bluuebunny/crossref_metadata_2025 huggingface dataset:
In situ monitoring of hydration and dehydration in pharmaceutical solids
Authors: Bond Andrew , Raijada Dhara , Rantanen Jukka , Sovago Ioana , van de Streek Jacco , Larsen Flemming , Thomas Diana
Published: November 2015

This talk will describe a multi-technique study of hydration and dehydration in pharmaceutical solids, using sodium naproxen as a case study. The aim of the work is to establish molecular-level structural understanding of the chemical changes that take place in the solid state as a function of temperature and relative humidity. Dynamic vapour sorption (DVS) analysis on the anhydrous compound carried out as a function of temperature provides a preliminary overview of the solid-form landscape and identifies static conditions to obtain four different hydrate forms [1]. Differences in the sorption and desorption cycles indicates the existence of a polymorphic dihydrate, and the two polymorphs show significant differences in their dehydration behaviour. Crystal structures are established for all phases in the system using either single-crystal or powder X-ray diffraction data, supplemented by dispersion-corrected density functional theory (DFT-D) calculations. The hydration and dehydration processes are monitored by powder X-ray diffraction (PXRD), as a function of relative humidity and temperature, and by variable-temperature solid-state 13C and 23Na NMR. Synchrotron PXRD is applied to the two dihydrate polymorphs to monitor the dehydration processes in approximately real time. The kinetic and structural details of dehydration are established by applying parametric Rietveld refinement [2] to the synchrotron data. This approach adds a structural picture to the kinetic processes. The PXRD studies indicate an essentially continuous dehydration pathway from one of the dihydrate polymorphs to the monohydrate, but a stepped dehydration pathway for the other dihydrate polymorph. The different mechanisms are linked to different degrees of structural similarity, and in particular to the existence of topotactic or non-topotactic transformations between the dihydrate polymorphs and the unique monohydrate and anhydrate phases.
Effect of pressure on a mixed valence FeiiFeiii2complex
Authors: Madsen Solveig , Overgaard Jacob , Iversen Bo
Published: November 2015

Intramolecular electron transfer (ET) in mixed valence (MV) oxo-centered [FeiiFeiii2O(carboxylate)6(ligand)3]·solvent complexes is highly dependent on temperature, on the nature of the ligands, and on the presence of crystal solvent molecules [1]. Whereas the effects of temperature, crystal solvent, and ligand variation on the details of the ET have been explored thoroughly, the effect of pressure is less well described [2]. The effect of pressure on the ET in MV Fe3O(cyanoacetate)6(water)3has been investigated with single crystal X-ray diffraction and Mössbauer spectroscopy. Previous multi-temperature studies have shown that at room temperature the ET between the three Fe sites is fast and the observed structure of the Fe3core is a perfectly equilateral triangle [3]. Cooling the complex below 130 K induces a phase transition as the ET slows down. Below 120 K the Fe3core is distorted due to the localization of the itinerant electron on one of the three Fe sites in the triangle (the complex is then in the valence trapped state). The valence trapping is complete within a temperature interval of just 10 K. The abruptness of the transition has been attributed to the extended hydrogen bond network involving water ligands and cyano groups, promoting intermolecular cooperative effects. The high-pressure X-ray diffraction data show that there is a 900flip of half the cyano groups at 3.5 GPa, which dramatically changes the hydrogen bond network. At a slightly higher pressure, a phase transition is found to occur. The five single crystals investigated all broke into minor fragments at the transition; however triclinic unit cells, similar to the low temperature unit cell, could be indexed from selected spots. Additional evidence that the complex is valence trapped comes from high pressure Mössbauer spectra measured above the phase transition (4 GPa). The relationship between valence trapping and the structural changes will in this work be highlighted using void space and Hirshfeld surface analysis.
Gas hydrates at high pressure
Authors: Loveday J. , Bull C. , Frantzana A. , Wilson C. , Amos D. , Nelmes R.
Published: November 2015

The behaviour of gas hydrates at high pressure is of wide interest and importance. Gas hydrates are stablised by water-gas repulsive interactions. Information on the effect of changing density on these water-gas interactions provides fundamental insight into the nature of the water potential. Gas hydrates are also widely found in nature and systems like the ammonia-water and methane-water systems form the basis of 'mineralogy' of planetary bodies like Saturn's moon Titan. Finally, gas hydrates offer the possibility of cheap environmentally inert transportation and storage for gases like carbon dioxide and hydrogen. We have been carrying out investigations of a range of gas hydrates at high pressure using neutron and x-ray diffraction as well as other techniques. Results from these studies including; the phase diagram of the ammonia water system, the occupancies of hexgonal clathrate structures, and new structures in the carbon dioxide water system, will be presented.
Dynamical effects in solid hydrogen and hydrogen-deuterium mixtures at elevated pressures.
Authors: Magdau Ioan , Howie Ross , Ackland Graeme , Gregoryanz Eugene
Published: November 2015

