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Find video protocols related to scientific articles indexed in Pubmed.
Reabsorption of soft x-ray emission at high x-ray free-electron laser fluences.
Phys. Rev. Lett.
PUBLISHED: 10-06-2014
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We report on oxygen K-edge soft x-ray emission spectroscopy from a liquid water jet at the Linac Coherent Light Source. We observe significant changes in the spectral content when tuning over a wide range of incident x-ray fluences. In addition the total emission yield decreases at high fluences. These modifications result from reabsorption of x-ray emission by valence-excited molecules generated by the Auger cascade. Our observations have major implications for future x-ray emission studies at intense x-ray sources. We highlight the importance of the x-ray pulse length with respect to the core-hole lifetime.
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Comparison of x-ray absorption spectra between water and ice: new ice data with low pre-edge absorption cross-section.
J Chem Phys
PUBLISHED: 07-24-2014
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The effect of crystal growth conditions on the O K-edge x-ray absorption spectra of ice is investigated through detailed analysis of the spectral features. The amount of ice defects is found to be minimized on hydrophobic surfaces, such as BaF2(111), with low concentration of nucleation centers. This is manifested through a reduction of the absorption cross-section at 535 eV, which is associated with distorted hydrogen bonds. Furthermore, a connection is made between the observed increase in spectral intensity between 544 and 548 eV and high-symmetry points in the electronic band structure, suggesting a more extended hydrogen-bond network as compared to ices prepared differently. The spectral differences for various ice preparations are compared to the temperature dependence of spectra of liquid water upon supercooling. A double-peak feature in the absorption cross-section between 540 and 543 eV is identified as a characteristic of the crystalline phase. The connection to the interpretation of the liquid phase O K-edge x-ray absorption spectrum is extensively discussed.
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A different view of structure-making and structure-breaking in alkali halide aqueous solutions through x-ray absorption spectroscopy.
J Chem Phys
PUBLISHED: 07-03-2014
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X-ray absorption spectroscopy measured in transmission mode was used to study the effect of alkali and halide ions on the hydrogen-bonding (H-bonding) network of water. Cl(-) and Br(-) are shown to have insignificant effect on the structure of water while I(-) locally weakens the H-bonding, as indicated by a sharp increase of the main-edge feature in the x-ray absorption spectra. All alkali cations act as structure-breakers in water, weakening the H-bonding network. The spectral changes are similar to spectra of high density ices where the 2nd shell has collapsed due to a break-down of the tetrahedral structures, although here, around the ions, the breakdown of the local tetrahedrality is rather due to non-directional H-bonding to the larger anions. In addition, results from temperature-dependent x-ray Raman scattering measurements of NaCl solution confirm the H-bond breaking effect of Na(+) and the effect on the liquid as similar to an increase in temperature.
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Facilitation of ipsilateral actions of corticospinal tract neurons on feline motoneurons by transcranial direct current stimulation.
Eur. J. Neurosci.
PUBLISHED: 02-02-2014
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Ipsilateral actions of pyramidal tract (PT) neurons are weak but may, if strengthened, compensate for deficient crossed PT actions following brain damage. The purpose of the present study was to examine whether transcranial direct current stimulation (tDCS) can strengthen ipsilateral PT (iPT) actions; in particular, those relayed by reticulospinal neurons co-excited by axon collaterals of fibres descending in the iPT and contralateral PT (coPT) and of reticulospinal neurons descending in the medial longitudinal fascicle (MLF). The effects of tDCS were assessed in acute experiments on deeply anaesthetized cats by comparing postsynaptic potentials evoked in hindlimb motoneurons and discharges recorded from their axons in a ventral root, before, during and after tDCS. tDCS was consistently found to facilitate joint actions of the iPT and coPT, especially when they were stimulated together with the MLF. Both excitatory postsynaptic potentials and inhibitory postsynaptic potentials evoked in motoneurons and the ensuing ventral root discharges were facilitated, even though the facilitatory effects of tDCS were not sufficient for activation of motoneurons by iPT neurons alone. Facilitation outlasted single tDCS periods by at least a few minutes, and the effects evoked by repeated tDCS by up to 2 h. The results of this study thus indicate that tDCS may increase the contribution of iPT actions to the recovery of motor functions after injuries to coPT neurons, and thereby assist rehabilitation, provided that corticoreticular and reticulospinal connections are preserved.
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Skilled reaching and grasping in the rat: lacking effect of corticospinal lesion.
