bluuebunny/crossref_metadata_2025 huggingface dataset:
Applications of X-ray Wavefunction Refinement
Authors: Grabowsky Simon , Woinska Magdalena , Bak Joanna , Jayatilaka Dylan
Published: November 2015

X-ray wavefunction refinement (XWR) is a way of modeling the total aspherical electron density from an X-ray diffraction experiment on a single crystal of a molecular compound. It is a combination of existing quantum-crystallographical techniques: In the first step, geometry is determined using Hirshfeld atom refinement,[1] which is based on a stockholder partitioning of quantum-mechanical aspherical electron densities. In the second step, the same wavefunction is fitted to the experimental data to reproduce the diffraction pattern and simultaneously minimize the molecular energy.[2] The XWR protocol involves embedding the molecule into a field of point charges and dipoles as well as termination strategies to avoid overfitting.[3] Results from an X-ray wavefunction refinement are not restricted to the analysis of electron density: the full reconstructed density matrix is available. Therefore, chemical problems can be tackled with suitable tools for any given question including, e.g., experimentally derived bond orders, electron-pair localisation information, or energetics. We will present first applications of this protocol for a selection of organic (hydrogen maleate salts, sulfur-containing protease inhibitors) and inorganic (siloxanes, sulfur dioxide) compounds, for which we measured high-resolution low-temperature X-ray diffraction data at various synchrotron facilities. We will show geometry improvements, anisotropic displacement parameters for hydrogens, anharmonic motion parameters for sulfur and chlorine atoms, and improved total electron-density distributions in comparison to results from multipole modeling. Moreover, we will discuss the contribution of the experimental data to the final constrained wavefunction (defect density) and demonstrate how the experimentally derived orbital-based descriptors assist in solving fundamental chemical problems.
Accurate Charge Densities from Synchrotron Powder Diffraction
Authors: Bindzus Niels , Wahlberg Nanna , Dippel Ann-Christin , Becker Jacob , Brummerstedt Iversen Bo
Published: November 2015

Advancements within the field of synchrotron powder X-ray diffraction (SPXRD) have rendered it a viable approach for probing subtle electronic features. It is especially powerful for highly crystalline inorganic extended materials, resolving severe extinction issues conventionally encountered with single-crystal diffraction. Furthermore, SPXRD data exhibit markedly reduced absorption and may be collected in a single exposure. The latter prevents systematic errors from merging a multitude of detector frames, each possessing a slightly different scale factor. These experimental advantages are counterbalanced by a more complicated data analysis, where the key problems are the inherent challenges of overlapping reflections and background subtraction. To evaluate the performance of SPXRD and to test the methodologies for estimating charge densities (CDs), we use benchmark data on diamond collected to low d-spacing. [1] The critical step is the recovery of observed structure factors from the powder pattern. This is the focal point of the present study, scrutinizing several traditional and novel approaches that deviate strongly in terms of model complexity and structure-dependency. All recovered sets of structure factors are evaluated with respect to their capability to determine the true atomic displacement parameter and to estimate the CD by both multipolar modelling and maximum entropy reconstruction. The data are of such exceptional quality that they even reveal how the innermost electron density responds to the formation of covalent bonding (figure below). Supporting their huge success over the last decades, only the Rietveld-based approaches are capable of quantifying this fine feature. The study of core polarization has emerged as a new frontier in chemical bonding studies, and the relevant experimental information may be reliably accessed by SPRXD for highly crystalline materials.
Recent developments in the structure of high temperature oxide melts
Authors: Benmore Chris , Skinner Lawrie , Alderman Oliver , Tamalonis Anthony , Weber J.K. , Parise John
Published: November 2015

Aerodynamic levitation with laser heating has now become a standard technique for studying the structure of oxide melts on synchrotron and neutron beamlines. Here we summarize the results of a growing number of findings that show a distinct decrease in the local cation-oxygen coordination number, for liquid state single and binary oxides, compared to their crystalline forms. This phenomenon is often correlated with a significant decrease in density upon melting and diffraction measurements show a distribution of lower coordinated polyhedra. The diffraction data allow us to refine interatomic potential parameters within molecular dynamics simulations to obtain very good agreement between the structural models and experiments. The feasibility of very high temperature experiments around and above 3000 degrees Celsius, as well as the safety aspects associated with measuring radioactive samples will be discussed. Future prospects on changing the oxidation state of high temperature oxide melts through reduction-oxidation reactions will also be considered. The photograph below shows a Uranium dioxide pellet being loaded into the aerodynamic levitator on a high energy x-ray beam line at the APS prior to melting.
In-situ Observation of Polymer Electrolyte Fuel Cell Using Deuterium Gas
Authors: Koizumi Satoshi
Published: November 2015

