bluuebunny/crossref_metadata_2025 huggingface dataset:
In-situ Gas Dosed Powder Diffraction Under Industrially Relevant Conditions
Authors: Hudson Matthew , Queen Wendy , Brown Craig
Published: November 2015

The adsorption of small molecules onto functionalized, high surface area microporous materials is important for the advancement of industrial and environmental processes ranging from catalysis and chemical separations, to CO2 sequestration and energy storage. Over the past several years we have focused our research efforts on understanding the molecular interactions of these small molecules with a variety of microporous materials using in-situ powder diffraction methods to correlate structure with chemical properties. Background will be given on the design of gas dosing apparatus for in-situ diffraction studies at synchrotron X-ray and neutron powder beamlines. The result is that accurate doses can be made per quantity of interest (moles of cations, per unit cell, per pore, etc.), or under high pressures (100 bar), and/or chemical reactions can be followed versus temperature/pressure. Several of our recent investigations of CO2/N2/CH4 sorption in cation-exchange zeolites including Zeolite A (5A) and CHA are presented. While many industrial processes use zeolites to carry out these functions, more emphasis has been placed on metal-organic frameworks (MOFs) on late since their properties can be tuned by varying the synthetic components. A number of studies on an isostructural series, M-MOF-74, have been considered investigating why certain functionalization leads to increased specificity for applications such as CO2, O2, CO, and hydrocarbon separations. The ultimate goal is to use the knowledge gained to improve the design of new MOF materials.
Pressure-induced spin crossover in a Prussian Blue analogue
Authors: Halder Gregory , Chapman Karena , Chupas Peter , dos Santos Antonio
Published: November 2015

The structural and chemical versatility of functional molecular materials, such as molecular magnets and metal-organic frameworks (MOFs), underlie important technological, industrial, and environmental applications. The extensive structural complexities now well-documented for these systems are likely to be associated with unprecedented pressure-induced behavior compared with the traditional solid state materials more commonly explored under high pressure conditions.1 Furthermore, the typically open (low density, often porous) nature of these materials is likely to induce such phenomena at more moderate pressures, such as may be routinely encountered in practical applications.2,3 Here we report pressure-induced spin-state switching in the Prussian Blue analogue, FePt(CN)6, including in situ Synchrotron (17-BM, Advanced Photon Source) and Neutron (SNAP, Spallation Neutron Source) powder diffraction studies. Work done at Argonne and use of the Advanced Photon Source (APS) was supported by the U.S. Department of Energy under Contract No. DE-AC02-06CH11357. Research at Oak Ridge National Laboratory's Spallation Neutron Source (SNS) was sponsored by the Scientific User Facilities Division, Office of Basic Energy Sciences, U. S. Department of Energy.
Neutron diffraction study of magnetic structure in multiferroics under pressure
Authors: Kimura Hiroyuki , Fujiyama Sei , Lin Jin , Fukunaga Mamoru , Noda Yukio , Hiraka Haruhiro , Oh In-Hwan , Kim Shin-Ae , Lee Chang-He
Published: November 2015

RMn2O5 (R = Y, Bi, rare-earth) is one of the prototypical multiferroic materials that exhibits a rich variety of magnetoelectric effects. Since the successive magnetic and ferroelectric phase transitions simultaneously take place, magnetic order has been thought to be a primary order parameter for the ferroelectricity in this system. We recently have found that in neutron diffraction study of 153EuMn2O5, magnetic phase transition is induced by applying hydrostatic pressure. As temperature decreases upon p = 1.4 GPa, the magnetic propagation wave vector changes from qM = (1/2, 0, 1/3) to (1/2, 0, 1/2), indicating that the period of magnetic unit cell as well as the magnetic structure change at the phase transition. We have also carried out the dielectric and polarization measurements under pressure and established magnetic and dielectric phase diagram as functions of temperature and pressure as shown in the figure. This study has revealed that the ferroelectric (FE1) – ferroelectric (FE2) phase transition concomitantly occurs at the magnetic phase transition, where the electric polarization is enhanced. To clarify the relevance between the ferroelectricity and the magnetic structure, we carried out single crystal magnetic structure analysis of 153EuMn2O5 upon ambient- and high-pressure. In the magnetic phase with qM = (1/2, 0, 1/3), cycloidal magnetic structure of manganese spins propagating along c-axis is realized. On the contrary in the magnetic phase with qM = (1/2, 0, 1/2), the spins arrange almost collinearly along c-axis. The result indicates that the presence of the cycloidal spin structure plays an important role for inducing (or reducing) the electric polarization in this compound. This study was supported by "KAKENHI"-programs of Scientific Research (B) (24340064), Scientific Research (A) (21244051), Challenging Exploratory Research (23654098) and of Scientific Research on Priority Areas "Novel States of Matter Induced by Frustration" (19052001).
Polarized 3He Neutron Spin Filters for Neutron Scattering at Oak Ridge National Laboratory
Authors: Jiang Chenyang , Tong Xin , Brown Daniel , Kadron Benjamin , Robertson Lee
Published: November 2015

