Calculated Structure Factors Research Articles

X-ray structure of junctional adhesion molecule: structural basis for homophilic adhesion via a novel dimerization motif.

Junctional adhesion molecules (JAMs) are a family of immunoglobulin-like single-span transmembrane molecules that are expressed in endothelial cells, epithelial cells, leukocytes and myocardia. JAM has been suggested to contribute to the adhesive function of tight junctions and to regulate leukocyte trans migration. We describe the crystal structure of the recombinant extracellular part of mouse JAM (rsJAM) at 2.5 A resolution. rsJAM consists of two immunoglobulin-like domains that are connected by a conformationally restrained short linker. Two rsJAM molecules form a U-shaped dimer with highly complementary interactions between the N-terminal domains. Two salt bridges are formed in a complementary manner by a novel dimerization motif, R(V,I,L)E, which is essential for the formation of rsJAM dimers in solution and common to the known members of the JAM family. Based on the crystal packing and studies with mutant rsJAM, we propose a model for homophilic adhesion of JAM. In this model, U-shaped JAM dimers are oriented in cis on the cell surface and form a two-dimensional network by trans-interactions of their N-terminal domains with JAM dimers from an opposite cell surface.

Spinodal Decompositions Driven by Orientation Fluctuations

We study early stages of spinodal decomposition (SD) in polymer/liquid crystal mixtures by solving linearized time-dependent Landau-Ginzburg equations for concentration (conserved order parameter) and orientation (nonconserved order parameter). We calculate structure factors for concentration and for orientation, depending on a quench temperature and concentration. We find a new SD process driven by instability of the orientational order parameter.

Calculated x-ray dichroic signals and resonant Bragg diffraction structure factors forDyB2C2

Low-temperature properties of dysprosium borocarbide display evidence of two phase transitions; it has been proposed that the first involves ordering of Dy quadrupole moments and the second, at a lower temperature, involves ordering of Dy magnetic moments. The latter has been established by magnetic neutron diffraction. Insight into the first phase transition, at ${T}_{Q},$ has been sought by resonant x-ray Bragg diffraction, which reveals charge-forbidden (Templeton-Templeton) intensities $(00l+\frac{1}{2})$ that increase with decreasing temperature. We show that this scattering is absent if the space group is $P4/mbm,$ which has been proposed for the high-temperature crystal structure. Tanaka et al. report evidence that at ${T}_{Q}$ the lattice distorts and the new space group is ${P4}_{2}/mnm.$ The lower point-group symmetry of Dy ions in this space group is shown by us to allow diffraction at $(00l+\frac{1}{2}).$ In the magnetically ordered phase two neighboring Dy moments along the c axis are mutually perpendicular and two neighboring moments in the plane normal to the c axis are almost oppositely aligned. This magnetic configuration and point-group symmetry $2/m$ for Dy sites lead us to predict magnetic and charge scattering at reflections $(00l+\frac{1}{2})$ in the magnetically ordered phase. At reflections $(h0l)$ and h odd calculated structure factors are purely magnetic. Our finding is consistent with data collected by Hirota et al. at the reflection (102). We report expressions for circular and linear dichroic signals and structure factors for Bragg scattering for the interpretation of future experiments. The structure factors are appropriate for azimuthal-angle scans in which the crystal is rotated about the $(00l+\frac{1}{2})$ or the $(h0l)$ Bragg scattering vectors.

On the calculation of the static structure factor of path-integral quantum simple fluids far from exchange

This paper addresses several points of interest concerning the computation of the static structure factor of path-integral monatomic quantum fluids. First of all, the connection between the structure factor and the path-integral linear response pair radial correlation function is shown as its defining quantity by assuming a generalized Fermi's potential for the neutron-nuclei interactions, which is to be included in the general expression of the dynamic structure factor. Second, the possibilities of finding Ornstein-Zernike equations for full path-integral fluids, and also for the effective potential models of fluids derived from the path-integral formalism, are explored by working in the grand canonical ensemble. By so doing, the success and features for improvement of the weak-field approach used previously in this context of determining quantum static structure factors [SESÉ, L. M., 1996, Molec. Phys., 89, 1783; SESÉ, L. M., and LEDESMA, R., 1997, J. chem. Phys., 106, 1134] can be understood. New numerical applications are performed within this weak-field approach taking as probes the quantum hard-sphere fluid and dense fluid helium-4, the latter being described through Lennard-Jones and Aziz-Slaman underlying interactions. The results show that the structure factors associated with the linear response and instantaneous path-integral pair radial correlation functions differ noticeably from each other with increasing quantum effects. In particular, the linear response description leads to more compressible fluids than the instantaneous one. Besides, the equality between the isothermal compressibilities fixed via the linear response and the quantum particle centre-of-gravity pair radial correlation functions does not hold beyond the situations that can be treated with the Gaussian Feynman-Hibbs effective potential picture. Comparison with experiment in the case of helium-4 (T = 4.2 K) reveals clearly that, under strong quantum conditions, an operative framework more elaborate than the weak-field approach is needed.