In order to visualize water distribution in an operating fuel cell, we combined two different methods using neutron as a probe, i.e., a combined method of small-angle & ultra-small-angle scattering (SANS) and radiography imaging. SANS observes water distribution in a membrane electrolyte assembly (MEA), whereas radiography observes bulk water appeared in a gas flow channel (so called "flooding"). The polymer electrolyte fuel cell (PEFC) was specially designed suitable for small-angle neutron scattering by replacing materials with aluminum in order to decrease background scattering. We employed hydrogen gas (H2) and deuterated gas (D2) as a fuel for operation. With exchange of H2 and D2, we aim to perform a contrast variation as for polyelectrolyte film (Nafion). When D gas is used as a fuel, D2O is produced at the cathode and diffuses back to the film. Then the film, originally swollen by H2O, exhibits change of coherent scattering contrast. By changing a fuel gas from H2 to D2, SANS quantitatively detected decrease of scattering intensity at scattering maximum originating from the ion-channel in the electrolyte. After quantitative analyses on scattering intensity, which is related to water ratio (H2O/D2O) in the ion channel, we found that 30 wt% of the total water is replaced by D2O by changing the gas from H2 to D2. In a stationary state of fuel cell operation using D2, the scattering intensity rhythmically oscillates (respiration of fuel cell). The rhythmic oscillation found for the peak intensity is a non-equilibrium and non-linear phenomenon, in which "flooding" in a flow field is a feedback mechanism to slow down chemical reaction or water production by affecting mass transportation of air at the cathode. A valance between two diffusions, (i) back diffusion of D2O from the cathode to the electrolyte and (ii) diffusion of H2O supplied as humidity, determines a time interval of the respiration.
Effect of organic Matter on RO Membrane Scaling in Wastewater Desalination
Authors: Schwahn Dietmar , Dahdal Yara , Pipich Vitaliy , Kasher Roni , Oren Yoram
Published: November 2015

Biofouling and scaling are major limitations of membrane-based desalination techniques. In particular scaling by calcium phosphate on reverse osmosis (RO) membranes limits the desalination efficiency of secondary wastewater effluents. The exploration of biofilm formation and of scaling is the topic of our research. Our particular interest is the effect of components representing the biofilm on calcium mineralization at a molecular level using the experimental technique of small-angle neutron scattering (SANS). To this end we are studying the formation of calcium minerals in a model solution simulating a secondary waste water effluent (SSE) [1] after adding biopolymers as single molecules or as grafted at gold nanoparticles. The latter experiment should simulate mineralization at surfaces such as membranes. SANS is a promising tool in this field as was demonstrated on similar studies in the related field of biomineralization [2]. We will present data showing the process of mineralization in SSE solutions stimulated by some relevant proteins (BSA, lysozyme) and polysaccharides (alginic acid, chitosan) using stopped-flow technique in combination with classical as well as with focusing ultra-small SANS techniques [3]. This work was funded by the Ministry of Science, Culture and Sport (MOST) and the Bundesministerium für Bildung und Forschung (BMBF).
Partially Oxidised Cellulose Nanofibril Gels for Rheology Modification
Authors: Edler Karen , Celebi Duygu , Jin Yun , Scott Janet
Published: November 2015

Partially C6-oxidised cellulose nanofibrils form a transparent, slightly viscous suspension in water. These materials, sourced from soft-wood waste, have shown excellent potential for use as a rheology modifier in aqueous formulations, when mixed with salt and minimal amounts of anionic surfactants [1] or with short chain alcohols. The interaction with anionic surfactants is particularly surprising as the cellulose fibrils themselves carry a net negative charge. The gels formed are transparent, mild on the skin and have excellent suspending properties while also being strongly shear thinning making application eg via spraying possible. The partially oxidised cellulose nanofibrils can also be used to stabilize oil-in-water Pickering emulsions. Both the gels and emulsions are of interest for use in personal care products such as creams, sanitizers and shower gels. We have probed the micelle-fibril interactions in water and in the presence of ethanol using contrast matching SANS on the gels and also on the cellulose-stabilized Pickering emulsion droplets. SAXS has also been used to probe the effect of short chain alcohols on the nanofibril structures in the gels as a function of alcohol chain length, while neutron reflectivity was used to probe surfactant-fibril binding for anionic and nonionic surfactants in thin nanofibril layers. The nanostructures formed in suspensions of partially oxidised cellulose nanofibrils with a range of salts, alcohols and surfactants will be correlated with their rheological behaviour. These factors will be discussed and brought together to give insights into how and why these systems form gels.
1913-1914: the First Truly International Year of Crystallography
Authors: Schwalbe Carl
Published: November 2015

It is appropriate that 2014 has been chosen as the International Year of Crystallography since it was a century ago that crystallography as we know it emerged as a truly international science. The pattern becomes clearer if one considers academic years starting on September 1. Thus 1911-1912, when the first successful diffraction experiments were carried out, becomes the German year of crystallography. With the statement of Bragg's Law and the first structure determinations, 1912-1913 can be called the British year of crystallography. By late 1913 our science had achieved truly international scope, demonstrated by publications describing advances in experimental design, theory and structure determination emanating from France, Japan, the Netherlands, Russia and Switzerland as well as Germany and Britain. While many countries worked on the first two areas, structure determination was done mainly in Britain (dominated by the Braggs) and Japan (to a limited extent). In the belligerent countries this magnificent flowering was sadly curtailed by the outbreak of World War I. However, at about this time the United States entered the field. The international spread followed by curtailment is readily visualised when presented in the form of a timeline.
Agilent Technologies: Proud Global Sponsors of the IYCr2014
Authors: Presly Oliver
Published: November 2015

