On the equation of state and atomic mean square displacement of crystals

We have presented a Green's function method for the calculation of the atomic mean square displacement (MSD) for an anharmonic Hamil toni an . This method effectively sums a whole class of anharmonic contributions to MSD in the perturbation expansion in the high temperature limit. Using this formalism we have calculated the MSD for a nearest neighbour fcc Lennard Jones solid. The results show an improvement over the lowest order perturbation theory results, the difference with Monte Carlo calculations at temperatures close to melting is reduced from 11% to 3%. We also calculated the MSD for the Alkali metals Nat K/ Cs where a sixth neighbour interaction potential derived from the pseudopotential theory was employed in the calculations. The MSD by this method increases by 2.5% to 3.5% over the respective perturbation theory results. The MSD was calculated for Aluminum where different pseudopotential functions and a phenomenological Morse potential were used. The results show that the pseudopotentials provide better agreement with experimental data than the Morse potential. An excellent agreement with experiment over the whole temperature range is achieved with the Harrison modified point-ion pseudopotential with Hubbard-Sham screening function. We have calculated the thermodynamic properties of solid Kr by minimizing the total energy consisting of static and vibrational components, employing different schemes: The quasiharmonic theory (QH), ).2 and).4 perturbation theory, all terms up to 0 ().4) of the improved self consistent phonon theory (ISC), the ring diagrams up to o ().4) (RING), the iteration scheme (ITER) derived from the Greens's function method and a scheme consisting of ITER plus the remaining contributions of 0 ().4) which are not included in ITER which we call E(FULL). We have calculated the lattice constant, the volume expansion, the isothermal and adiabatic bulk modulus, the specific heat at constant volume and at constant pressure, and the Gruneisen parameter from two different potential functions: Lennard-Jones and Aziz. The Aziz potential gives generally a better agreement with experimental data than the LJ potential for the QH, ).2, ).4 and E(FULL) schemes. When only a partial sum of the).4 diagrams is used in the calculations (e.g. RING and ISC) the LJ results are in better agreement with experiment. The iteration scheme brings a definitive improvement over the).2 PT for both potentials.

Direct visualisation of lipid bilayer cubic phases using Atomic Force Microscopy

Inverse bicontinuous cubic (Q(II)) phases are nanostructured materials formed by lipid self-assembly. We have successfully imaged thin films of hydrated Q(II) phases from two different systems using AFM. The images show periodic arrays of water channels with spacing and symmetry consistent with published SAXS data on the bulk materials.

Imaging the atomic structure of activated carbon

The precise atomic structure of activated carbon is unknown, despite its huge commercial importance in the purification of air and water. Diffraction methods have been extensively applied to the study of microporous carbons, but cannot provide an unequivocal identification of their structure. Here we show that the structure of a commercial activated carbon can be imaged directly using aberration-corrected transmission electron microscopy. Images are presented both of the as-produced carbon and of the carbon following heat treatment at 2000 degrees C. In the 2000 degrees C carbon clear evidence is found for the presence of pentagonal rings, suggesting that the carbons have a fullerene-related structure. Such a structure would help to explain the properties of activated carbon, and would also have important implications for the modelling of adsorption on microporous carbons.

X‑ray crystal structure of rac-[Ru(phen)2dppz]2+ with d(ATGCAT)2 shows enantiomer orientations and water ordering

We report an atomic resolution X-ray crystal structure containing both enantiomers of rac-[Ru(phen)2dppz]2+ with the d-(ATGCAT)2 DNA duplex (phen = phenanthroline; dppz = dipyridophenazine). The first example of any enantiomeric pair crystallized with a DNA duplex shows different orientations of the Λ and Δ binding sites, separated by a clearly defined structured water monolayer. Job plots show that the same species is present in solution. Each enantiomer is bound at a TG/CA step and shows intercalation from the minor groove. One water molecule is directly located on one phenazine N atom in the Δ-enantiomer only.

Controlled dehydration of a ruthenium complex-DNA crystal induces reversible DNA kinking

Hydration-dependent DNA deformation has been known since Rosalind Franklin recognised that the relative humidity of the sample had to be maintained to observe a single conformation in DNA fibre diffraction. We now report for the first time the crystal structure, at the atomic level, of a dehydrated form of a DNA duplex and demonstrate the reversible interconversion to the hydrated form at room temperature. This system, containing d(TCGGCGCCGA) in the presence of Λ-[Ru(TAP)2(dppz)]2+ (TAP = 1,4,5,8-tetraazaphenanthrene, dppz = dipyridophenazine), undergoes a partial transition from an A/B hybrid to the A-DNA conformation, at 84-79% relative humidity. This is accompanied by an increase in kink at the central step from 22° to 51°, with a large movement of the terminal bases forming the intercalation site. This transition is reversible on rehydration. Seven datasets, collected from one crystal at room temperature, show the consequences of dehydration at near-atomic resolution. This result highlights that crystals, traditionally thought of as static systems, are still dynamic and therefore can be the subject of further experimentation.