Refinement of proteins at subatomic resolution withMOPRO

Crystallography at subatomic resolution permits the observation and measurement of the non-spherical character of the atomic electron density. Charge density studies are being performed on molecules of increasing size. TheMOPROleast-squares refinement software has thus been developed, by extensive modifications of the programMOLLY, for protein and supramolecular chemistry applications. The computation times are long because of the large number of reflections and the complexity of the multipolar model of the atomic electron density; the structure factor and derivative calculations have thus been parallelized. Stereochemical and dynamical restraints as well as the conjugate gradient algorithm have been implemented. A large number of the normal matrix off-diagonal terms turn out to be very small and the block diagonal approximation is thus particularly efficient in the case of large structures at very high resolution.

Quantitative Electron Crystallographic Determinations of Higher Fullerenes in the Hexagonal Close Packed Polymorph

The hexagonal closed packed crystal structures of the higher fullerenes, C76, C78, and C84, have been determined at room temperature in the [001] projection from single crystal electron diffraction intensity data. In all cases, the molecules in the crystal are rotating freely about their centers. As part of the structure analysis, independent determination of average molecular radii (a continuous variable in the structure factor calculation) yields values in reasonable agreement with predicted values for these molecules.

Structural study of chiral camphorsulfonic acid doped polyaniline

Chiral camphorsulfonic acid [R-(-)-CSA] doped polyaniline (PANI) films have been studied using X-ray diffraction in combination with structure factor calculations. Scattering studies of dedoped films, which exhibit chiral activity, have also been performed. All samples formed partially crystalline films and displayed significant molecular anisotropy in the crystal unit cell with respect to film orientation. The crystalline features are interpreted using a lamellar molecular model in which parallel stacks of the PANI main chains alternate with layers of the CSA dopant. This organization could, in part, explain the high conductivities often recorded in CSA-doped films. No obvious features within crystalline regions of the doped or dedoped films were observed which correlate with the chiral recognition seen in dedoped films.

A theoretical study of the polarized neutron scattering from Cs3CoCl5

Spin-orbit interactions play an essential part in elucidating the magnetic structures which are measured by the polarized neutron diffraction technique. This work extends our previous Hartree–Fock theory, with a one-electron spin-orbit term limitation, to incorporate both one- and two-electron terms exactly. This new theory, which is based on the current density, has been applied to calculate the low-temperature magnetic structure factors of the Cs3CoCl5 crystal. The crystal is assumed to be assembled from noninteracting molecular fragments. The calculated structure factors were compared directly with those observed from experiment. The agreement between these theoretical results and the experimental data shows great improvement compared with those from the usual unrestricted Hartree–Fock theory and with those from the previous generalized Hartree–Fock theory including one-electron terms. To examine the electron correlation effects, we use ab initio wave-function-based correlation methods, unrestricted second-order Møller–Plesset perturbation (UMP2) and quadratic configuration interaction including single and double excitations (QCISD), and also density functional theoretical methods, Xα, local-spin density approximation, generalized gradient approximation, Becke’s three-parameter hybrid methods, and modified half-and-half hybrid methods, to calculate magnetic structure factors. Results indicate that the effects of spin-orbit interactions are comparable to those of electron correlation, and both must be included in reproducing the experimental data. To consider both these effects simultaneously we employed a simple model. With only three parameters, this model reproduced the observed data almost exactly as reflected by a χ2 goodness of fit close to unity.

Local order in liquid oxygen: computer simulations with point charge model

Molecular dynamics (MD) simulations are performed to study liquid oxygen in the temperature range from 84 to 120 K. The oxygen molecule is modeled as the Lennard-Jones diatomic carrying three point charges. This potential model is shown to reproduce the second virial coefficient in the temperatures range from 80 to 400 K and the heats of vaporization. The calculated structure factor for liquid oxygen is found to be in good agreement with neutron scattering data at 84 K. The orientational correlations in liquid oxygen are examined.

Singular continuous diffraction component of the thue-morse sequence at 1/17 and 1/41 satellite positions

The reference lattice concept 1 has been successfully used to calculate the scaling exponents for intensities of singular diffraction component of the one-dimensional Thue-Morse sequence at positions indexed by 1/p, where p is a prime number, and especially for p = 17 and 41. Based on the average unit cell approach 1 the probability distribution of atomic displacements from the reference lattice points has been obtained. Specially defined δ-parameters significantly reduce the number of variables required for the structure factor calculation. Values of fractal exponents for scaling of diffraction intensities with the number of atoms have been checked numerically for numbers of atoms reaching 232.