"The International Year of Crystallography 2014 represents a unique chance to highlight crystallography to a wide audience of researchers, students, school children and members of the public. It also offers a platform for boosting the capabilities of research laboratories in less well developed parts of the world, with instruments and expertise helping a new generation of scientists to learn theory and techniques, to generate data and to form collaborations with experts in various crystallographic fields. Agilent is proud to support IYCr2014, to assist the International Union of Crystallography (IUCr) and its partners in achieving some of the key goals of the project. To this end, Agilent has teamed up with the IUCr in the IYCr2014 ""Crystallography in Everyday Life"" photo contest. A highlight of the IUCr Congress, this contest has been open throughout 2014, inviting all amateur and professional photographers to submit stunning images that capture the spirit of crystallography in the places, objects and experiences of everyday life. Entries have been submitted from across the world from both scientists and non-scientists alike. Two winning entries will each receive bursaries to attend the IUCr Congress, and their entries will be on display in the main exhibition area. These and 14 further notable entries will make up the Agilent-IUCr IYCr2014 academic calendar (2014-15), and copies will be available from the Agilent booth in Montreal. Agilent is also proudly supporting the IUCr-UNESCO OpenLab initiative; aiming to provide facilities and teaching to young scientists without access to their own instrumentation. Agilent and the IUCr have been working with a number of Agilent system users, specifically in Argentina, Hong Kong and Turkey, to develop OpenLab workshops organized by local researchers and supported by Agilent sponsorship and Application Scientists. This poster will highlight Agilent's IYCr participation, focusing on these initiatives."
Influence of Crystalline and Amorphous Phases on pre-Hispanic Adobes Properties
Authors: Perez Castellanos Nora , Bucio Galindo Lauro
Published: November 2015

Adobe earth bricks are part of the past and present in Mexican culture, they have shown to have the right mechanical strength and time resistance that is adequate for a good constructive system. Adobe bricks are built from natural soil, which is an abundant and therefore potentially sustainable material. The archaeological site of Cholula, Puebla, Mexico is one of the most important pre-Hispanic cities during 300-900 A.D. The pyramid at the site has the largest volume and basing in the world and plays a very important role in the community since pre-Hispanic times up until now when it is a symbol of religious syncretism. This research seeks to provide a comprehensive study of the type of adobe earth bricks that were used as building material. The crystallographic study of this type of cultural heritage materials enables the expansion of our knowledge about the details concerning the structure and properties. This was achieved by identifying the role that each mineral plays on the properties of the adobe by integrating knowledge from mineralogy with that of materials science. The relationship between structure and function was foundational to understanding materials and from this knowledge it is possible to develop pathways on how to control and forecast the properties of earth building materials [1]. The results obtained from the XRD analysis of the different granulometric phases showed that plagioclase and quartz constitute the larger aggregates forming the sand phase, whilst a mixture between cristobalite and tridymite, constituted the mineral opal CT, which together with amphibole minerals formed the silt phase, the clay sized particles corresponded to amorphous phases such as allophane, glass and organic material [2, 3]. We concluded that the combination of these minerals in both cohesive and non-cohesive phases that are present in the regional soils fulfill the requirements for building ancient cities and still remain functional up until today.
Japanese Crystallography in Culture and Art
Authors: Inoue Tsuyoshi , Sugawara Yoko , Nakagawa Atsushi , Takata Masaki
Published: November 2015

"We can find many seeds of crystallography in Japanese culture. Most of the family crests have symmetry elements such as rotation axes and mirror symmetry elements. Sekka-zue, a picture book of 86 kinds of crystals of snow, was made by Toshitura Doi, who is a feudal lord in Edo-period and he observed snow using a microscope in nineteenth century. In recent years, people enjoy to make crystal structures, polyhedrons, carbon nanotube, quasicrystal etc. by origami, the art of folding paper [1]. In the field of science, the Japanese crystallography has contributed to explore culture and art. An excellent example is unveiling the original color of Japanese painting "Red and White Plum Blossoms" by Korin Ogata [2]. Prof. Izumi Nakai (Tokyo University of Science) developed an X-ray fluorescence analyzer and an X-ray powder diffractometer designated to the investigation of cultural and art works and had succeeded in reproducing the silver-colored waves through computer graphics after X-ray analyses of crystals on the painting. The scientific approach by Prof. Nakai et al. unveiled the mystery of cultural heritage of ancient near east, ancient Egypt etc. and is being to contribute to insight into the history of human culture. [1] An event to enjoy making crystals by origami is under contemplation. [2] The symposium ""Crystallography which revives heritages"" was held on February 16, 2014 at Atami in Japan."
50 years of protein crystallography and allosteric interactions
Authors: Cherfils Jacqueline
Published: November 2015

