A detailed single chain model for molten poly(tetrafluoroethylene) from a novel structure refinement technique on neutron scattering data

We present a new methodology that couples neutron diffraction experiments over a wide Q range with single chain modelling in order to explore, in a quantitative manner, the intrachain organization of non-crystalline polymers. The technique is based on the assignment of parameters describing the chemical, geometric and conformational characteristics of the polymeric chain, and on the variation of these parameters to minimize the difference between the predicted and experimental diffraction patterns. The method is successfully applied to the study of molten poly(tetrafluoroethylene) at two different temperatures, and provides unambiguous information on the configuration of the chain and its degree of flexibility. From analysis of the experimental data a model is derived with CC and CF bond lengths of 1.58 and 1.36 Å, respectively, a backbone valence angle of 110° and a torsional angle distribution which is characterized by four isometric states, namely a split trans state at ± 18°, giving rise to a helical chain conformation, and two gauche states at ± 112°. The probability of trans conformers is 0.86 at T = 350°C, which decreases slightly to 0.84 at T = 400°C. Correspondingly, the chain segments are characterized by long all-trans sequences with random changes in sign, rather anisotropic in nature, which give rise to a rather stiff chain. We compare the results of this quantitative analysis of the experimental scattering data with the theoretical predictions of both force fields and molecular orbital conformation energy calculations.

Crystal structure refinement of Co-doped lanthanum chromites

Results of crystal structure refinements and phase quantification for samples of Co-doped lanthanum chromites with nominal composition LaCr(1-x)Co(x)O(3), for x=0.00, 0.10, 0.20, and 0.30, prepared by combustion synthesis are presented. The resulting powders were characterized by scanning electron microscopy and X-ray diffraction (XRD). The XRD patterns were obtained with Cu K alpha radiation for non-doped lanthanum chromite sample and additionally with Cr K alpha radiation for Co-doped lanthanum chromites samples, in order to enhance the signal from scattering. Rietveld analysis of XRD data showed that the studied samples presented the lanthanum chromite with an orthorhombic structure (Pnma), except for the composition with x=0.30, in which the space group was found to be R (3) over barc. (C) 2008 International Centre for Diffraction Data.

Hyalotekite, (Ba,Pb,K)(4)(Ca,Y)(2)Si-8(B,Be)(2)(Si,B)(2)O28F, a Tectosilicate Related to Scapolite: New Structure Refinement, Phase Transitions and a Short-Range Ordered 3B Superstructure

Hyalotekite, a framework silicate of composition (Ba,Pb,K)(4)(Ca,Y)(2)Si-8(B,Be)(2) (Si,B)(2)O28F, is found in relatively high-temperature(greater than or equal to 500 degrees C) Mn skarns at Langban, Sweden, and peralkaline pegmatites at Dara-i-Pioz, Tajikistan. A new paragenesis at Dara-i-Pioz is pegmatite consisting of the Ba borosilicates leucosphenite and tienshanite, as well as caesium kupletskite, aegirine, pyrochlore, microcline and quartz. Hyalotekite has been partially replaced by barylite and danburite. This hyalotekite contains 1.29-1.78 wt.% Y2O3, equivalent to 0.172-0.238 Y pfu or 8-11% Y on the Ca site; its Pb/(Pb+Ba) ratio ranges 0.36-0.44. Electron microprobe F contents of Langban and Dara-i-Pioz hyalotekite range 1.04-1.45 wt.%, consistent with full occupancy of the F site. A new refinement of the structure factor data used in the original structural determination of a Langban hyalotekite resulted in a structural formula, (Pb1.96Ba1.86K0.18)Ca-2(B1.76Be0.24)(Si1.56B0.44)Si8O28F, consistent with chemical data and all cations with positive-definite thermal parameters, although with a slight excess of positive charge (+57.14 as opposed to the ideal +57.00). An unusual feature of the hyalotekite framework is that 4 of 28 oxygens are non-bridging; by merging these 4 oxygens into two, the framework topology of scapolite is obtained. The triclinic symmetry of hyalotekite observed at room temperature is obtained from a hypothetical tetragonal parent structure via a sequence of displacive phase transitions. Some of these transitions are associated with cation ordering, either Pb-Ba ordering in the large cation sites, or B-Be and Si-B ordering on tetrahedral sites. Others are largely displacive but affect the coordination of the large cations (Pb, Ba, K, Ca). High-resolution electron microscopy suggests that the undulatory extinction characteristic of hyalotekite is due to a fine mosaic microstructure. This suggests that at least one of these transitions occurs in nature during cooling, and that it is first order with a large volume change. A diffuse superstructure observed by electron diffraction implies the existence of a further stage of short-range cation ordering which probably involves both (Pb,K)-Ba and (BeSi,BB)-BSi.

