Selective Wrapping and Supramolecular Structures of Polyfluorene-Carbon Nanotube Hybrids

We report on the photophysical properties of single-walled carbon nanotube (SWNT) suspensions In toluene solutions of poly[9,9-dioctylfluorenyl-2,7-diyl](PFO). Steady-state and time-resolved photoluminescence spectroscopy in the near-infrared and visible spectral regions are used to study the interaction of the dispersed SWNTs with the wrapped polymer. Molecular dynamics simulations of the PFO-SWNT hybrids in toluene were carried out to evaluate the energetics of different wrapping geometries. The simulated fluorescence spectra in the visible region were obtained by the quantum chemical ZINDO-CI method, using a sampling of structures obtained from the dynamics trajectories. The tested schemes consider polymer chains aligned along the nanotube axis, where chirality has a minimal effect, or forming helical structures, where a preference for high chiral angles is evidenced. Moreover, toluene affects the polymer structure favoring the helical conformation. Simulations show that the most stable hybrid system is the PFO-wrapped (8,6) nanotube, in agreement with the experimentally observed selectivity.

A Multitechnique Study of Structure and Dynamics of Polyfluorene Cast Films and the Influence on Their Photoluminescence

This article describes the microstructure and dynamics in the solid state of polyfluorene-based polymers, poly(9,)-dioctylfluorenyl-2,7-diyl) (PFO), a semicrystalline polymer, and poly [(9,9-dioctyl- 2,7-divinylene-fluorenylene)-alt-co-{2-methoxy-5-(2-ethyl-hexyloxy)- 1,4-phenylene vinylene}, a copolymer with mesomorphic phase properties. These Structures were determined by wide-angle X-ray scattering (WAXS) measurements, Assuming a packing model for the copolymer structure, where the planes of the phenyl rings are stacked and separated by an average distance of similar to 4.5 angstrom and laterally spaced by about similar to 16 angstrom, we followed the evolution of these distances as a function of temperature using WAXS and associated the changes observed to the polymer relaxation processes identified by dynamical mechanical thermal analysis. Specific molecular motions were studied by solid-state nuclear magnetic resonance. The onset of the side-chain motion at about 213 K (beta-relaxation) produced a small increase in the lateral spacing and in the stacking distance of the phenyl rings in them aggregated Structures, Besides, at about 383 K (alpha-relaxation) there occurs a significant increase in the amplitude of the torsion motion in the backbone, producing a greater increase in the stacking distance of the phenyl rings. Similar results were observed in the semicrystalline phase of PFO, but in this case the presence of the crystalline structure affects considerably the overall dynamics, which tends to be more hindered. Put together, Our data explain many features of the temperature dependence of the photoluminescence of these two polymers.

Orthogonal packing of identical rectangles within isotropic convex regions

A mixed integer continuous nonlinear model and a solution method for the problem of orthogonally packing identical rectangles within an arbitrary convex region are introduced in the present work. The convex region is assumed to be made of an isotropic material in such a way that arbitrary rotations of the items, preserving the orthogonality constraint, are allowed. The solution method is based on a combination of branch and bound and active-set strategies for bound-constrained minimization of smooth functions. Numerical results show the reliability of the presented approach. (C) 2010 Elsevier Ltd. All rights reserved.

Effect of the Y(2)O(3)-ZrO(2) support composition on nickel catalyst evaluated in dry reforming of methane

Nickel catalysts with a load of 5 wt.% Ni, supported on pure ZrO(2) and ZrO(2) stabilized with 4 mol%, 8 mol% and 12 mol% of Y(2)O(3), were prepared by the polymerization method. The samples were characterized by X-ray diffraction (XRD), temperature-programmed reduction with hydrogen (TPR-H(2)), specific surface area (BET) and electronic paramagnetic resonance (EPR) and tested as catalysts for carbon dioxide reforming of methane. The XRD patterns showed the presence of the oxide precursor (NiO) and the tetragonal phase of a Y(2)O(3)-ZrO(2) solid solution. According to the TPR-H(2) analysis, the reduction of various NiO species was influenced by the composition of the support. Catalytic tests were conducted at 800 degrees C for 6 h, and the composition of the gaseous products and the catalytic conversion rate depended on the composition of the Y(2)O(3)-ZrO(2) solid solution and its influence on the supported NiO species. A direct relation was observed between the variation in the support, the nickel species supported on it and the performance in the catalytic tests. (C) 2008 Elsevier B.V. All rights reserved.