Polarized neutron scattering is a very useful method of determining spin densities and magnetic structures. It can also be used to separate nuclear coherent scattering from spin-incoherent scattering. When compared to other neutron polarizing techniques like Heusler crystals and polarizing supermirrors, polarized 3He neutron spin filters provide several unique advantages: First, polarized 3He can effectively polarize neutrons over a broad range of energies. Second, it has a large acceptance angle for incoming neutron beams. Third, it does not change direction of, or add divergence to, neutron beams. At Oak Ridge National Laboratory (ORNL), a polarized 3He program has been established to meet the increasing needs from various neutron beamlines. 3He is polarized through spin-exchange optical pumping at ORNL. Both ex situ and in situ systems have been developed to accommodate the requirements of different instruments. We report the current status of our development and present test results on several neutron beamlines at ORNL. Future application in small angle neutron scattering will also be discussed.
Coercive force mechanism in Nd-Fe-B nanocrystalline magnet investigated by SANS
Authors: Ueno Tetsuro , Saito Kotaro , Yano Masao , Harada Masashi , Shoji Tetsuya , Sakuma Noritsugu , Manabe Akira , Kato Akira , Keiderling Uwe , Ono Kanta
Published: November 2015

Permanent magnet material with high maximum energy product is demanded for industrial applications such as high-efficiency motors for hybrid and electric vehicles. Maximum energy product depends on the coercive force and the saturation magnetization. In order to achieve the high maximum energy product, current Nd-Fe-B magnets are doped with heavy rare-earth element Dy to enhance the coercive force at the expense of reducing the saturation magnetization. Viewed from another side, a supply of Dy is highly concerned because of the inequitable distribution of rare-earth resources on the Earth. Therefore, development of a Dy-free Nd-Fe-B magnet is desired. In this context, we have fabricated the Dy-free Nd-Fe-B nanocrystalline magnet and performed the small-angle neutron scattering (SANS) experiment to reveal the mechanism of its coercive force. Hot-deformed Nd-Fe-B nanocrystalline magnets with and without the diffusion process of Pr-Cu eutectic alloy were prepared [1]. Coercive forces were 1.46 T and 2.64 T for as-deformed and Pr-Cu infiltrated sample, respectively. Magnetic field dependent SANS experiment was performed to observe the magnetization reversal process. The reversal magnetic field was swept from 0 T to 5 T. SANS intensities exhibit maxima around the coercive force for both as-deformed and infiltrated sample, which indicates the evolution of the magnetic domain structure. In addition, suppressed intensity variation in infiltrated sample compared to that in as-deformed sample indicates the magnetic isolation of Nd2Fe14B grains, which is responsible for the high coercive force. We will compare the results for Pr-Cu infiltrated sample with Nd-Cu infiltrated one [1]. This work was supported by the Elements Strategy Initiative Center for Magnetic Materials under the outsourcing project of the MEXT, Japan. We thank HZB for the allocation of neutron beamtime (Proposal No. MAT-04-2110). The sample preparation was performed under the MagHEM project.
Small Angle Neutron Scattering Studies of Skyrmion Lattices
Authors: Mühlbauer Sebastian
Published: November 2015

Skyrmion lattices in chiral magnets can be regarded as macroscopic lattices formed by topological entities with particle like properties where the particle-like character of the Skyrmions is reflected in the integer winding number of their magnetization [1]. Caused by their topology, Skyrmions cannot be destroyed or created by a smooth deformation of a trivial spin texture. Skyrmion lines can be seen as magnetic whirls – sharing strong similarities with vortices of type II superconductors. Analogous to the large variety of different phases of superconducting vortex matter, Skyrmion lattice melting transitions, Skyrmion liquids and Skyrmion glass phases are expected to exist in the various B20 materials. The structure of Skyrmion matter thereby sensitively reflects the underlying physical properties of the material carrying the Skyrmions. Moreover, due to their topology, Skyrmion lattices in chiral magnets provide an excellent showcase for the investigation of topological stability and phase conversion [2]. A further consequence of the special topological properties of Skyrmions is called emergent electrodynamics: While moving through the Skyrmion lattice, conduction electrons collect a Berry´s phase in real space which leads to a very efficient coupling of transport current and magnetic structure. This leads to considerable spin transfer torque effects at current densities as low as 10^6 A/m2 [3]. Small angle neutron scattering (SANS) has played a central role in the investigation of Skyrmion lattices. We show how SANS can be used for a detailed investigation of the structure, stability, transport properties and topological decay of Skyrmion lattices in B20 compounds. *Work in collaboration with: T. Adams, A. Bauer, H. Berger, P. Böni, S. Buhrandt, A. Chacon, S. Dunsiger, L. Eng, K. Everschor-Sitte, M. Garst, R. Georgii, M. Janoschek, F. Jonietz, J. Kindervater, P. Milde, A. Neubauer, C. Pfleiderer, A. Rosch, C. Schütte, J. Seidel, J. Waizner, W. Wünzer
Structure Determination of C23H19N4OBr from Synchrotron Data
Authors: Ozgen Ozen , Kendi Engin , Koyunoglu Semra , Yesilada Akgul , Sheu Hwo-Shuenn
Published: November 2015

