Bilipid membrane phase characterization by reflectance anisotropy spectroscopy (RAS)

In this work we propose the use of experimental and theoretical reflectance anisotropy spectra (RAS) as a new tool to identify structural and dynamical aspects of the bilipid membrane and its various constituent molecules. The role of geometric details at the atomic level and macroscopic quantities, such as the membrane curvature and tilt for the different gel phases, in the theoretical RAS spectra (using Kohn-Sham density functional theory (KS-DFT)) are presented. Then the results are compared to the experimentally measured spectra taken from other techniques.

Atomistic Study of Water Confined in Silica.

In this work, we have used a combined of atomistic simulation methods to explore the effects of confinement of water molecules between silica surfaces. Firstly, the mechanical properties of water severe confined (~3A) between two silica alpha-quartz was determined based on first principles calculations within the density functional theory (DFT). Simulated annealing methods were employed due to the complex potential energry surface, and the difficulties to avoid local minima. Our results suggest that much of the stiffness of the material (46%) remains, even after the insertion of a water monolayer in the silica. Secondly, in order to access typical time scales for confined systems, classical molecular dynamics was used to determine the dynamical properties of water confined in silica cylindrical pores, with diameters varying from 10 to 40A. in this case we have varied the passivation of the silica surface, from 13% to 100% of SiOH, and the other terminations being SiOH2 and SiOH3, the distribution of the different terminations was obtained with a Monte Carlo simulation. The simulations indicates a lowering of the diffusion coefficientes as the diameter decreases, due to the structuration of hydrogen bonds of water molecules; we have also obtained the density profiles of the confined water and the interfacial tension.

Study of the Influence of Localized Vibrational Modes in Charge Transport Properties at Nanoscale Systems.

In molecular and atomic devices the interaction between electrons and ionic vibrations has an important role in electronic transport. The electron-phonon coupling can cause the loss of the electron's phase coherence, the opening of new conductance channels and the suppression of purely elastic ones. From the technological viewpoint phonons might restrict the efficiency of electronic devices by energy dissipation, causing heating, power loss and instability. The state of the art in electron transport calculations consists in combining ab initio calculations via Density Functional Theory (DFT) with Non-Equilibrium Green's Function formalism (NEGF). In order to include electron-phonon interactions, one needs in principle to include a self-energy scattering term in the open system Hamiltonian which takes into account the effect of the phonons over the electrons and vice versa. Nevertheless this term could be obtained approximately by perturbative methods. In the First Born Approximation one considers only the first order terms of the electronic Green's function expansion. In the Self-Consistent Born Approximation, the interaction self-energy is calculated with the perturbed electronic Green's function in a self-consistent way. In this work we describe how to incorporate the electron-phonon interaction to the SMEAGOL program (Spin and Molecular Electronics in Atomically Generated Orbital Landscapes), an ab initio code for electronic transport based on the combination of DFT + NEGF. This provides a tool for calculating the transport properties of materials' specific system, particularly in molecular electronics. Preliminary results will be presented, showing the effects produced by considering the electron-phonon interaction in nanoscale devices.

First principles calculations for vacancies and antisites in PbSe and PbTe: bulk and nanowire.

The energetic stability and the electronic properties of vacancies (VX) and antisites (XY) in PbSe and PbTe are investigated. PbSe and PbTe are narrow band gap semiconductors and have the potential to be used in infrared detectors, laser, and diodes. They are also of special interest for thermoelectric devices (TE). The calculations are based in the Density Functional Theory (DFT) and the General Gradient Approximation (GGA) for the exchange-correlation term, as implemented in the VASP code. The core and valence electrons are described by the Projected Augmented Wave (PAW) and the Plane Wave (PW) methods, respectively. The defects are studied in the bulk and nanowire (NW) system. Our results show that intrinsec defects (vacancies and antisites) in PbTe have lower formation energies in the NW as compared to the bulk and present a trend in migrate to the surface of the NW. For the PbSe we obtain similar results when compare the formation energy for the bulk and NW. However, the Pb vacancy and the antisites are more stable in the core of the NW. The intrinsec defects are shallow defects for the bulk system. For both PbSe and PbTe VPb is a shallow acceptor defect and VSe and VT e are shallow donor defects for the PbSe and PbTe, respectively. Similar electronic properties are observed for the antisites. For the Pb in the anion site we obtain an n-type semiconductor for both PbSe and PbTe, SeP b is a p-type for the PbSe, and T eP b is a n-type for PbTe. Due the quantum con¯nement effects present in the NW (the band gap open), these defects have different electronic properties for the NW as compared to the bulk. Now these defects give rise to electronic levels in the band gap of the PbTe NW and the VT e present a metallic character. For the PbSe NW a p-type and a n-type semiconductor is obtained for the VP b and P bSe, respectively. On the other hand, deep electronic levels are present in the band gap for the VSe and SePb. These results show that due an enhanced in the electronic density of states (DOS) near the Fermi energy, the defective PbSe and PbTe are candidates for efficient TE devices.