The atomic structure of low-index surfaces of the intermetallic compound InPd

The intermetallic compound InPd (CsCl type of crystal structure with a broad compositional range) is considered as a candidate catalyst for the steam reforming of methanol. Single crystals of this phase have been grown to study the structure of its three low-index surfaces under ultra-high vacuum conditions, using low energy electron diffraction (LEED), X-ray photoemission spectroscopy (XPS), and scanning tunneling microscopy (STM). During surface preparation, preferential sputtering leads to a depletion of In within the top few layers for all three surfaces. The near-surface regions remain slightly Pd-rich until annealing to ∼580 K. A transition occurs between 580 and 660 K where In segregates towards the surface and the near-surface regions become slightly In-rich above ∼660 K. This transition is accompanied by a sharpening of LEED patterns and formation of flat step-terrace morphology, as observed by STM. Several superstructures have been identified for the different surfaces associated with this process. Annealing to higher temperatures (≥750 K) leads to faceting via thermal etching as shown for the (110) surface, with a bulk In composition close to the In-rich limit of the existence domain of the cubic phase. The Pd-rich InPd(111) is found to be consistent with a Pd-terminated bulk truncation model as shown by dynamical LEED analysis while, after annealing at higher temperature, the In-rich InPd(111) is consistent with an In-terminated bulk truncation, in agreement with density functional theory (DFT) calculations of the relative surface energies. More complex surface structures are observed for the (100) surface. Additionally, individual grains of a polycrystalline sample are characterized by micro-spot XPS and LEED as well as low-energy electron microscopy. Results from both individual grains and “global” measurements are interpreted based on comparison to our single crystals findings, DFT calculations and previous literature.

Shape and size of red blood cells from the Pygoscelid penguins of Antarctica using atomic force microscopy

Antarctic biodiversity is evolutionarily complex, reflecting the extreme ambient conditions. Therefore, Antarctic organisms exhibit sophisticated adaptations in all organization levels, including organs, tissues, and cells. Since red blood cells (RBCs) travel through the vertebrates blood delivering O(2) to all tissues and organs and purging the unwanted CO(2), they represent an interesting model to investigate biological adaptations. We have used atomic force microscopy (AFM) to compare the shape and size of RBCs of the Pygoscelid penguins. A total of 18 landmarks were measured in AFM images. When analyzed individually, the parameters were not capable of discriminating the RBCs of each species. However, the simultaneous use of multiple parameters discriminated (74%) among the RBCs. In addition, the use of RBC measurements was sufficient to hierarchically cluster the species in accordance to other common and reliable phylogenetic strategies. In light of these results, the use of RBC characters could effectively benefit taxonomic inferences.

Formation of beta-nickel hydroxide plate-like structures under mild conditions and their optical properties

Nanostructural beta-nickel hydroxide (beta-Ni(OH)(2)) plates were prepared using the microwave hydrothermal (MH) method at a low temperature and short reaction times. An ammonia solution was employed as the coordinating agent, which reacts with [Ni(H(2)O)(6)](2+) to control the growth of beta-Ni(OH)(2) nuclei. A trigonal beta-Ni(OH)(2) single phase was observed by X-ray diffraction (XRD) analyses, and the crystal cell was constructed with structural parameters and atomic coordinates obtained from Rietveld refinement. Field emission scanning electron microscopy (FE-SEM) images revealed that the samples consisted of hexagonal-shaped nanoplates with a different particle size distribution. Broad absorption bands assigned as transitions of Ni(2+) in oxygen octahedral sites were revealed by UV-vis spectra. Photoluminescence (PL) properties observed with a maximum peak centered in the blue-green region were attributed to different defects, which were produced during the nucleation process. We present a growth process scheme of the beta-Ni(OH)(2) nanoplates. (C) 2011 Elsevier Inc. All rights reserved.

The processes involved in the Se electrodeposition and dissolution on Au electrode: the H2Se formation