A significant part of medicine is based on the discovery and development of drugs. It is very important to know the crystal structure of pharmaceutical compounds for fundamental understanding of structure, physical and chemical properties. Many of these materials are available only as powders. So any structural information must be obtained from powder diffraction. I am going to present following the stages while solving the structure of C23H19N4OBr, 2-[3-phenyl-4(m-bromophenyl)-2-pyrazolin-1-yl]-3-methyl-4(3H)-quinazolinone, from 2-pyrazolines derivatives. The compounds are known to display various biological properties such as fungicidal insecticidal, anti bacterial, anti viral activities, pharmacological properties such as antiinflammatory agents and have industral properties(1). The powder diffraction data was collected with Debye Scherrer camera at the BL01C2 beamline at room temperature in National Synchrotron Radiation Research Center(NSRRC), Taiwan. X-ray of wavelength was 1.0333Å. This compound crystallizes in orthorhombic system space group P bca, Z=8, unit cell parameters of a=25.83(1)Å, b=15.55(5)Å, c=10.63(3)Å, and V=4266.0(10)Å3. Reliability factors were reached Rwp=0.075, Rp=0.053, RB=0.086 ve S=1.31 after Rietveld refinement.
Getting More from Powder Diffraction Experiment: Modulation-Enhanced Diffraction
Authors: Chernyshov Dmitry , van Beek Wouter , Emerich Hermann , Milanesio Marco , Palin Luca , Caliandro Rocco , Urakawa Atsushi
Published: November 2015

Introducing a periodic perturbation of structural parameters of a given frequency results in a modulated diffraction response that may have a complex frequency spectrum. Frequency analysis of the diffraction signal allows untangling contributions from the average and varying part of the scattering density as well as interference between them; both model and real proof-of principal experiments will be discussed. An analysis of advantages and drawbacks of the modulation approach will be given together with new opportunities for structure determination and refinement offered by MED for powder diffraction experiments with synchrotron radiation.
MHz pump and probe combined with XAS-XES
Authors: Glatzel Pieter
Published: November 2015

We implemented a MHz pump and probe scheme on beamline ID26 of the European Synchrotron Radiation Facility. The laser runs at 1.4 MHz in the ESRF 16b mode and thus pumps every fourth pulse with ca. 15 uJ per pulse and 350 fs pulse length. The beamline hosts an X-ray emission spectrometer and thus allows combining resonant inelastic X-ray scattering with a MHz pump and probe schemes. The scattered X-rays are recorded with an avalanche photodiode in single photon counting mode. We measured the transient spectra of the spin cross-over transition in [Fe(bpy)3]Cl2 of the non-resonant Ka lines and of 1s2p resonant inelastic X-ray scattering (RIXS) at the K absorption pre-edge of Fe. The Ka transient spectrum can be readily modeled using crystal field multiplet calculations because the spectra mainly depend on the Fe spin state. The 1s2p RIXS is richer in information because it also probes the unoccupied molecular orbitals and a theoretical interpretation is more challenging.
Saturation phenomena for ultra short Free Electron Laser pulses
Authors: Hatada Keisuke , Di Cicco Andrea
Published: November 2015

Saturable absorption was recently observed in transmission measurements above the LII,III edge of pure Al thin films using ultra short x-ray pulses at a free-electron-laser (FEL) facility . [1] The high fluence reachable by FEL pulses, the shortness of the pulse duration, and the typical lifetime of the excited state, are all important factors enabling observation of the phenomenon. We devised a simplified theoretical model describing the saturation phenomenon using a three- channel model containing ground, excited and relaxed states. This phenomenological model explicitly includes the interaction between the solid and photon field in semi classical way, and the resulting non-linear coupled equation is solved numerically. We successfully applied this model to recent experimental results obtained using FEL radiation. [2,3]
Structural study of the transmembrane and membrane proximal domains of HIV-1 gp41
Authors: Gong Zhen , Fromme Raimund , Craciunescu Felicia , Mor Tsafrir , Fromme Petra , Fromme Petra
Published: November 2015

The transmembrane subunit (gp41) of the envelope glycoprotein (Env) of HIV-1 associates non-covalently with the surface subunit (gp120) and together they play essential roles in viral mucosal transmission and infection of target cells. The membrane proximal region (MPR) of gp41 is highly conserved and contains epitopes of broadly neutralizing antibodies. The transmembrane (TM) domain of gp41 is involved in many essential biological functions and its primary role is to anchor the Env in both viral and cellular membranes. Despite having many important biological functions, the atomic structure of gp41 TM domain remains unknown. While high-resolution X-ray structures of some segments of the MPR were solved in the past, they represent the prefusion or post-fusion conformations, which could not be recognized by the broadly neutralizing antibodies 2F5 and 4E10. Here we describe the expression, purification, biophysical characterization and crystallization of a chimera construct including maltose binding protein (MBP) and MPR-TM of gp41. The purified MBP-MPR-TM protein reacts with the broadly neutralizing antibodies 2F5 and 4E10 with nanomolar affinities and thereby may represent an immunologically relevant conformation mimicking a pre-hairpin intermediate of gp41. Crystals could not be obtained initially when MPR-TM was fused to the C terminus of MBP with linker 1 (MBP-linker1-MPR-TM) but could be obtained after changing the linker (MBP-linker2-MPR-TM). The crystal belongs to space group P32 with unit cell constants of a=172 Å, b=172 Å, c= 70 Å and alpha=beta=90 and gamma=120. The 2.5 Å crystal structure reveals the conformation of MBP and part of the linker region of this chimera, but the MPR-TM segment is unstructured.
Kill HIV by Starvation–Mechanism of Allosteric Activation of SAMHD1
Authors: Ji Xiaoyun , Wu Ying , Yan Junpeng , Mehrens Jennifer , DeLucia Maria , Hao Caili , Gronenborn Angela , Skowronski Jacek , Anh Jinwoo , Xiong Yong
Published: November 2015

