Inner-shell electron spectroscopy and chemical properties of atoms and small molecules

The program has been concerned with gas-phase carbon 1s photoelectron spectroscopy of a number of molecules of potential chemical interest. The primary goals have been to determine carbon 1s ionization energies with a view of relating these to other chemical properties such as electronegativity, acidity, basicity, and reactivity, in order to provide a better understanding of these fundamental properties. The role of electron-donating (methyl) and electron-withdrawing (fluoro) substituents on the carbon 1s ionization energies of substituted benzenes has been studied., and these results have been related to measurements of the reactivities of the same molecule as well as to their affinities for protons (basicity). Opportunities for investigation in unplanned areas have arisen, and the program has been modified to take advantage of these. One has been the realization that, under certain circumstances, inner-shell ionization energies may depend on the molecular conformation. Several examples of this phenomenon have been investigated and it has been shown that this technique provides a tool for the measurement of the energy differences between different conformers of the same substance. The other has been the demonstration that photoelectron recoil can lead to the excitation of vibrational modes that are forbidden in the normal view of photoemission and to rotational heating of the molecule that increases with the energy of the exciting radiation

Small Molecule Photoelectron Spectroscopy : Recoil Effects, Stoichiometric Surprises, and Double-Core-Hole Ionization

This is an author's peer-reviewed final manuscript, as accepted by the publisher. The published article is copyrighted by Elsevier and can be found at: https://doi.org/10.1016/j.elspec.2012.12.004Three features of small-molecule photoelectron spectroscopy are considered (1) The atom from which a photoelectron is emitted must have a recoil momentum equal to that of the emitted electron. This is shared among the various modes of motion of the ion, leading to rotational and vibrational excitation. Furthermore, any initial velocity of the atom (due to either translational, rotational, or vibrational motion) will lead to Doppler broadening. These effects are observable and can, in general, be accounted for by simple models. In some cases, however, the simple models fail and a deeper insight is necessary. (2) Inner-shell photoionization is essentially an atomic process, and it is expected that the intensity for emission of a photoelectron from the core of an atom in a molecule will be independent of its chemical environment. Recent measurements on the carbon 1s photoelectron spectra of three chloroethanes show that this is not the case. At energies not far above the ionization threshold there are strong oscillations of the intensity ratio (C[subscript Cl]/C[subscript H]) with increasing photon energy. These are similar to those seen in EXAFS and can be accounted for by considering backscattering of the photoelectrons from the chlorine atoms. Moreover, even at high energies the cross section for ionization has been found to depend on the chemical environment of the atom. These results have important consequences for the use of inner-shell electron spectroscopy for quantitative analysis. (3) Single-core-hole ionization energies have long been used as a tool for investigating chemical phenomena. Double-core-hole ionization energies provide additional chemical information. By combining the single-hole and double-hole ionization energies it is possible to determine the effects of the initial-state charge distribution and final-state charge rearrangement on the chemical shifts and on other chemical properties. Until recently double-core-hole ionization energies have not been experimentally accessible for first-row elements. New experimental techniques have, however, made it possible to measure these not only for single sites in a molecule, but also for two different sites in the same molecule. The chemical information that can be obtained from such measurements is discussed

Calibration of oxygen 1s ionization energies. Accurate energies for CO2, H2O, CO, and O2

Access to accurate reference data is a prerequisite in order to translate chemical shifts to an absolute scale for inner-shell ionization energies. Calibration standards for oxygen 1s (O 1s) ionization energies are less well established than, for instance, for carbon 1s. To improve upon this situation, adiabatic and vertical O 1s ionization energies for gaseous carbon dioxide (CO2) are critically reviewed and used to establish the most accurate values currently available: 541.085(17) and 541.253(17) eV, respectively. Combining these with new precise measurements of shifts in O 1s ionization energies for H2O, CO, and O2 allows us to establish equally accurate absolute ionization energies for these molecules as for CO2. The resulting adiabatic and vertical energies are 539.728(17) and 539.827(17) eV for H2O, 542.439(17) and 542.495(17) eV for CO, 543.285(17) and 543.294(17) eV for O2 (4Σ final state), and 544.338(17) and 544.423(17) eV for O2 (2Σ final state). It is proposed that O 1s in CO2 be adopted as a standard of higher precedence, and that H2O, CO, and O2 be used also. The O 1s ionization energies in these molecules occur in the range 540–543 eV. These proposed standards should provide optimal internal calibration for a wide range of oxygen-containing compounds.publishedVersio

