bluuebunny/crossref_metadata_2025 huggingface dataset:
Precession Electron Diffraction studies of the phase transition in the (NbSe4)3I
Authors: Zubko Maciej , Kusz Joachim , Prodan Albert , Prusik Krystian , Bennett J. Craig
Published: November 2015

(NbSe4)3I is at room-temperature (RT) a semimetal, which changes at lower temperatures into a semiconductor [1]. The compound shows nonlinear transport properties with a second order phase transition at 274 K [2]. The symmetry of the RT (NbSe4)3I belongs to the P4/mnc space group and the structure is formed of NbSe4 antiprisms, stacked along the c axis. The Nb atoms are grouped into Nb2 segments and the Se-Se distances are correlated with the Nb chains. The I atoms occupy two types of channels; those running along the [00z] direction contain two I atoms connected to four Se atoms, while the channels along the [½½z] direction host two I atoms connected to eight Se atoms in a square anti-prismatic arrangement. At the (h,k,16n) planes a relatively strong diffuse scattering is present in the form of concentric rings. This scattering is explained by a similar model to the one recently suggested for (NbSe4)10/3I. The model is based on a mismatch between infinite NbSe4 chains, randomly shifted along the c direction. (NbSe4)3I was studied by means of X-ray and electron diffraction with beam precession (PED) [3]. PED patterns usually contain more Bragg peaks than the conventional selected area diffraction patterns, because the intensity of the diffracted beams is integrated over the selected volume of the reciprocal space. An additional advantage of using the beam precession technique is a reduction of the dynamical interactions. Electron diffraction patterns were recorded sequentially, while tilting the crystal around an arbitrary crystallographic axis. Such space tomography allows a three-dimensional inspection of the reciprocal space and a more precise investigation of the diffuse scattering from nano-areas.
Identifying almost identical phases by 3D electron diffraction
Authors: Kodjikian Stéphanie , Klein Holger , Lepoittevin Christophe , Darie Céline , Bordet Pierre , Payen Christophe , Deudon Catherine
Published: November 2015

Magnetically frustrated materials have been the subject of many studies over the last decades. In search for a 3-dimensional quantum spin liquid, where quantum-mechanical fluctuations prevent magnetic order, different phases of stoichiometry Ba3NiSb2O9 have recently [1] been synthesized some of them at high pressure. Two of these phases are hexagonal. The hexagonal phases (space groups P63/mmc and P63mc, respectively) have different structures but cell parameters that differ by less than 1%. Similar phases have been obtained with Cu [2] or Co [3]. These phases are well distinguished by powder X-ray diffraction when they appear in sufficient quantity in a newly synthesized powder. When these phases are present only in minor quantities, which is a common situation when synthesizing new materials, only transmission electron microscopy can give structural information on a very local scale. However, the accuracy of unit cell parameter determination by electron diffraction (usually 1% or worse) and the identical extinction conditions for the 2 space groups don't permit to distinguish between the two phases. Convergent beam electron diffraction could show the difference between the centrosymmetric and non-centrosymmetric space groups provided a suitably oriented particle can be found. In this work we propose a different method of distinguishing structures in such complicated cases by actually solving the structure. Sufficient in-zone axis precession electron diffraction and/or electron diffraction tomography data can be obtained from any crystal regardless of its orientation. In the subsequent structure solution we have tested both space groups. The quality (or absence thereof) of the structure solutions obtained clearly makes it possible to distinguish between the two hexagonal structures.
Categorization of electrochemical storage materials en route to new concepts
Authors: Meutzner Falk , Nestler Tina , Hanzig Juliane , Zschornak Matthias , Ureña de Vivanco Mateo , Münchgesang Wolfram , Schmid Robert , Cherkouk Charaf , Leisegang Tilmann , Meyer Dirk
Published: November 2015

Because of their broad range of applications, electrochemical energy storage devices are the subject of a growing field of science and technology. Their unique features of high practical energy and power densities and low prices allow mobile and stationary applications. A large variety of electrochemical systems has been tailored for specific applications: Lithium-ion batteries for example have been optimized for mobile applications ranging from mobile phones to electric vehicles. On the other hand, sodium-sulphur accumulators – among others – have been developed for stationary applications to account for the capricious nature of renewable energies. Chemistry, physics and materials science have led to the optimization of existing cell-chemistries and the development of new concepts such as all-liquid or all-solid state batteries as well as high-energy density metal-air batteries. The aim of the BMBF (Federal Ministry of Education and Research, Germany)-financed project "CryPhysConcept" is to develop new concepts for electrochemical energy storage applying a crystallographic approach. First, a categorization of the main solid components of batteries based on their underlying working principles is suggested. Second, an algorithm for the identification of suitable new materials and material combinations, based on economical, ecological and material properties as well as crystallographic parameters, is presented. Based on these results, new concepts using multi-valent metal ions are proposed. Theoretical as well as experimental results including an iron-ion approach are presented.
Pyroelectric Crystals: Structure, Properties and Applications
Authors: Leisegang Tilmann , Störr Bianca , Mehner Erik , Jachalke Sven , Cherkouk Charaf , Zschornak Matthias , Stöcker Hartmut , Urena Mateo , Wunderwald Ulrike , Meyer Dirk
Published: November 2015

