Precision Measurement of the 29Si, 33S, and 36Cl Binding Energies

The binding energies of 29Si, 33S, and 36Cl have been measured with a relative uncertainty $< 0.59 \times 10^{-6}$ using a flat-crystal spectrometer. The unique features of these measurements are 1) nearly perfect crystals whose lattice spacing is known in meters, 2) a highly precise angle scale that is derived from first principles, and 3) a gamma-ray measurement facility that is coupled to a high flux reactor with near-core source capability. The binding energy is obtained by measuring all gamma-rays in a cascade scheme connecting the capture and ground states. The measurements require the extension of precision flat-crystal diffraction techniques to the 5 to 6 MeV energy region, a significant precision measurement challenge. The binding energies determined from these gamma-ray measurements are consistent with recent highly accurate atomic mass measurements within a relative uncertainty of $4.3 \times 10^{-7}$. The gamma-ray measurement uncertainties are the dominant contributors to the uncertainty of this consistency test. The measured gamma-ray energies are in agreement with earlier precision gamma-ray measurements.Comment: 13 pages, 4 figure

Polarized X-ray-emission Studies of Methyl Chloride and the Chlorofluoromethanes

A new technique sensitive to molecular orientation and geometry, and based on measuring the polarization of x-ray emission, has been applied to the Cl-containing molecules methyl chloride (CH3Cl) and the chlorofluoromethanes (CF3Cl, CF2Cl2, and CFCl3) in the gas phase. Upon selective excitation using monochromatic synchrotron radiation in the Cl K-edge (Cl 1s) near-threshold region, polarization-selective x-ray emission studies reveal highly polarized molecular valence x-ray fluorescence for all four molecules. The degree and the orientation of the polarized emission are observed to be sensitive to the incident excitation energy near the Cl Kedge. In some cases, the polarization direction for x-ray emission reverses for small changes in incident excitation energy (a few eV). It is shown that the polarized x-ray emission technique can be used to infer, directly from experiment, symmetries of occupied and unoccupied valence molecular orbitals, an- isotropies in absorption and emission, and orientational and geometrical information. It is suggested that the x-ray polarized-fluorescence phenomenon, reported here for simple molecules, can be used as a new approach to study more complicated systems in a variety of environments

Molecular-orbital Studies Via Satellite-free X-ray Fluorescence: Cl-K Absorption and K–Valence-level Emission Spectra of Chlorofluoromethanes

X-ray absorption and emission measurements in the vicinity of the chlorine K edge of the three chlorofluoromethanes have been made using monochromatic synchrotron radiation as the source of excitation. By selectively tuning the incident radiation to just above the Cl 1s single-electron ionization threshold for each molecule, less complex x-ray-emission spectra are obtained. This reduction in complexity is attributed to the elimination of multielectron transitions in the Cl K shell, which commonly produce satellite features in x-ray emission. The resulting satellite-free x-ray-emission spectra exhibit peaks due only to electrons in valence molecular orbitals filling a single Cl 1s vacancy. These simplified emission spectra and the associated x-ray absorption spectra are modeled using straightforward procedures and compared with semiempirical ground-state molecular-orbital calculations. Good agreement is observed between the present experimental and theoretical results for valence-orbital energies and those obtained from ultraviolet photoemission, and between relative radiative yields determined both experimentally and theoretically in this work

Resonant inelastic x-ray scattering from molecules and atoms

X-ray fluorescence spectroscopy is one of the most powerful methods for the understanding of the electronic structure of matter. We report here on fluorescence experiments in the 2 to 6 keV photon energy range using tunable synchrotron radiation and the resulting experimental programs on resonant inelastic scattering in atoms and on polarization measurements in resonant molecular excitations

Calculation of quasi-degenerate energy levels of two-electron ions

Accurate QED calculations of the interelectron interaction corrections for the $(1s2p)2 {}^1 P_1$, $(1s2p)2 {}^3 P_1$ two-electron configurations for ions with nuclear charge numbers $10\le Z \le 92$ are performed within the line profile approach. Total energies of these configurations are evaluated. Employing the fully relativistic treatment based on the {$j$--$j$} coupling scheme these energy levels become quasi-degenerate in the region $Z\le 40$. To treat such states within the framework of QED we utilize the line profile approach. The calculations are performed within the Coulomb gauge.Comment: 22 pages, 11 figure