Bilipid Membrane Phase Characterization by Reflectance Anisotropy Spectroscopy (RAS)

In this work we propose the use of experimental and theoretical reflectance anisotropy spectra (RAS) as a new tool to identify structural and dynamical aspects of the bilipid membrane and its various constituent molecules. The role of geometric details at the atomic level and macroscopic quantities, such as the membrane curvature and tilt for the different gel phases, in the theoretical RAS spectra (using Kohn-Sham density functional theory (KS-DFT)) are presented. Then the results are compared to the experimentally measured spectra taken from other techniques.

Thiosaccharine disulfide: synthesis, crystal structure, spectroscopic characterization and theoretical study

The title compound, (thiosaccharine disulfide), bis[1,10dioxide-2,3-dihidro-1,2-benzoisothiazol]disulfide, (tsac)2 has been synthesized and fully characterized by UV–Visible, IR, Raman, 1H and 13C NMR spectroscopy elemental analysis and structural X-ray crystallography. A DFT theoretical study has been performed and good agreement between experimental and theoretical values of structural parameters and vibration frequencies have been achieved.

Structural and vibrational study of 8-hydroxyquinoline-2-carboxaldehyde isonicotinoyl hydrazone: a potential metal-protein attenuating compound (MPAC) for the treatment of Alzheimer's disease

A comprehensive structural and vibrational study of the potential metal-protein attenuating compound 8-hydroxyquinoline-2-carboxaldehyde isonicotinoyl hydrazone is reported. X-ray diffraction data, as well as FT-IR and Raman frequencies, were compared with the respective theoretical values obtained from DFT calculations. Theory agrees well with experiment. In this context, an attempt of total assignment concerning the FT-IR and Raman spectra of the title compound was performed, shedding new light on previous partial assignments published elsewhere.

Reaction intermediates of ethanol electro-oxidation on platinum investigated by SFG spectroscopy

Although electrochemical oxidation of simple organic molecules on metal catalysts is the basic ingredient of fuel cells, which have great technological potential as a renewable source of electrical energy, the detailed reaction mechanisms are in most cases not completely understood. Here, we investigate the ethanol-platinum interface in acidic aqueous solution using infrared-visible sum frequency generation (SFG) spectroscopy and theoretical calculations of vibrational spectra in order to identify the intermediates present during the electro-oxidation of ethanol. The complex vibrational spectrum in the fingerprint region imply on the coexistence of several adsorbates. Based on spectra in ultra-high-vacuum (UHV) and electrochemical environment from the literature and our density functional theory (DFT) calculations of vibrational spectra, new adsorbed intermediates, never before observed with conventional infrared (IR) spectroscopy, are proposed here: g2-acetaldehyde, g2-acetyl, ethylidyne, monodentate acetate, methoxy, tertiary methanol derivative, COH residue, g2-formaldehyde, mono and bidentate formate, CH3 and CH2 residues. In addition, we present new evidences for an ethoxy intermediate, a secondary ethanol derivative and an acetyl species, and we confirm the presence of previously observed adsorbates: a tertiary ethanol derivative, bidentate acetate, and COad. These results indicate that the platinum surface is much more reactive, and the reaction mechanism for ethanol electro-oxidation is considerably more complex than previously considered. This might be also true for many other molecule-catalyst systems.