Dynamic polarizability, Cauchy moments, and the optical absorption spectrum of liquid water: A sequential molecular dynamics/quantum mechanical approach

The dynamic polarizability and optical absorption spectrum of liquid water in the 6-15 eV energy range are investigated by a sequential molecular dynamics (MD)/quantum mechanical approach. The MD simulations are based on a polarizable model for liquid water. Calculation of electronic properties relies on time-dependent density functional and equation-of-motion coupled-cluster theories. Results for the dynamic polarizability, Cauchy moments, S(-2), S(-4), S(-6), and dielectric properties of liquid water are reported. The theoretical predictions for the optical absorption spectrum of liquid water are in good agreement with experimental information.

Electronic properties of liquid ammonia: A sequential molecular dynamics/quantum mechanics approach

The electronic properties of liquid ammonia are investigated by a sequential molecular dynamics/quantum mechanics approach. Quantum mechanics calculations for the liquid phase are based on a reparametrized hybrid exchange-correlation functional that reproduces the electronic properties of ammonia clusters [(NH(3))(n); n=1-5]. For these small clusters, electron binding energies based on Green's function or electron propagator theory, coupled cluster with single, double, and perturbative triple excitations, and density functional theory (DFT) are compared. Reparametrized DFT results for the dipole moment, electron binding energies, and electronic density of states of liquid ammonia are reported. The calculated average dipole moment of liquid ammonia (2.05 +/- 0.09 D) corresponds to an increase of 27% compared to the gas phase value and it is 0.23 D above a prediction based on a polarizable model of liquid ammonia [Deng , J. Chem. Phys. 100, 7590 (1994)]. Our estimate for the ionization potential of liquid ammonia is 9.74 +/- 0.73 eV, which is approximately 1.0 eV below the gas phase value for the isolated molecule. The theoretical vertical electron affinity of liquid ammonia is predicted as 0.16 +/- 0.22 eV, in good agreement with the experimental result for the location of the bottom of the conduction band (-V(0)=0.2 eV). Vertical ionization potentials and electron affinities correlate with the total dipole moment of ammonia aggregates. (c) 2008 American Institute of Physics.

Optical second harmonic generation in the centrosymmetric magnetic semiconductors EuTe and EuSe

The magnetic europium chalcogenide semiconductors EuTe and EuSe are investigated by the spectroscopy of second harmonic generation (SHG) in the vicinity of the optical band gap formed by transitions involving the 4f and 5d electronic orbitals of the magnetic Eu(2+) ions. In these materials with centrosymmetric crystal lattice the electric-dipole SHG process is symmetry forbidden so that no signal is observed in zero magnetic field. Signal appears, however, in applied magnetic field with the SHG intensity being proportional to the square of magnetization. The magnetic field and temperature dependencies of the induced SHG allow us to introduce a type of nonlinear optical susceptibility determined by the magnetic-dipole contribution in combination with a spontaneous or induced magnetization. The experimental results can be described qualitatively by a phenomenological model based on a symmetry analysis and are in good quantitative agreement with microscopic model calculations accounting for details of the electronic energy and spin structure.

Role of dipolar interactions in a system of Ni nanoparticles studied by magnetic susceptibility measurements

The role of dipolar interactions among Ni nanoparticles (NPs) embedded in an amorphous SiO(2)/C matrix with different concentrations has been studied performing ac magnetic susceptibility chi(ac) measurements. For very diluted samples, with Ni concentrations < 4 wt % Ni or very weak dipolar interactions, the data are well described by the Neacuteel-Arrhenius law. Increasing Ni concentration to values up to 12.8 wt % Ni results in changes in the Neacuteel-Arrhenius behavior, the dipolar interactions become important, and need to be considered to describe the magnetic response of the NPs system. We have found no evidence of a spin-glasslike behavior in our Ni NP systems even when dipolar interactions are clearly present.

Atomistic molecular dynamics study of interface formation: Al on poly(p-phenylene vinylene)

We model interface formation by metal deposition on the conjugated polymer poly-para-phenylene vinylene, studying direct aluminum and layered aluminum-calcium structures Al/PPV and Al/Ca/PPV. To do that we use classical molecular dynamics simulations, checked by ab initio density-functional theory calculations, for selected relevant configurations. We find that Al not only migrates easily into the film, with a strong charge transfer to the neighboring chains, but also promotes rearrangement of the polymer in the interfacial region to the hexagonal structure. On the other hand, our results indicate that a thin Ca layer is sufficient to protect the film and maintain a well-defined metal/polymer interface, and that also a thin Al capping layer may protect the whole from environmental degradation.

