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PubMed1997

A multicopy modeling of the water distribution in macromolecular crystals.

A multicopy protocol is proposed for modeling macromolecular hydration using diffraction experimental data (X-ray or neutron) to search for a better description of delocalized water sites than that given by point water models. The model consists of one macro-molecule and several copies of each water molecule, refined simultaneously against diffraction data using molecular dynamics techniques. The protocol was applied to BPTI and an RNA tetradecamer. The sites defined by the different copies range from very ordered ones to continuous channels; they fit the density maps and agree with the diffraction amplitudes with an accuracy comparable with usual crystallographic methods. The delocalization of water in channels agrees with the high mobility observed in NMR experiments.

Aprotinin↗

PubMed1996

Time-of-flight Laue fiber diffraction studies of perdeuterated DNA.

The diffractometer SXD at the Rutherford Appleton Laboratory ISIS pulsed neutron source has been used to record high resolution time-of-flight Laue fiber diffraction data from DNA. These experiments, which are the first of their kind, were undertaken using fibers of DNA in the A conformation and prepared using deuterated DNA in order to minimise incoherent background scattering. These studies complement previous experiments on instrument D19 at the Institut Laue Langevin using monochromatic neutrons. Sample preparation involved drawing large numbers of these deuterated DNA fibers and mounting them in a parallel array. The strategy of data collection is discussed in terms of camera design, sample environment and data collection. The methods used to correct the recorded time-of-flight data and map it into the final reciprocal space fiber diffraction dataset are also discussed. Difference Fourier maps showing the distribution of water around A-DNA calculated on the basis of these data are compared with results obtained using data recorded from hydrogenated A-DNA on D19. Since the methods used for sample preparation, data collection and data processing are fundamentally different for the monochromatic and Laue techniques, the results of these experiments also afford a valuable opportunity to independently test the data reduction and analysis techniques used in the two methods.

Crystallography↗

PubMed2000

Crystallographic analysis of protein conformational changes in the bacteriorhodopsin photocycle.

A variety of neutron, X-ray and electron diffraction experiments have established that the transmembrane regions of bacteriorhodopsin undergo significant light-induced changes in conformation during the course of the photocycle. A recent comprehensive electron crystallographic analysis of light-driven structural changes in wild-type bacteriorhodopsin and a number of mutants has established that a single, large protein conformational change occurs within 1 ms after illumination, roughly coincident with the time scale of formation of the M(2) intermediate in the photocycle of wild-type bacteriorhodopsin. Minor differences in structural changes that are observed in mutants that display long-lived M(2), N or O intermediates are best described as variations of one fundamental type of conformational change, rather than representing structural changes that are unique to the optical intermediate that is accumulated. These observations support a model for the photocycle of wild-type bacteriorhodopsin in which the structures of the initial state and the early intermediates (K, L and M(1)) are well approximated by one protein conformation in which the Schiff base has extracellular accessibility, while the structures of the later intermediates (M(2), N and O) are well approximated by the other protein conformation in which the Schiff base has cytoplasmic accessibility.

Bacteriorhodopsins↗

PubMed2002

Room-temperature synthesis and crystal, magnetic, and electronic structure of the first silver copper oxide.

Ag(2)Cu(2)O(3) is the first known silver copper oxide. It was prepared by coprecipitation at room temperature and ambient pressure and shows an increased thermal stability compared with silver oxides. The crystal structure (tetragonal, a = 5.8862(2) A, c = 10.6892(4) A, Z = 4, I4(1)/amd) was refined from neutron and X-ray powder diffraction data, and it is related to that of the mineral paramelaconite (Cu(4)O(3)). In addition to a thorough characterization (chemical and TG analyses, XPS, crystal structure, and electrochemical, magnetic, and transport properties), we have carried out band structure calculations [extended Hückel tight binding (EHTB) and spin polarized density functional (DFT) band calculations] for the title silver copper oxide and for the related paramelaconite structure (Cu(II)-Cu(I) mixed-valence system) with special incidence into the magnetic behavior and coupling constants in these magnetically novel 3-D compounds. This new oxide represents an important precedent in solid state inorganic chemistry but also has potential interest concerning its magnetic, electrochemical, and catalytic properties.

