Local alignment refinement using structural assessment.

Homology modeling is the most commonly used technique to build a three-dimensional model for a protein sequence. It heavily relies on the quality of the sequence alignment between the protein to model and related proteins with a known three dimensional structure. Alignment quality can be assessed according to the physico-chemical properties of the three dimensional models it produces.In this work, we introduce fifteen predictors designed to evaluate the properties of the models obtained for various alignments. They consist of an energy value obtained from different force fields (CHARMM, ProsaII or ANOLEA) computed on residue selected around misaligned regions. These predictors were evaluated on ten challenging test cases. For each target, all possible ungapped alignments are generated and their corresponding models are computed and evaluated.The best predictor, retrieving the structural alignment for 9 out of 10 test cases, is based on the ANOLEA atomistic mean force potential and takes into account residues around misaligned secondary structure elements. The performance of the other predictors is significantly lower. This work shows that substantial improvement in local alignments can be obtained by careful assessment of the local structure of the resulting models.

Assessment of the water chemistry and the macroinvertebrate community changes produced during the creation of the new Llobregat river mouth (Barcelona, NE Spain)

In 1999, a set of coordinated projects and investments whose principal objective was to transform Barcelona into one of the main distribution points of southern Europe resulted in the relocation of the Llobregat River mouth. The mouth was relocated by draining the old river mouth and constructing a new one. The aim of this study was to characterise the physico-chemical properties and the aquatic macroinvertebrate communities of the new river mouth and to monitor the changes experienced by the estuarine environment during its creation. A sampling point was established in the river 1.8 km upstream from its connection with the new mouth, and two sampling points were established in the new mouth. Samples of water and macroinvertebrates were collected every two months from May 2004 to June 2005, covering the periods before (from May to September 2004) and after (from September 2004 to June 2005) the new mouth was connected to the river and the sea. During the period before its connection to the river and the sea, the new mouth was functionally similar to a lagoon, with clear waters, charophytes and a rich invertebrate community. After the connection was completed, seawater penetrated the river mouth and extended to the connection point with the river (approximately 3.9 km upstream). An increase in conductivity from 4-6 mS cm 1 to 24-30 mS cm 1 caused important changes in the macroinvertebrate community of the new mouth. An initial defaunation was followed by a colonisation of the new mouth by brackish-water and marine invertebrate species. Due to its design (which allows the penetration of the sea) and the decreased discharge from the lower part of the Llobregat River, the new mouth has become an arm of the sea

Fluidos supercríticos em química analítica. I. Cromatografia com fluido supercrítico: conceitos termodinâmicos

Under the chromatographic point of view, the physico-chemical properties of a supercritical fluid are intermediate to those of the gases and liquids. Many times they approach the best features of each one, as for example, the solubilization power of liquids and low viscosity of gases. The thermodynamic definitions and main physico-chemical features of a supercritical fluid will be presented in this article. The use of supercritical fluids in analytical chemistry has been extremely modest in Brazil, even considering the enormous potential of their applications, and their use in several techniques, such as chromatography (SFC) and supercritical fluid extration (SFE). This article series is intended to discuss the historical evolution, instrumentation features and potential and limitations of the supercritical fluid use in analytical chemistry. A special focus will be centered on chromatography and extration techniques using supercritical fluids.

Novas estratégias terapêuticas para o tratamento da depressão: uma visão da química medicinal

Depression is a widespread humor disturbance promoted mainly by depletion of biogenic neurotransmitter amines involved in the CNS synapses. Effective drug treatments for depression have been available for more than forty years. Despite its remarkable structural diversity, this paper discuss under the medicinal chemistry point of view, all different classes of "monoamine based" antidepressant drugs, emphasizing the rational design, structure-activity relationships (SAR), biotransformation and physico-chemical properties related with antidepressant activity and molecular mechanism of action.

Esquizofrenia: quarenta anos da hipótese dopaminérgica sob a ótica da Química Medicinal

Schizophrenia is a devastating psychiatric illness that affects 1-2% of the world population and continues as a challenge to neuroscience. In this work, we describe an account about the historical evolution of the dopaminergic hypothesis of schizophrenia discussing, from the medicinal chemistry point of view all different classes of antipsychotic drugs, emphasizing the rational design, structure activity relationships (SAR) and physico-chemical properties related with its molecular mechanism of action.

