bluuebunny/crossref_metadata_2025 huggingface dataset:
Lanthanide Oxalates Under Pressure: Structural and Photoluminescence Properties
Authors: Spencer Elinor , Carter Korey , Cahill Christopher , Ross Nancy
Published: November 2015

Three dimensional lanthanide (Ln) framework compounds are renowned for their excellent photoluminescence properties, and there is growing interest in the development of this class of metal-organic framework (MOFs) materials for a diverse range of applications ranging from size-selective sensor technology to bio-imaging. Yet, although the physical and structural properties of Ln-MOFs under ambient conditions are well documented, there remains a distinct lack of information pertaining to the behaviour of these materials under non-ambient conditions. In this contribution we present both variable pressure (0–4 GPa) and temperature (100–300 K) single-crystal X-ray diffraction (XRD) studies of several Nd and Pr oxalate MOFs with different topologies (Fig. 1). Furthermore, these extensive XRD investigations have been complemented by variable pressure spectroscopic measurements that allow for evaluation of the influence of pressure on the photoluminescent emissions of these Ln-MOF compounds. This combined diffraction and spectroscopy study has enabled the structure-property relationships, which are so critical to the development of Ln-MOFs for practical usage, to be evaluated comprehensively. We will also show how the framework topology influences the structural behaviour of the Ln-MOF in response to pressure, resulting in the occurrence of unusual phenomena such as negative linear compression (NLC) in which one of the crystallographic axes expands, rather than contracts, with increasing pressure. Analysis of the high-pressure single-crystal XRD data has enabled the NLC mechanism to be elucidated and this will be presented.
HP-induced supra-molecular organization of guest molecules in FER-type zeolites
Authors: Arletti Rossella , Quartieri Simona , Vezzalini Giovanna , Fois Ettore , Tabacchi Gloria
Published: November 2015

The response to pressure of a synthetic all-silica ferrierite (Si-FER) and of a natural ferrierite from Monastir (Sardinia, Italy) (Mon-FER, Na0.56 K1.19 Mg2.02 Ca0.52 Sr0.14)(Al6.89Si29.04)O72 ·17.86 H2O) is here investigated combining HP synchrotron XRPD experiments and molecular dynamics simulations. The experiments were carried out by using penetrating (methanol:ethanol:water 16:3:1, m.e.w.; ethanol:water 1:3, e.w.) and non-penetrating (silicone oil, s.o.) pressure transmitting media (PTM). In Si-FER compressed in e.w., both water (w.) and ethanol molecules (e.) enter the pore system even at 0.2 GPa. The structural refinement of the data collected at 0.8 GPa reveals 8 w. and 4 e. molecules in the 10- and 6-membered ring channels, in tight agreement with the results of MD simulations. In Si-FER compressed at 0.2 GPa in m.e.w., only water molecules penetrate the 10-membered ring channels (15 per u.c.), organized in chains running along the channel axis. The interactions among the guest species and the framework oxygen atoms are very weak, due to the hydrophobicity of the framework. Upon decompression, the intruded extra-molecules are not completely released, so giving rise to new materials with different extra-framework contents. The results obtained for Si-FER compressed in m.e.w. and s.o. were compared to those obtained for Mon-FER, demonstrating that the zeolite composition and the PTM strongly influence the overall elastic parameters of the investigated samples. Specifically, Mon-FER shows a much higher rigidy than Si-FER in both media, due to the stiffening effect of the numerous extraframework species present in the natural sample. The higher rigidity of Si-FER in m.e.w. with respect to s.o. can be explained by the penetration, in the former case, of the PTM molecules, which contribute to stiffen the framework.
In situ studies of gas sorption in porous networks
Authors: Plonka Anna , Banerjee Debasis , Woerner William , Parise John
Published: November 2015

Selective gas separation is one of the key properties exploited in industrial processes utilizing porous materials. The crystal structure of the native and activated frameworks, along with those of ion exchanged and otherwise modified variants, provide the basis for rational development of gas-selective nanoporous solids. In situ scattering studies of gas-loaded materials provide an understanding of the nature of interactions between sorbed gas and pore surface, which can be vital to development of reliable interatomic potentials, used simulating adsorption behavior. We find that simultaneous observation of the Differential Scanning Calorimetry coupled with x-ray diffraction (DSC-XRD) measurements is a particularly powerful tool 1, 2. The powder diffraction pattern can be monitored for changes, such as framework collapse, as porous materials are heated and activated. Apart from monitoring structural changes, thermal responses accompanying dynamic exposure to gases at variable humidity, and as the temperature is varied, provides a reliable tool in order to screen for new and potentially selective porous materials. The DSC signal provides a reliable means to determine the enthalpy of interaction between framework and gas, and there is experimental evidence this signal may distinguish between gas interactions with bare metal sites in the activated framework and other gas-framework interactions. Studies where the enthalpy of interaction and X-ray scattering from low angle peaks, which are most sensitive to the filling and evacuation of pores of the porous materials are monitored, can be coupled with varying the nature of the gas and the relative humidity. These studies are conveniently carried out with a modified gas manifold interfaced to a slightly modified Rigaku corporation DSC-XRD, which allows studies from about 150 – 600 K. Illustrative examples of the use of this laboratory based equipment, which provide the underpinnings of detailed single crystal studies of gas-loaded materials, include studies of porous calcium based coordination network (CaSDB, SDB: 4,4' - sulfonyldibenzoate), which is selective for CO2, even in the presence of high relative humidity (RH). Recent results from a series of materials studied in the home laboratory and at synchrotron sources will be presented.
Nanoporous Structural Science Developed by the MEM/Rietveld Method
Authors: Takata Masaki , Nishibori Eiji , Kubota Yoshiki , Tanaka Hiroshi
Published: November 2015

