Tuning of redox potential and visible absorption band of ruthenium(II) complexes of (benzimidazolyl) derivatives: synthesis, characterization, spectroscopic and redox properties, X-ray structures and DFT calculations

Six ruthenium(II) complexes have been prepared using the tridentate ligands 2,6-bis(benzimidazolyl) pyridine and bis(2-benzimidazolyl methyl) amine and having 2,2'-bipyridine, 2,2':6',2 ''-terpyridine, PPh3, MeCN and chloride as coligands. The crystal structures of three of the complexes trans-[Ru(bbpH(2))(PPh3)(2)(CH3CN)I(ClO4)(2) center dot 2H(2)O (2), [Ru(bbpH(2))(bpy)Cl]ClO4 (3) and [Ru(bbpH(2))(terpy)](ClO4)(2) (4) are also reported. The complexes show visible region absorption at 402-517 nm, indicating that it is possible to tune the visible region absorption by varying the ancillary ligand. Luminescence behavior of the complexes has been studied both at RT and at liquid nitrogen temperature (LNT). Luminescence of the complexes is found to be insensitive to the presence of dioxygen. Two of the complexes [Ru(bbpH(2))(bpy)Cl]ClO4 (3) and [Ru(bbpH(2))(terpy]ClO4)(2) (4) show RT emission in the NIR region, having lifetime, quantum yield and radiative constant values suitable for their application as NIR emitter in the solid state devices. The DFT calculations on these two complexes indicate that the metal t(2g) electrons are appreciably delocalized over the ligand backbone. (C) 2006 Elsevier B.V. All rights reserved.

Syntheses, structures, some reactions, and electrochemical oxidation of ferrocenylethynyl complexes of iron, ruthenium, and osmium

The syntheses and characterizations of several complexes containing ferrocenylethynyl and ferrocene-1,1'-bis(ethynyl) groups attached to M(PP)Cp'[M = Fe, Ru, PP = dppe, Cp'= Cp*; M = Ru, Os, PP = (PPh3)(2), dppe, Cp' = Cp] are described. Reactions with tetracyanoethene have given either tetracyanobuta-1,3-dienyl or eta(3)-allylic derivatives, while addition of Me+ afforded the corresponding vinylidene derivatives. Some electrochemical measurements are discussed in terms of electronic communication between the redox-active M(PP)Cp' groups through the ferrocene nucleus. The molecular structures of 14 of these complexes have been determined by crystallographic methods.

Nickel(II) and copper(II) complexes of Schiff base ligands containing N4O2 and N4S2 donors with pyrrole terminal binding groups: synthesis, characterization, X-ray structures, DFT and electrochemical studies

A series of hexadentate ligands, H2Lm (m = 1−4), [1H-pyrrol-2-ylmethylene]{2-[2-(2-{[1H-pyrrol-2-ylmethylene]amino}phenoxy)ethoxy]phenyl}amine (H2L1), [1H-pyrrol-2-ylmethylene]{2-[4-(2-{[1H-pyrrol-2-ylmethylene]amino}phenoxy)butoxy]phenyl}amine (H2L2), [1H-pyrrol-2-ylmethylene][2-({2-[(2-{[1H-pyrrol-2-ylmethylene]amino}phenyl)thio]ethyl}thio)phenyl]amine (H2L3) and [1H-pyrrol-2-ylmethylene][2-({4-[(2-{[1H-pyrrol-2-lmethylene]amino}phenyl)thio]butyl}thio) phenyl]amine (H2L4) were prepared by condensation reaction of pyrrol-2-carboxaldehyde with {2-[2-(2-aminophenoxy)ethoxy]phenyl}amine, {2-[4-(2-aminophenoxy)butoxy]phenyl}amine, [2-({2-[(2-aminophenyl)thio]ethyl}thio)phenyl]amine and [2-({4-[(2-aminophenyl)thio]butyl}thio)phenyl]amine respectively. Reaction of these ligands with nickel(II) and copper(II) acetate gave complexes of the form MLm (m = 1−4), and the synthesized ligands and their complexes have been characterized by a variety of physico-chemical techniques. The solid and solution states investigations show that the complexes are neutral. The molecular structures of NiL3 and CuL2, which have been determined by single crystal X-ray diffraction, indicate that the NiL3 complex has a distorted octahedral coordination environment around the metal while the CuL2 complex has a seesaw coordination geometry. DFT calculations were used to analyse the electronic structure and simulation of the electronic absorption spectrum of the CuL2 complex using TDDFT gives results that are consistent with the measured spectroscopic behavior of the complex. Cyclic voltammetry indicates that all copper complexes are electrochemically inactive but the nickel complexes with softer thioethers are more easily oxidized than their oxygen analogs.

