Probing the electron delocalization in liquid water and ice at attosecond time scales

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.

Are recent water models obtained by fitting diffraction data consistent with infrared/Raman and x-ray absorption spectra?

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.

DNA methylation: its contribution to systemic lupus erythematosus

Recent studies on epigenetics, including the methylation of DNA and the enzymes regulating methylation, seem likely to contribute to understanding the pathogenesis of autoimmune diseases such as systemic lupus erythematosus (SLE). In fact, the relationship between DNA methylation and SLE has long been the subject of investigation. To obtain a deeper understanding of the role of DNA methylation in the onset of SLE, we reviewed the findings reported in the literature and our own data about DNA methylation and SLE. Various studies have indicated the possible importance of DNA methylation, especially hypomethylation, in the aetiology of SLE. Epigenetic studies may provide clues for elucidating the pathogenesis of SLE and for developing new strategies to treat this disease.

Endoscopic management of pancreaticopleural fistulas: a report of three patients

Pancreaticopleural fistulas are a rare complication of acute or chronic pancreatitis, and are usually treated by surgery. We report three patients whose pancreaticopleural fistulas were successfully treated by endoscopic retrograde cholangiopancreatography and drainage (stenting, nasopancreatic drainage). In one patient a pancreatic pseudocyst persisted despite successful initial closure of the leak using this method and, as it was also suspected to be infected, additional drainage of the pseudocyst was required. Endotherapy of pancreaticopleural fistulas could obviate the need for surgery when conventional medical treatment has failed in this condition.

The local structure of protonated water from x-ray absorption and density functional theory

We present a combined x-ray absorption spectroscopy/computational study of water in hydrochloric acid (HCl) solutions of varying concentration to address the structure and bonding of excess protons and their effect on the hydrogen bonding network in liquid water. Intensity variations and energy shifts indicate changes in the hydrogen bonding structure in water as well as the local structure of the protonated complex as a function of the concentration of protons. In particular, in highly acidic solutions we find a dominance of the Eigen form, H(3)O(+), while the proton is less localized to a specific water under less acidic conditions.

Physisorption-induced C-H bond elongation in methane

Physisorption of methane to a Pt surface was studied by x-ray absorption spectroscopy in combination with density functional theory spectrum calculations. The experiment shows new electronic states appearing upon physisorption. We find that these states are due to orbital mixing causing charge polarization as a means to minimize Pauli repulsion. The results can be explained by elongation of 1 C-H bond by 0.09 A in the physisorbed state even though no covalent chemical bond is formed.

Hydrogenation of single-walled carbon nanotubes

Towards the development of a useful mechanism for hydrogen storage, we have studied the hydrogenation of single-walled carbon nanotubes with atomic hydrogen using core-level photoelectron spectroscopy and x-ray absorption spectroscopy. We find that atomic hydrogen creates C-H bonds with the carbon atoms in the nanotube walls, and such C-H bonds can be completely broken by heating to 600 degrees C. We demonstrate approximately 65 +/- 15 at % hydrogenation of carbon atoms in the single-walled carbon nanotubes, which is equivalent to 5.1 +/- 1.2 wt % hydrogen capacity. We also show that the hydrogenation is a reversible process.

X-ray Absorption Spectroscopy Measurements of Liquid Water

Recent studies, based on X-ray absorption spectroscopy (XAS) and X-ray Raman scattering (XRS), have shown that the hydrogen bond network in liquid water consists mainly of water molecules with only two strong hydrogen bonds. Since this result is controversial, it is important to demonstrate the reliability of the experimental data, which is the purpose of this paper. Here we compare X-ray absorption spectra of liquid water recorded with five very different techniques sensitive to the local environment of the absorbing molecule. Overall, the spectra obtained with photon detection show a very close similarity and even the observable minor differences can be understood. The comparison demonstrates that XAS and XRS can indeed be applied reliably to study the local bonding of the water molecule and thus to reveal the hydrogen bond situation in bulk water.

X-ray Absorption Spectroscopy Study of the Hydrogen Bond Network in the Bulk Water of Aqueous Solutions

We utilized X-ray absorption spectroscopy (XAS) and X-ray Raman scattering (XRS) in order to study the ion solvation effect on the bulk hydrogen bonding structure of water. The fine structures in the X-ray absorption spectra are sensitive to the local environment of the probed water molecule related to the hydrogen bond length and angles. By varying the concentration of ions, we can distinguish between contributions from water in the bulk and in the first solvation sphere. We show that the hydrogen bond network in bulk water, in terms of forming and breaking hydrogen bonds as detected by XAS/XRS, remains unchanged, and only the water molecules in the close vicinity to the ions are affected.

