Calculated Structure Factors Research Articles

Structural Basis of Citrate-dependent and Heparan Sulfate-mediated Cell Surface Retention of Cobra Cardiotoxin A3

Anionic citrate is a major component of venom, but the role of venom citrate in toxicity other than its inhibitory effect on the cation-dependent action of venom toxins is poorly understood. By immobilizing Chinese hamster ovary cells in microcapillary tubes and heparin on sensor chips, we demonstrated that heparan sulfate-mediated cell retention of the major cardiotoxin (CTX) from the Taiwan cobra, CTX A3, near membrane surfaces is citrate-dependent. X-ray determination of a CTX A3-heparin hexasaccharide complex structure at 2.4 A resolution revealed a molecular mechanism for toxin retention in which heparin-induced conformational changes of CTX A3 lead to citrate-mediated dimerization. A citrate ion bound to Lys-23 and Lys-31 near the tip of loop II stabilizes hydrophobic contact of the CTX A3 homodimer at the functionally important loop I and II regions. Additionally, the heparin hexasaccharide interacts with five CTX A3 molecules in the crystal structure, providing another mechanism whereby the toxin establishes a complex network of interactions that result in a strong interaction with cell surfaces presenting heparan sulfate. Our results suggest a novel role for venom citrate in biological activity and reveal a structural model that explains cell retention of cobra CTX A3 through heparan sulfate-CTX interactions.

D−fCoulomb and quadrupole-strain interactions inDyB2C2observed by resonant x-ray scattering

Experimental evidence of the d-f Coulomb interaction responsible for the resonant x-ray scattering (RXS) from antiferroquadrupolar order in DyB2C2 is presented. The energy dependences of the RXS intensity with polarization analysis are analyzed by considering the interference between the resonances of dipolar (E1) and quadrupolar (E2) transition processes. It is found that the structure factors for the E1 and E2 processes have the same sign for sigma-pi' but the opposite sign for sigma-sigma' channel. This result, when compared with the calculated structure factors, means that the quadrupolar moments of the 4f and 5d electrons have opposite signs to each other. Interference between nonresonant Thomson scattering from the lattice distortion and the resonant scatterings is also studied and a direct coupling between 4f and the lattice is concluded.

Crystal Structure and Morphology of Poly(12-dodecalactone)

Poly(12-dodecalactone) (PDDL) crystals in the form of chain-folded lamellae were prepared by isothermal crystallization from a 1-hexanol solution. The lozenge-shaped crystals with and without spiral growth have been studied by transmission electron microscopy and atomic force microscopy. Wide-angle X-ray diffraction data, obtained from PDDL lamellae sedimented to form oriented mats and annealed solvent-cast film, were supplemented with morphological and structural data from electron microscopy. PDDL crystallizes as an orthorhombic form with a P2(1)2(1)2(1) space group and lattice constants of a = 0.746 +/- 0.001 nm, b = 0.500 +/- 0.001 nm, and c (chain axis) = 3.281 +/- 0.003 nm. There are two chains per unit cell, which existed in an antiparallel arrangement. The fiber repeat distance is appropriate for an all-trans backbone conformation for the straight stems. Molecular packing of this structure has been studied in detail, taking into account both diffraction data and energy calculations. The setting angles, with respect to the a axis, were +/-43 degrees for the corner and center chains according to intensity measurements and structure factor calculations. The optimized shift along the crystallographic c axis is 0.1c (0.328 nm). A final model was obtained to yield R = 0.180 with X-ray diffraction data and R = 0.162 with electron diffraction data. A brief comparison is also made with related polymer structures.