The International Year of Crystallography coincides with the celebration of the 50th anniversary of the landmark articles on allostery by Monod, Changeux & Jabob (1963) and Monod, Wyman and Changeux (1965). These articles defined "allosteric" interactions in proteins as "indirect interactions between topographically distinct sites" and devised the model (now known as the MWC model) for the conformational changes mediating them. The concept, which Jacques Monod reportedly described as the "second secret of life" second only to the genetic code, was invented to account for feedback inhibition and cooperativity properties in enzymes and regulatory proteins, including hemoglobin. The pioneering crystallographic analysis of hemoglobin, whose structure had been determined by Max Perutz at about the same time, provided evidence for the concept and likely contributed to inspire it. Half a century later, allosteric interactions and underlying conformational transitions have been captured in many crystallographic structures, uncovering a wide range of mechanisms whereby information that affects biological activities is propagated over a long distance between two binding sites. I will present examples of allostery in protein crystallographic structures that illustrate the expansion and widespread application of the original concept, notably in understanding diseases and aiding in drug design.
UNESCO activities in Africa for the 2014 International Year of Crystallography (IYCr)
Authors: Ngome Abiaga Jean-Paul
Published: November 2015

Following the United Nations General Assembly (Decision A/66/L.51) declaration of 2014 as the International Year of Crystallography (IYCr2014), UNESCO and IUCr received a strong mandate to coordinate the activities of the Year in order to tackle the global disaffection from science and scientific careers, namely in crystallography, that threatens scientific enterprise innovation and sustainability and, consequently, the prospects for using science for development, especially in Africa. In addition, the crystallography capacity-gap between the wealthiest and the poorest regions of the world is increasing due to brain drain, the weakness of local expertise, the absence of linkage between science policy and the regional community of crystallographers, as well as the lack of inclusion of Africa in international scientific cooperation. For developing countries in Africa, it is therefore vital to be in a position to exploit the opportunities that crystallography and the IYCr2014 offer in terms of building, nurturing and maintaining a critical mass of highly qualified, innovative scientists, students and engineers in crystallography-related fields. For all those reasons, UNESCO seizes the opportunities presented by the International Year to foster crystallography education, research and cooperation and its use and applications, which are providing solutions to some of the developmental challenges that Africa is facing today. Some of the UNESCO/IUCr flagships initiatives echoing to this strategy are both the IUCr-UNESCO OpenLabs (a network of operational crystallographic laboratories) in Africa and the Regional Summit meeting in Bloemfontein, South Africa.
High School Enrichment: Scientific Research
Authors: Wasserman Erin
Published: November 2015

Science Research is a three-year program that offers gifted students the opportunity to journey into scientific research under the apprenticeship of a research mentor, where they can gain an understanding of the underpinnings of modern scientific research – an opportunity that most high school students do not encounter in their formal science coursework. Come learn about this program, which skillfully marries the ideas of experiential learning and social experience, which is supported and structured by classroom learning. The talk will include information about the classroom course, which serves as a support system for the literacy skills needed to successfully design an original project, independently. In addition, an example of a high school crystallography partnership project will be presented. "Senior scientists (e.g., teachers, researchers, etc.) and students working together in a mutual learning process is the strongest model for student retention and personal involvement in science. Furthermore, there is no better way to excite students and to insure their continued involvement in scientific pursuits than to give them individualized active engagement and ownership of part of a creative scientific activity at an early stage in their development." Science Research provides a unique opportunity for students to join a professional laboratory where advanced skills and critical thinking strategies are developed with concomitant support from their school in the development of college-level scientific learning skills and an understanding of the true meaning of scientific inquiry.
Photosalient Effect: Dramatic conversion of light into mechanical motion
Authors: Sahoo Subash , Naumov Pance
Published: November 2015

Materials showing mechanical response in presence of external stimuli are of relevance for the design of nanoscale actuating devices for a variety of small-scale applications including actuators, flexible electronics, artificial muscles, and others. In recent years, molecular actuators[1] (molecular rotor, elevator, etc.) and several macroscopic systems based on liquid-crystal elastomers, gels, and other polymers[2] have been developed. The most recent efforts are aimed at achieving rapid, reversible, maximum and fatigueless response with single crystals which display optimum coupling between light and the mechanical energy. When exposed to light, certain single crystals can jump up to thousands times their own size. The term "photosalient" was introduced recently to describe this phenomenon.[3] The photosalient effect in the motile crystals represents a direct and visually impressive demonstration of the conversion of light into mechanical motion through a photochemical reaction on a macroscopic scale, which sets the platform for the design of fast biomimetic and technomimetic actuating materials that can mimic animal motions, dynamics of macromolecules, or dynamic technical elements, in the future. In this presentation, we will describe the mechanical response from photosalient single crystals that undergo photoinduced linkage isomerization. To understand the mechanistic details, the mechanism of the process was studied by X-ray photodiffraction, kinematic analysis, IR spectroscopy and mechanical characterization. In contrast to many other solid-state transformations that involve nucleation and propagation of the reaction interface, in this system the reaction proceeds homogeneously whereupon solid solutions form without apparent phase separation.
BioDiff - a neutron diffractometer for protein crystallography
Authors: Schrader Tobias , Ostermann Andreas , Monkenbusch Michael , Laatsch Bernhard , Jüttner Philipp , Petry Winfried , Richter Dieter
Published: November 2015

