| 1. |
|
|
| 2. |
- Imanishi, T., et al.
(author)
-
Integrative annotation of 21,037 human genes validated by full-length cDNA clones
- 2004
-
In: PLoS biology. - : Public Library of Science (PLoS). - 1544-9173 .- 1545-7885. ; 2:6, s. 856-875
-
Journal article (peer-reviewed)abstract
- The human genome sequence defines our inherent biological potential; the realization of the biology encoded therein requires knowledge of the function of each gene. Currently, our knowledge in this area is still limited. Several lines of investigation have been used to elucidate the structure and function of the genes in the human genome. Even so, gene prediction remains a difficult task, as the varieties of transcripts of a gene may vary to a great extent. We thus performed an exhaustive integrative characterization of 41,118 full-length cDNAs that capture the gene transcripts as complete functional cassettes, providing an unequivocal report of structural and functional diversity at the gene level. Our international collaboration has validated 21,037 human gene candidates by analysis of high-quality full-length cDNA clones through curation using unified criteria. This led to the identification of 5,155 new gene candidates. It also manifested the most reliable way to control the quality of the cDNA clones. We have developed a human gene database, called the H-Invitational Database (H-InvDB; http://www.h-invitational.jp/). It provides the following: integrative annotation of human genes, description of gene structures, details of novel alternative splicing isoforms, non-protein-coding RNAs, functional domains, subcellular localizations, metabolic pathways, predictions of protein three-dimensional structure, mapping of known single nucleotide polymorphisms (SNPs), identification of polymorphic microsatellite repeats within human genes, and comparative results with mouse full-length cDNAs. The H-InvDB analysis has shown that up to 4% of the human genome sequence (National Center for Biotechnology Information build 34 assembly) may contain misassembled or missing regions. We found that 6.5% of the human gene candidates (1,377 loci) did not have a good protein-coding open reading frame, of which 296 loci are strong candidates for non-protein-coding RNA genes. In addition, among 72,027 uniquely mapped SNPs and insertions/deletions localized within human genes, 13,215 nonsynonymous SNPs, 315 nonsense SNPs, and 452 indels occurred in coding regions. Together with 25 polymorphic microsatellite repeats present in coding regions, they may alter protein structure, causing phenotypic effects or resulting in disease. The H-InvDB platform represents a substantial contribution to resources needed for the exploration of human biology and pathology.
|
|
| 3. |
|
|
| 4. |
- Fomalont, E. B., et al.
(author)
-
THE 2014 ALMA LONG BASELINE CAMPAIGN: AN OVERVIEW
- 2015
-
In: Astrophysical Journal Letters. - : American Astronomical Society. - 2041-8213 .- 2041-8205. ; 808:1
-
Journal article (peer-reviewed)abstract
- A major goal of the Atacama Large Millimeter/submillimeter Array (ALMA) is to make accurate images with resolutions of tens of milliarcseconds, which at submillimeter (submm) wavelengths requires baselines up to similar to 15 km. To develop and test this capability, a Long Baseline Campaign (LBC) was carried out from 2014 September to late November, culminating in end-to-end observations, calibrations, and imaging of selected Science Verification (SV) targets. This paper presents an overview of the campaign and its main results, including an investigation of the short-term coherence properties and systematic phase errors over the long baselines at the ALMA site, a summary of the SV targets and observations, and recommendations for science observing strategies at long baselines. Deep ALMA images of the quasar 3C 138 at 97 and 241 GHz are also compared to VLA 43 GHz results, demonstrating an agreement at a level of a few percent. As a result of the extensive program of LBC testing, the highly successful SV imaging at long baselines achieved angular resolutions as fine as 19 mas at similar to 350 GHz. Observing with ALMA on baselines of up to 15 km is now possible, and opens up new parameter space for submm astronomy.
|
|
| 5. |
|
|
| 6. |
- LaRue, Jerry, et al.