As defined by the IUCr, a material is a crystal if it has essentially a sharp diffraction pattern. Crystalline materials are wide spread in our today's life. More than 98 % of the solid fraction of the earth comprises crystalline matter, most of which are oxides. Single-crystals in particular are the basis for many applications – lasers, LEDs, sensors, etc. – and play an important role in fundamental research – for instance in materials science. The discipline that elucidates the impact of the crystal structure on the physical properties of particularly crystalline materials – crystallography – is of specific importance for the design of new materials. Moreover, crystallography can be utilized to establish new concepts and thus may contribute solving today's challenges in science and technology. Several technologies exist for the conversion of electric energy into, e. g. heat, light and motion or vice versa. In this context, this work highlights an approach based on the crystal coupling phenomenon pyroelectricity that can be adopted for energy conversion concepts. By means of pyroelectric crystals, waste heat can be converted into surface charges, which provide a manifold of applications. First, a comprehensive overview of more than 3000 known pyroelectric materials is given, including a categorization in terms of properties and crystallographic characteristics. In order to provide a high pyroelectric coefficient at certain temperatures, taking economic, ecologic and further material properties into account, promising materials are suggested and verified by a computer controlled thermal/electrical stimulation set-up. Several possible applications as, for instance, disinfection [1], and anti-icing are presented. Finally, an approach to convert waste heat into chemical energy, i. e. the generation of hydrogen, is introduced.
In vivo protein crystallization in living insect cells
Authors: Redecke Lars , Klinge Marco , Schönherr Robert , Rehders Dirk , Oberthür Dominik , Sommer Björn Philip , Martinez-Costas Jose , Duszenko Michael , Duden Rainer , Betzel Christian
Published: November 2015

Spontaneous protein crystallization within living cells has been observed several times in nature, e.g. for storage proteins in seeds. In vivo crystal growth can also occur during gene over-expression, as particularly discovered in baculovirus-infected insect cells [1]. We have recently shown that these in vivo crystals represent valuable targets for structural biology after isolation from the cell. Applying serial crystallography techniques at an X-ray free-electron laser (XFEL) as well as using a highly brilliant synchrotron source, single crystal diffraction pattern were collected and combined to yield high-resolution structural information of the associated fully glycosylated protein [2,3]. So far, the cellular mechanisms involved in the in vivo crystallization process remain to be understood, preventing a more successful application of this novel approach. Thus, our study aims at identifying the parameters crucial for optimal crystal growth within baculovirus-infected Sf9 insect cells. Combining confocal microscopy with live-cell imaging techniques and compartment-specific staining methods, we systematically investigated the impact of the intracellular environment on in vivo crystallization by directing recombinant proteins into different cellular compartments using specific signal sequences. Moreover, the impact of cellular transport mechanisms and induced cellular stress on the quality and size of the in vivo crystals was investigated in detail. The presented results provide important insights into the process of protein crystallization within living cells and will therefore significantly contribute to increase the success rate for spontaneous crystal growth of other proteins. Considering that in vivo crystals represent highly suitable targets for structural biology, this approach offers exciting new possibilities for proteins that do not form crystals suitable for conventional X-ray diffraction in vitro.
Upgrade of a high flux MX beamline BL41XU at SPring-8
Authors: Hasegawa Kazuya , Okumura Hideo , Baba Seiki , Mizuno Nobuhiro , Hirata Kunio , Yamashita Keitaro , Ueno Go , Murakami Hironori , Yumoto Hirokatsu , Senba Yasunori , Ohashi Haruhiko , Yamamoto Masaki , Kumasaka Takashi
Published: November 2015

BL41XU is the oldest macromolecular crystallography (MX) beamline at SPring-8 [1]. Although it has been contributing to the structure determination of difficult samples since its start of operation in 1997, the targets for the structural study is still getting more challenging and the crystal quality brought to the beamline is getting worse. Therefore, we have upgraded the focusing optics and diffractometer of BL41XU to cope with these targets. Our goal is to achieve an environment which can offer a stable beam with a photon flux of >1013photons/s in the beam size range of 5 ~ 50μm. It is a complementary specification with our micro-focus beamline BL32XU [2], and allows both micro-crystallography and data collection using crystal volume. The new optics adopts a two-step focusing with elliptical figured mirrors: the first optics is a single horizontal mirror and the second one adopts Kirkpatrick–Baez (KB) configuration. At the middle of the two focusing optics, a high precision horizontal slit is installed to define secondary source size. The beam size can be changed either by changing the secondary source size, by offsetting the sample position, or by tilting the vertical mirror. For the stable use of small beam, both KB mirror and diffractometer were equipped on the granite stage, and enclosed in a booth in which the temperature is keep stable. On the new diffractometer, we equipped PILATUS3 6M that enables rapid data collection combining with high flux beam. Together with the upgrade of hardware, software tools, which support diffraction based centering and determination of measurement condition, have been implemented in order to make full use of the renewed beamline. The upgrade was conducted in the long shut-down period between January and March of this year, and the beamline was opened for users in the middle of May after commissioning of one month. The result of commissioning and initial results will be presented. This study was supported by the MEXT of Japan.
Data collection tools for challenging samples at the MX beamlines at Diamond
Authors: Flaig Ralf
Published: November 2015

