Hydrodynamic equations for attractive particle systems on ℤ

Hydrodynamic properties for a class of nondiffusive particle systems are investigated. The method allows one to study local equilibria for a class of asymmetric zero-range processes, and applies as well to other models, such as asymmetric simple exclusion and misanthropes. Attractiveness is an essential ingredient. The hydrodynamic equations present shock wave phenomena. Preservation of local equilibrium is proven to hold away from the shocks. The problem of breakdown of local ergodicity at the shocks, which was investigated by D. Wick in a particular model, remains open in this more general setup.     

Intramolecular hydrogen bonds and hydrogen-bonded systems in di-Schiff bases of 4-methyl-isophthalaldehyde with 4-substituted anilines

Three di-Schiff bases of 2-hydroxy-5-methyl-isophthalaldehyde with 4-R-anilines (R=H, CH₃, OCH₃) and their 1:1 complexes with HClO₄ were studied by FT-IR, ¹H, and ¹³C NMR spectroscopy in acetonitrile and [²H₃]acetonitrile solutions, respectively. In di-Schiff bases intramolecular OH…N hydrogen bonds have been detected; however, they show no proton polarizability. Hydrogen-bonded systems with fast proton fluctuation and large proton polarizability have been found in the 1:1 complexes of di-Schiff bases with HClO₄.     

Intra- and intermolecular fluorescence quenching in 7-(pyridyl)indoles

Three isomeric 7-(pyridyl)indoles reveal very different, solvent-dependent photophysical properties. Due to rapid excited state depopulation involving intramolecular hydrogen bonding, 7-(2′-pyridyl)indole is practically nonfluorescent at room temperature. In nonpolar and polar aprotic solvents, 7-(3′-pyridyl)indole and 7-(4′-pyridyl)indole fluorescence strongly, but the emission is quenched in alcohols. Syn and anti rotameric forms of 7-(3′-pyridyl)indole are detected, each quenched to a different degree. This differential quenching is interpreted as evidence of enhanced S₁ → S₀ internal conversion being more efficient in cyclic solvates, with alcohol molecules forming a bridge between the proton donor and acceptor groups of an excited chromophore.     

Parameterization of peptide 13C carbonyl chemical shielding anisotropy in molecular dynamics simulations.

NMR chemical shielding anisotropy (CSA) relaxation is an important tool in the study of dynamical processes in proteins and nucleic acids in solution. Herein, we investigate how dynamical variations in local geometry affect the chemical shielding anisotropy relaxation of the carbonyl carbon nucleus, using the following protocol: 1) Using density functional theory, the carbonyl (13)C' CSA is computed for 103 conformations of the model peptide group N-methylacetamide (NMA). 2) The variations in computed (13)C' CSA parameters are fitted against quadratic hypersurfaces containing cross terms between the variables. 3) The predictive quality of the CSA hypersurfaces is validated by comparing the predicted and de novo calculated (13)C' CSAs for 20 molecular dynamics snapshots. 4) The CSA fluctuations and their autocorrelation and cross correlation functions due to bond-length and bond-angle distortions are predicted for a chemistry Harvard molecular mechanics (CHARMM) molecular dynamics trajectory of Ca(2+)-saturated calmodulin and GB3 from the hypersurfaces, as well as for a molecular dynamics (MD) simulation of an NMA trimer using a quantum mechanically correct forcefield. We find that the fluctuations can be represented by a 0.93 scaling factor of the CSA tensor for both R(1) and R(2) relaxations for residues in helix, coil, and sheet alike. This result is important, as it establishes that (13)C' relaxation is a valid tool for measurement of interesting dynamical events in proteins.     

Vascular endothelial and smooth muscle cell culture on NaOH-treated poly(epsilon-caprolactone) films: a preliminary study for vascular graft development

Tissue engineering offers the potential of providing vessels that can be used to replace diseased and damaged native blood vessels. The endothelization of a synthetic vascular graft minimizes the failures associated with blood clotting and platelet activation. The aim of this study was to culture vascular-derived endothelial and smooth muscle cells on both untreated and NaOH-treated poly(epsilon-caprolactone) (PCL) films, a biocompatible and bio-resorbable polymer, and to evaluate the behavior of both cell types as a preliminary study for vascular graft development. PCL films were prepared by hot pressing; characterized by DSC, IR, SEM, and scanning force microscopy; and treated with NaOH to increase the surface hydrophilicity before cell culture. Endothelial and smooth muscle cells, isolated from pig cava vein, were characterized by immunofluorescence and confocal microscopy studies of endothelial nitric oxide synthase and alpha-smooth muscle actin. Good adhesion, growth, viability and morphology of both the endothelial and smooth muscle cells on PCL films were obtained, but a light stimulation of mitochondrial activity was observed during short culture times. NaOH treatment improved the adhesion and enhanced the proliferation in both cell types. This verified the possible use of this modified polymer as a support in the preparation of a synthetic vascular graft. [Diagram: see text] SEM micrograph of smooth muscle cells cultured on NaOH-treated PCL film. (Original magnification: 1000x).     