(author)
-
Real-Time Elucidation of Catalytic Pathways in CO Hydrogenation on Ru
- 2017
-
In: The Journal of Physical Chemistry Letters. - : American Chemical Society (ACS). - 1948-7185. ; 8:16, s. 3820-3825
-
Journal article (peer-reviewed)abstract
- The direct elucidation of the reaction pathways in heterogeneous catalysis has been challenging due to the short-lived nature of reaction intermediates. Here, we directly measured on ultrafast time scales the initial hydrogenation steps of adsorbed CO on a Ru catalyst surface, which is known as the bottleneck reaction in syngas and CO2 reforming processes. We initiated the hydrogenation of CO with an ultrafast laser temperature jump and probed transient changes in the electronic structure using real-time X-ray spectroscopy. In combination with theoretical simulations, we verified the formation of CHO during CO hydrogenation.
|
|
| 7. |
- Miller, D. J., et al.
(author)
-
Oxidation of Pt(111) under Near-Ambient Conditions
- 2011
-
In: Physical Review Letters. - 0031-9007 .- 1079-7114. ; 107:19, s. 195502-
-
Journal article (peer-reviewed)abstract
- The oxidation of Pt(111) at near-ambient O(2) pressures has been followed in situ using x-ray photoelectron spectroscopy (XPS) and ex situ using x-ray absorption spectroscopy (XAS). Polarization-dependent XAS signatures at the O K edge reveal significant temperature-and pressure-dependent changes of the Pt-O interaction. Oxide growth commences via a PtO-like surface oxide that coexists with chemisorbed oxygen, while an ultrathin alpha-PtO(2) trilayer is identified as the precursor to bulk oxidation. These results have important implications for understanding the chemical state of Pt in catalysis.
|
|
| 8. |
|
|
| 9. |
|
|
| 10. |
- Magnuson, Martin, et al.
(author)
-
Electronic-structure investigation of CeB6 by means of soft-x-ray scattering
- 2001
-
In: Physical Review B. Condensed Matter and Materials Physics. - 1098-0121 .- 1550-235X. ; 63:7, s. 075101-
-
Journal article (peer-reviewed)abstract
- The electronic structure of the heavy fermion compound CeB6 is probed by resonant inelastic soft-x-ray scattering using photon energies across the Ce 3d and 4d absorption edges. The hybridization between the localized 4f orbitals and the delocalized valence-band states is studied by identifying the different spectral contributions from inelastic Raman scattering and normal fluorescence. Pronounced energy-loss structures are observed below the elastic peak at both the 3d and 4d thresholds. The origin and character of the inelastic scattering structures are discussed in terms of charge-transfer excitations in connection to the dipole allowed transitions with 4f character. Calculations within the single-impurity Anderson model with full multiplet effects are found to yield consistent spectral functions to the experimental data.
|
|
| 11. |
|
|
| 12. |
- Weiss, K., et al.
(author)
-
XPS and XAS investigation of condensed and adsorbed n-octane on a Cu(110) surface
- 2003
-
In: Journal of electron spectroscopy and related phenomena. - : Elsevier. - 0368-2048. ; 128:2-3, s. 179-191
-
Journal article (peer-reviewed)abstract
- The electronic structure of n-octane adsorbed on Cu(110) is studied by using X-ray absorption spectroscopy (XAS) and X-ray photoelectron spectroscopy (XPS) in combination with cluster model calculations in the framework of density functional theory (DFT). The molecule is found to be well oriented on the surface, which is seen from the high degree of XAS dichroism. Saturated hydrocarbons are commonly considered to physisorb on metals such as Cu(110), but still the C 1s XAS spectra reveal large changes in the electronic structure of the adsorbed octane relative to the free molecule. We find that the XAS resonances corresponding to the molecular Rydberg-valence states are strongly quenched upon adsorption and that there is a significant hybridization of the molecular valence orbitals with the metal bands. In addition to a precise interpretation of the XAS spectra, we present details on the molecular orbital structure of the adsorbed octane molecule. We also discuss shifts in the relative binding energies of the chemically inequivalent carbon atoms in octane upon adsorption, which lead to a narrower XPS spectrum for the adsorbate than the condensed phase spectrum due to the existence of a new relaxation channel.
|
|
| 13. |
- Xin, H., et al.
