Changes In Core Structure Research Articles

Immobilization of partial dislocations bounding double Shockley stacking faults in 4H-SiC observed by in situ synchrotron X-ray topography

The expansion of double Shockley stacking faults (DSFs) in an n-type 4H-SiC substrate with a nitrogen concentration of 3.9 × 1019 cm−3 was investigated using in situ synchrotron X-ray topography. DSF expansion was observed to be suppressed and immobilized above 1590 K, along with the partial dislocation (PD) shape being changed from a straight to zig-zag configuration. For a different heating process (higher heating rate), the PDs could continue to expand, even above 1590 K. Ex situ topography experiments revealed that the DSFs close to the specimen surface expanded widely, although those expanding toward the specimen interior became immobile. One possible mechanism for this immobilization was proposed, where the core structural changes from a Si-core to the C-core by non-conservative motion induced by the interaction between the PDs and point defects (C interstitials).

Immobilization of Partial Dislocations Bounding Double Shockley Stacking Faults in 4h-Sic Observed by in Situ Synchrotron X-Ray Topography

The expansion of double Shockley stacking faults (DSFs) in an n-type 4H-SiC substrate with a nitrogen concentration of 3.9×10 19 cm −3 was investigated using in situ synchrotron X-ray topography. DSF expansion was observed to be suppressed and immobilized above 1590 K, along with the partial dislocation (PD) shape being changed from a straight to zig-zag configuration. For a different heating process (higher heating rate), the PDs could continue to expand, even above 1590 K. Ex situ topography experiments revealed that the DSFs close to the specimen surface expanded widely, although those expanding toward the specimen interior became immobile. One possible mechanism for this immobilization was proposed, where the core structural changes from a Si-core to the C-core by climb motion induced by the interaction between the PDs and point defects (C interstitials).

Terahertz Raman Spectroscopy of Ligand-Protected Au8 Clusters.

For ligand-protected gold clusters, geometrical differences of gold cores and/or the presence of secondary gold core-ligand interactions influence their unique optical and electronic properties and can, in principle, be detected by spectral changes of gold core vibrations (phonon modes) in ultralow-frequency Raman spectroscopy. We report experimental and theoretical Raman spectra of Au8 clusters protected by phosphine ligands particularly in the "gold cluster fingerprint" region from 50 to 150 cm-1 Raman shift (1.5 to 4.5 terahertz, THz). A characteristic core breathing mode observed at ca. 123 cm-1 was sensitive to differences of core geometries. A new band was found at ca. 150 cm-1, originating from a local strain on a polyhedral gold core caused by weak Au···π interactions. THz Raman spectroscopy can be utilized for metal nanoclusters to visualize core structural changes and Au···π interactions, which cannot be captured by single crystal X-ray analysis.

Identifying new topoisomerase II poison scaffolds by combining publicly available toxicity data and 2D/3D-based virtual screening

Molecular descriptor (2D) and three dimensional (3D) shape based similarity methods are widely used in ligand based virtual drug design. In the present study pairwise structure comparisons among a set of 4858 DTP compounds tested in the NCI60 tumor cell line anticancer drug screen were computed using chemical hashed fingerprints and 3D molecule shapes to calculate 2D and 3D similarities, respectively. Additionally, pairwise biological activity similarities were calculated by correlating the 60 element vectors of pGI50 values corresponding to the cytotoxicity of the compounds across the NCI60 panel. Subsequently, we compared the power of 2D and 3D structural similarity metrics to predict the toxicity pattern of compounds. We found that while the positive predictive value and sensitivity of 3D and molecular descriptor based approaches to predict biological activity are similar, a subset of molecule pairs yielded contradictory results. By simultaneously requiring similarity of biological activities and 3D shapes, and dissimilarity of molecular descriptor based comparisons, we identify pairs of scaffold hopping candidates displaying characteristic core structural changes such as heteroatom/heterocycle change and ring closure. Attempts to discover scaffold hopping candidates of mitoxantrone recovered known Topoisomerase II (Top2) inhibitors, and also predicted new, previously unknown chemotypes possessing in vitro Top2 inhibitory activity.

Research on key factors and their interaction effects of electromagnetic force of high-speed solenoid valve.