SAMHD1, a deoxyribonucleoside triphosphate triphosphohydrolase (dNTPase), prevents the infection of blood cells by retroviruses, including HIV, by depleting the cellular dNTP pool available for viral reverse transcription. SAMHD1 is a major regulator of cellular dNTP levels in mammalian cells. Mutations in SAMHD1 are associated with the autoimmune condition Aicardi Goutières Syndrome (AGS), whose clinical manifestations resemble congenital viral infection. The catalytic activity of SAMHD1 is regulated by allosteric binding of dGTP, which enables SAMHD1 monomers/dimers to assemble into the catalytically active tetrameric form. We have determined the crystal structure of the tetrameric human SAMHD1-dGTP complex. The structure reveals an elegant allosteric mechanism of activation via dGTP-induced assembly of the tetrameric complex from two inactive dimers. Intriguingly, GTP can also activate SAMHD1, and our data further show the binding promiscuity of other dNTPs at the allosteric site. These findings suggest a regulation system that may have a profound effect on the balancing of cellular dNTP pools. These results provide the basis for a mechanistic understanding of SAMHD1 function in HIV restriction, the pathogenesis of AGS, and regulation of cellular dNTP levels.
HIV-1 capsid binds host cofactors to mediate nuclear import
Authors: Price Amanda , Jacques David , Essig Sebastian , Elliott Tom , Halambage Upul , Chin Jason , Aiken Christopher , James Leo
Published: November 2015

The capsid (CA) protein of HIV-1, which forms the core of the virus, has been shown to have an increasingly important role in the early stages of the virus lifecycle, in particular during reverse transcription and nuclear import. We recently solved the structure of a fragment of the human cofactor CPSF6 in complex with the N-terminal domain of HIV-1 CA, revealing a previously unknown interface used by the virus to recruit CPSF6, which is required for the virus to successfully complete the early stages of its lifecycle. Using a recently developed hexameric unit of CA, we have solved the structure of the CPSF6 peptide with CA in a context that more closely resembles an intact CA lattice. This has revealed that CPSF6 contacts HIV-1 CA using an additional second site only present in the hexameric form of CA. Furthermore, we have now solved the structure of a fragment of NUP153 (an HIV-1 cofactor that is integral to the nuclear pore) in complex with hexameric CA and discovered that this also forms contacts specific to hexameric CA. Moreover, the binding sites for CPSF6 and NUP153 on CA overlap at one crucial residue, which is remarkably mimicked by two drugs independently discovered to bind at this same site. Together, these data provide evidence for an essential role for CA in HIV-1 infection, and highlights CA as an important target for antiretroviral drugs.
Targeting HIV using Structure-Based Rational Design of Antibodies
Authors: Diskin Ron , Scheid Johannes , West Anthony , Klein Florian , Nussenzweig Michel , Bjorkman Pamela
Published: November 2015

Isolating and studying broadly anti HIV neutralizing antibodies from infected individuals is a major effort in the combat against HIV. We hope to gain better understanding for vaccine design by elucidating the exact epitope of such antibodies. Furthermore, by providing evermore potent and broadly neutralizing antibodies new strategies like passive immunization or using antibodies as topical microbicides for HIV prevention become feasible. One class of promising antibodies is anti CD4 binding site antibodies. Such antibodies can show exceptional potency and breadth. We used X-ray crystallography to study the structure of NIH45-46, one of the most potent anti CD4 binding site antibodies ever described in complex with gp120, the HIV receptor binding domain. Our structural analysis identified a region in the inner domain of gp120 that is important for the binding and neutralization of NIH45-46 (Diskin et al., 2011). This region is contacted by a four-residue insertion in CDRH3 that does not exist in VRC01, a less potent clonal member of NIH45-46. We further used structure-based rational design to improve NIH45-46. By replacing Gly54 in the CDRH2 with a tryptophan we allowed NIH45-46G54W to bind a unique hydrophobic pocket on the surface of gp120 that is normally accommodating Phe43 of CD4. Remarkably, NIH45-46G54W shows increase both in breadth and potency compared with NIH45-46 (Diskin et al., 2011). We took this approach further and engineered NIH45-46G54W to bind a conserved glycan on gp120. This effort resulted with the most potent and broadly neutralizing anti HIV antibody ever described (Diskin et al., 2013). I will present this work and additional efforts to modify NIH45-46 to accommodate potential escape mutations of HIV.
HIV-1 Env structure and vaccine design
Authors: Kwong Peter
Published: November 2015

Roughly one third of the HIV-1 genome is devoted to the HIV-1 envelope (Env) glycoprotein spike, which comprises three gp120 and three gp41 subunits. Structural characterization of the HIV-1 Env by electron microscopy, NMR, and X-ray crystallography reveals considerable conformational alterations, not only between trimeric ground state, CD4 receptor-bound conformation, and postfusion conformation of the spike, but also between monomeric and trimeric configurations of the subunits as well as between free- and antibody–bound states. One important structure, however, that of the prefusion HIV-1 spike, has resisted atomic level determination. This structure has been on the 10 list of most wanted structure for more than 20 years, because it is the target of the majority of broad HIV-1-neutralizing antibodies – and therefore of importance to vaccine design. In late 2013, the structure of a prefusion HIV-1 spike, based on a BG505 SOSIP.R6.664 construct, was reported by both X-ray crystallography (4.7 Å) and electron microscopy (5.8 Å). While these structures described the trimeric configuration of most of the HIV-1 gp120 subunit, the description of the gp41 subunit was limited to two helical regions comprising only about half the gp41 ectodomain, and the sequence register for the alpha helices was not reported. Recently, we were able to obtain x-ray diffraction data to 3.5 Å resolution on a prefusion crystal structure of the entire HIV-1 spike. The structure utilizes the same BG505 SOSIP.R6.664 construct as previously published, but crystallized in space group P6(3) with the antigen-binding fragments (Fab) of two antibodies, PGT122 and 35O22. The new structure provides atomic-level details for the complete prefusion structure of gp120 and the majority of the trimeric ectodomain of gp41 (up to residue 664). Also visualized are details of the gp120-gp41 interface and of antibodies such as 35O22. In addition to the complete HIV-1 Env ectodomain structure, implications for HIV-1 vaccine design will be described.
Mapping protein binding stability on nucleosomal DNA by single-molecule approach
Authors: Jin Jianshi , Lian Teng-fei , Xie Xiaoliang , Su Xiao-Dong
Published: November 2015