The research reactor Heinz Maier-Leibnitz (FRM II) is a modern high flux neutron source which feeds some 30 state of the art neutron beam instruments. Currently 24 are operational, others in commissioning or under construction. The newly built neutron single crystal diffractometer BIODIFF is especially designed to collect data from crystals with large unit cells. The main field of application is the structural analysis of proteins, especially the determination of hydrogen atom positions. BIODIFF is a joint project of the Jülich Centre for Neutron Science (JCNS) and the FRM II. Typical scientific questions addressed are the determination of protonation states of amino acid side chains (see e. g. [1,2]) and the characterization of the hydrogen bonding network between the protein active centre and an inhibitor or substrate. BIODIFF is designed as a monochromatic instrument. By using a highly orientated pyrolytic graphite monochromator (PG002) the diffractometer is able to operate in the wavelength range of 2.4 Å to about 5.6 Å. Contaminations of higher order wavelengths are removed by a neutron velocity selector. To cover a large solid angle the main detector of BIODIFF consists of a neutron imaging plate in a cylindrical geometry with online read-out capability. A fast Li/ZnS scintillator CCD camera is available for additional detection abilities. An optical CCD-camera pointing at the sample position is used to quickly align the crystal with respect to the neutron beam. The main advantage of BIODIFF is the possibility to adapt the wavelength to the size of the unit cell of the sample crystal while operating with a clean monochromatic beam that keeps the background level low. BIODIFF is equipped with a standard Oxford Cryosystem "Cryostream 700+" which allows measurements in the temperature regime from 90 K up to 500 K (see Figure underneath).
Mechanism of IPPase shown by high resolution Neutron and X-ray crystallography
Authors: Ng Joseph , Hughes Ronny , Morris Michelle , Coates Leighton , Blakeley Matthew , García-Ruiz Juan , Schrader Tobias , Ostermann Andreas
Published: November 2015

Soluble inorganic pyrophosphatase (IPPase) catalyzes the hydrolysis of inorganic pyrophosphate (PPi) to form orthophosphate (Pi). The action of this enzyme shifts the overall equilibrium in favor of synthesis during a number of ATP-dependent cellular processes such as in the polymerization of nucleic acids, production of coenzymes and proteins and sulfate assimilation pathways. Two Neutron crystallographic (2.10-2.50Å) and five high-resolution X-ray (0.99Å-1.92Å) structures of the archaeal IPPase from Thermococcus thioreducens have been determined under both cryo and room temperatures. The structures determined include the recombinant IPPase bound to Mg+2, Ca+2, Br-, SO2-2 or PO4-2 involving those with non-hydrolyzed and hydrolyzed pyrophosphate complexes. All the crystallographic structures provide snapshots of the active site corresponding to different stages of the hydrolysis of inorganic pyrophosphate. As a result, a structure-based model of IPPase catalysis is devised showing the enzyme's low-energy conformations, hydration states, movements and nucleophile generation within the active site.
Proton Transfer through Function-Unknown Glu residue Highly Conserved in ADPRase
Authors: Furuike Yoshihiko , Akita Yuka , Tomita Yurie , Miyahara Ikuko , Kamiya Nobuo
Published: November 2015

ADP ribose pyrophosphatases (ADPRase) hydrolyze ADP ribose (ADPR) into AMP and ribose-5'-phosphate with the help of Mn2+. We are trying to explain how ADPRases split H2O to generate the nucleophilic OH- and exclude the unnecessary proton left behind from the catalytic core consisting of Nudix motif GX5E(1)X7RE(2)UXE(3)E(4)XGU. In this report, we focus on Glu residue at the position 3 (Glu3rd) whose role has not been uncovered despite a lot of previous crystallographic efforts and kinetic studies. In order to judge whether Glu3rd takes part in the proton transfer process or not, we performed two kinds of experiments using the crystals of ADPRase from Thermus themophilus HB8, which diffracted X-rays up to 0.9 Å resolutions. The 11 crystals of 18 were used for the investigation of the time-dependent structural changes based on the in-situ observation of ADPR hydrolysis at constant pH. We soaked Mn2+ into ADPRase-ADPR (ES) binary complex to start the reaction, and cryo-trapped ES-Mn ternary reaction intermediates. All data sets were refined with SHELXL and the C-O bond lengths of carboxylates were calculated by the full-matrix inversion following the removal of structural restraints on Glu residues. Carefully observing how the C-O bond lengths of Glu3rd behave along the reaction time, we found that Glu3rd contributes to activate the nucleophilic H2O and to exclude the proton left behind. When the reaction reached the climax of ADPR hydrolysis, its two C-O bond lengths were 1.30(2) and 1.23(2) Å, indicating the resultant structure after the proton extraction from the nucleophilic H2O. The remaining 7 crystals were used for the pH titration of ES binary complex to investigate its acid dissociation property. We achieved the various crystalline pHs by soaking buffer solution without any reaction triggers. Based on the pH-dependent changes of C-O bond lengths, we revealed the pKa value of Glu3rd around 4.6, which makes the catalyst workable even in the weak acidic condition.
UHR PX and NPC studies of H-FABP water network with tiny perdeuterated crystals
Authors: Podjarny Alberto , Blakeley Matthew , Haertlein Michael , Mitschler Andre , Cousido-Siah Alexandra , Petrova Tatiana , Guillot Benoit , Stote Roland , Moulin Martine , Howard Eduardo
Published: November 2015

