Odd-even oscillations of SHG efficiencies in twin NLO chromophores

Twin NLO chromophores having two azobenzene units linked by a flexible polymethylene spacer of varying lengths are shown to exhibit odd-even oscillations in their second harmonic generation (SHG) efficiencies, when measured in the powder form. These twin systems were designed to also exhibit liquid cystallinity, and indeed most of them do exhibit a nematic mesophase. The anticipated odd-even oscillations, in both their isotropization transition temperatures (Ti) and isotropization entropies (Delta Si), were also observed. The odd-even oscillation of the SHG efficiencies has been ascribed to a more effective cancellation of mesogenic dipoles in the even twins as compared to their odd counterparts, due to a preferred centrosymmetric packing in the former case. Based on the behaviour of these twin chromophoric molecules, it may be anticipated that such odd-even oscillations will also be observed in the analogous main chain NLO polymers.

Structure of basic winged-bean lectin and a comparison with its saccharide-bound form

The crystal structure of the saccharide-free form of the basic form of winged-bean agglutinin (WBAI) has been solved by the molecular-replacement method and refined at 2.3 Angstrom resolution The final R factor is 19.74b for all data in the resolution range 8.0-2.3 Angstrom. The asymmetric unit contains two half-dimers, each located on a crystallographic twofold axis. The structure of the saccharide-free form is compared with that of the complex of WBAI wi th methyl-alpha-D-galactoside. The complex is composed of two dimers in the asymmetric unit. The intersubunit interactions in the dimer are nearly identical in the two structures The binding site of the saccharide-free structure contains three ordered water molecules at positions similar to those of the hydroxyl groups of the carbohydrate which an hydrogen bonded to the protein. Superposition of the saccharide-binding sites of the two structures shows that the major changes involve expulsion of these ordered water molecules and a shift of about 0.6 Angstrom of the main-chain atoms of the variable loop.

Continuous distribution kinetics for the thermal degradation of LDPE in solution

Polymer degradation in solution has several advantages over melt pyrolysis, The degradation of low-density polyethylene (LDPE) occurs at much lower temperatures in solution (280-360degreesC) than in conventional melt pyrolysis (400-450degreesC). The thermal degradation kinetics of LDPE in solution was investigated in this work. LDPE was dissolved in liquid paraffin and degraded for 3 h at various temperatures (280-360degreesC). Samples were taken at specific times and analyzed with high-pressure liquid chromatography/gel permeation chromatography for the molecular weight distribution (MWD), The time evolution of the MWD was modeled with continuous distribution kinetics. Data indicated that LDPE followed random-chain-scission degradation. The rapid initial drop in molecular weight, observed up to 45 min, was attributed to the presence of weak links in the polymer. The rate coefficients for the breakage of weak and strong links were determined, and the corresponding average activation energies were calculated to be 88 and 24 kJ/mol, respectively. (C) 2002 John Wiley Sons, Inc.

Ramachandran plot on the web

A graphics package has been developed to display the main chain torsion angles phi, psi (phi, Psi); (Ramachandran angles) in a protein of known structure. In addition, the package calculates the Ramachandran angles at the central residue in the stretch of three amino acids having specified the flanking residue types. The package displays the Ramachandran angles along with a detailed analysis output. This software is incorporated with all the protein structures available in the Protein Databank.

Thermal degradation studies of para-substituted poly(styrene peroxide)s

The thermal degradation of a series of para-substituted poly(styrene peroxide)s with electron-donating [CH3, C(CH3)(3)] and electron-attracting (Br) substitutents are investigated by thermogravimetric analysis (TGA). The results indicate that the Hammett relationship can describe quantitatively the trends in maximum rate of polymer decomposition (T-max) observed in TGA and thus thermostability of substituted poly(styrene peroxide)s depends only on the electronic nature of substituents and their ability to stabilize macroradicals formed during chain scission. The experimental results are also substantiated by thermochemical calculations. (C) 2002 Elsevier Science Ltd. All rights reserved.

Grafting of m-isopropenyl-alpha, alpha-dimethylbenzyl-isocyanate (m-TMI) onto isotactic polypropylene: Synthesis and characterization

A novel vinyl monomer with an isocyanate functional group, m-isopropenyl-alpha,alpha-dimethylbenzyl-isocyanate (m-TMI), was grafted onto isotactic polypropylene (i-PP) using dicumyl peroxide (DCP) as the initiator. This would open up the possibility of using the grafted polymer with the reactive isocyanate group as compatibilizer for blending carbohydrates such as cellulose with. polypropylene. The grafting was carried out in a Brabender Plasticoder at 180degreesC. The effects of monomer and initiator concentrations on the yield of grafting were investigated by performing statistical analysis. While the grafting yield increased with the concentration of DCP at any given concentration of m-TMI, the variation of the grafting yield with m-TMI concentration, for a given concentration of DCP, went through a maximum, the optimum yield of 7.8% (w/w) being obtained at 10 wt.% concentration of both DCP and m-TMI. The grafting reaction is. accompanied by considerable chain scission of I-PP, resulting in a decrease in the molecular weight of the grafted polymer. While the molecular weight drops sharply even at a low concentration of DCP, there occurs no further significant change in the molecular weight even at much higher concentrations of the initiator.