(author)
-
Strong Influence of Coadsorbate Interaction on CO Desorption Dynamics on Ru(0001) Probed by Ultrafast X-Ray Spectroscopy and Ab Initio Simulations
- 2015
-
In: Physical Review Letters. - 0031-9007 .- 1079-7114. ; 114:15
-
Journal article (peer-reviewed)abstract
- We show that coadsorbed oxygen atoms have a dramatic influence on the CO desorption dynamics from Ru(0001). In contrast to the precursor-mediated desorption mechanism on Ru(0001), the presence of surface oxygen modifies the electronic structure of Ru atoms such that CO desorption occurs predominantly via the direct pathway. This phenomenon is directly observed in an ultrafast pump-probe experiment using a soft x-ray free-electron laser to monitor the dynamic evolution of the valence electronic structure of the surface species. This is supported with the potential of mean force along the CO desorption path obtained from density-functional theory calculations. Charge density distribution and frozen-orbital analysis suggest that the oxygen-induced reduction of the Pauli repulsion, and consequent increase of the dative interaction between the CO 5 sigma and the charged Ru atom, is the electronic origin of the distinct desorption dynamics. Ab initio molecular dynamics simulations of CO desorption from Ru(0001) and oxygen-coadsorbed Ru(0001) provide further insights into the surface bond-breaking process.
|
|
| 14. |
|
|
| 15. |
- Yamamoto, S., et al.
(author)
-
In situ x-ray photoelectron spectroscopy studies of water on metals and oxides at ambient conditions
- 2008
-
In: Journal of Physics. - : IOP Publishing. - 0953-8984 .- 1361-648X. ; 20:18, s. 184025-
-
Research review (peer-reviewed)abstract
- X-ray photoelectron spectroscopy (XPS) is a powerful tool for surface and interface analysis, providing the elemental composition of surfaces and the local chemical environment of adsorbed species. Conventional XPS experiments have been limited to ultrahigh vacuum (UHV) conditions due to a short mean free path of electrons in a gas phase. The recent advances in instrumentation coupled with third-generation synchrotron radiation sources enables in situ XPS measurements at pressures above 5 Torr. In this paper, we describe the basic design of the ambient pressure XPS setup that combines differential pumping with an electrostatic focusing. We present examples of the application of in situ XPS to studies of water adsorption on the surface of metals and oxides including Cu(110), Cu(111), TiO2(110) under environmental conditions of water vapor pressure. On all these surfaces we observe a general trend where hydroxyl groups form first, followed by molecular water adsorption. The importance of surface OH groups and their hydrogen bonding to water molecules in water adsorption on surfaces is discussed in detail.
|
|
| 16. |
- Yamamoto, S., et al.
(author)
-
Water adsorption on α-Fe2O3 (0001) at near ambient conditions
- 2010
-
In: Journal of Physical Chemistry C. - : American Chemical Society (ACS). - 1932-7447 .- 1932-7455. ; 114:5, s. 2256-2266
-
Journal article (peer-reviewed)abstract
- We have investigated hydroxylation and water adsorption on α Fe 2O3(0001) at water vapor pressures up to 2 Torr and temperatures ranging from 277 to 647 K (relative humidity (RH)
|
|
| 17. |
- Östrom, Henrik, et al.
(author)
-
Probing the transition state region in catalytic CO oxidation on Ru
- 2015
-
In: Science. - : American Association for the Advancement of Science (AAAS). - 0036-8075 .- 1095-9203. ; 347:6225, s. 978-982
-
Journal article (peer-reviewed)abstract
- Femtosecond x-ray laser pulses are used to probe the carbon monoxide (CO) oxidation reaction on ruthenium (Ru) initiated by an optical laser pulse. On a time scale of a few hundred femtoseconds, the optical laser pulse excites motions of CO and oxygen (O) on the surface, allowing the reactants to collide, and, with a transient close to a picosecond (ps), new electronic states appear in the OK-edge x-ray absorption spectrum. Density functional theory calculations indicate that these result from changes in the adsorption site and bond formation between CO and O with a distribution of OC-O bond lengths close to the transition state (TS). After 1 ps, 10% of the CO populate the TS region, which is consistent with predictions based on a quantum oscillator model.
|
|
| 18. |
|
|
| 19. |
- Öström, H., et al.