Analysis consisting of numerical simulations along with lab experiments of interaction effects between key parameters on the electromagnetic force based on response surface methodology (RSM) has been also proposed to optimize the design of high-speed solenoid valve (HSV) and improve its performance. Numerical simulation model of HSV has been developed in Ansoft Maxwell environment and its accuracy has been validated through lab experiments. Effect of change of core structure, coil structure, armature structure, working air gap, and drive current on the electromagnetic force of HSV has been analyzed through simulation model and influence rules of various parameters on the electromagnetic force have been established. The response surface model of the electromagnetic force has been utilized to analyze the interaction effect between major parameters. It has been concluded that six interaction factors including working air gap with armature radius, drive current with armature thickness, coil turns with side pole radius, armature thickness with its radius, armature thickness with side pole radius, and armature radius with side pole radius have significant influence on the electromagnetic force. Optimal match values between coil turns and side pole radius; armature thickness and side pole radius; and armature radius and side pole radius have also been determined.

Tetranuclear Copper(II) Complexes Bridged by α-d-Glucose-1-Phosphate and Incorporation of Sugar Acids through the Cu4 Core Structural Changes

Tetranuclear copper(II) complexes containing alpha-D-glucose-1-phosphate (alpha-D-Glc-1P), [Cu4(mu-OH){mu-(alpha-D-Glc-1P)}2(bpy)4(H2O)2]X3 [X = NO3 (1a), Cl (1b), Br (1c)], and [Cu4(mu-OH){mu-(alpha-D-Glc-1P)}2(phen)4(H2O)2](NO3)3 (2) were prepared by reacting the copper(II) salt with Na2[alpha-D-Glc-1P] in the presence of diimine ancillary ligands, and the structure of 2 was characterized by X-ray crystallography to comprise four {Cu(phen)}2+ fragments connected by the two sugar phosphate dianions in 1,3-O,O' and 1,1-O mu4-bridging fashion as well as a mu-hydroxo anion. The crystal structure of 2 involves two chemically independent complex cations in which the C2 enantiomeric structure for the trapezoidal tetracopper(II) framework is switched according to the orientation of the alpha-D-glucopyranosyl moieties. Temperature-dependent magnetic susceptibility data of 1a indicated that antiferromagnetic spin coupling is operative between the two metal ions joined by the hydroxo bridge (J = -52 cm(-1)) while antiferromagnetic interaction through the Cu-O-Cu sugar phosphate bridges is weak (J = -13 cm(-1)). Complex 1a readily reacted with carboxylic acids to afford the tetranuclear copper(II) complexes, [Cu4{mu-(alpha-D-Glc-1P)}2(mu-CA)2(bpy)4](NO3)2 [CA = CH3COO (3), o-C6H4(COO)(COOH) (4)]. Reactions with m-phenylenediacetic acid [m-C6H4(CH2COOH)2] also gave the discrete tetracopper(II) cationic complex [Cu4{mu-(alpha-D-Glc-1P)}2(mu-m-C6H4(CH2COO)(CH2COOH))2(bpy)4](NO3)2 (5a) as well as the cluster polymer formulated as {[Cu4{mu-(alpha-D-Glc-1P)}2(mu-m-C6H4(CH2COO)2)(bpy)4](NO3)2}n (5b). The tetracopper structure of 1a is converted into a symmetrical rectangular core in complexes 3, 4, and 5b, where the hydroxo bridge is dissociated and, instead, two carboxylate anions bridge another pair of Cu(II) ions in a 1,1-O monodentate fashion. The similar reactions were applied to incorporate sugar acids onto the tetranuclear copper(II) centers. Reactions of 1a with delta-D-gluconolactone, D-glucuronic acid, or D-glucaric acid in dimethylformamide resulted in the formation of discrete tetracopper complexes with sugar acids, [Cu4{mu-(alpha-D-Glc-1P)}2(mu-SA)2(bpy)4](NO3)2 [SA = D-gluconate (6), D-glucuronate (7), D-glucarateH (8a)]. The structures of 6 and 7 were determined by X-ray crystallography to be almost identical with that of 3 with additional chelating coordination of the C-2 hydroxyl group of D-gluconate moieties (6) or the C-5 cyclic O atom of D-glucuronate units (7). Those with D-glucaric acid and D-lactobionic acid afforded chiral one-dimensional polymers, {[Cu4{mu-(alpha-D-Glc-1P)}2(mu-D-glucarate)(bpy)4](NO3)2}n (8b) and {[Cu4{mu-(alpha-D-Glc-1P)}2(mu-D-lactobionate)(bpy)4(H2O)2](NO3)3}n (9), respectively, in which the D-Glc-1P-bridged tetracopper(II) units are connected by sugar acid moieties through the C-1 and C-6 carboxylate O atoms in 8b and the C-1 carboxylate and C-6 alkoxy O atoms of the gluconate chain in 9. When complex 7 containing d-glucuronate moieties was heated in water, the mononuclear copper(II) complex with 2-dihydroxy malonate, [Cu(mu-O2CC(OH)2CO2)(bpy)] (10), and the dicopper(II) complex with oxalate, [Cu2(mu-C2O4)(bpy)2(H2O)2](NO3)2 (11), were obtained as a result of oxidative degradation of the carbohydrates through C-C bond cleavage reactions.