New methods of structure refinement for macromolecular structure determination by NMR

Recent advances in multidimensional NMR methodology have permitted solution structures of proteins in excess of 250 residues to be solved. In this paper, we discuss several methods of structure refinement that promise to increase the accuracy of macromolecular structures determined by NMR. These methods include the use of a conformational database potential and direct refinement against three-bond coupling constants, secondary 13C shifts, 1H shifts, T1/T2 ratios, and residual dipolar couplings. The latter two measurements provide long range restraints that are not accessible by other solution NMR parameters.

Modeling Metal Protein Complexes from Experimental Extended X-ray Absorption Fine Structure using Computational Intelligence

Experimental Extended X-ray Absorption Fine Structure (EXAFS) spectra carry information about the chemical structure of metal protein complexes. However, pre- dicting the structure of such complexes from EXAFS spectra is not a simple task. Currently methods such as Monte Carlo optimization or simulated annealing are used in structure refinement of EXAFS. These methods have proven somewhat successful in structure refinement but have not been successful in finding the global minima. Multiple population based algorithms, including a genetic algorithm, a restarting ge- netic algorithm, differential evolution, and particle swarm optimization, are studied for their effectiveness in structure refinement of EXAFS. The oxygen-evolving com- plex in S1 is used as a benchmark for comparing the algorithms. These algorithms were successful in finding new atomic structures that produced improved calculated EXAFS spectra over atomic structures previously found.

THE CRYSTAL STRUCTURE OF A MICROLITE-GROUP MINERAL WITH A FORMULA NEAR NaCaTa(2)O(6)F FROM THE MORRO REDONDO MINE, CORONEL MURTA, MINAS GERAIS, BRAZIL

We present electron-microprobe and single-crystal X-ray-diffraction data for a microlite-group mineral with a formula near NaCaTa(2)O(6)F from the Morro Redondo mine, Coronel Murta, Minas Gerais, Brazil. On the basis of these data, the formula is A(Na(0.88)Ca(0.88)Pb(0.02)square(0.22))(Sigma 2.00) (B)(Ta(1.70)Nb(0.14)Si(0.12)As(0.04))(Sigma 2.00) (X)[(O(5.75)(OH)(0.25)](Sigma 6.00) (Y)(F(0.73)square(0.27))(Sigma 1.00). According to the new nomenclature for the pyrochlore-supergroup minerals, it is intermediate between fluornatromicrolite and "" fluorcalciomicrolite"". The crystal structure, F (d3) over barm, a = 10.4396(12) angstrom, has been refined to an R(1) value of 0.0258 (wR(2) = 0.0715) for 107 reflections (MoK alpha radiation). There is a scarcity of crystal-chemical data for pyrochlore-supergroup minerals in the literature. A compilation of these data is presented here.

Investigation on the structure of liquid N-methylformamide-dimethylsulfoxide mixtures

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Structure determination of proteins and peptides in solution: simulation, chirality and NMR studies

The study of protein fold is a central problem in life science, leading in the last years to several attempts for improving our knowledge of the protein structures. In this thesis this challenging problem is tackled by means of molecular dynamics, chirality and NMR studies. In the last decades, many algorithms were designed for the protein secondary structure assignment, which reveals the local protein shape adopted by segments of amino acids. In this regard, the use of local chirality for the protein secondary structure assignment was demonstreted, trying to correlate as well the propensity of a given amino acid for a particular secondary structure. The protein fold can be studied also by Nuclear Magnetic Resonance (NMR) investigations, finding the average structure adopted from a protein. In this context, the effect of Residual Dipolar Couplings (RDCs) in the structure refinement was shown, revealing a strong improvement of structure resolution. A wide extent of this thesis is devoted to the study of avian prion protein. Prion protein is the main responsible of a vast class of neurodegenerative diseases, known as Bovine Spongiform Encephalopathy (BSE), present in mammals, but not in avian species and it is caused from the conversion of cellular prion protein to the pathogenic misfolded isoform, accumulating in the brain in form of amiloyd plaques. In particular, the N-terminal region, namely the initial part of the protein, is quite different between mammal and avian species but both of them contain multimeric sequences called Repeats, octameric in mammals and hexameric in avians. However, such repeat regions show differences in the contained amino acids, in particular only avian hexarepeats contain tyrosine residues. The chirality analysis of avian prion protein configurations obtained from molecular dynamics reveals a high stiffness of the avian protein, which tends to preserve its regular secondary structure. This is due to the presence of prolines, histidines and especially tyrosines, which form a hydrogen bond network in the hexarepeat region, only possible in the avian protein, and thus probably hampering the aggregation.