Diamond Light Source [1] is the UK third generation synchrotron facility located south of Oxford and it started with the user programme in early 2007. Currently, there are five operational macromolecular crystallography (MX) beamlines that provide state of the art facilities to the user community and eventually there will be seven beamlines dedicated to MX [2]. All MX beamlines provide tools for standard data collection but given the increasing complexity and associated challenges with bigger macromolecular complexes, membrane proteins, smaller crystals, and radiation damage, different approaches are often required to get the best possible data out of these samples. Tools for sample location and characterization are a first step. Often, because of radiation damage and sample deterioration, multiple crystals are needed in order to obtain a complete data set and a number of tools and different experiment setups that help to address this problem will be described, including use of suitable software tools to get the best data set, fast data collection, crystal humidity control, in situ screening and use of a mini kappa goniometer. These tools enable new data collection strategies which can make the difference towards a successful structure determination. A special focus will be on the use and potential of multi-axis goniometers. Given the limited amount of beam time and ever faster data acquisition rates, quick decision making during the beam time becomes more important. Therefore, data collection strategies and crystal and diffraction image characterization are provided automatically. Very shortly after the data collection has finished the results from our automatic data processing routines are available and we also provide difference electron density map, molecular replacement and experimental phasing pipelines.
FEM: Feature Enhanced Map
Authors: Afonine Pavel
Published: November 2015

A method is proposed that modifies 2Fo-Fc σA-weighted map such that the resulting map has significantly reduced amount of noise and model bias, and at the same time the weak signal is enhanced so it is visible as good as the strong signal. We call the new map Feature Enhanced Map (FEM). An atomic model is a result of interpretation of the electron density map. There are at least three fundamentally different sources of map imperfections that affect quality of this interpretation. 1) Errors. Fourier map artifacts due to finite resolution and completeness of data, errors in experimental data and crystal model parameters result in noise peaks in map that oftentimes appear very much similar to the true atomic structure and in turn may be erroneously interpreted as such. Also, the noise may obscure or corrupt the signal making its meaningful interpretation difficult or even impossible. 2) Signal strength. Not all the signal presented in the map has the same strength: a strong signal arising from a heavy atom derivative may obscure weak signal arising from a partially occupied very mobile ligand or residue side chain alternative conformation or hydrogen atoms. It is common that such weak signals are near or below the noise level. 3) Model bias. Crystallographic maps are calculated using model phases alone or a combination of model and experimental phases. Once placed, correctly or not, atoms feed back revealing themselves in the map. Therefore erroneously placed atoms may be positively confirmed against the map resulting in an incorrect structure. All three sources of map imperfections are always present together. They make interpretation of crystallographic maps never unambiguous, trivial, or unique at typical macromolecular resolutions. The new method aims to overcome these problems and is available in Phenix software. More information: http://www.phenix-online.org/presentations/fem_SEP2013.pdf
Collecting and analyzing diffraction data from multiple crystals
Authors: Evans Gwyndaf
Published: November 2015

Recent years have witnessed a marked revival of multiple crystal data collection and analysis methods. This has been brought about in many ways by a proliferation of microfocus beamlines [1] that have provided convenient access to structural biologists who wish to measure from their tiny crystals. Further to this however has been a realization that in some cases careful data collection and analysis of multiple crystal data can replace months if not years of effort in wet labs optimizing crystals to be large enough to yield a single crystal data set. The presentation will briefly discuss recent progress in multiple crystal data collection and analysis and illustrate it with some case studies.
MauG catalysis: a tale of ferryl iron, radicals and long distance hopping
Authors: Wilmot Carrie , Yukl Erik , Jensen Lyndal , Davidson Victor
Published: November 2015

Methylamine dehydrogenase (MADH) enables some methylotrophic/autotrophic bacteria to grow on methylamine as a sole source of carbon and energy. MADH catalysis depends on the cofactor tryptophan tryptophylquinone (TTQ) that is a posttranslational modification of two Trp residues in the MADH β-subunit. The maturation of MADH depends on four gene products located in the methylamine utilization (mau) gene cluster. One of these, mauG, encodes a c-type di-heme enzyme that completes synthesis of the TTQ cofactor. The potent oxidant is an unusual bis-Fe(IV) MauG species composed of a ferryl heme (Fe(IV)=O) with an oxidizing equivalent stored as Fe(IV) at the second heme, which has an unusual His, Tyr axial ligation. The bis-Fe(IV) oxidant is formally Fe(V) and equivalent to Compound I. Completion of TTQ to generate active MADH involves long-range electron transfer and a radical hopping mechanism to effect catalysis over a 40 Å distance. The MauG catalyzed reaction occurs in three discrete 2-electron events in a hydrogen peroxide or molecular oxygen (+ reducing equivalents) dependent process. A crystal structure of MauG in complex with its protein substrate, a precursor form of MADH known as preMADH, has been solved. The crystals are catalytically active. The order of the 2-electron chemistry catalyzed by MauG was determined through a series of structures from crystals harvested after different amounts of time following crystallization. Hydrogen peroxide to initiate the reaction was generated by the slow breakdown of polyethylene glycol used in crystallization. These in crystallo data are corroborated by mass spectrometry in solution experiments.
Crystal Structure of Human α-2,6 Sialyltransferase
Authors: Kuhn Bernd , Benz Jörg , Greif Michael , Engel Alfred , Sobek Harald , Rudolph Markus
Published: November 2015