Influência do agente precipitante na preparação do óxido de nióbio (V) hidratado pelo método da precipitação em solução homogênea

This work reports the preparation, characterization and study of the ion exchange behavior of hydrous niobium oxide prepared by a homogeneous precipitation method. The precipitating agent was obtained in aqueous solution by thermal decomposition of urea or ammonium carbonate. The compounds were chemically and physically characterized by X-ray diffractometry, thermal analysis (TG/DTG), surface area measurements and ion exchange behavior with sodium. The materials prepared with ammonium carbonate presented a higher degree of crystallinity and better ion exchange capacity with sodium than materials prepared with urea. In the homogeneous precipitation method, materials were obtained with specific surface area of 123 - 224 m² g-1. A variation of the preparation process produced hydrous niobium oxide with a different degree of hydration and specific surface area. This provided materials with different physico-chemical properties.

On the application of knoevenagel condensation for the synthesis of benzylidene benzothiazine compounds and structural study

The synthesis and physico-chemical properties of new 6-acetylamino or 6-benzoyl-amino 2-benzylidene-4-methyl-4H-benzo[1,4]thiazin-3-ones and 6-benzoylamino or 6-nitro 2-benzylidene-4H-benzo[1,4]thiazin-3-ones are described. These benzylidene benzothiazine compounds were prepared by the Knoevenagel condensation with benzaldehydes. The configurations and conformations of benzylidene benzothiazine derivatives were optimised using the semi-empirical method AM1.

Composição centesimal do leite humano e caracterização das propriedades físico-químicas de sua gordura

Human milk fat is essential for development of newborn infants. Many studies detail chemical characteristics of human milk fat; however there are no studies about its physical properties. The objective of this work was to analyze the centesimal composition of human milk and to compare the calculated energy value with the estimated energy by the creamatocrit method. Chemical composition and physical properties of human milk lipids and Betapol - a structured lipid - were also studied. The results showed that energy values of human milk estimated by creamatocrit and calculated by the centesimal composition didn't present significant correlation. Human milk lipids and Betapol presented distinct physico-chemical properties.

Funcionalização de nanotubos de Carbono

Carbon nanotubes are very stable systems having considerable chemical inertness due to the strong covalent bonds of the carbon atoms on the nanotube surface. Many applications of carbon nanotubes require their chemical modification in order to tune/control their physico-chemical properties. One way of achieving this control is carrying out functionalization processes where atoms and molecules interact (covalent or non-covalent) with the nanotubes. We review some of the progress that has been made in chemical functionalization of carbon nanotubes. Emphasis is given to chemical strategies, the most used techniques, and applications.

Lipídios estruturados obtidos a partir da mistura de gordura de frango, sua estearina e triacilgliceróis de cadeia média: I- Composição em ácidos graxos e em triacilgliceróis

The purpose of this study is to analyze the interactions that occur in binary and ternary fat blends between medium and long chain triacylglycerols and their structured lipids obtained by chemical interesterification through the analysis of their physico-chemical properties. The synthesized structured triacylglycerols presented from 14.8 to 58.4% medium chain fatty acids, from 15.7 to 37.2% saturated fatty acids, from 19.2 to 47.5% monounsaturated fatty acids, and from 6.7 to 15.2% essential fatty acids. Chemical interesterification modified the behavior of binary and ternary mixtures and new types of triacylglycerol groups were formed.

Caracterização físico-química de complexo de inclusão entre hidroximetilnitrofurazona e hidroxipropil-beta-ciclodextrina

Hydroxymethylnitrofurazone (NFOH) is a prodrug that is active against Trypanosoma cruzi. It however presents low solubility and high toxicity. Hydroxypropyl-beta-cyclodextrin (HP-beta-CD) can be used as a drug-delivery system for NFOH modifying its physico-chemical properties. The aim of this work is to characterize the inclusion complex between NFOH and HP-beta-CD. The rate of NFOH release decreases after complexation and thermodynamic parameters from the solubility isotherm studies revealed that a stable complex is formed (deltaGº= 1.7 kJ/mol). This study focuses on the physico-chemical characterization of a drug-delivery formulation that comes out as a potentially new therapeutic option for Chagas disease treatment.