Colloidal Systems with Attractive Interactions: Evaluation of Scattering Data Using the Generalized Indirect Fourier Transformation Method

Different attractive interacting colloidal systems are characterized by means of static light scattering. As most of these samples are rather concentrated, multiple scattering is suppressed by partial contrast match and the use of very a thin sample cell (13 μm). This is possible with the laboratory built flat cell light scattering instrument, which is also capable of time-resolved measurements. The systems under investigation are oil-in-water emulsions with added polymer micelles or latex spheres, which give rise to depletion interaction. A second set of samples consists of electrostatically stabilized dense silica suspensions, which are destabilized by ionic strength or pH shift initiated by an in-situ reaction. The potential change from repulsive to attractive is measured time-resolved in real time. These suspensions are model systems for the so-called direct coagulation casting (DCC) method. Scattering data are evaluated using the generalized indirect Fourier transformation (GIFT) method. We added some new routines for calculating structure factors for attractively interacting systems to the already existing software package. We now can choose between a depletion interaction and an attractive square well potential, which was used for the DCC samples. The obtained results are in good agreement with the values known from preparation for the depletion samples and those predicted from DLVO calculations for the DCC series, respectively.

Structure of the Si(113) surface studied by surface X-ray diffraction

We carried out a grazing incidence X-ray diffraction analysis of the Si(1 1 3) 3 × 1 surface using synchrotron radiation. We compared the experimental structure factors obtained from the integrated intensities of the fractional-order reflections with the calculated structure factors of the dimerized structure model of Ranke. By minimizing the R-factor, we determined the position and the size of the pentagon in the 3 × 1 dimerized structure model of Ranke. In addition, we found that a model with randomly distributed interstitial atoms at the center of the pentagon gives a smaller R-factor value.

Free NH3 quantum rotations in Hofmann clathrates: structure factors and line widths studied by inelastic neutron scattering

Abstract Quantum rotations of NH 3 groups in Hofmann clathrates Ni–Ni–C 6 H 6 and Ni–Ni–C 12 H 10 have been studied using inelastic neutron scattering. Calculations of the dynamical structure factor for a free uniaxial quantum rotor reproduce the neutron scattering data with respect to their Q - and T -dependence as well as the relative intensities for the 0 → 1, 0 → 2 and 1 → 2 transitions. Though the effective NH 3 rotation constant is different from the gas phase value, the effective radius of rotation (i.e., the average distance of protons from the rotation axis) is equal or very close to the geometrical value r = 0.94 A for a NH 3 group. Comparing the experimental data with the calculated dynamical structure factor for the 0 → 3 transition it could be shown, that the corresponding transition line, in contrast to transitions between j = 0,1,2 levels measured so far, has a finite width at T = 0 K.

Unified study of electrical resistivity of simple and non-simple liquid metals

A model potential depending on an effective core radius but otherwise parameter free is used for the comparative study of electrical resistivity of simple and non-simple liquid metals. In the present paper electrical resistivity of simple and non-simple liquid metals have been calculated using Ziman’s formula, Ziman’s formula modified and used by Khajil and Tomak (Self consistent approximation) and t-matrix formulation given by Evans and Evans et al. Previously no one have reported such comparative study using pseudopotentials. In the electrical resistivity calculations we have used structure factor derived through charge hard sphere approximation. The beauty of this approximation is that it needs pseudopotential form factor for the calculation of structure factor. So this gives the better explanation of structure factor than any other approximations. From present investigations it is found that self consistent formulation results are excellently agrees with the experimental findings. A successful application is an evidence that our potential can predict wide class of physical properties of d and f shell metals as well as simple and non-simple metals.

Beyond locating the atoms towards addressing the electronic structure of crystals using advanced transmission electron microscopy