We employed molecular dynamics simulations together with some novel theoretical techniques to calculate finite temperature Raman spectra in both hydrogen (H) and hydrogen-deuterium (HD) mixtures. By conditioning the simulations with the experimental data, we have discovered the true nature of Phase IV in solid hydrogen. X-ray and neutron diffraction measurements are virtually impossible in current state of the art experiments. The experimental investigation, thus, relies mainly on spectroscopic methods which provide minimal data about crystallography. Extensive work done so far [1] has led to an impressive amount of Raman and IR data up to pressures of almost 400 GPa. By carefully investigating the positions and widths of the peaks, they discovered phase IV of solid hydrogen and mapped out the melting curve up to very high pressures. Phase IV is only stable at elevated temperatures and therefore static relaxation calculations cannot reproduce the correct crystal structure. Previous theoretical work has predicted a class of exotic crystal structures with alternating layers of different character: B (well-defined molecules) and G (poorly-defined molecules) [2] that could qualitatively describe the Raman signal. By means of MD simulations we show that at high temperature, the Pc structure acquires higher symmetry which is sufficient to reproduce the exact position of the Raman peaks. It had been suggested that in a mixed hydrogen-deuterium alloy, the heavier atoms would segregate in the B layers which would decrease the overall zero-point energy and stabilise the Pc structure. Joining efforts with the experimental team we thoroughly investigated this problem. We found no evidence of isotopic layer segregation, but our theoretical model correctly described the Raman spectra found experimentally. We concluded that the phase boundaries in HD mixtures are slightly offset which we attribute to the inhomogeneous mass effect on the temperature of the broken symmetries, but the general behaviour is similar to that of solid hydrogen. We uncovered a new effect in HD, namely mass induced phonon localization. Matching experimental and theoretical results in this respect are yet another validation of the crystallographic conformation of phase IV.
Growth mechanisms of self-assembled gold nanoparticles in Deep Eutectic Solvent
Authors: Raghuwanshi Vikram Singh , Ochmann Miguel , Polzer Frank , Hoell Armin , Rademann Klaus
Published: November 2015

Self-assembled metallic nanoparticles are attractive candidates for plasmonic heating, non-linear optical switching [1], bio-analytical, chemical [2], catalytic , and surface enhanced RAMAN scattering (SERS) [3]. These applications are strongly dependent on the shape, size, composition, size distribution and volume fraction of nanoparticles. Here, self-assembly of gold nanoparticles (AuNPs) was obtained by low energy sputter deposition on Deep Eutectic Solvent (DES ; choline chloride and urea) surfaces and elucidated by Small Angle X-ray Scattering (SAXS), Cryogenic Transmission Electron Microscopy (Cryo-TEM) and UV-Vis. Data analysis shows the formation of spherically shaped AuNPs of 5 nm in diameter with narrow size distributions. Moreover, analysis reveals that prolongation of gold-sputtering time has no effect on the size of the particles and only the concentration of AuNPs increases linearly. The growth of the maxima in evaluated structure factor S(q) and the distance distribution function G(r) at higher concentrations of AuNPs is caused by the interference effects. Moreover, it indicates that the particles are not arranged in random but have a self-assembly in short-range order. Prolonged gold-sputtering time leads to increase in the ordering of the AuNPs with strong interactions. It is proposed that the self-assembly of AuNPs is due to the ionic liquid template effects of DES and the balancing physical forces. Moreover, a disulfide based stabilizer bis ((2-Mercaptoethyl) trimethylammonium) disulfide dichloride was applied to supress the self-assembly. The stabilizer even reverses the self-assembled or agglomerated AuNPs back to stable 5 nm individual particles. The templating effect of DES is compared with the non-templating solvent Castor oil. Our results will also pave a way to understand and control self-assembly of metallic and bimetallic nanoparticles.
Computational prediction of an icosahedral quasicrystal
Authors: Engel Michael , Damasceno Pablo , Phillips Carolyn , Glotzer Sharon
Published: November 2015

From the first quasicrystal discovered in the laboratory 30 years ago to the only known specimen of naturally occurring quasicrystals, quasicrystals with icosahedral symmetry have received great attention. There are more than one hundred stable icosahedral quasicrystals in metallic alloys; all are identified by their diffraction spectra. Despite this abundance, resolving the positions of the atoms within the solid has been possible only indirectly. Moreover, unlike dodecagonal and other axial quasicrystals, icosahedral quasicrystals have been observed neither in simulations nor in non-atomic (e.g. micellar or colloidal) systems, where real-space information would be available. Here we present an icosahedral quasicrystal discovered in computer simulation via self-assembly from the liquid phase. We provide a structure model by analyzing atomic surfaces and report the presence of phason flips. Our results constitute a direct microscopic confirmation of the higher-dimensional crystallographic description of icosahedral quasicrystals.
Controlled Self-Assembly of Soft-Matter Quasicrystals
Authors: Barkan Kobi , Engel Michael , Diamant Haim , Lifshitz Ron
Published: November 2015

A large number of soft-matter systems, whose building blocks range in size from several nanometers to almost a micron, have been shown in recent years to form ordered phases with dodecagonal (12-fold) symmetry (for recent reviews see [1]). Contrary to metallurgic quasicrystals, whose source of stability remains a question of great debate to this day, we show that the stability of certain soft-matter quasicrystals–interacting via pair potentials with repulsive cores, which are either bounded or only slowly diverging–can directly be explained. Their stability is attributed to the existence of two natural length scales in their isotropic pair potentials, along with an effective three-body interaction arising from entropy. We establish the validity of this mechanism at the level of a mean-field theory [2], and then use molecular dynamics simulations in two dimensions to confirm it beyond mean field, and to show that it leads to the formation of cluster crystals [3]. We demonstrate that our understanding of the stability mechanism allows us to generate a variety of desired structures, including decagonal and dodecagonal quasicrystals [3], suggesting a practical approach for their controlled self-assembly in laboratory realizations using synthesized soft-matter particles.
Crystallization by thermal processing of Poly(lactide) stereocomplex thin films
Authors: Takahashi Isao , Ozaki Yukihiro , Raghunatha Reddy Kummetha
Published: November 2015

