Characterizing the molecular order of phosphonic acid self-assembled monolayers on indium tin oxide surfaces

Self-assembled monolayers (SAMs) of alkanephosphonic acids with chain lengths between 8 and 18 carbon units were formed on thin films of indium tin oxide (ITO) sputter-deposited on silicon substrates with 400 nm thermally grown SiO(2). The silicon substrates, while not intended for use in near-IR or visible optics applications, do provide smooth surfaces that permit systematic engineering of grain size and surface roughness as a function of the sputter pressure. Argon sputter pressures from 4 to 20 mTorr show systematic changes in surface morphology ranging from smooth, micrometer-sized grain structures to <50 nm grains with 3× higher surface roughness. Near-edge X-ray absorption fine structure (NEXAFS) spectroscopy experiments are conducted for alkanephosphonic acids deposited on these wide range of ITO surfaces to evaluate the effects of these morphological features on monolayer ordering. Results indicate that long-chain SAMs are more highly ordered, and have a smaller tilt angle, than short-chain SAMs. Surprisingly, the 1-octadecyl phosphonic acids maintain their order as the lateral grain dimensions of the ITO surface shrink to ～50 nm. It is only when the ITO surface roughness becomes greater than the SAM chain length (～15 ?) that SAMs are observed to become relatively disordered.     

Snooker: a structure-based pharmacophore generation tool applied to class A GPCRs

G-protein coupled receptors (GPCRs) are important drug targets for various diseases and of major interest to pharmaceutical companies. The function of individual members of this protein family can be modulated by the binding of small molecules at the extracellular side of the structurally conserved transmembrane (TM) domain. Here, we present Snooker, a structure-based approach to generate pharmacophore hypotheses for compounds binding to this extracellular side of the TM domain. Snooker does not require knowledge of ligands, is therefore suitable for apo-proteins, and can be applied to all receptors of the GPCR protein family. The method comprises the construction of a homology model of the TM domains and prioritization of residues on the probability of being ligand binding. Subsequently, protein properties are converted to ligand space, and pharmacophore features are generated at positions where protein ligand interactions are likely. Using this semiautomated knowledge-driven bioinformatics approach we have created pharmacophore hypotheses for 15 different GPCRs from several different subfamilies. For the beta-2-adrenergic receptor we show that ligand poses predicted by Snooker pharmacophore hypotheses reproduce literature supported binding modes for ～75% of compounds fulfilling pharmacophore constraints. All 15 pharmacophore hypotheses represent interactions with essential residues for ligand binding as observed in mutagenesis experiments and compound selections based on these hypotheses are shown to be target specific. For 8 out of 15 targets enrichment factors above 10-fold are observed in the top 0.5% ranked compounds in a virtual screen. Additionally, prospectively predicted ligand binding poses in the human dopamine D3 receptor based on Snooker pharmacophores were ranked among the best models in the community wide GPCR dock 2010.     

Faraday rotation enhancement of gold coated Fe2O3 nanoparticles: comparison of experiment and theory

Understanding plasmonic enhancement of nanoscale magnetic materials is important to evaluate their potential for application. In this study, the Faraday rotation (FR) enhancement of gold coated Fe(2)O(3) nanoparticles (NP) is investigated experimentally and theoretically. The experiment shows that the Faraday rotation of a Fe(2)O(3) NP solution changes from approximately 3 rad/Tm to 10 rad/Tm as 5 nm gold shell is coated on a 9.7 nm Fe(2)O(3) core at 632 nm. The results also show how the volume fraction normalized Faraday rotation varies with the gold shell thickness. From the comparison of experiment and calculated Faraday rotation based on the Maxwell-Garnett theory, it is concluded that the enhancement and shell dependence of Faraday rotation of Fe(2)O(3) NPs is a result of the shifting plasmon resonance of the composite NP. In addition, the clustering of the NPs induces a different phase lag on the Faraday signal, which suggests that the collective response of the magnetic NP aggregates needs to be considered even in solution. From the Faraday phase lag, the estimated time of the full alignment of the magnetic spins of bare (cluster size 160 nm) and gold coated NPs (cluster size 90 nm) are found to be 0.65 and 0.17 μs. The calculation includes a simple theoretical approach based on the Bruggeman theory to account for the aggregation and its effect on the Faraday rotation. The Bruggeman model provides a qualitatively better agreement with the experimentally observed Faraday rotation and points out the importance of making a connection between component properties and the average "effective" optical behavior of the Faraday medium containing magnetic nanoparticles.     