Enhanced protein isoform characterization through long-read proteogenomics

[Background] The detection of physiologically relevant protein isoforms encoded by the human genome is critical to biomedicine. Mass spectrometry (MS)-based proteomics is the preeminent method for protein detection, but isoform-resolved proteomic analysis relies on accurate reference databases that match the sample; neither a subset nor a superset database is ideal. Long-read RNA sequencing (e.g., PacBio or Oxford Nanopore) provides full-length transcripts which can be used to predict full-length protein isoforms.[Results] We describe here a long-read proteogenomics approach for integrating sample-matched long-read RNA-seq and MS-based proteomics data to enhance isoform characterization. We introduce a classification scheme for protein isoforms, discover novel protein isoforms, and present the first protein inference algorithm for the direct incorporation of long-read transcriptome data to enable detection of protein isoforms previously intractable to MS-based detection. We have released an open-source Nextflow pipeline that integrates long-read sequencing in a proteomic workflow for isoform-resolved analysis.[Conclusions] Our work suggests that the incorporation of long-read sequencing and proteomic data can facilitate improved characterization of human protein isoform diversity. Our first-generation pipeline provides a strong foundation for future development of long-read proteogenomics and its adoption for both basic and translational research.This work was supported by a National Institutes of Health (NIH) grant R35GM142647 (G.M.S.), NIH grant R35GM126914 (L.M.S.), and Jackson Laboratory (A.D.M.). The codeathon which initiated the project was supported by the NIH STRIDES Initiative at the NIH.Peer reviewe

SINGLE AND MULTIPLE VACANCY EFFECTS IN MOLECULAR X-RAY SPECTRA

Nous discutons le spectre d'émission X Kβ des gaz moléculaires en utilisant l'exemple particulier de CH3Cl. A l'aide d'une détermination expérimentale grossière de seuil, nous montrons que les processus à vacances multiples sont du côté des hautes énergies des raies spectrales saillantes de l'émission Kβ de Cl dans CH3Cl. D'après un récent calcul d'orbitale moléculaire, les raies d'émission molécuIaires Kβ de Cl s'identifient aux orbitales 3 e et 7 a1 de CH3Cl. Le spectre d'émission K de valence peut être interprété pour l'essentiel au terme de transitions à un électron et une vacance simple des couches internes vers les différentes orbitales moléculaires extérieures, la position de la raie spectrale et son intensité dépendant du niveau d'énergie moléculaire, de la symétrie et du recouvrement des orbitales. Pour étendre les études d'émission X moléculaires aux séries L des sulfures et chlorures, nous avons mesuré les spectres L23 de l'argon afin d'étudier la réponse instrumentale dans cette région. Une extra-particularité remarquable de l'émission aux basses énergies a été trouvée dans le spectre L23 de l'argon. Une particularité semblable est également observée dans l'émission L23 de Cl et de K dans KCl. Ces extra-particularités sont interprétées comme preuves d'un processus à deux électrons.The X-ray Kβ emission spectra from molecular gases is discussed with the use of a particular example, CH3Cl. With the help of a crude threshhold experiment, the multiple vacancy processes are shown to be on the high energy side of the prominent spectral lines in Cl Kβ emission from CH3Cl. From a recent molecular orbital calculation, the Cl Kβ molecular emission lines are identified as the 3 e and 7 a1 orbitals of CH3Cl. The valence K emission spectra can be interpreted for the most part in terms of one electron single vacancy transitions from inner shells to the various outer molecular orbitals, where the spectral line position and intensity are dependent on the molecular term value, symmetry and orbital overlap. In the course of extending the X-ray molecular emission studies to the L series of sulphur and chlorine we measured the L23 spectra from argon gas to study the instrumental response in this region. A prominent extra low energy emission feature was found in the Ar L23 spectra. A similar feature is also observed in the L23 emission of Cl and K from KCl. These extra features are interpreted as evidence of a double electron process