Journal Article↗

PubMed2005

Crystal structure of stoichiometric YBa2Fe3O8.

The oxygen-nonstoichiometry locus in YBa2Fe3O(8+w) changes with the sign of w. The singularity at w = 0 is studied by Rietveld refinement of combined high-resolution, high-intensity neutron and synchrotron X-ray diffraction data collected at room temperature on red-colored stoichiometric YBa2Fe3O8. A residual disorder of oxygen atoms is identified in a concentration of 0.03 vacancy/interstitials per formula, with corresponding anisotropy in thermal displacements of oxygen neighbors. The disorder improves accommodation of trivalent iron over the two unequal coordination polyhedra and is not identical with the charged Frenkel disorder induced thermally. The symmetry of the cooperative magnetic order is Ib'am, with opposite moments of equal magnitude (4.07 micro(B) at 295 K) at the two iron sites.

Journal Article↗

PubMed2007

Atomic distributions in the gamma-brass structure of the Cu-Zn system: a structural and theoretical study.

The crystal structures, atomic distributions, and theoretical electronic structures of five different Cu5-xZn8+x gamma-brass compounds (x = -0.59(3), -0.31(3), 0.00(3), 0.44(3), and 0.79(3)) are reported with the goal of identifying chemical influences on the observed phase width. These structures have been refined by both neutron and X-ray powder diffraction to obtain accurate crystal chemical parameters. All compounds crystallize in the space group Iz3m (No. 217) (Z = 4), and the unit cell parameters are a = 8.8565(4), 8.8612(5), 8.8664(3), 8.8745(4), and 8.8829(7) A, respectively, for Cu5.59Zn7.41, Cu5.31Zn7.69, Cu5.00Zn8.00, Cu4.56Zn8.44, and Cu4.21Zn8.79. The results indicate specific site substitutions on both sides of the ideal composition "Cu5Zn8". In all cases, the 26-atom cluster building up the -brass structure shows a constant inner [Cu4Zn4] tetrahedral star with compositional variation occurring at the outer octahedron and cuboctahedron. First principles and semiempirical electronic structure calculations using both a COHP and Mulliken population analysis were performed to understand the observed compositional range and to address the "coloring problem" for the site preferences of Cu and Zn atoms for this series of compounds.

Journal Article↗

PubMed2006

Effect of structure and thermodynamic stability on the response of lanthanide stannate pyrochlores to ion beam irradiation.

The lanthanide stannates, Ln2Sn2O7, Ln=La-Lu and Y, have the isometric pyrochlore structure, A2B2O7, and their structural properties have been refined by Rietveld analysis of powder neutron and synchrotron X-ray diffraction data. In this study, the enthalpies of formation of selected stannate pyrochlores, Ln=La, Nd, Sm, Eu, Dy, and Yb, were measured by high-temperature oxide melt solution calorimetry. Their radiation response was determined by 1 MeV Kr2+ ion irradiation combined with in situ TEM observation over the temperature range of 25 to 1000 K. The enthalpy of formation from binary oxides of stannate pyrochlores became more endothermic (from -145 to -40 kJ/mol) as the size of the lanthanide in the A-site decreases. A more exothermic trend of the enthalpy of formation was observed in stannate pyrochlores with larger lanthanide ions, particularly La, possibly as a result of increased covalency in the Sn-O bond. In contrast to lanthanide titanate pyrochlores, Ln2Ti2O7, that are generally susceptible to radiation-induced amorphization and zirconate pyrochlores, Ln2Zr2O7, that are generally resistant to radiation-induced amorphization, the lanthanide stannate pyrochlores show a much greater variation in their response to ion irradiation. La, Nd, and Gd stannates experience the radiation-induced transformation to the aperiodic state, and the critical amorphization temperatures are approximately 960, 700, and 350 K, respectively. Y and Er stannate pyrochlores cannot be amorphized by ion beam irradiation, even at 25 K, and instead disorder to a defect fluorite structure. Comparison of the calorimetric and ion irradiation data for titanate, zirconate, and stannate pyrochlores reveals a strong correlation among subtle changes in crystal structure with changing composition, the energetics of the disordering process, and the temperature above which the material can no longer be amorphized. In summary, as the structure approaches the ideal, ordered pyrochlore structure, radiation-induced amorphization is more easily attained. This is consistent with an increasingly exothermic trend in the enthalpies of formation of pyrochlores from the oxides, that is, the greater the thermochemical stability of the pyrochlore structure, the more likely it will be amorphized upon radiation damage rather than recover to a disordered fluorite structure.

