Multiple scattering calculations of step contrast in REM images of the Si(001) surface

Simulations of reflection electron microscopy (REM) images of both monolayer and bilayer steps on the bulk-terminated Si(001) surface, for the case when the primary electron beam azimuth is directed parallel to the line of the step, are presented. The simulations employ our previously reported theory of REM image formation which uses a 2D Bloch wave formulation of dynamical (multiple scattering) elastic RHEED theory to calculate diffracted amplitudes propagating from the surface. The only step contrast mechanism considered here is phase contrast and this is sufficient to produce the characteristic “black-white” appearance observed experimentally. Defocusing of the simulated images is also discussed.     

Some aspects of single-grain luminescence dating

Single-grain methods of luminescence dating have been developed in order to circumvent problems of variability among aliquots of the sample being dated. Sufficient single grains must be separated in order to make an appropriate interpretation of the variability among such grains. We describe an automated apparatus for sorting grains for routine age determinations by green light stimulation. The sorted grains are then available for study of their collective luminescence physics characteristics. Examples are given of statistical frequency functions of grain brightness obtained with the apparatus and their interpretation. These frequency functions are lognormal or similar, covering up to four orders of magnitude, with consequent implications for luminescence dating application.     

Vibrational manifestations of strong non-Condon effects in the H3O(+)·X3 (X = Ar, N2, CH4, H2O) complexes: a possible explanation for the intensity in the "association band" in the vibrational spectrum of water

The harmonic approximation provides a powerful approach for interpreting vibrational spectra. In this treatment, the energy and intensity of the 3N- 6 normal modes are calculated using a quadratic expansion of the potential energy and a linear expansion of the dipole moment surfaces, respectively. In reality, transitions are often observed that are not accounted for by this approach (e.g. combination bands, overtones, etc.), and these transitions arise from inherent anharmonicities present in the system. One interesting example occurs in the vibrational spectrum of H(2)O((l)), where a band is observed near 2000 cm(-1) that is commonly referred to as the "association band". This band lies far from the expected bend and stretching modes of the water molecule, and is not recovered at the harmonic level. In a recent study, we identified a band in this spectral region in gas-phase clusters involving atomic and molecular adducts to the H(3)O(+) ion. In the current study we probe the origins of this band through a systematic analysis of the argon-predissociation spectra of H(3)O(+)·X(3) where X = Ar, CH(4), N(2) or H(2)O, with particular attention to the contributions from the non-linearities in the dipole surfaces, often referred to as non-Condon effects. The spectra of the H(3)O(+) clusters all display strong transitions between 1900-2100 cm(-1), and theoretical modeling indicates that they can be assigned to a combination band involving the HOH bend and frustrated rotation of H(3)O(+) in the solvent cage. This transition derives its oscillator strength entirely from strong non-Condon effects, and we discuss its possible relationship to the association band in the spectrum of liquid water.     

Spatial localization of ligand binding sites from electron current density surfaces calculated from NMR chemical shift perturbations

Rapid, accurate structure determination of protein-ligand complexes is an essential component in structure-based drug design. We have developed a method that uses NMR protein chemical shift perturbations to spatially localize a ligand when it is complexed with a protein. Chemical shift perturbations on the protein arise primarily from the close proximity of electron current density from the ligand. In our approach the location of the center of the electron current density for a ligand aromatic ring was approximated by a point-dipole, and dot densities were used to represent ligand positions that are allowed by the experimental data. The dot density is increased in the region of space that is consistent for the most data. A surface can be formed in regions of the highest dot density that correlates to the center of the ligand aromatic ring. These surfaces allow for the rapid evaluation of ligand binding, which is demonstrated on a model system and on real data from HCV NS3 protease and HCV NS3 helicase, where the location of ligand binding can be compared to that obtained from difference electron density from X-ray crystallography.     