Tubulin Polymerization Promoting Protein Affects the Circadian Timing System in C57Bl/6 Mice

The circadian timing system (CTS) is a complex set of cyclic cellular mechanisms which serve to synchronize discrete cell groups across multiple organ systems to adapt the body’s physiology to a (roughly) 24-hour clock. Many genes and hormones have been shown to be strongly associated with the CTS, some of which include the genes 'Bmal1, Period1, Period2, Cryptochrome1', and 'Cryptochrome2', and the hormone melatonin. Previous data suggest that microtubule dynamics play an important role in melatonin function as it relates to the CTS in vitro, though this relationship has never been explored in vivo. The purpose of this study was to determine whether disruption of microtubule regulation in C57Bl/6 mice results in measurable changes to the CTS. To study the potential effects of microtubule dynamics on the CTS in vivo, we utilized a mouse model of microtubule instability, knocked out for the tubulin polymerization promoting protein gene ('Tppp' -/-), comparing them to their wild type (WT) littermates in three categories: locomotor activity (in light/dark and dark/dark photoperiods), serial clock gene expression, and serial serum melatonin concentration. These comparisons showed differences in all three categories, including significant differences in locomotor characteristics under dark/dark conditions. Our findings support and extend previous reports that microtubule dynamics are a modulator of circadian rhythm regulation likely through a mechanism involving melatonin induced phase shifting

Noble Gases Identify the Mechanisms of Fugitive Gas Contamination in Drinking-Water Wells Overlying the Marcellus and Barnett Shales

Horizontal drilling and hydraulic fracturing have enhanced energy production but raised concerns about drinking-water contamination and other environmental impacts. Identifying the sources and mechanisms of contamination can help improve the environmental and economic sustainability of shale-gas extraction. We analyzed 113 and 20 samples from drinking-water wells overlying the Marcellus and Barnett Shales, respectively, examining hydrocarbon abundance and isotopic compositions (e.g., C2H6/CH4, δ13C-CH4) and providing, to our knowledge, the first comprehensive analyses of noble gases and their isotopes (e.g., 4He, 20Ne, 36Ar) in groundwater near shale-gas wells. We addressed two questions. (i) Are elevated levels of hydrocarbon gases in drinking-water aquifers near gas wells natural or anthropogenic? (ii) If fugitive gas contamination exists, what mechanisms cause it? Against a backdrop of naturally occurring salt- and gas-rich groundwater, we identified eight discrete clusters of fugitive gas contamination, seven in Pennsylvania and one in Texas that showed increased contamination through time. Where fugitive gas contamination occurred, the relative proportions of thermogenic hydrocarbon gas (e.g., CH4, 4He) were significantly higher (P \u3c 0.01) and the proportions of atmospheric gases (air-saturated water; e.g., N2, 36Ar) were significantly lower (P \u3c 0.01) relative to background groundwater. Noble gas isotope and hydrocarbon data link four contamination clusters to gas leakage from intermediate-depth strata through failures of annulus cement, three to target production gases that seem to implicate faulty production casings, and one to an underground gas well failure. Noble gas data appear to rule out gas contamination by upward migration from depth through overlying geological strata triggered by horizontal drilling or hydraulic fracturing

Surface oxides, carbides, and impurities on RF superconducting Nb and Nb3Sn: A comprehensive analysis