Predicting protein structures and structural annotation of proteomes

Protein structure prediction methods aim to predict the structures of proteins from their amino acid sequences, utilizing various computational algorithms. Structural genome annotation is the process of attaching biological information to every protein encoded within a genome via the production of three-dimensional protein models.

Syntheses, structures and efficient catalysis for C–C coupling of some benzaldehyde thiosemicarbazone complexes of palladium

Reaction of the 4-R-benzaldehyde thiosemicarbazones (denoted in general as L-R; R = OCH(3), CH(3), H, Cl and NO(2)) with trans-[Pd(PPh(3))(2)Cl(2)] afforded a group of mixed-ligand complexes (denoted in general as 1-R) incorporating a N,S-coordinated thiosemicarbazone. a triphenylphosphine and a chloride. Similar reaction with Na(2)[PdCl(4)] afforded a family of bis-thiosemicarbazone complexes (denoted in general as 2-R), where each ligand is N,S-coordinated. Crystal structures of 1-CH(3), 1-NO(2), 2-OCH(3), 2-NO(2) and L-NO(2) have been determined. In all the complexes the thiosemicarbazones are coordinated to the metal center, via dissociation of the acidic proton, as bidentate N,S-donors forming five-membered chelate rings. With reference to the structure of the uncoordinated thiosemicarbazone, this coordination mode is associated with a conformational change around the C=N bond. All the 1-R and 2-R complexes display intense absorptions in the visible region. Catalytic activity of the 1-R and 2-R complexes towards some C-C coupling reactions (e.g. Suzuki, Heck and Sonogashira) has been examined and while both are found to be efficient catalysts, 1-R is much better catalyst than 2-R.

The vertical structure of oceanic Rossby waves: a comparison of high-resolution model data to theoretical vertical structures

Tests of the new Rossby wave theories that have been developed over the past decade to account for discrepancies between theoretical wave speeds and those observed by satellite altimeters have focused primarily on the surface signature of such waves. It appears, however, that the surface signature of the waves acts only as a rather weak constraint, and that information on the vertical structure of the waves is required to better discriminate between competing theories. Due to the lack of 3-D observations, this paper uses high-resolution model data to construct realistic vertical structures of Rossby waves and compares these to structures predicted by theory. The meridional velocity of a section at 24° S in the Atlantic Ocean is pre-processed using the Radon transform to select the dominant westward signal. Normalized profiles are then constructed using three complementary methods based respectively on: (1) averaging vertical profiles of velocity, (2) diagnosing the amplitude of the Radon transform of the westward propagating signal at different depths, and (3) EOF analysis. These profiles are compared to profiles calculated using four different Rossby wave theories: standard linear theory (SLT), SLT plus mean flow, SLT plus topographic effects, and theory including mean flow and topographic effects. Our results support the classical theoretical assumption that westward propagating signals have a well-defined vertical modal structure associated with a phase speed independent of depth, in contrast with the conclusions of a recent study using the same model but for different locations in the North Atlantic. The model structures are in general surface intensified, with a sign reversal at depth in some regions, notably occurring at shallower depths in the East Atlantic. SLT provides a good fit to the model structures in the top 300 m, but grossly overestimates the sign reversal at depth. The addition of mean flow slightly improves the latter issue, but is too surface intensified. SLT plus topography rectifies the overestimation of the sign reversal, but overestimates the amplitude of the structure for much of the layer above the sign reversal. Combining the effects of mean flow and topography provided the best fit for the mean model profiles, although small errors at the surface and mid-depths are carried over from the individual effects of mean flow and topography respectively. Across the section the best fitting theory varies between SLT plus topography and topography with mean flow, with, in general, SLT plus topography performing better in the east where the sign reversal is less pronounced. None of the theories could accurately reproduce the deeper sign reversals in the west. All theories performed badly at the boundaries. The generalization of this method to other latitudes, oceans, models and baroclinic modes would provide greater insight into the variability in the ocean, while better observational data would allow verification of the model findings.

Epidemics in networks of spatially correlated three-dimensional root-branching structures

Using digitized images of the three-dimensional, branching structures for root systems of bean seedlings, together with analytical and numerical methods that map a common susceptible-infected- recovered (`SIR`) epidemiological model onto the bond percolation problem, we show how the spatially correlated branching structures of plant roots affect transmission efficiencies, and hence the invasion criterion, for a soil-borne pathogen as it spreads through ensembles of morphologically complex hosts. We conclude that the inherent heterogeneities in transmissibilities arising from correlations in the degrees of overlap between neighbouring plants render a population of root systems less susceptible to epidemic invasion than a corresponding homogeneous system. Several components of morphological complexity are analysed that contribute to disorder and heterogeneities in the transmissibility of infection. Anisotropy in root shape is shown to increase resilience to epidemic invasion, while increasing the degree of branching enhances the spread of epidemics in the population of roots. Some extension of the methods for other epidemiological systems are discussed.