(author)
-
Orbital rehybridization in n-octane adsorbed on Cu(110)
- 2003
-
In: Journal of Chemical Physics. - : American Institute of Physics. - 0021-9606. ; 118:8, s. 3782-3789
-
Journal article (peer-reviewed)abstract
- We have investigated the local electronic structure of n-octane adsorbed on the Cu(110) surface using symmetry-resolved x-ray absorption spectroscopy (XAS) and x-ray emission spectroscopy (XES) in combination with density functional theory (DFT) spectrum calculations. We found new adsorption-induced states in the XE spectra, which we assign to interaction between the bonding CH orbitals and the metal surface. By performing a systematic investigation of the influence of different structural parameters on the XA and XE spectra, we conclude that the molecular geometry is significantly distorted relative to the gas-phase structure. The bonding to the surface leads to a strengthening of the carbon–carbon bonds and a weakening of the carbon–hydrogen bonds, consistent with a rehybridization of the carbons from sp3 to sp2.8. ©2003 American Institute of Physics.
|
|
| 20. |
|
|
| 21. |
|
|
| 22. |
|
|
| 23. |
- Beye, M., et al.
(author)
-
Selective Ultrafast Probing of Transient Hot Chemisorbed and Precursor States of CO on Ru(0001)
- 2013
-
In: Physical Review Letters. - 0031-9007 .- 1079-7114. ; 110:18
-
Journal article (peer-reviewed)abstract
- We have studied the femtosecond dynamics following optical laser excitation of CO adsorbed on a Ru surface by monitoring changes in the occupied and unoccupied electronic structure using ultrafast soft x-ray absorption and emission. We recently reported [M. Dell'Angela et al. Science 339, 1302 (2013)] a phonon-mediated transition into a weakly adsorbed precursor state occurring on a time scale of >2 ps prior to desorption. Here we focus on processes within the first picosecond after laser excitation and show that the metal-adsorbate coordination is initially increased due to hot-electron-driven vibrational excitations. This process is faster than, but occurs in parallel with, the transition into the precursor state. With resonant x-ray emission spectroscopy, we probe each of these states selectively and determine the respective transient populations depending on optical laser fluence. Ab initio molecular dynamics simulations of CO adsorbed on Ru(0001) were performed at 1500 and 3000 K providing insight into the desorption process.
|
|
| 24. |
|
|
| 25. |
- Brena, Barbara, et al.
(author)
-
Ultrafast Molecular Dissociation of Water in Ice
- 2004
-
In: Physical Review Letters. - : The American Physical Society. - 1079-7114 .- 0031-9007. ; 93, s. 148302-148305
-
Journal article (peer-reviewed)abstract
- Using x-ray emission and photoemission spectroscopies to measure the occupied valence levels in a thin crystalline ice film, we resolve the ionization-induced dissociation of water in ice on a femtosecond time scale. Isotope substitution confirms proton transfer during the core-hole lifetime in spite of the nonresonant excitation. Through ab initio molecular dynamics on the core-ionized state, the dissociation and spectrum evolution are followed at femtosecond intervals. The theoretical simulations confirm the experimental analysis and allow for a detailed study of the dissociative reaction path.
|
|
| 26. |
|
|
| 27. |
|
|
| 28. |
- Cavalleri, M., et al.
(author)
-
X-absorption spectra of water within a plane-wave Car-Parrinello molecular dynamics framework
- 2004
-
In: Journal of Chemical Physics. - : American Institute of Physics. - 0021-9606 .- 1089-7690. ; 121:20, s. 10065-10075
-
Journal article (peer-reviewed)abstract
- We describe the implementation of a simple technique to simulate core-level spectra within the Car-Parrinello plane-waves molecular dynamics framework. The x-ray absorption (XA) spectra are generated using the transition potential technique with the effect of the core hole included through a specifically developed pseudopotential for the core-excited atom. Despite the lack of 1s core orbitals in the pseudopotential treatment, the required transition moments are accurately calculated without reconstruction of the all-electron orbitals. The method is applied to the oxygen XA spectra of water in its various aggregation states, but it is transferable to any first-row element. The computed spectra are compared favorably with the results from all-electron cluster calculations, as well as with experimental data. The periodicity of the plane-wave technique improves the description of condensed phases. The molecular dynamics simulation enables in principle a proper treatment of thermal effects and dynamical averaging in complex systems.
|
|
| 29. |
|
|
| 30. |
|
|
| 31. |
- Chen, Zhen, et al.
