Calculated Structure Factors Research Articles

Local strains induced in silicon channel by a periodic array of nitride capped poly lines investigated by high resolution X-ray diffraction

In the framework of the development of strained channel materials, the mechanical stress induced in silicon by a silicon nitride stressor layer is studied. The investigated samples are sub-micrometric periodic arrays of polysilicon lines deposited on thermally oxidised single crystal (0 0 1) Si substrate and capped with silicon nitride. We compare the stress induced in the silicon substrate by three layouts: without Si 3N 4, with a tensile Si 3N 4 or with a compressive Si 3N 4 layer on top of the poly lines. The periodic strain field in silicon is investigated by high resolution X-ray diffraction which is very sensitive to local strain (<10 −4) and is non-destructive. The lines array induces a periodic strain field in silicon, which gives rise to distinct satellites in reciprocal space. The intensity of these satellites is related to the strain field in one cell. X-ray reciprocal space maps are measured on a 4 circles goniometer with a laboratory source. First experimental mappings around the symmetrical 0 0 4 Si Bragg peak are presented here. Elastic calculations are performed with a Finite Element Modelling code in order to extract the displacement field that is useful for structure factor calculations within kinematical approximation. The calculations are necessary for explaining the experimental reciprocal space maps intensity envelope and comparing the strain induced by the three investigated layouts.

Concentration dependence of structural and bonding properties of liquid Tl-Se alloys byab initiomolecular dynamics simulations

The structural and electronic properties of liquid ${\text{Tl}}_{x}{\text{Se}}_{1\ensuremath{-}x}$ for $0\ensuremath{\le}x\ensuremath{\le}1$ are investigated by means of ab initio molecular dynamics simulations. It is shown that calculated structure factors are in good agreement with experiments over the whole range of composition. It is confirmed from calculated electronic densities of states that the liquid Tl-Se alloys have semiconducting properties for Tl concentrations not exceeding the stoichiometric composition $(x=2/3)$, while they are metallic for $x&gt;2/3$. In Se-rich composition range, Se atoms form chain molecules, whose average length becomes shorter with increasing Tl concentration. In the equiatomic liquid Tl-Se alloy, short Se chains, mostly negatively charged ${\text{Se}}_{2}$ dimers, coexist with a few Se ions, while most of Se atoms exist as ions at the stoichiometric composition. Based on a population analysis, we discuss the concentration dependence of the bonding properties in comparison with that in liquid alkali-metal chalcogenides.

Direct structural evidence of the change in N-III bonding in (GaIn)(NAs) before and after thermal annealing

The blueshift of the fundamental energy gap of (GaIn)(NAs) upon thermal treatment is well established. However, the physical reason is still controversially discussed in literature. In the present paper we give direct structural evidence using transmission electron microscopy in combination with structure factor calculation that this blueshift—for the metal organic vapor phase epitaxy grown samples investigated here—results solely from a change in the local environment of nitrogen. N is bound to Ga upon growth and moves into an In-rich environment upon annealing to minimize the strain energy of the crystal. The technique presented here can be used to unambiguously determine the reason for the blueshift of differently grown and annealed dilute nitride materials.

Monte Carlo Simulation of the Reactive Formation of Co-Continuous Nanostructured Polymers

Structure formation during high-temperature reactive blending of randomly functionalized poly-disperse backbone polymers (such as polyethylene) with end-functionalized graft polymers (such as polyamide 6) forming co-continuous nanostructured microphases was investigated by means of MC simulations using the bond fluctuation algorithm. We compared reacted and non-reacted systems under the same conditions. For the non-reacted system at low temperatures, phase separation was observed. In the system with grafting reactions, macroscopic phase separation was inhibited even if the consumption of reactive sites was only 50%. The calculated structure factor indicates a distinct difference between the two simulation states in accordance with the 3D visualization of the system and the box-counting method.

Displacement of the Occluding Loop by the Parasite Protein, Chagasin, Results in Efficient Inhibition of Human Cathepsin B