First-principles study of the adsorption of atomic and molecular hydrogen on BC(2)N nanotubes

The adsorption of atomic and molecular hydrogen on armchair and zigzag boron carbonitride nanotubes is investigated within the ab initio density functional theory. The adsorption of atomic H on the BC(2)N nanotubes presents properties which are promising for nanoelectronic applications. Depending on the adsorption site for the H, the Fermi energy moves toward the bottom of the conduction band or toward the top of the valence band, leading the system to exhibit donor or acceptor characteristics, respectively. The H(2) molecules are physisorbed on the BC(2)N surface for both chiralities. The binding energies for the H(2) molecules are slightly dependent on the adsorption site, and they are near to the range to work as a hydrogen storage medium.

Anisotropic Confinement, Electronic Coupling and Strain Induced Effects Detected by Valence-Band Anisotropy in Self-Assembled Quantum Dots

A method to determine the effects of the geometry and lateral ordering on the electronic properties of an array of one-dimensional self-assembled quantum dots is discussed. A model that takes into account the valence-band anisotropic effective masses and strain effects must be used to describe the behavior of the photoluminescence emission, proposed as a clean tool for the characterization of dot anisotropy and/or inter-dot coupling. Under special growth conditions, such as substrate temperature and Arsenic background, 1D chains of In(0.4)Ga(0.6) As quantum dots were grown by molecular beam epitaxy. Grazing-incidence X-ray diffraction measurements directly evidence the strong strain anisotropy due to the formation of quantum dot chains, probed by polarization-resolved low-temperature photoluminescence. The results are in fair good agreement with the proposed model.

Artificial molecular quantum rings under magnetic field influence

The ground states of a few electrons confined in two vertically coupled quantum rings in the presence of an external magnetic field are studied systematically within the current spin-density functional theory. Electron-electron interactions combined with inter-ring tunneling affect the electronic structure and the persistent current. For small values of the external magnetic field, we recover the zero magnetic field molecular quantum ring ground state configurations. Increasing the magnetic field many angular momentum, spin, and isospin transitions are predicted to occur in the ground state. We show that these transitions follow certain rules, which are governed by the parity of the number of electrons, the single-particle picture, Hund's rules, and many-body effects. (C) 2009 American Institute of Physics. [doi:10.1063/1.3223360]

Internal Strain Distribution in Freestanding Porous Silicon

Elastic properties of freestanding porous silicon layers fabricated by electrochemical anodization were studied by Raman scattering. Different anodization currents provided different degrees of porosity in the nanometer scale. Raman lines corresponding to the longitudinal optical phonons of crystalline and amorphous phases were observed. The amorphous volume fraction increased and the phonon frequencies for both phases decreased with increasing porosity. A strain distribution model is proposed whose fit to the experimental results indicates that the increasing nanoscale porosity causes strain relaxation in the amorphous domains and strain buildup in the crystalline ones. The present analysis has significant implications on the estimation of the crystalline Si domain's characteristic size from Raman scattering data. (C) 2009 The Electrochemical Society. [DOI: 10.1149/1.3225832] All rights reserved.

Optimized architecture for Tyrosinase-containing Langmuir-Blodgett films to detect pyrogallol

The control of molecular architectures has been a key factor for the use of Langmuir-Blodgett (LB) films in biosensors, especially because biomolecules can be immobilized with preserved activity. In this paper we investigated the incorporation of tyrosinase (Tyr) in mixed Langmuir films of arachidic acid (AA) and a lutetium bisphthalocyanine (LuPc(2)), which is confirmed by a large expansion in the surface pressure isotherm. These mixed films of AA-LuPc(2) + Tyr could be transferred onto ITO and Pt electrodes as indicated by FTIR and electrochemical measurements, and there was no need for crosslinking of the enzyme molecules to preserve their activity. Significantly, the activity of the immobilised Tyr was considerably higher than in previous work in the literature, which allowed Tyr-containing LB films to be used as highly sensitive voltammetric sensors to detect pyrogallol. Linear responses have been found up to 400 mu M, with a detection limit of 4.87 x 10(-2) mu M (n = 4) and a sensitivity of 1.54 mu A mu M(-1) cm(-2). In addition, the Hill coefficient (h = 1.27) indicates cooperation with LuPc(2) that also acts as a catalyst. The enhanced performance of the LB-based biosensor resulted therefore from a preserved activity of Tyr combined with the catalytic activity of LuPc(2), in a strategy that can be extended to other enzymes and analytes upon varying the LB film architecture.

Molecular determinants of improved cathepsin B inhibition by new cystatins obtained by DNA shuffling

Background: Cystatins are inhibitors of cysteine proteases. The majority are only weak inhibitors of human cathepsin B, which has been associated with cancer, Alzheimer's disease and arthritis. Results: Starting from the sequences of oryzacystatin-1 and canecystatin-1, a shuffling library was designed and a hybrid clone obtained, which presented higher inhibitory activity towards cathepsin B. This clone presented two unanticipated point mutations as well as an N-terminal deletion. Reversing each point mutation independently or both simultaneously abolishes the inhibitory activity towards cathepsin B. Homology modeling together with experimental studies of the reverse mutants revealed the likely molecular determinants of the improved inhibitory activity to be related to decreased protein stability. Conclusion: A combination of experimental approaches including gene shuffling, enzyme assays and reverse mutation allied to molecular modeling has shed light upon the unexpected inhibitory properties of certain cystatin mutants against Cathepsin B. We conclude that mutations disrupting the hydrophobic core of phytocystatins increase the flexibility of the N-terminus, leading to an increase in inhibitory activity. Such mutations need not affect the inhibitory site directly but may be observed distant from it and manifest their effects via an uncoupling of its three components as a result of increased protein flexibility.