Reformulation of two Ni(Ⅱ)-8-hydroxyquinoline complexes from Calculated Structure Factors

晶体学研究曾认为,分子式是Na[NiQ2(HQ)](CI O4)的结构并不含有钠而应为[H3O][NiQ2(HQ)](CI O4).相似地,稀土-Ni络合物[YQ(HQ)2][NiQa](CI O4)也不含有钇而应为[H3O][Ni2Qs(HQ)s](CI O4).晶体结构描述的修正系根据文献报导的原子坐标计算结构因子所导出的结果.

Wavefunctions derived from experiment. II. A wavefunction for oxalic acid dihydrate.

A wavefunction has been derived for the oxalic acid dihydrate molecule using accurate low-temperature X-ray electron-density structure-factor data. The electron density from this constrained theoretical wavefunction is compared to those of unconstrained theoretical wavefunctions. Fitted electron densities around hydrogen atoms show significant deviation compared to Hartree-Fock calculations. In particular, hydrogen bonding appears enhanced in the crystal over theoretical predictions, while the density usually attributed to lone-pair electrons of the oxalic acid oxygen atoms is decreased. The constrained fitting procedure improves the overall agreement of the calculated structure factors even for structure factors that were not used as input to the fitting procedure. The pictures obtained from the constrained fitting procedure are insensitive to random errors introduced into the data. Similarly, the fitting procedure is able to reproduce features that arise from more accurate theoretical calculations. However, we are unable to fit our wavefunction to within the experimentally quoted error bounds without allowing an unreasonably large change in the energy of the constrained wavefunction. Large Hartree-Fock and density functional theory (DFT) cluster calculations involving up to 86 atoms in size also do not show significantly improved agreement with the experimentally observed structure factors. Derived properties from the constrained wavefunction fragments, such as the kinetic energy, electrostatic potential and the electron localization function, are also presented. In general, there are no difficulties in extracting experimental wavefunctions and the associated derived properties from elastic X-ray scattering data for crystal fragments of the order of 20 atoms.

Influence of the Screening Function on Theoretical Calculations of the Structure Factor of Liquid Aluminum

The structure factor S(k) of liquid aluminum is calculated using the Metropolis Monte Carlo method. The effective two-body ion-ion interaction used in the calculations are the Shaw optimized model and the local approximation suggested by Harrison calculated using two screening function in each case, the screening function of Vashishta and Singwi and that of Utsumi and Ichimaru. The calculated structure factors from each case are compared with experiment.

Effect of excess Bi2O3 on the ferroelectric properties of SrBi2Ta2O9 ceramics

In this study, the effect of bismuth content on phase-transition behavior, ferroelectric property, and crystal structure of strontium–bismuth–tantalate (SBT) ceramics was explored with the aid of εr(T), ferroelectric hysteresis loop, x-ray diffraction (XRD), and Raman spectroscopy. Both the phase-transition behavior and ferroelectric properties such as spontaneous polarization (Ps) showed a dependence on Bi content. The ferroelectric Curie temperature Tc, was found to decrease with increasing the Bi content and Ps was maximized when 2–3 mol % excess Bi2O3 was added. It was found that Raman spectroscopy and XRD can explain the Bi-content dependence of SBT ceramics. The frequency and the width of the mode below 60 cm−1 in Raman spectra revealed that a site exchange of Sr2+ and Bi3+ ions occurred. The formation of antisite defects was confirmed by the change in the intensity ratio of I(008)/I(105) in the XRD patterns. The calculation of structure factors showed it was also related to antisite defects (SrBi,BiSr).

A flexible and efficient procedure for the solution and phase refinement of protein structures.

An ab initio method is described for solving protein structures for which atomic resolution (better than 1.2 A) data are available. The problem is divided into two stages. Firstly, a substructure composed of a small percentage ( approximately 5%) of the scattering matter of the unit cell is positioned. This is used to generate a starting set of phases that are slightly better than random. Secondly, the full structure is developed from this phase set. The substructure can be a constellation of atoms that scatter anomalously, such as metal or S atoms. Alternatively, a structural fragment such as an idealized alpha-helix or a motif from some distantly related protein can be orientated and sometimes positioned by an extensive molecular-replacement search, checking the correlation coefficient between observed and calculated structure factors for the highest normalized structure-factor amplitudes |E|. The top solutions are further ranked on the correlation coefficient for all E values. The phases generated from such fragments are improved using Patterson superposition maps and Sayre-equation refinement carried out with fast Fourier transforms. Phase refinement is completed using a novel density-modification process referred to as dynamic density modification (DDM). The method is illustrated by the solution of a number of known proteins. It has proved fast and very effective, able in these tests to solve proteins of up to 5000 atoms. The resulting electron-density maps show the major part of the structures at atomic resolution and can readily be interpreted by automated procedures.

