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Electron–ion recoil vector correlations are examined for the ionization and subsequent dissociation of ? state CF 3 I + . The magnitude of the electron and fragment ion recoil vectors permits the energetics of two alternative decays to I + and CF 3 + to be compared, while differences between the angular correlations are interpreted as molecule-frame photoelectron angular distributions which, in the I + channel, are smeared by molecular rotation between ionization and dissociation. Quantitative estimates of sub-ps I + decay lifetimes are extracted, indicating very different decay rates for the alternative dissociation channels. Surprisingly, the k a 1 and k e photoelectron continua exchange polarization dependence in the I + channel correlations and vibronic interactions are postulated in explanation. This can also rationalize the non-adiabatic ? CF 3 I + →I + decay mechanism and the branching competition between the CF 3 + and I + channels.

Alamethicin (Alm) is a 20 residue peptide which forms a kinked α-helix in membrane and membrane-mimetic environments. Ion channels formed by intramembraneous aggregates of Alm are thought to be formed by bundles of approximately parallel Alm helices surrounding a central bilayer pore. Different channel conductance levels correspond to different numbers of helices per bundle, ranging from N =5 to N 8. Calculation of the predicted p K A values of the ring of Glu18 sidechains at the C-terminal mouth of the pore suggests that at neutral pH most or all of these sidechains will remain protonated. Nanosecond molecular dynamics (MD) simulations of N =5, 6, 7 and 8 bundles of Alm helices in a POPC bilayer have been run, corresponding to a total simulation time of 4 ns. These simulations explore the stability and conformational dynamics of these helix bundle channels when embedded in a full phospholipid bilayer in an aqueous environment. The structural and dynamic properties of water in these model channels are examined. As in earlier in vacuo simulations (J. Breed, R. Sankararamakrishnan, I. D. Kerr and M. S. P. Sansom, Biophys . J ., 1996, 70 , 1643) the dipole moments of water molecules within the pores are aligned antiparallel to the helix dipoles. This helps to contribute to the stability of the helix bundles.

Allostery is a universal phenomenon that couples the information induced by a local perturbation (effector) in a protein to spatially distant regulated sites. Such an event can be described in terms of a large scale transmission of information (communication) through a dynamic coupling between structurally rigid (minimally frustrated) and plastic (locally frustrated) clusters of residues. To elaborate a rational description of allosteric coupling, we propose an original approach – MOdular NETwork Analysis (MONETA) – based on the analysis of inter-residue dynamical correlations to localize the propagation of both structural and dynamical effects of a perturbation throughout a protein structure. MONETA uses inter-residue cross-correlations and commute times computed from molecular dynamics simulations and a topological description of a protein to build a modular network representation composed of clusters of residues ( dynamic segments ) linked together by chains of residues ( communication pathways ). MONETA provides a brand new direct and simple visualization of protein allosteric communication. A GEPHI module implemented in the MONETA package allows the generation of 2D graphs of the communication network. An interactive PyMOL plugin permits drawing of the communication pathways between chosen protein fragments or residues on a 3D representation. MONETA is a powerful tool for on-the-fly display of communication networks in proteins. We applied MONETA for the analysis of communication pathways (i) between the main regulatory fragments of receptors tyrosine kinases (RTKs), KIT and CSF-1R, in the native and mutated states and (ii) in proteins STAT5 (STAT5a and STAT5b) in the phosphorylated and the unphosphorylated forms. The description of the physical support for allosteric coupling by MONETA allowed a comparison of the mechanisms of (a) constitutive activation induced by equivalent mutations in two RTKs and (b) allosteric regulation in the activated and non-activated STAT5 proteins. Our theoretical prediction based on results obtained with MONETA was validated for KIT by in vitro experiments. MONETA is a versatile analytical and visualization tool entirely devoted to the understanding of the functioning/malfunctioning of allosteric regulation in proteins – a crucial basis to guide the discovery of next-generation allosteric drugs.

The adsorption behavior of ions at liquid–vapor interfaces exhibits several unexpected yet generic features. In particular, energy and entropy are both minimum when the solute resides near the surface, for a variety of ions in a range of polar solvents , contrary to predictions of classical theories. Motivated by this generality, and by the simple physical ingredients implicated by computational studies, we have examined interfacial solvation in highly schematic models, which resolve only coarse fluctuations in solvent density and cohesive energy. Here we show that even such lattice gas models recapitulate surprising thermodynamic trends observed in detailed simulations and experiments. Attention is focused on the case of two dimensions, for which approximate energy and entropy profiles can be calculated analytically. Simulations and theoretical analysis of the lattice gas highlight the role of capillary wave-like fluctuations in mediating adsorption . They further point to ranges of temperature and solute– solvent interaction strength where surface propensity is expected to be strongest.