Cathepsin B is a papain-like cysteine protease showing both endo- and exopeptidase activity, the latter due to a unique occluding loop that restricts access to the active site cleft. To clarify the mode by which natural protein inhibitors manage to overcome this obstacle, we have analyzed the structure and function of cathepsin B in complexes with the Trypanosoma cruzi inhibitor, chagasin. Kinetic analysis revealed that substitution of His-110e, which anchors the loop in occluding position, results in 3-fold increased chagasin affinity (Ki for H110A cathepsin B, 0.35 nm) due to an improved association rate (kon, 5 x 10(5) m(-1)s(-1)). The structure of chagasin in complex with cathepsin B was solved in two crystal forms (1.8 and 2.67 angstroms resolution), demonstrating that the occluding loop is displaced to allow chagasin binding with its three loops, L4, L2, and L6, spanning the entire active site cleft. The occluding loop is differently displaced in the two structures, indicating a large range of movement and adoption of conformations forced by the inhibitor. The area of contact is slightly larger than in chagasin complexes with the endopeptidase, cathepsin L. However, residues important for high affinity to both enzymes are mainly found in the outer loops L4 and L6 of chagasin. The chagasin-cathepsin B complex provides a structural framework for modeling and design of inhibitors for cruzipain, the parasite cysteine protease and a virulence factor in Chagas disease.

Electron density of a new EGFR Tyrokinase-inhibitor at 100 K, consideration of different models

Abstract The electron density (ED) of a substituted 4-(indol-3-yl)-quinazoline, a newly developed anti-cancer drug, was determined from a high resolution X-ray data set measured at 100 K using synchrotron radiation. Because the structure contains a chlorine atom, which has a diffuse outer electron shell and is therefore beyond standard modeling, the influence of the model on the bond topological and atomic properties was studied following Bader's approach of ‘Atoms In Molecules’ (AIM). The expansion/contraction parameters κ and κ′ of the four atoms being constitutive for the Cl—C-bond and the F—C-bond were obtained by calculation of theoretical structure factors of a model compound and assigned in subsequent multipole refinements. The κ and κ′-values for all other non H-atoms atoms were taken from the literature. The effect of two different sets of κ and κ′ (1.20/1.20 and 1.13/1.29) for the hydrogen atoms was evaluated for the topological properties at bonds to hydrogen atoms (including hydrogen bonds) and to the atomic properties of the hydrogen atoms. Furthermore the effect of particular n l -sets for the chlorine atom to bond topological descriptors of the Cl—C-bond was investigated for the theoretical structure factors and compared with experiment. All results were compared with corresponding theoretical findings from a single point calculation at experimental geometry.

Exfoliated Nanosheet Crystallite of Cesium Tungstate with 2D Pyrochlore Structure: Synthesis, Characterization, and Photochromic Properties

Layered cesium tungstate, Cs(6+x)W(11)O(36), with two-dimensional (2D) pyrochlore structure was exfoliated into colloidal unilamellar sheets through a soft-chemical process. Interlayer Cs ions were replaced with protons by acid exchange, and quaternary ammonium ions were subsequently intercalated under optimized conditions. X-ray diffraction (XRD) measurements on gluelike sediment recovered from the colloidal suspension by centrifugation showed a broad pattern of a pronounced wavy profile, which closely matched the square of calculated structure factor for the single host layer. This indicates the total delamination of the layered tungstate into nanosheets of Cs(4)W(11)O(36)(2-). Microscopic observations by transmission electron microscopy and atomic force microscopy clearly revealed the formation of unilamellar crystallites with a very high 2D anisotropy, a thickness of only approximately 2 nm versus lateral size up to several micrometers. In-plane XRD analysis confirmed that the 2D pyrochlore structure was retained. The colloidal cesium tungstate nanosheet showed strong absorption of UV light with sharp onset, suggesting a semiconducting nature. Analysis of the absorption profile provided 3.6 eV as indirect band gap energy, which is 0.8 eV larger than that of the bulk layered precursor, probably due to size quantization. The nanosheet exhibited highly efficient photochromic properties, showing reversible color change upon UV irradiation.

Domain-swapped dimerization of ZO-1 PDZ2 generates specific and regulatory connexin43-binding sites

PDZ domain scaffold proteins are capable of assembling macromolecular protein complexes in diverse cellular processes through PDZ-mediated binding to a short peptide fragment at the carboxyl tail of target proteins. How each PDZ domain specifically recognizes its target protein(s) remains a major conceptual question, as at least a few out of the several hundred PDZ domains in each eukaryotic genome share overlapping binding properties with any given target protein. Here, we show that the domain-swapped dimerization of zonula occludens-1 PDZ2 generates a distinct interface that functions together with the well-separated canonical carboxyl tail-binding pocket in each PDZ unit in binding to connexin43 (Cx43). We further demonstrate that the charge-charge interaction network formed by residues in the PDZ dimer interface and upstream residues of the Cx43 peptide not only provides the unprecedented interaction specificity for the complex but may also function as a phosphorylation-mediated regulatory switch for the dynamics of the Cx43 gap junctions. Finally, we provide evidence that such domain-swapped dimer assembly also occurs in other PDZ domain scaffold proteins. Therefore, our findings present a new paradigm for understanding how some PDZ domain proteins specifically bind to and regulate the functions of their target proteins.