We have obtained very detailed information about the internal water molecules in the large internal cavity inside fatty acid binding (FABP) proteins , in the presence of bound fatty acids (FA), by Ultra High Resolution X-Ray Crystallography (UHR) to 0.7 Å and Neutron Protein Crystallography (NPC) to 1.9 Å using a "radically small" (V=0.05 mm3) crystal. These waters form a very well ordered dense cluster of 12 molecules, positioned between the hydrophilic internal wall of the cavity and the fatty acid molecule. This information has been used for a detailed electrostatic analysis based on the charge distribution description modeled in the multipole formalism and on the Atoms in Molecules theory. This information is also being used in molecular dynamics simulations of H-FABP and its complex with FA in order to quantify the energetic contribution of these internal waters to the binding energy. The experiment has been done with oleic acid, coming with the protein expressed in E. Coli. The results have been analyzed in order to understand the interactions between the FA, the internal water and the protein, and in particular the role played by the water molecules in determining the potency and specificity of FA binding to FABPs. The major tool for visualizing the water molecules inside the H-FABP cavity is UHR X-Ray Crystallography combined with NPC. UHR crystallographic structures give the positions of hydrogen and oxygen atoms for well-ordered water molecules. NPC determines hydrogen atom positions, particularly of water molecules which have multiple conformations, leading to the best possible crystallographic model. This model was then complemented by a transferred charge distribution to accurately determine the electrostatic and topological properties in the binding pocket, providing a description of the way water molecules in hydration layer contribute to the binding of ligand, which is essential to understand and model ligand binding.
Direct methods for the 21st century
Authors: Elser Veit
Published: November 2015

We describe a general method for obtaining structures from diffraction data that can be applied to non-crystalline and magnetic materials.
The phase problem for quasicrystals in reciprocal space
Authors: Wolny Janusz , Buganski Ireneusz , Chodyn Maciej , Kozakowski Bartlomiej , Kuczera Pawel , Strzalka Radoslaw
Published: November 2015

The phase problem is very well-known in crystallography and is particularly important for structure solution of quasicrystals. Structure solution ( initial phasing of the diffraction pattern) is the first step of atomic structure determination against the diffraction data. Many tools for solving the phase problem in crystallography were developed over the years. Besides the pioneer Patherson function method or direct methods, also the low density elimination method and, more recently, maximum entropy method or charge flipping algorithm are widely used. We propose another way of phase recovery, directly from the diffraction pattern. It has been shown, that diffraction patterns of aperiodic structures (quasicrystals and modulated structures) consists of periodic series of peaks [1,2]. The peaks are, of course, aperiodically distributed in reciprocal space. However, the envelopes of such peaks are strictly periodic. For Fibonacci sequence the shape of envelopes is given by a sinx/x – type function. In the centrosymmetric case all peaks belonging to a given series have the same phase (0 or π). Moreover, once we rescale peak positions to obtain the reduced envelope of structure factor (intensity), we can easily find the shape of the average unit cell, by applying the inverse Fourier transform. The functionality of such approach has been shown in [3] for d-AlNiCo quasicrystal. In this paper we show a few examples of model structures with recovered phases. Decorated Fibonacci sequence, Penrose tiling and Ammann tiling are used as model structures for 1D, 2D, and 3D quasicrystals respectively. We compare the results with conventionally used charge flipping method.
Electron Microscopy for Atomic/Electronic Structure of Quasicrystals
Authors: Abe Eiji
Published: November 2015

As stated with special emphasis in the Noble Lecture by Dr. Shechtman, the quasicrystal discovery is definitely the victory of electron microscopy – the first icosahedral stereogram was constructed by a series of electron diffraction patterns from a tiny quasicrystalline grain, and the following high-resolution electron microscope images indeed confirmed a unique aperiodic order that can never be consistent with twinning of normal crystals. Almost thirty years after these early electron microscopy studies, we are now in the era of aberration-corrected electron microscopy which realizes a remarkable resolution beyond an Ångstrom scale [1, 2]. In the talk, I will describe the local atomic/electronic structure of quasicrystals using state-of-the-art scanning transmission electron microscopy, providing several striking insights that may lead to the answers for the longstanding key questions; "Where are the atoms? And why do quasicrystals form?"
Influence of high pressure on amino acids and their multicomponent crystals
Authors: Zakharov Boris , Boldyreva Elena , Kolesov Boris , Losev Evgeniy , Arkhipov Sergey
Published: November 2015

