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Short-range Order (short-range + order)
Selected AbstractsStructural Characterization of the Transient Amorphous Calcium Carbonate Precursor Phase in Sea Urchin Embryos,ADVANCED FUNCTIONAL MATERIALS, Issue 10 2006Y. Politi Abstract Sea urchin embryos form their calcitic spicular skeletons via a transient precursor phase composed of amorphous calcium carbonate (ACC). Transition of ACC to calcite in whole larvae and isolated spicules during development has been monitored using X-ray absorption spectroscopy (XAS). Remarkably, the changing nature of the mineral phase can clearly be monitored in the whole embryo samples. More detailed analyses of isolated spicules at different stages of development using both XAS and infrared spectroscopy demonstrate that the short-range order of the transient ACC phase resembles calcite, even though infrared spectra show that the spicules are mostly composed of an amorphous mineral phase. The coordination sphere is at first distorted but soon adopts the octahedral symmetry typical of calcite. Long-range lattice rearrangement follows to form the calcite single crystal of the mature spicule. These studies demonstrate the feasibility of real-time monitoring of mineralized-tissue development using XAS, including the structural characterization of transient amorphous phases at the atomic level. [source] Investigation of penetratin peptides Part 1.JOURNAL OF PEPTIDE SCIENCE, Issue 4 2002The environment dependent conformational properties of penetratin, two of its derivatives Abstract The homeodomain, the DNA-binding domain of Antennapedia homeoprotein, is composed of three ,-helices and one ,-turn between helices II and III. Its third helix from the N -terminal (helix III) can translocate through the cell membrane into the nucleus and can be used as an intracellular vehicle for the delivery of oligopeptides and oligonucleotides. To the best of our knowledge, this helix III, called penetratin, which consists of 16 amino acids, is internalized by cells in a specific, non-receptor-mediated manner. For a better understanding of the mechanism of the transfer, the structure of penetratin was examined in both extracellular matrix-mimetic and membrane-mimetic environments; 1H-NMR and CD spectroscopic measurements were performed in mixtures of TFE/water with different ratios. The molecular conformations of two analogue peptides [(6,14-Phe)-penetratin and a 12 amino acid penetratin derivative (peptide 3)] were also studied. An atomic level comprehensive analysis of penetratin and its two analogues was performed. In a membrane-mimetic solvent system (TFEd2/water = 9 : 1), on the basis of 553 distance restraints, the 4,12 region of penetratin exhibits a bent, irregular helical structure on NMR examination. Interactions between hydrophobic amino acid residues in conjunction with H-bonds stabilize the secondary structure of the molecule. Thus, both derivatives adopt a helix-like conformation. However, while (6,14-Phe)-penetratin displays both ,-helical and 310 -helical features, the structure of peptide 3 is predominantly a 310 -helix. Of the three peptides, surprisingly (6,14-Phe)-penetratin has the largest helical content. An increase in the polarity of the molecular environment gradually disintegrates these helix-like secondary structures. In a highly aqueous molecular system (TFEd2/water = 1 : 9), the fast exchange of multiple conformers leads to too few distance restraints being extracted, therefore the NMR structures can no longer be determined. The NMR data show that only short-range order can be traced in these peptides. Under these conditions, the molecules adopt nascent helix-like structures. On the other hand, CD spectra could be recorded at any TFE/water ratio and the conformational interconversion could therefore be monitored as a function of the polarity of the molecular environment. The CD data were analysed comprehensively by the quantitative deconvolution method (CCA+). All three penetratin peptides display helical conformational features in a low dielectric medium, with significant differences as a function of their amino acid composition. However, these conformational features are gradually lost during the shift from an apolar to a polar molecular environment. Copyright © 2002 European Peptide Society and John Wiley & Sons, Ltd. [source] Order and Disorder in Powder Mixtures: Spatial Distribution Functions as Tools to Assess Powder HomogeneityPARTICLE & PARTICLE SYSTEMS CHARACTERIZATION, Issue 5-6 2008Albert Mihranyan Abstract In interactive mixtures with small carrier particles, the content variability is often higher than predicted by available models despite the significant degree of interaction visualized with Scanning Electron Microscopy (SEM). The present work details how pair-correlation functions can be used to reveal information about the spatial distribution of mixture constituents and their interactions. SEM pictures of a 2,% w/w oxazepam/sodium starch glycolate (SSG) mixture