Probing the dependence of long-range, four-atom interactions on intermolecular orientation. 1. Molecular hydrogen and iodine monochloride

The dependence of the long-range interactions between molecular hydrogen and iodine monochloride on the geometry between the molecules is investigated. Laser-induced fluorescence and action spectroscopy experiments have identified multiple conformers of the o,p-H2...I35,37Cl(X,v' '=0) van der Waals complexes. A conformer with the hydrogen molecule localized at the iodine end of the dihalogen, most likely with C2v symmetry, is significantly more stable than an asymmetric conformer with the hydrogen localized in the well oriented orthogonally to the I-Cl bond axis, D0' ' = 186.4(3) cm-1 versus 82.8(3) 相似文献   

Pyrene‐Based Quantitative Detection of the 5‐Formylcytosine Loci Symmetry in the CpG Duplex Content during TET‐Dependent Demethylation

Methylcytosine (5mC) is mostly symmetrically distributed in CpG sites. Ten‐eleven‐translocation (TET) proteins are the key enzymes involved in active DNA demethylation through stepwise oxidation of 5mC. However, oxidation pathways of TET enzymes in the symmetrically methylated CpG context are still elusive. Employing the unique fluorescence properties of pyrene group, we designed and synthesized a sensitive fluorescence‐based probe not only to target 5‐formylcytosine (5fC) sites, but also to distinguish symmetric from asymmetric 5fC sites in the double stranded DNA context during TET‐dependent 5mC oxidation process. Using this novel probe, we revealed dominant levels of symmetric 5fC among total 5fC sites during in vitro TET‐dependent 5mC oxidation and novel mechanistic insights into the TET‐dependent 5mC oxidation in the mCpG context.     

Probing the dependence of long-range, four-atom interactions on intermolecular orientation: 2. Molecular deuterium and iodine monochloride

Laser-induced fluorescence and action spectroscopy experiments have identified multiple conformers of the D2...ICl van der Waals complex for both ortho-D2 (o-D2) and para-D2 (p-D2). As with the analogous H2...ICl van der Waals complexes [Darr, J. P.; Crowther, A. C.; Loomis, R. A.; Ray, S. E.; McCoy, A. B. J. Phys. Chem. A 2007, 111, 13387], the C2v conformer with the deuterium molecule localized at the iodine atom end of the dihalogen is significantly more stable than the asymmetric conformer that has the deuterium positioned orthogonally to the ICl bond axis, D0' = 223.9(2.4) versus 97.3(8)-103.9(3) cm(-1) for p-D2...I(35)Cl(X, v'=0). For both conformers, complexes containing p-D2 are found to be more strongly bound than those with o-D2. The electronically excited D2...ICl(A, v') and D2...ICl(B, v') complexes are found to have equilibrium geometries that are nearly the same as those of the ground-state asymmetric structures. Calculated D2...ICl(B, v'=3) energies and probability amplitudes obtained using a simple scaled He + ICl(B, v'=3) potential provide clues to the nature of the different excited-state levels accessed.     

Partitioning and adsorption in gas-liquid-solid chromatography: Models of temporal moments for retention and variance

Summary The resolution of gaseous chemical species in gasliquid-solid chromatography is influenced by absorption (partitioning) in the liquid and adsorption at the liquid-solid interface. We consider fundamental mass transfer models with adsorption and partitioning effects for solid chromatographic supports covered with thin films of stationary liquid. The dynamic models, based on mass-balance partial-differential equations, include the significant phenomena: convection, axial dispersion, gas-liquid mass transfer, intraparticle diffusion, and liquid-solid adsorption. Expressions for retention time and band variance (first and second temporal moments) are presented and evaluated for four distinct models: (1) capillary tube with inner surface covered with a uniform-thickness liquid film, (2) column of nonporous spheres covered with a uniform-thickness liquid film, (3) porous spherical particles with intraparticle pores covered with a uniform-thickness liquid film, (4) porous spherical particles with intraparticle pores completely filled with liquid.     

Ebselen and congeners inhibit NADPH oxidase 2-dependent superoxide generation by interrupting the binding of regulatory subunits

NADPH oxidases (Nox) are a primary source of reactive oxygen species (ROS), which function in normal physiology and, when overproduced, in pathophysiology. Recent studies using mice deficient in Nox2 identify this isoform as a novel target against Nox2-implicated inflammatory diseases. Nox2 activation depends on the binding of the proline-rich domain of its heterodimeric partner p22phox to p47phox. A high-throughput screen that monitored this interaction via fluorescence polarization identified ebselen and several of its analogs as inhibitors. Medicinal chemistry was performed to explore structure-activity relationships and to optimize potency. Ebselen and analogs potently inhibited Nox1 and Nox2 activity but were less effective against other isoforms. Ebselen also blocked translocation of p47phox to neutrophil membranes. Thus, ebselen and its analogs represent a class of compounds that inhibit ROS generation by interrupting the assembly of Nox2-activating regulatory subunits.