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X-ray Data (x-ray + data)
Terms modified by X-ray Data Selected AbstractsSynthesis and crystal structure determination of 6,7-dihydro-2-methoxy-4-(substituted)-5H -benzo[6,7]cyclohepta[1,2- b ]pyridine-3-carbonitrileCRYSTAL RESEARCH AND TECHNOLOGY, Issue 4 2007A. M. Moustafa Abstract The compounds 6,7-dihydro-2-methoxy-4-(4-methylphenyl)-5H -benzo[6.7]cyclohepta[1,2 -b ]pyridine-3-carbonitrile (compound IIIa) and 4-(4-chlorophenyl)-6,7-dihydro-2-methoxy-5H -benzo[6,7]cyclohepta[1,2- b ]pyridine-3-carbonitrile (compound IIIb) were synthesized and their structures have been determined from three dimensional X-ray data using direct method and refined by full matrix least squares with anisotropic thermal parameters for non-hydrogen atoms to conventional R(gt) of 0.036 and 0.038 for the two compounds respectively. For compound (IIIa) the crystals are monoclinic, space group Cc, with a=11.2909 (5) Å, b=17.7755(8) Å, c=9.1437(4) Å and ,=95.428(3)°, while the crystals of the second compound (IIIb) are triclinic, space group P1, with a=8.7465(3)Å, b=10.3958(3)Å, c=10.9011(4)Å, ,= 108.3870(10)°, ,=101.3741(12)°, ,=97.9594(12)°. The molecular structure of the two compounds have nearly the same configuration, where the cyclohepta ring takes the boat shape and the methoxy and the carbonitrile groups are attached at the same position C2 and C8. The difference occurs only at the position C4, where the substituent is methylphenyl for compound (IIIa) and chlorophenyl for the other. The bond lengths, valency angles and the hydrogen bonding were calculated and fully discussed. (© 2007 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim) [source] Heterometallic CoIII,LnIII (Ln = Gd, Tb, Dy) Complexes on a p -Sulfonatothiacalix[4]arene Platform Exhibiting Redox-Switchable Metal-to-Metal Energy TransferEUROPEAN JOURNAL OF INORGANIC CHEMISTRY, Issue 25 2008Viktoriya Skripacheva Abstract Nuclear magnetic relaxation along with pH metric data have been used to reveal pH-dependent heterometallic CoIII,LnIII (Ln = Gd, Tb, and Dy) complex formation on a p -sulfonatothiacalix[4]arene (TCAS) platform in aqueous solution. The previously obtained 1D and 2D 1H NMR spectroscopic and X-ray data prove the outer sphere binding of the CoIII block with the upper rim of TCAS, whereas the LnIII ion is coordinated with the phenolate groups of the lower rim of TCAS. The inclusive outer-sphere binding of CoIII tris(dipyridyl) and tris(ethylendiaminate) complexes with the upper rim of TCAS favors binding of the inner-sphere lanthanide ions through the lower rim of TCAS, whereas noninclusive binding of CoIII bis(histidinate) provides no effect on the binding of lanthanide ions. The emission properties of [Co(dipy)3]3+,LnIII (Ln = Gd, Tb, Dy) complexes indicate the quenching of 4f luminescence by the 3d block. This quenching can be switched off by electrochemical CoIII/CoII reduction with further switching on by reoxidation. (© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2008) [source] Towards Understanding of the Selective Precipitation of Alkali Metal Cations in Presence of Dipicrylamine AnionEUROPEAN JOURNAL OF INORGANIC CHEMISTRY, Issue 11 2005Suresh Eringathodi Abstract Dipicrylamine anion (DPA,) precipitates out [K(DPA)] with high selectivity from salt bitterns containing Na+, K+, and Mg2+, whereas the same ligand shows poor selectivity towards K+ , and much higher selectivity towards Cs+ , in studies conducted with a mixture of K+, Rb+, and Cs+. Their single-crystal structures reveal that the K+ and Rb+ salts have similar layered structures, with 8 oxygen atoms from seven DPA, anions encapsulating the metal cation, whereas the Cs+ salt possesses a channel-like structure with the metal ion encapsulated by ten oxygen atoms from six DPA,. The conformation of DPA, in the [Cs(DPA)] single crystal matches closely that of DPA in crystalline state. M···O and intermolecular C,H···O interactions together stabilize the structures. The 133Cs NMR spectrum of the poorly soluble [Cs(DPA)] shows an upfield shift of the peak with respect to CsCl as a result of the interaction with the oxygen atoms of DPA,, whereas 23Na NMR spectrum of the highly soluble [Na(DPA)] shows no such upfield shift compared to NaCl. Powder XRD patterns of bulk [M(DPA)] (M = K+, Rb+, and Cs+) precipitates show that these are similar to the patterns obtained by simulation of the single-crystal X-ray data. The selectivity of precipitation correlates qualitatively with the size and hydration enthalpies of the ions. (© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2005) [source] Structure, Electrochemistry and Hydroformylation Catalytic Activity of the Bis(pyrazolylborato)rhodium(I) Complexes [RhBp(CO)P] [P = P(NC4H4)3, PPh3, PCy3, P(C6H4OMe-4)3]EUROPEAN JOURNAL OF INORGANIC CHEMISTRY, Issue 7 2004Anna M. Trzeciak Abstract Rhodium complexes of formula [RhBp(CO)P] [Bp = bis(pyrazolylborate), P = P(NC4H4)31, PPh32, PCy33, P(C6H4OMe-4)34] have been prepared by exchange of the acetylacetonate (acac,) ligand in [Rh(acac)(CO)P] complexes. The spectroscopic and electrochemical properties as well as X-ray data of [Rh(acac)(CO)P] and [RhBp(CO)P] complexes have been compared with the aim to estimate the relative donor properties of both anionic ligands (acac, and Bp,). The cyclic voltammetric results indicate that the Bp, ligand behaves as a much stronger electron donor than acac, and a value of the Lever EL ligand parameter identical to that of the