From Rational Design of Drug Crystals to Understanding of Nucleic Acid Structures: Lamivudine Duplex

A DNA-like duplex of nucleosides is probable to exist even without the 5`-phosphate groups needed to assemble the chain backbone. However, double-stranded helical structures of nucleosides are unknown. Here, we report a duplex of nucleoside analogs that is spontaneously assembled due to stacking of the neutral and protonated molecules of lamivudine, a nucleoside reverse transcriptase inhibitor (NTRI) widely used in anti-HIV drug combinatory medication. The left-handed lamivudine duplex has features similar to those of i-motif DNA, as the face-to-face base stacking and the helix rise per base pair. Furthermore, the protonation pattern on alternate bases expected for it DNA-like duplex stabilized by pairing of neutral and protonated cytosine fragments was observed for the first time in the lamivudine double-stranded helix. This structure demonstrates that hydrogen bonds can substitute for covalent phosphodiester linkage in the stabilization of the duplex backbone. This interesting example of spontaneous molecular self-organization indicates that the 5`-phosphate group could not be a requirement for duplex assembly.

Crystal structures and thermal behavior of alkaline earth tricyanomethanides

The alkaline earth tricyanomethanides Mg(tcm)(2) center dot 2H(2)O, Ca(tcm)(2), Sr(tcm)(2) - H2O and Ba(tcm)(2) center dot 2H(2)O were prepared from aqueous solutions of the respective chlorides and silver tricyanomethanide. Their IR spectra and thermal behavior are described. The crystal structures of Ca(tcm)(2) and Ba(tcm)(2) center dot 2H(2)O were determined by single crystal X-ray diffraction. The structure of Ca(tcm)(2) is of the type found for several transition metal tricyanomethanides [1], containing two independent interpenetrating networks. Ba(tcm)(2) center dot 2H(2)O has a unique crystal structure corresponding to a three-dimensional coordination polymer with nine fold coordinated Ba atoms connected by water molecules and tricyanomethanide anions.

Structural requirement for PPAR gamma binding revealed by a meta analysis of holo-crystal structures

PPAR gamma is a ligand regulated transcriptional factor that modulates the transcription of several genes involved in fat and sugar metabolism. Due to its easy bacterial expression and crystallization, several crystal structures of holo-PPAR gamma have been reported and deposited in the Protein Data Bank. Here, we investigated the three-dimensional electrostatic properties of 55 PPAR gamma ligands and used this information for clustering them through principal component analysis. We found out that, according to their electrostatic potential, these ligands can be separated in three groups, with different binding features. We also observed that non-selective and selective ligands show different 3D electrostatic properties and are separated in different clusters. The relevance of this analysis for the development of new binders is discussed. (C) 2010 Elsevier Masson SAS. All rights reserved.

Effect Of Different Hydrological Model Structures On The Assimilation Of Distributed Uncertain Observations

The reliable evaluation of the flood forecasting is a crucial problem for assessing flood risk and consequent damages. Different hydrological models (distributed, semi-distributed or lumped) have been proposed in order to deal with this issue. The choice of the proper model structure has been investigated by many authors and it is one of the main sources of uncertainty for a correct evaluation of the outflow hydrograph. In addition, the recent increasing of data availability makes possible to update hydrological models as response of real-time observations. For these reasons, the aim of this work it is to evaluate the effect of different structure of a semi-distributed hydrological model in the assimilation of distributed uncertain discharge observations. The study was applied to the Bacchiglione catchment, located in Italy. The first methodological step was to divide the basin in different sub-basins according to topographic characteristics. Secondly, two different structures of the semi-distributed hydrological model were implemented in order to estimate the outflow hydrograph. Then, synthetic observations of uncertain value of discharge were generated, as a function of the observed and simulated value of flow at the basin outlet, and assimilated in the semi-distributed models using a Kalman Filter. Finally, different spatial patterns of sensors location were assumed to update the model state as response of the uncertain discharge observations. The results of this work pointed out that, overall, the assimilation of uncertain observations can improve the hydrologic model performance. In particular, it was found that the model structure is an important factor, of difficult characterization, since can induce different forecasts in terms of outflow discharge. This study is partly supported by the FP7 EU Project WeSenseIt.