Human β-galactoside α-2,6 sialyltransferase I (ST6Gal-I) establishes the final glycosylation pattern of many glycoproteins by transferring a sialyl moiety to a terminal galactose. Complete sialylation of therapeutic immunoglobulins is essential for their anti-inflammatory activity and for protein stability. However, a complete glycan tree is difficult to achieve in vitro due to limited activity of ST6Gal-I for some galactose acceptors. No structural information on ST6Gal-I that could help to improve the enzymatic properties of ST6Gal-I for biotechnological purposes was previously available. We describe the crystal structure of human ST6Gal-I, which allows rationalizing the inhibitory activity of cytosine-based nucleotides. ST6Gal-I differs from related sialyltransferases by several large insertions and deletions that determine its regio- and substrate specificity. Excitingly, a large glycan binds to the active site in a catalytically competent orientation, representing the general binding mode of any substrate glycoprotein. This binding mode also rationalizes why some galactose acceptors are incompletely sialylated. Comparison with a bacterial sialyltransferase lends first insight into the Michaelis complex. The results support an SN2 mechanism with inversion of configuration at the sialyl residue and suggest substrate-assisted catalysis with a charge relay mechanism that bears conceptual similarity to serine proteases.
Crystal structures of 2OG oxygenases involved in ribosomal protein hydroxylation
Authors: Horita Shoichiro , Scotti John , McDonough Michael , Sekirnik Rok , Chowdhury Rashed , Krojer Tobias , Thalhammer Armin , Aik WeiShen , Oppermann Udo , Schofield Christopher
Published: November 2015

Post-translational modifications play diverse biological functions. Hydroxylation of collagen proteins has long been a recognised post-translational modification in eukaryotes. In the case of collagen, hydroxylation of prolyl residues, by 2-oxoglutarate and iron dependent enzymes (2OG oxygenases), in collagen proteins allows for the stabilisation of the collagen triple helix structure through conformational restraint and through the addition of a hydrogen bond donor. Additionally, hydroxylation of lysine side chains of collagen is required for cross-linking collagen (and possibly other proteins) in the extra-cellular matrix. Post-translational prolyl hydroxylation also plays a pivotal role in transcriptional regulation of the hypoxic response, as catalyzed by the hypoxia inducible factor / HIF prolyl hydroxylases (PHDs or EGLN enzymes). Recently, ribosomal protein hydroxylation catalyzed by 2OG- and Fe(II)-dependent oxygenases has been found to be a highly conserved post-translational modification in eukaryotes and prokaryotes (Ge et al and Loenarz et al). We present several crystal structures of 2OG oxygenases involved in ribosomal protein hydroxylation.
Structure of pneumococcal GtfA reveals a novel prokaryotic O-GlcNAc transferase
Authors: Shi Wei-Wei , Jiang Yong-Liang , Zhu Fan , Wu Hui , Zhou Cong-Zhao , Chen Yuxing
Published: November 2015

Protein glycosylation is increasingly recognized as an important process for bacterial physiology and pathophysiology. Glycosylation of serine-rich repeat (SRR) glycoprotein PsrP is essential for the pathogenesis of Streptococcus pneumoniae, one of the most common human pathogens. This glycosylation process is initiated by a glycosyltransferase complex comprising two components, a core enzyme GtfA and a co-activator GtfB. Here we report the 2.0-Å crystal structure of GtfA in complex with GlcNAc and UDP. The structure possesses a core domain of GT-B fold and an unprecedented "add-on" domain of DUF1975, which adopts a β-meander structure. This novel DUF1975 domain is critical for the intact glycosyltransferase activity of GtfA–GtfB complex via mediating their self-recognition and the binding to the acceptor protein PsrP. The glycoproteomic analysis revealed a novel pattern of protein O-linked glycosylation at the serine residue cluster. The findings suggest that GtfA is a new glycosyltransferase and provide a structural basis for the future design of inhibitors against the biogenesis of bacterial SRRPs.
Structural elucidation of innate immune signaling
Authors: Wu Hao
Published: November 2015

Signal transduction in the Toll-like receptor and interleukin-1 receptor pathways requires both kinase activation and ubiquitination. Here, we will present our recent structural studies on critical mediators of the pathways.
Particle orientation from distribution of explosion fragments in XFEL experiment
Authors: Gyula Faigel , Jurek Zoltan
Published: November 2015

