| 1. |
- Asahina, Shunsuke, et al.
(författare)
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Direct observation and analysis of york-shell materials using low-voltage high-resolution scanning electron microscopy : Nanometal-particles encapsulated in metal-oxide, carbon, and polymer
- 2014
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Ingår i: APL Materials. - : AIP Publishing. - 2166-532X. ; 2:11, s. 113317-
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Tidskriftsartikel (refereegranskat)abstract
- Nanometal particles show characteristic features in chemical and physical properties depending on their sizes and shapes. For keeping and further enhancing their features, the particles should be protected from coalescence or degradation. One approach is to encapsulate the nanometal particles inside pores with chemically inert or functional materials, such as carbon, polymer, and metal oxides, which contain mesopores to allow permeation of only chemicals not the nanometal particles. Recently developed low-voltage high-resolution scanning electron microscopy was applied to the study of structural, chemical, and electron state of both nanometal particles and encapsulating materials in york-shell materials of Au@C, Ru/Pt@C, Au@TiO2, and Pt@Polymer. Progresses in the following categories were shown for the york-shell materials: (i) resolution of topographic image contrast by secondary electrons, of atomic-number contrast by back-scattered electrons, and of elemental mapping by X-ray energy dispersive spectroscopy; (ii) sample preparation for observing internal structures; and (iii) X-ray spectroscopy such as soft X-ray emission spectroscopy. Transmission electron microscopy was also used for characterization of Au@C. (C) 2014 Author(s). All article content, except where otherwise noted, is licensed under a Creative Commons Attribution 3.0 Unported License.
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| 2. |
- Ginya, Harumi, et al.
(författare)
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Development of the Handy Bio-Strand and its application to genotyping of OPRM1 (A118G)
- 2007
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Ingår i: Analytical Biochemistry. - : Elsevier BV. - 0003-2697 .- 1096-0309. ; 367:1, s. 79-86
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Tidskriftsartikel (refereegranskat)abstract
- We previously developed a three-dimensional microarray system, the Bio-Strand, which exhibits advantages in automated DNA analysis in combination with our Magtration Technology. In the current study, we have developed a compact system for the Bio-Strand, the Handy Bio-Strand, which consists of several tools for the preparation of Bio-Strand Tip, hybridization, and detection. Using the Handy Bio-Strand, we performed single nucleotide polymorphism (SNP) genotyping of OPRM1 (A118G) by allele-specific oligonucleotide competitive hybridization (ASOCH). DNA fragments containing SNP sites were amplified from genomic DNA by PCR and then were fixed on a microporous nylon thread. Thus, prepared Bio-Strand Tip was hybridized with allele-specific Cy5 probes (<15mer), on which the SNP site was designed to be located in the center. By optimizing the amount of competitors, the selectivity of Cy5 probes increased without a drastic signal decrease. OPRM1 (A118G) genotypes of 23 human genomes prepared from whole blood samples were determined by ASOCH using the Handy Bio-Strand. The results were perfectly consistent with those determined by PCR direct sequencing. ASOCH using the Handy Bio-Strand would be a very simple and reliable method for SNP genotyping for small laboratories and hospitals.
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| 3. |
- Harada, Yoshihisa, et al.
(författare)
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Selective Probing of the OH or OD Stretch Vibration in Liquid Water Using Resonant Inelastic Soft-X-Ray Scattering
- 2013
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Ingår i: Physical Review Letters. - 0031-9007 .- 1079-7114. ; 111:19, s. 193001-
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Tidskriftsartikel (refereegranskat)abstract
- High-resolution O 1s resonant inelastic x-ray scattering spectra of liquid H2O, D2O, and HDO, obtained by excitation near the preedge resonance show, in the elastic line region, well-separated multiple vibrational structures corresponding to the internal OH stretch vibration in the ground state of water. The energy of the first-order vibrational excitation is strongly blueshifted with respect to the main band in the infrared or Raman spectra of water, indicating that water molecules with a highly weakened or broken donating hydrogen bond are correlated with the preedge structure in the x-ray absorption spectrum. The vibrational profile of preedge excited HDO water is well fitted with 50% +/- 20% greater OH-stretch contribution compared to OD, which strongly supports a preference for OH being the weakened or broken H-bond in agreement with the well-known picture that D2O makes stronger H-bonds than H2O. Accompanying path-integral molecular dynamics simulations show that this is particularly the case for strongly asymmetrically H-bonded molecules, i.e., those that are selected by preedge excitation.