With the present focus on nanostructures, the role of the transmission electron microscope (TEM) as a research tool is becoming increasingly important. Among themajor strengths of TEM are the capability of obtaining diffraction patterns and electron energy loss spectra (EELS) from nanometer sized areas. In addition, advanced TEMmay serve as a supplement to synchrotron x-ray diffraction and absorption spectroscopy in efforts to study bonding and electronic structure of bulk materials. This is in particular the case when only small-grained polycrystalline samples are available, but TEM may also provide valuable input in studies of single crystals. For example, the near edge fine structure at EELS absorption edges was used to locate different valence states of Fe within the unit cell of a mixed valence crystal already two decades ago [1], and more recently precision convergent beam electron diffraction (CBED)was used in combination with x-ray diffraction to study the spatial distribution of valence electrons in Cu2O [2]. In this presentation, we report our recent study of the MgB2 where we use both EELS [3] and CBED [4] to gain insight into the electronic structure of this new superconductor with Tc=39K. Using angle-resolved EELS we studied the fine structure at the K-edge of boron in order to probe the empty boron pxy and pz states near the Fermi level in this anisotropic hexagonal crystal. Similar information can be obtained using polarized soft x-rays in absorption spectroscopy (XANES) if sufficiently large single crystals become available. Using quantitative CBED we determine the structure factors at short g-vectors. These structure factors at short g-vectors, which are strongly influenced by the valence electron redistribution, can be determined with very high accuracy using electron diffraction. For example, after converting to x-ray structure factors, we measure F001 of MgB2 to be 2.15±0.03 electrons while the calculated structure factor for the procrystal differs 20 standard deviations from this value (2.75 electrons).We also did DFT calculations, and found good agreement between experimental and theoretical structure factors.

Crystal Structure and Morphology of Poly(11-undecalactone) Solution-Grown Single Crystals

Solution-grown lamellar single crystals of poly(11-undecalactone) (PUDL) have been prepared in 1-hexanol. The lozenge and hexagonal-shaped single crystals were grown simultaneously, and these crystals gave well-resolved electron diffraction diagrams from which the orthogonal reciprocal lattice with the parameters a* = 1.346 nm-1, b* = 2.004 nm-1, and γ* = 90° could be determined. The growth faces of both crystals were considered as mainly {110}, and the average chain-folding direction was parallel to these growth planes, suggesting that the hexagonal crystal has pseudohexagonal symmetry but actual orthogonal packing of the PUDL molecules. The diffraction analysis combined with X-ray and electron diffraction diagrams indicated that PUDL crystallized in the orthorhombic system which had the lattice parameters of a = 0.743 ± 0.001 nm, b = 0.499 ± 0.001 nm, and c(chain axis) = 1.519 ± 0.003 nm. There are two chains per unit cell, which existed in an antiparallel arrangement. The fiber repeat distance is appropriate for an all-trans backbone conformation for the straight stems. Molecular packing of this structure has been studied in detail, taking into account both diffraction data and energy calculations. The setting angles, with respect to a axis, were 59° for the corner and center chains according to intensity measurements and structure factor calculations. A final model was obtained to yield R = 0.173 with X-ray diffraction data and R = 0.152 with electron diffraction data. A brief comparison is also made with related polymer structures.

Structure of the Si(1 1 3) surface studied by surface X-ray diffraction

We carried out a grazing incidence X-ray diffraction analysis of the Si(113) 3 × 1 surface using synchrotron radiation. We compared the experimental structure factors obtained from the integrated intensities of the fractional-order reflections with the calculated structure factors of the dimerized structure model of Ranke. By minimizing the R-factor, we determined the position and the size of the pentagon in the 3 × 1 dimerized structure model of Ranke. In addition, we found that a model with randomly distributed interstitial atoms at the center of the pentagon gives a smaller R-factor value.

Analytical Solution of the Ornstein–Zernike Equation for the Structure Factor of Ordered Plasmas Using Sogami–Ise Potential

An analytic solution of Ornstein–Zernike (OZ) equation for the structure factor for plasmas has been obtained using Sogami–Ise (SI) potential amongst plasma particles that contains attractive tail at large distances. Pastore et al. 's criterion and a characteristic feature of the pair interaction potential have helped in reaching to the final expressions. The calculated structure factors compare well with that obtained by using Pastore et al. 's expressions derived with the Derjaguin, Landau, Verwey and Overbeek (DLVO) potential in case of H + -plasmas. The excess energy per particle and the values of the compressibility determined with the help of the calculated structure factors in the limit of momentum transfer becoming zero have been reported.