In many XFEL experiments small objects with unknown orientations are introduced into the x-ray beam. However, understanding the measured quantities it would be desirable to know their orientations. This is the situation in the case of single-molecule imaging one of the main target areas of X-ray free-electron lasers. Here, the solution to the orientation problem is based on the possibility of orienting the large number of low-counting-statistics 2D diffraction patterns taken at random orientations of identical replicas of the sample. This is a difficult process and the low statistics limits the usability of these methods and ultimately it could prevent single-molecule imaging. We suggest a new approach, which avoids the use of the diffraction patterns. We propose to determine the sample orientation through identifying the direction of ejection fragments. The orientation of the sample is measured together with the diffraction pattern by detecting some fragments of the Coulomb explosion. We show by molecular-dynamics simulations that from the angular distribution of the fragments one can obtain the orientation of the samples [1].The figure shows the distribution of heavy atoms coming from different depth of the sample ( upper panel homogeneous, lower panel inhomogeneous model samples, and left to right is heavy atom at the outer boundary, halfway to center and at the center).
Development of Single Molecule Imaging Using XFELs: Recent Results and Prospects
Authors: Boutet Sébastien
Published: November 2015

X-ray Free Electron Lasers such as the Linac Coherent Light Source (LCLS) were built on the promise of single molecule imaging. The extremely intense pulses of x-rays such sources can deliver can in principle provide at the same time the large number of photons required to produce sufficient signal from a single molecule while keeping the pulse duration short enough to prevent radiation damage from destroying the sample before the measurement is complete. This diffract-then-destroy concept allows the measurement to occur rapidly, before the sample is completely damaged after the x-rays have interacted with the sample. After close to 5 years of operation of the first hard x-ray free electron laser in the world, the LCLS, some data exists which makes it possible to review past experiments and technical developments aimed at the single particle imaging. Furthermore, one can discuss the still required technical, computational and theoretical developments to make this a reality. Recent results and future prospects of the technique will be presented in this talk.
Single-Shot X-Ray Coherent Diffractive Imaging of Superfluid He Nanodroplets
Authors: Gessner Oliver , Bostedt Christoph , Vilesov Andrey
Published: November 2015

Single-shot coherent diffractive imaging (CDI) experiments were performed on pure and doped helium nanodroplets using femtosecond X-ray pulses from the Linac Coherent Light Source (LCLS). The superfluid nature of helium droplets presents a rare opportunity to study the onset of macroscopic quantum phenomena in finite, sub-micron scale systems. Despite the small X-ray scattering cross sections of atomic helium, high-quality single-shot CDI data were obtained that give direct access to sizes and shapes of individual nanodroplets. The diffraction patterns from helium droplets doped with xenon atoms differ starkly from the patterns from pure droplets. Strong indications for the formation of complex xenon structures inside the superfluid helium environment are observed, giving access to information about the structure and aggregation dynamics of the dopant species. The results are discussed with respect to the hydrodynamic properties of the superfluid droplets and compared to those of classical drops. An outlook on femtosecond time-resolved CDI experiments to study dynamics in pure and Xe-doped He nanodroplets will be given based on a new undulator-based X-ray pump/X-ray probe technique that is currently under development at LCLS.
Charge-density analysis and electrostatic properties of a new hybrid compound
Authors: Dadda Noureddine , Direm Amani , Guillot Benoit , Jelsch Christian , Bnelai-cherif Nourredine
Published: November 2015

2-carboxy-4-methylaniline is a biologically active molecule serving as a pharmaceutical intermediate [1]. We've synthesized, studied and refined the crystal structure of its derivative 2-carboxy-4-methylanilinium chloride monohydrate using three different electron-density models. In the first model, the ELMAM2 multipolar electron-density database [2] was transferred to the molecule. Theoretical structure factors were also computed from periodic density functional theory calculations [3] and yielded, after multipolar-atoms refinement, the second charge-density model. An alternative electron-density modelling, based on spherical atoms and additional charges on the covalent bonds and electron lone-pair sites, was used in the third model in the refinement versus the theoretical data. The crystallographic refinements, structural properties, electron-density distributions and molecular electrostatic potentials obtained from the different charge-density models were compared.
Experimental core electron density of cubic boron nitride
Authors: Wahlberg Nanna , Bindzus Niels , Bjerg Lasse , Becker Jacob , Iversen Bo
Published: November 2015

The resent progress in powder diffraction provides data of quality beyond multipolar modeling of the valence density. As was recently shown in a benchmark study of diamond by Bindzus et al.[1] The next step is to investigate more complicated chemical bonding motives, to determine the effect of bonding on the core density. Cubic boron nitride lends itself as a perfect candidate because of its many similarities with diamond: bonding pattern in the extended network structure, hardness, and the quality of the crystallites.[2] However, some degree ionic interaction is a part of the bonding in boron nitride, which is not present in diamond. By investigating the core density in boron nitride we may obtain a deeper understanding of the effect of bonding on the total density. We report here a thorough investigation of the charge density of cubic boron nitride with a detailed modelling of the inner atom charge density. By combining high resolution powder X-ray diffraction data and an extended multipolar model an experimental modeling of the core density is possible.[3] The thermal motion is a problem since it is strongly correlated to the changes of the core density, but by combining the average displacement from a Wilson plot and a constrained refinement, a reasonable result has been obtained. The displacement parameters reported here are significantly lower than those previously reported, stressing the importance of an adequate description of the core density. The charge transfer from boron to nitrogen clearly affects the inner electron density, which is evident from theoretical as well as experimental result. The redistribution of electron density will, if not accounted for, result in increased thermal parameters. It is estimated that 1.7-2 electrons is transferred from boron to nitrogen.
Importance of multiple diffraction avoidance for charge density observation
Authors: Sakakura Terutoshi , Nakano Takahiro , Kimura Hiroyuki , Noda Yukio , Ishikawa Yoshihisa , Takenaka Yasuyuki , Tanaka Kiyoaki , Kishimoto Shunji , Tokura Yoshinori , Miyasaka Shigeki
Published: November 2015