Ultrafast core-hole-induced dynamics in water probed by x-ray emission spectroscopy

The isotope effect and excitation-energy dependence have been measured in the oxygen K-edge x-ray emission spectrum (XES). The use of XES to monitor core decay processes provides information about molecular dynamics (MD) on an ultrafast time scale through the O1s lifetime of a few femtoseconds. Different nuclear masses give rise to differences in the dynamics and the observed isotope effect in XES is direct evidence of the importance of such processes. MD simulations show that even the excitation-energy dependence in the XES is mainly related to differences in core-excited-state dynamics.

The hydrogen bond in ice probed by soft x-ray spectroscopy and density functional theory

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.

Water dissociation on Ru(001): an activated process

It is shown using x-ray photoelectron spectroscopy that water is adsorbed either nondissociatively or partially dissociatively on Ru(001) under ultrahigh vacuum conditions. We found an activated dissociation process with a barrier slightly larger than that of desorption. A difference in dissociation barriers is found between H2O and D2O that explains the anomalous isotope effects in the thermal desorption. Previous theoretical and experimental disagreements can be rationalized based on electron or x-ray beam-induced dissociation of the water overlayer and an earlier underestimation of the dissociation barrier.

Ultrafast molecular dissociation of water in ice

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.

Possible mechanisms of gender bias in SLE: a new hypothesis involving a comparison of SLE with atopy

The prevalence of systemic lupus erythematosus (SLE) is far higher in females than in males, and numerous investigations of this gender bias have been performed from several perspectives. Sex hormones, particularly estrogens, may be significant in causing the gender discrepancy. This article discusses the possible importance of estrogens in regulating the expression of and responsivity to autoantigens in SLE and in atopic disorders, which are associated with hyperreactivity to exogenous antigens. Estrogens seem to play an important role in the overexpression of endogenous autoantigens, such as human endogenous retroviruses (HERV), and this may be related to the existence of a gender bias in the incidence of SLE but not atopy.

The structure of the first coordination shell in liquid water

X-ray absorption spectroscopy and x-ray Raman scattering were used to probe the molecular arrangement in the first coordination shell of liquid water. The local structure is characterized by comparison with bulk and surface of ordinary hexagonal ice Ih and with calculated spectra. Most molecules in liquid water are in two hydrogen-bonded configurations with one strong donor and one strong acceptor hydrogen bond in contrast to the four hydrogen-bonded tetrahedral structure in ice. Upon heating from 25 degrees C to 90 degrees C, 5 to 10% of the molecules change from tetrahedral environments to two hydrogen-bonded configurations. Our findings are consistent with neutron and x-ray diffraction data, and combining the results sets a strong limit for possible local structure distributions in liquid water. Serious discrepancies with structures based on current molecular dynamics simulations are observed.

Possible role of DNA hypomethylation in the induction of SLE: relationship to the transcription of human endogenous retroviruses

OBJECTIVE

We investigated the contribution of DNA methyltransferase activity to the transcription of human endogenous retroviruses (HERV), which have been reported to be a plausible causative agent for systemic lupus erythematosus (SLE).

METHODS

The reverse transcriptase-polymerase chain reaction (RT-PCR) and real-time quantitative-PCR (RQ-PCR) were used.

RESULTS

Our results indicated that treatment with 5-aza-deoxycytidine (5-aza C), a demethylating agent, increased the transcription of messenger RNA (mRNA) for HERV clone 4-1 and decreased mRNA for DNA methyltransferase-1 (DNMT-1; methylation-regulating enzyme) in peripheral blood mononuclear cells (PBMC) from normal individuals. Also, transcription of DNMT-1 mRNA in PBMC from patients with SLE was lower than in cells from normal controls.

CONCLUSION

DNA hypomethylation seems to play a significant role in the transcription of HERV clone 4-1 and may be related to the pathogenesis of SLE.

DNA methylation in systemic lupus erythematosus

Recent studies on epigenetics, including DNA methylation and its regulatory enzymes, seem likely to contribute to elucidation of the pathogenesis of autoimmune diseases such as systemic lupus erythematosus (SLE), although the relationship between DNA methylation and SLE has long been the subject of investigation. To obtain a deeper understanding of the role of DNA methylation in the induction of SLE, we reviewed the relationship between DNA methylation and SLE based on findings reported in the literature and our own data. Various studies, including ours, have indicated the possible importance of DNA methylation, especially hypomethylation, in the etiology of SLE. These epigenetic studies may give us clues towards elucidation of the pathogenesis of SLE and development of new therapeutic strategies for this disease.

Bonding of saturated hydrocarbons to metal surfaces

The adsorption of octane on Cu(110) was studied by x-ray absorption and x-ray emission spectroscopy, in combination with spectrum calculations in the framework of density functional theory, as a model system for alkane adsorption on transition metals. Significant electron sharing between the adsorbate and metal surface and involvement of both bonding and antibonding C-H molecular orbitals in the molecule-metal bond was found. The calculations were extended to the case of octane adsorbed on Ni(110), and the position of the metal d band was found to be important for the bonding. The results were generalized to show that this is important for the efficiency as an alkane dehydrogenation catalyst.