Wide-spread functionalization research of Metal Organic Frameworks(MOFs) has brought rapid increase in variety of materials since the beginning of structural study in nanoporous of MOFs were made by SR(Synchrotron Radiation) powder diffraction using the MEM(Maximum Entropy Method)/Rietveld Method(Kitaura et al, 2002). The MEM/Rietveld method has successfully applied to refine the structural position of absorbed molecules and to investigate a bonding nature between the molecules and MOF's pore walls. Noise-resistance electron density mapping with incomplete data set was a key advantage of MEM to visualize unmodeled feature of molecules in nanoporous. Since then, the charge density studies by the MEM/Rietveld Method have uncovered various ordering structure of absorbed molecules into nanoporous more and more(Takata, 2008). Those findings ignited trends to design the nanoporous as the space to be functionalized. Recently, the MEM/Rietveld method has been further developed as the method to map an electrostatic potential and electric field(Tanaka 2006). This technique is making a progress in structural science of MOFs since the visualized electrostatic potential in the nanoporous ought to provide information of interplay between the molecule and the pore walls. The talk will present the recent progress and challenges of the MEM/Rietveld method to the structural science of the MOFs.
Resonant X-ray magnetic scattering study of Ti-Mn-doped Ba ferrites
Authors: Sasaki Yo , Okube Maki , Sasaki Satoshi , Toyoda Takeshi
Published: November 2015

BaFe12O19 has M-type hexaferrite structure, giving strong uniaxial anisotropy of the magnetization along c axis. In doped BaTixMnxFe12-2xO19, the substitution of Fe3+ by a pair of Ti4+ and Mn2+ results in a weakening of the magnetic interactions due to the canting of magnetic moments. The crystal structure has a sequence of (Fe6O8) spinel and (BaFe6O11) hcp blocks, associated with five independent Fe sites: tetrahedral 4f1, bipyramidal 2b, and octahedral 2a, 4f2 and 12k sites. Single crystals synthesized by a flux method have cell dimensions of a = 5.8953(2) and c = 23.1887(8) Å and a = 5.9039(2) and c = 23.2047(8) Å for samples of x = 0.5 and 1.0, respectively. Each crystal was mounted with short glass fiber on rare-earth magnet and goniometer head. Conventional intensity measurements were made using a Rigaku AFC7 four-circle diffractometer with a graphite (002) monochromator for Mo Kα radiation. Site-occupancy experiments were performed by using a vertical-type four-circle diffractometer at PF-BL-10A. In this study the magnetic structure has been examined to use resonant X-ray magnetic scattering (RXMS) at the Fe K absorption edge in PF-BL-6C. Circularly polarized X rays produced by a diamond phase retarder were switched between right-handed (helicity=+1) and left-handed polarizations. An AFC-5u four-circle diffractometer was used in the geometry of horizontal scattering plane. Intensity measurements were made to collect as many as possible of Bragg reflections. Based on an asymmetrical ratio of the intensities between right- and left- handed circular polarizations, the intensity difference in the RXMS was estimated for each of reflections. A set of observed asymmetrical ratios was fitted to a model of spin orientation in crystal-structure calculations with the resonant magnetic scattering factors. A residual function in the least-squares fitting is useful to evaluate magnetic moments for individual sites, which is a multiplicity parameter refined in terms of atomic scattering factor. It gives a minimum in plot between site-multiplicity and residual function, assigning the multiplicity related to the canting of magnetic moment in the Fe sites. The magnetic structure obtained in this study is compared with those of M-type BaFe12O19 and BaTiCoFe10O19.
Magnetism and its interplay with lattice in the iron-based ladder compounds
Authors: Nambu Yusuke , Hawai Takafumi , Sato Taku , Ohgushi Kenya
Published: November 2015

