Simulation of electron solid interactions in NbC and NbN using Monte Carlo method

A computer program has been developed using Rutherford’s Screened Scattering Model and Energy loss model due to Bethe and applied to simulate the electron interaction pattern in the sample of NbC and NbN with a resist layer of PMMA (Polymethyl Methylacrylate). Using the program we have studied the extent of penetration, lateral spread for different electron energies and the degree of electron back scattering. It has been found that backscattering and lateral spread is more in case of NbC than in NbN signifying hard, refractory and ceramic properties of NbC.     

Structural Wall-modeled LES Using a High-order Spectral Difference Scheme for Unstructured Meshes

The combination of the high-order unstructured Spectral Difference (SD) spatial discretization scheme with Sub-Grid Scale (SGS) modeling for Wall-Modeled Large-Eddy Simulation (WMLES) is investigated. Particular focus is given to the use of wall-function approaches and to the relevant optimal coupling with the numerical scheme and the SGS model, a similarity mixed type model featuring newly designed discrete filters with specified cutoff length scale. To take full advantage of the discontinuous Finite Element (FE) structure which characterizes the SD scheme, wall-modeling is accomplished within the first wall element by using the information from the farthest solution points from the wall. Compared to the customary used first off-wall node, this point provides more accurate information to the wall-function, thus improving the quality of the solution. Two different law-of-the-wall are tested, a classical three-layers wall-function based on the equilibrium assumption and a more general formulation to account for the pressure gradient in more complex configurations. Moreover, the mixed scale-similarity SGS model is used in the entire computational domain without any particular adjustment inside the wall-modeled region. Numerical tests on the classical test case of the turbulent channel flow at different Reynolds numbers and on the channel with periodic constrictions at Re _h = 10,595 give evidence that the results are extremely sensitive to the choice of the solution points used to provide the informations to the law-of-the-wall. In particular, it is shown that significant improvements in the results can be attained by solving the wall-function away from the wall, rather than at the first off-wall solution point as customary done. The combination of the selected wall-modeling strategies and the similarity mixed formulation proves to be remarkably accurate, even in the presence of boundary layer separation, thus opening the path to further exploit the high-order SD platform, as well as a broad range of other similar methodologies, for WMLES. Extensions of the methodology are envisaged to include more sophisticated wall-modeling approaches incorporating turbulent sensors to switch to no-slip conditions in laminar regions.     

Prediction of Henry's constants of xenon in cyclo-alkanes from molecular dynamics simulations

Using the molecular dynamics (MD) method, we demonstrate that intermolecular nuclear magnetic resonance (NMR) chemical shifts can be used to evaluate and develop intermolecular potentials for cross-interactions for use in solubility studies. The calculation of chemical shifts in MD is an order of magnitude more efficient than solubilities, which makes it an attractive tool for fine-tuning potential models. We examine the average Xe chemical shifts in cyclo-alkanes over a range of temperatures to develop a suitable potential model for the cross-interactions between Xe and a series of cyclo-alkanes. Our results clearly demonstrate that potential models that show better agreement with experiments for chemical shift, invariably lead to better agreement with experiment for Henry's constant and solubility of gases in solvents.     

Factors influencing tetranuclear [2 x 2] grid vs dinuclear side-by-side structures for silver(I) complexes of pyridazine-based bis-bidentate ligands

Silver(I) complexes of five bis-bidentate Schiff-base ligands, derived from 3,6-diformylpyridazine and substituted anilines (2,4-dimethylaniline L ( o,p - Me ); 3,5-dichloroaniline L ( m,m - Cl ); 2-aminobiphenyl L ( o - Ph ); p-toluidine L ( p - Me ); 4-aminophenol L ( p - OH ); p-anisidine L ( p - OMe )), have been prepared. The ligands have a wide range of steric and electronic properties due to variation in the extent and nature of the substitution of the aniline rings. Four of the resulting complexes were structurally characterized by X-ray crystallography: three of the four, [Ag 2( L ( o,p - Me )) 2](BF 4) 2, [Ag 2( L ( m,m - Cl )) 2](BF 4) 2 and [Ag 2( L ( o - Ph )) 2](BF 4) 2 formed dinuclear side-by-side complexes, while [Ag 4( L ( p - Me )) 4](BF 4) 4 gave a tetranuclear [2 x 2] grid. The previously reported tetranuclear [2 x 2] grid [Ag 4( L ( p - OMe )) 4](BF 4) 4 was recrystallized in the presence of benzene to see if this would alter the architecture of this complex. It did not: the [2 x 2] grid architecture was retained despite the benzene molecules of solvation. Given the flexibility of silver(I) with regard to coordination geometry, the molecular structure of these complexes is influenced mostly by the ligand rather than the metal ion. In each case, the factors which influence the molecular architecture are presented and discussed. Substituent effects on the electrostatics of the intramolecular ligand-ligand pi-pi interactions (XED2.8) account for some of the differences observed in the structures.     