It might not be well recognized, most reflections are contaminated by multiple diffractions (MD). Therefore high redundancy data could not coincide with high accuracy data when MDs are not avoided. We collected both data set of MD-avoided and no MD-avoided ones and investigated its effectiveness in electron density measurement. For data collection, four-circle diffractometer at KEK-PF BL14A (Tsukuba, Japan) was used. In MD-avoided measurement, each reflection is collected at angle setting of least of MD contamination which calculated by psi-scan simulation software MDC [1]. In no MD-avoided measurement, usual bisect setting were used. In no MD-avoided measurement, intensities of forbidden reflections of YMn2O5 are more than 10 times largely observed than for MD-avoided one, and resulting residual density map is also highly contaminated reflecting the tendency of Fo>>Fc which is typical for reflections of weak intensity. Figure 1 shows this situation. Figure 2 is the deformation density of YTiO3 for MD-avoided data. Where model density of without Ti-3d1 valence electrons is subtracted from experimentally observed electron density. In the figure, quenching of angular momentum of Ti-3d1 electron is clearly observed. Although Rint could not be an ideal indicator of data accuracy since it cannot perceive Fo>>Fc, Rint(F) of MD-avoided measurement for YTiO3 is significantly reduced to ~0.5%. For no MD-avoided one, Rint(F) is ~1.2%. Since accuracy of MD-avoidance technique is confirmed, the next step is to exploit informations of only a few numbers of valence electrons among F(000) electrons. To accomplish this, wave function based refinement such as XAO [2] should be applied and studied.
MoProViewer: a tool to study proteins from a charge density science perspective
Authors: Guillot Benoit , Enrique Espinosa , Huder Loïc , Jelsch Christian
Published: November 2015

Applying the charge density science methods to the structural biology field remains a considerable challenge. Several approaches were followed in the past years, focusing either on multipolar refinement of the rare available subatomic resolution protein structures or on the application of the transferability principle for the evaluation of electrostatic and energetic properties in protein-ligand complexes. However, the usually large size of macromolecules and the consequently large number of multipolar parameters in the Hansen & Coppens formalism [1] obviously complicates the feasibility of such kind of studies. In this presentation, we introduce the tools implemented in the MoProViewer software, part of the MoPro Suite for charge density refinement, especially designed to ease the analysis of a protein structure from a charge density perspective. These tools focus on helping the user in the computation of properties deriving from a refined or transferred [2] protein charge distribution and to manage a large number of atoms described in the multipole formalism in terms for instance of atomic local axis, symmetry or chemical equivalences constraints definitions. Moreover we will present new methods based on the topological analysis of the electrostatic potential [3]. They are designed to allow an original use of the electrostatic properties of a protein-ligand complex structure and rely on the computation and the representation of electrophilic and nucleophilic influence zones of atoms involved in protein-ligand interactions or in a biochemical process. The computational details of these methods as well as application examples on selected protein-ligand complexes will be given.
Novel lanthanide borohydrides: magnetism of all flavours
Authors: Grochala Wojciech , Jaron Tomasz , Wegner Wojciech , Pancerz Dawid
Published: November 2015

The rare-earth metals have high magnetic moments and a diverse range of magnetic structures. However, due to the inner-transition nature of lanthanide elements, the valence f orbitals of their trivalent cations usually do not mix substantially with the ligands' orbitals in the chemical compounds. The majority of lanthanide compounds is thus characterized by a rather ionic metal–ligand bonding and is hosting only weak crystal field effects. Several exceptions known encompass the valence fluctuation systems consisting of Sm, Ey, Tm or Yb combined with less electronegative nonmetal ligands (Si, S, Se, B etc.) or metals (Murani 2003 and references therein). This important class of lanthanide compounds for which crystal field effects are strong includes the classical systems: Yb3Si5 (Iandelli et al., 1979), YbB12 (Altshuler et al., 1998), and Yb3H8 (Drulis et al., 1999) . Even elemental Yb and Eu metals show valence transition at elevated pressure from di- to trivalent (Takemura & Syassen, 1985). These valence fluctuations are typically accompanied by electric resistivity changes: Ln(2+) → Ln(3+) + e–. Lanthanide borohydrides, Ln(BH4)3, constitute a rather poorly explored and novel group of compounds (Olsen et al., 2014). They are conveniently prepared via mechanochemical synthesis approach (high-energy milling). Quasi-ternary alkali metal-lanthanide borohydrides, MLn(BH4)4, are also available using this synthetic procedure (Wegner et al., 2013 [1] & Wegner et al., 2014 [2]). Here we explore for the first time the magnetic properties of Ln(BH4)3 and MLn(BH4)4 compounds, with particular emphasis on the thermally unstable systems (Ln= Sm, Yb and Eu) as contrasted with the reference case of much more thermally stable derivatives of ordinary lanthanides (Ln = Ho). We show that remarkably strong mixing of Ln(4f) and H(1s) states which causes thermal instability: Ln(3+) + BH4–→ Ln(2+) + BH4· leads in some cases to strong magnetic superexchange interactions between Ln(3+) centers [3].
Study of structural response of chlorpropamide polymorphs to external stress
Authors: Ivanenko Alisa , Minkov Vasily , Zakharov Boris , Janković Biljana , Srčič Stanko , Stare Jernej , Boldyreva Elena
Published: November 2015