Front Neurol
PUBLISHED: 01-01-2014
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The corticospinal system is a major motor pathway in the control of skilled voluntary movements such as reaching and grasping. It has developed considerably phylogenetically to reach a peak in humans. Because rodents possess advanced forelimb movements that can be used for reaching and grasping food, it is commonly considered that the corticospinal tract (CST) is of major importance for this control also in rodents. A close homology to primate reaching and grasping has been described but with obvious limitations as to independent digit movements, which are lacking in rodents. Nevertheless, it was believed that there are, as in the primate, direct cortico-motoneuronal connections. Later, it was shown that there are no such connections. The fastest excitatory pathway is disynaptic, mediated via cortico-reticulospinal neurons and in the spinal cord the excitation is mainly polysynaptically mediated via segmental interneurons. Earlier behavioral studies have aimed at investigating the role of the CST by using pyramidotomy in the brainstem. However, in addition to interrupting the CST, a pyramidal transection abolishes the input to reticulospinal neurons. It is therefore not possible to conclude if the deficits after pyramidotomy result from interruption of the CST or the input to reticulospinal neurons or both. We have re-investigated the role of the CST by examining the effect of a CST lesion in the C1-C2 spinal segments on the success rate of reaching and grasping. This lesion spares the cortico-reticulospinal pathway. In contrast to investigations using pyramidal transections, the present study did not demonstrate marked deficits in reaching and grasping. We propose that the difference in results can be explained by the intact cortical input to reticulospinal neurons in our study and thus implicate an important role of this pathway in the control of reaching and grasping in the rat.
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Endogenous plasticity in neuro-rehabilitation following partial spinal cord lesions.
Front Neurosci
PUBLISHED: 01-01-2014
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Currently, much interest in neuro-rehabilitation is focused on mechanisms related to axonal outgrowth and formation of new circuits although still little is known about the functionality in motor behavior. This is a highly exciting avenue of research and most important to consider when dealing with large lesions. Here, we address endogenous mechanisms with the potential of modifying the function of already existing spinal circuits via associative plasticity. We forward a hypothesis based on experimental findings suggesting that potentiation of synaptic transmission in un-injured pathways can be monitored and adjusted by a Cerebellar loop involving the Reticulospinal, Rubrospinal and Corticospinal tracts and spinal interneurons with projection to motoneurons. This mechanism could be of relevance when lesions are less extensive and the integrity of the neural circuits remains in part. Endogenous plasticity in the spinal cord could be of clinical importance if stimulated in an adequate manner, e.g., by using optimal training protocols.
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Geographic and habitat origin influence biomass production and storage translocation in the clonal plant Aegopodium podagraria.
PLoS ONE
PUBLISHED: 01-01-2014
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Through physiological integration, clonal plants can support ramets in unfavourable patches, exploit heterogeneously distributed resources and distribute resources that are taken up over large areas. Physiological integration generally increases in adverse conditions, but it is not well known which factors determine the evolution of physiological integration. The aim of this study was to investigate if clonal plants from Southern and Northern populations of the clonal herb Aegopodium podagraria differed in physiological integration in terms of translocation of carbon to the rhizomes, and in biomass production using a reciprocal transplant experiment. Aegopodium podagraria from shaded conditions have been suggested to share more resources than clones from open conditions and therefore, plants from forest and open populations within the Southern and Northern regions were included. The regional growing conditions greatly affected biomass production. Plants grown in North Sweden produced more biomass and allocated more biomass to shoots, while plants grown in South Sweden allocated more biomass to rhizomes. There was a regional origin effect as plants originating from North Sweden produced more biomass in both regions. Within the Northern region, plants from shaded habitats translocated more (14)C to the rhizomes, suggesting more storage there than in plants from open habitats. In addition to genetic differentiation in biomass production between Northern and Southern populations, probably as a response to a shorter growing season in the North, there appeared to be genetic differentiation in physiological integration within the Northern region. This shows that both regional and local conditions need to be taken into account in future studies of genetic differentiation of physiological integration in clonal plants.
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Selective Probing of the OH or OD Stretch Vibration in Liquid Water Using Resonant Inelastic Soft-X-Ray Scattering.
Phys. Rev. Lett.
PUBLISHED: 11-08-2013
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High-resolution O 1s resonant inelastic x-ray scattering spectra of liquid H_{2}O, D_{2}O, 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 D_{2}O makes stronger H-bonds than H_{2}O. 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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The Boson peak in supercooled water.
Sci Rep
PUBLISHED: 05-22-2013
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We perform extensive molecular dynamics simulations of the TIP4P/2005 model of water to investigate the origin of the Boson peak reported in experiments on supercooled water in nanoconfined pores, and in hydration water around proteins. We find that the onset of the Boson peak in supercooled bulk water coincides with the crossover to a predominantly low-density-like liquid below the Widom line TW. The frequency and onset temperature of the Boson peak in our simulations of bulk water agree well with the results from experiments on nanoconfined water. Our results suggest that the Boson peak in water is not an exclusive effect of confinement. We further find that, similar to other glass-forming liquids, the vibrational modes corresponding to the Boson peak are spatially extended and are related to transverse phonons found in the parent crystal, here ice Ih.
