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.

A microscopic view of substitution reactions solvated by ionic liquids

The solvation effect of the ionic liquid 1-N-butyl-3-methylimidazolium hexafluorophosphate on nucleophilic substitution reactions of halides toward the aliphatic carbon of methyl p-nitrobenzenesulfonate (pNBS) was investigated by computer simulations. The calculations were performed by using a hybrid quantum-mechanical/molecular-mechanical (QM/MM) methodology. A semiempirical Hamiltonian was first parametrized on the basis of comparison with ab initio calculations for Cl(-) and Br(-) reaction with pNBS at gas phase. In condensed phase, free energy profiles were obtained for both reactions. The calculated reaction barriers are in agreement with experiment. The structure of species solvated by the ionic liquid was followed along the reaction progress from the reagents, through the transition state, to the final products. The simulations indicate that this substitution reaction in the ionic liquid is slower than in nonpolar molecular solvents proper to significant stabilization of the halide anion by the ionic liquid in comparison with the transition state with delocalized charge. Solute-solvent interactions in the first solvation shell contain several hydrogen bonds that are formed or broken in response to charge density variation along the reaction coordinate. The detailed structural analysis can be used to rationalize the design of new ionic liquids with tailored solvation properties. (c) 2008 American Institute of Physics.

Molecular dynamics simulation of liquid trimethylphosphine

Structural and dynamical properties of liquid trimethylphosphine (TMP), (CH(3))(3)P, as a function of temperature is investigated by molecular dynamics (MD) simulations. The force field used in the MD simulations, which has been proposed from molecular mechanics and quantum chemistry calculations, is able to reproduce the experimental density of liquid TMP at room temperature. Equilibrium structure is investigated by the usual radial distribution function, g(r), and also in the reciprocal space by the static structure factor, S(k). On the basis of center of mass distances, liquid TMP behaves like a simple liquid of almost spherical particles, but orientational correlation due to dipole-dipole interactions is revealed at short-range distances. Single particle and collective dynamics are investigated by several time correlation functions. At high temperatures, diffusion and reorientation occur at the same time range as relaxation of the liquid structure. Decoupling of these dynamic properties starts below ca. 220 K, when rattling dynamics of a given TMP molecules due to the cage effect of neighbouring molecules becomes important. (C) 2011 American Institute of Physics. [doi: 10.1063/1.3624408]

Distinct conformational properties determined by implicit and explicit representation of protein-solvent interactions. An analytical and computer simulation study

In the protein folding problem, solvent-mediated forces are commonly represented by intra-chain pairwise contact energy. Although this approximation has proven to be useful in several circumstances, it is limited in some other aspects of the problem. Here we show that it is possible to achieve two models to represent the chain-solvent system. one of them with implicit and other with explicit solvent, such that both reproduce the same thermodynamic results. Firstly, lattice models treated by analytical methods, were used to show that the implicit and explicitly representation of solvent effects can be energetically equivalent only if local solvent properties are time and spatially invariant. Following, applying the same reasoning Used for the lattice models, two inter-consistent Monte Carlo off-lattice models for implicit and explicit solvent are constructed, being that now in the latter the solvent properties are allowed to fluctuate. Then, it is shown that the chain configurational evolution as well as the globule equilibrium conformation are significantly distinct for implicit and explicit solvent systems. Actually, strongly contrasting with the implicit solvent version, the explicit solvent model predicts: (i) a malleable globule, in agreement with the estimated large protein-volume fluctuations; (ii) thermal conformational stability, resembling the conformational hear resistance of globular proteins, in which radii of gyration are practically insensitive to thermal effects over a relatively wide range of temperatures; and (iii) smaller radii of gyration at higher temperatures, indicating that the chain conformational entropy in the unfolded state is significantly smaller than that estimated from random coil configurations. Finally, we comment on the meaning of these results with respect to the understanding of the folding process. (C) 2009 Elsevier B.V. All rights reserved.

Substitutional Impurities in PPV Crystals: An Intrinsic Donor-Acceptor System for High V(oc) Photovoltaic Devices

Defects are usually present in organic polymer films and are commonly invoked to explain the low efficiency obtained in organic-based optoelectronic devices. We propose that controlled insertion of substitutional impurities may, on the contrary, tune the optoelectronic properties of the underivatized organic material and, in the case studied here, maximize the efficiency of a solar cell. We investigate a specific oxygen-impurity substitution, the keto-defect -(CH(2)-C=O)- in underivatized crystalline poly(p-phenylenevinylene) (PPV), and its impact on the electronic structure of the bulk film, through a combined classical (force-field) and quantum mechanical (DFT) approach. We find defect states which suggest a spontaneous electron hole separation typical of a donor acceptor interface, optimal for photovoltaic devices. Furthermore, the inclusion of oxygen impurities does not introduce defect states in the gap and thus, contrary to standard donor-acceptor systems, should preserve the intrinsic high open circuit voltage (V(oc)) that may be extracted from PPV-based devices.