The processes involved in the Se electrodeposition, mainly the one related to the formation of H2Se species on Au electrode in perchloric acid solutions, have been investigated through cyclic voltammetry, electrochemical quartz crystal microbalance (EQCM), rotating ring-disc electrode (RRDE), and atomic force microscopy (AFM) techniques. In the experiments performed with the EQCM, with the potential sweep in the negative direction, the responses for the mass variation were divided in three well-defined potential regions: A (from 1.55 to 0.35 V), B (from 0.35 to -0.37 V), and C (from -0.37 to -0.49 V). It was verified that the following processes can occur, respectively: the species (AuO)(2)H2SeO3 was desorbed during the AuO reduction, the reduction of Se(IV) to Se(0), and the formation of H2Se. When the potential was swept in the positive direction, the responses for the mass variation were divided in four well-defined potential regions: D (from -0.49 to 0.66 V), E (from 0.66 to 0.99 V), F (from 0.99 to 1.26 V), and G (from 1.26 to 1.55 V), and the described processes in these regions were, respectively: the Se deposition and adsorption of water molecules and/or perchlorate ions, the Se dissolution, the Se incorporating mass in the form of HO-Se, and the Au oxidation (all potentials are referred to the Ag/AgCl electrode). Making use of the RRDE, using the collection technique, the formation of H2Se species during the Se electrodeposition was investigated. Therefore, it was confirmed that this species is formed on the disc electrode between -0.3 and -0.55 V vs the Ag/AgCl potential range (collecting the oxidized compound onto the ring electrode). AFM images also indicated that the surface topography of the Se-massive deposit on Au is different from the images registered after the formation of H2Se species, confirming the cathodic stripping of Se.

Physical Vapor Deposited Thin Films of Lignins Extracted from Sugar Cane Bagasse: Morphology, Electrical Properties, and Sensing Applications

The concern related to the environmental degradation and to the exhaustion of natural resources has induced the research on biodegradable materials obtained from renewable sources, which involves fundamental properties and general application. In this context, we have fabricated thin films of lignins, which were extracted from sugar cane bagasse via modified organosolv process using ethanol as organic solvent. The films were made using the vacuum thermal evaporation technique (PVD, physical vapor deposition) grown up to 120 nm. The main objective was to explore basic properties such as electrical and surface morphology and the sensing performance of these lignins as transducers. The PVD film growth was monitored via ultraviolet-visible (UV-vis) absorption spectroscopy and quartz crystal microbalance, revealing a linear relationship between absorbance and film thickness. The 120 nm lignin PVD film morphology presented small aggregates spread all over the film surface on the nanometer scale (atomic force microscopy, AFM) and homogeneous on the micrometer scale (optical microscopy). The PVD films were deposited onto Au interdigitated electrode (IDE) for both electrical characterization and sensing experiments. In the case of electrical characterization, current versus voltage (I vs V) dc measurements were carried out for the Au IDE coated with 120 nm lignin PVD film, leading to a conductivity of 3.6 x 10(-10) S/m. Using impedance spectroscopy, also for the Au IDE coated with the 120 nm lignin PVD film, dielectric constant of 8.0, tan delta of 3.9 x 10(-3)) and conductivity of 1.75 x 10(-9) S/m were calculated at 1 kHz. As a proof-of-principle, the application of these lignins as transducers in sensing devices was monitored by both impedance spectroscopy (capacitance vs frequency) and I versus time dc measurements toward aniline vapor (saturated atmosphere). The electrical responses showed that the sensing units are sensible to aniline vapor with the process being reversible. AFM images conducted directly onto the sensing units (Au IDE coated with 120 nm lignin PVD film) before and after the sensing experiments showed a decrease in the PVD film roughness from 5.8 to 3.2 nm after exposing to aniline.

Deposition of selenium thin layers on gold surfaces from sulphuric acid media: Studies using electrochemical quartz crystal microbalance, cyclic voltammetry and AFM

In this paper we report here new considerations about the relationship between the mass and charge variations (m/z relationship) in underpotential deposition (UPD), bulk deposition and also in the H(2)Se formation reaction. Nanogravimetric experiments were able to show the adsorption of H(2)SeO(3) on the AuO surface prior to the voltammetric sweep and that, after the AuO reduction, 0.40 monolayer of H(2)SeO(3) remains adsorbed on the newly reduced Au surface, which was enough to gives rise to the UPD layer. The UPD results indicate that the maximum coverage with Se(ads) on polycrystalline gold surface corresponds to approximately 0.40 monolayer, in good agreement with charge density results. The cyclic voltammetry experiments demonstrated that the amount of bulk Se obtained during the potential scan to approximately 2 Se monolayers, which was further confirmed by electrochemical quartz crystal microbalance (EQCM) measurements that pointed out a mass variation corresponding of 3 monolayers of Se. In addition, the Se thin films were obtained by chronoamperometric experiments, where the Au electrode was polarized at +0.10V during different times in 1.0 M H(2)SO(4) + 1.0 mM SeO(2). The topologic aspects of the electrodeposits were observed in Atomic Force Microscope (AFM) measurements. Finally, in highly negative potential polarizations, the H(2)Se formation was analyzed by voltammetric and nanogravimetric measurements. These finding brings a new light on the selenium electrodeposition and point up to a proposed electrochemical model for molecule controlled surface engineering. (c) 2009 Elsevier Ltd. All rights reserved.