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| 4. |
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| 5. |
- Morokuma, Tomoki, et al.
(författare)
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OISTER optical and near-infrared monitoring observations of peculiar radio-loud active galactic nucleus SDSSJ110006.07+442144.3
- 2017
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Ingår i: Nippon Tenmon Gakkai obun kenkyu hokoku. - : Oxford University Press (OUP). - 0004-6264. ; 69:5
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Tidskriftsartikel (refereegranskat)abstract
- We present monitoring campaign observations at optical and near-infrared (NIR) wavelengths for a radio-loud active galactic nucleus (AGN) at z = 0.840, SDSSJ110006.07+442144.3 (hereafter, J1100+4421), which was identified during a flare phase in late 2014 February. The campaigns consist of three intensive observing runs from the discovery to 2015 March, mostly within the scheme of the OISTER collaboration. Optical-NIR light curves and simultaneous spectral energy distributions (SEDs) are obtained. Our measurements show the strongest brightening in 2015 March. We found that the optical-NIR SEDs of J1100+4421 show an almost steady shape despite the large and rapid intranight variability. This constant SED shape is confirmed to extend to similar to 5 mu m in the observed frame using the archival WISE data. Given the lack of absorption lines and the steep power-law spectrum of alpha(upsilon) similar to -1.4, where f(v) proportional to v(alpha upsilon), synchrotron radiation by a relativistic jet with no or small contributions from the host galaxy and the accretion disk seemsmost plausible as an optical-NIR emission mechanism. The steep optical-NIR spectral shape and the large amplitude of variability are consistent with this object being a low.peak jet-dominated AGN. In addition, sub-arcsecond resolution optical imaging data taken with Subaru Hyper Suprime-Cam does not show a clear extended component and the spatial scales are significantly smaller than the large extensions detected at radio wavelengths. The optical spectrum of a possible faint companion galaxy does not show any emission lines at the same redshift, and hence a merging hypothesis for this AGN-related activity is not supported by our observations.
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| 6. |
- Nordlund, Dennis, et al.
(författare)
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Probing the Electron Delocalization in Liquid Water and Ice at Attosecond Time Scales
- 2007
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Ingår i: Physical Review Letters. - : American Physical Society. - 1079-7114 .- 0031-9007. ; 99, s. 217406-
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Tidskriftsartikel (refereegranskat)abstract
- We determine electron delocalization rates in liquid water and ice using core-hole decay spectroscopy. The hydrogen-bonded network delocalizes the electrons in less than 500 as. Broken or weak hydrogen bonds—in the liquid or at the surface of ice—provide states where the electron remains localized longer than 20 fs. These asymmetrically bonded water species provide electron traps, acting as a strong precursor channel to the hydrated electron.
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| 7. |
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| 8. |
- Pettersson, Lars Gunnar Moody, 1951-, et al.
(författare)
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The local structure of water from combining diffraction and X-ray spectroscopy
- 2022
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Ingår i: Journal of Non-Crystalline Solids: X. - : Elsevier BV. - 2590-1591. ; 14
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Tidskriftsartikel (refereegranskat)abstract
- We build a large (~3400 structures) library of X-ray absorption (XAS) and X-ray emission (XES) spectra computed at high level, which together with their associated structures form the basis for a Monte Carlo fit to the experimental oxygen‑oxygen pair-distribution, XAS and XES spectra for ambient liquid water. The procedure results in weights giving the relative importance of each structure to reproduce the experimental properties. We show that the information content in the X-ray spectroscopic data is strongly complementary to that of X-ray diffraction, and dependent on specific structures that are still consistent with the diffraction data. We fit simultaneously to the X-ray spectroscopy and diffraction experimental data and obtain weights on each structure that give a structural distribution that is consistent with the three experimental datasets. These weights are applied to structural parameters characterizing the local environment of each structure and result in the emergence of more preferred values of these parameters.
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| 9. |
- Pettersson, Lars G. M., et al.