Improvement of protein structure comparison using a structural alphabet

The three dimensional structure of a protein provides major insights into its function. Protein structure comparison has implications in functional and evolutionary studies. A structural alphabet (SA) is a library of local protein structure prototypes that can abstract every part of protein main chain conformation. Protein Blocks (PBS) is a widely used SA, composed of 16 prototypes, each representing a pentapeptide backbone conformation defined in terms of dihedral angles. Through this description, the 3D structural information can be translated into a 1D sequence of PBs. In a previous study, we have used this approach to compare protein structures encoded in terms of PBs. A classical sequence alignment procedure based on dynamic programming was used, with a dedicated PB Substitution Matrix (SM). PB-based pairwise structural alignment method gave an excellent performance, when compared to other established methods for mining. In this study, we have (i) refined the SMs and (ii) improved the Protein Block Alignment methodology (named as iPBA). The SM was normalized in regards to sequence and structural similarity. Alignment of protein structures often involves similar structural regions separated by dissimilar stretches. A dynamic programming algorithm that weighs these local similar stretches has been designed. Amino acid substitutions scores were also coupled linearly with the PB substitutions. iPBA improves (i) the mining efficiency rate by 6.8% and (ii) more than 82% of the alignments have a better quality. A higher efficiency in aligning multi-domain proteins could be also demonstrated. The quality of alignment is better than DALI and MUSTANG in 81.3% of the cases. Thus our study has resulted in an impressive improvement in the quality of protein structural alignment. (C) 2011 Elsevier Masson SAS. All rights reserved.

Thermal degradation kinetics of poly(trimethylol propane triacrylate)/poly(hexane diol diacrylate) interpenetrating polymer network

Interpenetrating polymer networks (IPNs) of trimethylol propane triacrylate (TMPTA) and 1,6-hexane diol diacrylate (HDDA) at different weight ratios were synthesized. Temperature modulated differential scanning calorimetry (TMDSC) was used to determine whether the formation resulted in a copolymer or interpenetrating polymer network (IPN). These polymers are used as binders for microstereolithography (MSL) based ceramic microfabrication. The kinetics of thermal degradation of these polymers are important to optimize the debinding process for fabricating 3D shaped ceramic objects by MSL based rapid prototyping technique. Therefore, thermal and thermo-oxidative degradation of these IPNs have been studied by dynamic and isothermal thermogravimetry (TGA). Non-isothermal model-free kinetic methods have been adopted (isoconversional differential and KAS) to calculate the apparent activation energy (E a) as a function of conversion (α) in N 2 and air. The degradation of these polymers in N 2 atmosphere occurs via two mechanisms. Chain end scission plays a dominant role at lower temperature while the kinetics is governed by random chain scission at higher temperature. Oxidative degradation shows multiple degradation steps having higher activation energy than in N 2. Isothermal degradation was also carried out to predict the reaction model which is found to be decelerating. It was shown that the degradation of PTMPTA follows a contracting sphere reaction model in N 2. However, as the HDDA content increases in the IPNs, the degradation reaction follows Avrami-Erofeev model and diffusion governed mechanisms. The intermediate IPN compositions show both type of mechanism. Based on the above study, debinding strategy for MSL based microfabricated ceramic structure has been proposed. © 2012 Elsevier B.V.

Packing in molten globules and native states

Close packing of hydrophobic residues in the protein interior is an important determinant of protein stability. Cavities introduced by large to small substitutions are known to destabilize proteins. Conversely, native states of proteins and protein fragments can be stabilized by filling in existing cavities. Molten globules (MGs) were initially used to describe a state of protein which has well-defined secondary structure but little or no tertiary packing. Subsequent studies have shown that MGs do have some degree of native-like topology and specific packing. Wet molten globules (WMGs) with hydrated cores and considerably decreased packing relative to the native state have been studied extensively. Recently there has been renewed interest in identification and characterization of dry molten globules (DMGs). These are slightly expanded forms of the native state which show increased conformational flexibility, native-like main-chain hydrogen bonding and dry interiors. The generality of occurrence of DMGs during protein unfolding and the extent and nature of packing in DMGs remain to be elucidated. Packing interactions in native proteins and MGs can be probed through mutations. Next generation sequencing technologies make it possible to determine relative populations of mutants in a large pool. When this is coupled to phenotypic screens or cell-surface display, it becomes possible to rapidly examine large panels of single-site or multi-site mutants. From such studies, residue specific contributions to protein stability and function can be estimated in a highly parallelized fashion. This complements conventional biophysical methods for characterization of packing in native states and molten globules.