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With that diet, you will go far: trait-based analysis reveals a link between rapid range expansion and a nitrogen-favoured diet.
Proc. Biol. Sci.
PUBLISHED: 05-01-2013
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Recent global change has had a substantial influence on the distribution of organisms, and many species are currently expanding their ranges. To evaluate the underlying processes, long-term data with good geographic resolution are essential. One important but generally overlooked data source is offered by the taxon-specific national catalogues of first provincial records that are kept in many countries. Here, we use such data to quantify trait-based influences on range expansion in Swedish butterflies and moths between 1973 and 2010. Of 282 species meeting pre-defined quality criteria, 170 expanded their northern range margin, with a mean expansion rate of 2.7 km per year. The analyses demonstrate that habitat and diet generalists, forest species and species active during warm conditions have expanded their ranges more rapidly than other species. Notably, range expansion in diet specialists was positively related to a nitrogen-favoured larval diet, an effect not found among oligo- or polyphagous species. In contrast to the general view, this shows that specialist species can undergo rapid range expansion. We suggest that increased areas of nitrogen-rich habitat, and increased availability of a nitrogen-favoured diet, are among the most important drivers of range expansions, potentially having far-reaching consequences for a wide variety of organisms.
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Solvation structures of protons and hydroxide ions in water.
J Chem Phys
PUBLISHED: 04-26-2013
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X-ray Raman spectroscopy (XRS) combined with small-angle x-ray scattering (SAXS) were used to study aqueous solutions of HCl and NaOH. Hydrated structures of H(+) and OH(-) are not simple mirror images of each other. While both ions have been shown to strengthen local hydrogen bonds in the hydration shell as indicated by XRS, SAXS suggests that H(+) and OH(-) have qualitatively different long-range effects. The SAXS structure factor of HCl (aq) closely resembles that of pure water, while NaOH (aq) behaves similar to NaF (aq). We propose that protons only locally enhance hydrogen bonds while hydroxide ions induce tetrahedrality in the overall hydrogen bond network of water.
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Predator faunas past and present: quantifying the influence of waterborne cues in divergent ecotypes of the isopod Asellus aquaticus.
Oecologia
PUBLISHED: 04-17-2013
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Waterborne chemical cues are an important source of information for many aquatic organisms, in particular when assessing the current risk of predation. The ability to use chemical cues to detect and respond to potential predators before an actual encounter can improve prey chances of survival. We investigated predator recognition and the impact of chemical cues on predator avoidance in the freshwater isopod Asellus aquaticus. This isopod has recently colonised a novel habitat and diverged into two distinct ecotypes, which encounter different predator communities. Using laboratory-based choice experiments, we have quantified behavioural responses to chemical cues from predators typical of the two predator communities (larval dragonflies in the ancestral habitat, perch in the newly colonised habitat) in wild-caught and lab-reared Asellus of the two ecotypes. Individuals with prior experience of predators showed strong predator avoidance to cues from both predator types. Both ecotypes showed similar antipredator responses, but sexes differed in terms of threat-sensitive responses with males avoiding areas containing predator cues to a larger extent than females. Overall, chemical cues from fish elicited stronger predator avoidance than cues from larval dragonflies. Our results indicate that in these isopods, prior exposure to predators is needed to develop antipredator behaviour based on waterborne cues. Furthermore, the results emphasise the need to analyse predator avoidance in relation to waterborne cues in a sex-specific context, because of potential differences between males and females in terms of vulnerability and life history strategies.
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Evidence for long-lasting subcortical facilitation by transcranial direct current stimulation in the cat.