Ab initio molecular dynamics simulations on structure change of liquid Te from normal- tosupercooled-state

Using ab initio molecular dynamics simulations and inherent structure formalism, the localatomic structures and electronic properties of liquid Te from the normal- to supercooled-statewere studied. The calculated structure factors agree acceptably with available experimentaldata. There is a noticeable maximum at around 723 K in the curve of first-peak-height ofS(Q) versus temperature. With increasing temperature, in the low-temperature region from 573to 673 K, the average coordination number increases gradually in contrast to the behaviorof a classical isotropic fluid; but in the high-temperature region from 843 to 1073 K, itremains nearly constant. Our calculated angular limited bond–bond correlationfunctions first show that there are two types of Peierls distorted local atomicstructures in liquid Te: the lengths of short and long bonds in the first type aresimilar to those in crystalline Te, while the lengths of short and long bonds inthe second one are very different from those in crystalline Te. With decreasingtemperature, the lengths of the two short intrachain bonds are unchanged, but thoseof the two long interchain bonds become longer, indicating that the interchaincorrelation reduces with decreasing temperature. Our results suggest that the changeof the Peierls-type distorted local atomic structures with temperature may beresponsible for the striking anomalies of many thermophysical properties of liquid Te.The calculated DOS and LDOS shows that there is an obvious dip in DOS atEF, but the dip at 1073 K is shallower than that at 573 K. The variation of the dip in DOSmainly results from the change of Te p orbital.

Novel type of Ras effector interaction established between tumour suppressor NORE1A and Ras switch II

A class of putative Ras effectors called Ras association domain family (RASSF) represents non-enzymatic adaptors that were shown to be important in tumour suppression. RASSF5, a member of this family, exists in two splice variants known as NORE1A and RAPL. Both of them are involved in distinct cellular pathways triggered by Ras and Rap, respectively. Here we describe the crystal structure of Ras in complex with the Ras binding domain (RBD) of NORE1A/RAPL. All Ras effectors share a common topology in their RBD creating an interface with the switch I region of Ras, whereas NORE1A/RAPL RBD reveals additional structural elements forming a unique Ras switch II binding site. Consequently, the contact area of NORE1A is extended as compared with other Ras effectors. We demonstrate that the enlarged interface provides a rationale for an exceptionally long lifetime of the complex. This is a specific attribute characterizing the effector function of NORE1A/RAPL as adaptors, in contrast to classical enzymatic effectors such as Raf, RalGDS or PI3K, which are known to form highly dynamic short-lived complexes with Ras.

Obtainment of precise experimental data on diffractometers with 2D and point detectors

A measurement method based on the use of diffractometers with a point detector is proposed that makes it possible to reduce the measurement time by a factor of about 2 in comparison with the conventional experiment. Measures are proposed that allow one to increase the measurement precision for diffractometers with a 2D CCD detector. Refinement of the model of independent atoms from the experimental data obtained by these methods is characterized by consistency between the experimental and calculated structure factors at a level of 1–1.5%. A further significant decrease in refinement Rfactors in going to the multipole model indicates that the data precision is sufficient for studying the charge density in crystals.

Implementing the LIM code: the structural basis for cell type-specific assembly of LIM-homeodomain complexes

LIM-homeodomain (LIM-HD) transcription factors form a combinatorial 'LIM code' that contributes to the specification of cell types. In the ventral spinal cord, the binary LIM homeobox protein 3 (Lhx3)/LIM domain-binding protein 1 (Ldb1) complex specifies the formation of V2 interneurons. The additional expression of islet-1 (Isl1) in adjacent cells instead specifies the formation of motor neurons through assembly of a ternary complex in which Isl1 contacts both Lhx3 and Ldb1, displacing Lhx3 as the binding partner of Ldb1. However, little is known about how this molecular switch occurs. Here, we have identified the 30-residue Lhx3-binding domain on Isl1 (Isl1(LBD)). Although the LIM interaction domain of Ldb1 (Ldb1(LID)) and Isl1(LBD) share low levels of sequence homology, X-ray and NMR structures reveal that they bind Lhx3 in an identical manner, that is, Isl1(LBD) mimics Ldb1(LID). These data provide a structural basis for the formation of cell type-specific protein-protein interactions in which unstructured linear motifs with diverse sequences compete to bind protein partners. The resulting alternate protein complexes can target different genes to regulate key biological events.

