Insights into the molecular architecture of a peptide nanotube using FTIR and solid-state NMR spectroscopic measurements on an aligned sample

The self-assembly of proteins and peptides into b-sheet-rich amyloid fibers is a process that has gained notoriety because of its association with human diseases and disorders. Spontaneous self-assembly of peptides into nonfibrillar supramolecular structures can also provide a versatile and convenient mechanism for the bottom-up design of biocompatible materials with functional properties favoring a wide range of practical applications.[1] One subset of these fascinating and potentially useful nanoscale constructions are the peptide nanotubes, elongated cylindrical structures with a hollow center bounded by a thin wall of peptide molecules.[2] A formidable challenge in optimizing and harnessing the properties of nanotube assemblies is to gain atomistic insight into their architecture, and to elucidate precisely how the tubular morphology is constructed from the peptide building blocks. Some of these fine details have been elucidated recently with the use of magic-angle-spinning (MAS) solidstate NMR (SSNMR) spectroscopy.[3] MAS SSNMR measurements of chemical shifts and through-space interatomic distances provide constraints on peptide conformation (e.g., b-strands and turns) and quaternary packing. We describe here a new application of a straightforward SSNMR technique which, when combined with FTIR spectroscopy, reports quantitatively on the orientation of the peptide molecules within the nanotube structure, thereby providing an additional structural constraint not accessible to MAS SSNMR.

Array based detection of antibiotic resistance genes in Gram negative bacteria isolated from retail poultry meat in the UK and Ireland

The use of antibiotics in birds and animals intended for human consumption within the European Union (EU) and elsewhere has been subject to regulation prohibiting the use of antimicrobials as growth promoters and the use of last resort antibiotics in an attempt to reduce the spread of multi-resistant Gram negative bacteria. Given the inexorable spread of antibiotic resistance there is an increasing need for improved monitoring of our food. Using selective media, Gram negative bacteria were isolated from retail chicken of UK-Intensively reared (n = 27), Irish-Intensively reared (n = 19) and UK-Free range (n = 30) origin and subjected to an oligonucleotide based array system for the detection of 47 clinically relevant antibiotic resistance genes (ARGs) and two integrase genes. High incidences of β-lactamase genes were noted in all sample types, acc (67%), cmy (80%), fox (55%) and tem (40%) while chloramphenicol resistant determinants were detected in bacteria from the UK poultry portions and were absent in bacteria from the Irish samples. Denaturing Gradient Gel Electrophoresis (DGGE) was used to qualitatively analyse the Gram negative population in the samples and showed the expected diversity based on band stabbing and DNA sequencing. The array system proved to be a quick method for the detection of antibiotic resistance gene (ARG) burden within a mixed Gram negative bacterial population.

Adsorption of organic molecules at the TiO2(110) surface: the effect of van der Waals interactions

Understanding the interaction of organic molecules with TiO2 surfaces is important for a wide range of technological applications. While density functional theory (DFT) calculations can provide valuable insight about these interactions, traditional DFT approaches with local exchange-correlation functionals suffer from a poor description of non-bonding van der Waals (vdW) interactions. We examine here the contribution of vdW forces to the interaction of small organic molecules (methane, methanol, formic acid and glycine) with the TiO2 (110) surface, based on DFT calculations with the optB88-vdW functional. The adsorption geometries and energies at different configurations were also obtained in the standard generalized gradient approximation (GGA-PBE) for comparison. We find that the optB88-vdW consistently gives shorter surface adsorbate-to-surface distances and slightly stronger interactions than PBE for the weak (physisorbed) modes of adsorption. In the case of strongly adsorbed (chemisorbed) molecules both functionals give similar results for the adsorption geometries, and also similar values of the relative energies between different chemisorption modes for each molecule. In particular both functionals predict that dissociative adsorption is more favourable than molecular adsorption for methanol, formic acid and glycine, in general agreement with experiment. The dissociation energies obtained from both functionals are also very similar, indicating that vdW interactions do not affect the thermodynamics of surface deprotonation. However, the optB88-vdW always predicts stronger adsorption than PBE. The comparison of the methanol adsorption energies with values obtained from a Redhead analysis of temperature programmed desorption data suggests that optB88-vdW significantly overestimates the adsorption strength, although we warn about the uncertainties involved in such comparisons.