Dynamics of meso and thermo citrate synthases with implicit solvation

The dynamics of hydration of meso and thermo citrate synthases has been investigated using the EEF1 methodology implemented with the CHARNM program. The native enzymes are composed of two identical subunits, each divided into a small and large domain. The dynamics behavior of both enzymes at 30 degrees C and 60 degrees C has been compared. The results of simulations show that during the hydration process, each subunit follows a different pathway of hydration, in spite of the identical sequence. The hydrated structures were compared with the crystalline structure, and the root mean square deviation (RMSD) of each residue along the trajectory was calculated. The regions with larger and smaller mobility were identified. In particular, helices belonging to the small domain are more mobile than those of the large domain. In contrast, the residues that constitute the active site show a much lower displacement compared with the crystalline structure. Hydration free energy calculations point out that Thermoplasma acidophilum citrate synthase (TCS) is more stable than chicken citrate synthase (CCS), at high temperatures. Such result has been ascribed to the higher number of superficial charges in the thermophilic homologue, which stabilizes the enzyme, while the mesophilic homologue denatures. These results are in accord with the experimental found that TCS keeps activity at temperatures farther apart from the catalysis regular temperature than the CCS. (c) 2005 Wiley Periodicals, Inc.

Molecular characterization and phylogenetic analysis of JussuMP-I: A RGD-P-III class hemorrhagic metalloprotease from Bothrops jararacussu snake venom

Snake venom metalloproteases (SVMPs) embody zinc-dependent multidomain enzymes responsible for a relevant pathophysiology in envenomation. including local and systemic hemorrhage. The molecular features responsible for hemorrhagic potency of SVMPs have been associated with their multidomains structures which can target these proteins them to several receptors of different tissues and cellular types. BjussuMP-I. a SVMP isolated from the Bothrops jararacussu venom, has been characterized as a P-III hemorrhagic metalloprotease. The complete cDNA sequence of BjussuMP-I with 1641bp encodes open reading frames of 547 amino acid residues, which conserve the common domains of P-III high molecular weight hemorrhagic metalloproteases: (i) pre-pro-peptide, (ii) metalloprotease, (iii) disintegrin-like and (iv) rich cysteine domain. BjussuMP-I induced lyses in fibrin clots and inhibited collagen- and ADP-induced platelet aggregation. We are reporting, for the first time, the primary structure of an RGD-P-III class snake venom metalloprotease. A phylogenetic analysis of the BjussuMP-1 metalloprotease/catalytic domain was performed to get new insights into the molecular evolution of the metalloproteases. A theoretical molecular model of this domain was built through folding recognition (threading) techniques and refined by molecular dynamics simulation. Then, the final BjussuMP-I catalytic domain model was compared to other SVMPs and Reprolysin family proteins in order to identify eventual structural differences, which could help to understand the biochemical activities of these enzymes. The presence of large hydrophobic areas and some conserved surface charge-positive residues were identified as important features of the SVMPs and other metalloproteases. (C) 2006 Elsevier B.V. All rights reserved.