pyrazolate ligand (,0.24 V vs. NHE for each coordinating arm) is proposed for the bis- and tris(pyrazolyl)borate ligands, whereas P(C6H4OMe-4)3 is also shown to have an identical EL value (0.69 V) to that of P(NC4H4)3. An improved linear relationship between the oxidation potential and the sum of the ligand EL values for square-planar RhI complexes is also obtained and adjusted values for the Lever SM and IM parameters for the RhI/RhII redox couple are given. The trans influence of phosphanes was not observed in crystals of complexes 2 and 3, in contrast to analogous acetylacetonato complexes in which the Rh,O bonds differ by ca. 0.04,0.06 Å. Complexes 1,4 are very attractive precursors for hydroformylation catalysts and yields of aldehydes of 80,87% have been obtained with all complexes without extra phosphane as co-catalyst. During the hydroformylation reaction, however, small amounts of a catalytically inactive [RhBp(CO)2] complex were formed. (© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2004) [source] Dewetting of an Organic Semiconductor Thin Film Observed in Real-time,ADVANCED ENGINEERING MATERIALS, Issue 4 2009Stefan Kowarik We study the growth and the post-growth dewetting process of the organic semiconductor diindenoperylene (DIP) using real-time X-ray reflectivity measurements. We show that a DIP monolayer deposited in UHV onto silicon oxide dewets via the formation of bilayer islands. From the time resolved structural data we estimate the rate constant for interlayer diffusion of DIP molecules. Post-growth AFM measurements confirm the conclusions from the X-ray data and show the morphology of the dewetted film. [source] Molecular dynamics simulations of solvated UDP,glucose in interaction with Mg2+ cationsFEBS JOURNAL, Issue 20 2001Pavla Petrová ,Glycosyltransferases are key enzymes involved in biosynthesis of oligosaccharides. Nucleotide-sugars, the glycosyltransferase substrates, serve as activated donors of sugar residues during the enzymatic reaction Although very little is known about the catalytic mechanism of these enzymes, it appears that the catalytic activity in most glycosyltransferases is dependent upon the presence of a divalent cation, for example Mn2+ or Mg2+. It is not known whether the ion is bound to the enzyme before its interaction with the substrate, or if it binds the substrate before the enzymatic reaction to modify its conformation to fit better the active site of the enzyme. We have inspected the latter possibility by running four 2-ns molecular dynamics trajectories on fully solvated UDP-glucose in the presence of Mg2+ ions. Our results indicate that the divalent cation interacts strongly with the nucleotide-sugar in solution, and that it can alter its conformational behavior. It is also shown that a conformation of the pyrophosphate moiety that results in an eclipsed or almost eclipsed orientation of two of the oxygen atoms, and which is found in protein interacting with a nucleotide di- or tri-phosphate X-ray data, is energetically favored. The results are also discussed in light of existing NMR data, and are found to be in a good agreement with them. [source] Solvent effect on the reactivity of CIS -platinum (II) complexes: A density functional approachINTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 8 2008Pubalee Sarmah Abstract The structure and chemical reactivity of some selected cis -platinum(II) complexes, including clinically used drug molecules, cisplatin, carboplatin, and oxaliplatin are investigated using density functional theory (DFT) calculations. Calculated geometries of the complexes are in agreement with their available X-ray data. The global and local reactivity descriptors, such as hardness, chemical potential, electrophilicity index, Fukui function, and local philicity are calculated to investigate the usefulness of these descriptors for understanding the reactive nature and reactive sites of the complexes. Inclusion of solvent effect shows that both global and local descriptors change the trend of reactivity with respect to their trend in the gas phase. The stability of the complexes increases with the inclusion of water molecules. Simple regression analysis is applied to build up a quantitative structure-activity relationship (QSAR) model based on DFT derived electrophilicity index for the Pt(II) complexes against A2780 human ovarian adenocarcinoma cell line to establish the importance of the descriptor in predicting cytotoxicity. © 2008 Wiley Periodicals, Inc. Int J Quantum Chem, 2008 [source] PDB_REDO: automated re-refinement of X-ray structure models in the PDBJOURNAL OF APPLIED CRYSTALLOGRAPHY, Issue 3 2009Robbie P. Joosten Structural biology, homology modelling and rational drug design require accurate three-dimensional macromolecular coordinates. However, the coordinates in the Protein Data Bank (PDB) have not all been obtained using the latest experimental and computational methods. In this study a method is presented for automated re-refinement of existing structure models in the PDB. A large-scale benchmark with 16,807 PDB entries showed that they can be improved in terms of fit to the deposited experimental X-ray data as well as in terms of geometric quality. The re-refinement protocol uses TLS models to describe concerted atom movement. The resulting structure models are made available through the PDB_REDO databank (http://www.cmbi.ru.nl/pdb_redo/). Grid computing techniques were used to overcome the computational requirements of this