Various properties of polymers such as optical, barrier and mechanical properties are substantially anisotropic, since molecular orientations of polymer chains strongly affect the physical properties. Controlling the chain orientation in the semicrystalline polymers can thus lead us to valuable technological breakthroughs. Polymer ultrathin films have attracted great attention due to their vast applications. In thin films, the molecular chain orientation depends on the method of processing, thickness and substrate interactions. In the present study, we report on the crystallization condition dependent molecular chain orientation and crystallinity peculiar to the ultrathin films of biodegradable Poly(lactide) (PLA) stereocomplex (SC) with thicknesses ranging from several nm to several hundred nm. Equimolar solution of two enantiomers of PLA, poly(L-lactide) (PLLA) and poly(D-lactide) (PDLA) has attracted great attention because of the formation of SC which shows decent physical properties better than PLLA and PDLA. Combination of surface sensitive X-ray diffraction and scattering techniques, including grazing incidence wide angle X-ray diffraction (GIWAXD), X-ray reflectivity (XRR) and grazing incidence small angle X-ray scattering (GISAXS) measured at synchrotron radiation facility (SPring-8, Japan) and infrared reflection absorption spectroscopy (IR-RAS) were used to characterize the film structures. In the SC films, two different polymer chain configurations, i.e., lying molecules and standing molecules revealed to be controlled by simple thermal processes.
GISAXS studies of mesoporous films using a standard laboratory diffractometer
Authors: Gateshki Milen , Kharchenko Alexander , Kidd Patricia
Published: November 2015

With the increasing number of GISAXS (Grazing-Incidence Small-Angle X-ray Scattering) applications for the investigation of materials surface nano-structures, comes the demand for a mainstream laboratory capability to run alongside the more established synchrotron facilities. GISAXS poses considerable challenges when scaling the method to fit a multipurpose laboratory instrument, including the achievement of good angular resolution at small scattering radius, the reduction of scatter from the direct beam and the observation of low intensity signals. We have developed a hardware solution that addresses these challenges. The recent availability of small size pixel (55 micron) photon counting detectors with very low noise characteristics has enabled the implementation of new 2D imaging GISAXS hardware for a standard 1.8KW laboratory X-ray source. In this work we present a number of results that illustrate the capabilities of the new experimental set-up based on a standard multipurpose diffractometer. We present GISAXS images and analysis of a mesoporous silica thin film with close-packed hexagonal type ordering of the pores. In [1] we have reported reflectometry results and analysis of this sample structure. The addition of GISAXS information demonstrates the versatility of the multipurpose diffractometer and the strength in combining methods on one instrument. Strongly scattering Ti-filled silica mesoporous films illustrate the relative ease with which GISAXS signals can be recorded, including even the weak signal below the critical angle of the sample (fig.1). The scattering patterns from both samples exhibit subtle departures from a simple symmetry, suggesting that the films may exhibit residual strain. Thin films with vertical mesopores provide their own challenges in the observation of scatter close and parallel to the specularly reflected beam. We present results in which scattering from Co-filled mesopore structures with 37nm pitch can be clearly resolved.
In-Situ Neutron Reflectometry on Polymer Thin Films in Different Environments
Authors: Torikai Naoya
Published: November 2015

Neutron reflectometry is indispensable for the studies on material interfaces and thin films, since it can probe the interfaces non-destructively with a quite high depth resolution. Here, the interfacial structures of polymer thin films in different environments: hot and wet, were examined by means of in-situ neutron reflectometry. The neutron reflectivity measurements were performed on a time-of-flight reflectometer SOFIA [1, 2] at the Japan Proton Accelerator Research Complex (J-PARC). The depth distribution of components was investigated for binary blend thin films of polystyrenes with different molecular weights to clarify the mechanism of de-wetting suppression effect by blending a small amount of the longer homologue. It was found by static measurements that the longer chains deplete from the air surface of the film, while they slightly localize at the interface with the substrate. The time evolution of the component distribution was also examined by in-situ measurements above the glass transition temperature in a vacuum. The structural change of lamellarly-ordered styrene-2-vinylpyridine (PS-P2VP) diblock copolymer thin film in contact with solvent was explored by in-situ neutron reflectometry with a conventional solid/liquid cell. During the block copolymer thin film was in contact with methanol, which is selective for P2VP, some of methanol penetrated into the film causing the structural change. However, the original structure was almost recovered after drying, though annealing effect was slightly observed. When toluene was made contact, which is selective for PS, the block copolymer thin film was immediately dissolved into, and never recovered.
Vapor Treatment of Block Copolymer Thin Films: GISAXS and Simulations
Authors: Zhang Jianqi , Posselt Dorthe , Sepe Alessandro , Perlich Jan , Smilgies Detlef-M. , Rudov Andrey , Patyukova Elena , Potemkin Igor , Papadakis Christine
Published: November 2015