Mimicking the action of GroEL in molecular dynamics simulations: Application to the refinement of protein structures

Bacterial chaperonin, GroEL, together with its co-chaperonin, GroES, facilitates the folding of a variety of polypeptides. Experiments suggest that GroEL stimulates protein folding by multiple cycles of binding and release. Misfolded proteins first bind to an exposed hydrophobic surface on GroEL. GroES then encapsulates the substrate and triggers its release into the central cavity of the GroEL/ES complex for folding. In this work, we investigate the possibility to facilitate protein folding in molecular dynamics simulations by mimicking the effects of GroEL/ES namely, repeated binding and release, together with spatial confinement. During the binding stage, the (metastable) partially folded proteins are allowed to attach spontaneously to a hydrophobic surface within the simulation box. This destabilizes the structures, which are then transferred into a spatially confined cavity for folding. The approach has been tested by attempting to refine protein structural models generated using the ROSETTA procedure for ab initio structure prediction. Dramatic improvements in regard to the deviation of protein models from the corresponding experimental structures were observed. The results suggest that the primary effects of the GroEL/ES system can be mimicked in a simple coarse-grained manner and be used to facilitate protein folding in molecular dynamics simulations. Furthermore, the results Sur port the assumption that the spatial confinement in GroEL/ES assists the folding of encapsulated proteins.

Protein crystallography and examples of its applications in medicinal chemistry

The field of protein crystallography inspires and enthrals, whether it be for the beauty and symmetry of a perfectly formed protein crystal, the unlocked secrets of a novel protein fold, or the precise atomic-level detail yielded from a protein-ligand complex. Since 1958, when the first protein structure was solved, there have been tremendous advances in all aspects of protein crystallography, from protein preparation and crystallisation through to diffraction data measurement and structure refinement. These advances have significantly reduced the time required to solve protein crystal structures, while at the same time substantially improving the quality and resolution of the resulting structures. Moreover, the technological developments have induced researchers to tackle ever more complex systems, including ribosomes and intact membrane-bound proteins, with a reasonable expectation of success. In this review, the steps involved in determining a protein crystal structure are described and the impact of recent methodological advances identified. Protein crystal structures have proved to be extraordinarily useful in medicinal chemistry research, particularly with respect to inhibitor design. The precise interaction between a drug and its receptor can be visualised at the molecular level using protein crystal structures, and this information then used to improve the complementarity and thus increase the potency and selectivity of an inhibitor. The use of protein crystal structures in receptor-based drug design is highlighted by (i) HIV protease, (ii) influenza virus neuraminidase and (iii) prostaglandin H-2-synthetase. These represent, respectively, examples of protein crystal structures that (i) influenced the design of drugs currently approved for use in the treatment of HIV infection, (ii) led to the design of compounds currently in clinical trials for the treatment of influenza infection and (iii) could enable the design of highly specific non-steroidal anti-inflammatory drugs that lack the common side-effects of this drug class.

Reduction of symmetry in grandite solid solution

The results of a crystal structure refinement of an anisotropic grandite garnet specimen with composition Gro36-4 And63-6 are given. The structure obtained has orthorrombic symmetry (space group Fddd) and is compared with similar results obtained by other authors. In all cases the reduction of symmetry is due to the ordering of Fe3+ and Al in octahedral sites. Non cubic structures of grandites are discussed in connection with optical, morphological an grou-th features of these minerals.

Real-time Image-based RGB-D Camera Motion Tracking and Environment Mapping

In this work, image based estimation methods, also known as direct methods, are studied which avoid feature extraction and matching completely. Cost functions use raw pixels as measurements and the goal is to produce precise 3D pose and structure estimates. The cost functions presented minimize the sensor error, because measurements are not transformed or modified. In photometric camera pose estimation, 3D rotation and translation parameters are estimated by minimizing a sequence of image based cost functions, which are non-linear due to perspective projection and lens distortion. In image based structure refinement, on the other hand, 3D structure is refined using a number of additional views and an image based cost metric. Image based estimation methods are particularly useful in conditions where the Lambertian assumption holds, and the 3D points have constant color despite viewing angle. The goal is to improve image based estimation methods, and to produce computationally efficient methods which can be accomodated into real-time applications. The developed image-based 3D pose and structure estimation methods are finally demonstrated in practise in indoor 3D reconstruction use, and in a live augmented reality application.