endeavour. [source] Pressure-induced high-density amorphous ice in protein crystalsJOURNAL OF APPLIED CRYSTALLOGRAPHY, Issue 1 2008Chae Un Kim Crystal cryocooling has been used in X-ray protein crystallography to mitigate radiation damage during diffraction data collection. However, cryocooling typically increases crystal mosaicity and often requires a time-consuming search for cryoprotectants. A recently developed high-pressure cryocooling method reduces crystal damage relative to traditional cryocooling procedures and eases or eliminates the need to screen for cryoprotectants. It has been proposed that the formation of high-density amorphous (HDA) ice within the protein crystal is responsible for the excellent diffraction quality of the high-pressure cryocooled crystals. This paper reports X-ray data that confirm the presence of HDA ice in the high-pressure cryocooled protein crystallization solution and protein crystals analyzed at ambient pressure. Diffuse scattering with a spacing characteristic of HDA ice is seen at low temperatures. This scattering then becomes characteristic successively to low-density amorphous, cubic and hexagonal ice phases as the temperature is gradually raised from 80 to 230,K, and seems to be highly correlated with the diffraction quality of crystals. [source] Polyaniline-multiwalled carbon nanotube composites: Characterization by WAXS and TGAJOURNAL OF APPLIED POLYMER SCIENCE, Issue 1 2008T. Jeevananda Abstract Polyaniline/carboxylated multi-walled carbon nanotube (PAni/c-MWNT) nanocomposites have been synthesized by micellar aided emulsion polymerization with various c-MWNTs compositions, viz., 0.5, 1, 5, and 10 wt %. The microcrystalline parameters such as the nanocrystal size (,N,), lattice strain (g), interplanar distance (dhkl), width of the crystallite size distribution, surface weighted crystal size (Ds), and volume of the ordered regions were calculated from the X-ray data by using two mathematical models, namely the Exponential distribution and Reinhold distribution methods. The effects of heat ageing on the microcrystalline parameters of the PAni/c-MWNT nanocomposites were also studied and the results are correlated. The thermal stability and electrical resistivity of the PAni/c-MWNT nanocomposites were examined with thermogravimetric analysis (TGA) and a conventional two-probe method. The TGA data indicate that the thermal stability of the nanocomposites improved after the incorporation of c-MWNTs. The influence of temperature on the resistivity of the nanocomposites was also measured. © 2008 Wiley Periodicals, Inc. J Appl Polym Sci 2008 [source] Nanocrystallite regions of guar gum filled PU/PAN composites before and after biodegradation using WAXSJOURNAL OF APPLIED POLYMER SCIENCE, Issue 5 2008H. Kumar Abstract Polyurethane/polyacrylonitrile semi-interpenetrating polymer network containing varying weight percent of guar gum were prepared. The resulting composites were subjected to biodegradation with the help of specific fungi Aspergillus niger. The composite before and after biodegradation were subjected to wide angle X-ray scattering studies. The nanocrystallite regions, area, and size are determined from X-ray data using three different asymmetric column length functions. A comparison of these parameters does explain the nature of biodegradation at microlevel. © 2008 Wiley Periodicals, Inc. J Appl Polym Sci, 2008 [source] PSRK method for gas hydrate equilibria: I. Simple and mixed hydratesAICHE JOURNAL, Issue 1 2004Ji-Ho Yoon Abstract A thermodynamic model using the predictive Soave-Redlich-Kwong (PSRK) group contribution method to calculate the fugacities of all components in the vapor and liquid phases in equilibrium with the coexisting hydrate phase is proposed. Since the PSRK method together with the UNIFAC model takes the gas,gas interaction in the vapor and liquid phases into account, the phase equilibria of mixed gas hydrates can be successfully reproduced. This approach greatly improves upon the accuracy of the modified Huron-Vidal second-order (MHV2) model, especially for three-guest hydrate systems. Based on experimentally determined X-ray data, an accurate representation for the molar volume of the structure I (sI) hydrate is provided and used for predicting the equilibrium dissociation of methane hydrate at high pressures. Using this correlation, it is possible to reduce noticeable errors in dissociation predictions of high-pressure hydrate formers. Complete phase behavior, including a new quadruple point, which is predicted to be 272.6 K and 7.55 MPa, for cyclopropane hydrate, is presented by the proposed model calculation. © 2004 American Institute of Chemical Engineers AIChE J, 50: 203,214, 2004 [source] Structural study of ethyl 3-arylcarbamoyl-2,3-diazabicyclo[2.2.1]hept-5-ene-2-carboxylates: conformation and transmission of substituent effects across the diazabicycloheptene ring,JOURNAL OF PHYSICAL ORGANIC CHEMISTRY, Issue 11 2001A. Perjéssy Abstract Nine new ethyl 3-arylcarbamoyl-2,3-diazabicyclo[2.2.1]hept-5-ene-2-carboxylates were prepared by a [4,+,2] cycloaddition and their FTIR, 1H, 13C and 15N NMR spectra were measured and assigned. Single crystals were grown for five compounds and their X-ray data were obtained. The electronic structure and the conformations were calculated by the semi-empirical AM1 method. Using correlations between the spectral, empirical and theoretical structural data, the transmission of substituent effects and the preferential