The structural evolution in poly(styrene-b-butadiene) (P(S-b-B)) diblock copolymer thin films during treatment with cyclohexane vapor is investigated in-situ and in real-time using grazing-incidence small-angle X-ray scattering (GISAXS) [1]. Both the swelling and the drying process are investigated. The lamellae are initially perpendicular to the film surface, i.e. the film is laterally nanostructured. Cyclohexane is a good solvent for PB and a theta solvent for PS, i.e., it is slightly selective. Using incident angles above and below the polymer critical angle, structural changes near the film surface and in the entire film are distinguished. We find that, during swelling, the initially perpendicular lamellae tilt within the film. Our computer simulations [2] show that this is due to the tendency of the copolymers to assume less stretched chain conformations, i.e. the lamellae shrink upon solvent uptake. Since long-range mass transport is not easily possible, tilting allows satisfying the space-filling condition when the lamellae are shrinking. Surface-sensitive GISAXS experiments show that, at the film surface, the lamellae eventually vanish at the expense of a thin PB wetting layer. During the subsequent drying, the perpendicular lamellae reappear at the surface, and finally, PS blocks protrude because of the solvent selectivity. By modeling the 2D GISAXS images, the time-dependent height of the protrusions can be quantitatively extracted. Figure 1. (a) 2D GISAXS images during swelling (top row) and drying (bottom row). The times after the beginning of the vapor treatment are indicated. (b) Snapshots from computer simulations of perpendicular lamellae which tilt during the film swelling. From left to right, the degree of swelling increases.
Grazing-Transmission Scattering for Measuring Nano-structured Thin Films
Authors: Yager Kevin
Published: November 2015

We describe a new scattering geometry which can be used to quantify three-dimensional nanoscale order in thin films: Grazing-Transmission Small-Angle X-ray Scattering (GTSAXS). This technique collects sub-horizon scattering which exits from the edge of the sample, and does not suffer from the large refraction-distortions and multiple-scattering terms that complicate GISAXS data analysis. We also present a new modelling formalism applicable to superlattices of nano-objects, where lattice symmetry and nano-object size/shape can be arbitrarily defined.
In-situ grazing incidence scattering in information and communication technology
Authors: Roth Stephan
Published: November 2015

Novel functional materials rely on a profound understanding of nanoscale structure and processing. Employed as multilayered thin films and coatings, they find applications in smart sensors, organic electronics, organic photovoltaics and barrier layers. To create such organic and inorganic multilayers a multitude of deposition methods is used. These include processing from liquid phase, such as ink-jet printing, spray-coating, spin-coating, as well as vacuum deposition. Grazing incidence X-ray scattering (GIXS) is a very powerful tool to investigate processes in-situ and in-operando and in real-time [1,2,3]. GIXS allows for combining with micro- and nanofocused X-ray beams as well as complementary investigation tools at the same time. Therefore one obtains full structural and morphological understanding of functional materials and to correlate this knowledge with the desired functionality. I will present selected examples for application of GIXS in information and communication technology. This comprises vacuum deposition with millisecond time resolution and on functional materials. Combining GIXS and imaging ellipsometry, we are able to follow in-situ the installation of functional thin films by droplet casing. Furthermore, this powerful combination allows for examining the stability of nanostructure and optical constants in nanostructured polymeric films for high temperature applications. I complement my talk with the example of GIXS and spray deposition as one rapid deposition method to obtain functional coatings.
Magic Sized Clusters in ZnO Nanoparticle Formation – an in-situ PDF study
Authors: Zobel Mirijam , Neder Reinhard
Published: November 2015

Semiconductor nanoparticles (NP) such as zinc oxide (ZnO) are commonly produced in sol-gel processes. The final NP powders are well characterized with respect to their crystallinity, which fundamentally governs their physical and chemical properties. Nevertheless, the nucleation process and the evolution of crystallinity of the nucleating NPs is not yet understood [1]. With the advent of the Rapid Acquisition Pair Distribution Function (PDF) method, time-resolved PDF studies have become possible, and the distinction between molecular clusters and nanoparticles in 1 M aqueous solutions of metal oxide NPs [2] has been demonstrated. However, nucleation in dilute sol-gel processes in more complex organic solutions remains untackled [1]. Our experiments are, to our knowledge, the first in-situ PDF studies in organic solvents. We used a 30 mM ethanolic solution of zinc acetate dihydrate. Several hours after the addition of the organic base tetramethylammonium hydroxide, monodisperse ZnO powders can be obtained. However, directly upon the base addition primary tetrahedral precursors Zn4OAc6 form. Approx. 1 hour later, they evolve into stable magic sized clusters (MSC) of 1.3 nm diameter and wurtzitic structure. Though known to exist for II-VI semiconductor NP such as CdSe [3], MSCs have not been demonstrated for ZnO before. With ongoing reaction time, the final spherical NPs of 2.5 nm diameter evolve at the expense of the MSCs and exist for several hours without undergoing further growth. SAXS studies confirm the PDF data. Fig. 1 shows the experimental PDFs and their fits. The fits are multiphase models of the precursor, the MSC and NP. The solvent shows intermolecular ordering effects whose contribution to the PDF was modelled by a low-frequency wave function. The MSC and NP sketches show a view along the crystallographic c-axis. Based upon these state-of-the art in-situ PDF studies, we suggest a nucleation model based on the existence of magic-sized clusters.
PDF Analysis on a Laboratory System: Adapting the Experiment to the Material
Authors: Reiss Céleste , Gateshki Milen , Sommariva Marco
Published: November 2015

