Many-body energy decomposition of hydrogen-bonded glycine clusters in gas-phase

A detailed analysis of the many-body contribution to the interaction energies of the gas-phase hydrogen-bonded glycine clusters, (Gly)(N), N = 1-4 is presented. The energetics of the hydrogen-bonded dimer, trimer and tetramer complexes have been analyzed using density-functional theory. The magnitude of the two-through four-body energy terms have been calculated and compared. The relaxation energy and the two-body energy terms are the principal contributors to the total binding energy. Four-body contribution is negligible. However, the three-body contribution is found to be sizable and the formation of the cyclic glycine trimer presents geometric strains that make it less favorable. (C) 2010 Elsevier B.V. All rights reserved.

Group IV Graphene- and Graphane-Like Nanosheets

We performed a first-principles investigation on the structural and electronic properties of group IV (C, SiC, Si, Ge, and Sn) graphene-like sheets in flat and buckled configurations and the respective hydrogenated or fluorinated graphane-like ones. The analysis on the energetics, associated with the formation of those structures, showed that fluorinated graphane-like sheets are very stable and should be easily synthesized in the laboratory. We also studied the changes of the properties of the graphene-like sheets as a result of hydrogenation or fluorination. The interatomic distances in those graphane-like sheets are consistent with the respective crystalline ones, a property that may facilitate integration of those sheets within three-dimensional nanodevices.

The role of carbon impurities on the Si(001)-c(4 x 4) surface reconstruction: Theoretical calculations

In this work we employ the state-of-the-art pseudopotential method, within a generalized gradient approximation to the density functional theory, combined with a recently developed method for the calculation of HREELS spectra to study a series of different proposed models for carbon incorporation on the silicon (001) surface. A fully discussion on the geometry, energetics and specially the comparison between experimental and theoretical STM images and electron energy loss spectra indicate that the Si(100)-c(4 x 4) is probably induced by Si-C surface dinners, in agreement with recent experimental findings. (C) 2009 Elsevier B.V. All rights reserved.

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.

Combined Crystallographic and Solution Molecular Dynamics Study of Allosteric Effects in Ester and Ketone p-tert-Butylcalix[4]arene Derivatives and Their Complexes with Acetonitrile, Cd(II), and Pb(II)

We describe here a procedure to bridge the gap in the field of calixarene physicochemistry between solid-state atomic-resolution structural information and the liquid-state low-resolution thermodynamics and spectroscopic data. We use MD simulations to study the kinetics and energetics involved in the complexation of lower rim calix[4]arene derivatives (L), containing bidentate ester (1) and ketone (2) pendant groups, with acetonitrile molecule (MeCN) and Cd2+ and Pb2+ ions (M2+) in acetonitrile solution. On one hand, we found that the prior inclusion of MeCN into the calix to form a L(MeCN) adduct has only a weak effect in preorganizing the hydrophilic cavity toward metal ion binding. On the other hand, the strong ion-hydrophilic cavity interaction produces a wide open calix which enhances the binding of one MeCN molecule (allosteric effect) to stabilize the whole (M2+)1(MeCN) bifunctional complex. We reach two major conclusions: (i) the MD results for the (M2+)1(MeCN) binding are in close agreement with the ""endo"", fully encapsulated, metal complex found by X-ray diffraction and in vacuo MD calculations, and (ii) the MD structure for the more flexible 2 ligand, however, differs from the also endo solid-state molecule. In fact, it shows strong solvation effects at the calixarene lower bore by competing MeCN molecules that share the metal coordination sphere with the four C=O oxygens of an ""exo"" (M2+)2(MeCN) complex.