Since the discovery, research on iron-based superconductivity (SC) has become one of the main streams in condensed matter physics [1]. The interplay between structure, magnetism and SC is one of most intriguing subjects of this field. The common structural feature is the presence of square planar sheets of Fe atoms coordinated tetrahedrally by pnictogens or chalcogens. They have been, at the early stage, realized in the ZrCuSiAs (1111), ThCr2Si2 (122), anti-PbO (11) and Cu2Sb (111) structures. To gain further insight into the mechanism of the SC and variation of magnetic orders, investigation of Fe-based compounds with a separate spatial dimension is important. This is because the dimensionality should influence magnetism and can control itinerancy of electrons by changing Fermi surface topology. As spin ladders in copper oxides shed a new light on the mechanism of SC, a study on an analogue with ladder geometry among Fe-based compounds is highly desired. Here we report our recent studies of iron-based ladder compounds AFe2X3 (A = K, Rb, Cs, Ba; X = S, Se, Te) [2,3]. Crystal structure is novel, comprising of FeX4 tetrahedra with channels which host A atoms, and four-fold coordinated Fe2+ ions form two-leg ladder geometry. Unlike most of parent compounds of the Fe-based SCs, the ladder compounds are insulating down to the lowest measured temperature. Through bulk properties and neutron diffraction measurements, a variety of magnetic structures and low dimensional characteristics were elucidated. These would provide a clue of the SC realized in a separate dimension systems. The description of theory that accounts for the observed magnetic structures will be also presented.
Magnetic structure analysis of rare earth permanent magnet Sm2Fe17N3
Authors: Saito Kotaro , Inami Nobuhito , Takeichi Yasuo , Ueno Tetsuro , Sagayama Ryoko , Kumai Reiji , Hansen Thomas , Ono Kanta
Published: November 2015

Rare earth intermetallic compound Sm2Fe17N3 exhibits notalble magnetic properties such as high Curie temperature and high coercivity which are very suitable for permanent magnets [1,2]. Although microscopic magnetic structure is one of the basic information for magnetic materials, there is no report about the magnetic structure of Sm2Fe17N3 for our knowledge. This is because samarium's neutron absorption cross section is huge enough to make researchers hesitate to have neutron diffraction experiments of Sm compounds. We have carried out powder neutron diffraction measurement of Sm2Fe17N3 with a straightforward solution to the problem by taking long measurement time. Synchrotron x-ray diffraction measurements with single crystal has also been done to obtain initial crystal structure parameters for magnetic structure analysis and we have succeeded to analyze the magnetic structure of Sm2Fe17N3 at room temperature. Among four Fe sites in the unit cell, while one Fe site which is the nearest neighbor of nitrogen shows smaller magnetic moment than normal iron, two Fe sites show enhancement in their magnetic moments. This phenomenon can be understood as 'cobaltization' of Fe by the adjacent nitrogen through hybridization.
Extracting Local Crystallographic Structure Using 4D-STEM Datasets
Authors: Ophus Colin , Ercius Peter , Sarahan Michael , Czarnik Cory , Ciston Jim
Published: November 2015

Traditional scanning transmission electron microscopy (STEM) detectors are monolithic and integrate a subset of the transmitted electron beam signal scattered from each electron probe position. These convergent beam electron diffraction patterns (CBED) are extremely rich in information, containing localized information on sample structure, composition, phonon spectra, three-dimensional defect crystallography and more. Many new imaging modes become possible if the full CBED pattern is recorded at many probe positions with millisecond dwell times. In this study, we have used a Gatan K2-IS direct electron detection camera installed on an uncorrected FEI Titan-class transmission electron microscope to record 4D-STEM probe diffraction patterns on a variety of samples at up to 1600 frames per second. As an example, a 4D-STEM dataset for a multilayer stack of epitaxial SrTiO3 and mixed LaMnO3-SrTiO3 is plotted in Figure 1. Figure 1A shows a HAADF micrograph of the multilayer along a (001) zone axis. Only the A sites (Sr and La) are visible in this micrograph and the composition can be roughly determined from the relative brightness. One possible 4D-STEM technique is position-averaged convergent beam electron diffraction (PACBED) described by LeBeau et al. [1]. We can easily construct ideal PACBED patterns by averaging the probe images over each unit cell fitted from Figure 1A, which is shown in Figure 1B. By matching these patterns to PACBED images simulated with the multislice method we can precisely determine parameters such as sample thickness and composition, the latter of which is plotted in Figure 1C. For comparison, the composition has also been determined with electron energy loss spectroscopy (EELS) in a separate experiment, shown in Figure 1D. The composition range of 0-85% LaMnO3 measured by PACBED is in good agreement with the EELS measurements. In this talk we will demonstrate several other possible uses for 4D-STEM datasets.
Characterization of Crystal Lattices
Authors: Santoro Antonio
Published: November 2015

At present time, crystal lattices are characterized by means of the 44 reduced forms tabulated in Int. Tables for Crystallography, Vol. A, 1983, pag.737. Recently, we have found that this classification can be improved by a more careful analysis of the metric properties of each reduced form. Foe example, we know that the reciprocal cell of a face-centered lattice is body-centerd, and vice-versa. In the orthorhombic system there are two oF reduced forms (#16 and #26) and three oI (#8, 19 and 42) and therefore there is no one to one relationship between direct and reciprocal reduced forms. In fact, form oF #16 can be split into two sub-forms, both obeying the conditions AAC/DDF plus [2D+F]=A (Int.Tables, loc.cit.) but with different metric properties, one of which has reciprocal form oI #8 and the other reciprocal form oI #19. This method is being extended to all reduced forms of centerd lattices and a new list of will be presented.
High-Resolution STEM and EELS as Tools to Study Structure and Bonding of Oxides
Authors: Botton Gianluigi , Bugnet Matthieu , Gauquelin Nicolas , Zhu Guo-zhen
Published: November 2015

