bluuebunny/crossref_metadata_2025 huggingface dataset:
Structural behavior of organic zeolites on guest sorption/desorption
Authors: Lipkowski Janusz , Justyniak Iwona
Published: November 2015

The term organic zeolites, originally has been introduced to chemical literature by R.M. Barrer, to describe molecular crystals having open porous structures, able to reversibly absorb and desorb organic species with relatively weak, if any, sorption of water or other hydrophilic molecules. A characteristic feature of the organic zeolite structures, when compared to classical `inorganic' zeolites based on aluminosilicates, is the relatively weak intermolecular bonding within the host component. This is the reason for significant flexibility of the host crystal structure which changes its parameters upon guest absorption, desorption or exchange. The most characteristic property in this respect is absorption with `adsorbate generated sorption sites' which is the basis for design and control of selectivity and efficiency of sorption-desorption processes. In general, organic zeolite behavior may be observed on a large variety of supramolecular materials, including solvates of macrocyclic compounds and in the very important, so-called- MOFs. In the paper solvation of cyclodextrins and their complexes will be used as the convenient example, based on brand new, mostly yet unpublished large structures of heavily solvated cyclodextrin complexes in the solid state. Cyclodextrins are commonly known as materials having intra-molecular cavity able to accommodate guest species. This property, when combined with sorption in the inter-molecular space in the solid state structures of CDs leads to very interesting structures and properties. In general, such behavior may be observed only when CD moieties are at equilibrium with a solution of the respective guest and solvent species. The equilibria are quite sensitive to minor changes of solution chemical composition what may be observed microscopically as morphology changes of the crystalline phases. This phenomenon will be illustrated with short movies demonstrating crystal behavior on change of its environment. Novel x-ray structures will also be demonstrated and commented. This work was supported by grant POIG.01.01.02-14-102/09.
Studies on Cocrystal Formation of Metaxalone with Short-chain Dicarboxylic Acids
Authors: Lin Hong-Liang , Wu Tieh-Kang , Huang Yu-Ting , Lin Shan-Yang
Published: November 2015

A possible cocrystal formation between metaxalone and short-chain dicarboxylic acids (HOOC-(CH2)n-COOH, n=0-3) was quickly investigated using a solvent-assisted grinding approach. Differential scanning calorimetry (DSC), Fourier transform infrared (FTIR) microspectroscopy, and powder X-ray diffraction (PXRD) were used to verify the cocrystal formation between metaxalone and each dicarboxylic acid. A solvent evaporation method was used to prepare the standard cocrystal. The cocrystal formation was also estimated by using a one-step simultaneous DSC-FTIR microspectroscopy. The present study indicates that only n=2 of short-chain dicarboxylic acids such as succinic acid, fumaric acid and maleic acid could form a cocrystal with metaxalone. Both solvent-assisted grinding technique and solvent evaporation method were successfully applied to prepare the metaxalone cocrystal with n=2 of short-chain dicarboxylic acids. Moreover, this cocrystal formation was also easily screened and estimated using a unique DSC-FTIR microspectroscopy in real time. Acknowledgement This work was supported by National Science Council, Taipei, Taiwan, ROC (NSC 100-2320-B- 264-001-MY3).
Supramolecular organization of complexes of aryl hydrazones with SnCl3and SnCl4
Authors: Korlyukov Alexander , Vologzhanina Anna , Voronova Evgenia , Shmatkova Natalia , Seifullina Inna
Published: November 2015

Chelate complexes of main group metals with N,O-chelating Schiff Base ligands have been reported as perspective models for biologically active species. The derivatives of aryl hydrazones are among the most widely used ligands of such type. In our study, crystal structures of aryl hydrazones with SnCl3and SnCl4are discussed: the presence of aromatic fragments, amine groups and chlorine atoms therein are responsible for the coexistence of strong hydrogen and halogen bonds as well as stacking and Cl...π interactions. Interplay between these types of interactions and their role in stabilization of crystal structures is the subject of particular interest. We studied all these aspects in complexes of aryl hydrazones using different theoretical approaches: those based on Stockholder partitioning, molecular electrostatic potential, non-covalent interaction index, AIM theory – together with Espinosa-Mollins-Lecomte correlation to estimate the energy of all intermolecular interactions in crystals by means of electron density analysis from periodic quantum chemical calculations (VASP code). Our results showed that the presence of intermolecular interactions led to a noticeable redistribution of electron density in crystal as compared to an isolated molecule. Although Cl...π, stacking interactions and halogen bonds are numerous in the crystals of these complexes, their contribution to the energy of their crystal lattice does not exceed 30%. The work was supported by Council of the President of the Russian Federation (grant MD-3589.2014.3).
Photochromism change by conformation control in macrocyclic boronic ester cavity
Authors: Johmoto Kohei , Uekusa Hidehiro , Kikuchi Yuji , Takahagi Hiroki , Ono Kosuke , Iwasawa Nobuharu
Published: November 2015