Correlation and prediction of moisture-mediated dissolution stability for benazepril hydrochloride tablets.

This report investigated dissolution stability of benazepril hydrochloride tablets. Reduction in dissolution rate was observed for benazepril hydrochloride tablets when they were subjected to stressed storage condition (40 degrees C/75% RH) for prolonged periods of time (1-3 months). Moisture contents of initial and stressed tablets were measured by Karl Fischer method. Comparative thermal and physical characterizations of initial and stressed tablets were also performed. A mathematical model that was used to predict possible reduction in dissolution rate was proposed and validated using experimental data. It was found that there was a direct correlation between moisture content of benazepril hydrochloride tablets and their percentage of dissolution at 10 min. At moisture content below 3.5%, there were no significant changes in dissolution values. Beyond that point, however, a close to linear decrease in dissolution was observed as a function of increase in moisture content. Results from thermal and X-ray analysis have ruled out possible changes in drug substance. Other physical characterization, such as scanning electron microscope and mercury porosimetry measurements, revealed changes in core structure of stressed tablets vs. initial tablets. Based on results from these measurements, "preactivation" of disintegrant was identified as the mechanism for reduction in dissolution rate above critical moisture content. A simple physical model for moisture uptake of benazepril hydrochloride tablets was also proposed for predicting when, based on water vapor transmission and critical moisture content, dissolution rate will decline. Physical changes of tablets mediated by moisture were the main cause for reduction in dissolution. Inclusion of desiccant, although beneficial, cannot prevent reduction in dissolution completely. The simple physical model proposed in this report was found to be useful in predicting the dissolution stability of the dosage form.

Domain dislocation: a change of core structure in periplasmic binding proteins in their evolutionary history

Periplasmic binding proteins (PBPs) serve as receptors for various water-soluble ligands in ATP-binding cassette (ABC) transport systems, and form one of the largest protein families in eubacterial and archaebacterial genomes. They are considered to be derived from a common ancestor, judging from their similarities of three-dimensional structure, their mechanism of ligand binding and the operon structure of their genes. Nevertheless, there are two types of topological arrangements of the central β-sheets in their core structures. It follows that there must have been differentiation in the core structure, which we call “domain dislocation”, in the course of evolution of the PBP family. To find a clue as to when the domain dislocation occurred, we constructed phylogenetic trees for PBPs based on their amino acid sequences and three-dimensional structures, respectively. The trees show that the proteins of each type clearly cluster together, strongly indicating that the change in the core structure occurred only once in the evolution of PBPs. We also constructed a phylogenetic tree for the ABC proteins that are encoded by the same operon of their partner PBP, and obtained the same result. Based on the phylogenetic relationship and comparison of the topological arrangements of PBPs, we obtained a reasonable genealogical chart of structural changes in the PBP family. The present analysis shows that the unidirectional change of protein evolution is clearly deduced at the level of protein three-dimensional structure rather than the level of amino acid sequence.

Conformational changes in the core structure of bacteriorhodopsin.