Gaining ligand selectivity in thyroid hormone receptors via entropy

Nuclear receptors are important targets for pharmaceuticals, but similarities between family members cause difficulties in obtaining highly selective compounds. Synthetic ligands that are selective for thyroid hormone (TH) receptor beta (TR beta) vs. TR alpha reduce cholesterol and fat without effects on heart rate; thus, it is important to understand TR beta-selective binding. Binding of 3 selective ligands (GC-1, KB141, and GC-24) is characterized at the atomic level; preferential binding depends on a nonconserved residue (Asn-331 beta) in the TR beta ligand-binding cavity (LBC), and GC-24 gains extra selectivity from insertion of a bulky side group into an extension of the LBC that only opens up with this ligand. Here we report that the natural TH 3,5,3`-triodothyroacetic acid (Triac) exhibits a previously unrecognized mechanism of TR beta selectivity. TR x-ray structures reveal better fit of ligand with the TR alpha LBC. The TR beta LBC, however, expands relative to TR alpha in the presence of Triac (549 angstrom(3) vs. 461 angstrom(3)), and molecular dynamics simulations reveal that water occupies the extra space. Increased solvation compensates for weaker interactions of ligand with TR beta and permits greater flexibility of the Triac carboxylate group in TR beta than in TR alpha. We propose that this effect results in lower entropic restraint and decreases free energy of interactions between Triac and TR beta, explaining subtype-selective binding. Similar effects could potentially be exploited in nuclear receptor drug design.

Defeitos pontuais nos compostos intermetálicos ZrNi e Zr/sub 2/Ni estudados por dinâmica molecular

Empregamos a técnica de Dinâmica Molecular para estudar propriedades de defeitos pontuais nos compostos intermetálicos ZrNi e Zr2Ni. Descrevemos as configurações estáveis de defeitos e mecanismos de migração, assim como as energias envolvidas. Os potenciais interatômicos foram derivados do Embedded Atom Model. No intuito de levar em conta a variação de estequiometria causada pela presença de alguns tipos de defeitos em intermetálicos, apresentamos um método numérico que fornece a energia efetiva de formação de defeitos e aplicamos o método ao ZrNi e Zr2Ni. Os resultados mostraram que vacâncias são mais estáveis na sub—rede do Ni, com energia de formação de 0,83 e-0,61 eV em ZrNi e Zr2Ni, respectivamente. Vacâncias de Zr são instáveis em ambos compostos; elas decaem espontaneamente em pares anti—sítio e vacância de Ni. Configurações e energias de formação de intersticiais também foram calculadas e mostraram comportamentos similares. Em ZrNi, a migração de vacâncias ocorre preferencialmente nas direções [025] e [100], com as respectivas energias de migração 0,67 e 0,73 eV, e é um processo essencialmente bidimensional no plano (001). Em Zr,Ni, a migração de vacâncias é unidimensional, ocorrendo na direção [001], com energia de migração de 0,67 eV. Em ambos compostos a presença de defeitos de anti—sítio de Ni diminui a energia de migração da vacância de Ni em até 3 vezes e facilita a movimentação em três dimensões. Mecanismos de anel não são energeticamente eficientes em comparação com saltos diretos. As configurações estáveis de intersticiais em ambos compostos consistem em um átomo de Ni sobre o plano (001) entre dois vizinhos de Zr fora do plano. Intersticiais de Zr são instáveis e tendem a deslocar um átomo de Ni, ocupando seu sítio. Energias de deslocamento foram estudadas através de simulações de irradiação de ambos compostos. Durante o processo de colisão binária, um potencial universal ZBL foi usado para colisões a curta distância. Para distâncias intermediárias usamos um potencial de união arbitrário. Zr mostrou—se mais difícil de ser arrancado de seu sítio do que Ni. Encontramos valores de energia de deslocamento no intervalo de aproximadamente 29 eV até 546 eV. Alguns resultados experimentais são mostrados e apresentam boa concordância com os cálculos.

Neustonic distribution of decapod planktonic stages and competence of brachyuran megalopae in coastal waters

Settlement rate may not reflect larval supply to coastal waters in different marine invertebrates and demersal fishes. The importance of near-shore oceanography and behaviour of late larval stages may be underestimated. The present study conducted neustonic sampling over station grids and along full-length transects at two embayments in south-eastern Brazil to (1) compare diurnal and nocturnal occurrence of most frequent decapod stages to assess their vertical movements, (2) describe the formation of larval patches and (3) measure competence of crab megalopae according to their distance to recruitment grounds. Several shrimp species apparently undergo a diel vertical migration, swimming crab megalopae showed no vertical movements and megalopae of the intertidal crab Pachygrapsus transversus revealed a reversed vertical migration. During the day, crab megalopae aggregated in convergence zones just below surface slicks. These larvae consisted of advanced, pre-moult stages, at both mid-bay and near-shore patches. Competence, measured as the time to metamorphosis in captivity, was similar between larval patches within each taxon. Yet, subtidal portunids moulted faster to juveniles than intertidal grapsids, possibly because they were closer to settlement grounds. Megalopae of Pachygrapsus from benthic collectors moulted faster than those from bay areas. These results suggest that alternative vertical migration patterns of late megalopae favour onshore transport, and actual competence takes place very close to suitable substrates, where larvae may remain for days before settlement. Lack of correlation between larval supply and settlement for Pachygrapsus suggests that biological processes, besides onshore transport, may play an important role in determining settlement success of coastal crabs.