Precise analysis of array usage in scientific programs

The automatic transformation of sequential programs for efficient execution on parallel computers involves a number of analyses and restructurings of the input. Some of these analyses are based on computing array sections, a compact description of a range of array elements. Array sections describe the set of array elements that are either read or written by program statements. These sections can be compactly represented using shape descriptors such as regular sections, simple sections, or generalized convex regions. However, binary operations such as Union performed on these representations do not satisfy a straightforward closure property, e.g., if the operands to Union are convex, the result may be nonconvex. Approximations are resorted to in order to satisfy this closure property. These approximations introduce imprecision in the analyses and, furthermore, the imprecisions resulting from successive operations have a cumulative effect. Delayed merging is a technique suggested and used in some of the existing analyses to minimize the effects of approximation. However, this technique does not guarantee an exact solution in a general setting. This article presents a generalized technique to precisely compute Union which can overcome these imprecisions.

Quantitative structure of an acetate dye molecule analogue at the TiO2- acetic acid interface

The positions of atoms in and around acetate molecules at the rutile TiO2(110) interface with 0.1 M acetic acid have been determined with a precision of ±0.05 Å. Acetate is used as a surrogate for the carboxylate groups typically employed to anchor monocarboxylate dye molecules to TiO2 in dye-sensitised solar cells (DSSC). Structural analysis reveals small domains of ordered (2 x 1) acetate molecules, with substrate atoms closer to their bulk terminated positions compared to the clean UHV surface. Acetate is found in a bidentate bridge position, binding through both oxygen atoms to two five-fold titanium atoms such that the molecular plane is along the [001] azimuth. Density functional theory calculations provide adsorption geometries in excellent agreement with experiment. The availability of these structural data will improve the accuracy of charge transport models for DSSC.

Spatial and temporal variability of the concentration field from localized releases in a regular building array

Spatial and temporal fluctuations in the concentration field from an ensemble of continuous point-source releases in a regular building array are analyzed from data generated by direct numerical simulations. The release is of a passive scalar under conditions of neutral stability. Results are related to the underlying flow structure by contrasting data for an imposed wind direction of 0 deg and 45 deg relative to the buildings. Furthermore, the effects of distance from the source and vicinity to the plume centreline on the spatial and temporal variability are documented. The general picture that emerges is that this particular geometry splits the flow domain into segments (e.g. “streets” and “intersections”) in each of which the air is, to a first approximation, well mixed. Notable exceptions to this general rule include regions close to the source, near the plume edge, and in unobstructed channels when the flow is aligned. In the oblique (45 deg) case the strongly three-dimensional nature of the flow enhances mixing of a scalar within the canopy leading to reduced temporal and spatial concentration fluctuations within the plume core. These fluctuations are in general larger for the parallel flow (0 deg) case, especially so in the long unobstructed channels. Due to the more complex flow structure in the canyon-type streets behind buildings, fluctuations are lower than in the open channels, though still substantially larger than for oblique flow. These results are relevant to the formulation of simple models for dispersion in urban areas and to the quantification of the uncertainties in their predictions.

Surfactant-nanotube interactions in water and nanotube separation by diameter: atomistic simulations

A non-destructive sorting method to separate single-walled carbon nanotubes (SWNTs) by diameter was recently proposed. By this method, SWNTs are suspended in water by surfactant encapsulation and the separation is carried out by ultracentrifugation in a density gradient. SWNTs of different diameters are distributed according to their densities along the centrifuge tube. A mixture of two anionic surfactants, namely sodium dodecylsulfate (SDS) and sodium cholate (SC), presented the best performance in discriminating nanotubes by diameter. Unexpectedly, small diameter nanotubes are found at the low density part of the centrifuge tube. We present molecular dynamics studies of the water-surfactant-SWNT system to investigate the role of surfactants in the sorting process. We found that surfactants can actually be attracted towards the interior of the nanotube cage, depending on the relationship between the surfactant radius of gyration and the nanotube diameter. The dynamics at room temperature showed that, as the amphiphile moves to the hollow cage, water molecules are dragged together, thereby promoting the nanotube filling. The resulting densities of filled SWNT are in agreement with measured densities.