J. Physiol. (Lond.)
PUBLISHED: 03-18-2013
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The main aim of the study was to examine the effects of transcranial polarization on neurons in two descending motor systems, rubro- and reticulospinal. Anodal DC current was applied through an electrode in contact with the skull over the contralateral sensori-motor cortex, against an electrode placed between the skull and the ipsilateral temporal muscles in deeply anaesthetized cats. Its effects were estimated from changes in descending volleys evoked by electrical stimuli applied in the red nucleus (RN), medial longitudinal fascicle (MLF; to reticulospinal fibres) and the pyramidal tract (PT; to corticospinal or corticoreticular fibres). The descending volleys were recorded from the surface of the spinal cord at a cervical level. Rubrospinal neurones were activated either directly or indirectly, via interpositorubral fibres. Reticulospinal neurons were likewise activated directly and indirectly, via other reticulospinal or corticospinal fibres. Transcranial polarization facilitated transsynaptic activation of both rubrospinal and reticulospinal neurons, shortening the latency of the indirect descending volleys and/or increasing them, Direct activation of descending axons was much less affected. The facilitation of all subcortical neurons examined was potentiated by repeated applications of transcranial direct current stimulation (tDCS) and outlasted the polarization by at least 1-2 h, replicating tDCS effects on indirect activation of cortical neurons. The results indicate that the beneficial effects of tDCS on motor performance in humans may be due to more efficient activation of not only cortical but also subcortical neuronal systems. Combined actions of tDCS on cortical and subcortical neurones might thus further improve recovery of motor functions during rehabilitation after central injuries. 249/250.
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Benchmark oxygen-oxygen pair-distribution function of ambient water from x-ray diffraction measurements with a wide Q-range.
J Chem Phys
PUBLISHED: 03-01-2013
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Four recent x-ray diffraction measurements of ambient liquid water are reviewed here. Each of these measurements represents a significant development of the x-ray diffraction technique applied to the study of liquid water. Sources of uncertainty from statistical noise, Q-range, Compton scattering, and self-scattering are discussed. The oxygen-hydrogen contribution to the measured x-ray scattering pattern was subtracted using literature data to yield an experimental determination, with error bars, of the oxygen-oxygen pair-distribution function, g(OO)(r), which essentially describes the distribution of molecular centers. The extended Q-range and low statistical noise of these measurements has significantly reduced truncation effects and related errors in the g(OO)(r) functions obtained. From these measurements and error analysis, the position and height of the nearest neighbor maximum in g(OO)(r) were found to be 2.80(1) A? and 2.57(5) respectively. Numerical data for the coherent differential x-ray scattering cross-section I(X)(Q), the oxygen-oxygen structure factor S(OO)(Q), and the derived g(OO)(r) are provided as benchmarks for calibrating force-fields for water.
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Highly compressed two-dimensional form of water at ambient conditions.
Sci Rep
PUBLISHED: 01-15-2013
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The structure of thin-film water on a BaF(2)(111) surface under ambient conditions was studied using x-ray absorption spectroscopy from ambient to supercooled temperatures at relative humidity up to 95%. No hexagonal ice-like structure was observed in spite of the expected templating effect of the lattice-matched (111) surface. The oxygen K-edge x-ray absorption spectrum of liquid thin-film water on BaF(2) exhibits, at all temperatures, a strong resemblance to that of high-density phases for which the observed spectroscopic features correlate linearly with the density. Surprisingly, the highly compressed, high-density thin-film liquid water is found to be stable from ambient (300 K) to supercooled (259 K) temperatures, although a lower-density liquid would be expected at supercooled conditions. Molecular dynamics simulations indicate that the first layer water on BaF(2)(111) is indeed in a unique local structure that resembles high-density water, with a strongly collapsed second coordination shell.
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X-ray Raman scattering provides evidence for interfacial acetonitrile-water dipole interactions in aqueous solutions.
J Chem Phys
PUBLISHED: 11-04-2011
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Aqueous solutions of acetonitrile (MeCN) have been studied with oxygen K-edge x-ray Raman scattering (XRS) which is found to be sensitive to the interaction between water and MeCN. The changes in the XRS spectra can be attributed to water directly interacting with MeCN and are reproduced by density functional theory calculations on small clusters of water and MeCN. The dominant structural arrangement features dipole interaction instead of H-bonds between the two species as revealed by the XRS spectra combined with spectrum calculations. Small-angle x-ray scattering shows the largest heterogeneity for a MeCN to water ratio of 0.4 in agreement with earlier small-angle neutron scattering data.
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Ab initio van der waals interactions in simulations of water alter structure from mainly tetrahedral to high-density-like.