Role of invariant water molecules and water-mediated ionic interactions in D-xylose isomerase from Streptomyces rubiginosus

The enzyme, D-xylose isomerase (D-xylose keto-isomerase; EC 5.3.1.5) is a soluble enzyme that catalyzes the conversion of the aldo-sugar D-xylose to the keto-sugar D-xylulose. A total of 27 subunits of D-xylose isomerase from Streptomyces rubiginosus were analyzed in order to identify the invariant water molecules and their water-mediated ionic interactions. A total of 70 water molecules were found to be invariant. The structural and/or functional roles of these water molecules have been discussed. These invariant water molecules and their ionic interactions may be involved in maintaining the structural stability of the enzyme D-xylose isomerase. Fifty-eight of the 70 invariant water molecules (83%) have at least one interaction with the main chain polar atom.

Crystal structures of SCP2-thiolases of Trypanosomatidae, human pathogens causing widespread tropical diseases: the importance for catalysis of the cysteine of the unique HDCF loop

Thiolases are essential CoA-dependent enzymes in lipid metabolism. In the present study we report the crystal structures of trypanosomal and leishmanial SCP2 (sterol carrier protein, type-2)-thiolases. Trypanosomatidae cause various widespread devastating (sub)-tropical diseases, for which adequate treatment is lacking. The structures reveal the unique geometry of the active site of this poorly characterized subfamily of thiolases. The key catalytic residues of the classical thiolases are two cysteine residues, functioning as a nucleophile and an acid/base respectively. The latter cysteine residue is part of a CxG motif. Interestingly, this cysteine residue is not conserved in SCP2-thiolases. The structural comparisons now show that in SCP2-thiolases the catalytic acid/base is provided by the cysteine residue of the HDCF motif, which is unique for this thiolase subfamily. This HDCF cysteine residue is spatially equivalent to the CxG cysteine residue of classical thiolases. The HDCF cysteine residue is activated for acid/base catalysis by two main chain NH-atoms, instead of two water molecules, as present in the CxG active site. The structural results have been complemented with enzyme activity data, confirming the importance of the HDCF cysteine residue for catalysis. The data obtained suggest that these trypanosomatid SCP2-thiolases are biosynthetic thiolases. These findings provide promise for drug discovery as biosynthetic thiolases catalyse the first step of the sterol biosynthesis pathway that is essential in several of these parasites.

PROPENSITIES OF AMINO ACID RESIDUES IN PROTEINS FOR DIFFERENT REGIONS OF THE RAMACHANDRAN MAP

Using a dataset of 1164 crystal structures of largely non-homologous proteins defined at a resolution of 1.5 angstrom or better, we have investigated the (phi,psi) preferences of 20 residue types by considering the residues which occur in loops. Propensities of residue types to occur in the loops with (phi,psi) values in the aa region of the Ramachandran map has a poor correlation coefficient of 0.48 to the Chou-Fasman propensities of the residue types to occur in the a-helical segments. However the correlation coefficient between propensities of residues in loops to adopt beta conformations and those in beta-sheet is much higher (0.95). These observations suggest that a-helix formation is well influenced by the local amino acid sequence while intrinsic preference of residue types for beta-sheet plays a major role in the formation of beta-sheet. The main chain polar groups of residues in loops, that can affect the (phi,psi) values, can be involved in intra-molecular hydrogen bonding. Therefore we investigated further by considering subset of residues in loops with low (0 to 2) number of intra-molecular hydrogen bonds per residue involving main chain polar atoms. For this subset, the correlation coefficients between propensities for alpha-helix and alpha(R) region and between beta-sheet and beta-region are 0.26 and 0.64 respectively. This reiterates higher intrinsic tendency of beta-region favouring residues to adopt beta-sheet than alpha(R) region favouring residues to adopt alpha-helical structure.

Peptide delta-Turn: Literature Survey and Recent Progress

Among the various types of a-peptide folding motifs, delta-turn, which requires a central cis-amide disposition, has been one of the least extensively investigated. In particular, this main-chain reversal topology has been studied in-depth neither in linear/cyclic peptides nor in proteins. This Minireview article assembles and critically analyzes relevant data from a literature survey on the d-turn conformation in those compounds. Unpublished results from recent conformational energy calculations and a preliminary solution-state analysis on a small model peptide, currently ongoing in our laboratories, are also briefly outlined.