Comparative compressibility and equation of state of orthorhombic and tetragonal edingtonite

The high-pressure (HP) behaviour of a natural orthorhombic and tetragonal edingtonite from Ice River, Canada, has been investigated using in situ single-crystal X-ray diffraction. The two isothermal equations of state up to 6.74(5) GPa were determined. V 0, KT0 and K′ refined with a third-order Birch–Murnaghan equation of state (BM-EoS) are: V 0 = 598.70(7) A3, KT0 = 59(1) GPa and K′=3.9(4) for orthorhombic edingtonite and V 0 = 600.9(2) A3, KT0 = 59(1) GPa and K′=4.2(5) for tetragonal edingtonite. The experiments were conducted with nominally hydrous pressure penetrating transmitting medium. No overhydration effect was observed within the pressure range investigated. At high-pressures the main deformation mechanism is represented by cooperative rotation of the secondary building unit (SBU).Si/Al distribution slightly influences the elastic behaviour of the tetrahedral framework: the SBU bulk moduli are 125(8) GPa and 111(4) GPa for orthorhombic and tetragonal edingtonite, respectively. Extra-framework contents of both zeolites show an interesting behaviour under HP conditions: the split Ba2 site at P >2.85 GPa is completely empty; only the position Ba1 is occupied. Electronic Supplementary Material. Supplementary material to this paper (Observed and calculated structure factors) is available in electronic form at http://dx.doi.org/10.1007/s00269-004-0394-y.

High Resolution Crystal Structures of Piscine Transthyretin Reveal Different Binding Modes for Triiodothyronine and Thyroxine

Transthyretin (TTR) is an extracellular transport protein involved in the distribution of thyroid hormones and vitamin A. So far, TTR has only been found in vertebrates, of which piscine TTR displays the lowest sequence identity with human TTR (47%). Human and piscine TTR bind both thyroid hormones 3,5,3'-triiodo-l-thyronine (T(3)) and 3,5,3',5'-tetraiodo-l-thyronine (thyroxine, T(4)). Human TTR has higher affinity for T(4) than T(3), whereas the reverse holds for piscine TTR. X-ray structures of Sparus aurata (sea bream) TTR have been determined as the apo-protein at 1.75 A resolution and bound to ligands T(3) and T(4), both at 1.9 A resolution. The apo structure is similar to human TTR with structural changes only at beta-strand D. This strand forms an extended loop conformation similar to the one in chicken TTR. The piscine TTR.T(4) complex shows the T(4)-binding site to be similar but not identical to human TTR, whereas the TTR.T(3) complex shows the I3' halogen situated at the site normally occupied by the hydroxyl group of T(4). The significantly wider entrance of the hormone-binding channel in sea bream TTR, in combination with its narrower cavity, provides a structural explanation for the different binding affinities of human and piscine TTR to T(3) and T(4).

The structure factor and equation of state of hard-sphere fluids

In a paper by Verberg et al (2002 Dynamics: Models and Kinetic Methods for Non-Equilibrium ManyBody Systems ed J Karkheck (Dordrecht: Kluwer)) it was shown that the static structure factorS(k) of a hard-sphere fluid plays an important role in the computation of the transportproperties of colloidal suspensions. To perform actual calculations, those authors used asemiempirical form due to Grundke and Henderson which stems out of the Percus–Yevickapproximation. In this work we present calculations of the static structure factor of ahard-sphere fluid within the rational function approximation method (Bravo Yuste et al 1996 Phys. Rev. E 53 4820) which is wholly compatible with the equation ofstate used for the fluid. The Carnahan–Starling equation of state (Carnahanand Starling 1969 J. Chem. Phys. 51 635), the Padé (4, 3) of van Rensburg (1993J. Phys. A: Math. Gen. 26 4805) and Sánchez (1994 J. Chem. Phys. 101 7003), the equation ofstate of Malijevský and Veverka (1999 Phys. Chem. Chem. Phys. 1 4267) and a recent proposalby us (Robles and López de Haro 2003 Europhys. Lett. 62 56) will be explicitlyexamined.