Crystal structure and theoretical calculations of Julocrotine, a natural product with antileishmanial activity

Julocrotine, N-(2,6-dioxo-l-phenethyl-piperidin-3-yl)-2-methyl-butyramide, is a potent antiproliferative agent against the promastigote and amastigote forms of Leishmania amazonensis (L.). In this work, the crystal structure of Julocrotine was solved by X-ray diffraction, and its geometrical parameters were compared with theoretical calculations at the B3LYP and HF level of theory. IR and NMR spectra also have been obtained and compared with theoretical calculations. IR absorptions calculated with the B3LYP level of theory employed together with the 6-311G+(d,p) basis set, are close to those observed experimentally. Theoretical NMR calculations show little deviation from experimental results. The results show that the theory is in accordance with the experimental data. (C) 2007 Wiley Periodicals, Inc.

Influência dos parâmetros de processo na deposição de nitreto de titânio por plasma em gaiola catódica

Titanium nitride films were grown on glass using the Cathodic Cage Plasma Deposition technique in order to verify the influence of process parameters in optical and structural properties of the films. The plasma atmosphere used was a mixture of Ar, N2 and H2, setting the Ar and N2 gas flows at 4 and 3 sccm, respectively and H2 gas flow varied from 0, 1 to 2 sccm. The deposition process was monitored by Optical Emission Spectroscopy (OES) to investigate the influence of the active species in plasma. It was observed that increasing the H2 gas flow into the plasma the luminescent intensities associated to the species changed. In this case, the luminescence of N2 (391,4nm) species was not proportional to the increasing of the H2 gas into the reactor. Other parameters investigated were diameter and number of holes in the cage. The analysis by Grazing Incidence X-Ray Diffraction (GIXRD) confirmed that the obtained films are composed by TiN and they may have variations in the nitrogen amount into the crystal and in the crystallite size. The optical microscopy images provided information about the homogeneity of the films. The atomic force microscopy (AFM) results revealed some microstructural characteristics and surface roughness. The thickness was measured by ellipsometry. The optical properties such as transmittance and reflectance (they were measured by spectrophotometry) are very sensitive to changes in the crystal lattice of the material, chemical composition and film thicknesses. Therefore, such properties are appropriate tools for verification of this process control. In general, films obtained at 0 sccm of H2 gas flow present a higher transmittance. It can be attributed to the smaller crystalline size due to a higher amount of nitrogen in the TiN lattice. The films obtained at 1 and 2 sccm of H2 gas flow have a golden appearance and XRD pattern showed peaks characteristics of TiN with higher intensity and smaller FWHM (Full Width at Half Maximum) parameter. It suggests that the hydrogen presence in the plasma makes the films more stoichiometric and becomes it more crystalline. It was observed that with higher number of holes in the lid of the cage, close to the region between the lid and the sample and the smaller diameter of the hole, the deposited film is thicker, which is justified by the most probability of plasma species reach effectively the sample and it promotes the growth of the film

Interaction of small amounts of bovine serum albumin with phospholipid monolayers investigated by surface pressure and atomic force microscopy

The influence of small amounts of bovine serum albumin (BSA) (nM concentration) on the lateral organization of phospholipid monolayers at the air-water interface and transferred onto solid substrates as one-layer Langmuir-Blodgett (LB) films was investigated. The kinetics of adsorption of BSA onto the phospholipid monolayers was monitored with surface pressure isotherms in a Langmuir trough, for the zwitterionic dipalmitoylphosphatidyl ethanolamine (N,N-dimethyl-PE) and the anionic dimyristoylphosphatidic acid (DMPA). A monolayer of N,N-dimethyl-PE or DMPA incorporating BSA was transferred onto a solid substrate using the Langmuir-Blodgett technique. Atomic force microscopy (AFM) images of one-layer LB films displayed protein-phospholipid domains, whose morphology was characterized using dynamic scaling theories to calculate roughness exponents. For DMPA-BSA films the surface is characteristic of self-affine fractals, which may be described with the Kardar-Parisi-Zhang (KPZ) equation. on the other hand, for N,N-dimethyl-PE-BSA films, the results indicate a relatively flat surface within the globule. The height profile and the number and size of globules varied with the type of phospholipid. The overall results, from kinetics of adsorption on Langmuir monolayers and surface morphology in LB films, could be interpreted in terms of the higher affinity of BSA to the anionic DMPA than to the zwitterionic N,N-dimethyl-PE. Furthermore, the effects from such small amounts of BSA in the monolayer point to a cooperative response of DMPA and N,N-dimethyl-PE monolayers to the protein. (c) 2005 Elsevier B.V. All rights reserved.

Physical Vapor Deposited Thin Films of Lignins Extracted from Sugar Cane Bagasse: Morphology, Electrical Properties, and Sensing Applications

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