Due to the developments of aberration correctors, bright electron sources, stable microscopes and electron monochromators, electron microscopy has dramatically evolved in the recent years. The current microscopes provide structural, chemical and spectroscopic information with sub-angstrom resolution and with synchrotron-quality spectroscopic performance ranging from the mid-infrared to the hard X-ray regime. Using a combination of scanning transmission electron microscopy (STEM) and electron energy loss spectroscopy (EELS) with better than 0.1eV energy resolution (down to 10meV), we provide here a review of recent studies where EELS and STEM have allowed us to probe the structure, the local chemistry and the nature of the local electronic structure of a range of complex oxides. These studies show that it is possible to determine the location of particular atomic species used as dopants in a crystal [1], the local coordination and valence of atoms in crystals and at surfaces [2,3], and also the nature of the hybridization and valence in perovskites [4] and superconductors [5,6]. These applications show that EELS and STEM can be used to resolve ambiguities in structure refinements of oxides by deducing the site preference of transition metal atoms and their coordination. We also show that it is possible to extract valence information and localization of electron charge in a range of materials, thus providing essential information on termination at interfaces [7]. With these techniques, we explore defects in materials and the nature of the electronic structure at interfaces.
Quantitative determination of site-specific magnetic structure in TEM
Authors: Zhu jing , Wang Ziqiang , Zhong Xiaoyan , Yu Rong , Song Dongsheng , Cheng Zhiying
Published: November 2015

Determining the magnetic structure of material on a nanometer scale is fundamental for understanding its nano-scale magnetic property and developing nano-scale magnetic devices. Site-specific electron energy-loss magnetic chiral dichroism (site-specific EMCD[1],[2]) method is come up with to get the crystallographic site-specific magnetic information of nanostructures. By constructively using the dynamical diffraction conditions in EMCD experiments, we experimentally achieve the crystallographic site-specific magnetic structure of a nanostructure of NiFe2O4 as an example in transmission electron microscope, with its site-specific magnetic circular dichroism spectra, and its site-specific spin/orbital magnetic moments extracted. The site-specific EMCD method shows its unique capability for solving the crystallographic site-specific magnetic structure on nano-scale, compared with X-ray magnetic circular dichroism and neutron diffraction. This work may benefit the research and application of magnetic materials on a nanometer scale. Acknowledgement: This work is financially supported by National 973 Project of China (2009CB623701) and Chinese National Nature Science Foundation (11374174,51390471 ). This work made use of the resources of the Beijing National Center for Electron Microscopy.
Quantitative ADF-STEM and STEM-EELS at the atomic level
Authors: Dwyer Christian
Published: November 2015

The ability to count, locate and distinguish the atoms in a material is one of the ultimate pursuits of nanomaterials characterization. In recent decades, significant advances toward this goal have occurred in the field of scanning transmission electron microscopy (STEM), with the establishment of a class of imaging modes capable of ~0.1 nm spatial resolution and high chemical sensitivity. High-angle annular dark-field (ADF) imaging and chemical mapping via core-level spectroscopy are prominent techniques in this class, with applicability to a wide variety of nanostructured materials, such as nanoparticles, interfaces, and embedded phases. With such advances comes the ability to perform fully quantitative imaging for unprecedented accuracy in nanostructure characterization. However, full realization of this goal requires that we must be able to isolate and quantify all of the experimental parameters pertinent to imaging at 0.1 nm resolution, so that the only remaining unknown is the nanostructure itself. This is demonstrated in the present work. We present a systematic study of the influence of experimental factors pertinent to 0.1 nm ADF-STEM. We demonstrate that ADF-STEM images can be interpreted on a quantitative basis, in terms of the number, positions and species of atoms in the material, *without* recourse to adjustable parameters [1]. The figure presents a demonstration for [001]-oriented LaB6. A similar demonstration will be shown for atomic-resolution chemical mapping based on core-level electron energy-loss spectroscopy (EELS) [2]. The approach demonstrated here improves on previous works by removing instrumental unknowns from the analysis. Applications of this approach will be presented.
Debye function and Reverse Monte Carlo refinement of nano-sized FeOOH
Authors: Sestu Matteo , Corrias Anna , Casula Maria , Navarra Gabriele
Published: November 2015

Debye scattering equation is known since 1915 [1]. Altought this formula can, in principle, describe scattering from any multiple particle systems, its application is normally limited to small domains as clusters or low-sized nanoparticles. This is mostly due to the very high computational effort needed. Indeed, computing time strongly depends on the number of atoms. In recent years, the availability of highly performant graphics processing units (GPU) allowed their use for general purposes including strongly demanding scientific applications. This feature was exploited in the Debye Function Analysis to study more complex systems with several thousand of atoms [2]. Here, we present a refinement code using both the Debye scattering equation implemented on a commercial GPU and the Reverse Monte Carlo algorithm [3] to study the structure of two disordered nano-sized iron oxy-hydroxides, feroxyhite and ferrihydrite. The determination of their structure appears rather complex. Different interpretations of the X-ray diffraction pattern have been put forward and debates remain about the exact nature of their crystalline structure. The proposed models show some structural features that are not in accordance with the known structures of other iron oxy-hydroxides: goethite, akaganeite and lepidocrocite. To evaluate their validity, these models are used as starting atom sets in the refinement procedure. To reach a quantitative agreement between the experimental diffraction pattern and the calculated one, the atom positions are randomly modified. X-ray diffraction pattern is calculed using Debye scattering equation; to speed up calculation time, a parallelized version of the equation is optimized to run on Nvidia GeForce 690 GPU.
Ab initio and DFT study on Cu (II) complex salicylate derivative
Authors: Natarajan Karthikeyan , Duraisamy Sathya , Kandasamy Sivakumar
Published: November 2015