J Phys Chem B
PUBLISHED: 08-01-2011
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The structure of liquid water at ambient conditions is studied in ab initio molecular dynamics simulations in the NVE ensemble using van der Waals (vdW) density-functional theory, i.e., using the new exchange-correlation functionals optPBE-vdW and vdW-DF2, where the latter has softer nonlocal correlation terms. Inclusion of the more isotropic vdW interactions counteracts highly directional hydrogen bonds, which are enhanced by standard functionals. This brings about a softening of the microscopic structure of water, as seen from the broadening of angular distribution functions and, in particular, from the much lower and broader first peak in the oxygen-oxygen pair-correlation function (PCF) and loss of structure in the outer hydration shells. Inclusion of vdW interactions is shown to shift the balance of resulting structures from open tetrahedral to more close-packed. The resulting O-O PCF shows some resemblance with experiment for high-density water (Soper, A. K. and Ricci, M. A. Phys. Rev. Lett. 2000, 84, 2881), but not directly with experiment for ambient water. Considering the accuracy of the new functionals for interaction energies, we investigate whether the simulation protocol could cause the deviation. An O-O PCF consisting of a linear combination of 70% from vdW-DF2 and 30% from low-density liquid water, as extrapolated from experiments, reproduces near-quantitatively the experimental O-O PCF for ambient water. This suggests the possibility that the new functionals may be reliable and that instead larger-scale simulations in the NPT ensemble, where the density is allowed to fluctuate in accordance with proposals for supercooled water, could resolve the apparent discrepancy with the measured PCF.
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Increased fraction of low-density structures in aqueous solutions of fluoride.
J Chem Phys
PUBLISHED: 06-21-2011
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X-ray absorption spectroscopy (XAS) and small angle x-ray scattering (SAXS) were utilized to study the effect of fluoride (F(-)) anion in aqueous solutions. XAS spectra show that F(-) increases the number of strong H-bonds, likely between F(-) and water in the first hydration shell. SAXS data show a low-Q scattering intensity increase similar to the effect of a temperature decrease, suggesting an enhanced anomalous scattering behavior in F(-) solutions. Quantitative analysis revealed that fluoride solutions have larger correlation lengths than chloride solutions with the same cations but shorter compared to pure water. This is interpreted as an increased fraction of tetrahedral low-density structures in the solutions due to the presence of the F(-) ions, which act as nucleation centers replacing water in the H-bonding network and forming stronger H-bonds, but the presence of the cations restricts the extension of strong H-bonds.
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Evidence for Fe(2+) in wurtzite coordination: iron doping stabilizes ZnO nanoparticles.
Small
PUBLISHED: 05-18-2011
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First-principles calculations are used to investigate the structural and electronic properties of Fe-doped ZnO nanoparticles. Based on extensive validation studies surveying various density functionals, the hybrid functional PBE0 is employed to calculate the structures, formation energies, and electronic properties of Fe in ZnO with Fe concentrations of 6.25, 12.5, and 18.75 at%. Substitution of Zn by Fe, zinc vacancies, and interstitial oxygen defects is studied. High-resolution inner-shell electron energy loss spectroscopy measurements and X-ray absorption near-edge structure calculations of Fe and O atoms are performed. The results show that Fe-doped ZnO nanoparticles are structurally and energetically more stable than the isolated FeO (rocksalt) and ZnO (wurtzite) phases. The Fe dopants distribute homogeneously in ZnO nanoparticles and do not significantly alter the host ZnO lattice parameters. Simulations of the absorption spectra demonstrate that Fe(2+) dominates in the Fe-doped ZnO nanoparticles reported recently, whereas Fe(3+) is present only as a trace.
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The structure of water in the hydration shell of cations from x-ray Raman and small angle x-ray scattering measurements.
J Chem Phys
PUBLISHED: 02-17-2011
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X-ray Raman scattering (XRS) spectroscopy and small angle x-ray scattering (SAXS) are used to study water in aqueous solutions of NaCl, MgCl(2), and AlCl(3) with the particular aim to provide information about the structure of the hydration shells of the cations. The XRS spectra show that Na(+) weakens the hydrogen bonds of water molecules in its vicinity, similar to the effect of increased temperature and pressure. Mg(2+) and Al(3+), on the other hand, cause the formation of short and strong hydrogen bonds between the surrounding water molecules. The SAXS data show that Mg(2+) and Al(3+) form tightly bound hydration shells that give a large density contrast in the scattering data. From the form factors extracted from the SAXS data, we found that Mg(2+) and Al(3+) have, respectively, an equivalent of one and one and a half stable hydration shells that appear as a density contrast. In addition, we estimated that the density of water in the hydration shells of Mg(2+) and Al(3+) is, respectively, ?61% and ?71% higher than in bulk water.
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In situ X-ray probing reveals fingerprints of surface platinum oxide.
Phys Chem Chem Phys
PUBLISHED: 11-09-2010
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In situ X-ray absorption spectroscopy (XAS) at the Pt L(3) edge is a useful probe for Pt-O interactions at polymer electrolyte membrane fuel cell (PEMFC) cathodes. We show that XAS using the high energy resolution fluorescence detection (HERFD) mode, applied to a well-defined monolayer Pt/Rh(111) sample where the bulk penetrating hard X-rays probe only surface Pt atoms, provides a unique sensitivity to structure and chemical bonding at the Pt-electrolyte interface. Ab initio multiple-scattering calculations using the FEFF code and complementary extended X-ray absorption fine structure (EXAFS) results indicate that the commonly observed large increase of the white-line at high electrochemical potentials on PEMFC cathodes originates from platinum oxide formation, whereas previously proposed chemisorbed oxygen-containing species merely give rise to subtle spectral changes.