N-salicylideneaniline derivatives are known to show photochromism by UV light, and it depends on the molecular conformation in the crystal. The twisted molecule is photochromic but the planar one is not[1,2]. N-salicylidene-2-aminopyridine (2SAP) always has a planar conformation due to the chemical structure without steric hindrance, therefore 2SAP is known as non-photochromic. However, by confining the molecule in a cavity of the macrocyclic boronic ester 1[3], the conformation and photochromism can be controlled. The inclusion crystal of 1 (homo-parallel form) has a special feature to have a channel type crystal structure in which the macrocyclic ring aligned one-dimensionally to include guest molecules. Interestingly, the crystals can reversibly absorb/desorb guests maintaining the crystal structure, because the channel structure is robust. To exchange the included guests, the crystal of 1(homo-parallel form) was immersed in the melt of 2SAP at 90°C. The obtained inclusion crystal showed photochromism. In the crystal structure, the shape of residual electron density for 2SAP indicated the conformation of 2SAP was twisted due to the confining in the cavity, which is the reason for photochromism. On the other hand, the recrystallization of 1 and 2SAP from THF / hexane solution unexpectedly gave hetero-antiparallel form of 1 because of the dynamic covalent bond formation in the boronic esters (Fig.). As this hetero-antiparallel form has planar cavity in the molecule, the conformation of the included guest molecule, 2SAP, is also planar as always seen. Therefore the inclusion crystal is non-photochromic. Thus, photochromism change of 2SAP was realized by conformational control through confining in the cavity of macrocyclic boronic ester.
Rampant Polymorphism in Pharmaceuticals: An Isoniazid Derivative
Authors: Hean Duane , Lemmerer Andreas , Michael Joseph
Published: November 2015

Investigations into the polymorphic forms of Active Pharmaceutical Ingredients (APIs) are of vital importance to drug formulations and are often kept a closely guarded secret by pharmaceutical companies. This secrecy is maintained as the nature of the polymorph could either make or break a drug formulation. Polymorphism is the ability of a solid crystalline form to exist in more than one structural arrangement. The variation in the crystalline forms often displays different mechanical, thermal, and chemical properties. These changes can remarkably influence the bioavailability, hygroscopicity, stability and other performance characteristics of the API [1]. Isoniazid, a well-known pharmaceutical, is used as a first-line treatment against Mycobacterium tuberculosis (TB) which is known to possess multiple polymorphs. Derivatives of isoniazid were developed in response to TB drug resistance. One such derivative, isonicotinic acid-(1-phenyl-ethylidenehydrazide) (IPH) [2] was found to exhibit an array of polymorphic behaviour as a result of its hydrogen bond acceptors, donors and conformational freedom along its backbone. To date only one crystal structure of IPH has been reported in the literature [3]. We have discovered and isolated an additional five novel polymorphs of IPH from various crystallization techniques, namely slow cooling, rapid evaporation, sublimation, as well as from hot-stage experiments. All of the polymorphs display hydrogen bonding through the carbonyl acceptor and hydrazide donor. However the torsion of these hydrogen bond acceptors and donors, relative to the molecular backbone, deviate due to the conformational flexibility of the molecule. Structural information of the polymorphs was obtained by SCXRD, PXRD, IR and Raman. The thermal phase relationships of these polymorphs were also investigated using DSC and HSM. Elucidating these novel polymorphs and establishing phase relationships are a key step in the design of isoniazid based pharmaceuticals.
Coordination modes of novel 4,5-dicyanoimidazolato ligand in alkali metal salts
Authors: Dranka Maciej , Zachara Janusz
Published: November 2015