X -ray diffraction becomes a routine process these decades for determining crystal structure of the materials. Most of the crystal structures solved nowadays is based on single crystal X-ray diffraction because it solves the crystal and molecular structures from small molecules to macro molecules without much human intervention. However it is difficult to grow single crystals of sufficient size and quality for conventional single-crystal X-ray diffraction studies. In such cases it becomes essential that structural information can be determined from powder diffraction data. With the recent developments in the direct-space approaches for structure solution, ab initio crystal structure analysis of molecular solids can be accomplished from X-ray powder diffraction data. It should be recalled that crystal structure determination from laboratory X-ray powder diffraction data is a far more difficult task than that of its single-crystal counterpart, particularly when the molecule possesses considerable flexibility or there are multiple molecules in the asymmetric unit. Salicylic acid and its derivatives used as an anti-inflammatory drug are known for its numerous medicinal applications. In our study, we synthesized mononuclear copper (II) complex of salicylate derivative. The structural characterization of the prepared compound was carried out using powder X-ray diffraction studies. Crystal structure of the compound has been solved by direct-space approach and refined by a combination of Rietveld method using TOPAS Academic V4.1. Density Functional Theory (DFT) calculations have to be carried in the solid state for the compound using GaussianW9.0 in the frame work of a generalized-gradient approximation (GGA). The geometry optimization was to be performed using B3LYP density functional theory. The atomic coordinates were taken from the final X-ray refinement cycle.
A lattice-dynamical refinement approach based on periodic ab-initio calculations
Authors: Madsen Anders
Published: November 2015

The use of synchrotron radiation and large area detectors has increased the quality and quantity of X-ray and neutron diffraction data within the last decades. These advances call for new and better approaches to model and to interpret the data. Elastic X-ray diffraction corresponds to the Fourier transform of the thermally averaged electron density in the unit cell. This density is normally approximated as the convolution of a sum of static atomic densities and the thermal motion of the individual atoms. The static densities and thermal motion are equally important: Together they conform the entire model refined against a single set of measured data, and they must both be modeled correctly, or neither is. The advent of high-performance computers has made it feasible to obtain lattice-dynamical models based on periodic quantum-mechanical calculations, to describe the concerted motion of atoms and molecules through the crystal. Our recent calculations of Debye-Waller factors based on periodic ab-initio calculations for various molecular test systems [1] has prepared the ground for proposing the refinement of quantum-mechanically derived normal modes of vibration against diffraction experiments. As opposed to the standard approach using independent atomic motion, some of the advantages and possibilities that emerge are: 1. A physically reasonable picture of the molecular motion in the crystal. 2. Refinement against data obtained at multiple temperatures in a common model. 3. Modeling thermal diffuse scattering. 4. Reduction of the number of model parameters. 5. Anisotropic motion of H atoms. The approach is computationally expensive, but may prove useful for electron density studies, studies of thermal effects in crystals, i.e. studies of thermochromic and thermoelectric compounds, solid-state phase-transitions and to derive thermodynamic properties, e.g. free energies of polymorphic crystals. We will introduce the method and present some first results for model systems.
Accurate water site determination in macromolecular refinement using 3D-RSIM
Authors: Borbulevych Oleg , Truchon Jean-François , Labute Paul , Westerhoff Lance
Published: November 2015

"Structure Based Drug Discovery (SBDD) is employed by virtually all pharmaceutical R&D organizations, and understanding the protein:ligand complex structure along with explicit solvent effects is necessary to obtain meaningful results from docking, thermodynamic calculations, and active site exploration. Phenix/DivCon is able to accurately elucidate the protein:ligand complex structure through in situ treatment of the structure using quantum mechanics; however, at standard SBDD resolutions, the crystallographic data unambiguously reveals only a small fraction of water molecules in protein crystals - even within the first hydrogen shell of the protein molecule. Further, the implicit solvent correction in conventional methods does not take into account non-linear effects of hydrogen bonding and dispersion interactions introduced by the nearest hydration shells. To address this deficiency, we have used the 3D Reference Interaction Site Model (3D-RISM) method as implemented in MOE to filter crystallographic map data and create a more complete first solvation shell of the biomolecular complex. The combination, implemented within the Phenix/DivCon refinement workflow, allows us to capture weaker difference density peaks and thus ""rescue"" water sites that are normally undetectable using conventional crystallographic protocols. This workflow has been applied to ""standard"" resolution structures, and the results have been compared to corresponding higher-resolution structures. We have observed consistent improvements in R-factors and in water site determination. For example, the lysozyme structure PDBid:2EPE (2.5 Å) has 48 crystallographic waters while PDBid:193L (1.33 Å) has 142 waters. When considering overlapping sites, 2EPE captures 30% of the waters found in 193L. When our method is applied to 2EPE however, it is able to find almost 60% of the waters observed in the higher-resolution, and it is able to predict sites that may have been missed at the higher resolution."
The Extended PLATON/SQUEEZE Tool in the Context of Twinning and SHELXL2014
Authors: Spek Anthony
Published: November 2015