conformation connected with the consecutive double nitrogen inversion and regarding the mutual orientation of NH and CO bonds were investigated. The results are compared with those for a previously reported series of analogous ethyl 2-arylcarbamoyl-4,5-dimethyl-1,2,3,6-tetrahydropyridazine-1-carboxylates. Copyright © 2001 John Wiley & Sons, Ltd. [source] A systematic study of low-mass X-ray binaries in the M31 globular cluster systemMONTHLY NOTICES OF THE ROYAL ASTRONOMICAL SOCIETY, Issue 4 2010Mark B. Peacock ABSTRACT We investigate low-mass X-ray binaries (LMXBs) in the M31 globular cluster (GC) system using data from the 2XMMi catalogue. These X-ray data are based on all publicly available XMM,Newton observations of the galaxy. This new survey provides the most complete and homogeneous X-ray survey of M31's GCs to date, covering >80 per cent of the confirmed old clusters in the galaxy. We associate 41 X-ray sources with confirmed old clusters in the recent M31 cluster catalogue of Peacock et al. Comparing these data with previous surveys of M31, it is found that three of these clusters are newly identified, including a bright transient source in the cluster B128. Four additional clusters, that are not detected in these 2XMMi data, have previously been associated with X-ray sources from Chandra or ROSAT observations. Including these clusters, we identify 45 clusters in M31 which are associated with X-ray emission. By considering the latest optical GC catalogues, we identify that three of the previously proposed X-ray clusters are likely to be background galaxies and two have stellar profiles. We consider the properties of LMXB hosting clusters and confirm significant trends between the presence of an LMXB and the metallicity, luminosity and stellar collision rate of a cluster. We consider the relationship between the luminosity and stellar collision rate of a cluster and note that LMXB hosting clusters have higher than average stellar collision rates for their mass. Our findings strongly suggest that the stellar collision rate is the dominant parameter related to the presence of LMXBs. This is consistent with the formation of LMXBs in GCs through dynamical interactions. [source] Are fossil groups a challenge of the cold dark matter paradigm?MONTHLY NOTICES OF THE ROYAL ASTRONOMICAL SOCIETY, Issue 2 2009Stefano Zibetti ABSTRACT We study six groups and clusters of galaxies suggested in the literature to be ,fossil' systems (i.e. to have luminous diffuse X-ray emission and a magnitude gap of at least 2 mag R between the first and the second ranked member within half of the virial radius), each having good quality X-ray data and Sloan Digital Sky Survey (SDSS) spectroscopic or photometric coverage out to the virial radius. The poor cluster AWM 4 is clearly established as a fossil system, and we confirm the fossil nature of four other systems (RX J1331.5+1108, RX J1340.6+4018, RX J1256.0+2556 and RX J1416.4+2315), while the cluster RX J1552.2+2013 is disqualified as fossil system. For all systems, we present the luminosity functions within 0.5 and 1 virial radius that are consistent, within the uncertainties, with the universal luminosity function of clusters. For the five bona fide fossil systems, having a mass range 2 × 1013,3 × 1014 M,, we compute accurate cumulative substructure distribution functions (CSDFs) and compare them with the CSDFs of observed and simulated groups/clusters available in the literature. We demonstrate that the CSDFs of fossil systems are consistent with those of normal observed clusters and do not lack any substructure with respect to simulated galaxy systems in the cosmological , cold dark matter (,CDM) framework. In particular, this holds for the archetype fossil group RX J1340.6+4018 as well, contrary to earlier claims. [source] Structures of the magnetoionic media around the Fanaroff,Riley Class I radio galaxies 3C 31 and Hydra AMONTHLY NOTICES OF THE ROYAL ASTRONOMICAL SOCIETY, Issue 2 2008R. A. Laing ABSTRACT We use high-quality Very Large Array (VLA) images of the Fanaroff,Riley Class I radio galaxy 3C 31 at six frequencies in the range 1365,8440 MHz to explore the spatial scale and origin of the rotation measure (RM) fluctuations on the line of sight to the radio source. We analyse the distribution of the degree of polarization to show that the large depolarization asymmetry between the north and south sides of the source seen in earlier work largely disappears as the resolution is increased. We show that the depolarization seen at low resolution results primarily from unresolved gradients in a Faraday screen in front of the synchrotron-emitting plasma. We establish that the residual degree of polarization in the short-wavelength limit should follow a Burn law and we fit such a law to our data to estimate the residual depolarization at high resolution. We discuss how to interpret the structure function of RM fluctuations in the presence of a finite observing beam and how to address the effects of incomplete sampling of RM distribution using a Monte Carlo approach. We infer that the observed RM variations over selected areas of 3C 31, and the small residual depolarization found at high resolution, are consistent with a power spectrum of magnetic fluctuations in front of 3C 31 whose power-law slope changes significantly on the scales sampled by our data. The power spectrum P(f) can only have the form expected for Kolmogorov turbulence [P(f) ,f,11/3] on scales ,5 kpc. On larger scales, we find . We briefly discuss the physical interpretation of these results. We also compare the global variations of RM across 3C 31 with the results of three-dimensional simulations of the magnetic-field fluctuations in the surrounding magnetoionic medium. We infer that the RM variation across 3C 31 is qualitatively as expected from relativistic-jet models of the brightness asymmetry wherein the apparently brighter jet is on the near side of the nucleus and is seen through less magnetoionic material than the fainter jet. We show that our data are inconsistent with observing 3C 31 through a spherically symmetric magnetoionic medium, but that they are consistent with a field distribution that favours the plane perpendicular to the jet axis , probably because the radio source has evacuated a large cavity in the surrounding medium. We also apply our analysis techniques to the case of Hydra A, where the shape and the size of the cavities produced by the source in the surrounding medium are known from X-ray data. We emphasize that it is essential to account for the potential exclusion of magnetoionic material from a large volume containing the radio source when using the RM variations to derive statistical properties of the fluctuations in the foreground magnetic field. [source] Anomalous SZ contribution to three-year WMAP dataMONTHLY NOTICES OF THE ROYAL ASTRONOMICAL SOCIETY, Issue 3 2007R. M. Bielby ABSTRACT We first show that the new Wilkinson Microwave Anisotropy Probe (WMAP) 3-yr data confirm the detection by Myers et al. of an extended SZ signal centred on 606 Abell (ACO) clusters with richness class, R, 2. Our results also show SZ decrements around APM and 2MASS groups at increased significance than previously detected. We then follow the approach of Lieu, Mittaz & Zhang and compare the stacked WMAP results for the decrement in 31 clusters with ROSAT X-ray profiles where Lieu et al. found on average less SZ decrement in the WMAP 1-yr data than predicted. We confirm that in the 3-yr data these same clusters again show less SZ decrement than the X-ray data predict. We then analysed the WMAP results for the 38 X-ray clusters with OVRO/BIMA measured SZ decrements as presented by Bonamente et al.. We again find that the average decrement is measured to be significantly less (5.5,) than predicted by the Chandra X-ray data. Thus while we confirm the original detection of an extended SZ effect by Myers et al., these X-ray comparisons may now suggest that the central SZ amplitudes detected by WMAP may actually be lower than expected. One possible explanation is that there is contamination of the WMAP SZ signal by radio sources in the clusters but we argue that this appears implausible. We then consider the possibility that the SZ decrement has been lensed away by foreground galaxy groups. Such a model predicts that the SZ decrement should depend on cluster redshift. A reduction in the SZ decrement with redshift is suggested from the ACO cluster sample and also from comparing the samples of Lieu et al. and Bonamente et al.. However, the mass power spectrum would require a far higher amplitude than currently expected if lensing was to explain the SZ deficit in high-redshift clusters. [source] The XMM-SSC survey of hard-spectrum XMM,Newton sources , I. Optically bright sourcesMONTHLY NOTICES OF THE ROYAL ASTRONOMICAL SOCIETY, Issue 4 2007M. J. Page ABSTRACT We present optical and X-ray data for a sample of serendipitous XMM,Newton sources that are selected to have 0.5,2 versus 2,4.5 keV X-ray hardness ratios which are harder than the X-ray background. The sources have 2,4.5 keV X-ray flux ,10,14 erg cm,2 s,1, and in this paper we examine a subsample of 42 optically bright (r < 21) sources; this subsample is 100 per cent spectroscopically identified. All but one of the optical counterparts are extragalactic, and we argue that the single exception, a Galactic M star, is probably a coincidental association rather than the correct identification of the X-ray source. The X-ray spectra of all the sources are consistent with heavily absorbed power laws (21.8 < log NH < 23.4), and all of them, including the two sources with 2,10 keV intrinsic luminosities of <1042 erg s,1, appear to be absorbed active galactic nuclei (AGN). The majority of the sources show only narrow emission lines in their optical spectra, implying that they are type 2 AGN. Three sources have 2,10 keV luminosities of >1044 erg s,1, and two of these sources have optical spectra which are dominated by narrow emission lines, that is, are type 2 QSOs. Only a small fraction of the sources (7/42) show broad optical emission lines, and all of these have NH < 1023 cm,2. This implies that ratios of X-ray absorption to optical/ultraviolet extinction equivalent to >100 times the Galactic gas-to-dust ratio are rare in AGN absorbers (at most a few per cent of the population), and may be restricted to broad absorption line QSOs. Seven objects appear to have an additional soft X-ray component in addition to the heavily absorbed power law; all seven are narrow emission-line objects with z < 0.3 and 2,10 keV intrinsic luminosities <1043 erg s,1. We consider the implications of our results in the light of the AGN unified scheme. We find that the soft components in narrow-line objects are consistent with the unified scheme provided that >4 per cent of broad-line AGN (BLAGN) have ionized absorbers that attenuate their soft X-ray flux by >50 per cent. In at least one of the X-ray-absorbed BLAGN in our