Shape resonances in slow electron scattering by aromatic molecules. I. Anthraquinone derivatives

A series of anthraquinone (C(14)O(2)H(8)) derivatives has been studied by means of electron capture negative ion mass spectrometry (ECNI-MS), photoelectron spectroscopy (PES), and AM1 quantum chemical calculations. Mean lifetimes of molecular negative ions M(-.) (MNI) have been measured. The mechanism of long-lived MNI formation in the epithermal energy region of incident electrons has been investigated. A simple model of a molecule (a spherical potential well with the repulsive centrifugal term) has been applied for the analysis of the energy dependence of cross sections at the first stage of the electron capture process. It has been shown that a temporary resonance of MNI at the energy approximately 0.5 eV corresponds to a shape resonance with lifetime 1-2.10(-13) s in the f-partial wave (l = 3) of the incident electron. The next resonant state of MNI at the energy approximately 1.7 eV has been associated with the electron excited Feshbach resonance (whose parent state is a triplet npi* transition). In all cases the initial electron state of the MNI relaxes into the ground state by means of a radiationless transition, and the final state of the MNI is a nuclear excited resonance with a lifetime measurable on the mass spectrometry timescale. Copyright 1999 John Wiley & Sons, Ltd.     

A finite element formulation for global linear stability analysis of a nominally two‐dimensional base flow

A stabilized finite element method, to carry out the linear stability analysis of a two‐dimensional base flow to three‐dimensional perturbations that are periodic along span, is presented. The resulting equations for the time evolution of the disturbance requires a solution to the generalized eigenvalue problem. The analysis is global in nature and is also applicable to non‐parallel flows. Equal‐order‐interpolation functions for velocity and pressure are utilized. Stabilization terms are added to the Galerkin formulation to admit the use of equal‐order‐interpolation functions and to eliminate node‐to‐node oscillations that might arise in advection‐dominated flows. The proposed formulation is tested on two flow problems. First, the mode transitions in the circular Couette flow are investigated. Two scenarios are considered. In the first one, the outer cylinder is at rest, while the inner one spins. Two linearly unstable modes are identified. The primary mode is real and represents the axisymmetric Taylor vortices. The second mode is complex and consists of spiral vortices. For the counter‐rotating cylinders, the primary transition is via the appearance of spiral vortices. Excellent agreement with results from earlier studies is observed. The formulation is also utilized to investigate the parallel and oblique modes of vortex shedding past a cylinder for the Re = 100 flow. It is found that the flow is associated with a large number of unstable oblique shedding modes. The parallel mode of vortex shedding is a special case of this family of modes and is associated with the largest growth rate. Copyright © 2014 John Wiley & Sons, Ltd.     

Practical aspects of fluorescent staining for proteomic applications

SYPRO Orange and SYPRO Ruby staining methods, modified for use with large-format two dimensional (2-D) gels, are compared to the manufacturer's recommended protocols to determine sensitivity and reproducibility of the new methods. This study examines the critical aspects of fixation, washing, and staining to develop an optimized fluorescent staining method. It was determined that careful control of sodium dodecyl sulfate (SDS) levels and pH in the gel was critical for successful staining with SYPRO Orange. Overnight fixation in 40% ethanol/2% acetic acid/0.0005% SDS preserved protein content, eliminated ampholyte-generated staining artifacts, and had no detrimental effects on staining. Three one-hour washes in 2% acetic acid/0.0005% SDS, followed by staining with SYPRO Orange diluted 1:5,000 with washing solution for 3 or more hours, produced high sensitivity, low background images using a STORM 860 laser scanner. Gels viewed two years after staining showed no significant changes with respect to the initial protein patterns, and allowed successful mass spectrometric postgel characterization of protein spots. Protocol changes applied to SYPRO Ruby staining improved the contrast of STORM 860-generated images, but had little impact on staining sensitivity. A comparison of the cost benefits of staining with SYPRO Orange vs. SYPRO Ruby is also discussed.     

Fluorogenic Tagging of Peptide and Protein 3-Nitrotyrosine with 4-(Aminomethyl)benzenesulfonic Acid for Quantitative Analysis of Protein Tyrosine Nitration

Protein 3-nitrotyrosine (3-NT) has been recognized as an important biomarker of nitroxidative stress associated with inflammatory and degenerative diseases, and biological aging. Analysis of protein-bound 3-NT continues to represent a challenge since in vivo it frequently does not accumulate on proteins in amounts detectable by quantitative analytical methods. Here, we describe a novel approach of fluorescent tagging and quantitation of peptide-bound 3-NT residues based on the selective reduction to 3-AT followed by reaction with 4-(aminomethyl)benzenesulfonic acid (ABS) in the presence of K₃Fe(CN)₆ to form a highly fluorescent 2-phenylbenzoxazole product. Synthetic 3-NT peptide (0.005-1 μM) upon reduction with 10 mM sodium dithionite and tagging with 2 mM ABS and 5 μM K₃Fe(CN)₆ in 0.1 M Na₂HPO₄ buffer (pH 9.0) was converted with yields >95% to a single fluorescent product incorporating two ABS molecules per 3-NT residue, with fluorescence excitation and emission maxima at 360 ± 2 and 490 ± 2 nm, respectively, and a quantum yield of 0.77 ± 0.08, based on reverse-phase LC with UV and fluorescence detection, fluorescence spectroscopy and LC–MS–MS analysis. This protocol was successfully tested for quantitative analysis of in vitro Tyr nitration in a model protein, rabbit muscle phosphorylase b, and in a complex mixture of proteins from C2C12 cultured cells exposed to peroxynitrite, with a detection limit of ca. 1 pmol 3-NT by fluorescence spectrometry, and an apparent LOD of 12 and 40 pmol for nitropeptides alone or in the presence of 100 μg digested cell proteins, respectively. LC–MS–MS analysis of ABS tagged peptides revealed that the fluorescent derivatives undergo efficient backbone fragmentations, allowing for sequence-specific characterization of protein Tyr nitration in proteomic studies. Fluorogenic tagging with ABS also can be instrumental for detection and visualization of protein 3-NT in LC and gel-based protein separations.     

Oscillator models for multiphoton optical bistability and phase conjugacy

Nonlinear oscillator models are constructed to treat the bistability in situations involving elementary excitations in solids. Such models are shown to be useful not only in describing single photon but also multiphoton bistability. The resulting bistability both with and without cavity is considered. The two-photon excitonic bistability in CuCl is in detail. The effect of local field corrections can also be incorporated, in a simple manner, in such models.