Polymorphism in molecular crystals is a remarkable property of Nature to create a wide range of various combinations of limited amount of components. Studies of the polymorphic crystals upon different types of external influence could be very useful in terms of analysis of molecular packing, nature and dynamics of the intermolecular interactions. When applied to pharmaceuticals, crystal structure may noticeably affect on stability, solubility, bioavailability, etc. which are essential for drug development. Sulfonyl urea derivatives represent a great example of compounds which are potentially inclined to conformational polymorphism. In particular generation drug chlorpropamide could be crystallized in a five different polymorphs. Chlorpropamide molecule is highly flexible in the crystal structure whereby we obtain various types of molecular conformations and their relative arrangements within the main structural forming motif – directed hydrogen bonded chains. Although polymorphic properties of chlorpropamide have been well-known for a decade there are still a lot of open questions regarding relative stability and crystallization conditions of the polymorphs as well as their behavior under extreme conditions such as cryogenic temperatures, hydrostatic pressure and mechanical stress. In order to follow dynamics of molecular fragments and to observe possible phase transitions on cooling and compression polarized Raman spectroscopy was used. Low temperature spectra were recorded in a wide temperature (5-300 K) range. The effect of hydrostatic pressure was studied using diamond anvil cell up to 5 – 5.5 GPa. Nanoindentation was applied to five polymorphs of chlorpropamide to examine and compare their mechanical properties. Experimental results were also supported by quantum-mechanical calculations. The research was supported by a grant for Russia-Slovenia collaboration BI-RU-12-13-038, a grant from RFBR and the Integration project 108 of the SB RAS.
Periodicity and its breaking in compressed ferroelectric dabco monosalts
Authors: Olejniczak Anna , Katrusiak Andrzej
Published: November 2015

1,4-Diazabicyclo[2.2.2]octane (dabco) monosalts form a fascinating group of compounds, which exhibit exceptional dielectric properties. They can be described by a general formula: dabcoHX, where X= Br-, I-, ClO4-, BF4-and ReO4-. DabcoHI is the first material for which anisotropic relaxor properties were reported.[1] The ferroelectric relaxors are particularly desired for numerous practical applications in electronics, including miniature electronic devices and new methods of storing electricity in capacitors. Moreover, organic relaxors are environment friendly and easier to produce and to dispose off, than inorganic ceramic relaxors of mixed perovskites and doped with lead. DabcoHI undergoes a large number of transformations at elevated pressure and temperature, however analogous dabcoHBr exists only in three forms. Exceptionally rich phase diagram of ten phases was also revealed for dabcoHClO4. At normal conditions in dabco monosalts the dabcoH+cations are NH+···N bonded into linear chains, but pressure can considerably modify that pattern, and the weak hydrogen bonds are relevant for the formation of new polymorphs at high pressure.[2,3] In all dabcoHI polymorphs the NH+···N bonded chains of dabcoH+cations are retained, however the chains are linear at 0.1 MPa and high pressure induces modulation of the chain with gradually increased periodicity. In dabcoHBr only phase III is NH+···N bonded. Although phase II of dabcoHClO4isostructural with phase II of dabcoHBF4, it behaves differently on lowering temperature than it was observed in dabcoHBF4. The polymorphic structures of dabco salts differ mainly in the arrangement of the chains and iodide anions, in the dabco conformation, and in the location of protons. When crystallized from methanol, above 1.70 GPa, dabcoHI forms solvates, and the high-pressure crystallization from aqueous solution leads to hydration already at 0.50 GPa.
The impact of pressure on β-Cyclodextrin·acetaminophen inclusion complexes
Authors: Saouane Sofiane , Morgenroth Wolfgang , Liermann Hanns-Peter , Paulmann Carsten , Fabbiani Francesca
Published: November 2015

Cyclodextrins (CDs) have attracted considerable interest as model systems in supramolecular host-guest chemistry. They are described as hollow truncated cones with a hydrophilic outer surface and a nonpolar inner cavity suitable for small molecules' encapsulation.[1] By virtue of their character, CDs are used as excipients to improve the aqueous solubility of active pharmaceutical ingredients (APIs). High-pressure crystallisation techniques have been established as a suitable tool for exploring the phenomenon of polymorphism and solvate formation of pharmaceutical compounds throughout numerous examples reported in the literature.[2] Thus, exploring the inclusion-complex formation and the polymorphic behaviour of CDs with APIs at high pressure would be an interesting extension of the technique. The present work describes the attempt of an in-situ crystallisation of β-CD·acetaminophen inclusion complex and compression studies of the known β-CD·acetaminophen complex[3] in different crystallisation media at pressures up to 1.0 GPa. A new high-pressure crystal form observed at 0.8 GPa as well as unexpected results are presented herein. The crystals have been characterised by means of polarised optical microscopy, Raman spectroscopy and single-crystal X-ray diffraction using both home and synchrotron sources.
Aglycosylated knob and hole Fc homodimers are anti-parallel
Authors: Ultsch Mark , Elliott J. , Lee Joshua , Tong Raymond , Takeda Kentaro , Spiess Christoph , Scheer Justin , Eigenbrot Charles
Published: November 2015

