X-ray Intensity Data Research Articles

Electron Density Distribution in AgBr

The electron density distribution in AgBr was investigated on the basis of X-ray intensity data collected by single crystal diffractometry. It was verified from difference Fourier map that the charge tends to accumulate in the intermediate region between the neighbouring unlike atoms. The origin of the extra charge on the difference Fourier map is investigated in terms of the radial distribution of the valence electrons.It is pointed out that the estimated value of the diamagnetic susceptibility of AgBr based on the present result agrees consistently with the observed one.

The use of an imaging proportional counter in macromolecular crystallography

A multiwire proportional chamber known as an imaging proportional counter has been used to collect X-ray intensity data for the determination of several structures by molecular replacement or difference Fourier analysis and has provided data for numerous other macromolecular crystallographic projects. Results obtained with an imaging proportional counter mounted on a rotating-anode X-ray generator indicate that the detector produces accurate intensity information and that its reliability is high.

A diamond-anvil high-pressure cell for X-ray diffraction on a single crystal

A new diamond-anvil high-pressure cell is described which can be used in single-crystal X-ray diffraction instruments to collect X-ray intensity data from single-crystal samples up to hydrostatic pressures of about 10 GPa. A unique design allows two types of diffraction geometry to be applied in single-crystal high-pressure diffraction experiments. More than 85% of the Ewald sphere is accessible, and a continuous range of 2θ values is available from 0 up to about 160°. Pressure may be calibrated by the ruby fluorescence technique or by the use of an internal X-ray-standard single-crystal. The design of our diamond-anvil cell would allow, with little or no modification, operation at high and low temperatures, optical studies and powder diffractometer work.

Conformations of Acyclonucleosides: Crystal Structure of 9-(4-Hydroxybutyl)Guanine, an Analogue of Acyclovir

Abstract 9-(4-Hydroxybutyl)guanine is an analogue of acyclovir in which the ether oxygen is replaced by a methylene group. Crystals of the monohydrate belong to the monoclinic space group P21/n with a = 4.350 (1), b = 10.859 (1), c = 23.684 (4) Å, β = 90.65 (1)°. X-ray intensity data were measured with a diffractometer and the structure was determined by direct methods. Least-squares refinement converged at R = 0.055 for 1982 reflections. The side chain is fully extended and almost perpendicular to the guanine base.

Electron Density Distribution in β-AgI

The electron density distribution in β-AgI was investigated on the basis of X-ray intensity data obtained by single crystal diffractometry. Several broad peaks observed on the difference Fourier map indicate that β-AgI is not a highly ionic-bonded compound. The charge accumulation on Ag-I bond along the c -axis explains the existence of a low-lying TO mode and the fact that β-AgI is easily cleaved parallel to the hexagonal plane like a layered compound. Present result in the charge distribution suggests an importance of the d-s hybridization in hexagonal AgI as well as linear coordinated silver compounds.

Conformations of Ammonium 3-Deoxy-D-manno-2-octulosonate (KDO) and Methyl α- and β-Ketopyranosides of KDO: X-Ray Structure and1H NMR Analyses

Abstract Ammonium 3-deoxy-D-manno-2-octulosonate monohydrate (KDO) crystallizes in the orthorhombic space group P212121, and the cell dimensions are a - 6.9700(4)Å, b = 7.7230(4) Å, c = 23.4067 (12) Å. X-ray intensity data were measured on a diffractometer, and the structure was determined by direct methods. Least-squares refinement, which included all hydrogen atoms, converged at R = 0.034 for 1526 observed reflections. The pyranose ring exists in an almost perfect 5C2 (D) chair conformation. The COO-, 4-OH and 6-CHOHCH2OH groups are In equatorial orientation, while the 2-OH and 5-OH groups are axial. The solution conformations of the ammonium salts of methyl α- and β-ketopyranosides of KDO were determined by high-resolution 1H NMR spectroscopy. The conformation of the ethylene glycol side chain in the α-methyl glycopyranoside of KDO was found to be indistinguishable from that in the solid state. However, the solution conformation of the side chain is different in the β-anomer, possibly indicative of an intramolecular hydrogen bond between the 8-OH and carboxylate groups.