Substrates and Cyclic Peptide Inhibitors of the Oligonucleotide-Activated Sirtuin 7**

The sirtuins are NAD⁺-dependent lysine deacylases, comprising seven isoforms (SIRT1–7) in humans, which are involved in the regulation of a plethora of biological processes, including gene expression and metabolism. The sirtuins share a common hydrolytic mechanism but display preferences for different ϵ-N-acyllysine substrates. SIRT7 deacetylates targets in nuclei and nucleoli but remains one of the lesser studied of the seven isoforms, in part due to a lack of chemical tools to specifically probe SIRT7 activity. Here we expressed SIRT7 and, using small-angle X-ray scattering, reveal SIRT7 to be a monomeric enzyme with a low degree of globular flexibility in solution. We developed a fluorogenic assay for investigation of the substrate preferences of SIRT7 and to evaluate compounds that modulate its activity. We report several mechanism-based SIRT7 inhibitors as well as de novo cyclic peptide inhibitors selected from mRNA-display library screening that exhibit selectivity for SIRT7 over other sirtuin isoforms, stabilize SIRT7 in cells, and cause an increase in the acetylation of H3 K18.     

Rotation-Inversion Isomerization of Tertiary Carbamates: Potential Energy Surface Analysis of Multi-Paths Isomerization Using Boltzmann Statistics

Potential energy surface (PES) analyses at the SMD[MP2/6–311++G(d,p)] level and higher-level energies up to MP4(fc,SDTQ) are reported for the fluorinated tertiary carbamate N-ethyl-N-(2,2,2-trifluoroethyl) methyl carbamate ( VII ) and its parent system N,N-dimethyl methyl carbamate ( VI ). Emphasis is placed on the analysis of the rotational barrier about the CN carbamate bond and its interplay with the hybridization of the N-lone pair (NLP). All rotational transition state (TS) structures were found by computation of 1D relaxed rotational profiles but only 2D PES scans revealed the rotation-inversion paths in a compelling fashion. We found four unique chiral minima of VII , one pair each of E- and Z-rotamers, and we determined the eight unique rotational TS structures associated with every possible E/Z-isomerization path. It is a significant finding that all TS structures feature N-pyramidalization whereas the minima essentially contain sp²-hybridized nitrogen. We will show that the TS stabilities are affected by the synergetic interplay between NLP/CO₂ repulsion minimization, NLP→σ^*(CO) negative hyperconjugation, and two modes of intramolecular through-space electrostatic stabilization. We demonstrate how Boltzmann statistics must be applied to determine the predicted experimental rotational barrier based on the energetics of all eight rotamerization pathways. The computed barrier for VII is in complete agreement with the experimentally measured barrier of the very similar fluorinated carbamate N-Boc-N-(2,2,2-trifluoroethyl)-4-aminobutan-1-ol II . NMR properties of VII were calculated with a variety of density functional/basis set combinations and Boltzmann averaging over the E- and Z-rotamers at our best theoretical level results in good agreement with experimental chemical shifts δ(¹³C) and J(¹³C,¹⁹F) coupling constants of II (within 6 %).     