The conformation of nucleosomal DNA is significantly different from that of a canonical B-form double stranded DNA (dsDNA), and is generally regarded to be less flexible and less accessible than free dsDNA due to the tight association of histone cores. Previous studies have demonstrated that the key mechanism involved in nucleosomal DNA-protein interaction is the protein accessibility to the DNA binding site. In this work, we used single molecule assays to measure the stability of two transcriptional factors (glucocorticoid receptor DNA binding domain (GRDBD) and estrogen receptor DNA-binding domain (ERDBD)) bound to their binding sites on different positions of the nucleosomal DNA. Interestingly, the results demonstrated that the nucleosomal DNA-GRDBD binding is not always consistent with the histone shielding effect, but adjusted by additional structural changes. Furthermore, the changes of these DNA-GRDBD interaction profiles were confirmed using molecular modeling and docking approaches based on their crystal structures. Very differently, ERDBD essentially is unable to bind to the nucleosomal DNA anywhere including the unblocked positions. We thus have concluded that the nucleosomal DNA-protein interaction is regulated not only by the histone shielding of the DNA binding sites, but also by the conformational changes of the nucleosomal DNA.
Single-molecule imaging uncover novel pathways in transcriptional regulation
Authors: Chen Peng
Published: November 2015

Metalloregulators regulate transcription in response to metal ions. Many studies have provided insights into how transcription is activated upon metal binding by MerR-family metalloregulators. In contrast, how transcription is turned off after activation is unclear. Turning off transcription promptly is important, however, as the cells would not want to continue expressing metal resistance genes and thus waste energy after metal stress is relieved. Using single-molecule FRET measurements, we studied the dynamic interactions of CueR, a Cu+-responsive MerR-family metalloregulator, with DNA. We discovered that a CueR molecule coming from solution can directly substitute for a DNA-bound CueR or assist the dissociation of the incumbent CueR. The kinetics of the direct protein substitution and assisted dissociation reactions indicate that these two novel processes can provide efficient pathways to replace a DNA-bound holo-CueR with apo-CueR, thus turning off transcription promptly and facilely. Using single-molecule tracking experiments, we further show that these novel pathways also operate in living bacterial cells.
Characterization of Local Distortions in Thermoelectric Lead Chalcogenides
Authors: Bindzus Niels , Christensen Sebastian , Christensen Mogens , Iversen Bo
Published: November 2015

Thermoelectric materials are functional materials with the unique ability to interconvert heat and electricity, holding much promise for green energy solutions such as efficient waste heat recovery. The extraordinary thermoelectric performance of binary lead chalcogenides has caused huge research activity, but the mechanisms governing their unexpected low thermal conductivity still remain a controversial topic. It has been proposed to result from giant anharmonic phonon scattering or from local fluctuating dipoles on the Pb site, emerging with temperature on the Pb site.[1,2] No macroscopic symmetry change are associated with these effects, rendering them invisible to conventional crystallographic techniques. For this reason lead chalcogenides were until recently believed to adopt the ideal, undistorted rock-salt structure. In the present study, we probe the peculiar structural features in PbX (X = S, Se, Te) using multi-temperature synchrotron powder X-ray diffraction data in combination with the maximum entropy method. Distorted atoms are detected and quantified by refinement of anharmonic probability density functions. The charge density analysis is complemented by nuclear density distributions (NDDs) reconstructed from neutron diffraction data and by a novel method: Nuclear Enhanced X-ray Maximum Entropy Method (NEXMEM). NEXMEM offers an alternative route to experimental NDDs, exploiting the superior quality of synchrotron X-ray data compared to neutron diffraction data. The increased atomic resolution introduced by NEXMEM proved essential for resolving atomic distortions, see figure below showing Pb in the (100) plane. Our findings outline the extent of disorder and anharmonicity in binary lead chalcogenides, promoting our fundamental understanding of this class of high-performance thermoelectric materials. The applied approach can be used in general, opening up for widespread characterization of subtle features in crystals with unusual properties.
Evaluating structures derived from X-ray powder diffraction data using entropy
Authors: Sisak Jung Dubravka , McCusker Lynne , Baerlocher Christian , Gilmore Christopher
Published: November 2015