Population structure and sexual maturity of the calico box crab Hepatus epheliticus Linnaeus (Brachyura, Hepatidae) from Yucatan Peninsula, Mexico

The calico box crab Hepatus epheliticus is an abundant species from shallow and continental shelf waters of the Atlantic coast of USA and Mexico. Information about population structure and sexual maturity is absent, even though this crab is caught to be used as bait for the octopus fishery in the Campeche Bank, Mexico. In order to achieve such information, a total of 768 individuals were collected from January to March 2010 through baited traps installed in the Yucatan Peninsula, Mexico. Our results showed that sex ratio is biased towards more males than females (1:0.55), contradicting to that reported in other brachyuran crabs. The absence of ovigerous females suggests that they did not enter into the traps during embryogenesis. Males reached a larger maximum size than females (64.0 +/- 6.15 and 58.4 +/- 5.60 mm carapace width, respectively). The general scheme of growth being positive allometric throughout ontogeny of both sexes. Males presented a transition phase from juveniles to adult corresponding to the puberty moult. The estimation of the onset of functional sexual maturity revealed a steady situation for the population, with 21.5 and 13.8% of males and females, respectively, morphologically immature at the time of catch. This study constitutes the first report on population structure and sexual maturity in a population of the calico box crab H. epheliticus.

Biology of Grapsus grapsus (LINNAEUS, 1758) (Brachyura, Grapsidae) in the Saint Peter and Saint Paul Archipelago, Equatorial Atlantic Ocean

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Infestation rates of the pedunculated barnacle Octolasmis lowei (Cirripedia: Poecilasmatidae) on the spider crab Libinia spinosa (Decapoda: Majoidea)

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

Histoarchitectural Features of the Hepatopancreas of the Amazon River Prawn Macrobrachium amazonicum

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Eficiência do processo de obtenção do biodiesel de girassol usando o catalisador KNO3/Al2O3

It is known that the head office world energetics is leaning in the fossil fuels. However, the world panorama is changing quickly, for linked reasons to three of the humanity's great concerns in that century beginning: environment, global economy and energy. The biodiesel production is based on the transesterificação of vegetable oils or animal fats, using catalysts homogeneous or heterogeneous. The process of heterogeneous transesterificação presents lower conversions in comparison with the homogeneous, however, it doesn't present corrosion problems and it reduces to the occurrence of parallel reactions as saponification. In this sense, this work has for purpose the synthesis of a heterogeneous catalyst, KNO3/Al2O3, that soon afterwards was used in the reaction of transesterificação of the oil of the Helianthus annuus L. (sunflower). The solid materials (it supports and catalyst) they were analyzed by diffraction of ray-X (XRD) and electronic microscope of sweeping (MEV). After the analysis of Al2O3, a structure monophase amorphous tetragonal was verified, with characteristic patterns of that material, what could not be visualized in the difratograma of the catalyst. The biodiesel obtained with 4% wt. of KNO3/Al2O3 it was what obtained a better cinematic viscosity 8,3 mm2/s, comparing with the norms of ANP, and it also presented the best conversion tax in ethyl ésteres, in accordance with the quantitative measure starting from TG, that was of 60%. While the biodiesel with 6% wt. and with 8% wt. of KNO3/Al2O3 it was it that no transesterificou, because it was observed in the analysis termogravimétrica of those two materials, a single thermal event, that it corresponds the decomposition or volatilization of the triglycerides

Phosphorus magnetic resonance spectroscopy in malformations of cortical development

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

Early juvenile development of Armases rubripes (Rathbun 1897) (Crustacea, Brachyura, Sesarmidae) and comments on the morphology of the megalopa and first crab

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