Structure and conformation of 2′,5′-anhydroarabinosylcytosine: X-ray, 1H nmr and 13C nmr analyses

Crystals of 2′,5′-anhydroarabinosylcytosine hemihydrate belong to the monoclinic space group P21. The cell dimensions are a = 9.643(2), b = 10.328(1), c = 10.544(2) Å, β = 94.55(1)°. X-ray intensity data were measured on a diffractometer and the structure was determined by direct methods. Least-squares refinement, which included all nucleoside hydrogen atoms, converged at R = 0.041 for 2298 observed reflections. The asymmetric unit contains two molecules of the nucleoside and one molecule of water. In both nucleoside molecules, the conformation about the glycosyl bond is and, with XCN values of 15.5(3) and 26.3(3)°, respectively. In the bicyclic sugar moiety, the arabinofuranose rings adopt a C(3′)exo/C(2′)endo conformation and are highly puckered (τm = 57°). The solution conformation was studied by 1H and 13C nmr spectroscopy. A difference nOe proton nmr spectrum and 3J(C,H) coupling constants reveal an anti conformation in solution, with torsion angles very similar to those obtained from X-ray analysis. A comparison of observed 3J(H,H) coupling constants with those calculated on the basis of a modified Karplus equation shows significant differences, probably due to the presence of the bicyclic system.

Structure Refinement of BaxTiO3(x=0.992) from X-ray Powder Intensity Data

BaxTiO3 prepared through coprecipitation method may contain vacancies in either Ba-position or Ti-position. Since by chemical analysis it has been ascertained that the mole content of Ti-ion is in excess of that required to maintain the stoichiometric ratio of Ba: Ti as 1:1 it is assumed that there occur vacancies in Ba-position in the structure of BaTiO3. On this assumption, when exact positional coordinates in the lattice structure, P4mmm, are determined on refinement of X-ray intensity data with respect to the calculated intensities, it is found that more agreeable results are obtained when atomic positions in the lattice structure are such that a certain portion of Ba-positions is lying vacant than when the ratio of Ba: Ti is 1:1. In this paper, the methodology adopted for structure refinement from powder diffraction data will be discussed at length, focussing on the various assumptions that are required to be made to simplify the procedure.

The stability and structure of [formula omitted

The stability of the phase Cs x[ Ti 2− x 4 □ x 4 ] O 4 , □ = vacancy, in the Cs 2OTiO 2 system has been studied in the temperature range 800−1120°C. The phase has a narrow range of homogeneity with 0.61 < x < 0.65. Structure refinements were carried out for X-ray intensity data from two crystals obtained from melts with TiO 2:CsO 0.5 molar ratios of 2.0 and 3.2. The crystals have orthorhombic symmetry, Immm, a 0 = 3.83, b 0 = 17.00, c 0 = 2.96 Å. The refinements are consistent with the structural model of Hervieu and Raveau ( Rev. Chim. Minér. 18, 642 (1981)) in which (010) corrugated layers of titanium-oxygen octahedra, containing disordered titanium vacancies, are separated by planes of cesium ions. Long-exposure precession photographs showed diffuse superlattice diffraction effects in the form of continuous streaks parallel to b∗ 0 . These have been analyzed in terms of models for two-dimensional ordering of the interlayer cesium ions. Annealing of melted samples below 700°C causes a transformation of the I-centered structure to a C-centered structure of the K x ( M y Ti 2− y )O 4 type in which 3-D ordering of cesium occurs.

Crystal structure analysis of cytochrome c' by the multiwavelength anomalous diffraction method using synchrotron radiation

A multiwavelength X-ray diffraction study was performed at 6 Å resolution on the native cytochrome c′ crystal from Rhodospirillum rubrum, which contains heme irons. The X-ray intensity data from the crystal were collected on a four-circle diffractometer with three wavelengths, λ1 = 1.077, λ2 = 1.730 and λ3 = 1.757 Å, using the synchrotron radiation produced by the storage ring in the Photon Factory, National Laboratory for High Energy Physics. λ2 and λ3 are above and below the energy of the K absorption edge of iron (λe = 1.743 Å) respectively, while λ1 is far from the edge. The positions of the two iron atoms in the crystal could be determined from the difference Patterson maps based on either the real or imaginary components of the anomalous scattering effect caused by iron. The best phase angles for the crystal were calculated from the X-ray intensity data measured with λ1 and λ2 by the method which is basically the same as the isomorphous replacement method. Although the resulting best phase angles differed 75° on the average from those obtained by the multiple isomorphous replacement method, the molecular boundary and α helices could be recognized on the electron density map.

X-ray and 1H nmr analyses of 5-(m-benzyloxybenzyl)-1-[(1,3-dihydroxy-2-propoxy)methyl]uracil, an acyclonucleoside inhibitor of uridine phosphorylase

The title compound crystallizes in the triclinic space group [Formula: see text] and the cell dimensions are a = 16.890(3), b = 9.586(2), c = 6.316(1) Å, α = 91.09(1), β = 93.50(1), γ = 93.04(1)°. X-ray intensity data were measured on a diffractometer, and the crystal structure was determined by direct methods. Least-squares refinement, which included all hydrogen atoms, converged at R = 0.056 for 3454 observed reflections. Adjacent six-membered rings are approximately perpendicular to one another. The glycosidic torsion angle [C(6)—N(1)—C(1′)—O(4′)] is 96.2(2)°. In the acyclic moiety, both C—OH bonds are gauche with respect to C(4′)—O(4′). The gauche conformation is also dominant in solution, as determined by high-resolution 1H nmr spectroscopy. Results of nuclear Overhauser experiments lead to conclusions about the flexibility of the molecule.