So far, in the field of X-ray powder diffraction, the maximum entropy method (MEM) has been used to (i) solve the phase problem, (ii) estimate the intensities of overlapping reflections, (iii) predict the intensities of missing reflections, and (iv) improve electron density maps generated during Rietveld refinement. We found a new application for MEM in a recent study, in which the powder charge flipping algorithm [1] in Superflip was applied to all-light-atom structures [2]. It proved to be difficult to identify the few fully interpretable maps within in the 200 generated in a typical Superflip job using the standard evaluation criteria. In 1992, Sato reported that entropy could be used as a solution evaluation criterion if the basis set is large, the phases are close to the correct ones, and the structure contains a small molecule [3]. Reasoning that these requirements would be fulfilled by the better Superflip solutions, all solutions were input to the MEM program MICE to calculate the corresponding ME maps and their entropies. Tests performed on several datasets showed no direct correlation between entropy and the solution quality. However, it was noted that a certain number of solutions show entropy values significantly lower than the others. This group usually contained one fully interpretable map. Refinement of the approach led to a relatively straightforward method for recognizing the better solutions. Furthermore, phase recycling based on this approach proved to be useful. As a result, guidelines for solving structures of different levels of complexity using the pCF algorithm could be devised.
Direct Visualization of Energy-transferred Excited State in Eu Complex
Authors: Sugimoto Kunihisa , Fujiwara Akihiko , Takata Masaki , Tanaka Hiroshi , Hasegawa Miki
Published: November 2015

Highly luminescent lanthanide (Ln) complexes have attracted much attention because Ln3+ions show long-lived ff-emissions with narrow band shape. Their unique photo-optical properties are promising for the design of light-emitting materials and sensing devices. Although the ff-emissions are essentially weak because of Laporte forbidden, chelate ligands is effective to strengthen the intramolecular energy transfer from photo-excited organic ligands to Ln3+ions. The direct evidence of energy transfer from ligands to Ln3+and details of excited state, however, are still veiled. Here, we report direct visualization of energy-transferred excited state in Eu complex with a hexadentate ligand (L) consisting of two bipyridine moieties bridged by an ethylendiamine unit, [Eu3+(L)(NO3)2](PF6) (Eu(L))[1] by Maximum Entropy Method (MEM) charge density[2] and electrostatic potential analysis[3] based on SR X-ray diffraction. First, we confirmed that the electron numbers of Eu and ligand L in the excited state are the same as those in the ground state, which is a direct evidence of energy transfer instead of charge transfer. Next, we observed charge re-distribution in the Eu ion and the ligand L. The electrostatic potential distributions calculated using MEM charge density give an experimental evidence for the existence of polarization of ligand L both in the ground and photo-excited states. The orientation polarization in the ground state changed during pumping at 315 nm, and the charge re-distribution are qualitatively consistent with a theoretical prediction. This characteristic luminescence behavior based on the energy relaxation process have not been detected by fundamental crystal structural analysis. We have succeeded in visualization of subtle but important change due to energy transfer in the mononuclear Europium complex with hexadentate ligand at the first time.
Application of maximum-entropy electrostatic potential in Materials Science.
Authors: Nishibori Eiji
Published: November 2015

Charge density (CD) studies by Maximum Entropy Method (MEM) (Sakata & Sato, 1990) from x-ray diffraction data have been widely applied to solve problems and questions in materials science during past two decades. Encapsulations of metal atoms (Takata et al, 1995), gas molecules, as well as protein molecules in the materials have been visualized as MEM CDs. The MEM CD technique is now regarded as a sophisticated technique for visualization in atomic scale. Electrostatic potential (EP) and electric field (EF) from x-ray diffraction data using MEM have been developed in 2006 (Tanaka et al, 2006). The EP & EF successfully applied to ferroelectric material PbTiO3 and a charge ordered manganite system. The method has huge potential in materials science since interaction in the non-atomic region can be visualized experimentally. One of the promising target for EP & EF analysis is host-guest systems, such as porous coordination polymers (PCPs), zeolites, clathrates as well as endohedral metallofullerenes[3]. In the case of host-guest systems, the guest atom(s) or molecule(s) are located in spatially wider sites in comparison to other type of materials. Therefore the detailed structural information in the spatially wider sites is one of the most important issues. In the present study, I present an application of MEM EP & EF analysis to host-guest related system, icosahedral B12 cluster materials and hydrogen adsorbed PCP. The EP studies clearly visualize doping sites in B12 based superconductor and adsorption sites in PCP. The EF enables us to estimate quantitative interaction from host to guest. The quantitative evaluation really bridges between experiment and theory in materials science.
Intermediate-valence Yb-based quasicrystals and approximants
Authors: Watanuki Tetsu , Yamada Tsunetomo , Nakamura Yoko , Tanaka Yukinori , Machida Akihiko , Tsai AnPang , Ishimasa Tsutomu
Published: November 2015

We are searching for intermediate-valence (IV) quasicrystals where IV ions are quasi-periodically arranged. Our previous study revealed that an icosahedral Au-Al-Yb quasicrystal forms an IV system [1]. X-ray absorption spectroscopy near the Yb L_3 edge indicated that the Yb ions in the quasicrystal assume a mean valence of 2.61, between a divalent state (4f^14, J = 0) and a trivalent one (4f^13, J = 7/2). Additionally we found that non-Fermi-liquid behaviour appears at low temperatures without doping, pressure, or field tuning. In this study we examined Au-M-Yb system, where M = Sn, Ge, and Ga. X-ray absorption spectroscopy measurements at SPring-8 (BL22XU) showed that each compounds forms IV system. The Yb valence values are respectively 2.27 for a Au-Sn-Yb 2/1 crystalline approximant, 2.24 for a Au-Ge-Yb 1/1 approximant, and 2.36 for a Au-Ga-Yb 1/1 approximant. By following the trend of Yb-based IV compounds, these valence values close to divalent suggest that the Yb 4f character in these compounds would be itinerant rather than localized one.
High temperature structural study of decagonal Al-Cu-Rh quasicrystal.
Authors: Kuczera Pawel , Steurer Walter
Published: November 2015

