A TDDFT study of the excited states of DNA bases and their assemblies

We present a detailed study of the optical absorption spectra of DNA bases and base pairs, carried out by means of time dependent density functional theory. The spectra for the isolated bases are compared to available theoretical and experimental data and used to assess the accuracy of the method and the quality of the exchange-correlation functional. Our approach turns out to be a reliable tool to describe the response of the nucleobases. Furthermore, we analyze in detail the impact of hydrogen bonding and pi-stacking in the calculated spectra for both Watson-Crick base pairs and Watson-Crick stacked assemblies. We show that the reduction of the UV absorption intensity (hypochromicity) for light polarized along the base-pair plane depends strongly on the type of interaction. For light polarized perpendicular to the basal plane, the hypochromicity effect is reduced, but another characteristic is found, namely a blue shift of the optical spectrum of the base-assembly compared to that of the isolated bases. The use of optical tools as fingerprints for the characterization of the structure (and type of interaction) is extensively discussed.     

Effect of SiO2 on relaxation phenomena and mechanism of ion conductivity of [Nafion/(SiO2)x] composite membranes

This report describes a study of the effect of SiO2 nanopowders on the mechanism of ionic motion and interactions taking place in hybrid inorganic-organic membranes based on Nafion. Five nanocomposite membranes of the formula [Nafion/(SiO2)x] with SiO2 ranging from 0 to 15 wt % were prepared by a solvent casting procedure. TG measurements demonstrated that the membranes are thermally stable up to 170 degrees C but with the loss water it changes the cluster environments and changes the conductivity properties. MDSC investigations in the 90-300 degrees C temperature range revealed the presence of three intense overlapping endothermal peaks indicated as I, II, and III. Peak I measures the order-disorder molecular rearrangement in hydrophilic polar clusters, II corresponds to the endothermic decomposition of -SO3 groups, and III describes the melting process in microcrystalline regions of hydrophobic fluorocarbon domains of the Nafion moiety. ESEM with EDAX measurements revealed that the membranes are homogeneous materials with smooth surfaces. DMA studies allowed us to measure two relaxation modes. The mechanical relaxation detected at ca. 100 degrees C is attributed to the motion of cluster aggregates of side chains and is diagnostic for R-SO3H...SiO2 nanocluster interactions. DMA disclosed that at SiO2/-SO3H (psi) molar ratios lower than 1.9, the oxoclusters act to restrict chain mobility of hydrophobic domains of Nafion and the dynamics inside polar cages of [Nafion/(SiO2)x] systems; at psi higher than 1.9, the oxoclusters reduce the cohesiveness of hydrophilic polar domains owing to a reduction in the density of cross-links. FT-IR and FT-Raman studies of the [Nafion/(SiO2)x] membranes indicated that the fluorocarbon chains of Nafion hydrophobic domains assume the typical helical conformation structure with a D(14pi/15) symmetry. These analyses revealed four different species of water domains embedded inside polar cages and their interconnecting channels: (a) bulk water [(H2O)n]; (b) water solvating the oxonium ions directly interacting with sulfonic acid groups [H3O+...SO3(-)-].(H2O)n; (c) water aggregates associated with H3O+ ions [H3O+.(H2O)n]; and (d) low associated water species in dimer form [(H2O)2]. The conductivity mechanism and relaxation events were investigated by broadband dielectric spectroscopy (BDS). [Nafion/(SiO2)x] nanocomposite membranes were found to possess two different molecular relaxation phenomena which are associated with the alpha-relaxation mode of PTFE-like fluorocarbon domains and the beta-relaxation mode of acid side groups of the Nafion component. Owing to their strong coupling, both these relaxation modes are diagnostic for the interactions between the polar groups of the Nafion host polymer and the (SiO2)x oxoclusters and play a determining role in the conductivity mechanism of the membranes. The studies support the proposal that long-range proton charge transfer in [Nafion/(SiO2)x] composites takes place due to a mechanism involving exchange of the proton between the four water domains. This latter proton transfer occurs owing to a subsequent combination of domain intersections resulting from the water domain fluctuations induced by the molecular relaxation events of host Nafion polymer.     

Morphology-controlled synthesis of ZnO nanostructures by a simple round-to-round metal vapor deposition route

One-dimensional ZnO nanostructures with different morphologies have been successfully synthesized through a simple round-to-round metal vapor deposition route at 550 degrees C with a zinc powder covered indium film as the source material. The structures and morphologies of the products were characterized in detail by using X-ray diffraction, scanning electron microscopy, and transmission electron microscopy. Studies found that the morphology of the products can be easily tuned from one experimental round to another. Possible growth mechanisms for the formation of one-dimensional ZnO nanostructures with different morphologies are discussed. Photoluminescence studies show that there are sharp UV emission and broad defect-related green emissions for the products obtained in all experimental rounds. Relative intensity of the UV emission to defect-related emissions gradually increased from one experimental round to another.     