Bacteriorhodopsin (bR) is the light-driven proton pump found in the purple membrane of Halobacterium salinarium. In this work, structural changes occurring during the bR photocycle in the core structure of bR, which is normally inaccessible to hydrogen/deuterium (H/D) exchange, have been probed. FTIR difference bands due to vibrations of peptide groups in the core region of bR have been assigned by reconstituting and regenerating delipidated bR in the presence of D2O. Exposure of bR to D2O even after long periods causes only a partial shift of the amide II band due to peptide NH --> ND exchange only of peripheral peptide structure. However, the amide II band completely downshifts when reconstitution/regeneration of bR is performed in the presence of D2O, indicating that almost the entire core backbone structure of bR undergoes H/D exchange. Peripheral regions can then be reexchanged in H2O, leaving the core backbone region deuterated. Low-temperature FTIR difference spectra on these core-deuterated samples reveal that peptide groups in the core region respond to retinal isomerization as early as the K intermediate. By formation of the M intermediate, infrared differences in the amide I region are dominated by much larger structural changes occurring in the core structure. In the amide II region, difference bands appear upon K formation and increase upon M formation which are similar to those observed upon the cooling of bacteriorhodopsin. This work shows that retinal isomerization induces conformational changes in the bacteriorhodopsin core structure during the early photocycle which may involve an increase in the strength of intramolecular alpha-helical hydrogen bonds.

Molecular Dynamics Simulation of (c+a) Edge Dislocation Core Structure in HCP Crystal

The core structures of (c+a) edge dislocation in a HCP crystal have been investigated by computer simulation. An elastic perfect edge dislocation with Burgers vector (c+a) was introduced into the crystal, which was relaxed by molecular dynamic method. In this calculation, a Lennard-Jones type pair potential is used. Two types of core are stable at OK ; one is a perfect dislocation and the other is two 1/2(c+a) partial dislocations. While the core spreaded into two 1/2(c+a) partial dislocations was still stable at higher temperatures, the core of perfect dislocation extended parallel to basal plane. Changes of these core structures by application of shear stress have been also investigated. The two 1/2(c+a) partial dislocations glided separately on the slip plane. In contrast, the extended core emitted a 1/2(c+a) partial dislocations and expand stacking fault with increasing stress, but the rest part of dislocation did not move. These results suggest that the (c+a) edge dislocation glides on the plane as two 1/2(c+a) partial dislocations and becomes to be sessile due to change of core structure. This change of core structure from glissile to sessile causes the anormalous temperature dependence of yield stress observed in HCP metals.

Nonpairing like-nucleon valence residual interactions.

Nonpairing like-nucleon residual interactions, \ensuremath{\delta}${\mathit{V}}_{\mathit{n}\mathit{n}}$ and \ensuremath{\delta}${\mathit{V}}_{\mathit{p}\mathit{p}}$, of the last two neutrons or protons are extracted from double differences of nuclear binding energies for all even-even nuclei. They are found to be weakly repulsive and, combined with analogous information on p-n interactions, provide an alternate way of demonstrating that the T=0 interaction is strongly attractive. Anomalies in \ensuremath{\delta}${\mathit{V}}_{\mathit{n}\mathit{n}}$ and \ensuremath{\delta}${\mathit{V}}_{\mathit{p}\mathit{p}}$ are shown to correlate with changes in core structure, and repulsive spikes for N=Z nuclei are interpreted in terms of shell-model calculations with realistic interactions.

On non-glide stresses and their influence on the screw dislocation core in body-centred cubic metals. II. The core structure

The change in core structure of the screw dislocation in a body-centred cubic lattice subjected to a general applied stress tensor is studied by means of computer simulation. The large variations observed are found not to be correlated with the applied stress, in that the same deformed core structure can be realized by many different combinations of stress components. Instead, the core structure is found to be characterized almost exclusively by the magnitude and orientation of the induced glide strain, with a much smaller dependence on the glide stress. This means that while the force acting on a dislocation is defined by the applied stress, it is the elastic strain within the lattice that determines the resistance to motion. This explains the anomalously large dependence of the Peierls stress upon non-glide components of the applied stress tensor. The Peierls stress varies strongly with the shape of the dislocation core, which depends upon the glide strain. However, the glide strain is in turn dependent on non-glide components of the applied stress by way of anisotropic elastic couplings. Therefore the Peierls stress is itself dependent on the non-glide stresses, to an extent governed by the elastic anisotropy. The possible origin of the strain-dependence of the core structure in elastic strain multiplet forces (equal and opposite generalized forces acting on the dislocation) is discussed briefly, as are implications for the phenomenon of ductile fracture.