As the use of lithium batteries became more and more wide-spread, the importance of the research on novel salts for batteries' electrolytes grew more and more important. The focus has been put on designing novel lithium and sodium salts which dissociate well in aprotic solvents and are electrochemically and thermally stable. Salts with heteroaromatic anions such as 2-trifluoromethane-4,5-dicyanoimidazolate (LiTDI) [1,2] are a promising alternative for the salts commonly used as charge carriers in lithium and sodium batteries. The class of new 4,5-dicyanoimidazolates ligands is based on N-heterocyclic five-membered ring substituted with nitrile group. Such a type of anions possesses four nitrogen donor centers able to coordinate cation, and is characterized by charge delocalization, both on imidazole ring and cyano substituents resulting in extended π electron system. In solid as well as liquid electrolytes one should expect the co-existence of a variety of ionic species, such as iosolated anions and cations solvated by solvent molecules, ionic pairs, for which the coordination sphere of cations is completed with solvent molecules, as well as dimers and aggregates with varied stoichiometry. The observed degree of aggregation depends mostly on the coordination properties of anions, their ability to form hydrogen bonds and their compatibility with the acidic properties of cations. The increase of the salt concentration should result in association process and the emergence of higher aggregates, up to polymeric systems, possessing structure of chains, ribbons, layers or networks. In order to define the coordination ability of the class of new ligands, we examined their organization modes in the alkali metal salts and have found a wide variety of mentioned motifs. Discovering and understanding the phenomena related to the organization of such systems in the solid state is crucial for the elaboration of novel electrolytes and should give information about cation and anion coordination in electrolytes. Our single-crystal diffraction studies have shown that new salts comprising 4,5-dicyano-2-(trifluoromethyl)imidazolato anion are interesting from the point of view of their crystalline structure, offering variety of possible coordination modes and are, therefore, worthy of examination.
A new family of [IrCl5(NO)]-salts. Structural diversity tuned by aryl embraces
Authors: Di Salvo Florencia , Foi Ana , Baggio Ricardo , Bikiel Damian , Doctorovich Fabio
Published: November 2015

The interactions experimented by multiple phenyl or other aromatic groups in crystals have been described as ``embraces'' since 1995, when Dance and co-workers developed the embrace paradigm as an important and widespread tool of supramolecular chemistry. There are three main classes of Multiple Phenyl Embraces (MPE) depending on the total number of phenyl rings (Ph) located in the interaction domain: sextuple (6PE), quadruple (4PE), and double phenyl embrace (2PE) [1]. Recently, an accurate theoretical evaluation of the MPE motifs between PPh4+was presented by Novoa et al [2]. In our laboratory we demonstrated that by changing the counterion of the [IrCl5(NO)]-salts from K+to PPh4+, it was possible to stabilize an excited state of the metal complex anion. The electronic distribution of the IrNO moiety in K[IrCl5(NO)] can be depicted as the closed-shell electronic structure IrIII–NO+. However, in PPh4[IrCl5(NO)] an unprecedented electronic perturbation takes place favouring the open-shell electronic structure IrIv–NO* [3]. These results together with the interesting systematic studies on MPE, encouraged us to explore the synthesis of new phosphonium salts. In this work we report new phosphonium ions of the type Ph3PR+and five new Ph3PR[IrCl5(NO)] salts (R = aryl, methylaryl). Structural analyses of these compounds were done in the context of the multiple embraces motifs. For the new unsymmetrical [IrCl5(NO)]-salts, the supramolecular arrangements are different from the one observed for the PPh4+one. In the last one, the 4PE infinite chains run parallel to the columns described by the anions [3] and for the others, the presence of bulkier substituents give place to symmetries that favours other kinds of aryl embraces resulting in a side by side location of the anions. Finally, DFT calculations were performed to evaluate the theoretical concerns regarding the structural behaviour, as well as the electronic distribution along the family of compounds.
Design of Mechanically Flexible Organic Crystals: A Crystal Engineering Approach
Authors: Krishna Gamidi , Devarapalli Ramesh , Lal Garima , Reddy C.
Published: November 2015

Utilization of organic single crystal materials is increasing day by day owing to their promising applications in organic light emitting diodes [1], organic solar cells, mechanochromic luminescence [2] and tablatability [3] of APIs etc. These desirable functions, especially mechanical properties, can be achieved by imparting soft nature in organic materials, however unfortunately there is no simple strategy to attain this. Till date all the findings are serendipitous discoveries, so a rational design strategy is necessary to accomplish such soft mechanical behavior in molecular crystals. Here we propose a design strategy to attain plastically deformable organic materials by introducing slip planes in the crystal structures. The high plasticity can be achieved by introducing hydrophobic groups, such as t-Bu, -OMe, -Me and multiple –Cl (or) –Br groups on -Ar building blocks, for example on naphthalene diimide (NDI), which leads to the formation of slip planes in the crystal structures (as shown in attached figure), hence facilitate the plastic (irreversible) bending [2].
Stabilising peroxyacids in niche microenvironments
Authors: Cruickshank Dyanne , Wilson Chick
Published: November 2015