Journal Article↗

PubMed1980

The higher order structure of chicken erythrocyte chromosomes in vivo.

Recently eukaryotic chromosomes have been shown to consist of a repeating subunit, called the nucleosome. Although electron microscopy, neutron scattering and X-ray diffraction have been used to determine the low resolution structure of the nucleosome, these techniques have yielded little information about the disposition of nucleosomes within chromosomes. Electron microscopy has produced many models for chromosome structure based on uniform fibres of 150-500A diameter or on globular 'superbeads. Unfortunately the models are based on microscope images that fail to reveal the strong structural periodicities shown by X-ray scattering to be characteristic of isolated chromatin in solution. Moreover it has not been demonstrated that the chromosomes of living cells are composed of such fibres. We have used low-angle X-ray scattering to investigate the organization of chromosomes in vivo and to account for the previously observed inconsistencies in many X-ray and electron microscope observations. We report here that chicken erythrocytes have a 400 A periodicity due to a nuclear structure that is directly related to the 300 A side-by-side packing of chromosome fibres revealed by electron microscopy of embedded cells, and that this periodicity can be preserved in isolated nuclei provided that the proper buffers are used.

Animals↗

PubMed2001

Stable methane hydrate above 2 GPa and the source of Titan's atmospheric methane.

Methane hydrate is thought to have been the dominant methane-containing phase in the nebula from which Saturn, Uranus, Neptune and their major moons formed. It accordingly plays an important role in formation models of Titan, Saturn's largest moon. Current understanding assumes that methane hydrate dissociates into ice and free methane in the pressure range 1-2 GPa (10-20 kbar), consistent with some theoretical and experimental studies. But such pressure-induced dissociation would have led to the early loss of methane from Titan's interior to its atmosphere, where it would rapidly have been destroyed by photochemical processes. This is difficult to reconcile with the observed presence of significant amounts of methane in Titan's present atmosphere. Here we report neutron and synchrotron X-ray diffraction studies that determine the thermodynamic behaviour of methane hydrate at pressures up to 10 GPa. We find structural transitions at about 1 and 2 GPa to new hydrate phases which remain stable to at least 10 GPa. This implies that the methane in the primordial core of Titan remained in stable hydrate phases throughout differentiation, eventually forming a layer of methane clathrate approximately 100 km thick within the ice mantle. This layer is a plausible source for the continuing replenishment of Titan's atmospheric methane.

Journal Article↗

PubMed2004

Anomalous pressure dependence of the structure factor in 1,4-polybutadiene melts: a molecular dynamics simulation study.

Neutron scattering has shown the first diffraction peak in the structure factor of a 1,4-polybutadiene melt under compression to move to larger q values as expected but to decrease significantly in intensity. Simulations reveal that this behavior does not result from loss of structure in the polymer melt upon compression but rather from the generic effects of differences in the pressure dependence of the intermolecular and intramolecular contributions to the melt structure factor and differences in the pressure dependence of the partial structure factors for carbon-carbon and carbon-deuterium intermolecular correlations. This anomalous pressure dependence is not seen for protonated melts.