The studies of molecular crystals at high pressures help to understand intermolecular interactions, their role in the formation of crystal structures and in crystal structure response to external actions. Multicomponent crystals are promising for high-pressure research since a large number of phenomena has been observed for them [1]. Crystals of amino acids, their salts and co-crystals are of special interest in this respect. They are promising as new materials and can serve as biomimetics since the structure forming units of these crystals are similar to those in biomolecules. The aim of this study was to follow the effect of increasing pressure on crystal structures of amino acid salts and co-crystals to compare the results with those obtained for individual amino acids. Glycine, alanine, serine and their corresponding salts with carboxylic acids were chosen as objects of the study. Single-crystal X-ray diffraction and Raman spectroscopy were used as main experimental techniques. Three different types of behavior of salts on increasing pressure as compared with individual crystals were observed. For some salts, adding the second component stabilized the crystal structure with respect to phase transitions [2]. In the second group, on the contrary, the salts underwent phase transitions at relatively low pressures, though individual components did not undergo phase transitions at least up to 8-10 GPa. The last, third group of salts showed phase transitions in a similar pressure range as the individual components, but the mechanism of the transition changed. The phase transitions were accompanied either by crystal structure disordering, or by switching-over hydrogen bonds [3]. This work was supported by a grant from RFBR (12-03-31541 mol_a), by the Ministry of Education and Science of Russia, Russian Academy of Sciences, and by a grant of President of Russia for State support of Russian leading Scientific Schools (project NSh-279.2014.3).
In situ synchrotron powder diffraction for an ionic conductor transition
Authors: Kasai Hidetaka , Kato Kenichi , Hori Akihiro , Takata Masaki , Kitagawa Susumu , Tanaka Hiroshi , Arikawa Hidekazu , Takeguchi Tatsuya , Sadakiyo Masaaki , Yamauchi Miho
Published: November 2015

In situ synchrotron X-ray powder diffraction can be one of the most powerful probes to investigate the structure evolution by a chemical reaction thanks to simultaneity of data collection. It is not, however, with ease to produce a homogeneous chemical reaction in the limited spaces, which is essential to see an atomic-scale structure evolution. We have developed an in situ capillary cell for both high-temperature H2reduction and precise humidity control at the SPring-8 BL44B2. We successfully applied this in situ system to an electronic conductor LaSr3Fe3O10, which is transformed into an ionic conductor by the two-step chemical treatments [1]. LaSr3Fe3O10has a triple-layer structure with a FeO6octahedral unit. One triple layer is bonded with another layer through van der Waals interaction. Structure refinements with in situ synchrotron powder diffraction data revealed that the H2reduction at 613 K produced in-plane oxygen vacancies, which resulted in suppression of the interlayer interaction. We found from charge density studies and Raman spectroscopy measurements that the following humidification intercalated H2O and OH-into the interlayer and intralayer, respectively. That means that H2O plays a role for suppression of three-dimensional electronic conductivity, stabilizing the intercalation structure. On the other hand, the OH-ions behave as carriers for ionic conductivity, maintaining the charge neutrality in the intralayer. Finally we determined the composition of the ionic conductor to be LaSr3Fe3O8.0(OH)1.2·2H2O, which indicates a transformation of LaSr3Fe3O10into an OH-ionic conductor. In the presentation, I will discuss the OH-ionic conduction channel based on electrostatic potentials obtained from charge densities.
Growth kinetics of metal nanoparticles on solid surfaces
Authors: Metwalli Ezzeldin
Published: November 2015

Dispersed metal nanoparticles (nps) in a polymer matrix are essential for many technological applications, including biological imaging, thin film technology, magnetic recording media, optoelectronics and sensors. Real time investigation of the evolution of nps size and shape during the in-situ metal deposition on polymer thin films enables a fine tune of magnetic and electric properties. Metals in their atomic state are deposited on several homopolymer and block copolymer films by DC magnetron system (Metwalli et al., 2013, Metwalli et al., 2008, Buffet et al., 2011). With the unprecedented time resolution of 10 milliseconds, the growth kinetics of the metal nps on the polymer surfaces is monitored using in-situ GISAXS. An exponential growth of nps size on all polymer surfaces is observed. Below a certain critical nps size, an initial fast particle growth is due to high particle mobility. A slower kinetics at concentrated metal dispersion is due to the strong metal-metal interactions. The metal growth kinetics study for many chemically different homopolymer films explains the long-time debated high selectivity characteristics of metals towards one block in block copolymer based nano-templates.
In operando and wide-d neutron diffraction measurements at J-PARC
Authors: Ishigaki Toru , Yonemura Masao , Hoshikawa Akinori , Yoshida Yukihiko , Matsukawa Takeshi , Torii Shuki , Kamiyama Takashi
Published: November 2015