(författare)
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X-ray emission spectroscopy : a genetic algorithm to disentangle core-hole-induced dynamics
- 2021
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Ingår i: Theoretical Chemistry accounts. - : Springer Science and Business Media LLC. - 1432-881X .- 1432-2234. ; 140:12
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Tidskriftsartikel (refereegranskat)abstract
- A genetic algorithm (GA) is developed and applied to make proper connections of final-state potential-energy surfaces and X-ray emission (XES) cross sections between steps in the time-propagation of H-bonded systems after a core–hole is created. We show that this modification results in significantly improved resolution of spectral features in XES with the semiclassical Kramers–Heisenberg approach which takes into account important interference effects. We demonstrate the effects on a water pentamer model as well as on two 17-molecules water clusters representing, respectively, tetrahedral (D2A2) and asymmetric (D1A1) H-bonding environments. For D2A2, the applied procedure improves significantly the obtained intensities, whereas for D1A1 the effects are smaller due to milder dynamics during the core–hole life-time as only one hydrogen is involved. We reinvestigate XES for liquid ethanol and, by properly disentangling the relevant states in the dense manifold of states using the GA, now resolve the important 3a′′ state as a peak rather than a shoulder. Furthermore, by applying the SpecSwap-RMC procedure, we reweigh the distribution of structures in the sampling of the liquid to fit to experiment and estimate the ratio between the main anti and gauche conformers in the liquid at room temperature. This combination of techniques will be generally applicable to challenging problems in liquid-phase spectroscopy.
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| 10. |
- Puettner, Ralph, et al.
(författare)
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Si 1s(-1), 2s(-1) and 2p(-1) lifetime broadening of SiX4 (X = F, Cl, Br, CH3) molecules : SiF4 anomalous behaviour reassessed
- 2019
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Ingår i: Physical Chemistry, Chemical Physics - PCCP. - : ROYAL SOC CHEMISTRY. - 1463-9076 .- 1463-9084. ; 21:17, s. 8827-8836
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Tidskriftsartikel (refereegranskat)abstract
- The Si 1s(-1), Si 2s(-1), and Si 2p(-1) photoelectron spectra of the SiX4 molecules with X = F, Cl, Br, CH3 were measured. From these spectra the Si 1s(-1) and Si 2s(-1) lifetime broadenings were determined, revealing a significantly larger value for the Si 2s(-1) core hole of SiF4 than for the same core hole of the other molecules of the sequence. This finding is in line with the results of the Si 2p(-1) core holes of a number of SiX4 molecules, with an exceptionally large broadening for SiF4. For the Si 2s(-1) core hole of SiF4 the difference to the other SiX4 molecules can be explained in terms of Interatomic Coulomb Decay (ICD)-like processes. For the Si 2p(-1) core hole of SiF4 the estimated values for the sum of the Intraatomic Auger Electron Decay (IAED) and ICD-like processes are too small to explain the observed linewidth. However, the results of the given discussion render for SiF4 significant contributions from Electron Transfer Mediated Decay (ETMD)-like processes at least plausible. On the grounds of our results, some more molecular systems in which similar processes can be observed are identified.
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| 11. |
- Schiros, Theanne, et al.
(författare)
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Structure of water adsorbed on the open Cu(110) surface: H-up, H-down, or both?
- 2006
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Ingår i: Chemical Physics Letters. - : Elsevier BV. - 0009-2614 .- 1873-4448. ; 429:4-6, s. 415-419
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Tidskriftsartikel (refereegranskat)abstract
- We investigated the structure of the water monolayer on an open surface, Cu(1 1 0), at low temperature. We found that water adsorbs molecularly, adopting a 2:1 ratio of H-down and H-up configurations. This behavior of water on an open surface is quite different to the behavior on close-packed surfaces, such as Pt(1 1 1) and Ru(0 0 0 1), where water adsorbs primarily H-down, but can be understood on the basis of a range of different water adsorption sites across the observed (7 × 8) unit cell.
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| 12. |
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| 13. |
- Schiros, Theanne, et al.
(författare)
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The Role of Substrate Electrons in the Wetting of a Metal Surface
- 2010
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Ingår i: Journal of Chemical Physics. - : AIP Publishing. - 0021-9606 .- 1089-7690. ; 132:9, s. 094701-
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Tidskriftsartikel (refereegranskat)abstract
- We address how the electronic and geometric structures of metal surfaces determine water-metal bonding by affecting the balance between Pauli repulsion and electrostatic attraction. We show how the rigid d-electrons and the softer s-electrons utilize different mechanisms for the redistribution of charge that enables surface wetting. On open d-shell Pt(111), the ligand field of water alters the distribution of metal d-electrons to reduce the repulsion. The closed-shell Cu d10 configuration of isostructural Cu(111), however, does not afford this mechanism, resulting in a hydrophobic surface and three-dimensional ice cluster formation. On the geometrically corrugated Cu(110) surface, however, charge depletion involving the mobile sp-electrons at atomic rows reduces the exchange repulsion sufficiently such that formation of a two-dimensional wetting layer is still favored in spite of the d10 electronic configuration
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| 14. |
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| 15. |
- Takahashi, Osamu, et al.