were recorded (n = 14). The constituent coordinates were extracted and pair-correlation functions as well as the cross-correlation function were calculated. A significant degree of interaction was observed between the constituents in the experimental mixture, compared to a randomized control system. In particular, the probability of finding an oxazepam particle was especially high inside the perimeter of the carrier particle and along its edges. The observed cross-correlation between oxazepam and SSG particles was periodic and repeated at distances corresponding to 1,1.5 carrier diameters. It was concluded that interactive mixtures of powders can be compared to disordered/amorphous solids since both exhibit short-range order, whilst lacking long-range translational periodicity. [source] Short-range order diffuse scattering in quasicrystalsACTA CRYSTALLOGRAPHICA SECTION A, Issue 3 2010Akiji Yamamoto A theory for the diffuse scattering intensity owing to short-range order (SRO) in quasicrystals is given. The diffuse scattering intensity can be calculated based on higher-dimensional cluster models of quasicrystals. It is determined by the overlapped area (or volume) of occupation domains separated from each other by distances up to the correlation length and the SRO correlation functions. It is applied to a random atom distribution in phason flip sites in the Penrose pattern. To confirm the validity of the derived formula, analytical and numerical results for this case have been compared. Both results give similar diffuse scattering intensity, suggesting the validity of the theory. [source] Magnetic short-range order diffuse scattering in quasicrystalsACTA CRYSTALLOGRAPHICA SECTION A, Issue 3 2010Akiji Yamamoto An analytical expression is derived for the short-range order (SRO) magnetic neutron diffuse scattering intensity in quasicrystals, and it is applied to a fictitious model of spin-orientation disorder in the Penrose pattern. The SRO diffuse scattering intensity depends on the overlapped volume of the occupation domains which are separated from each other by distances less than the correlation length and the SRO correlation functions. Analytical results for four different spin arrangements in the Penrose pattern are compared with numerical ones. The corresponding analytical and numerical results for all the cases are quite similar, suggesting the validity of the analytical expression. [source] Simultaneous fitting of X-ray and neutron diffuse scattering dataACTA CRYSTALLOGRAPHICA SECTION A, Issue 1 2007D. J. Goossens Conventional crystallographic refinement uses the Bragg-peak intensities and gives the single-site average crystal structure. Information about short-range order and local order is contained in the diffuse scattering that is distributed throughout reciprocal space. Models of the short-range order in materials can now be automatically refined. The complementarity of X-ray and neutron diffraction data, and the value of simultaneously refining a structural model against both types of data, has long been known. This paper presents the first refinement of a short-range-order model against comprehensive X-ray and neutron diffuse scattering data simultaneously. The sample is the organic molecular crystal benzil, C14H10O2 (for neutron work H is replaced by D). The technique gives new insights into local order in crystalline materials, including the dynamic correlation structure indicative of the dynamics of molecules in the crystalline state, and successfully overcomes limitations of using only the X-ray data set. [source] Diffuse scattering and short-range order in uranium iodine phthalocyanine [U1,xPc2]I2,y and the X-ray structure analysis of crystals with diffuse superstructure reflectionsACTA CRYSTALLOGRAPHICA SECTION B, Issue 3 2003J. Krawczyk Crystals of uranium iodine phthalocyanine present an example of a disordered commensurate modulated structure of the intergrowth type. The short-range order of both uranium ions and iodine chains [I]n has been analysed by Reverse Monte Carlo (RMC) simulation of X-ray diffuse scattering. The diffraction pattern of uranium iodine phthalocyanine contains diffuse superstructure reflections. In the routine crystal structure analysis diffuse superstructure reflections may be either omitted or measured and classified along with other Bragg reflections. The crystal structure of uranium iodine phthalocyanine is an example of such ambiguity. The crystal structures of two specimens of [U1,xPc2]I2,y with slightly different composition have been published in the literature with different space groups and unit cells. We have shown that the structure of both specimens differs only in the degree of short-range order and is isostructural with [YbPc2]I2. We have also shown that while the omission of diffuse reflections results in the average crystal structure, the treatment of these reflections as normal Bragg reflections is incorrect and produces the structure averaged over a limited small range. [source] | |||||||||||||