Avaliação de modelos preditivos de sorção em membranas de pervaporação para a remoção de sulfurados da nafta

A remoção de compostos sulfurados da gasolina é um assunto de grande interesse na indústria de refino de petróleo em função das restrições ambientais cada vez mais rígidas em relação ao teor máximo de enxofre de produtos acabados. A solução mais comum para remoção de contaminantes são as unidades de hidrotratamento que operam a alta pressão e possuem alto custo de instalação e de operação além de levarem à perda de octanagem do produto acabado. O uso de membranas é uma alternativa promissora para a redução do teor de enxofre de correntes de gasolina e possui diversas vantagens em relação ao hidrotratamento convencional. O conhecimento aprofundado dos parâmetros que influenciam as etapas de sorção e difusão é crítico para o desenvolvimento da aplicação. Este trabalho avalioua seletividade e sorção do sistema formado por n-heptano e tiofeno em polímeros através de modelos termodinâmicos rigorosos, baseados em contribuição de grupos. O modelo UNIFAC-FV, variante do tradicional modelo UNIFAC para sistemas poliméricos, foi o modelo escolhido para cálculo de atividade dos sistemas estudados. Avaliou-se ainda a disponibilidade de parâmetros para desenvolvimento da modelagem e desenvolveu-se uma abordagem com alternativas para casos de indisponibilidade de parâmetros UNIFAC. Nos casos com ausência de parâmetros, o cálculo do termo residual da atividade das espécies é feito na forma proposta por Flory-Hugginsutilizando-se parâmetros de solubilidade obtidos também por contribuição de grupos. Entre os métodos de contribuição de grupos existentes para cálculo de parâmetros de solubilidade, o método de Hoy mostrou menores desvios para os sistemas estudados. A abordagem utilizada neste trabalho permite, ao final, uma análise de alterações da configuração da cadeia principal de polímeros de forma a influenciar sua seletividade e sorção para dessulfurização de naftas

主链含六元氮杂环聚酰亚胺的合成及性能

聚酰亚胺是一类综合性能优异的耐热高分子材料，不仅具有很高的热性能，机械性能，和化学稳定性，还具有较低的介电常数和热膨胀系数，使它在航空，航天工业，微电子工业等诸多领域获得了广泛的应用。研究发现芳杂环的引入能为聚酰亚胺带来一定特殊的性能，因而由芳杂环单体合成的聚酰亚胺一直备受关注。近年来由含氮杂环的单体合成的聚酰亚胺及其性能不断被报道，这些聚合物具有很优异的性能。研究表明这些优异的性能与酰亚胺环的对称性，芳香性和杂原子带来的极性有关。吡啶、嘧啶等芳杂环是刚性的芳杂环分子，具有很好的耐热性能及化学稳定性能，而且杂环中的N 原子又可与金属离子配位和质子化。因而，含吡啶(或嘧啶)环聚合物在具有很好的热稳定性及化学稳定性同时，还会具有较好的可加工性。本论文以硝基取代的vinamidinium salts，amidine salts和易烯醇化的羰基化合物为原料，通过在碱性条件下的环化反应得到得含吡啶环(或嘧啶环)的硝基化合物；硝基化合物用Pd/C和水合肼还原得到棒状含氮芳杂环二胺：2,5-二(4-氨基苯基)嘧啶，2-氨基-5-(4-氨基苯基)嘧啶，2-(4-氨基苯基)-5-氨基嘧啶，2,5-二(4-氨基苯基)吡啶，和2-(4-氨基苯基)-5-氨基吡啶。通过1H-NMR、13C-NMR、IR、MS及元素分析确证了含氮芳杂环二胺及其中间产物的结构。这种二胺或加一定量对苯二胺与均苯二酐(PMDA)或联苯二酐(BPDA)通过两步法聚合获得一系列聚酰亚胺，通过红外、动态力学、静态力学、热重分析、广角X-Ray衍射等实验测试了该类聚合物的结构、热性能、机械性能及结晶性能。研究表明，所得聚酰亚胺的分子链有很高的规整性，表现出很好的化学稳定性，优异的热性能和机械性能。当PPD的含量为50%时，由相同二酐单体所得的聚合物具有最好的综合性能，其中杂环中氮原子的极性对维持聚合物的热稳定性和聚合物在高温条件下的机械性能性起着很重要的作用。并将PPD的含量为50%的聚酰胺酸胶液通过干-湿纺，热亚胺化，和高温牵伸获得聚酰亚胺纤维，并研究了亚胺化条件和牵伸条件对聚酰亚胺纤维性能的影响。