The increased interest in recent years regarding the properties and applications of nanomaterials has also created the need to characterize the structures of these materials. However, due to the lack of long-range atomic ordering, the structures of nanostructured and amorphous materials are not accessible by conventional diffraction methods used to study crystalline materials. One of the most promising techniques to study nanostructures using X-ray diffraction is by using the total scattering (Bragg peaks and diffuse scattering) from the samples and the pair distribution function (PDF) analysis. The pair distribution function provides the probability of finding atoms separated by a certain distance. This function is not direction-dependent; it only looks at the absolute value of the distance between the nearest neighbors, the next nearest neighbors and so on. The method can therefore also be used to analyze non-crystalline materials. From experimental point of view a typical PDF analysis requires the use of intense high-energy X-ray radiation (E ≥ 20 KeV) and a wide 2θ range. After the initial feasibility studies regarding the use of standard laboratory diffraction equipment for PDF analysis [1-3] this application has been further developed to achieve improved data quality and to extend the range of materials, environmental conditions and geometrical configurations that can be used for PDF experiments. Studies performed on different nanocrystalline and amorphous materials of scientific and technological interest, including organic substances, oxides, metallic alloys, etc. have demonstrated that PDF analysis with a laboratory diffractometer can be a valuable tool for structural characterization of nanomaterials. This contribution presents several examples of laboratory PDF studies, in which the experimental conditions have been successfully adapted to match the specific requirements of materials under investigation.
Local Structure of Iridate Pyrochlores from Hydrothermal Synthesis
Authors: Playford Helen , SINGH Ravi , Chang Lieh Jeng , Sardar Kripasindhu , Hannon Alex , Tucker Matt , Lees Martin , Balakrishnan Geetha , Walton Richard
Published: November 2015

Iridate pyrochlores of general formula M2Ir2O7have potential applications in catalysis [1]. They also often exhibit unusual magnetic and electronic properties caused by spin-orbit coupling and geometric frustration [2]. A detailed understanding of structure is necessary to enable these properties to be understood and exploited. Because of the propensity of the pyrochlore structure to accommodate structural disorder, we have chosen to utilise the technique of total scattering to examine the structure of M2Ir2O7(M = Bi, Nd). The sensitivity of our measurements to all the constituent elements is maximised by the combination of both neutron and X-ray total scattering. We find no evidence for magnetic ordering in our samples of Nd2Ir2O7, in contrast to literature reports [3]. By comparing the local structure of our samples with that of one reported to exhibit magnetic ordering, we explore the possibility of a structural origin for the differences in magnetic behaviour. We have found that synthesis method can directly influence the structure of these iridate pyrochlores. Local structural analysis provides evidences of A-site cation deficiency and partial oxidation of Ir(IV) to Ir(V) in samples produced by hydrothermal techniques. Irreversible changes to the lattice parameter upon heating these samples at 400 – 9000C further support the inference that the cation content is somewhat variable. We report the results of reverse Monte Carlo (RMC) refinements using the program RMCProfile, which is capable of simultaneously fitting to X-ray and neutron data, and therefore provides structural models of the greatest possible accuracy. We also report the results of in situ X-ray total scattering measurements which provide local-scale insight into the interesting thermal behaviour and apparent flexible cation content of these materials.
Tracking morphotropic phase boundary through total scattering technique
Authors: Datta Kaustuv , Neder Reinhard
Published: November 2015

Morphotropic phase boundary (MPB) is an important theme in the research of ferroelectric materials since materials often exhibit enhanced physical properties at MPB. Although an established understanding of creating MPB behaviour relies on invoking instability of average crystal structure or a low-symmetry monoclinic phase in the system driven by composition [1], the actual mechanism is far more complex and heavily dependent on the local ordering of cations as evidences found in recent diffuse scattering studies [2] on both lead-based and lead-free systems. We have studied an important and popular ferroelectric system xBiScO3-(1-x) PbTiO3 (BS-PT), which was first reported in 2001 with MPB characteristics [3], through total scattering technique to understand its structural evolution as a function composition in the vicinity of the MPB. Total scattering technique which is essentially the analysis of the pair distribution function (PDF) of a system, provides crucial structural information at the microscopic level which are not easily available from conventional structural analysis like Rietveld refinement. Both x-ray and neutron powder diffraction experiments were carried out on six different compositions of BS-PT in the range 0.30 < x < 0.40 and neutron PDFs were analysed through RMC simulations to extract the behaviour of individual cations. It was observed that locally there was no abrupt change in any of the cation-cation correlations to assign the MPB unambiguously, however a trend was noticed in the sigmas of individual cationic displacements where the reported MPB composition show a minimum.
2-D cyanides from square planar M(CN)4units (M(II) = Ni, Pd, Pt, Cu)
Authors: Chippindale Ann , Hibble Simon , Marelli Elena
Published: November 2015