3-Nitrophenol-4,4 '-bipyridyl N,N '-dioxide (2/1): a DFT study and CSD analysis of DPNO molecular complexes

The title 2:1 complex of 3-nitrophenol (MNP) and 4,4'-bipyridyl N, N'-dioxide (DPNO), 2C(6)H(5)NO(3)center dot C(10)H(8)N(2)O(2) or 2MNP center dot DPNO, crystallizes as a centrosymmetric three-component adduct with a dihedral angle of 59.40 (8)degrees between the planes of the benzene rings of MNP and DPNO (the DPNO moiety lies across a crystallographic inversion centre located at the mid-point of the C-C bond linking its aromatic rings). The complex owes its formation to O-H center dot center dot center dot O hydrogen bonds [O center dot center dot center dot O = 2.605 (3) angstrom]. Molecules are linked by intermolecular C-H center dot center dot center dot O and C-H center dot center dot center dot N interactions forming R(2)(1) (6) and R(2)(2) (10) rings, and R(6)(6) (34) and R(4)(4) (26) macro-rings, all of which are aligned along the [(1) over bar 01] direction, and R(2)(2) (10) and R(2)(1) (7) rings aligned along the [010] direction. The combination of chains of rings along the [(1) over bar 01] and [010] directions generates the three-dimensional structure. A total of 27 systems containing the DNPO molecule and forming molecular complexes of an organic nature were analysed and compared with the structural characteristics of the dioxide reported here. The N-O distance [1.325 (2) angstrom] depends not only on the interactions involving the O atom at the N-O group, but also on the structural ordering and additional three-dimensional interactions in the crystal structure. A density functional theory (DFT) optimized structure at the B3LYP/6-311G(d,p) level is compared with the molecular structure in the solid state.

Adenosine binding to low-molecular-weight purine nucleoside phosphorylase: the structural basis for recognition based on its complex with the enzyme from Schistosoma mansoni

Schistosomes are unable to synthesize purines de novo and depend exclusively on the salvage pathway for their purine requirements. It has been suggested that blockage of this pathway could lead to parasite death. The enzyme purine nucleoside phosphorylase (PNP) is one of its key components and molecules designed to inhibit the low-molecular-weight (LMW) PNPs, which include both the human and schistosome enzymes, are typically analogues of the natural substrates inosine and guanosine. Here, it is shown that adenosine both binds to Schistosoma mansoni PNP and behaves as a weak micromolar inhibitor of inosine phosphorolysis. Furthermore, the first crystal structures of complexes of an LMW PNP with adenosine and adenine are reported, together with those with inosine and hypoxanthine. These are used to propose a structural explanation for the selective binding of adenosine to some LMW PNPs but not to others. The results indicate that transition-state analogues based on adenosine or other 6-amino nucleosides should not be discounted as potential starting points for alternative inhibitors.

Energy transfer upconversion determination by thermal-lens and Z-scan techniques in Nd(3+)-doped laser materials

The Z-scan and thermal-lens techniques have been used to obtain the energy transfer upconversion parameter in Nd(3+)-doped materials. A comparison between these methods is done, showing that they are independent and provide similar results. Moreover, the advantages and applicability of each one are also discussed. The results point to these approaches as valuable alternative methods because of their sensitivity, which allows measurements to be performed in a pump-power regime without causing damage to the investigated material. (C) 2009 Optical Society of America

Influence of film thickness on the crystallization of Ni-doped amorphous silicon samples

This work reports on the crystallization of amorphous silicon (a-Si) films doped with 1 at. % of nickel. The films, with thicknesses ranging from 10 to 3000 nm, were deposited using the cosputtering method onto crystalline quartz substrates. In order to investigate the crystallization mechanism in detail, a series of undoped a-Si films prepared under the same deposition conditions were also studied. After deposition, all a-Si films were submitted to isochronal thermal annealing treatments up to 1000 degrees C and analyzed by Raman scattering spectroscopy. Based on the present experimental results, it is possible to state that (a) when compared to the undoped a-Si films, those containing 1 at. % of Ni crystallize at temperatures similar to 100 degrees C lower, and that (b) the film thickness influences the temperature of crystallization that, in principle, tends to be lower in films thinner than 1000 nm. The possible reasons associated to these experimental observations are presented and discussed in view of some experimental and thermodynamic aspects involved in the formation of ordered Si-Si bonds and in the development of Ni-silicide phases. (c) 2008 American Institute of Physics.