Ab Initio Molecular Dynamics Simulation of a 1-Ethyl-3-methylimidazolium Fluoride−Hydrogen Fluoride Mixture

The intermolecular structure and dynamics of an acidic 1-ethyl-3-methylimidazolium fluoride-hydrogen fluoride solution ([emim][F].2.3HF) have been studied through a Car-Parrinello molecular dynamics simulation. The calculated structure factor is found to be in good agreement with X-ray scattering data. The solution consists of [emim] cations and polyfluoride anions of the kind F(HF)n(-). With increasing n, the length of the H-F covalent bond in the polyfluoride species is found to decrease, with a concomitant blue shift in the frequency of its stretching mode. Evidence for the presence of a hydrogen bond between the acidic ring hydrogen of the cation and the fluoride ion is presented.

Convergence study of a Schrödinger-equation algorithm and structure-factor determination from the wavefunction

The algorithm [Bethanis, Tzamalis, Hountas & Tsoucaris (2002). Acta Cryst. A58, 265-269] which reformulates the quantum-mechanical problem of solving a Schrödinger (S) equation in a crystallographic context has been upgraded and tested for many aspects of convergence. The upgraded algorithm in reciprocal space aims at determining a wavefunction Phi(H) such that (a) Phi(H) fulfils the S equation within certain precision and (b) Phi(H) minimizes by least squares the differences between the calculated structure factors from the wavefunction and the observed ones. Calculations have been made with three molecules (11, 41 and 110 non-H atoms in the asymmetric unit) for different numbers of initially given phases. Three main questions have been addressed: (I) Does the iterative calculation of the wavefunction converge? (II) Do the calculated wavefunctions converge to a unique set of Phi(H) values independent of the initial random set of Phi(H)? (III) Is the calculated Phi(H) set a good approximation of a wavefunction able to produce within certain errors the correct values of the phases of the structure factors? Concerning questions (I) and (II), our results give a strong hint about fast convergence to a unique wavefunction independent of the arbitrary starting wavefunction. This is an essential prerequisite for practical applications. For question (III) in the case closer to the ab initio situation, the final mean phase error, respectively, for the three structures is 3, 26 and 28 degrees. The combination of (a) and (b) in the upgraded algorithm has been proved crucial especially for the results concerning the larger structures.

Spin dynamics in the one-dimensional [formula omitted] antiferromagnet with Dzyaloshinskii–Moriya interaction

We present a calculation of the in-plane dynamical structure factor for the S = 1 one-dimensional antiferromagnet with a Dzyaloshinskii–Moriya interaction using the Schwinger boson mean-field theory.

Influence of crystallographic orientation on local strains in silicon: A combined high-resolution X-ray diffraction and finite element modelling investigation

The processing of Si-based devices induces very high local strains in silicon. This strain field is worth investigating in particular in Shallow Trench Isolation, which is a key step in the production of non-volatile-memories and transistors. In this study we investigate by high high-resolution X-ray diffraction the periodic strain field induced in silicon by the STI process. High-resolution X-ray diffraction is shown to be very sensitive (< 10 − 4 ) to local strains and has the distinct advantage of being non-destructive. Investigated samples are periodic arrays of SiO 2-filled trenches in single crystal (001) Si. The trenches are etched either along [100] or along [110]. The experiments have been performed on a 4 circles goniometer with a laboratory source. We have recorded Si 004 and asymmetric Si 224 or Si 404 reciprocal space maps in order to extract axial strains in the 3 directions. The trenches array induces a periodic strain field in silicon, which gives rise to distinct satellites in reciprocal space. The intensity of these satellites is related to the strain field. We also performed elastic calculations with a finite element modelling code. Finally structure factor calculations are performed using the displacement field determined from mechanical modelling. We focus here on the effect of silicon elastic anisotropy on the strain field in 580 nm and 200 nm period samples. The influence of line crystallographic orientation ([100] or [110]) on the strain field is evaluated by finite element modelling and compared with experimental ones. The silicon anisotropy has a weak effect on strain and is compensated by process variations due to the line orientation.