Classical simulation of deposition of thiophene oligomers on TiO(2)-anatase: Relevance of long-range electrostatic interactions

We performed classical molecular dynamics simulations of the vapor-deposition of alpha-T4 oligomers on the TiO(2)-anatase (101) surface, comparing different sets of charges associated with the atoms of the model. The potential energy surfaces for alpha-T4 and TiO(2) were described by re-parametrizations of the Universal force field with charges given by the charge equilibration (QEq) scheme, or with fixed charges obtained by an ab initio method using the Hirshfeld partition. The two sets of charges lead to completely different results for the interface formation, and for the characteristics of the organic film, with a clearly defined alpha-T4 contact layer in the QEq case, and a more homogeneous molecular distribution when using Hirshfeld charges. The main reason for the discrepancy was found to be the incorrect charge assignment given by QEq to the sulfur and alpha-carbon atoms in thiophenes, and highlight the relevance of long-range interactions in the organization of molecular films. (C) 2009 Elsevier B.V. All rights reserved.

Ligand dissociation from estrogen receptor is mediated by receptor dimerization: Evidence from molecular dynamics simulations

Estrogen Receptor (ER) is an important target for pharmaceutical design. Like other ligand-dependent transcription factors, hormone binding regulates ER transcriptional activity. Nevertheless, the mechanisms by which ligands enter and leave ERs and other nuclear receptors remain poorly understood. Here, we report results of locally enhanced sampling molecular dynamics simulations to identify dissociation pathways of two ER ligands [the natural hormone 17 beta-estradiol (E-2) and the selective ER modulator raloxifene (RAL)] from the human ER alpha ligand-binding domain in monomeric and dimeric forms. E-2 dissociation occurs via three different pathways in ER monomers. One resembles the mousetrap mechanism (Path I), involving repositioning of helix 12 (H12), others involve the separation of H8 and H11 (Path II), and a variant of this pathway at the bottom of the ligand-binding domain (Path II`). RAL leaves the receptor through Path I and a Path I variant in which the ligand leaves the receptor through the loop region between H11 and H12 (Path I`). Remarkably, ER dimerization strongly suppresses Paths II and II` for E-2 dissociation and modifies RAL escape routes. We propose that differences in ligand release pathways detected in the simulations for ER monomers and dimers provide an explanation for previously observed effects of ER quaternary state on ligand dissociation rates and suggest that dimerization may play an important, and hitherto unexpected, role in regulation of ligand dissociation rates throughout the nuclear receptor family.

Flexibility and inhibitor binding in Cdc25 phosphatases

Cdc25 phosphatases involved in cell cycle checkpoints are now active targets for the development of anti-cancer therapies. Rational drug design would certainly benefit from detailed structural information for Cdc25s. However, only apo- or sulfate-bound crystal structures of the Cdc25 catalytic domain have been described so far. Together with previously available crystalographic data, results from molecular dynamics simulations, bioinformatic analysis, and computer-generated conformational ensembles shown here indicate that the last 30-40 residues in the C-terminus of Cdc25B are partially unfolded or disordered in solution. The effect of C-terminal flexibility upon binding of two potent small molecule inhibitors to Cdc25B is then analyzed by using three structural models with variable levels of flexibility, including an equilibrium distributed ensemble of Cdc25B backbone conformations. The three Cdc25B structural models are used in combination with flexible docking, clustering, and calculation of binding free energies by the linear interaction energy approximation to construct and validate Cdc25B-inhibitor complexes. Two binding sites are identified on top and beside the Cdc25B active site. The diversity of interaction modes found increases with receptor flexibility. Backbone flexibility allows the formation of transient cavities or compact hydrophobic units on the surface of the stable, folded protein core that are unexposed or unavailable for ligand binding in rigid and densely packed crystal structures. The present results may help to speculate on the mechanisms of small molecule complexation to partially unfolded or locally disordered proteins.

Host-guest system of 4-nerolidylcatechol in 2-hydroxypropyl-beta-cyclodextrin: preparation, characterization and molecular modeling

The interaction of 4-nerolidylcatechol (4-NRC), a potent antioxidant agent, and 2-hydroxypropyl-beta-cyclodextrin (HP-beta-CD) was investigated by the solubility method using Fourier transform infrared (FTIR) methods in addition to UV-Vis, (1)H-nuclear magnetic resonance (NMR) spectroscopy and molecular modeling. The inclusion complexes were prepared using grinding, kneading and freeze-drying methods. According to phase solubility studies in water a B(S)-type diagram was found, displaying a stoichiometry complexation of 2:1 (drug:host) and stability constant of 6494 +/- A 837 M(-1). Stoichiometry was established by the UV spectrophotometer using Job`s plot method and, also confirmed by molecular modeling. Data from (1)H-NMR, and FTIR, experiments also provided formation evidence of an inclusion complex between 4-NRC and HP-beta-CD. 4-NRC complexation indeed led to higher drug solubility and stability which could probably be useful to improve its biological properties and make it available to oral administration and topical formulations.