sample the X-ray spectrum requires an ionized absorber, consistent with this picture. [source] Chandra monitoring observations of the ultraluminous X-ray source NGC 5204 X-1MONTHLY NOTICES OF THE ROYAL ASTRONOMICAL SOCIETY, Issue 4 2006T. P. Roberts ABSTRACT We report the results of a two-month campaign conducted with the Chandra X-ray observatory to monitor the ultraluminous X-ray source (ULX) NGC 5204 X-1. This was composed of a 50-ks observation, followed by ten 5-ks follow-ups spaced initially at ,3, then at ,10-d intervals. The ULX flux is seen to vary by factors ,5 on time-scales of a few days, but no strong variability is seen on time-scales shorter than an hour. There is no evidence for a periodic signal in the X-ray data. An examination of the X-ray colour variations over the period of the campaign shows the ULX emission consistently becomes spectrally harder as its flux increases. The X-ray spectrum from the 50-ks observation can be fitted by a number of disparate spectral models, all of which describe a smooth continuum with, unusually for a ULX, a broad emission feature evident at 0.96 keV. The spectral variations, both within the 50-ks observation and over the course of the whole campaign, can then be explained solely by variations in the continuum component. In the context of an optically thick corona model (as found in other recent results for ULXs) the spectral variations can be explained by the heating of the corona as the luminosity of the ULX increases, consistent with the behaviour of at least one Galactic black hole system in the strongly Comptonized very high state. We find no new evidence supporting the presence of an intermediate-mass black hole in this ULX. [source] Relativistic ionized accretion disc models of MCG,6-30-15MONTHLY NOTICES OF THE ROYAL ASTRONOMICAL SOCIETY, Issue 2 2001D.R. Ballantyne We present results from fitting of ionized accretion disc models to three long ASCA observations of the Seyfert 1 galaxy MCG,6-30-15. All three data sets can be fitted by a model consisting of ionized reflection from the inner region of the accretion disc (with twice solar Fe abundance) and a separate disc-line component from farther out on the disc. The disc-line is required to fit the height of the observed Fe K, line profile. However, we show that a much simpler model of reflection from a very weakly ionized constant-density disc also fits the data. In this case only a single cold Fe K, line at 6.4 keV is required to fit the observed line. The ionized disc models predict that O viii K,, C vi K,, Fe xvii L, and Fe xviii L, lines will appear in the soft X-ray region of the reflection spectrum, but are greatly blurred as a result of Compton scattering. The equivalent width (EW) of O viii K, is estimated to be about 10 eV and seems to be as strong as the blend of the Fe L lines. This result creates difficulty for the claim of a strong relativistic O viii line in the XMM - Newton grating spectrum of MCG,6-30-15, although we cannot strictly rule it out since MCG,6-30-15 was in an anomalously low state during that observation. We find that increasing the O abundance or breaking the continuum below 2 keV will not significantly strengthen the line. The second Fe K, line component in the ionized disc model may arise from neutral reflection from a flared disc, or from a second illumination event. The data cannot distinguish between the two cases, and we conclude that single-zone ionized disc models have difficulty fitting these hard X-ray data of MCG,6-30-15. [source] X-ray constrained unrestricted Hartree,Fock and Douglas,Kroll,Hess wavefunctionsACTA CRYSTALLOGRAPHICA SECTION A, Issue 1 2010Martin Hudák The extension of the X-ray constrained (XC) wavefunction approach to open-shell systems using the unrestricted Hartree,Fock formalism is reported. The XC method is also extended to include relativistic effects using the scalar second-order Douglas,Kroll,Hess approach. The relativistic effects on the charge and spin density on two model compounds containing the copper and iron atom are reported. The size of the relativistic effects is investigated in real and reciprocal space; in addition, picture-change effects are investigated and discussed for the isolated Cu atom. It is found that the relativistic terms lead to changes in the densities that are much smaller than those from the X-ray constraint. Nevertheless, the use of the relativistic corrections in the ab initio model always leads to an improvement in the agreement statistics. An interesting result of the unrestricted XC technique is the possibility of obtaining experimentally derived spin densities from X-ray data. [source] Towards the best model for H atoms in experimental charge-density refinementACTA CRYSTALLOGRAPHICA SECTION A, Issue 4 2009Anna A. Hoser The consequences of different treatments of H atoms in experimental charge-density studies are discussed. Geometric and topological parameters obtained after applying four different H-atom models in multipolar refinement on high-resolution X-ray data only were compared with the results obtained for a reference joint high-resolution X-ray/neutron refinement. The geometry and the topological critical point and integrated parameters closest to the reference values were obtained after a mixed refinement (high-order refinement of heavy atoms, low-angle refinement of H atoms and elongation of the X,H distance to the average neutron bond lengths) supplemented by an estimation of the anisotropic thermal motions