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Functional groups and sulfur K-edge XANES spectra: divalent sulfur and disulfides.
J Phys Chem A
PUBLISHED: 08-19-2010
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Sulfur K-edge XANES was measured for two divalent sulfurs (dibenzyl and benzyl phenyl) and two disulfides (dibenzyl and diphenyl). The absorption spectra could be assigned using density functional theory with the "half core hole" approximation for the core hole including relaxation of selected excited states at the absorption edge. Analysis of the molecular orbitals shows that the characteristic double peak of the dibenzyl disulfide arises as a consequence of the enhanced splitting of the LUMO (lowest unoccupied molecular orbital) and the LUMO + 1. Exchange of the ligand benzyl by phenyl introduces more transitions at the absorption edge, which enhance the broadening in the divalent sulfur and splitting of the peaks of the disulfide. It is shown that different ligand groups introduce significant differences in the absorption edge, which poses a problem for the speciation analysis when the ligand groups are not clearly defined.
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Complementarity between high-energy photoelectron and L-edge spectroscopy for probing the electronic structure of 5d transition metal catalysts.
Phys Chem Chem Phys
PUBLISHED: 05-05-2010
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We demonstrate the successful use of hard X-ray photoelectron spectroscopy (HAXPES) for selectively probing the platinum partial d-density of states (DOS) in a Pt-Cu nanoparticle catalyst which shows activity superior to pure Pt towards the oxygen-reduction reaction (ORR). The information about occupied Pt d-band states was complemented by Pt L(2)-edge X-ray absorption near-edge spectroscopy (XANES), which probes unoccupied valence states. We found a significant electronic perturbation of the Pt projected d-DOS which was narrowed and shifted to higher binding energy compared to pure platinum. The effect of this electronic structure perturbation on the chemical properties of the nanoparticle surface is discussed in terms of the d-band model. We have thereby demonstrated that the combination of L-edge spectroscopy and HAXPES allows for an experimental derivation of the valence electronic structure in an element-specific way for 5d metal catalysts.
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Oxygen-oxygen correlations in liquid water: addressing the discrepancy between diffraction and extended x-ray absorption fine-structure using a novel multiple-data set fitting technique.
J Chem Phys
PUBLISHED: 03-18-2010
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The first peak of the oxygen-oxygen pair-correlation function (O-O PCF) is a critical measure of the first coordination-shell distances in liquid water. Recently, a discrepancy has been uncovered between diffraction and extended x-ray absorption fine-structure (EXAFS) regarding the height and position of this peak, where EXAFS gives a considerably more well-defined peak at a shorter distance compared to the diffraction results. This discrepancy is here investigated through a novel multiple-data set structure modeling technique, SpecSwap-RMC, based on the reverse Monte Carlo (RMC) method. Fitting simultaneously to both EXAFS and a diffraction-based O-O PCF shows that even though the reported EXAFS results disagree with diffraction, the two techniques can be reconciled by taking into account a strong contribution from the photoelectron scattering focusing effect in EXAFS originating from nearly linear hydrogen bonds. This many-body contribution, which is usually neglected in RMC modeling of EXAFS data, is included in the fits by precomputing and storing EXAFS signals from real-space multiple-scattering calculations on a large number of unique water clusters. On the other hand, fitting also the O-O PCF from diffraction is seen to enhance the amount of structural disorder in the joint fit. Thus, both structures containing nearly linear hydrogen bonds and local structural disorder are important to reproduce diffraction and EXAFS simultaneously. This work also illustrates a few of many possible uses of the SpecSwap-RMC method in modeling disordered materials, particularly for fitting computationally demanding techniques and combining multiple data sets.
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SpecSwap-RMC: a novel reverse Monte Carlo approach using a discrete set of local configurations and pre-computed properties.
J Phys Condens Matter
PUBLISHED: 02-25-2010
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We present a novel approach to reverse Monte Carlo (RMC) modeling, SpecSwap-RMC, specifically applicable to structure modeling based on properties that require significant computer time to evaluate. In this approach pre-computed property data from a discrete set of local configurations are used and the configuration space is expressed in this basis. Atomistic moves are replaced with swap moves of contributions to a sample set representing the state of the simulated system. We demonstrate the approach by fitting jointly and separately the EXAFS signal and x-ray absorption spectrum (XAS) of ice Ih using a SpecSwap sample set of 80 configurations from a library of 1382 local structures with associated pre-computed spectra. As an additional demonstration we compare SpecSwap and FEFFIT fits of EXAFS data on crystalline copper, finding excellent agreement. SpecSwap-RMC thus extends RMC structure modeling to any property that can be computed from a structure irrespective of computational expense, but at the cost of a reduced configuration space. The method is general enough that it can be applied to any sets of computed properties, not necessarily limited to structure determination.