The binary cyanide, Cu(CN)2, has never been synthesised. However, by using Ni(CN)42-as a structural synthon, copper(II) can be stabilised in a cyanide-only environment in CuNi(CN)4and in the solid-solution CuxNi1+x(CN)2(0 ≤ x < 1/4). The atomic structure of the layers in CuNi(CN)4and the stacking relationship between nearest-neighbour layers have been determined from total neutron diffraction studies at 10 and 300 K. The structure consists of flat layers of square-planar, ordered [Ni(CN)4] and [Cu(NC)4] units. (NB it is very unusual to find Cu(II) in a genuine square-planar environment within an extended solid). The layered structure of this new material is closely related to those of the Group 10 cyanides, Ni(CN)2, Pd(CN)2.xNH3and Pt(CN)2.xH2O, except that these are generated from vertex-sharing square-planar metal-cyanide units with head-to-tail disorder of the C≡N groups. The overall appearance of the powder X-ray diffraction pattern of CuNi(CN)4, including the unusual peak shapes of the observed Bragg reflections, has been successfully explained using models incorporating stacking disorder between next nearest neighbour layers. CuNi(CN)4forms less extended sheets than Ni(CN)2[1, 2], but larger sheets than those found in Pd(CN)2.xNH3and Pt(CN)2.xH2O, which are nanocrystalline [3]. CuNi(CN)4, like Ni(CN)2[1], shows interesting thermal expansion behavior i.e. intralayer negative thermal expansion (αa = -9.7 MK-1) and interlayer positive thermal expansion (αc = +89 MK-1). CuNi(CN)4forms as an anhydrous material from aqueous solution, unlike Ni(CN)2, which can form hydrates such as Ni(CN)2.nH2O (n = 3, 3/2, 2, 1). However, on investigating the Cu-Ni-CN phase diagram, it is found that nickel-rich compounds, CuxNi1+x(CN)2(0 ≤ x < 1/4), can be formed via hydrated phases, CuxNi1+x(CN)2.3H2O, and readily rehydrate. Attempts to form copper-rich phases results in partial reduction of Cu(II) with the formation of copper(I) cyanide, CuCN, in addition to CuNi(CN)4, suggesting that Cu(II) ions are stable in a cyanide environment only when connected to the nitrogen ends of bridging C≡N ligands. Hence the non existence of Cu(CN)2can now be explained.
Intermolecular interactions in molecular crystals and glasses
Authors: Beake Edward , Dove Martin , Phillips Anthony
Published: November 2015

The local structure of materials may not be apparent from Bragg crystallography, but emerges naturally from refinement against a pair distribution function (PDF). In molecular systems, the most prominent features in the PDF are the low-r peaks corresponding to the intramolecular interactions, yet these features are often the least interesting. The domination of the PDF by intramolecular interactions makes it difficult in the case of molecular materials to investigate the more interesting intermolecular interactions. In particular, few amorphous framework materials or molecular glasses have been characterized in any detail. Using reverse Monte Carlo (RMC) refinement against total neutron and x-ray scattering data we have studied the intermolecular interactions in two families of molecular materials, each including both crystalline and glassy phases. To overcome the problem posed by intramolecular interactions prior chemical knowledge of the molecular structure is incorporated into the refinement using empirical intramolecular potentials. One family consists of three phases of ZIF-4, a metal-organic framework consisting of tetrahedrally coordinated Zn2+ ions connected by imidazolate rings. In this material, we identify the molecular motion responsible for the greater flexibility shown by the amorphous phase compared to two crystalline phases [1]. The other family consists of the isomeric molecules para- and ortho-terphenyl (PTP/OTP). OTP is a paradigmatic glass-former, with a critical cooling rate of less than 0.1 K/min. PTP, on the other hand, is a crystalline material that undergoes an order-disorder phase transition at 178 K. We have characterized these materials' flexibility with the aid of molecular dynamics simulations. Our results demonstrate that RMC refinement with appropriate intramolecular potentials is capable of elucidating the intermolecular interactions of molecular systems, revealing new structural details in glassy and amorphous structures.
Real time study of wet-chemical reaction dynamics at beamline P02.1 @ PETRA III
Authors: Dippel Ann-Christin , Delitz Jan Torben , Liermann Hanns-Peter , Tyrsted Christoffer , Saha Dipankar , Bøjesen Espen , Christensen Mogens , Iversen Bo
Published: November 2015

The high brilliance synchrotron light source PETRA III in Hamburg, Germany, provides a dedicated X-ray powder diffraction beamline called P02.1 [1]. It is a side station to the hard X-ray diffraction beamline and runs at a fixed photon energy of 60 keV. Its dispersive monochromator produces a highly collimated photon beam of very narrow energy bandwidth and high intensity. These excellent beam characteristics turn P02.1 into an ideal instrument for many different kinds of experiments, ranging from high resolution powder diffraction of polycrystalline materials for structure solution and refinement or microstructure analysis, to the study of nanocrystalline and disordered materials to determine their local structure. In particular, it is the scope of P02.1 to study dynamic processes such as chemical and crystallographic transitions under non-ambient conditions in real time. For this purpose, the beamline is equipped with a large and fast area detector which enables sub-second time-resolution. The accessible range in reciprocal space is beyond Q = 30 Å-1. Hence, P02.1 is a powerful tool for total scattering experiments as it provides high resolution in real and reciprocal space which are determined by the max. Q and the instrumental resolution, respectively. This presentation describes some recent experiments carried out at P02.1 that relate to pair distribution function (PDF) and total scattering analysis. The focus will be on the investigation of structural changes on the atomic scale during the wet-chemical synthesis of nanoparticles, e.g. in the system ZrO2. By means of evaluating the changes of bond distances and atomic coordination on a time scale of seconds, it is possible to describe the molecular structure of intermediates and, thus, to deduce the underlying reaction mechanism. On the basis of this information, synthesis processes may be optimised with respect to tuning the properties of the product and to maximize its yield.
Complexity in Cubic Crystals
Authors: Keen David
Published: November 2015