X-ray crystal structure analysis of tetrakis(indenyl) thorium

Th(C 9H 7) 4 crystallizes in space group Pna2 1 with cell dimensions a = 22.403(5), b = 36.034(7), c = 9.566(2) A ̊ . There are 12 molecules in the whole cell of which three are symmetrically independent. Three dimensional X-ray intensity data were collected with an Enraf-Nonius four-circle diffractometer. The structure was solved by direct methods, Fourier techniques and full-matrix refinement. The agreement factors are R = 0.04 and R w = 0.04 for 3468 independent reflections ( I ⩾ 1.5 σ( I)). The crystal structure exhibits stacking disorder, a simple basic pseudostructure being modulated over the b-axis to give the triple true cell. Coordination about each thorium atom is a slightly distorted tetrahedron. The Th-C distances to the five membered rings of the indenide ligands indicate trihapto character of the metal-carbon bonding.

Ionic conduction in one dimension: A structural study of the hollandite K1.54Mg0.77Ti7.23O16 over the range 133≤T≤919 K

Joint probability density functions (pdf) of the mobile K atom (and their corresponding pseudopotentials) have been obtained from seven x-ray (MoKα) intensity data sets collected on a one-dimensional conductor with the hollandite structure (K1.54Mg0.77Ti7.23O16; space group I4/m; Z=1). The data were collected at high resolution [(sin θ/λ)max ≥0.9 Å−1] and at several temperatures (133, 298, 387, 459, 540, 707, and 919 K) in order to determine the conduction mechanism. Two models of the K distribution within the strand of cavities making up the conduction tunnel have been refined. In the most complex model B [Rw(F) =0.02], up to four atomic positions are needed to describe the observed electron density. The pdfs show that—already at room temperature and within undamaged segments of the conduction tunnel—potassium ions diffuse at a high rate across the bottleneck between two neighboring cavities. Below about 430 K the potassium ions preferentially occupy sites shifted off the cavity center in the direction of the bottleneck; above this temperature the cavity center becomes the preferred location. At 298 K the potential barrier at the bottleneck amounts to 0.032(4) eV. In a plot of the cell constants vs T an inflection shows up at 387&amp;lt;T&amp;lt;459 K, indicating a second order transition. Within the same temperature interval we also observe a sharp break in a plot of U33 (refined from the one-atom model A) vs T. A comparative study of two other hollandites K1.92V8O16 and (Ba0.98Ca0.03 Zr0.02) [Al1.1 Ni0.48 Ti6.4] with different tunnel stoichiometry underscores the importance of the values of ionic density and charge in the conduction column to the conductivity.

Protein, DNA, and virus crystallography with a focused imaging proportional counter.

A set of programs has been developed for rapid collection of x-ray intensity data from protein and virus crystals with a commercially available two-dimensional focused geometry electronic detector. The detector is compact and portable, with unusually high spatial resolution comparable to that used in oscillation photography. It has allowed x-ray data collection on weakly diffracting crystals with large unit cells, as well as more conventional "diffractometer-quality" crystals. The quality of the data is compared with that from oscillation photography and automated diffractometry in the range of unit cells from 96.3 to 383.2 angstroms. Isomorphous and anomalous difference Pattersons, based on detector data, are shown for a variable surface glycoprotein mercury derivative and for a repressor-DNA bromine derivative, which has been solved at 7 angstroms with detector data only.

Crystallographic determination of lanthanide ion binding to troponin C

X-ray intensity data to 2.8 Å resolution were collected from each of three crystals of turkey skeletal troponin C(TnC) that had been soaked individually in solutions containing the lanthanide ions europium, thulium and lutetium. Each of the resulting difference electron density maps computed for the three data sets showed three lanthanide ion-binding sites on the TnC molecule. Two of the sites are approximately coincident with the Ca 2+ positions in binding loops III and IV and the third site is near the Ca 2+-free loop I. The mode of ion binding in loop I is different from that commonly observed for Ca 2+ in the Ca 2+-binding proteins.