Shielding of ionic interactions by sulfur dioxide in an ionic liquid

The effect of adding SO(2) on the structure and dynamics of 1-butyl-3-methylimidazolium bromide (BMIBr) was investigated by low-frequency Raman spectroscopy and molecular dynamics (MD) simulations. The MD simulations indicate that the long-range structure of neat BMIBr is disrupted resulting in a liquid with relatively low viscosity and high conductivity, but strong correlation of ionic motion persists in the BMIBr-SO(2) mixture due to ionic pairing. Raman spectra within the 5 < omega < 200 cm(-1) range at low temperature reveal the short-time dynamics, which is consistent with the vibrational density of states calculated by MD simulations. Several time correlation functions calculated by MD simulations give further insights on the structural relaxation of BMIBr-SO(2).

Total syntheses of trikentrins and of herbindoles

CNPq

Modelling water adsorption on Au(210) surfaces: II. Monte Carlo simulations

Canonical Monte Carlo simulations for the Au(210)/H(2)O interface, using a force field recently proposed by us, are reported. The results exhibit the main features normally observed in simulations of water molecules in contact with different noble metal surfaces. The calculations also assess the influence of the surface topography on the structural aspects of the adsorbed water and on the distribution of the water molecules in the direction normal to the metal surface plane. The adsorption process is preferential at sites in the first layer of the metal. The analysis of the density profiles and dipole moment distributions points to two predominant orientations. Most of the molecules are adsorbed with the molecular plane parallel to surface, while others adsorb with one of the O-H bonds parallel to the surface and the other bond pointing towards the bulk liquid phase. There is also evidence of hydrogen bond formation between the first and second solvent layers at the interface. (c) 2007 Elsevier B.V. All rights reserved.

Cooperative scattering and radiation pressure force in dense atomic clouds

Atomic clouds prepared in ""timed Dicke"" states, i.e. states where the phase of the oscillating atomic dipole moments linearly varies along one direction of space, are efficient sources of superradiant light emission [Scully et al., Phys. Rev. Lett. 96, 010501 (2006)]. Here, we show that, in contrast to previous assertions, timed Dicke states are not the states automatically generated by incident laser light. In reality, the atoms act back on the driving field because of the finite refraction of the cloud. This leads to nonuniform phase shifts, which, at higher optical densities, dramatically alter the cooperative scattering properties, as we show by explicit calculation of macroscopic observables, such as the radiation pressure force.

Acoustic Simulation of a Special Switched Reluctance Drive by Means of Field-Circuit Coupling and Multiphysics Simulation

The approach presented in this paper consists of an energy-based field-circuit coupling in combination with multi-physics simulation of the acoustic radiation of electrical machines. The proposed method is applied to a special switched reluctance motor with asymmetric pole geometry to improve the start-up torque. The pole shape has been optimized, subject to low torque ripple, in a previous study. The proposed approach here is used to analyze the impact of the optimization on the overall acoustic behavior. The field-circuit coupling is based on a temporary lumped-parameter model of the magnetic part incorporated into a circuit simulation based on the modified nodal analysis. The harmonic force excitation is calculated by means of stress tensor computation, and it is transformed to a mechanical mesh by mapping techniques. The structural dynamic problem is solved in the frequency domain using a finite-element modal analysis and superposition. The radiation characteristic is obtained from boundary element acoustic simulation. Simulation results of both rotor types are compared, and measurements of the drive are presented.

Determining the effect of grain size and maximum induction upon coercive field of electrical steels

Although theoretical models have already been proposed, experimental data is still lacking to quantify the influence of grain size upon coercivity of electrical steels. Some authors consider a linear inverse proportionality, while others suggest a square root inverse proportionality. Results also differ with regard to the slope of the reciprocal of grain size-coercive field relation for a given material. This paper discusses two aspects of the problem: the maximum induction used for determining coercive force and the possible effect of lurking variables such as the grain size distribution breadth and crystallographic texture. Electrical steel sheets containing 0.7% Si, 0.3% Al and 24 ppm C were cold-rolled and annealed in order to produce different grain sizes (ranging from 20 to 150 mu m). Coercive field was measured along the rolling direction and found to depend linearly on reciprocal of grain size with a slope of approximately 0.9 (A/m)mm at 1.0 T induction. A general relation for coercive field as a function of grain size and maximum induction was established, yielding an average absolute error below 4%. Through measurement of B(50) and image analysis of micrographs, the effects of crystallographic texture and grain size distribution breadth were qualitatively discussed. (C) 2011 Elsevier B.V. All rights reserved.