The structure of d(ecagonal)-Al-Cu-Rh has been studied as a function of temperature by in-situ single-crystal X-ray diffraction in order to contribute to the discussion on energy or entropy stabilization of quasicrystals (QC) [1]. The experiments were performed at 293 K, 1223 K, 1153 K, 1083 K, and 1013 K. A common subset of 1460 unique reflections was used for the comparative structure refinements at each temperature. The results obtained for the HT structure refinements of d-Al-Cu-Rh QC seem to contradict a pure phasonic-entropy-based stabilization mechanism [2] for this QC. The trends observed for the ln func(I(T1 )/I(T2 )) vs.|k⊥ |^2 plots indicate that the best on-average quasiperiodic order exists between 1083 K and 1153 K, however, what that actually means is unclear. It could indicate towards a small phasonic contribution to entropy, but such contribution is not seen in the structure refinements. A rough estimation of the hypothetic phason instability temperature shows that it would be kinetically inaccessible and thus the phase transition to a 12 Å low T structure (at ~800 K) is most likely not phason-driven. Except for the obvious increase in the amplitude of the thermal motion, no other significant structural changes, in particular no sources of additional phason-related configurational entropy, were found. All structures are refined to very similar R-values, which proves that the quality of the refinement at each temperature is the same. This suggests, that concerning the stability factors, some QCs could be similar to other HT complex intermetallic phases. The experimental results clearly show that at least the ~4 Å structure of d-Al-Cu-Rh is a HT phase therefore entropy plays an important role in its stabilisation mechanism lowering the free energy. However, the main source of this entropy is probably not related to phason flips, but rather to lattice vibrations, occupational disorder unrelated to phason flips like split positions along the periodic axis.
A cubic quasicrystal in a rapidly-solidified Mg-Al alloy
Authors: Kato Takeshi , Seki Takehito , Abe Eiji
Published: November 2015

It is commonly accepted that the definition of quasicrystal should include a rotational symmetry forbidden in periodic crystals. On the other hand, the quasicrystal with a conventional point group is theoretically possible [1,2]. In a rapidly-solidified Mg-Al alloy, intriguing electron diffraction patterns (EDPs) were reported, which show a cubic symmetry with aperiodic arrays of Bragg reflections [2]. In the present work, we investigate the detailed structure of the rapidly-solidified Mg-Al phase based on direct structure observations using STEM. In a rapidly-solidified Mg-61 at.% Al alloy, 2-fold, 3-fold, and 4-fold EDPs are obtained (Fig. a), which shows that the structure has the cubic point group. However, the relevant diffraction spots are arranged aperiodically. Especially in the 2-fold EDP, a high density of the spots is observed, and the corresponding HADDF-STEM image shows several remarkable features (Fig. b). Two length scales, L and S, can be definitely observed, and they are arranged quasiperiodically along the 3-fold axis. Their arrangement can be well described by the hyperspace crystallography; a physical space tilted by the angle θ , where tanθ ∼ 1.4, successfully generates the observed quasiperiodic pattern. Simulated EDPs from a simple model without detailed atomic decoration reproduces fairly well the experimental patterns. Further analysis of the images reveals that the present quasiperiodic structure has similar local structure to the stable β-Mg2Al3phase; two lengths correspond to L and S may be reasonably defined. The quasicrystal with a cubic symmetry is unambiguously determined for the first time, based on a direct structural observation. The present results strongly suggest that the noncrystallographic rotational symmetry is not an essential factor to form the quasiperiodic structure, raising a very fundamental, universal question on the physical origin of a long-range order of condensed matters.
Ferromagnetic transition in Au- based Approximants
Authors: Hiroto Takanobu , Tokiwa Kazuyasu , Sato Taku , Tamura Ryuji
Published: November 2015

The structure of Tsai-type magnetic quasicrystals and its related compounds (called approximants) are characterized by the space-filling of an icosahedral cluster which has a rare-earth icosahedron [1]. From an experimental point of view, such compounds have been known to show the spin glass like behavior without exception [2]. However, the discovery of the antiferromagnetic phase transition in the Cd-Tb approximant [3] gives a counterexample to this trend. Moreover, ferromagnetic transitions were observed in the Au-based approximant recently. In this paper, magnetic phase transitions in Au-Si-R (R= Gd ,Tb, Dy and Ho) approximants are discussed. In all the systems, the temperature dependence of magnetization show ferromagnetic transition at Tc. On the other hand, the magnetization curves below Tc are different between Gd-compound and non-Gd compounds. The difference in the magnetization may be attributed to the existence of the CEF effect in the non-Gd compounds which have non-zero orbital angular momentum.
Phason dynamics of quasicrystals
Authors: Agiasofitou Eleni , Lazar Markus
Published: November 2015