The completion of a single crystal structure determination is often hampered by the presence of disordered solvent molecules of crystallization. The often not interesting details of that solvent disorder and its contribution to the calculated structure factors has to be modelled in some way in order to obtain publishable results. Current refinement programs include suitable constraints and restraints for a stable refinement of a discrete disorder model. This is often the preferred procedure, in particular when charge balances and valence states are relevant. Unfortunately, a discrete disorder model is not always feasible. Examples include solvent molecules in infinite channels or structures including unknown solvents or solvent mixtures. In such cases the iterative back-Fourier transformation of the content of the disordered solvent volume in a difference density map can be attempted as the contribution to the calculated structure factors. Back-Fourier transformation of disordered solvent regions was prototyped by us nearly 25 years ago (van der Sluis & Spek, 1990) around the, at that time widely used, SHELX76 refinement program. The original reason for its development was the structure determination of a pharmaceutical that contained infinite channels filled with ridges of electron density in the difference density map rather than discrete density peaks (van der Sluis & Spek, 1990). The preliminary implementation of a successful prototype procedure (called BYPASS) was complex and found not to be easily distributable due to its dependence on many (local) ad-hoc programs. A new distributable version, compatible with the next generation refinement program SHELXL97, was implemented as the SQUEEZE tool in the program package PLATON Spek, 2009). The new SHELXL2014 refinement program allows for an even more elegant implementation of the SQUEEZE tool including the possibility to apply it also for twinned structures. Examples and restrictions will be discussed.
A new approach to time-resolved X-ray crystallography
Authors: Yorke Briony , Pearson Arwen , Beddard Godfrey , Owen Robin
Published: November 2015

Time-resolved crystallography is able to provide four-dimensional structural information about short-lived intermediate states, with near-atomic resolution. This information can be used to elucidate molecular mechanisms relevant to areas such as drug-design, chemical and biological sensors, and energy and information storage. The current state of the art time-resolved experiments can reach picosecond time-resolutions using Laue crystallography but such experiments can only be carried out at a few beamlines worldwide.We have developed a new transform time-resolved method that can be performed using a monochromatic beamline at a synchrotron and still achieve high time-resolution, vastly increasing the accessibility of such experiments. Here we present initial results demonstrating the method.
RMCProfile: A step towards complex modelling
Authors: Tucker Matt
Published: November 2015

The importance of local structure and disorder in crystalline materials is being recognised more and more as a key property of many functional materials. From negative thermal expansion to improved fuel cell technology and solid state amorphisation to the 'nanoscale' problem, a clear picture of the local atomic structure is essential to understanding these phenomena and solving the associated problems. Total scattering, an extension of the powder diffraction method, is increasingly being used to study crystalline materials. The unique combination of Bragg and diffuse scattering can be used to determine both the average structure and the short-range fluctuations from this average within a single experiment. To maximise the structural information from such data, three-dimensional atomic models consistent with all aspects of the data are required. RMCProfile[1] (see www.rmcprofile.org) expands the reverse Monte Carlo (RMC) modelling technique[2] to take explicit account of the Bragg intensity profile from crystalline materials. Analysis of the RMCProfile-generated atomic models gives more detailed information than is available directly from the data alone. I will give several examples where RMCProfile has been used to successfully study the structure and disorder of crystalline materials to illustrate its potential. As the systems being studied become more complex, the information from many experimental techniques and any prior chemical knowledge needs to be combined into one consistent atomic model. The continued development of RMCProfile and its new capabilities is moving us closer to the complex modelling paradigm[3] required to drive the discovery of new functional materials.
Crowdsourcing the Phase Problem: Progress in Low Resolution Ab Initio Phasing
Authors: Jorda Julien , Sawaya Michael , Yeates Todd
Published: November 2015

Solving molecular structures from X-ray diffraction data without knowledge of the phases is an example of an inverse problem. Solving such problems requires searching a potentially high dimensional parameter space (e.g. of phases) and recognizing when a correct solution is encountered. Computers are good at performing rapid searches, whereas teaching a computer to recognize subtle patterns is generally challenging. Humans are naturally better at the latter task, but lack the search speed required for many scientific problems. We have begun experiments to `crowd-source' the ab-initio phase problem in crystallography by harnessing the pattern recognition capabilities of a large group of human game players to drive a computational search for good phase sets given only low resolution structure factor magnitudes [1]. The search framework is based on a genetic algorithm; each `individual' in a population has a genome that encodes a set of (initially random) phases for the given diffraction magnitudes. In an iterative procedure of Darwinian evolution (i.e. survival of the fittest), human gamers use a multi-player web-interface (CrowdPhase) to select the most fit individuals for survival based on the qualities of their corresponding electron density maps. Through mutation, recombination, and selection, the population then evolves over many generations toward a final solution. Preliminary experiments with groups of users numbering around 20 show that good phases can be obtained for very low resolution test problems. New results on more challenging test cases will be discussed.
Crystal Prediction using the Point Groups: an Application of Group Theory
Authors: McColm Gregory
Published: November 2015