(author)
-
Design, Synthesis, and Evaluation of Reversible and Irreversible Monoacylglycerol Lipase Positron Emission Tomography (PET) Tracers Using a "Tail Switching" Strategy on a Piperazinyl Azetidine Skeleton
- 2019
-
In: Journal of Medicinal Chemistry. - : American Chemical Society (ACS). - 0022-2623 .- 1520-4804. ; 62:7, s. 3336-3353
-
Journal article (peer-reviewed)abstract
- Monoacylglycerol lipase (MAGL) is a senile hydrolase that degrades 2-arachidonoylglycerol (2-AG) in the endocannabinoid system (eCB). Selective inhibition of MAGL has emerged as a potential therapeutic approach for the treatment of diverse pathological conditions, including chronic pain, inflammation, cancer, and neurodegeneration. Herein, we disclose a novel array of reversible and irreversible MAGL inhibitors by means of "tail switching" on a piperazinyl azetidine scaffold. We developed a lead irreversible-binding MAGL inhibitor 8 and reversible-binding compounds 17 and 37, which are amenable for radiolabeling with C-11 or F-18. [C-11]8 ([C-11]MAGL-2-11) exhibited high brain uptake and excellent binding specificity in the brain toward MAGL. Reversible radioligands [C-11]17 ([C-11]PAD) and [F-18]37 ([F-18]MAGL-4-11) also demonstrated excellent in vivo binding specificity toward MAGL in peripheral organs. This work may pave the way for the development of MAGL-targeted positron emission tomography tracers with tunability in reversible and irreversible binding mechanisms.
|
|
| 32. |
- Cheng, Ran, et al.
(author)
-
In Vitro and in Vivo Evaluation of C-11-Labeled Azetidinecarboxylates for Imaging Monoacylglycerol Lipase by PET Imaging Studies
- 2018
-
In: Journal of Medicinal Chemistry. - : American Chemical Society (ACS). - 0022-2623 .- 1520-4804. ; 61:6, s. 2278-2291
-
Journal article (peer-reviewed)abstract
- Monoacylglycerol lipase (MAGL) is the principle enzyme for metabolizing endogenous cannabinoid ligand 2-arachidonoyglycerol (2-AG). Blockade of MAGL increases 2-AG levels, resulting in subsequent activation of the endocannabinoid system, and has emerged as a novel therapeutic strategy to treat drug addiction, inflammation, and neurodegenerative diseases. Herein we report a new series of MAGL inhibitors, which were radiolabeled by site-specific labeling technologies, including C-11-carbonylation and spirocyclic iodonium ylide (SCIDY) radio fluorination. The lead compound [C-11]10 (MAGL-0519) demonstrated high specific binding and selectivity in vitro and in vivo. We also observed unexpected washout kinetics with these irreversible radiotracers, in which in vivo evidence for turnover of the covalent residue was unveiled between MAGL and azetidine carboxylates. This work may lead to new directions for drug discovery and PET tracer development based on azetidine carboxylate inhibitor scaffold.
|
|
| 33. |
- Dell'Angela, M., et al.
(author)
-
Real-Time Observation of Surface Bond Breaking with an X-ray Laser
- 2013
-
In: Science. - : American Association for the Advancement of Science (AAAS). - 0036-8075 .- 1095-9203. ; 339:6125, s. 1302-1305
-
Journal article (peer-reviewed)abstract
- We used the Linac Coherent Light Source free-electron x-ray laser to probe the electronic structure of CO molecules as their chemisorption state on Ru(0001) changes upon exciting the substrate by using a femtosecond optical laser pulse. We observed electronic structure changes that are consistent with a weakening of the CO interaction with the substrate but without notable desorption. A large fraction of the molecules (30%) was trapped in a transient precursor state that would precede desorption. We calculated the free energy of the molecule as a function of the desorption reaction coordinate using density functional theory, including van der Waals interactions. Two distinct adsorption wells-chemisorbed and precursor state separated by an entropy barrier-explain the anomalously high prefactors often observed in desorption of molecules from metals.
|
|
| 34. |
- Dell'Angela, M., et al.
(author)
-
Vacuum space charge effects in sub-picosecond soft X-ray photoemission on a molecular adsorbate layer
- 2015
-
In: Structural Dynamics. - : AIP Publishing. - 2329-7778. ; 2:2
-
Journal article (peer-reviewed)abstract
- Vacuum space charge induced kinetic energy shifts of O 1s and Ru 3d core levels in femtosecond soft X-ray photoemission spectra (PES) have been studied at a free electron laser (FEL) for an oxygen layer on Ru(0001). We fully reproduced the measurements by simulating the in-vacuum expansion of the photoelectrons and demonstrate the space charge contribution of the high-order harmonics in the FEL beam. Employing the same analysis for 400 nm pump-X-ray probe PES, we can disentangle the delay dependent Ru 3d energy shifts into effects induced by space charge and by lattice heating from the femtosecond pump pulse.
|
|
| 35. |
- Gladh, Jörgen, et al.