Phason dynamics constitutes a challenging and interesting subject in the study of quasicrystals, since there is not a unique model in the literature for the description of the dynamics of the phason fields. Here, we introduce the elastodynamic model of wave-telegraph type for the description of dynamics of quasicrystals [1, 2]. Phonons are represented by waves, and phasons by waves damped in time and propagating with finite velocity; that means the equations of motion for the phonons are partial differential equations of wave type, and for the phasons partial differential equations of telegraph type. The proposed model constitutes a unified theory in the sense that already established models in the literature can be recovered as asymptotic cases of it. Several noteworthy features characterize the proposed model. The influence of the damping in the dynamic behavior of the phasons is expressed by the tensor of phason friction coefficients, which gives the possibility to take into account that the phason waves can be damped anisotropically. In terms of the phason friction coefficient and the average mass density of the material an important quantity, the characteristic time of damping, can been defined. Another important advantage of the model is that it provides a theory valid in the whole regime of possible wavelengths for the phasons. In addition, with the telegraph type equation there is no longer the drawback of the infinite propagation velocity that exists with the equation of diffusion type.
Magnetic quasicrystals: Current Status and Open Questions
Authors: Goldman Alan
Published: November 2015

The magnetic properties of quasicrystals have been the subject of intense theoretical and experimental interest since Dan Shechtman's discovery of icosahedral quasicrystals in 1982 [1]. The first generation of Al-TM (TM = 3d transition metal) quasicrystals with moment bearing elements, such as Al-Mn and Al-Pd-Mn, provided some insight into the fate of magnetism in quasiperiodic systems: only a small fraction of the Mn ions carry a moment and these moments appear to be distributed randomly on the quasilattice. The discovery of the Zn-Mg-R and Cd-Mg-R (R = rare earth) quasicrystals with sizeable local moments that interact via indirect exchange (i.e. the RKKY interaction) reinvigorated the search for long-range magnetic order in the icosahedral phase. However, to date, all of the known quasicrystals with moment bearing elements exhibit frustration and spin-glass-like behavior at low temperature. The recent discovery of binary magnetic quasicrystals in the R-Cd system [2] is particularly exciting because their closely related crystalline approximants, RCd6, exhibit long-range antiferromagnetic order at low temperature [3] permitting a detailed investigation of the effects of aperiodicity on magnetic interactions in this system. Here, I will describe the status of investigations of the R-Cd quasicrystals and RCd6 approximants with regard to their structural and magnetic properties. This research was supported by the Office of the Basic Energy Sciences, Materials Sciences Division, US Department of Energy (DOE).
RKKY interactions and magnetic structure of rare-earth quasicrystals
Authors: Thiem Stefanie
Published: November 2015

We study the structure of the RKKY interactions and the corresponding low-temperature behaviour of magnetic moments for quasiperiodic tilings. The alignment of magnetic moments in rare-earth quasicrystals remains a fundamental open problem despite the continuous effort since the discovery of this material class. We compute the RKKY interactions between the localized magnetic moments by means of a continued fraction expansion of the Green's function of the conduction electrons. Thus, our approach takes the structure of the critical electronic wave functions into account. The results show the emergence of strongly coupled spin clusters while the inter-cluster coupling is significantly weaker. Monte Carlo simulations reveal with decreasing temperature first the freezing of spins within the clusters followed by the freezing of the clusters. Thus, the low-temperature phase behaves has similarities to a cluster spin glass which is in good agreement with previous experimental findings.
Observations of Local Electronic States in Al-based quasicrystals by STEM-EELS
Authors: Seki Takehito , Abe Eiji
Published: November 2015

Most quasicrystals (QCs) reveal pseudogaps in their density of states around Fermi level, and hence the stability of QCs have been discussed in terms of energetic gains in electron systems. In fact, many QCs have been discovered by tuning valence electron density based on Hume-Rothery rule. Therefore, understanding electronic structures in QCs may provide an important clue for their stabilization mechanism. Generally, it has been frequently discussed based on an interaction between Fermi surface and Brillouin zone boundary within the framework of nearly free electron model, which is believed to be an underlying physics of a Hume-Rothery's empirical criteria. However, the electronic structures of QCs have not yet been fully understood, particularly being in microscopic-macroscopic relations. In the present work, we investigate local electronic states in Al-based QCs using electron energy loss spectroscopy (EELS) combined with scanning transmission electron microscopy (STEM), by which EELS spectra with sub-Å probe and atomic structure can be obtained simultaneously. We report STEM-EELS results on AlCuIr decagonal phases [1]. Principal components analysis clearly shows up the atomic-site dependence of plasmon loss spectra in a two-dimensional map. Qualitatively, there seems to be certain correlations between the plasmon peaks and the core-loss edges, Al L1, Ir O23, Ir N67and Cu L23, all of which reveal different behaviours at the cluster centers and the edges. All results indicate the cluster centers have metallic states and the cluster edges have covalent states in comparison. First-principles calculations confirm the unusual electronic state. We analyse a distribution of covalent electrons by Fourier transformation of electron localization function. The distribution seems like a 10-fold charge density wave with Fermi wave length. It suggests that the Hume-Rothery mechanism is important even when hybridization effect mainly contributes to pseudogap formation. The cluster centers can be regarded as the regions which are unable to contribute to the Hume-Rothery mechanism. It may be origin of the unusual electronic states. This work was conducted in Research Hub for Advanced Nano Characterization, The University of Tokyo, supported by the Ministry of Education, Culture, Sports, Science and Technology (MEXT), Japan. It is acknowledged that T. Seki is a research fellow of Japan Society for the Promotion of Science.