Propriedades e aplicações recentes das ciclodextrinas

Cyclodextrins (CDs) are cyclic oligosaccharides comprised of six or more glucose units connected by alpha-1,4 bonds. They have hydrophobic cavities with a hydrophilic exterior, and are versatile receptors for a variety of substrates. This ability allows them to be applied in many fields, as distinct as supramolecular chemistry, nanotechnology, pharmaceuticals, green chemistry, agrochemicals, analytical chemistry, toiletries, foods, and cosmetics. This review summarizes several aspects related to the physico-chemical properties of CDs and discusses their potential applications illustrated by recent examples. The prospects for their use in several areas are also described.

Síntese e caracterização de nanopartículas de óxido de ferro suportadas em matriz carbonácea: remoção do corante orgânico azul de metileno em água

In this work were prepared composites of iron oxide and carbonaceous materials in two different weight proportions (Carbon/Fe 1/1 and 1/2). The physico-chemical properties of the composites were determined by temperature programmed reduction (TPR), adsorption/dessorption of N2, X-ray diffraction (XRD), X-ray photoelectron spectroscopy (XPS) and pulse titration H2. The XRD and XPS analysis showed a cubic iron oxide phase, identified as maghemite, formed over the carbon surface. The particle size of maghemite showed to be within 10-30 nm. Carbon/Fe 1/2 was the most active in MB removal kinetics and ESI-MS studies showed that MB removal by both composites leads to oxidized intermediates.

Magnetic, thermal and spectral behaviour of 3-chloro-2-nitrobenzoates of Co(II), Ni(II), and Cu(II)

Physico-chemical properties of 3-chloro-2-nitrobenzoates of Co(II), Ni(II) and Cu(II) were synthesized and studied. The complexes were obtained as mono- and dihydrates with a metal ion to ligand ratio of 1 : 2. All analysed 3-chloro-2-nitrobenzoates are polycrystalline compounds with colours depending on the central ions: pink for Co(II), green for Ni(II) and blue for Cu(II) complexes. Their thermal decomposition was studied in the range of 293 ­ 523 K, because it was found that on heating in air above 523 K 3-chloro-2-nitrobenzoates decompose explosively. Hydrated complexes lose crystallization water molecules in one step and anhydrous compounds are formed. The final products of their decomposition are the oxides of the respective transition metals. From the results it appears that during dehydration process no transformation of nitro group to nitrite takes place. The solubilities of analysed complexes in water at 293 K are of the order of 10-4 ­ 10-2 mol / dm³. The magnetic moment values of Co2+, Ni2+ and Cu2+ ions in 3-chloro-2-nitrobenzoates experimentally determined at 76 ­ 303 K change from 3.67µB to 4.61µB for Co(II) complex, from 2.15µB to 2.87µB for Ni(II) 3-chloro-2-nitrobenzoate and from 0.26µB to 1.39µB for Cu(II) complex. 3-Chloro-2-nitrobenzoates of Co(II) and Ni(II) follow the Curie-Weiss law. Complex of Cu(II) forms dimer.

Complexes of 3,4-dimethoxybenzoic acid anion with Cu(II), Co(II), La(III), and Nd(III)

Physico-chemical properties of 3,4-dimethoxybenzoates of Co(II), Cu(II), La(III) and Nd(III) were studied. The complexes were obtained as hydrated or anhydrous polycrystalline solids with a metal ion-ligand mole ratio of 1 : 2 for divalent ions and of 1 : 3 in the case of trivalent cations. Their colours depend on the kind of central ion: pink for Co(II) complex, blue for Cu(II), white for La(III) and violet for Nd(III) complexes. The carboxylate groups in these compounds are monodentate, bidentate bridging or chelating and tridentate ligands. Their thermal decomposition was studied in the range of 293-1173 K. Hydrated complexes lose crystallization water molecules in one step and form anhydrous compounds, that next decompose to the oxides of respective metals. 3,4 - Dimethoxybenzoates of Co(II) is directly decomposed to the appropriate oxide and that of Nd(III) is also ultimately decomposed to its oxide but with the intemediate formation of Nd2O2CO3.. The magnetic moment values of 3,4-dimethoxybenzoates determined in the range of 76-303 K change from 4.22 µB to 4.61 µB for Co(II) complex , from 0.49 µB to 1.17 µB for Cu(II) complex , and from 2.69 µB to 3.15 µB for Nd(III) complex.