Gold(I)-selenium bond: synthesis and x-ray structure of chloro(triphenylphosphine selenide)gold(I)

The crystal and molecular structures of chloro(triphenylphosphineselenide)gold(I), [(C6H5)3PSe]AuCl, have been determined from three-dimensional X-ray intensity data collected on a CAD4 diffractometer. The compound crystallizes in the triclinic space groupPl witha=9.322(3),b=10.639(5),c=9.252(3) A, α=104.74(4), β=99.52(3), γ=76.97(3)°, andZ=2. Atomic parameters were refined by full-matrix least-squares to anR value of 5.7% for 2591 observed reflections. This is one of the few known examples of linear gold(I) complexes having an Au-Se linkage. The Se-Au-Cl angle is 178.6(1)°, and the Au-Se and Au-Cl distances are 2.371(2) and 2.277(6) A, respectively. As expected, the Au-Se bond length is 0.10–0.18 A longer than the Au-S bond length observed in similar two-coordinate linear gold(I) complexes.

An intercomparison of spectral data processing techniques in PIXE

Least-squares fitting codes developed independently at five different laboratories are used to analyse PIXE spectra of a set of biological, environmental and geological specimens. A detailed comparison of the resulting five sets of X-ray intensity data reveals a remarkably good agreement among the five techniques, despite major differences in their methodologies. This conclusion strengthens PIXE's claim to have reached maturity as a trace element analysis technique.

Crystal structure and chirality of sodium tetrathionate dihydrate, Na2S4O6· 2H2O

The crystal structure of Na2S4O6 · 2H2O has been redetermined from three-dimensional X-ray intensity data and refined to R = 0.025 (Rw = 0.018) for 1620 observed reflections. The structure is monoclinic, space group C2, with a = 14.4726(5), b = 6.3716(3), c = 5.4402(3) Å, β = 105.53(1) °, Z = 2. Except for the chirality of the structure and the hydrogen positions, for which no information is given in the earlier work of Foss and Hordvik (1964), their structural model was confirmed by the present study. The tetrathionate anion possesses a two-fold symmetry axis. From the two independent S – S bonds of the anion the central bond is significantly shorter than the terminal one [2.019(1) Å versus 2.115(1) Å]. The S–S–S bond angle formed about the central S – S bond by the sulfur atoms is 89.55(2)°. The terminal SO3 groups of the anion have almost perfect trigonal symmetry [S–O: 1.447(1)–1.450(1) Å, O–S–O: 113.39(6)– 113.82(5)°]. The sodium cation is surrounded by six oxygen atoms in a distorted octahedral arrangement. [Na–O: 2.358(1)–2.465(1) Å]. By sharing opposite faces, columns of NaO6 octahedra are formed, which run parallel to b axis and are linked together through the sulfonate groups of the tetrathionate anions and through hydrogen bonds, in which the water molecules are involved. The chirality of the structure was determined with the Hamilton and the Bijvoet methods. Both indicated that the earlier structure proposal of Foss and Hordvik (1964) should be inversed for our crystal.

Crystal structure and infrared spectra of an inclusion compound of cyclotriveratrylene and water

A crystal grown by slow evaporation from a solution of cyclotriveratrylene (CTV) in toluene was found to be an inclusion compound with water as the only encaged guest. Its stoichiometry is C27H30O6•xH2O (x = 0.16) and it belongs to the monoclinic space group C2/c, with a = 24.216(21), b = 9.636(2), c = 23.117(4) Å, β = 118.08(5)°, Z = 8. X-ray intensity data were measured with a diffractometer and the structure was solved by direct methods. Least-squares refinement, which included all hydrogen atoms of the host molecule, converged at R = 0.046 for 3986 observed reflections. The geometry of the host molecule is compared to that of analogous structures and to cyclononatriene. Significant differences are ascribed to the effects of homoaromaticity and steric strain. Both the X-ray analysis and an FTIR study of the OH stretching show that the water molecules are weakly bound to the methoxy oxygen atoms of CTV. The molecular packing of CTV clathrates is discussed on the basis of crystallographic and spectroscopic evidence.

Arrangement of subunits in peanut lectin. Rotation function and chemical cross-linking studies.

X-ray intensity data from the native orthorhombic crystals of peanut lectin have been collected using oscillation photography. Rotation function studies using data up to a resolution of 4.5 A indicate that the four subunits in the molecule, which constitute the asymmetric unit in the crystals, are related to one another by three mutually perpendicular noncrystallographic 2-fold axes. Chemical cross-linking experiments in solution followed by sodium dodecyl sulfate gel electrophoresis, carried out in parallel, suggest that there is more than one type of intersubunit approach in the molecule. Rotation function and cross-linking studies thus show that the tetrameric molecule of peanut lectin is a dimer of a dimer. The two monomers in a dimer are related by a 2-fold axis. The two dimers are in turn related by another 2-fold axis perpendicular to the one that relates the two monomers in the dimer, endowing the molecule with 222 (D2) symmetry.