Multistep energy transfer in single molecular photonic wires

We demonstrate the synthesis and spectroscopic characterization of an unidirectional photonic wire based on four highly efficient fluorescence energy-transfer steps (FRET) between five spectrally different chromophores covalently attached to double-stranded DNA. The DNA-based modular conception enables the introduction of various chromophores at well-defined positions and arbitrary interchromophore distances. While ensemble fluorescence measurements show overall FRET efficiencies between 15 and 30%, single-molecule spectroscopy performed on four spectrally separated detectors easily uncovers subpopulations that exhibit overall FRET efficiencies of up to approximately 90% across a distance of 13.6 nm and a spectral range of approximately 200 nm. Fluorescence trajectories of individual photonic wires show five different fluorescence intensity patterns which can be ascribed to successive photobleaching events.     

Energetic and topological analysis of the reaction of Mo and Mo2 with NH3, C2H2, and C2H4 molecules

The Density functional theory has been applied to characterize the structural features of Mo(1,2)-NH(3),-C(2)H(4), and -C(2)H(2) compounds. Coordination modes, geometrical structures, and binding energies have been calculated for several spin multiplets. It has been shown that in contrast to the conserved spin cases (Mo(1,2)-NH(3)), the interaction between Mo (or Mo(2)) and C(2)H(4) (or C(2)H(2)) are the low-spin (Mo-C(2)H(4) and -C(2)H(2)) and high-spin (Mo(2)-C(2)H(4) and -C(2)H(2)) complexes. In the ground state of Mo(1,2)-C(2)H(4) and -C(2)H(2), the metal-center always reacts with the C-C center. The spontaneous formation of the global minima is found to be possible due to the crossing between the potential energy surfaces (ground and excited states with respect to the metallic center). The bonding characterization has been performed using the topological analysis of the Electron Localization Function. It has been shown that the most stable electronic structure for a pi-acceptor ligand correlates with a maximum charge transfer from the metal center to the C-C bond of the unsaturated hydrocarbons, resulting in the formation of two new basins located on the carbon atoms (away from hydrogen atoms) and the reduction of the number of attractors of the C-C basin. The interaction between Mo(1,2) and C(2)H(4) (or C(2)H(2)) should be considered as a chemical reaction, which causes the multiplicity change. Contrarily, there is no charge transfer between Mo(1,2) and NH(3), and the partners are bound by an electrostatic interaction.     

Ascorbate-induced oxidation of formate by peroxodisulfate: product yields,kinetics and mechanism

The slow reaction between peroxodisulfate and formate is significantly accelerated by ascorbate at room temperature. The products of this induced oxidation, CO₂ and oxalate (C₂O^2– ₄), were analyzed by several methods and the kinetics of this reaction were measured. The overall mechanism involves free radical species. Ascorbate reacts with peroxodisulfate to initiate production of the sulfate radical ion (SO^– ₄), which reacts with formate to produce carbon dioxide radical ion (CO^– ₂) and sulfate. The carbon dioxide radical reacts with peroxodisulfate to form CO₂ or self-combines to form oxalate. Competition occurring between these two processes determines the overall fate of the carbon dioxide radical species. As pH decreases, protonation of the carbon dioxide radical ion tends to favor production of CO₂.     

Efficient RNase H-directed cleavage of RNA promoted by antisense DNA or 2'F-ANA constructs containing acyclic nucleotide inserts

The ability of modified antisense oligonucleotides (AONs) containing acyclic interresidue units to support RNase H-promoted cleavage of complementary RNA is described. Manipulation of the backbone and sugar geometries in these conformationally labile monomers shows great benefits in the enzymatic recognition of the nucleic acid hybrids, while highlighting the importance of local strand conformation on the hydrolytic efficiency of the enzyme more conclusively. Our results demonstrate that the duplexes support remarkably high levels of enzymatic degradation when treated with human RNase HII, making them efficient mimics of the native substrates. Furthermore, interesting linker-dependent modulation of enzymatic activity is observed during in vitro assays, suggesting a potential role for this AON class in an RNase H-dependent pathway of controlling RNA expression. Additionally, the butyl-modified 2'F-ANA AONs described in this work constitute the first examples of a nucleic acid species capable of eliciting high RNase H activity while possessing a highly flexible molecular architecture at predetermined sites along the AON.     

Characterization of Mercury – Humic Acids Interaction by Potentiometric Titration with a Modified Carbon Paste Mercury Sensor

Stability constant for mercury binding by commercial and natural humic acids (HA) were determined using a new potentiometric mercury(II) sensor based on dithiosalicylic acid modified carbon paste electrode. The sensor present a high selective and sensitive response to mercury(II) ions, and a low detection limit of 1.8×10^?8 M. The potentiometric titrations curves of humic acids against mercury(II) ions were modeled. For 1.00×10^?7 to 3.00×10^?4 M mercury(II) ion concentration levels the results are consistent with the presence of two different binding sites in the humic acid macromolecule. The strongest binding sites (log K₁ ranging from 10.1 to 6.8) are probably due to interaction with carboxylic acid and amine groups in the molecule, whereas weakest binding sites (log K₂ ranging from 8.8 to 4.5) can be associated to phenolic groups.