Photo-induced structural change in liquid sulphur

The structure of liquid sulphur at 400 K, below the polymerizationtemperature Tp = 432 K, is investigated by first-principlesmolecular-dynamics simulations. The calculated structure factor isin excellent agreement with the experimental data. To investigatethe microscopic mechanism of the photo-induced structural change inliquid sulphur below Tp, simulations are performedby exciting electrons in the valence band to the conduction band.It is found that a bond in one of the S8 rings is easily broken andconsequently the S8 ring turns out to be the S8 chain after anelectron excitation, in the same way as was seen for an isolated S8ring. After the electron excitation is stopped, the S8 chain doesnot reconstruct the S8 ring; instead a `tadpole' structure is formed.Since the tadpole structure persists for a long time, it isconsidered that the tadpole is one of possible structures for theexperimentally observed long-lived product in the relaxationprocess. We have shown that photo-induced polymerization occursin liquid sulphur when the S8 chains or the S8 tadpoles areclose to each other at their ends.

Adsorption of Li on Ni(110) surfaces at low and room temperature

We present the investigation of Li adsorption on Ni(110) surfaces at low temperature (LT) and room temperature (RT) by means of Auger electron spectroscopy, low-energy electron diffraction, thermal desorption spectroscopy and work function measurements, in ultrahigh vacuum. At RT, from the early stages of deposition ( Θ≤0.1 ML) Li induces a (1×2) reconstruction of the Ni(110) surface. The (1×2) reconstruction is lifted at 0.5 ML. A further increase of Li coverage leads to a disordered surface, with an intermixing of Li adatoms and the Ni substrate with a tendency toward Li–Ni alloy formation. A gradual heating of the Li-covered Ni(110) surface gives an Li(3×1), an Li(5×1) structure and the (1×2) reconstruction before the complete desorption of Li. Near saturation ( Θ≈2 ML), Li forms a nearly metallic overlayer. At LT (150 K), deposition of Li up to 1 ML gives a sequence of c(2×2), (7×2), (3×2), (4×2), (5×4) and finally (1×1) structures, which have been determined using structure factor calculations. These structures are attributed to a continuous stretching of deposited Li atoms along the [11̄0] direction of the Ni(110) surface. The Li–Ni interaction is a thermally activated process and decreases the stability of the Ni surface, leading to its reconstruction at RT. However, at LT the Li–Li interaction dominates and the effect of Li adatoms on the substrate structure is limited. The change of the (1×2) reconstruction to the ideal (1×1) bulk-like surface occurs at the beginning of the transition of ionic to metallic bonding of the Li overlayer.

Absolute Orientation of Molecules of Amphiphilic Alcohols in Crystalline Monolayers at the Air−Water Interface

The absolute orientations of the amphiphilic molecules α-hydroxy ω-bromo alcohols BrCnH2n OH, n = 21, 22, and the alkyl hydroxy esters CmH2m+1COO(CH2)nOH, m = 14, 15, n = 10, in crystalline monolayer forms on water have been determined, the former by grazing incidence X-ray diffraction (GIXD) and the latter by sum frequency generation (SFG). The assignment was made for the alkyl hydroxy esters by establishing the polar angle between the terminal CH3−C bond and the normal to the plane of the monolayer; for the bromo alcohols the assignment was made by a determination of the two-dimensional crystal structure via X-ray structure factor calculations. The SFG results are in agreement with reported GIXD and lattice energy analyses of the alkyl hydroxy esters m = 19, n = 9, 10. These studies have further revealed the absolute orientation of the alcohol C−OH bonds at the water surface, which in turn can be correlated with the ice-nucleating behavior of the monolayers on supercooled water drops in terms of the odd and even values of n.

Structure of phosphorus-selenium glasses: results from ab initio molecular dynamics simulations

Car-Parrinello molecular dynamics calculations have been carried out for phosphorus-selenium mixtures of compositions corresponding to overall stoichiometrics PSe and P2Se. Comparison of the calculated structure factors with those obtained in neutron scattering experiements suggests that the real materials are characterized by the presence of substantial numbers of well defined molecular units.

An introductory exercise in Fourier synthesis and structure-factor calculation for undergraduates, using anEXCELworkbook

AnEXCEL(Microsoft Corp.) workbook has been configured to enable spreadsheet calculation of two-dimensional structure factors and Fourier syntheses. An exercise in which it can be used by undergraduate students to solve the structure of potassium bicarbonate in projection is described. The package is available from the internet.