of H atoms using the SHADE program. Such a procedure works very well even for strong hydrogen bonds. The worst fit to the reference results for both critical point and integrated parameters was obtained when only the standardization to the average neutron X,H distances was applied. The non-H-atom parameters are also systematically influenced by the H-atom modeling. In order to compare topological and integrated properties calculated for H and non-H atoms in multipolar refinement when there are no neutron data, the same treatment of H atoms (ideally the mixed refinement + estimated anisotropic atomic displacement parameters for H atoms) should be applied. [source] Dynamics of molecules in crystals from multi-temperature anisotropic displacement parameters.ACTA CRYSTALLOGRAPHICA SECTION A, Issue 5 2000A new model for analysing the temperature evolution of anisotropic displacement parameters (ADP's) is presented. It allows for a separation of temperature-dependent from temperature-independent contributions to ADP's and provides a fairly detailed description of the temperature-dependent large-amplitude molecular motions in crystals in terms of correlated atomic displacements and associated effective vibrational frequencies. It can detect disorder in the crystal structure, systematic error in the diffraction data and the effects of non-spherical electron-density distributions on ADP's in X-ray data. The analysis requires diffraction data measured at multiple temperatures. [source] Intersubsystem chemical bonds in the misfit layer compounds (LaS)1.13TaS2 and (LaS)1.14NbS2ACTA CRYSTALLOGRAPHICA SECTION B, Issue 2 2002Andreas Jobst The modulated structures of incommensurate composite crystals (La0.912S)1.13TaS2 at room temperature and of (La0.949S)1.14NbS2 at T = 115,K are refined against high-resolution X-ray data. The compounds are isostructural with superspace group F,m2m(,,0,0)00s. For (LaS)1.13TaS2, lattice parameters of the first subsystem TaS2 were obtained as a = 3.2922,(1), b = 5.7776,(2) and c = 23.013,(2),Å. For the second subsystem LaS, the same b and c parameters were found, but a = 5.8090,(8),Å. Refinements led to a final structure model with R = 0.036 for 4767 observed unique reflections (R = 0.023 for 2147 main reflections, R = 0.099 for 1554 first-order satellites and R = 0.112 for 1042 second-order satellites). The final model includes modulation parameters up to the second-order harmonics for the displacements of the atoms, for the occupational parameters and for the temperature parameters. A clear correlation is found between the relative positions of the subsystems, the displacement modulation, the occupational modulation and the modulation of the temperature parameters. The analysis shows that the variations in environments are resolved by correlated variations in the temperature factors. For (LaS)1.14NbS2, lattice parameters at T = 115,K of the NbS2 subsystem were obtained as a = 3.3065,(4), b = 5.7960,(5) and c = 22.956,(3),Å. For the LaS subsystem, the same values for b and c were obtained, but a = 5.7983,(7),Å. Refinements led to a final structure model with R = 0.048 for 5909 observed unique reflections (R = 0.034 for 2528 main reflections, R = 0.092 for 2171 first-order satellites and R = 0.113 for 1103 second-order satellites). The final structure model is similar to that of (LaS)1.13TaS2. In particular, it is found that the values of the modulation parameters are almost equal and it is concluded that the modulations are independent of the temperature and the replacement of Ta with Nb, and thus represent a general mechanism of resolving the strain between the mutually incommensurate layers. [source] Structure of Nd10W22O81 from high-resolution electron microscopy and X-ray powder diffractionACTA CRYSTALLOGRAPHICA SECTION B, Issue 1 2001Carl Grenthe The crystal structure of Nd10W22O81, neodymium tungstate, has been determined using a combination of high-resolution transmission electron microscopy and X-ray powder diffraction methods. The unit-cell dimensions determined from X-ray data are a = 3.8613,(1), b = 35.9431,(1), c = 21.8900,(1),Å, V = 3038.05,Å3, Z = 2, space group Pbcm. The structure is built up of pentagonal columns (PCs) connected to ReO3 -type fragments consisting of three octahedra, thus forming W9O32 units. These units form `pillars' along a. These `pillars' are joined by pairs of tilted octahedra (W2O11 groups) to form corrugated layers perpendicular to b. The Nd atoms are located in the space between these layers and form the only link between them. Interstitial O atoms are located between two of the Nd atoms. The formula Nd10W22O81 can thus be alternatively given as Nd5W11O39,+,x (x, 1.5), where x represents the interstitial O atoms. Nd10W22O81 is a new type of PC structure. [source] A novel route to perovskite lead zirconate titanate from glycolate precursors via the sol,gel processAPPLIED ORGANOMETALLIC CHEMISTRY, Issue 2 2008N. Tangboriboon Abstract A perovskite lead zirconate titanate was synthesized by the sol-gel process, using lead glycolate, sodium tris(glycozirconate) and titanium glycolate as the starting precursors. For the mole ratio Pb:Zr:Ti of 1:0.5:0.5 [Pb(Zr0.5Ti0.5)O3], TGA-DSC thermal analysis indicated that the percentage of ceramic yield was 55.8, close to the calculated chemical composition value of 49.5. The exothermic peak occurred at 268 °C below the theoretical Curie temperature of 400 °C. The pyrolysis of Pb(Zr0.5Ti0.5)O3 of the perovskite phase was investigated