means that the majority of AOT molecules go into the aqueous subphase as monomers and/or normal micelles. When a waiting time elapses between spreading and compression, the surfactant monolayer tends to reorganize partially at the air-water interface, with a monolayer expansion being observed for waiting times as large as 12 h. The incorporation of very small amount of BSA (10(-9) M) at the interface, also inferred from BAM, increases the monolayer stability as revealed by pi - A and DeltaV - A results. For a waiting time of circa 3 h, the mixed monolayer reaches its maximum stability. This must be related to protein (and/or protein-surfactant complexes) adsorbed onto the AOT monolayer, thus altering the BSA conformation to accommodate its hydrophobic/hydrophilic residues. Furthermore, the effects from such small amounts of BSA in the monolayer formation and stabilization mean that the AOT monolayer responds cooperatively to BSA. (C) 2004 Elsevier B.V. All rights reserved.

Self-assembling of phenothiazine compounds investigated by small-angle X-ray scattering and electron paramagnetic resonance spectroscopy

Small-angle X-ray scattering (SAXS) and electron paramagnetic resonance (EPR) have been carried out to investigate the structure of the self-aggregates of two phenothiazine drugs, chlorpromazine (CPZ) and trifluoperazine (TFP), in aqueous solution. In the SAXS studies, drug solutions of 20 and 60 mM, at pH 4.0 and 7.0, were investigated and the best data fittings were achieved assuming several different particle form factors with a homogeneous electron density distribution in respect to the water environment. Because of the limitation of scattering intensity in the q range above 0.15 angstrom(-1), precise determination of the aggregate shape was not possible and all of the tested models for ellipsoids, cylinders, or parallelepipeds fitted the experimental data equally well. The SAXS data allows inferring, however, that CPZ molecules might self-assemble in a basis set of an orthorhombic cell, remaining as nanocrystallites in solution. Such nanocrystals are composed of a small number of unit cells (up to 10, in c-direction), with CPZ aggregation numbers of 60-80. EPR spectra of 5- and 16-doxyl stearic acids bound to the aggregates were analyzed through simulation, and the dynamic and magnetic parameters were obtained. The phenothiazine concentration in EPR experiments was in the range of 5-60 mM. Critical aggregation concentration of TFP is lower than that for CPZ, consistent with a higher hydrophobicity of TFP. At acidic pH 4.0 a significant residual motion of the nitroxide relative to the aggregate is observed, and the EPR spectra and corresponding parameters are similar to those reported for aqueous surfactant micelles. However, at pH 6.5 a significant motional restriction is observed, and the nitroxide rotational correlation times correlate very well with those estimated for the whole aggregated particle from SAXS data. This implies that the aggregate is densely packed at this pH and that the nitroxide is tightly bound to it producing a strongly immobilized EPR spectrum. Besides that, at pH 6.5 the differences in motional restriction observed between 5- and 16-DSA are small, which is different from that observed for aqueous surfactant micelles.

Crystal Structures of Xanthomonas Small Heat Shock Protein Provide a Structural Basis for an Active Molecular Chaperone Oligomer

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Small angle X-ray scattering study of surface modified tin oxide nanoparticles prepared by sol-gel route

The surface properties of SnO2 nanoparticles were modified by grafting ionic (Tiron (R). (OH)(2)C6H2(SO3Na)(2)(H2O)-H-.) or non-ionic (Catechol (R). C6H4-1,2-(OH)(2)) capping Molecules during aqueous sol-gel processing to improve the redispersibility of powdered xerogel. The effect of the amount of grafted organic molecules on the redispersibility of powders in aqueous solution at several basic pH values was Studied. The nanostructural features of the colloidal suspensions were analyzed by small angle X-ray scattering (SAXS) measurements. Irrespective of the nature and amount of grafted molecules, complete redispersion was obtained in aqueous solution at pH = 13. The redispersion at pH = 11 results in a mixture of dispersed primary particles and aggregates. The proportion of well dispersed nanoparticles and aggregates (and their average size) can be tuned by the quantity of grafted ionic molecules.

Immune receptors and adhesion molecules in human pulmonary leptospirosis

Pulmonary involvement in leptospirosis has been increasingly reported in the last 20 years, being related to the severity and mortality of the disease. The pathogenesis of pulmonary hemorrhage in leptospirosis is not understood. Lung endothelial cells have been proposed as targets in the pathogenesis of lung involvement in leptospirosis through the activation of Toll-like receptor 2 or the complement system, which stimulates the release of cytokines that lead to the activation of adhesion molecules. The aim of this study was to investigate the involvement of immune pathways and of the intercellular and vascular cell adhesion molecules (intercellular adhesion molecule and vascular cell adhesion molecule, respectively) in the lungs of patients with pulmonary involvement of leptospirosis. We studied the lungs of 18 patients who died of leptospirosis and compared them with 2 groups of controls: normal and noninfectious hemorrhagic lungs. Using immunohistochemistry and image analysis, we quantified the expression of the C3a anaphylatoxin receptor, intercellular adhesion molecule, vascular cell adhesion molecule, and Toll-like receptor 2 in small pulmonary vessels and in the alveolar septa. There was an increased expression of intercellular adhesion molecule (P <.03) and C3a anaphylatoxin receptor (P <.008) in alveolar septa in the leptospirosis group compared with the normal and hemorrhagic controls. In the vessels of the leptospirosis group, there was an increased expression of intercellular adhesion molecule (P=.004), vascular cell adhesion molecule (P=.030), and Toll-like receptor 2 (P=.042) compared with the normal group. Vascular cell adhesion molecule expression in vessels was higher in the leptospirosis group compared with the hemorrhagic group (P=.015). Our results indicate that immune receptors and adhesion molecules participate in the phenomena leading to pulmonary hemorrhage in leptospirosis. (C) 2012 Elsevier Inc. All rights reserved.

Footprints of a trypanosomatid RNA world: pre-small subunit rRNA processing by spliced leader addition trans-splicing

The addition of a capped mini-exon [spliced leader (SL)] through trans-splicing is essential for the maturation of RNA polymerase (pol) II-transcribed polycistronic pre-mRNAs in all members of the Trypanosomatidae family. This process is an inter-molecular splicing reaction that follows the same basic rules of cis-splicing reactions. In this study, we demonstrated that mini-exons were added to precursor ribosomal RNA (pre-rRNA) are transcribed by RNA pol I, including the 5' external transcribed spacer (ETS) region. Additionally, we detected the SL-5' ETS molecule using three distinct methods and located the acceptor site between two known 5' ETS rRNA processing sites (A' and A1) in four different trypanosomatids. Moreover, we detected a polyadenylated 5' ETS upstream of the trans-splicing acceptor site, which also occurs in pre-mRNA trans-splicing. After treatment with an indirect trans-splicing inhibitor (sinefungin), we observed SL-5' ETS decay. However, treatment with 5-fluorouracil (a precursor of RNA synthesis that inhibits the degradation of pre-rRNA) led to the accumulation of SL-5' ETS, suggesting that the molecule may play a role in rRNA degradation. The detection of trans-splicing in these molecules may indicate broad RNA-joining properties, regardless of the polymerase used for transcription.