Journal Article↗

PubMed2000

Orientational ordering of N2O molecules adsorbed on graphite (0001): A novel commensurate pinwheel structure

The structure and orientational ordering of N2O molecules physisorbed on graphite (0001) is investigated applying x-ray, neutron, and low-energy electron diffraction techniques. Combining the results of the three techniques, we find that N2O forms a highly ordered, hexagonal, commensurate (sqrt[21]xsqrt[21])R10.89 degrees phase. The unit cell contains seven molecules which are arranged in a seven-sublattice pinwheel structure, unexpected for linear molecules on a hexagonal lattice. Potential energy calculations corroborate these results.

Journal Article↗

PubMed2000

Determination of the magnetic symmetry of hexagonal manganites by second harmonic generation

Optical second harmonic spectroscopy is introduced as a powerful supplement for the determination of complex magnetic structures. Experimental efforts are simplified and new degrees of freedom are opened. Thereby, some principal or technical restrictions of neutron or magnetic x-ray diffraction experiments are overcome. High spatial resolution leads to additional information about magnetically ordered matter. As an example, the noncollinear magnetic structure of the hexagonal manganites RMnO3 ( R = Sc, Y, Ho, Er, Tm, Yb, Lu) is analyzed. The results show that some earlier conclusions on their magnetic symmetry and properties should be revised.

Journal Article↗

PubMed2001

Transition from cage clathrate to filled ice: the structure of methane hydrate III.

The structure of a new methane hydrate has been solved at 3 GPa from neutron and x-ray powder diffraction data. It is a dihydrate in which a 3D H-bonded network of water molecules forms channels surrounding the methane molecules. The network is closely related to that of ice-Ih and the methane-water system appears to be the first in which a cage clathrate hydrate is transformed into an ice-related hydrate (a "filled ice").

Journal Article↗

PubMed2003

Oxygen stripes in La0.5Ca0.5MnO3 from ab initio calculations.

We investigate the electronic, magnetic, and orbital properties of La0.5Ca0.5MnO3 perovskite by means of an ab initio electronic structure calculation within the Hartree-Fock approximation. Using the experimental crystal structure reported by Radaelli et al. [Phys. Rev. B 55, 3015 (1997)]], we find a charge-ordering stripelike ground state. The periodicity of the stripes, and the insulating magnetic structure, consisting of antiferromagnetically coupled zigzag chains, are in agreement with neutron x-ray and electron diffraction experiments. However, the detailed structure is more complex than that envisaged by simple models of charge and orbital order on Mn d levels alone, and is better described as a charge-density wave of oxygen holes, coupled to the Mn spin/orbital order.

Journal Article↗

PubMed2003

Ca2MgWO6 from neutron and X-ray powder data.

The room-temperature structure of the B-site-ordered complex perovskite dicalcium magnesium tungstate, Ca(2)MgWO(6), has been determined by simultaneous Rietveld refinement of neutron and X-ray powder diffraction patterns. Ca(2)MgWO(6) is characterized by B-site ordering and an a(-)a(-)c(+)-type BO(6) octahedral tilt mechanism.

Journal Article↗

PubMed2006

Structure determination of A2M3+TaO6 and A2M3+NbO6 ordered perovskites: octahedral tilting and pseudosymmetry.

The room-temperature crystal structures of six A(2)M(3+)M(5+)O(6) ordered perovskites have been determined from neutron and X-ray powder diffraction data. Ba(2)YNbO(6) adopts the aristotype high-symmetry cubic structure (space group Fm\overline 3m, Z = 4). The symmetries of the remaining five compounds were lowered by octahedral tilting distortions. Out-of-phase rotations of the octahedra about the c axis were observed in Sr(2)CrTaO(6) and Sr(2)GaTaO(6), which lowers the symmetry to tetragonal (space group = I4/m, Z = 2, Glazer tilt system = a(0)a(0)c(-)). Octahedral tilting analogous to that seen in GdFeO(3) occurs in Sr(2)ScNbO(6), Ca(2)AlNbO(6) and Ca(2)CrTaO(6), which lowers the symmetry to monoclinic (space group P2(1)/n, Z = 2, Glazer tilt system = a(-)a(-)c(+)). The Sr(2)MTaO(6) (M = Cr, Ga, Sc) compounds have unit-cell dimensions that are highly pseudo-cubic. Ca(2)AlNbO(6) and Ca(2)CrTaO(6) have unit-cell dimensions that are strongly pseudo-orthorhombic. This high degree of pseudosymmetry complicates the space-group assignment and structure determination. The space-group symmetries, unit-cell dimensions and cation ordering characteristics of an additional 13 compositions, as determined from X-ray powder diffraction data, are also reported. An analysis of the crystal structures of 32 A(2)MTaO(6) and A(2)MNbO(6) perovskites shows that in general the octahedral tilt system strongly correlates with the tolerance factor.