As a blueprint for designing a crystal, a crystal net should be a geometric object. So a crystal design regime might be based on an algorithm that generates crystal nets using geometry. The "Crystal Turtlebug" is such a program, generating crystal nets as graphs embedded in 3-space. McColm et al (2011) described a "Maple" version; it generated crystal nets of one or two kinds of vertices and one or two kinds of edges. A new "Python" version can generate crystal nets of any number of kinds of vertices and edges. The algorithm employs matrix representations of point groups. The "core" of the program takes a fragment of the prospective crystal (e.g. for a crystal of 3 kinds of atoms and 2 kinds of bonds, a "transversal" of 3 vertices and 2 edges). The core assigns point groups to the vertices and isometries to the edges. The core then repeatedly applies groups to isometries and vice versa to generate a unit cell. The computational problem is finding a transversal that produces a chemically plausible crystal net, as most crystal nets found are implausible. We follow a breadth-first search and enumerate some transversals, screen them, generate crystal nets from the screened transversals, and screen the results. This process can entail generating millions of transversals to obtain a handful of crystal nets for users to view manually. Although such a geometric approach is somewhat different from the more popular directions of contemporary research in crystal prediction, there is precedent in the work of A. F. Wells, A. Le Bail, C. Wilmer et al, and in particular M. Treacy et al (2004). In principle, the Crystal Turtlebug will generate every crystal net up to topological equivalence. In practice, there is an exponential explosion in the number of transversals, so the time spent enumerating crystal nets within fixed parameters explodes exponentially with the number of kinds of atoms and bonds (McColm (2012)).
Quasi-Groups and the Configuration Space of Symmetry-Constrained Motions
Authors: Chirikjian Gregory
Published: November 2015

In this work, the set of all possible positions and orientations of a large molecule within the crystallographic asymmetric unit is equated to the coset space of the continuous group of proper rigid-body motions modulo the chiral space group of the macromolecular crystal. Since every chiral space group is a co-compact subgroup in the full group of rigid-body motions (which is a six-dimensional Lie group), the resulting coset space is a compact 6D manifold. However, since none of the crystallographic groups are normal in the full group of rigid-body motions, this coset space is not a group. However, it can be endowed with an operation that satisfies all of the group axioms except for associativity, thereby giving it the structure of a quasi-group. The quasi-group properties of such spaces are explored in this work as an example of generalized symmetry. The mathematical formulation presented here, which builds on the author's prior work cited below, is relevant to both the Molecular Replacement (MR) method in biomolecular crystallography, and in the design of new engineered crystals.
Interplay of symmetry and topology in science
Authors: Zhilinskii Boris
Published: November 2015

Qualitative methods in natural science are based mainly on simultaneous use of symmetry and topology arguments. The idea of the present talk is to demonstrate how the corresponding mathematical tools (based on symmetry and topology arguments) initially applied to describe classification of different phases of matter and transitions between them are extended to construct qualitative theory of finite particle systems and more general dynamical systems. I start with reminding basic notions and tools associated with application of group action ideas to physics as initiated and developed by Louis Michel (1923-1999) [1,2]. Then geometric combinatorial and topological ideas are used to give qualitative description of singularities of dynamical integrable classical system and their quantum analogs. Quantum monodromy and its various generalizations as well as description of energy bands of isolated finite particle quantum systems in terms of topological invariant, Chern number [3], will be discussed on concrete molecular and atomic examples.
Optical Properties of Ag3O4/Ag2O Films Synthesized From Recovered Ag Solution
Authors: Ekpunobi Uchenna , Akumuo Anthonia , Ogbuagu Adaora , Duru Chiamara , Ajiwe Vincent
Published: November 2015

Silver was recovered from x-ray films by dissolving the silver compounds with three different solvents (concentrated nitric acid, cassava juice and NaCN solution) and the resultant solutions were labeled Electrolyte B, C, and D. A fourth solution comprising of silver nitrate made from commercial product was labeled Electrolyte A. The solution thus formed was used as electrolyte in the electrodeposition of silver oxide. Silver oxides (Ag3O4, AgO and Ag2O) thin films of optical thicknesses, 0.2μm to 1.25μm were electrodeposited on a transparent FTO conducting glass substrates at room temperature from the silver solutions. The FTO conducting glass served as cathode while a carbon electrode served as the anode. Electrodeposition was done under dc current of 0.2A, 4V for 20seconds at 26oC. From the results, prominent peaks of orientation (031) and (111) planes of reflection of high intensity gave monoclinic structures of Ag3O4 and AgO in the films produced from all the four electrolytes with intergrowth of cubic structure of Ag2O in the film produced from electrolyte C. The average crystalline grain size calculated gave a range of 5.274 Å – 5.432Å. Optical measurements show ultra violet range of 0.36-0.45 microns and have almost zero absorbance in VIS-IR regions of the spectrum. The films have a band gap range of 2.3 – 2.7eV. Transmittance and reflectance data have been used to calculate the spectral variation of their optical constants. From the results films produced from electrolyte C compared well with others.
In- and ex situ PXRD studies of ZnO nanoparticle growth in sub-critical water
Authors: Bøjesen Espen , Jensen Kirsten , Tyrsted Christoffer , Lock Nina , Christensen Mogens , Iversen Bo
Published: November 2015