Surface structures on radio-frequency (RF) superconductors are crucially important in determining their interaction with the RF field. Here we investigate the surface compositions, structural profiles, and valence distributions of oxides, carbides, and impurities on niobium (Nb) and niobium-tin (Nb3Sn) in situ under different processing conditions. We establish the underlying mechanisms of vacuum baking and nitrogen processing in Nb and demonstrate that carbide formation induced during high-temperature baking, regardless of gas environment, determines subsequent oxide formation upon air exposure or low-temperature baking, leading to modifications of the electron population profile. Our findings support the combined contribution of surface oxides and second-phase formation to the outcome of ultra-high vacuum baking (oxygen processing) and nitrogen processing. Also, we observe that vapor-diffused Nb3Sn contains thick metastable oxides, while electrochemically synthesized Nb3Sn only has a thin oxide layer. Our findings reveal fundamental mechanisms of baking and processing Nb and Nb3Sn surface structures for high-performance superconducting RF and quantum application

The Grizzly, November 12, 2015

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Electronic Properties of Chlorine, Methyl, and Chloromethyl as Substituents to the Ethylene Group-Viewed from the Core of Carbon

“Substituent effects” is an important and useful concept in organic chemistry. Although there are many approaches to parametrizing the electronic and steric effects of substituents, the physical basis for the parameters is often unclear. The purpose of the present work is to explore the properties of chemical shifts in carbon 1s energies as a well-defined basis for characterizing substituents to an ethylene C═C moiety. To this end, high-resolution carbon 1s photoelectron spectra of six chloro-substituted ethenes and seven chloro-substituted propenes have been measured in the gas phase. Site-specific adiabatic ionization energies have been determined from the spectra using theoretical ab initio calculations to predict the vibrational structures. For two molecules, 3-chloropropene and 2,3-dichloropropene, the spectral analyses give quantitative results for the conformer populations. The observed shifts have been analyzed in terms of initial-state (potential) and relaxation effects, and charge relaxation has also been analyzed by means of natural resonance theory. On the basis of core-level spectroscopy and models, chlorine, methyl, and chloromethyl have been characterized in terms of their effect on the carbon to which they are attached (α site) as well as the neighboring sp² carbon (β site). The derived spectroscopic substituent parameters are characterized by both inductive (electronegativity) effects and the ability of each substituent to engage in electron delocalization via the π system. Moreover, the adopted approach is extended to include substituent–substituent interaction parameters

Elevated levels of diesel range organic compounds in groundwater near Marcellus gas operations are derived from surface activities

Author Posting. © The Author(s), 2015. This is the author's version of the work. It is posted here by permission of National Academy of Sciences for personal use, not for redistribution. The definitive version was published in Proceedings of the National Academy of Sciences of the United States of American 112 (2015): 13184-13189, doi: 10.1073/pnas.1511474112 .Hundreds of organic chemicals are utilized during natural gas extraction via high volume hydraulic fracturing (HVHF). However, it is unclear if these chemicals, injected into deep shale horizons, reach shallow groundwater aquifers and impact local water quality, either from deep underground injection sites or from the surface or shallow subsurface. Here, we report detectable levels of organic compounds in shallow groundwater samples from private residential wells overlying the Marcellus Shale in northeastern Pennsylvania. Analyses of purgeable and extractable organic compounds from 64 groundwater samples revealed trace levels of volatile organic compounds, well below the Environmental Protection Agency’s maximum contaminant levels, and low levels of both gasoline range (GRO; 0-8 ppb) and diesel range organic compounds (DRO; 0-157 ppb). A compound-specific analysis revealed the presence of bis(2-ethylhexyl)phthalate, which is a disclosed HVHF additive, that was notably absent in a representative geogenic water sample and field blanks. Pairing these analyses with 1) inorganic chemical fingerprinting of deep saline groundwater, 2) characteristic noble gas isotopes, and 3) spatial relationships between active shale gas extraction wells and wells with disclosed environmental health and safety (EHS) violations, we differentiate between a chemical signature associated with naturally occurring saline groundwater and a one associated with alternative anthropogenic routes from the surface (e.g., accidental spills or leaks). The data support a transport mechanism of DRO to groundwater via accidental release of fracturing fluid chemicals derived from the surface rather than subsurface flow of these fluids from the underlying shale formation.The authors thank Duke University’s Pratt School of Engineering and the National Science Foundation’s CBET Grant Number 1336702 and NSF EAGER (EAR-1249255) for financial support.2016-04-1