Since the operation start for J-PARC/MLF at 2008, neutron diffraction experiment using high intensity pulse neutron beam became possible. For example, if there are 1g typical oxide samples, it is possible to get one diffraction pattern in about ten minutes for `Rietveld-analysis-quality' at iMATERIA. Four neutron powder diffractometer, iMATERIA (IBARAKI Materials Design Diffractometer[1]), SPICA (special environment powder diffractometer dedicated for battery study), SuperHRPD (Super high resolution powder diffractometer, d/d = 0.03 %) and NOVA (high intensity total scattering diffractometer) are operating at J-PARC/MLF. In our previous neutron facility, the neutron intensity is not so strong to carry out routinely in operando neutron diffraction experiments. In J-PARC, however, it became possible to measure quickly changing neutron diffraction patterns in operando condition. iMATERIA is a versatile neutron diffractometer funded by Ibaraki prefecture for industrial application. In iMATERIA, Some user group was trying to in-situ measurements for battery. SPICA is optimized for an in operando neutron diffraction study to clarify the structural changes of battery materials at the atomic level. It has already typical results of time resolved measurements for a commercialized Li-ion battery. The structural changes of the material, which is dependent on the lithium content, were clearly observed. We will report the status of J-PARC/MLF diffractometers and recent result of in operando experiments.
Molecular Analysis of a G-actin Sensor
Authors: Mouilleron Stephane , McDonald Neil , McDonald Neil
Published: November 2015

Actin dynamics control many aspects of cell shape and cell motility through regulatory interactions with a large variety of actin-binding proteins. Signalling to these actin regulators frequently involves a Rho GTPase-stimulated pathway that leads to a dramatic fluctuation in the levels of monomeric actin (G-actin) following polymerisation to F-actin. Recent studies have identified a molecular G-actin sensor called the RPEL domain that links RPEL-containing proteins and their subcellular localisation to actin dynamics. The RPEL domain contains a tandem array of typically three RPEL motifs, each of which is competent to bind a G-actin molecule [1]. The domain is present in two otherwise unrelated protein families; the MRTF family of serum response factor (SRF) transcriptional co-activator proteins and the Phactr family of actin and PP1 phosphatase-binding proteins. We have begun to investigate how the RPEL domain operates in both of these protein contexts and how it modulates subcellular localisation, transcriptional regulation and actomyosin contractility. To define the molecular basis for the sensor we have reconstituted pentameric and trimeric G-actin complexes with the RPEL domain from both MRTF-A and Phactr and used crystallography to reveal discrete supramolecular assemblies with repetitive arrangements of the G-actin subunits around the "crankshaft"-shaped RPEL domain [2,3]. These arrangements are quite different from F-actin intermolecular contacts and are quite unexpected. Our crystal structures reveal cooperative loading of G-actin onto the RPEL domain that we show by several cell-based reporter assays to be of functional importance. These structures explain how G-actin interaction alters the subcellular localisation of both MRTF-A and Phactr by inhibiting nuclear import through competing with importin alpha-beta binding [2,3].
Mechanisms of membrane protein biogenesis
Authors: Sinning Irmgard
Published: November 2015

More than 25% of the cellular proteome comprise membrane proteins that have to be inserted into the correct target membrane. Most membrane proteins are delivered to the membrane by the signal recognition particle (SRP) pathway which relies on the recognition of an N-terminal signal sequence. In contrast to this co-translational mechanism, which avoids problems due to the hydrophobic nature of the cargo proteins, tail-anchored (TA) membrane proteins utilize a post-translational mechanism for membrane insertion – the GET pathway (guided entry of tail-anchored membrane proteins). The SRP and GET pathways are both regulated by GTP and ATP binding proteins of the SIMIBI family. However, in the SRP pathway the SRP RNA plays a unique regulatory role. Recent insights into eukaryotic SRP will be discussed.
Structure determination from in situ diffraction with the Rigaku PlateMate
Authors: Le Magueres Pierre , Criswell Angela , Ferrara Joseph
Published: November 2015

As crystallographers face increasing problems with crystallizing new proteins, in-situ screening in crystallization trays at room temperature is experiencing a renaissance. It saves a lot of time when screening large numbers of crystallization hits and it helps avoid crystal damage caused by human manipulation error (harsh manual handling, bad freezing) or changes in crystal properties (dehydration, wrong cryo-conditions). In certain cases, it is also possible to go beyond screening and collect enough data for structure solution, especially on an X-ray home source where a less intense beam helps minimize the devastations of radiation damage occurring at room temperature. The Rigaku PlateMate has proved itself as an efficient and easy-to-use in-situ screening tool on the field for the past two years. It is as easily mounted on a goniometer as a regular goniometer head and thanks to a plate adapter with SBS footprints, it accommodates most 96-wells plate types, from sitting and hanging drop to LCP plates. In addition, thanks to its narrow dimensions and aided by software to prevent collisions with the detector and the crystal viewing camera, the PlateMate can be used to easily collect data from crystals in situ. In this work, we present structure solution results obtained from data collected with the PlateMate on crystals from various proteins (native crystals or containing gold or iodine) and using one or multiple crystals to make up a complete data set.