in terms of calcination temperature and time. The structure obtained was of the tetragonal form when calcined at temperatures below 400 °C; it transformed to the tetragonal and the cubic forms of the perovskite phase on calcination above the Curie temperature, as verified by X-ray data. The lead zirconate titanate synthesized and calcined at 400 °C for 1 h had the highest dielectric constant, the highest electrical conductivity and the dielectric loss tangent of 10 190, 0.803 × 10,3 (,.m),1 and 1.513 at 1000 Hz, respectively. The lead zirconate titanate powder synthesized has potential applications as an electronic material. Copyright © 2008 John Wiley & Sons, Ltd. [source] Tetrastrontium dimanganese copper nonaoxide, Sr4Mn2CuO9ACTA CRYSTALLOGRAPHICA SECTION C, Issue 10 2002Ahmed El Abed Single crystals of Sr4Mn2.09Cu0.91O9 have been grown by flux synthesis and the structure, closely related to the hexagonal perovskite 2H, was solved from single-crystal X-ray data in space group P321. The structure of Sr4Mn2CuO9 is composed of chains of face-sharing polyhedra with a sequence of two octahedra and one trigonal prism. The octahedra are filled by Mn atoms and the Cu atoms are randomly distributed at the centres of the square faces of the trigonal prism. A stacking fault is observed within one of the two chains, which can be attributed to a shifting of the chain along the c axis. [source] Inclusion of weak high-resolution X-ray data for improvement of a group II intron structureACTA CRYSTALLOGRAPHICA SECTION D, Issue 9 2010Jimin Wang It is common to report the resolution of a macromolecular structure with the highest resolution shell having an averaged I/,(I) , 2. Data beyond the resolution thus defined are weak and often poorly measured. The exclusion of these weak data may improve the apparent statistics and also leads to claims of lower resolutions that give some leniency in the acceptable quality of refined models. However, the inclusion of these data can provide additional strong constraints on atomic models during structure refinement and thus help to correct errors in the original models, as has recently been demonstrated for a protein structure. Here, an improved group II intron structure is reported arising from the inclusion of these data, which helped to define more accurate solvent models for density modification during experimental phasing steps. With the improved resolution and accuracy of the experimental phases, extensive revisions were made to the original models such that the correct tertiary interactions of the group II intron that are essential for understanding the chemistry of this ribozyme could be described. [source] Unambiguous determination of H-atom positions: comparing results from neutron and high-resolution X-ray crystallographyACTA CRYSTALLOGRAPHICA SECTION D, Issue 5 2010Anna S. Gardberg The locations of H atoms in biological structures can be difficult to determine using X-ray diffraction methods. Neutron diffraction offers a relatively greater scattering magnitude from H and D atoms. Here, 1.65,Å resolution neutron diffraction studies of fully perdeuterated and selectively CH3 -protonated perdeuterated crystals of Pyrococcus furiosus rubredoxin (D-rubredoxin and HD-rubredoxin, respectively) at room temperature (RT) are described, as well as 1.1,Å resolution X-ray diffraction studies of the same protein at both RT and 100,K. The two techniques are quantitatively compared in terms of their power to directly provide atomic positions for D atoms and analyze the role played by atomic thermal motion by computing the , level at the D-atom coordinate in simulated-annealing composite D-OMIT maps. It is shown that 1.65,Å resolution RT neutron data for perdeuterated rubredoxin are ,8 times more likely overall to provide high-confidence positions for D atoms than 1.1,Å resolution X-ray data at 100,K or RT. At or above the 1.0, level, the joint X-ray/neutron (XN) structures define 342/378 (90%) and 291/365 (80%) of the D-atom positions for D-rubredoxin and HD-rubredoxin, respectively. The X-ray-only 1.1,Å resolution 100,K structures determine only 19/388 (5%) and 8/388 (2%) of the D-atom positions above the 1.0, level for D-rubredoxin and HD-rubredoxin, respectively. Furthermore, the improved model obtained from joint XN refinement yielded improved electron-density maps, permitting the location of more D atoms than electron-density maps from models refined against X-ray data only. [source] Getting the best out of long-wavelength X-rays: de novo chlorine/sulfur SAD phasing of a structural protein from ATVACTA CRYSTALLOGRAPHICA SECTION D, Issue 3 2010Adeline Goulet The structure of a 14,kDa structural protein from Acidianus two-tailed virus (ATV) was solved by single-wavelength anomalous diffraction (SAD) phasing using X-ray data collected at 2.0,Å wavelength. Although the anomalous signal from methionine sulfurs was expected to suffice to solve the structure, one chloride ion turned out to be essential to achieve phasing. The minimal data requirements and the relative contributions of the Cl and S atoms to phasing are discussed. This work supports the feasibility of a systematic approach for the solution of protein crystal structures by SAD based on intrinsic protein light atoms along with associated chloride ions from the solvent. In such cases, data collection at long wavelengths may be a time-efficient alternative to selenomethionine substitution and heavy-atom derivatization. [source] | ||||||||||||||||