Structure and dynamics of the fast lithium ion conductor "Li7La3Zr2O12"

The solid lithium-ion electrolyte "Li(7)La(3)Zr(2)O(12)" (LLZO) with a garnet-type structure has been prepared in the cubic and tetragonal modification following conventional ceramic syntheses routes. Without aluminium doping tetragonal LLZO was obtained, which shows a two orders of magnitude lower room temperature conductivity than the cubic modification. Small concentrations of Al in the order of 1 wt% were sufficient to stabilize the cubic phase, which is known as a fast lithium-ion conductor. The structure and ion dynamics of Al-doped cubic LLZO were studied by impedance spectroscopy, dc conductivity measurements, (6)Li and (7)Li NMR, XRD, neutron powder diffraction, and TEM precession electron diffraction. From the results we conclude that aluminium is incorporated in the garnet lattice on the tetrahedral 24d Li site, thus stabilizing the cubic LLZO modification. Simulations based on diffraction data show that even at the low temperature of 4 K the Li ions are blurred over various crystallographic sites. This strong Li ion disorder in cubic Al-stabilized LLZO contributes to the high conductivity observed. The Li jump rates and the activation energy probed by NMR are in very good agreement with the transport parameters obtained from electrical conductivity measurements. The activation energy E(a) characterizing long-range ion transport in the Al-stabilized cubic LLZO amounts to 0.34 eV. Total electric conductivities determined by ac impedance and a four point dc technique also agree very well and range from 1 × 10(-4) Scm(-1) to 4 × 10(-4) Scm(-1) depending on the Al content of the samples. The room temperature conductivity of Al-free tetragonal LLZO is about two orders of magnitude lower (2 × 10(-6) Scm(-1), E(a) = 0.49 eV activation energy). The electronic partial conductivity of cubic LLZO was measured using the Hebb-Wagner polarization technique. The electronic transference number t(e-) is of the order of 10(-7). Thus, cubic LLZO is an almost exclusive lithium ion conductor at ambient temperature.     

Effect of pH on the synthesis and properties of luminescent SiO2/calcium phosphate:Eu3+ core-shell nanoparticles

A novel method for the synthesis of luminescent SiO(2)/calcium phosphate (CaP):Eu(3+) core-shell nanoparticles (NPs) was developed via a sol-gel route followed by annealing at a temperature of 800 °C. The object of this study was the investigation of the effect of pH on the formation of a CaP shell around the silica core. The resulting annealed NPs exhibited an amorphous SiO(2) core and a crystalline luminescent shell. The formation of a CaP layer was possible at pH below 4.5 and above 6.5 during the coating step. The crystal structure of the shell was studied by X-ray diffraction analysis. Hydroxyapatite (HAp) and α-tricalcium phosphate were detected as crystal phases of the surrounding layer. However, NPs produced under basic conditions exhibited a higher crystallinity of the CaP layer than did samples coated at pH below 4.5. In the pH interval between 4.5 and 6.5, no shell growth but the formation of secondary NPs containing CaO and Ca(OH)(2) was observed. Furthermore, SiO(2)/CP:Eu(3+) core-shell NPs were investigated by transmission electron microscopy, dynamic light scattering, Fourier transform infrared spectroscopy, inductively coupled plasma optical emission spectrometry, and photoluminescence spectroscopy. The resulting HAp-coated NPs were successfully tested by a cell-culture-based viability assay with respect to a later application as a luminescent marker for biomedical applications.     

Simulation of photoelectron spectra using the reflection principle in combination with unrestricted excitation ADC2 to assess the accuracy of excited-state calculations

The gas-phase photoelectron spectra of ethene, formaldehyde, formic acid and difluoromethane are simulated using the reflection principle and the unrestricted second-order algebraic diagrammatic construction [UADC(2)] scheme of the polarization propagator for the computation of the vertical-excited states of the cations at the equilibrium geometry of the parent neutral molecule. Comparison is made with experimental spectra and the established highly accurate ionization IP-ADC(3) theory to gain insight into the accuracy and applicability of recently developed excitation UADC schemes. Within UADC(2), we distinguish between the strict and extended schemes UADC(2)-s and UADC(2)-x. While the latter approach is found to slightly underestimate the experimental photoelectron spectra by 0.3 eV and can thus be regarded as a reliable scheme within the limits of the applied reflection principle and the underlying approximations, the UADC(2)-s scheme tends to overestimate the excitation energies by about 0.5 eV. Time-dependent density functional theory is also applied in combination with the standard B3LYP xc functional and turns out to be a useful computational tool for the simulation of the photoelectron spectra of the studied species.