(författare)
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Dynamical and interference effects in X-ray emission spectroscopy of H-bonded water – origin of the split lone-pair peaks
- 2023
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Ingår i: Molecular Physics. - : Informa UK Limited. - 0026-8976 .- 1362-3028. ; 121:7-8
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Tidskriftsartikel (refereegranskat)abstract
- We examine the effects of core-hole-induced dynamics and vibrational interference on computed x-ray emission spectra of H-bonded water. Two model pentamers were investigated, tetrahedral and distorted, representing possible local environments in proposed low- and high-density water. Core-hole-induced dynamics were considered in the simulations, and the semi-classical Kramers-Heisenberg (SCKH) scheme to convolute theoretical spectra was applied. We determine the origin of the split two peaks in XES of liquid water to be a combination of the initial H-bonding and subsequent dynamics, where we find faster dynamics for tetrahedrally bonded. We further find that H-bond acceptors move towards the core-excited molecule while donors move away and we analyse the origin of this dynamics in terms of charge-redistributions during the dynamics.We determine the origin of the split two peaks in X-ray emission spectra of liquid water to be a combination of the initial H-bonding and subsequent dynamics, where we find faster dynamics for tetrahedrally H-bonded water. We further find that H-bond acceptors move towards the core-excited molecule while donors move away and we analyse the origin of this dynamics in terms of charge-redistributions during the dynamics.
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| 16. |
- Takahashi, Osamu, et al.
(författare)
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Interpretation of the X-Ray Emission Spectra of Liquid Water through Temperature and Isotope Dependence
- 2022
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Ingår i: Physical Review Letters. - 1079-7114. ; 128:8
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Tidskriftsartikel (refereegranskat)abstract
- The interpretation of x-ray emission spectroscopy (XES) spectra in terms of their sensitivity to the hydrogen bonding and the consequent microheterogeneity in liquid water has been debated over a decade. To shed a light on this problem, we report the theoretical reproduction of the debated 1b_{1} peaks observed in the XES spectra of liquid water using semiclassical Kramers-Heisenberg formula. The essence of the temperature and isotope dependence of the 1b_{1} double peaks is explained by molecular dynamics simulations including full vibrational (O─H stretching, bending, and) modes, rotational combined with the density functional theory and core-hole induced dynamics. Some inconsistencies exist with the experimental XES profile, which illustrates the need to employ a more precise theoretical calculations for both geometry sampling and electronic structure using a more sophisticated procedure.
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| 17. |
- Takahashi, Osamu, et al.
(författare)
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Site-selective bond scission of methylbenzoate following core excitation
- 2018
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Ingår i: Physical Chemistry, Chemical Physics - PCCP. - : Royal Society of Chemistry. - 1463-9076 .- 1463-9084. ; 20:14, s. 9591-9599
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Tidskriftsartikel (refereegranskat)abstract
- The chemical bond scission of methylbenzoate (C6H5CO2CH3) following core excitation at the C and O K edges was examined from partial ion yield measurements across these edges using synchrotron radiation. Site-specific scission of the C-O bonds was observed at both edges. Theoretical X-ray absorption spectra (XAS) were obtained using density functional theory. Peak assignments in the observed spectra were found to be consistent with the theory. From core-excited state dynamics calculations, an elongation of the C-O bond was predicted and provides an explanation of the observed partial ion yield enhancement of CH3+ and C6H5CO+ at the core-excited resonances at both edges.
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| 18. |
- Takahashi, Osamu, et al.
(författare)
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Theoretical study of the X-ray natural circular dichroism of some crystalline amino acids
- 2015
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Ingår i: Chemical Physics. - : Elsevier BV. - 0301-0104 .- 1873-4421. ; 450-451, s. 109-114
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Tidskriftsartikel (refereegranskat)abstract
- X-ray natural circular dichroism (XNCD) spectra of alanine and serine were calculated at the C, N, and O K-edges within the framework of density functional theory. Basis set and gauge dependence of D-alanine were examined as a test case. XNCD spectra of crystalline D-alanine and L-serine were obtained using cluster models of increasing size. The absolute intensities of the XNCD spectra were found to be reduced in the solid phase compared to the gas phase monomers, suggesting that a monomer model is not necessarily a good representation of the solid phase.