Selective Wrapping and Supramolecular Structures of Polyfluorene-Carbon Nanotube Hybrids

We report on the photophysical properties of single-walled carbon nanotube (SWNT) suspensions In toluene solutions of poly[9,9-dioctylfluorenyl-2,7-diyl](PFO). Steady-state and time-resolved photoluminescence spectroscopy in the near-infrared and visible spectral regions are used to study the interaction of the dispersed SWNTs with the wrapped polymer. Molecular dynamics simulations of the PFO-SWNT hybrids in toluene were carried out to evaluate the energetics of different wrapping geometries. The simulated fluorescence spectra in the visible region were obtained by the quantum chemical ZINDO-CI method, using a sampling of structures obtained from the dynamics trajectories. The tested schemes consider polymer chains aligned along the nanotube axis, where chirality has a minimal effect, or forming helical structures, where a preference for high chiral angles is evidenced. Moreover, toluene affects the polymer structure favoring the helical conformation. Simulations show that the most stable hybrid system is the PFO-wrapped (8,6) nanotube, in agreement with the experimentally observed selectivity.

Low-Frequency Noise in Field-Effect Devices Functionalized With Dendrimer/Carbon-Nanotube Multilayers

Low-frequency noise in an electrolyte-insulator- semiconductor (EIS) structure functionalized with multilayers of polyamidoamine (PAMAM) dendrimer and single-walled carbon nanotubes (SWNT) is studied. The noise spectral density exhibits 1/f(gamma) dependence with the power factor of gamma approximate to 0.8 and gamma = 0.8-1.8 for the bare and functionalized EIS sensor, respectively. The gate-voltage noise spectral density is practically independent of the pH value of the solution and increases with increasing gate voltage or gate-leakage current. It has been revealed that functionalization of an EIS structure with a PAMAM/SWNTs multilayer leads to an essential reduction of the 1/f noise. To interpret the noise behavior in bare and functionalized EIS devices, a gate-current noise model for capacitive EIS structures based on an equivalent flatband-voltage fluctuation concept has been developed.

Trigger and aperture of the surface detector array of the Pierre Auger Observatory

The surface detector array of the Pierre Auger Observatory consists of 1600 water-Cherenkov detectors, for the study of extensive air showers (EAS) generated by ultra-high-energy cosmic rays. We describe the trigger hierarchy, from the identification of candidate showers at the level of a single detector, amongst a large background (mainly random single cosmic ray muons), up to the selection of real events and the rejection of random coincidences. Such trigger makes the surface detector array fully efficient for the detection of EAS with energy above 3 x 10(18) eV, for all zenith angles between 0 degrees and 60 degrees, independently of the position of the impact point and of the mass of the primary particle. In these range of energies and angles, the exposure of the surface array can be determined purely on the basis of the geometrical acceptance. (C) 2009 Elsevier B.V. All rights reserved.

Dinuclear Azide-Bridged Copper(II) Complex as Building Block for the Assembly of a 2D-Supramolecular Array

A novel Schiff base-copper(II) complex [Cu(2)L(2)(N(3))(2)](ClO(4))(2) 1, where L = (4-imidazolyl)ethylene-2-amino-1-ethylpyridine (apyhist), containing azide-bridges between adjacent copper ions in a dinuclear arrangement was isolated and characterized both in the solid state and in solution by X-ray crystallography and different spectroscopic techniques. Azide binding constants were estimated from titrations of the precursor [CuL(H(2)O)(2)](2+) solutions with sodium azide, giving rise to the azido-bridged species, [Cu(2)L(2)(N(3))(2)](2+). Raman spectra showed asymmetric stretching band at 2060 cm(-1), indicating the presence of azido ligands with a symmetric mu(1,) (1) binding geometry. EPA spectra, in frozen methanol/water solutions at 77 K, exhibited characteristic features of copper centers in tetragonal pyramidal coordination geometry, exhibiting magnetic interactions between them. Further, in solid state, two different values for magnetic coupling in this species were obtained, J/k = -(5.14 +/- 0.02) cm(-1) attributed to the mu(1, 1) azide-bridge mode, and J`z`/k = -(2.94 +/- 0.11) cm(-1) for the interaction between dinuclear moieties via water/perchorate bridges. Finally, an attempt was made to correlate structure and magnetic data for this dinuclear asymmetric end-on azido bridged-copper(II) 1 complex with those of another correlated dinuclear system, complex [Cu(2)L(2)Cl(2)](ClO(4))(2) 2, containing the same tridentate diimine ligand, but with chloro-bridged groups between the copper centres.