Cupin: A candidate molecular structure for the Nep1-like protein family

Background: NEP1-like proteins (NLPs) are a novel family of microbial elicitors of plant necrosis. Some NLPs induce a hypersensitive-like response in dicot plants though the basis for this response remains unclear. In addition, the spatial structure and the role of these highly conserved proteins are not known.Results: We predict a 3d-structure for the beta-rich section of the NLPs based on alignments, prediction tools and molecular dynamics. We calculated a consensus sequence from 42 NLPs proteins, predicted its secondary structure and obtained a high quality alignment of this structure and conserved residues with the two Cupin superfamily motifs. The conserved sequence GHRHDWE and several common residues, especially some conserved histidines, in NLPs match closely the two cupin motifs. Besides other common residues shared by dicot Auxin-Binding Proteins (ABPs) and NLPs, an additional conserved histidine found in all dicot ABPs was also found in all NLPs at the same position.Conclusion: We propose that the necrosis inducing protein class belongs to the Cupin superfamily. Based on the 3d-structure, we are proposing some possible functions for the NLPs.

Molecular cloning and biochemical characterization of a myotoxin inhibitor from Bothrops alternatus snake plasma

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

SMase II, a new sphingomyelinase D from Loxosceles laeta venom gland: Molecular cloning, expression, function and structural analysis

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

Coordinate and time-dependent diffusion dynamics in protein folding

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Application of a new reverse Monte Carlo algorithm to polyatomic molecular systems. I. Liquid water

Using a new reverse Monte Carlo algorithm, we present simulations that reproduce very well several structural and thermodynamic properties of liquid water. Both Monte Carlo, molecular dynamics simulations and experimental radial distribution functions used as input are accurately reproduced using a small number of molecules and no external constraints. Ad hoc energy and hydrogen bond analysis show the physical consistency and limitations of the generated RMC configurations. (C) 2001 American Institute of Physics.

Generalized simulated annealing: Application to silicon clusters

We have compared the recently introduced generalized simulated annealing (GSA) with conventional simulated annealing (CSA). GSA was tested as a tool to obtain the ground-state geometry of molecules. We have used selected silicon clusters (Sin, n=4-7,10) as test cases. Total energies were calculated through tight-binding molecular dynamics. We have found that the replacement of Boltzmann statistics (CSA) by Tsallis's statistics (GSA) has the potential to speed up optimizations with no loss of accuracy. Next, we applied the GSA method to study the ground-state geometry of a 20-atom silicon cluster. We found an original geometry, apparently lower in energy than those previously described in the literature.

Dynamics of a collapsing and exploding Bose-Einstein condensed vortex state

The dynamics of small repulsive Bose-Einstein condensed vortex states of 85Rb atoms in a cylindrical traps with low angular momentum was studied. The time-dependent mean-field Gross-Pitaevskii equation was used for the study. The condensates collapsed and atoms ejected via explosion and a remnant condensate with a smaller number of atoms emerges that survived for a long time.

Electromagnetic form factor of the pion in the space- and time-like regions within the front-form dynamics

The pion electromagnetic form factor is calculated in the space- and time-like regions from -10 (GeV/c)2 up to 10 (GeV/c)2, within a front-form model. The dressed photon vertex where a photon decays in a quark-antiquark pair is depicted generalizing the vector meson dominance ansatz, by means of the vector meson vertex functions. An important feature of our model is the description of the on-mass-shell vertex functions in the valence sector, for the pion and the vector mesons, through the front-form wave functions obtained within a realistic quark model. The theoretical results show an excellent agreement with the data in the space-like region, while in the time-like region the description is quite encouraging. © 2003 Elsevier B.V. All rights reserved.

Multiple minima hypersurfaces procedures for biomimetic ligands screening

In this work the interaction of the pesticide carbaryl with two groups of biomimetic ligands, peptides and MIPs was screened by multiple minima hypersurfaces (MMH) procedures, through the AM1 semiempirical method. Data related to the properties of the molecular association of the complex biomimetic ligand-pesticide were obtained and compared with another molecular modeling algorithm named Leapfrog, as included in the Sybyl software package, and experimental results from the literature, remarking good correlation between them. All important MMH program parameters (cells number, box size, conformers) were studied and optimized with the aim of getting the minimum computation time without losing the correlation with experimental data. The data demonstrated that MMH approach can be used as a fast biomimetic ligand screening tool for MIPs. In the case of peptides the computation time was not comparable with the molecular dynamics methods conventionally used for this approach. © 2011 Springer Science+Business Media B.V.