Preliminary X-ray diffraction analysis of YcdB from Escherichia coli: a novel haem-containing and Tat-secreted periplasmic protein with a potential role in iron transport

YcdB is a periplasmic haem-containing protein from Escherichia coli that has a potential role in iron transport. It is currently the only reported haem-containing Tat-secreted substrate. Here, the overexpression, purification, crystallization and structure determination at 2.0 angstrom resolution are reported for the apo form of the protein. The apo-YcdB structure resembles those of members of the haem-dependent peroxidase family and thus confirms that YcdB is also a member of this family. Haem-soaking experiments with preformed apo-YcdB crystals have been optimized to successfully generate haem-containing YcdB crystals that diffract to 2.9 angstrom. Completion of model building and structure refinement are under way.

THE PYROCHLORE SUPERGROUP OF MINERALS: NOMENCLATURE

A new scheme of nomenclature for the pyrochlore supergroup, approved by the CNMNC-IMA, is based on the ions at the A, B and Y sites. What has been referred to until now as the pyrochlore group should be referred to as the pyrochlore supergroup, and the subgroups should be changed to groups. Five groups are recommended, based on the atomic proportions of the B atoms Nb, Ta, Sb, Ti, and W. The recommended groups are pyrochlore, microlite, romite, betafite, and elsmoreite, respectively. The new names are composed of two prefixes and one root name (identical to the name of the group). The first prefix refers to the dominant anion (or cation) of the dominant valence [or H(2)O or rectangle] at the Y site. The second prefix refers to the dominant cation of the dominant valence [or H(2)O or rectangle] at the A site. The prefix "" keno-"" represents "" vacancy"". Where the first and second prefixes are equal, then only one prefix is applied. Complete descriptions are missing for the majority of the pyrochlore-supergroup species. Only seven names refer to valid species on the grounds of their complete descriptions: oxycalciopyrochlore, hydropyrochlore, hydroxykenomicrolite, oxystannomicrolite, oxystibiomicrolite, hydroxycalcioromite, and hydrokenoelsmoreite. Fluornatromicrolite is an IMA-approved mineral, but the complete description has not yet been published. The following 20 names refer to minerals that need to be completely described in order to be approved as valid species: hydroxycalciopyrochlore, fluornatropyrochlore, fluorcalciopyrochlore, fluorstrontiopyrochlore, fluorkenopyrochlore, oxynatropyrochlore, oxyplumbopyrochlore, oxyyttropyrochlore-(Y), kenoplumbopyrochlore, fluorcalciomicrolite, oxycalciomicrolite, kenoplumbomicrolite, hydromicrolite, hydrokenomicrolite, oxycalciobetafite, oxyuranobetafite, fluornatroromite, fluorcalcioromte, oxycalcioromite, and oxyplumboromite. For these, there are only chemical or crystalstructure data. Type specimens need to be defined. Potential candidates for several other species exist, but are not sufficiently well characterized to grant them any official status. Ancient chemical data refer to wet-chemical analyses and commonly represent a mixture of minerals. These data were not used here. All data used represent results of electron-microprobe analyses or were obtained by crystal-structure refinement. We also verified the scarcity of crystal-chemical data in the literature. There are crystalstructure determinations published for only nine pyrochlore-supergroup minerals: hydropyrochlore, hydroxykenomicrolite, hydroxycalcioromite, hydrokenoelsmoreite, hydroxycalciopyrochlore, fluorcalciopyrochlore, kenoplumbomicrolite, oxycalciobetafite, and fluornatroromite. The following mineral names are now discarded: alumotungstite, bariomicrolite, bariopyrochlore, bindheimite, bismutomicrolite, bismutopyrochlore, bismutostibiconite, calciobetafite, ceriopyrochlore-(Ce), cesstibtantite, ferritungstite, jixianite, kalipyrochlore, monimolite, natrobistantite, partzite, plumbobetafite, plumbomicrolite, plumbopyrochlore, stannomicrolite, stetefeldtite, stibiconite, stibiobetafite, stibiomicrolite, strontiopyrochlore, uranmicrolite, uranpyrochlore, yttrobetafite-(Y), and yttropyrochlore-(Y).

A Monte Carlo Revisiting of N-Methylformamide and Acetone

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)