T2384, a Novel Antidiabetic Agent with Unique Peroxisome Proliferator-activated Receptor γ Binding Properties

The nuclear hormone receptor peroxisome proliferator-activated receptor gamma (PPARgamma) plays central roles in adipogenesis and glucose homeostasis and is the molecular target for the thiazolidinedione (TZD) class of antidiabetic drugs. Activation of PPARgamma by TZDs improves insulin sensitivity; however, this is accompanied by the induction of several undesirable side effects. We have identified a novel synthetic PPARgamma ligand, T2384, to explore the biological activities associated with occupying different regions of the receptor ligand-binding pocket. X-ray crystallography studies revealed that T2384 can adopt two distinct binding modes, which we have termed "U" and "S", interacting with the ligand-binding pocket of PPARgamma primarily via hydrophobic contacts that are distinct from full agonists. The different binding modes occupied by T2384 induced distinct patterns of coregulatory protein interaction with PPARgamma in vitro and displayed unique receptor function in cell-based activity assays. We speculate that these unique biochemical and cellular activities may be responsible for the novel in vivo profile observed in animals treated systemically with T2384. When administered to diabetic KKAy mice, T2384 rapidly improved insulin sensitivity in the absence of weight gain, hemodilution, and anemia characteristics of treatment with rosiglitazone (a TZD). Moreover, upon coadministration with rosiglitazone, T2384 was able to antagonize the side effects induced by rosiglitazone treatment alone while retaining robust effects on glucose disposal. These results are consistent with the hypothesis that interactions between ligands and specific regions of the receptor ligand-binding pocket might selectively trigger a subset of receptor-mediated biological responses leading to the improvement of insulin sensitivity, without eliciting less desirable responses associated with full activation of the receptor. We suggest that T2384 may represent a prototype for a novel class of PPARgamma ligand and, furthermore, that molecules sharing some of these properties would be useful for treatment of type 2 diabetes.

X-ray Scattering of Vinyl Polyolefin Liquids and Random Copolymers: Theory and Experiment

Polymer reference interaction site model (PRISM) calculations and wide-angle X-ray experiments were performed on vinyl polyolefin melts of polyethylene (PE), isotactic polypropylene (iPP), and poly(1-butene) (P1B). PRISM calculations were also carried out on poly(1-hexene) (P1H). For PE and iPP melts a single main peak in the scattering pattern was observed near wave vectors k ∼ 1 A−1; for P1B and P1H we observed this main peak to split with the development of a prepeak that moves to lower wave vectors as the side chain size increased. By calculation of the various partial structure factors, we found that the prepeak formation is due to a combination of two effects: (1) an increase in the average distance between the chain backbones due to screening of the side chains and (2) increased intermolecular ordering of the pendant methyl groups as the side chains become longer. The scattering of random copolymers (PEP, PEB, PEH) of PE with iPP, P1B, and P1H, respectively, was also studied with PRISM theory as a ...

Structural and electronic properties of liquid InAs under pressure

The structural and bonding properties of liquid InAs under pressure are investigated by ab initio molecular-dynamics simulations. The calculated structure factors are in good agreement with the recent X-ray diffraction measurements over a wide range of pressure. It is shown that the pressure dependence of the spatial correlation between atoms depends on the species of atomic pairs reflecting the strength of the covalent bonding. A detailed investigation of the pair distribution functions confirms that different pressure-induced structural changes occur below and above 6 ∼ 10 GPa. It is suggested that such structural changes are related to the reduction of the covalent nature under pressure.

Refining real structure parameters of disordered layer structures within the Rietveld method

A new approach is proposed for the refinement of disordered layered structures within the Rietveld method. It is shown that it is possible to introduce the existing recursive treatments of stacking disorder in a Rietveld refinement by using a supercell approach in combination with a complex manipulation of the structure factor calculation. The applicability of this approach is demonstrated by the refinement of disordering parameters of data simulated by the established program DIFFaX (1). In addition, structural parameters and contents of disordered layered double hydroxides in mixtures with a reference material were successfully refined from measured laboratory diffraction data. 1. Introduction physicochemical properties of materials are often directly related to their structural char- acteristics. X-ray powder diffractometry in combination with the Rietveld method (2) proved to be a suitable method for the determination of microstructural parameters. Unfortunately, this approach fails in the presence of materials which show strong structural defects like stacking disorder in layered materials. In the reciprocal space, structural disorder leads to intensity fractions continuously distributed along reciprocal rods. Therefore it is not treatable by the classical Rietveld method. To overcome this problem in the case of turbostratic disor- der, a partly filled supercell was introduced (3). Further treatments are necessary for stacking disorder consisting of translations/rotations with distinctive amounts and probabilities or mixed layer stacking. The literature reports several attempts for the treatment of stacking faults, e.g. the explicit calculation of finite stacks (4) or a recursive treatment (1). Numerous