Journal Article↗

PubMed1999

Structures des phases paraélectrique et ferroélectrique de Pb2KNb5O15.

The paraelectric and the ferroelectric/ferroelastic structures of Pb(2)KNb(5)O(15) have been refined by the Rietveld method from neutron and X-ray powder diffraction data. The paraelectric phase is tetragonal (space group P4/mbm) with lattice parameters a(t) = 12.646 (1) and c(t) = 3.9551 (2) Å at 790 K. The Pb- and K-atom distribution has been determined. It was established that the Pb atoms situated on the 15-coordinate sites are not on the special position (2mm) but are distributed over two disordered positions as in the tetragonal phase of Pb(2)KTa(5)O(15). The ferroelectric/ferroelastic phase is orthorhombic. The space group of the average structure is Cm2m and the lattice parameters are a(o) = 17.779 (2), b(o) = 18.015 (2), c(o) = 3.9209 (4) Å at 294 K and a(o) = 17.756 (1), b(o) = 18.019 (1), c(o) = 3.9141 (2) Å at 81 K. It is isostructural with the average ferroelectric/ferroelastic structure of PbNb(2)O(6). The orthorhombic distortion is of the same order but the Curie temperature is lowered by the substitution 2K(+)-Pb(2+). The structures of PbNb(2)O(6), PbTa(2)O(6), Pb(2)KNb(5)O(15) and Pb(2)KTa(5)O(15) are compared. The ferroelectric polarization of the niobates is due to both the Pb off-site position and the Nb displacements, which induce a distortion of the oxygen lattice. In PbTa(2)O(6), the oxygen-lattice distortion is very weak. The polarization seems to be due only to the Pb atom. In the tantalates the substitution 2K(+)-Pb(2+) should weaken the correlations between the Pb atoms and consequently suppress the ferroelectric transition. Only a local polarization should take place; this might be the origin of the dielectric relaxation observed in this compound.

Journal Article↗

PubMed1989

Hydration structure in natural DNA observed by thermal neutron scattering.

Films of highly oriented Na- and LiDNA showing the typical X-ray diffraction patterns for the A-, B-, and C-conformation have been investigated by elastic and quasielastic neutron scattering. Information concerning the question of the DNA-water interaction has been obtained by varying the parameters H2O/D2O contrast, humidity, and temperature. Main observations are: A coexistence of one- and three-dimensionally correlated DNA which shifts towards the one-dimensionally correlated C-conformation for high humidity; a coexistence of A-, B-, and C-conformation for NaDNA with a similar humidity dependence; a factor of two increase between the average degree of localization of water hydrogens compared with DNA hydrogens at 75% r.h. for NaDNA; a strong water contribution to layer peaks which are close to the susceptibility maximum of water; a strong temperature dependence of the axial repeat distance for C-DNA; broad quasielastic spectra around the inverse of this distance. The observations are interpreted in terms of a competition between finite three-dimensional correlation and an optimized spatial resonance of nearly one-dimensionally correlated DNA with the correlation of bulk water. The observations are compatible with the concept of water spine formation (Dickerson 1983). The interpretation emphasizes the dynamic character of this mechanism in the region of nearly one-dimensionally correlated DNA.

DNA↗