Cubic crystals have been studied in detail ever since the advent of X-ray crystallography 101 years ago when Lawrence Bragg first solved the cubic structure of rocksalt. Despite this long history they still hold a fascination with many topical materials such as C60, PbTe-based thermoelectrics, ZrW2O8-related negative thermal expansion materials and several ice phases, all crystallising into cubic structures. This talk will briefly outline the early heritage of (cubic) crystallography and will then highlight the key role of complexity on the physical properties of many cubic crystals. I define complexity as a local breaking of the overall crystal symmetry, rather than the creation of ever larger unit cells, and therefore accurate understanding cannot be gained through analysis of Bragg diffraction alone. Instead I will describe methods for quantifying this complexity via models refined by reverse Monte Carlo analysis of total scattering (pair distribution function) data and using a range of different examples, some taken from the list given above.
Materials for energy storage and conversion: Probing functionality with PDF
Authors: Chapman Karena
Published: November 2015

In the last decade, the potential of the pair distribution function (PDF) method as a versatile tool for materials characterization has expanded enormously, driven by accelerated data acquisition (from hours to sub-second) and the advent of dedicated PDF instruments, such as 11-ID-B at the Advanced Photon Source. New time-resolved, in-situ/operando, parametric, and combined experimental capabilities coupled with innovative model-independent approaches to data analysis are being developed to harness the growing potential of this methodology. For example, while the complex multicomponent architecture of batteries and their coupled electronic, chemical and structural transformations complicate investigations of functionality, through the development of new insitu PDF measurement capabilities and analytical approaches, we have been able to gain insight into the structure and reactivity of these electrochemical energy storage systems.[1] This presentation will describe recent studies of electrode reactions during cycling and the atomic structure of electrolytes.[2]
Conformational heterogeneity of the AAA ATPase p97 characterized by single particle cryo-EM
Authors: Mountassif Driss , Fabre Lucien , Basu Kaustuv , Bostina Mihnea , Jonic Slavica , Rouiller Isabelle
Published: November 2015

p97, a member of the AAA (ATPase Associated with various Activities) ATPase family, is essential and centrally involved in a wide variety of cellular processes. Single amino-acid substitutions in p97 have been associated with the severe degenerative disorder of Inclusion Body Myopathy associated with Paget disease of bone and Frontotemporal Dementia (IBMPFD) as well as amytropic leteral sclerosis (ALS). Current models propose that p97 acts as a motor transmitting the energy from the ATPase cycle to conformational changes of substrate protein complexes causing segregation, remodeling or translocation. Mutations at the interface between the N and the D1 domains impact the ATPase activity and the conformation of D2 on the opposite side of the protein complex, suggesting intermolecular communication. Because of limited structural information, the molecular mechanisms on how p97 drives its activities and the molecular basis for transmission of information within the molecule remain elusive. Structural heterogeneity is observed in vitro and is likely relevant for the in vivo biological function of p97. Single particle cryo-EM is the method of choice to study a flexible complex. The technique allows study in solution and also deals with sample heterogeneity by image classification. We have set-up the characterization of the conformational heterogeneity in WT and disease relevant p97 mutant using multi-likelihood classification and Hybrid Electron Microscopy Normal Mode Analysis HEMNMA. The multi-likelihood analysis shows a link between the conformations of the N and D2 domains. HEMNMA allows the analysis of the asymmetry of the conformational changes. Together these studies describe the structural flexibility of p97 and the coupling of the ATPase activity with conformational changes in health and in disease. Study of this model system also allows the development of new methods to understand the conformational heterogeneity of other protein complexes.
Structural basis for filament formation of MAVS on mitochondria by cryoEM
Authors: Jiang Qiu-Xing , He Xiaojing , Zheng Hui , Huang Lily , Hou Fajian , Yu Zhiheng , de la Cruz Michael , Borkowski Brian , Zhang Xuewu , Chen Zhijian , Jiang Qiu-Xing
Published: November 2015