Fast batch injection analysis of H(2)O(2) using an array of Pt-modified gold microelectrodes obtained from split electronic chips

A fast and robust analytical method for amperometric determination of hydrogen peroxide (H(2)O(2)) based on batch injection analysis (BIA) on an array of gold microelectrodes modified with platinum is proposed. The gold microelectrode array (n = 14) was obtained from electronic chips developed for surface mounted device technology (SMD), whose size offers advantages to adapt them in batch cells. The effect of the dispensing rate, volume injected, distance between the platinum microelectrodes and the pipette tip, as well as the volume of solution in the cell on the analytical response were evaluated. The method allows the H(2)O(2) amperometric determination in the concentration range from 0.8 mu mol L(-1) to 100 mu mol L(-1). The analytical frequency can attain 300 determinations per hour and the detection limit was estimated in 0.34 mu mol L(-1) (3 sigma). The anodic current peaks obtained after a series of 23 successive injections of 50 mu L of 25 mu mol L(-1) H(2)O(2) showed an RSD < 0.9%. To ensure the good selectivity to detect H(2)O(2), its determination was performed in a differential mode, with selective destruction of the H(2)O(2) with catalase in 10 mmol L(-1) phosphate buffer solution. Practical application of the analytical procedure involved H(2)O(2) determination in rainwater of Sao Paulo City. A comparison of the results obtained by the proposed ampermetric method with another one which combines flow injection analysis (FIA) with spectrophotometric detection showed good agreement. (C) 2011 Elsevier B.V. All rights reserved.

Evidences for charge-transfer complex formation in the benzene adsorption on sulfated TiO2-a resonance Raman spectroscopy investigation

Benzene adsorbed on highly acidic sulfated TiO2 (S-TiO2) shows an intriguing resonance Raman (RR) effect, with excitation in the blue-violet region. There are very interesting spectral features: the preferential enhancement of the e(2g) mode (1595 cm(-1)) in relation to the a(1g) mode (ring-breathing mode at 995 cm(-1)) and the appearance of bands at 1565 and 1514 cm(-1). The band at 1565 cm(-1) is probably one of the components of the e(2g) split band, originally a doubly degenerate mode (8a, 8b) in neat benzene, and the band at 1514 cm(-1) is assigned to the 19a mode, an inactive mode in neat benzene. These facts indicate a lowering of symmetry in adsorbed benzene, which may be caused by a strong interaction between S-TiO2 and the benzene molecule with formation of a benzene to Ti (IV) charge transfer (CT) complex or by the formation of a benzene radical cation species. However, the RR spectra of the adsorbed benzene cannot be assigned to the benzene radical cation because the observed wavenumber of the ring-breathing mode does not have the value expected for this species. Moreover, it was found by ESR measurements that the amount of radicals was very low, and so it was concluded that a CT complex is the species that originates the RR spectra. The most favorable intensification of the band at 1595 cm(-1) in the RR spectra of benzene/S-TiO2 at higher excitation energy corroborates this hypothesis, as an absorption band in this energy range, assigned to a CT transition, is observed. Copyright (C) 2008 John Wiley & Sons, Ltd.

XPS characterization of sensitized n-TiO2 thin films for dye-sensitized solar cell applications

TiO2 thin films, employed in dye-sensitized solar cells, were prepared by the sol-gel method or directly by Degussa P25 oxide and their surfaces were characterized by X-ray photoelectron spectroscopy (XPS) and scanning electron microscopy (SEM). The effect of adsorption of the cis-[Ru(dcbH(2))(2)(NCS)(2)] dye, N3, on the surface of films was investigated. From XPS spectra taken before and after argon-ion sputtering procedure, the surface composition of inner and outer layers of sensitized films was obtained and a preferential etching of Ru peak in relation to the Ti and N ones was identified. The photoelectrochemical parameters were also evaluated and rationalized in terms of the morphological characteristics of the films. (c) 2007 Elsevier B.V. All rights reserved.