(author)
-
X-ray emission spectroscopy and density functional study of CO/Fe(100)
- 2012
-
In: Journal of Chemical Physics. - : AIP Publishing. - 0021-9606 .- 1089-7690. ; 136:3
-
Journal article (peer-reviewed)abstract
- We report x-ray emission and absorption spectroscopy studies of the electronic structure of the pre-dissociative alpha(3) phase of CO bound at hollow sites of Fe(100) as well as of the on-top bound species in the high-coverage alpha(1) phase. The analysis is supported by density functional calculations of structures and spectra. The bonding of lying down CO in the hollow site is well described in terms of pi to pi* charge transfer made possible through bonding interaction also at the oxygen in the minority spin-channel. The on-top CO in the mixed, high-coverage alpha(1) phase is found to be tilted due to adsorbate-adsorbate interaction, but still with bonding mainly characteristic of vertical on-top adsorbed CO similar to other transition-metal surfaces.
|
|
| 36. |
|
|
| 37. |
|
|
| 38. |
- Hou, Lu, et al.
(author)
-
Positron Emission Tomography Imaging of the Endocannabinoid System : Opportunities and Challenges in Radiotracer Development
- 2021
-
In: Journal of Medicinal Chemistry. - : American Chemical Society (ACS). - 0022-2623 .- 1520-4804. ; 64:1, s. 123-149
-
Research review (peer-reviewed)abstract
- The endocannabinoid system (ECS) is involved in a wide range of biological functions and comprises cannabinoid receptors and enzymes responsible for endocannabinoid synthesis and degradation. Over the past 2 decades, significant advances toward developing drugs and positron emission tomography (PET) tracers targeting different components of the ECS have been made. Herein, we summarized the recent development of PET tracers for imaging cannabinoid receptors 1 (CB1R) and 2 (CB2R) as well as the key enzymes monoacylglycerol lipase (MAGL) and fatty acid amide hydrolase (FAAH), particularly focusing on PET neuroimaging applications. State-of-the-art PET tracers for the ECS will be reviewed including their chemical design, pharmacological properties, radiolabeling, as well as preclinical and human PET imaging. In addition, this review addresses the current challenges for ECS PET biomarker development and highlights the important role of PET ligands to study disease pathophysiology as well as to facilitate drug discovery.
|
|
| 39. |
- Janin, Emmanuelle, et al.
(author)
-
Adsorption and bonding of propene and 2-butenal on Pt(111)
- 2001
-
In: Surface Science. - 0039-6028 .- 1879-2758. ; 482, s. 83-89
-
Journal article (peer-reviewed)abstract
- The adsorption of propene and 2-butenal on the Pt(1 1 1) surface has been studied by high resolution photoelectron spectroscopy, both in the mono-and multi-layer regime. The results obtained indicate an involvement of both aliphatic and carbonyl groups in the bonding of 2-butenal with the platinum surface in the sub-monolayer regime.
|
|
| 40. |
- Katayama, T., et al.
(author)
-
Ultrafast soft X-ray emission spectroscopy of surface adsorbates using an X-ray free electron laser
- 2013
-
In: Journal of Electron Spectroscopy and Related Phenomena. - : Elsevier BV. - 0368-2048 .- 1873-2526. ; 187, s. 9-14
-
Journal article (peer-reviewed)abstract
- We report on an experimental system designed to probe chemical reactions on solid surfaces on a sub-picosecond timescale using soft X-ray emission spectroscopy at the Linac Coherent Light Source (LCLS) free electron laser (FEL) at the SLAC National Accelerator Laboratory. We analyzed the O 1s X-ray emission spectra recorded from atomic oxygen adsorbed on a Ru(0001) surface at a synchrotron beamline (SSRL, BL13-2) and an FEL beamline (LCLS, SXR). We have demonstrated conditions that provide negligible amount of FEL induced damage of the sample. In addition we show that the setup is capable of tracking the temporal evolution of electronic structure during a surface reaction of submonolayer quantities of CO molecules desorbing from the surface.
|
|
| 41. |
- Leetmaa, Mikael, et al.