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Assessing the electric-field approximation to IR and Raman spectra of dilute HOD in D2O.
J Chem Phys
PUBLISHED: 07-24-2009
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We analyze the validity of the commonly used electric-field (E-field) approximation to vibrational OH stretch Raman spectra of dilute HOD in D(2)O by computing the OH stretch frequency of all molecules in several different structure models, each containing around 2000 molecules. The calculations are done at the B3LYP level using clusters containing 32 molecules centered around the molecule for which the frequencies are calculated; the large cluster size is required due to significant nonlocal contributions influencing the computed frequencies. The vibrational frequencies are determined using a six-point potential optimized discrete variable representation. Raman and infrared intensities are furthermore computed to generate the spectra. We find that a quadratic fit of E-field versus frequency gives a reasonable representation of the calculated distribution of frequencies. However, the mapping depends significantly on the structural model and is thus not universal. Anharmonic couplings are calculated for several optimized clusters showing a general trend to compress the computed frequency distributions, which is in agreement with dynamical simulations (motional narrowing).
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Increased fraction of weakened hydrogen bonds of water in aerosol OT reverse micelles.
J Chem Phys
PUBLISHED: 07-24-2009
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Water in aerosol OT reverse micelles has been extensively studied as a model system for nanoconfined water. Results from previous vibrational studies suggest that water confined this way has slower dynamics compared to bulk water; however, the effects on the hydrogen bonding network are unclear. From our study of the structure of water hydrogen bonding using x-ray Raman spectroscopy, we found an increased fraction of weakened hydrogen bonds upon confinement, similar to the effect seen in temperature increase and NaCl solvation, as evidenced by the changes in specific spectral features.
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On the range of water structure models compatible with X-ray and neutron diffraction data.
J Phys Chem B
PUBLISHED: 04-11-2009
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We use the reverse Monte Carlo (RMC) method to critically evaluate the structural information content of diffraction data on bulk water by fitting simultaneously or separately to X-ray and neutron data; the O-H and H-H, but not the O-O, pair-correlation functions (PCFs) are well-described by the neutron data alone. Enforcing at the same time different H-bonding constraints, we generate four topologically different structure models of liquid water, including a simple mixture model, that all equally well reproduce the diffraction data. Although earlier work [Leetmaa, M.; et al. J. Chem. Phys. 2008, 129, 084502] has focused on tetrahedrality in the H-bond network in liquid water, we show here that, even for the O-O-O three-body correlation, tetrahedrality is not strictly defined by the data. We analyze how well two popular MD models (TIP4P-pol2 and SPC/E) reproduce the neutron data in q-space and find differences in important aspects from the experiment. From the RMC fits, we obtain pair-correlation functions (PCFs) that are in optimal agreement with the diffraction data but still show a surprisingly strong variability both in position and height of the first intermolecular (H-bonding) O-H peak. We conclude that, although diffraction data impose important constraints on the range of possible water structures, additional data are needed to narrow the range of possible structure models.
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Theoretical and experimental sulfur K-edge X-ray absorption spectroscopic study of cysteine, cystine, homocysteine, penicillamine, methionine and methionine sulfoxide.
