A novel derivatization method for peptides to increase sensitivity and backbone fragmentation in liquid secondary-ion mass spectra.

Derivatization is used to increase both negative-ion sensitivity and positive-ion sequence information in the liquid secondary-ion mass spectra (LSIMS) of a series of peptides. The derivatization method involves acylation with pentafluorobenzoyl fluoride in a single-step reaction, and the reaction mixture is applied directly to the probe tip for analysis. Acylation takes place at the unprotected N-terminus, tyrosine, and lysine. The derivatives exhibit increased signal-to-noise ratio for [M-H]- ions, especially where there is not already an acidic amino acid residue in the peptide. In positive-ion LSIMS, the N-terminal group acts to retain the charge at the N-terminus, simplifying the fragmentation by producing N-terminal fragment ions. It also increases positive-ion fragmentation, sometimes very dramatically, making sequence determination more straightforward. The simplicity of the process, together with the enhancements it provides, make this a generally useful method for obtaining peptide structural information.     

Practical Considerations for Selection of Representative Elementary Volumes for Fluid Permeability in Fibrous Porous Media

We investigate the lower bound of the area of a square-shaped representative elementary volume (REV) for the permeability tensor for transverse Stokes flow through randomly packed, parallel, and monodisperse cylinders. The investigation is significant to flow models using small calculation regions for fibrous porous media, such as modeling defect formation during directional solidification in the mushy zone of dendritic alloys. Using 90 ensembles of 1,000 domains, where each ensemble comprises domains with the same number and size of cylinders, we develop correlations between the permeability tensor invariants and macroscopic features of the domain. We find that for ensembles of domains with fewer than 200 cylinders, the eigenvectors of the permeability tensors exhibit preferential alignment with the domain axes, demonstrating that the estimated permeability is significantly affected by the periodic boundary conditions for these cases. Our results also suggest that the anisotropy of the permeability tensor may not be insignificant even for large sampling volumes. These results provide a practical lower bound for the calculation volumes used in permeability simulations in fibrous porous media, and also suggest that modelers should consider using an anisotropic tensor for small calculation volumes if phenomena such as channeling are important.     

Longitudinal focusing and cooling of a molecular beam

A neutral polar molecule experiences a force in an inhomogeneous electric field. This electric field can be designed such that a beam of polar molecules is exposed to a harmonic potential in the forward direction. In this potential the longitudinal phase-space distribution of the ensemble of molecules is rotated uniformly. This property is used to longitudinally focus a pulsed beam of ammonia molecules and to produce a beam with a longitudinal velocity spread of 0.76 m/s, corresponding to a temperature of 250 mu K.     

Using an incremental mean first passage approach to explore the viscosity dependent dynamics of the unbiased translocation of a polymer through a nanopore

Noting the limitations of the standard characterization of translocation dynamics, an incremental mean first passage process methodology is used to more completely map the unbiased translocation of a polymer through a nanopore. In this approach, the average time t(0) required to reach successively increasing displacements for the first time is recorded - a measure shown to be more commensurate with the mean first passage nature of translocation. Applying this methodology to the results of Langevin dynamics simulations performed in three dimensions across a range of viscosities, a rich set of dynamics spanning regular diffusion at low viscosities to sub-diffusion at higher viscosities is revealed. Further, while the scaling of the net translocation time τ with polymer length N is shown to be viscosity-dependent, common regimes are found across all viscosities: super-diffusive behaviour at short times, an N-independent backbone consistent with τ ～ N(2.0) at low viscosities and τ ～ N(2.2) at higher viscosities for intermediate times, and N-dependent deviations from the backbone near the completion of translocation.     

Excitation of analytes and enhancement of emission intensities in a d.c. plasma jet: a critical review leading to proposed mechanistic models

Experimental data and theoretical criteria are used to critically review existing models for analyte emission enhancement in the 3-electrode d.c. plasma (DCP). The analytical zone is characterized as a non-optically thin recombining plasma in partial thermodynamic equilibrium (PTE). Spectrochemical excitation the authors ascribe largely to: (1) argon resonance line radiative transport; (2) inversion of optically pumped argon states; (3) inversion of analyte populations by Franck-Condon collisions with argon; (4) energy cascading in analytes via a multitude of channels. Adding an easily ionized element (EIE): (1) induces additional resonance line radiative transfer; (2) raises electron densities in cooler, analyte-rich plasma margins; (3) locally increases argon optical absorption cross sections via Stark broadening; (4) redistributes ohmic heating. Coupling between the proposed mechanisms is non-linear. Relationships between radiative transfer and collisional redistribution and (1) background suppression by EIE and (2) analyte emission enhancement by helium are also examined. Similarities between DCP and inductively coupled plasma (ICP) excitation mechanisms are noted and practical implications are addressed.     

Characterization and complementation of a Pichia stipitis mutant unable to grow on d-xylose or l-arabinose

Pichia stipitis CBS 6054 will grow on d-xylose, d-arabinose, and l-arabinose. d-Xylose and l-arabinose are abundant in seed hulls of maize, and their utilization is important in processing grain residues. To elucidate the degradation pathway for l-arabinose, we obtained a mutant, FPL-MY30, that was unable to grow on d-xylose and l-arabinose but that could grow on d-arabinitol. Activity assays of oxidoreductase and pentulokinase enzymes involved in d-xylose, d-arabinose, and l-arabinose pathways indicated that FPL-MY30 is deficient in d-xylitol dehydrogenase (D-XDH), d- and l-arabinitol dehydrogenases, and d-ribitol dehydrogenase. Transforming FPL-MY30 with a gene for xylitol dehydrogenase (PsXYL2), which was cloned from CBS 6054 (Gen Bank AF127801), restored the D-XDH activity and the capacity for FPL-MY30 to grow on l-arabinose. This suggested that FPL-MY30 is critically deficient in XYL2 and that the d-xylose and l-arabinose metabolic pathways have xylitolas a common intermediate. The capacity for FPL-MY30 to grow on d-arabinitol could proceed through d-ribulose.     

Copper‐Catalyzed Electrophilic Amination of Heteroarenes and Arenes by CH Zincation

Direct amination of heteroarenes and arenes has been achieved in a one‐pot C? H zincation/copper‐catalyzed electrophilic amination procedure. This amination method provides an efficient and rapid approach to access a diverse range of heteroaromatic and aromatic amines including those previously inaccessible using C? H amination methods. The mild reaction conditions and good functional‐group compatibility demonstrate its great potential for the synthesis of important and complex amines.     

On deflection fields, weak-focusing and strong-focusing storage rings for polar molecules

In this paper, we analyze electric deflection fields for polar molecules in terms of a multipole expansion and derive a simple but rather insightful expression for the force on the molecules. Ideally, a deflection field exerts a strong, constant force in one direction, while the force in the other directions is zero. We show how, by a proper choice of the expansion coefficients, this ideal can be best approximated. We present a design for a practical electrode geometry based on this analysis. By bending such a deflection field into a circle, a simple storage ring can be created; the direct analog of a weak-focusing cyclotron for charged particles. We show that for realistic parameters a weak-focusing ring is only stable for molecules with a very low velocity. A strong-focusing (alternating-gradient) storage ring can be created by arranging many straight deflection fields in a circle and by alternating the sign of the hexapole term between adjacent deflection fields. The acceptance of this ring is numerically calculated for realistic parameters. Such a storage ring might prove useful in experiments looking for an EDM of elementary particles.     

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