Micromagnetic modelling of SANS in longitudinal recording media

A micromagnetic calculation of the magnetic structure factor is performed for a model sample of longitudinal medium to investigate the dependence of the scattering intensity profile I m( q) on the intrinsic parameters of the magnetocrystalline anisotropy and intergranular exchange coupling. It is demonstrated that changes in the ratio of the external to the anisotropy field H/ H k lead to significant differences in the profile. The formation of domains, owing to increased coupling, can also change the period and the amplitude of the profile oscillations.

Fluctuating charge stripes in an antiferromagnetic background

The charge stripe fluctuating in an antiferromagnetic background is studied numerically within an effective model of the stripe picture. We carry out a direct investigation on the correlation between the charge and spin orderings by calculating structure factors and the corresponding order parameter by means of the quantum Monte Carlo simulation. The spin long-range order with an antiphase boundary structure consistent with the topology of the static-stripe order is obtained in the thermodynamic limit for the ground state. The spin long-range order is enhanced by the increase in the stripe kinetic energy. A further increase, however, leads to results which suggest the reduction of the spin long-range order by the reformation of the static-stripe order.

Ab initio molecular dynamics simulations of local structure of supercooled Ni.

We report results of first-principles molecular dynamics simulations for stable and undercooled nickel liquids. The calculated structure factors as a function of temperature are discussed with respect to recent experimental measurements. In addition, structural analysis using bonding orientational order and three-dimensional pair analysis techniques have been performed in detail and the effect of undercooling on the microstructure has been analyzed. More particularly, we show the importance of fivefold symmetry local structures.

A model for velocity fluctuations in sedimentation

We present a model for velocity fluctuations of dilute sedimenting spheres at low Reynolds number. The central idea is that a vertical stratification causes the fluctuations to decrease below those of an independent uniform distribution of particles, such a stratification naturally occurring from the broadening of the sedimentation front. We use numerical simulations, scaling arguments, structure factor calculations, and experiments to show that there is a critical stratification above which the characteristics of the density and velocity fluctuations change significantly. For thin cells, the broadening of the sediment front (and the resulting stratification) is small, so the velocity fluctuations are predicted by independent-Poisson-distribution estimates. In very thick cells, the stratification is significant, leading to persistent decay of the velocity fluctuations for the duration of the experiment. Estimated stratifications quantitatively agree with the simulations, and indicate the likelihood that previous experimental measurements were also affected by stratification. The velocity fluctuations in sedimentation are therefore not universal but instead depend on both the cell shape and developing stratification.

Connection between the observable and centroid structural properties of a quantum fluid: application to liquid para-hydrogen.

It is shown that the discrepancy between path integral Monte Carlo [M. Zoppi et al., Phys. Rev. B 65, 092204 (2002)] and path integral centroid molecular dynamics [F. J. Bermejo et al., Phys. Rev. Lett. 84, 5359 (2000)] calculations of the static structure factor of liquid para-hydrogen can be explained based on a deconvolution equation connecting centroid and physical radial distribution functions. An explicit expression for the kernel of the deconvolution equation has been obtained using functional derivative techniques. In the superposition approximation, this kernel is given by the functional derivative of the effective potential with respect to the pairwise classical potential. Results of path integral Monte Carlo calculations for the radial distribution function and the static structure factor of liquid para-hydrogen are presented.

Valence-electron distribution inMgB2by accurate diffraction measurements and first-principles calculations

We use synchrotron x-ray and precision electron-diffraction techniques to determine accurately the structure factors of reflections that are sensitive to the valence-electron distribution in the superconductor ${\mathrm{MgB}}_{2}.$ These values deviate significantly from those calculated using the scattering factors of free (or neutral) atoms, but agree well with our calculated structure factors based on density-functional theory. Having experimentally established the reliability of our first-principles-based structure factors, we present electron-density maps of the redistribution of the valence electrons that takes place when hypothetical free atoms of Mg and B in ${\mathrm{MgB}}_{2}$ interact to form the real crystal.