Antimicrobial resistance of heterotrophic marine bacteria isolated from seawater and sands of recreational beaches with different organic pollution levels in southeastern Brazil: evidences of resistance dissemination

Antimicrobial resistance of marine heterotrophic bacteria to different antimicrobials agents were evaluated in seawater, dry and wet sands from three marine recreational beaches with different pollution levels. In all studied beaches, the greatest frequencies of resistance were found in relation to penicillin. on Gonzaguinha, the most polluted beach, 72.3% of all isolated strains showed simple resistance, whilst 8.33% had multiple resistance. The values found on Ilha Porchat beach, were 70.8% and 6.9% for simple and multiple resistances, respectively. on GuaraA(0), the less polluted beach, only 35.3% of isolated strains had simple resistance. Multiple resistance was not observed. While samples from Gonzaguinha and Ilha Porchat beach showed isolated strains resistant to seven and six different antimicrobial agents, respectively, samples from GuaraA(0) beach were resistant only to penicillin and erytromicin. The positive correlations obtained between the degree of seawater contamination and frequency and variability of bacterial resistance indicate that polluted marine recreational waters and sands are sources of resistant bacteria contributing thus, to the dissemination of bacterial resistance.

Digestibility and metabolizable energy of maize gluten feed for dogs as measured by two different techniques

Maize gluten feed (MGF) is a co-product of wet milling of maize, and is composed of structures that remain after most starch, gluten and germ has been extracted from the grain. Although currently used in dog foods, its digestibility and energy values have not been documented. Two techniques were used to determine nutrient digestibility of MGF for dog foods. Both techniques used extruded diets fed to Beagle dogs, with six replicates per diet. The first study used a difference method in which 300 g/kg of a reference diet was replaced by MGF. Based on the difference method, the coefficient of total tract apparent digestibility (CTTAD) of MGF was 0.53 for dry matter (DM), 0.69 for crude protein (CP), 0.74 for fat, 0.99 for starch, and 0.55 for gross energy (GE). The calculated metabolizable energy (ME) of MGF was 7.99 MJ/kg (as-fed). The second study used a regression method and included a basal diet and a basal diet with 70, 140 and 210 g MGF/kg of diet (as a substitute for maize starch). Maize gluten feed inclusion resulted in a linear reduction of CTTAD of DM (R(2)=0.99; P<0.001), CP (R(2)=0.95; P=0.002), fat (R(2)=0.87; P=0.009). starch (R(2)=0.81; P<0.001), and GE (R(2)=0.99; P<0.001). Faecal production increased linearly from 56 g to 107 g/dog/d (R(2)=0.99; P<0.001), with a linear reduction of faecal DM (R(2)=0.99: P<0.001) and a linear increase in faecal lactic acid concentration (P<0.02). Both urine (R(2)=0.77; P=0.029) and faeces (R(2)=0.92: P=0.019) showed a linear reduction in pH. Results of ingredient MAD obtained by the regression and difference methods were close (6% or less of variation) for CP, fat, and starch, and also for ME content (1.4% higher for the difference method), but the two methods disagreed on calculated CTTAD of DM and organic matter. The high dietary fiber content of MGF (382 g/kg) may explain the low digestibility of this ingredient. Maize gluten feed could be a useful ingredient for formulations designed to have low energy or reduce the urine pH of dogs. (C) 2011 Elsevier B.V. All rights reserved.

Dominance of legume trees alters nutrient relations in mixed species forest restoration plantings within seven years

Failures in reforestation are often attributed to nutrient limitation for tree growth. We compared tree performance and nitrogen and phosphorus relations in adjacent mixed-species plantings of contrasting composition, established for forest restoration on Ultisol soil, originally covered by tropical semi-deciduous Atlantic Forest in Southeast Brazil. Nutrient relations of four tree species occurring in both planting mixtures were compared between a legume-dominated, species-poor direct seeding mixture of early-successional species ("legume mixture"), and a species-diverse, legume-poor mixture of all successional groups ("diverse mixture"). After 7 years, the legume mixture had 6-fold higher abundance of N(2)-fixing trees, 177% higher total tree basal area, 22% lower litter C/N, six-fold higher in situ soil resin-nitrate, and 40% lower in situ soil resin-P, compared to the diverse mixture. In the legume mixture, non-N(2)-fixing legume Schizolobium parahyba (Fabaceae-Caesalpinioideae) had significantly lower proportional N resorption, and both naturally regenerating non-legume trees had significantly higher leaf N concentrations, and higher proportional P resorption, than in the diverse mixture. This demonstrate forms of plastic adjustment in all three non-N(2)-fixing species to diverged nutrient relations between mixtures. By contrast, leaf nutrient relations in N(2)-fixing Enterolobium contortisiliquum (Fabaceae-Mimosoideae) did not respond to planting mixtures. Rapid N accumulation in the legume mixture caused excess soil nitrification over nitrate immobilization and tighter P recycling compared with the diverse mixture. The legume mixture succeeded in accelerating tree growth and canopy closure, but may imply periods of N losses and possibly P limitation. Incorporation of species with efficient nitrate uptake and P mobilization from resistant soil pools offers potential to optimize these tradeoffs.

Phosphorus, nitrogen, and carbon contents of macrophytes in lakes lateral to a tropical river (Paranapanema River, São Paulo, Brazil)

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