Modulation of hydrophobic effect by cosolutes

This work concerns a comparison of the hydration properties and self-association behavior in aqueous solution of three biologically relevant simple molecules: tert-butyl alcohol (TBA), trimethylamine-n-oxide (TMAO), and glycine betaine (GB). These molecules were used as a model to study hydrophobic behavior in water solutions. In particular, water perturbation induced by TBA, TMAO, and GB molecules was studied as a function of the solute molar fraction X(2) (0 < X(2) < 0.04) by Raman spectra of water in the fundamental OH-stretching region (3,800-2,800 cm(-1)). Furthermore, possible hydrophobic clustering of these molecules was investigated by studying the behavior of the alkyl CH stretching band in the 3,100-2,900 cm(-1) frequency region as a function of X(2). To establish the existence of a correlation between the effects of these three solutes on the micellization process and changes in the properties of the solvent, the behavior of the critical micelle concentration of sodium dodecyl sulfate was also investigated as a function of the added amount of TBA, TMAO, and GB. On the whole, these data show that there is no direct correlation between a solute's effect on the water structure and its effect on micelle or protein stability. Results indicate that, while TBA starts to self-aggregate at approximately X(2) = 0.025, both TMAO and GB do not exhibit any significant self-aggregation up to the highest concentration considered. In addition, nonadditive perturbations of the H-bonded networks of solvent water are observed in the case of TBA solutions, but are absent in both the TMAO and GB cases. The absence of these nonlinear effects in TMAO and GB water solutions allow for tracing the microscopical mechanism of the neutrality of these osmolytes toward hydrophobic effects. This confers the compatibility to these two osmolytes, which can be accumulated at high concentrations without interfering with biochemical processes in the cell.     

Multipoint holographic optical velocimetry in microfluidic systems

We show how holographic optical trapping can be used for the multipoint measurement of fluid flow in microscopic geometries. An array of microprobes can be simultaneously trapped and used to map out the fluid flow in a microfluidic device. The optical traps are alternately turned on and off such that the probe particles are displaced by the flow of the surrounding fluid and then retrapped. The particles' displacements are monitored by digital video microscopy and directly converted into velocity field values. This technique enables the measurement of a two-dimensional flow field at points arbitrarily distributed in a three-dimensional volume. The validity of the technique is demonstrated for the case of the flow around a spinning sphere and the flow at the outlet of a microchannel.     

New 64Cu PET imaging agents for personalised medicine and drug development using the hexa-aza cage, SarAr

The success of positron emission tomography (PET) in personalised medicine and drug development requires radioisotopes that provide high quality images and flexible chemistry for a broad application. 64Cu is arguably one of the most suitable PET isotopes for imaging with the evolving target agents, but there are not many appropriate chelating agents for 64Cu and this has limited its wider application. The bi-functional chelator, SarAr is known to bind 64Cu2+ quantitatively (i.e. one metal per ligand present) and rapidly (<2 min) at 10(-6) M over a range of pH (4-9). In this paper the conjugation of SarAr to the whole and fragmented antibody is described. Conjugation of the SarAr to the protein does not impair its coordination of the 64Cu. It complexes the 64Cu2+ rapidly, quantitatively and essentially irreversibly at pH 5. Animal studies show that the 64Cu-SarAr-immunoconjugates maintain their specificity for the target and are stable in vivo. Also, SarAr is a platform technology, is easy to use in a kit formulation and is readily adaptable for the wider application in 64Cu PET imaging.     

On the effect of a point mutation on the reactivity of CuZn superoxide dismutase: a theoretical study

In this paper, we investigate the effects of a point mutation on the enzymatic activity of copper-zinc superoxide dismutase, which we recently studied in detail by means of a theoretical-computational procedure. Comparison of the reactivity of the initial catalytic steps in this mutant (G93A mutation far from the active site) with our previous data, reveals the beautiful mechanical-dynamical architecture of the enzyme, altered by such an apparently irrelevant mutation. Finally, our results suggest a possible atomic-molecular-based explanation for the mutant-pathology correlation, in line with the most recent experimental data.     

Monte Carlo vs molecular dynamics for all-atom polypeptide folding simulations

An efficient Monte Carlo (MC) algorithm including concerted rotations is directly compared to molecular dynamics (MD) in all-atom statistical mechanics folding simulations of small polypeptides. The previously reported algorithm "concerted rotations with flexible bond angles" (CRA) has been shown to successfully locate the native state of small polypeptides. In this study, the folding of three small polypeptides (trpzip2/H1/Trp-cage) is investigated using MC and MD, for a combined sampling time of approximately 10(11) MC configurations and 8 micros, respectively. Both methods successfully locate the experimentally determined native states of the three systems, but they do so at different speed, with 2-2.5 times faster folding of the MC runs. The comparison reveals that thermodynamic and dynamic properties can reliably be obtained by both and that results from folding simulations do not depend on the algorithm used. Similar to previous comparisons of MC and MD, it is found that one MD integration step of 2 fs corresponds to one MC scan, revealing the good sampling of MC. The simplicity and efficiency of the MC method will enable its future use in folding studies involving larger systems and the combination with replica exchange algorithms.     

Single-phase bimetallic system for the selective oxidation of glycerol to glycerate

Single phase bimetallic Au/Pd catalyst was prepared and characterised by TEM techniques. The high activity in the selective liquid phase oxidation of glycerol towards glycerate is unambiguously attributed to the synergistic effect of alloy.     

Study on the interaction of copper-zinc superoxide dismutase with aluminum ions by electrochemical and fluorescent method

The interaction of superoxide dismutase (SOD) with aluminum (Al) ions was investigated by cyclic voltammetry, fluorescence spectroscopy and synchronous fluorescence spectroscopy. The electrochemical activity of the SOD enzyme electrode was inhibited irreversibly by the addition of Al. Meanwhile, the static fluorescence quenching mechanism further revealed the existing of molecular complex of SOD with Al(3+). The association constant was obtained from Lineweaver-Burk plot. The experimental results of voltammetry and fluorescence spectroscopy indicated that the conformation of SOD molecule was altered by the formation of Al-SOD complex. It may influence the activity of SOD enzyme since the optimum action of SOD depends upon a particular configuration of electrostatic charges in the enzyme molecule.