(author)
-
Are Recent Water Models Obtained by Fitting Diffraction Data Consistent with IR/Raman and X-ray Absorption Spectra?
- 2006
-
In: Journal of Chemical Physics. - : AIP Publishing. - 0021-9606 .- 1089-7690. ; 125, s. 244510-
-
Journal article (peer-reviewed)abstract
- X-ray absorption (XA) spectra have been computed based on water structures obtained from a recent fit to x-ray and neutron diffraction data using models ranging from symmetrical to asymmetrical local coordination of the water molecules [A. K. Soper, J. Phys.: Condens. Matter 17, S3273 (2005)]. It is found that both the obtained symmetric and asymmetric structural models of water give similar looking XA spectra, which do not match the experiment. The fitted models both contain unphysical structures that are allowed by the diffraction data, where, e.g., hydrogen-hydrogen interactions may occur. A modification to the asymmetric model, in which the non-hydrogen-bonded OH intramolecular distance is allowed to become shorter while the bonded OH distance becomes longer, improves the situation somewhat, but the overall agreement is still unsatisfactory. The electric field (E-field) distributions and infrared (IR) spectra are also calculated using two established theoretical approaches, which, however, show significant discrepancies in their predictions for the asymmetric structural models. Both approaches predict the Raman spectrum of the symmetric model fitted to the diffraction data to be significantly blueshifted compared to experiment. At the moment no water model exists that can equally well describe IR/Raman, x-ray absorption spectroscopy, and diffraction data. ©2006 American Institute of Physics
|
|
| 42. |
- Madanian, H., et al.
(author)
-
The Dynamics of a High Mach Number Quasi-perpendicular Shock : MMS Observations
- 2021
-
In: Astrophysical Journal. - : American Astronomical Society. - 0004-637X .- 1538-4357. ; 908:1
-
Journal article (peer-reviewed)abstract
- Shock parameters at Earth's bow shock in rare instances can approach the Mach numbers predicted at supernova remnants. We present our analysis of a high Alfven Mach number (M-A = 27) shock utilizing multipoint measurements from the Magnetospheric Multiscale spacecraft during a crossing of Earth's quasi-perpendicular bow shock. We find that the shock dynamics are mostly driven by reflected ions, perturbations that they generate, and nonlinear amplification of the perturbations. Our analyses show that reflected ions create modest magnetic enhancements upstream of the shock, which evolve in a nonlinear manner as they traverse the shock foot. They can transform into proto-shocks that propagate at small angles to the magnetic field and toward the bow shock. The nonstationary bow shock shows signatures of both reformation and surface ripples. Our observations indicate that although shock reformation occurs, the main shock layer never disappears. These observations are at high plasma beta, a parameter regime that has not been well explored by numerical models.
|
|
| 43. |
|
|
| 44. |
- Myneni, S., et al.
(author)
-
Spectroscopic probing of local hydrogen-bonding structures in liquid water
- 2002
-
In: Journal of Physics. - : IOP Publishing. - 0953-8984 .- 1361-648X. ; 14:8, s. L213-L219
-
Journal article (peer-reviewed)abstract
- We have studied the electronic structure of liquid water using x-ray absorption spectroscopy at the oxygen K edge. Since the x-ray absorption process takes less than a femtosecond, it allows probing of the molecular orbital structure of frozen, local geometries of water molecules at a timescale that has not previously been accessible. Our results indicate that the electronic structure of liquid water is significantly different from that of the solid and gaseous forms, resulting in a pronounced pre-edge feature below the main absorption edge in the spectrum. Theoretical calculations of these spectra suggest that this feature originates from specific configurations of water, for which the H-bond is broken on the H-donating site of the water molecule. This study provides a fingerprint for identifying broken donating H-bonds in the liquid and shows that an unsaturated H-bonding environment exists for a dominating fraction of the water molecules.
|
|
| 45. |
- Nakanishi, T., et al.