Zinc oxide (ZnO) is a material of great scientific and industrial relevance and is used widely in a variety of applications. Synthesis of ZnO nanoparticles can be performed by a wide range of methods resulting in a tremendous variety of sizes and shapes. Different in situ characterization methods have been used to investigate the ZnO formation under various synthesis conditions; these include numerous spectroscopic methods and small angle scattering. Common for these studies is that the primary focus has been to extract information on particle size and shape of ZnO, while a more rigorous microstructural and structural analysis has been lacking. Furthermore, the aforementioned studies have primarily been focused on soft chemical synthesis methods, at low temperatures and in non-aqueous media, thus omitting the widely used environmentally benign and versatile hydrothermal method. In the present work the formation of ZnO during hydrothermal synthesis has been followed using in situ powder X-ray diffraction (PXRD) combined with Rietveld refinement, thus enabling the extraction of crystallographic as well as microstructural information during the formation and growth of ZnO. Supporting ex situ syntheses and characterization by electron microcopy, high resolution PXRD and other techniques have been used to corroborate the findings from the in situ experiments. Mapping out a vast parameter space has led to a deeper understanding of the intricate mechanisms governing the nucleation and growth of ZnO nanoparticles during hydrothermal synthesis. Among the parameters studied were the influence of temperature, type of base used and the influence of different ionic salts as synthesis directing agents. The various synthesis parameters were found to influence the following structural and microstructural features: crystallite shape, morphology and size as well as the twin-fault concentration, degree of doping and crystallinity.
Pulsed laser deposition of functional oxides - towards a transparent electronics
Authors: Lorenz Michael
Published: November 2015

Metal oxides, in particular with transition metals, show strong electronic correlations which determine a huge variety of electronic properties, together with other functionalities. For example, ZnO and Ga2O3 as wide-bandgap semiconductors have a high application potential as transparent functional layers in future oxide electronics [1-2]. Other oxides of current interest are ferrimagnetic spinels of the type MFe2O4 (M=Zn,Co,Ni), see K. Brachwitz et al. Appl. Phys. Lett. 102, 172104 (2013), or highly correlated iridate films, see M. Jenderka et al. Phys. Rev. B 88, 045111 (2013). Furthermore, combinations of ferroelectric and magnetic oxides in multiferroic composites and multilayers show promising magnetoelectric coupling. For the exploratory growth of the above mentioned novel oxides into nm-thin films, pulsed laser deposition (PLD) appears as the method of choice because of its extremely high flexibility in terms of material and growth conditions, high growth rate and excellent structural properties [3]. This talk highlights recent developments of new functional oxides using unique large-area PLD processes running for more than two decades in the lab of the author [3].
Optical applications of wide-band-gap gallium oxide
Authors: Oshima Takayoshi
Published: November 2015

Ga2O3 have been attracting much attention as a wide-band-gap semiconductor owing to a large band-gap of 4.8 eV and the availability of high-quality and large-sized single crystals, which are advantageous over conventional wide-band-gap semiconductors. This presentation focuses on optical applications using Ga2O3 single crystals: photodetectors and photoelectrodes, both of which show interesting and promising properties[1,2]. As for photodetectors, a PEDOT-PSS Schottky and In ohmic contacts were prepared on front and back surfaces of a n-type Ga2O3 single crystal plate, respectively, to fabricate a photovoltaic detector. The detector operated at zero bias (V = 0 V) exhibited high responsivities in the solar-blind region (< 280 nm). Incident photon to current conversion efficiency (IPCE) was as high as 21% at 240 nm and a 240-to-300 nm rejection ratio was as large as 10^4, indicating that the detector can be applicable for flame sensing. In fact, the detector successfully detected a flame by distinguishing several nW/cm2 weak solar-blind light from a flame under a strong fluorescent lamp illumination without using visible-cut filters. As for photoelectrodes, an n-type Ga2O3 single crystal plate with In ohmic contact on the back side was used for characterization. From impedance analysis, the conduction and valence band-edges in aqueous solutions were found to be 1.1 V higher and 2.5 V lower than the H+/H2 and O2/H2O redox potentials, respectively. These potential differences, or overpotentials for water splitting, are large enough for photolysis of water. When the photoelectrode was excited by photons, H2 and O2 gases evolved from a counter Pt electrode and the photoelectrode, respectively. The highest IPCE of 36% was obtained at 240 nm. Stoichiometric water splitting was demonstrated at V = 1V without using co-catalysts. These results encourage the notion of Ga2O3 optical applications and also contribute for developing Ga2O3 semiconductor studies.