Bispecific antibody and antibody-like molecules are of wide interest as potential therapeutics that can recognize two distinct targets. Among the variety of ways such molecules have been engineered is by creating ""knob"" and ""hole"" heterodimerization sites in the CH3 domains of two antibody heavy chains. The molecules produced in this manner maintain their biological activities while differing very little from the native human IgG sequence. To better understand the knob-into-hole interface, the molecular mechanism of heterodimerization, and to engineer Fc domains that could improve the assembly and purity of bispecific antibodies, we sought crystal structures of heterodimeric and homodimeric aglycosylated Fc fragments bearing ""knob"" and ""hole"" mutations. The structure of the knob-into-hole Fc was determined at 2.64Å. Except for the sites of mutation, the structure is very similar to that of the native human IgG1 Fc, consistent with a hetero-dimer interaction kinetic KD <1 nM. Homodimers of the ""knob"" and ""hole"" mutants were also obtained and their X-ray structures were determined at resolutions of 2.5Å and 2.1Å, respectively. Both kinds of homodimers adopt a head-to-tail quaternary structure and thus do not contain direct knob-knob or hole-hole CH3 interactions. By adding site-directed mutations at F241 and F243 in the CH2 domains, the head-to-tail arrangement was disfavored, leading to increases in both the rate and efficiency of bispecific (heterodimer) assembly.
Crystal chemistry of layered single and double hydroxides
Authors: Richardson Ian
Published: November 2015

Layered double hydroxides (LDH) are derived from layered single hydroxides by the substitution of a fraction (x) of the divalent metal cations by trivalent cations, with the charge balanced by anions in the space between the main hydroxide layers. LDH phases can have a range of metal cations and interlayer anions and the value of x can vary quite widely. Straightforward crystal-chemical and geometrical reasoning has resulted in new yet fundamental information about these phases [1, 2]. In particular: (1) It is now possible to calculate x from the `a' parameter of the unit cell or vice versa (whichever is known with the most confidence) for LDH phases that are based on Mg, Ni, Zn or Co; (2) The phase at x = 0 is shown to be an alpha form of M(OH)2 rather than the beta polymorph; (3) The extent to which the metal-oxygen octahedra in the main layer of LDH phases are squashed is now known to be independent of the type of the interlayer anions or the type of trivalent ion, which also has no substantial effect on the reduction in layer spacing that occurs as x increases; (4) It is now easy to create reliable structural models for hydrotalcite- and takovite-type LDH phases that have any trivalent ion (or ions) and any value of x; (5) The ordered distributions of trivalent cations that are possible in LDH phases have been clarified and a plausible explanation provided for the observed variation in the lower solid-solution limit [3]; (6) A reliable model for the crystal structure of beta-Zn(OH)2.
The role of point defects in multinary chalcogenide compound semiconductors
Authors: Schorr Susan
Published: November 2015

The electronic properties of multinary chalcogenide compound semiconductors, like chalcopyrite type ternary Cu(In,Ga)Se2 and quaternary kesterite type Cu2ZnSnSe4, depend strongly on their intrinsic point defects. For instance it is generally believed that in CuInSe2 the copper vacancies (VCu) cause p-type conductivity, whereas copper on interstitial positions (Cui) or InCu anti-sites act as donors and promote a n-type character. These defects are resulting from deviations from the stoichiometric composition. In order to keep the charge balance in the non-stoichiometric compounds, only a number of cation substitution reactions are possible: for example the transition to Cu-poor CuInSe2 goes via the defect pair 2VCu+InCu, whereas the transition to Cu-poor and Zn-rich Cu2ZnSnSe4 goes via the substitution 2Cu+->ZnCu + VCu. The presentation will give a comparison of the role of cationic point defects in chalcopyrite and kesterite type compound semiconductors concerning the following features: (i) Phase stability: the chalcopyrite type structure is very flexible to hold defects and can adapt itself to substitutions. Beyond a given copper vacancy rate, a vacancy compound (for instance CuIn3Se5) is formed, thus avoiding the occurrence of binary secondary phases (like copper selenides). For kesterite type Cu2ZnSnSe4 the situation is different: due to the lower flexibility of the kesterite type structure and the absence of vacancy compounds, secondary phases, like ZnSe, occur when the compound becomes Cu-poor. (ii) Atomic disorder: The cationic point defects cause an atomic disorder on the short range level which also influences the electronic properties (for instance the bandgap energy). For instance in Cu(In,Ga)Se2 defects such as antisites or interstitials lead to variations in the local atomic arrangements and thus broaden the bond distance distribution due to static disorder. The discussion will be underlined by the experimental results of neutron diffraction [1], anomalous scattering of synchrotron X-rays [2] as well as X-ray absorption spectroscopy [3].