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| 19. |
- Takahashi, Osamu, et al.
(författare)
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X-ray Emission Spectrum of Liquid Ethanol : Origin of Split Peaks
- 2017
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Ingår i: Journal of Physical Chemistry B. - : American Chemical Society (ACS). - 1520-6106 .- 1520-5207. ; 121:49, s. 11163-11168
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Tidskriftsartikel (refereegranskat)abstract
- The X-ray emission spectrum of liquid ethanol was calculated using density functional theory and a semiclassical approximation to the Kramers Heisenberg formula including core hole-induced dynamics. Our spectrum agrees well with the experimental spectrum. We found that the intensity ratio between the two peaks at 526 and 527 eV assigned as 10a ' and 3a '' depends not only on the hydrogen bonding network around the target molecule but also on the intramolecular conformation. This effect is absent in liquid methanol and demonstrates the high sensitivity of X-ray emission to molecular structure. The dependence of spectral features on hydrogen bonding as well as on dynamical effects following core excitation are also discussed.
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| 20. |
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| 21. |
- Tokushima, Takashi, et al.
(författare)
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High resolution X-ray emission spectroscopy of water and its assignment based on two structural motifs
- 2010
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Ingår i: Journal of Electron Spectroscopy and Related Phenomena. - : Elsevier BV. - 0368-2048 .- 1873-2526. ; 177:03-feb, s. 192-205
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Tidskriftsartikel (refereegranskat)abstract
- We evaluate proposed interpretations of previous X-ray emission spectroscopy (XES) data on liquid water. The split peak in the lone-pair orbital region has been interpreted in terms of either two different structural motifs, tetrahedral and distorted, or as due to core-hole-induced dissociative dynamics; here we add new data on a 1:1 H2O/D2O isotopic mixture and additional spectrum simulations including the core-hole-induced dynamics. The XES spectrum of HDO is quite nicely reproduced as the sum of spectra of H2O and D2O, which we interpret as that core-hole-induced dynamics contribute only to the peak shape and do not affect the intensity ratio between tetrahedrally coordinated and distorted. We find the simulation-based interpretation of the two lone-pair peaks as being of completely different symmetries, molecular 1b(1) and dissociated 3a(1), difficult to reconcile with the experimental intensities in the 1b(2) and 3a(1) spectral regions. We report extensive theoretical simulations of spectra probing both the distance and velocity quantum distributions of the internal OH stretch; sharp features not associated with the lone-pair, that are seen when the OH stretch is treated as a classical oscillator, become smeared out when the zero-point Franck-Condon profile and momentum distribution in the v=0 level of the OH stretch are taken into account. This demonstrates that neglecting zero-point motion in simulating XES spectra of water generates artificially sharp structures. XES spectra of 1 M and 4 M hydrochloric acid (HCl) and sodium hydroxide (NaOH) are reported. These spectra indicate that dissociated species most likely can be excluded as the origin of the double 1b(1) peak structure. We thus argue that the experimental observation of two distinct peaks in the lone-pair region is less likely to be explained by an unstructured continuum model of the liquid, but is easily explained within a two-component fluctuating model.
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| 22. |
- Tokushima, Takashi, et al.
(författare)
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Polarization dependent resonant x-ray emission spectroscopy of D2O and H2O water : Assignment of the local molecular orbital symmetry
- 2012
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Ingår i: Journal of Chemical Physics. - : AIP Publishing. - 0021-9606 .- 1089-7690. ; 136:4, s. 044517-
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Tidskriftsartikel (refereegranskat)abstract
- The polarization dependence of the split two peaks in the lone-pair region in the x-ray emission spectra has been determined at several different excitation energies for both D2O and H2O water. In contrast to predictions based on a narrow range of local water structures where the two peaks would be of different molecular orbital symmetry and arise from, respectively, intact and dissociated molecules, we show that the two peaks in the lone-pair region are both of lone-pair 1b(1) orbital symmetry. The results support the interpretation that the two peaks appear due to fluctuations between two distinct different main structural environments.
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