(author)
-
Role of cathepsins and cystatins in patients with recurrent miscarriage
- 2005
-
In: Mol Hum Reprod. - 1360-9947. ; 11:5, s. 351-5
-
Journal article (peer-reviewed)abstract
- In the implantation, trophoblasts penetrate maternal decidua by secreting proteases. It has been reported that cathepsins are highly expressed in the mouse villi, and play an important role in normal embryonal growth and decidualization. In this study, we evaluated cathepsins and their endogenous inhibitors, cystatins, in tissue and serum of patients with recurrent miscarriage. Decidua and villi were surgically collected from 22 patients and 12 healthy women. Immunohistochemistry was performed with antibodies against cathepsins, stefin A (cystatin A), stefin B (cystatin B) and cystatin C. The concentrations of cathepsins, stefins and cystatin C were measured by Enzyme-linked immunosorbent assay. In addition, we measured the serum level of cystatin C in 85 Japanese women with recurrent miscarriage. Staining of cathepsin B, D, H, L, stefin B and cystatin C was observed in the cytoplasm of epithelial cells in decidua. Stefin A was expressed on the surface of the trophoblast. The concentration of cathepsin B and H in patients' decidua was significantly higher than in control individuals. The serum level of cystatin C was significantly lower in patients than in control individuals. Our findings suggest that the regulation of the cathepsin-cystatin system may play an important role in patients with recurrent miscarriage.
|
|
| 46. |
|
|
| 47. |
- Nilsson, Anders, et al.
(author)
-
Catalysis in real time using X-ray lasers
- 2017
-
In: Chemical Physics Letters. - : Elsevier BV. - 0009-2614 .- 1873-4448. ; 675, s. 145-173
-
Journal article (peer-reviewed)abstract
- We describe how the unique temporal and spectral characteristics of X-ray free-electron lasers (XFEL) can be utilized to follow chemical transformations in heterogeneous catalysis in real time. We highlight the systematic study of CO oxidation on Ru(0001), which we initiate either using a femtosecond pulse from an optical laser or by activating only the oxygen atoms using a THz pulse. We find that CO is promoted into an entropy-controlled precursor state prior to desorbing when the surface is heated in the absence of oxygen, whereas in the presence of oxygen, CO desorbs directly into the gas phase. We monitor the activation of atomic oxygen explicitly by the reduced split between bonding and antibonding orbitals as the oxygen comes out of the strongly bound hollow position. Applying these novel XFEL techniques to the full oxidation reaction resulted in the surprising observation of a significant fraction of the reactants at the transition state through the electronic signature of the new bond formation.
|
|
| 48. |
|
|
| 49. |
- Nilsson, A., et al.
(author)
-
The hydrogen bond in ice probed by soft x-ray spectroscopy and density functional theory
- 2005
-
In: Journal of Chemical Physics. - : American Institute of Physics. - 1089-7690 .- 0021-9606. ; 122, s. 154505-
-
Journal article (peer-reviewed)abstract
- We combine photoelectron and x-ray absorption spectroscopy with density functional theory to derive a molecular orbital picture of the hydrogen bond in ice. We find that the hydrogen bond involves donation and back-donation of charge between the oxygen lone pair and the O–H antibonding orbitals on neighboring molecules. Together with internal s-p rehybridization this minimizes the repulsive charge overlap of the connecting oxygen and hydrogen atoms, which is essential for a strong attractive electrostatic interaction. Our joint experimental and theoretical results demonstrate that an electrostatic model based on only charge induction from the surrounding medium fails to properly describe the internal charge redistributions upon hydrogen bonding.
|
|
| 50. |
- Nilsson, Anders, et al.
(author)
-
X-ray absorption spectroscopy and X-ray Raman scattering of water and ice; an experimental view
- 2010
-
In: Journal of Electron Spectroscopy and Related Phenomena. - : Elsevier BV. - 0368-2048 .- 1873-2526. ; 177:03-feb, s. 99-129
-
Journal article (peer-reviewed)abstract
- Here we present a review of X-ray absorption spectroscopy and X-ray Raman scattering with the perspective to understand the spectra of water including changes with temperature, mass of the water molecule and presence of monovalent ions. The different detection schemes are discussed and it is concluded that transmission X-ray absorption measurements, using a small area where the thickness is uniform, and X-ray Raman scattering give the most reliable spectra. Different model systems are discussed such as the surface and bulk of ice and various adsorbed monolayer structures on metal surfaces.
|
|