Inspired by earlier attempts in organic electronics aiming at controlling charge injection from metals into organic materials by manipulating the Schottky energy barrier using self-assembled monolayers (SAMs), recent experimental and theoretical work in molecular electronics showed that metal–organic interfaces can be controlled via changes in the metal work function that are induced by SAMs. In this paper we indicate a different route to achieve interface-driven control over the charge transfer/transport at the molecular scale. It is based on the fact that, in floppy molecule based SAMs, the molecular conformation can be tuned by varying the coverage of the adsorbate. We demonstrate this effect with the aid of benchmark molecules that are often used to fabricate nanojunctions and consist of two rings that can easily rotate relative to each other. We show that, by varying the coverage of the SAM, the twisting angle φ of the considered molecular species can be modified by a factor of two. Given the fact that the low bias conductance G scales as cos 2 ? φ , this results in a change in G of over one order of magnitude for the considered molecular species. Tuning the twisting angle by controlling the SAM coverage may be significant, e.g. , for current efforts to fabricate molecular switches. Conversely, the lack of control over the local SAM coverage may be problematic for the reproducibility and interpretation of the STM (scanning tunneling microscope) measurements on repeatedly forming single molecule break junctions.

A series of model catalysts were prepared by depositing different size Pd n clusters on alumina films grown to variable thickness on a Ta(110) support. Samples were characterized by a combination of X-ray photoelectron spectroscopy , low energy He + scattering, and temperature-programmed reaction and desorption (TPR/ TPD ). For the activity studies, the samples were first exposed to 18 O 2 at T ox , and then to 13 CO at 180 K, where CO sticks to Pd, but not to the alumina support. CO oxidation activity increased with increasing thickness of the alumina support up to ～4.5 nm, but was constant for greater thicknesses. Activity increased, with T ox up to 400 K, but then declined for T ox = 500 K. Activity was also found to be non-monotonically dependent on deposited cluster size, with Pd n ( n ≤ 6) being generally more reactive than the larger clusters studied. Activity was only weakly correlated with exposed Pd binding sites, which decreased with increasing cluster size, however, there does appear to be a correlation between activity and electronic structure, as probed via the Pd 3d binding energy. Unlike previous systems we have studied, the activity of small Pd n on these alumina films was quite stable, with essentially no changes observed in up to eight successive TPR experiments.

Ambient measurements of PM 1 aerosol chemical composition at Cabauw, the Netherlands, implicate higher ammonium concentrations than explained by the formation of inorganic ammonium salts. This additional particulate ammonium is called excess ammonium ( e NH 4 ). Height profiles over the Cabauw Experimental Site for Atmospheric Research (CESAR) tower, of combined ground based and airborne aerosol mass spectrometric (AMS) measurements on a Zeppelin airship show higher concentrations of e NH 4 at higher altitudes compared to the ground. Through flights across the Netherlands, the Zeppelin based measurements furthermore substantiate e NH 4 as a regional phenomenon in the planetary boundary layer. The excess ammonium correlates with mass spectral signatures of (di-)carboxylic acids, making a heterogeneous acid–base reaction the likely process of NH 3 uptake. We show that this excess ammonium was neutralized by the organic fraction forming particulate organic ammonium salts. We discuss the significance of such organic ammonium salts for atmospheric aerosols and suggest that NH 3 emission control will have benefits for particulate matter control beyond the reduction of inorganic ammonium salts.

In this study, a systematic series of AuPd bimetallic particles were prepared by colloidal synthesis methods, in order to gain better control over the particle size distribution and structure. Particles having random alloy structures, as well as ‘designer’ particles with Pd-shell/Au-core and Au-shell/Pd-core morphologies, have been prepared and immobilized on both activated carbon and TiO 2 supports. Aberration corrected analytical electron microscopy (ACEAM) has been extensively used to characterize these sol-immobilized materials. In particular, state-of-the-art z- contrast STEM-HAADF imaging and STEM-XEDS spectrum imaging has been employed. These techniques have provided invaluable new (and often unexpected) information on the atomic structure, elemental distribution within particles, and compositional variations between particles for these controlled catalyst preparations. In addition, we have been able to compare their differing thermal stability, sintering and wetting behaviors on activated carbon and TiO 2 supports. These sol immobilized materials have also been compared as catalysts for (i) benzyl alcohol oxidation and (ii) the direct production of H 2 O 2 in an attempt to elucidate the optimum particle morphology/support combination for each reaction.

The coupling of acoustic waves across interfacial boundaries depends upon the morphology of the surface and the orientation of the waves at the boundary. The dependence of the wave propagation at the boundary as a function of the physical properties of the liquid is described. The primary influence comes from the density and viscosity. However, the electrical conductivity of the liquid may also contribute to the interactions at such boundaries. The structure of the interface is an important parameter in discriminating the influences of the density and viscosity of the liquid. It is possible to optimise the surface structure for sensitivity to either density or viscosity and to achieve a high sensitivity to liquid densities despite samples with a broad range of viscosities. The influence of surface morphology of the thickness shear mode resonator on the liquid properties is studied by using different structured electrodes to separate the density and viscosity of the liquid. Finally, a sensor was developed to measure antifreeze concentration in water.

Peptide amphiphiles consisting of a hydrophobic alkyl tail coupled to the eight-amino acid GANPNAAG have been studied extensively for their fibre forming properties. However, detailed characteristics of the fibre structure, such as peptide conformation and molecular organisation, are unknown to date. In this report a range of characterization techniques is described that have been employed to elucidate the internal structure of these fibres. Based on the results obtained by circular dichroism spectroscopy, X-ray diffraction and solid state NMR spectroscopy it was concluded that in a self-assembled state the peptide is in a stretched β-sheet conformation, with the alkyl tails interdigitated and hydrogen-bonded along the axis of the fibre.