Mitochondrial anti-viral signaling (MAVS) protein is required for innate immune responses against RNA viruses. In virus-infected cells MAVS forms prion-like aggregates to activate antiviral signaling cascades, but the underlying structural mechanism is unknown. Here we report cryo-electron microscopic structures of the helical filaments formed by both the N-terminal caspase activation and recruitment domain (CARD) of MAVS and a truncated MAVS lacking part of the proline-rich region and the C-terminal transmembrane domain. Iterative helical real space refinement was used to analyze cryoEM images of the filaments. The CARD filament structure was resolved at 9.6 angstrom with rod-like densities fitting with four alpha helices of the domain. That of the truncated MAVS was resolved at 16.4 angstroms, showing the arrangement of the middle segment of MAVS at the periphery of the CARD filament. Both structures are left-handed three-stranded helical filaments, revealing specific interfaces between individual CARD subunits that are dictated by electrostatic interactions between neighboring strands and hydrophobic interactions within each strand. Point mutations at multiple locations of these two interfaces impaired filament formation and antiviral signaling. Super-resolution imaging of virus-infected cells revealed rod-shaped MAVS clusters on mitochondria. These results elucidate the structural mechanism of MAVS polymerization, and explain how an α-helical domain uses distinct chemical interactions to form self-perpetuating filaments.
Rocking, rolling, sliding: structural transitions in actin:tropomyosin
Authors: Stroupe M Elizabeth , Tao Yeqing
Published: November 2015

Tropomyosin is a key factor in the molecular mechanisms that regulate the binding of myosin motors to actin filaments in most eukaryotic cells. This regulation is achieved by the azimuthal repositioning of tropomyosin along the actin:tropomyosin:troponin thin filament to block or expose myosin binding sites on actin. In striated muscle, including involuntary cardiac muscle, tropomyosin regulates muscle contraction by coupling Ca2+ binding to troponin with myosin binding to the thin filament. In smooth muscle, the switch is the post-translational modification of the myosin. Depending on the activation state of troponin and the binding state of myosin, tropomyosin can occupy the blocked, closed, or open position on actin. Using native cryogenic 3DEM, we have directly resolved and visualized cardiac and gizzard muscle tropomyosin on filamentous actin in the position that corresponds to the closed state. From the 8-Å resolution structure of the reconstituted Ac:Tm filament formed with gizzard-derived Tm we discuss two possible mechanisms for the transition from closed to open state and describe the role Tm plays in blocking myosin tight binding in the closed state position.
Electron cryomicroscopy of rotary ATPases
Authors: Rubinstein John
Published: November 2015

Ion-translocating rotary ATPases serve either as adenosine triphosphate (ATP) synthases, using energy from a transmembrane ion motive force to create the cell's supply of ATP, or as transmembrane ion pumps that are powered by ATP hydrolysis. The members of this family of enzymes each contain two rotary motors: one that couples ion translocation to rotation and one that couples rotation to ATP synthesis or hydrolysis. Our group uses electron cryomicroscopy (cryo-EM) of single protein particles to study the structures of rotary ATPases. We also work to develop new methods for cryo-EM to facilitate these studies. The structures that we have obtained have illuminated several aspects of how structure relates to function in these remarkable molecular motors.
Structure and function of the CagA oncoprotein from Helicobacter pylori
Authors: Senda Toshiya , Senda Miki , Hayashi Takeru , Hatakeyama Masanori
Published: November 2015

CagA is known as a major bacterial virulence determinant from Helicobacter pylori and is critical for gastric cancer. Upon delivery into the gastric epithelial cells, CagA localizes to the inner leaflet of the plasma membrane and promiscuously interacts with host proteins such as PAR1b and SHP2. The CagA-PAR1-SHP2 complex potentiates oncogenic signaling. Biochemical and physicochemical analyses revealed that CagA is comprises a structured N-terminal region (residues 1-876) and an intrinsically disordered C-terminal region (residues 877-1186). To understand the structure and function relationship of CagA, we determined the crystal structure of the N-terminal region (residues 1-876) of CagA [1]. The N-terminal CagA is rich in α-helices and composed of three domains. Domain I (residues 24-221) is linked to domain II (residues 303-644) by a disordered loop with about 80 amino acid residues. Domain II has a basic patch composed of 14 lysine and 2 arginine residues. Biological experiments revealed that the basic patch mediates the CagA-phosphatidylserine interaction to localize the inner face of the plasma membrane. In addition, we found that C-terminal disordered region forms a lariat-like loop by the interaction between NBS (residues 645 - 824) and CBS (residues 998 - 1038) in the disordered C-terminal region. The formation of the lariat-like loop facilitates promiscuous interaction of CagA with target protein such as SHP2.
InlC of L. monocytogenes Binds Human Tuba for Bacterial Cell-Cell Spreading
Authors: Polle Lilia , Rigano Luciano , Ireton Keith , Schubert Wolf-Dieter
Published: November 2015

The human pathogen Listeria monocytogenes is able to directly spread to neighboring cells of host tissues, a process recently linked to the virulence factor InlC. InlC targets the sixth SH3 domain (SH3-6) of human Tuba, disrupting its physiological interaction with the cytoskeletal protein N-WASP. The resulting loss of cortical actin tension proposedly slackens the junctional membrane allowing protrusion formation by motile Listeria. Complexes of Tuba SH3-6 with physiological partners N-WASP and Mena reveal equivalent binding modes but distinct affinities. The interaction surface of the infection complex InlC/Tuba SH3-6 is centered on phenylalanine146 of InlC stacking upon asparagine1569 of Tuba. Replacing Phe146 by alanine largely abrogates molecular affinity and in vivo mimics deletion of inlC. Collectively, our findings indicate that InlC hijacks Tuba through its LRR domain, blocking the peptide binding groove to prevent recruitment of its physiological partners.