Ground-and Excited-State Characterization of an Electrostatic Complex between Tetrakis-(4-Sulfonatophenyl)porphyrin and 16-Pyrimidinium Crown-4

Abstract— We report the formation of an electrostatic complex between (16-pyrimidinium crown-4)tetranitrate (16PC4) and tetrakis-(4-sulfonatophenyl)porphyrin (4SP) in aqueous solution. Ground-state complex formation results in a red shift of the 4SP visible absorption bands and a decrease in absorbance of the Soret band. The equilibrium constant for complex formation (determined from optical titrations) is found to be (2.0 ± 0.2) × 10⁵ M ⁻¹. In addition, the data fit to an expression describing a 1:1 stoichiometry. Excitation of the complex results in quenching of both the excited singlet and triplet states of the associated porphyrin. The singlet-state lifetime decreases from 10 ns for the free porphyrin to 1.5 ns in the presence of 16PC4 at low solution ionic strengths. In addition, evidence is presented for triplet-state quenching within the complex with k _q= (1.1 ± 0.1) × 10⁴ s⁻¹. The mechanism of quenching is tentatively assigned to electron transfer from either the excited singlet or excited triplet state of the porphyrin to the ground state of the 16PC4.     

ANALYSIS AND IMPLEMENTATION OF THE GAS-KINETIC BGK SCHEME FOR COMPUTATIONAL GAS DYNAMICS

Gas-kinetic schemes based on the BGK model are proposed as an alternative evolution model which can cure some of the limitations of current Riemann solvers. To analyse the schemes, simple advection equations are reconstructed and solved using the gas-kinetic BGK model. Results for gas-dynamic application are also presented. The final flux function derived in this model is a combination of a gas-kinetic Lax– Wendroff flux of viscous advection equations and kinetic flux vector splitting. These two basic schemes are coupled through a non-linear gas evolution process and it is found that this process always satisfies the entropy condition. Within the framework of the LED (local extremum diminishing) principle that local maxima should not increase and local minima should not decrease in interpolating physical quantities, several standard limiters are adopted to obtain initial interpolations so as to get higher-order BGK schemes. Comparisons for well-known test cases indicate that the gas-kinetic BGK scheme is a promising approach in the design of numerical schemes for hyperbolic conservation laws. © 1997 by John Wiley & Sons, Ltd.     

Utility of membrane preconcentration-capillary electrophoresis-mass spectrometry in overcoming limited sample loading for analysis of biologically derived drug metabolites, peptides, and proteins

The limited loading of capillary electrophoresis (CE) leads to relatively poor concentration limits of detection. In this work a unique method for analyte preconcentration with capillary electrophoresis-mass spectrometry (CE-MS) is described. A cartridge containing an impregnated membrane is installed at the inlet of the CE capillary, and we term this approach membrane preconcentration capillary electrophoresis-mass spectrometry (mPC-CE-MS). The analysis of in vivo derived metabolites, peptides, and proteins is described showing the wide applicability of the technology in the analysis of numerous compound classes ranging in molecular weight from 200–60,000 u. In particular, we describe the direct mPC-CE-MS analysis of urine obtained from a patient receiving the neuroleptic drug haloperidol. Three metabolites were found in the urine, and two of them are implicated in the Parkinsonian-like side effects caused by taking this drug. The technique is also applied to the analysis of major histocompatibility complex class I peptides obtained from EG-7 cells. Furthermore, the clinical potential of this approach is described by the direct analysis of urine from a patient suffering from multiple myeloma, as well as aqueous humor derived from a patient undergoing surgery. Finally we show that the use of mPC-ME-MS in conjunction with either analyte stacking (small organic molecules such as metabolites) or moving-boundary transient isotachophoresis (peptides and proteins) after analytes have been eluted from the adsorptive membrane affords optimal performance and no compromise in CE mass spectrometry performance.     

Kinetic study of the complex reaction between copper(II) and 2-(2′-hydroxy-3′-methoxyphenyl)benzothiazole

2-(2′-Hydroxy-3′-methoxyphenyl)benzothiazole reacts with copper(II) in an ethanol/water mixture to form an O,S chelate which exhibits the remarkable property of changing the chelation site above a pH of ca. 5.0, to the O,N site. The detailed kinetics of this reaction in an ethanol/water mixture (3:1) at a temperature of 25 °C was investigated using a stopped-flow spectrophotometric technique employing a wavelength of 400 nm. The initial complex, Cu(O,S), is formed via a fast, reversible second-order complex formation step whereupon the formation of the Cu (O,N) follows first order kinetics. The Cu(O,N) complex is, however, unstable towards internal electron exchange and after the reaction is complete, a black polymeric material very slowly precipitates out of solution. Rate and equilibrium constants for the postulated reactions are presented and discussed.