Dalton Trans
PUBLISHED: 03-10-2009
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The experimental sulfur K-edge X-ray absorption near-edge structure (XANES) spectra of the amino acids cysteine, homocysteine, penicillamine, methionine, including the oxidation products methionine sulfoxide and the disulfide cystine, have been analyzed by transition potential DFT calculations. The absolute energies and intensities of the main pre-edge sulfur 1s electron transitions have been computed to determine the character of the receiving unoccupied molecular orbitals (MO), and to investigate the influence of external interactions, especially by introducing water molecules hydrogen-bonded to the ionic species present in different pH ranges. When the thiol group deprotonates for cysteine, homocysteine and penicillamine and also for the cysteine residue in glutathione the energy of the main transition, to an MO with antibonding sigma*(S-H) character, reduces by approximately 1.1 eV and the receiving MO obtains sigma*(S-C) character. The changes in transition energy due to hydrogen-bonding were in most cases found to be relatively small, although the transition intensities could vary significantly due to the changes induced in the molecular charge distribution, thereby affecting the shapes of the spectral features. For the cysteine and penicillamine zwitterions deconvolution of the experimental spectra allowed the microscopic acid dissociation constants to be extracted separately for the thiol and the protonated amine groups, pK(a)(S) = 8.5 +/- 0.1 and 8.2 +/- 0.1, and pK(a)(N) = 8.9 +/- 0.1 and 8.8 +/- 0.1, respectively, with the thiol group in both cases being the more acidic. Coordination of cysteine to nickel(II) or mercury(II) introduced a new low energy transition involving metal ion orbitals in the receiving LUMO. The small experimentally observed energy differences between the similar main absorption features of the cysteine and methionine zwitterions, 0.2-0.3 eV in comparable surrounding, as well as a minor difference in their intensities, are reflected in the calculated transitions. The S K-edge XANES spectrum of the disulfide cystine displays a characteristic double peak with the lower energy transition (2469.9 eV) into the antibonding sigma*(S-S) MO. The second peak, at 2471.5 eV in aqueous solution, contains several transitions into MOs with sigma*(S-C) character involving also charge transfer to the water molecules hydrating the protonated amine groups (NH(3)(+)) of cystine. For solid cystine without hydrogen bonding the experimental energy difference between the two peaks is 0.2 eV larger, while no such increase occurs for the oxidized disulfide of glutathione, with a similar -S-S- bond between its cysteine residues as in cystine, because the amine groups are engaged in peptide bonds. This study shows that externally induced changes in the intramolecular bonding, e.g., by coordination, conformation geometry or hydrogen-bonding, can significantly influence the S K-edge spectra, and emphasizes the importance of a similar chemical surrounding when choosing the model compounds for standard spectra of sulfur functional groups, used to deconvolute composite experimental spectra.
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Seasonal migration to high latitudes results in major reproductive benefits in an insect.
Proc. Natl. Acad. Sci. U.S.A.
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Little is known of the population dynamics of long-range insect migrants, and it has been suggested that the annual journeys of billions of nonhardy insects to exploit temperate zones during summer represent a sink from which future generations seldom return (the "Pied Piper" effect). We combine data from entomological radars and ground-based light traps to show that annual migrations are highly adaptive in the noctuid moth Autographa gamma (silver Y), a major agricultural pest. We estimate that 10-240 million immigrants reach the United Kingdom each spring, but that summer breeding results in a fourfold increase in the abundance of the subsequent generation of adults, all of which emigrate southward in the fall. Trajectory simulations show that 80% of emigrants will reach regions suitable for winter breeding in the Mediterranean Basin, for which our population dynamics model predicts a winter carrying capacity only 20% of that of northern Europe during the summer. We conclude not only that poleward insect migrations in spring result in major population increases, but also that the persistence of such species is dependent on summer breeding in high-latitude regions, which requires a fundamental change in our understanding of insect migration.
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Connecting dopant bond type with electronic structure in N-doped graphene.
Nano Lett.
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Robust methods to tune the unique electronic properties of graphene by chemical modification are in great demand due to the potential of the two dimensional material to impact a range of device applications. Here we show that carbon and nitrogen core-level resonant X-ray spectroscopy is a sensitive probe of chemical bonding and electronic structure of chemical dopants introduced in single-sheet graphene films. In conjunction with density functional theory based calculations, we are able to obtain a detailed picture of bond types and electronic structure in graphene doped with nitrogen at the sub-percent level. We show that different N-bond types, including graphitic, pyridinic, and nitrilic, can exist in a single, dilutely N-doped graphene sheet. We show that these various bond types have profoundly different effects on the carrier concentration, indicating that control over the dopant bond type is a crucial requirement in advancing graphene electronics.
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Microscopic probing of the size dependence in hydrophobic solvation.
J Chem Phys
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We report small angle x-ray scattering data demonstrating the direct experimental microscopic observation of the small-to-large crossover behavior of hydrophobic effects in hydrophobic solvation. By increasing the side chain length of amphiphilic tetraalkyl-ammonium (C(n)H(2n+1))(4)N(+) (R(4)N(+)) cations in aqueous solution we observe diffraction peaks indicating association between cations at a solute size between 4.4 and 5 A?, which show temperature dependence dominated by hydrophobic attraction. Using O K-edge x-ray absorption we show that small solutes affect hydrogen bonding in water similar to a temperature decrease, while large solutes affect water similar to a temperature increase. Molecular dynamics simulations support, and provide further insight into, the origin of the experimental observations.
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Polarization dependent resonant x-ray emission spectroscopy of D2O and H2O water: assignment of the local molecular orbital symmetry.
J Chem Phys
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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 D(2)O and H(2)O 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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