There has been dramatic evolution in the formulation of household cleaning products over the last decade, this is mainly due to the influence of social change, regulatory pressure and the need for new less toxic, safer formulations with increased performance. Due to their high chemical reactivity, peroxides are found in a wide range of bleaching agents, they are known for their instability which is a direct consequence of their high reactivity (in turn essential for function). Stabilising such materials for implementation in a range of product types is a significant target within the domestic products industry. Supramolecular approaches are already being explored to try stabilise other chemically reactive species such as explosives [1,2] thus illustrating the feasibility of this research. The work to be presented will deal with peroxyacids that include small model compounds such as m-chloroperbenzoic acid as well as a commericially relevant bleaching agent and their inclusion in both crystalline and amorphous hosting systems. Single crystal X-ray diffraction methods are used to elucidate the ordered crystalline structures and to confirm whether or not the peroxo group is still intact within the crystalline host environments. Simple reactivity tests are used to demonstrate whether or not the amorphous host-guest complexes contain the active peroxy acid within their host cavity. Other complementary analytical techniques such as powder X-ray diffraction, differential scanning calorimetry and thermogravimetry have also been used to characterise the newly-hosted peroxyacid materials. By hosting these molecules in microenvironments it is possible to prepare formulations that are less pH sensitive, thus making their storage safer while allowing their reactivity to be controlled and tuned.
Exploration of supramolecular interactions in a series of UO22+hybrid materials
Authors: Carter Korey , Thangavelu Sonia , Cahill Christopher
Published: November 2015

Previous work from our group has focused on uranyl hybrid materials with para-substituted halogen benzoic acids.1 Applying a `cap and link' strategy we have successfully controlled the nuclearity of UO22+ in a series of coordination polymers and Ln3+ in a family of molecular materials.2,3 Here we have expanded on this strategy and produced a series of 12 unique uranyl hybrid materials. The hydrothermally synthesized complexes all feature bromo-substituted benzoic acid linkers and the UO22+ metal centers are capped with a chelating N-donor. Single crystal X-ray diffraction analyses of these materials allowed for the exploration of the structural relationship between the benzoic acid group and the chelating N-donor as well as the influence of pH on uranyl speciation. At an unadjusted pH (~3) a mix of molecular monomers and dimers are observed while at higher pH (5-6) molecular uranyl dimers are exclusively produced. A systematic study of the supramolecular interactions that governed extended solid-state assembly was investigated by varying the bromine position on the benzoic acid groups along with the chelating N-donor with pH. Assembly via halogen-halogen, halogen-π, π-π, and halogen-oxygen interactions was observed and the influence of these interactions on uranyl emission was also investigated. Solid-state luminescence and lifetime measurements were used to explore the effects of speciation and chelating N-donor ligands on the spectroscopic properties of the uranyl cation.
The relevance of polymorphism in rifampicin
Authors: Nogueira Luciana , Raffin Fernanda , Ayala Alejandro
Published: November 2015

Tuberculosisis is an infectious Neglected Tropical Disease (NTD) considered a public health problem in several countries. Rifampin (RIF) is one of the first choice drugs in the treatment of this disease since it has bactericidal action on susceptible strains of Mycobacterium tuberculosis, the etiological agent of tuberculosis affecting humans. According to the literature RIF can exist in two polymorphic forms, namely forms I and II, a penta-hydrate and an amorphous solid1. Each form has different solubility in aqueous medium affecting the bioavailability of the drug when it formulated in solid dosage forms for oral administration since they are expected to content form II2. The objective of this research is to characterize and understand in detail the pharmaceutically relevant forms of RIF. It is an important and challenging problem related to the development of formulations because the physical mixture of these forms is usually observed in raw materials from generic suppliers. Thus, the reference sample (USP standard) and two lots from different suppliers were investigated by electron microscopy, Raman and infrared spectroscopies, X-ray diffraction powder and thermal analysis. In addition, pure samples of these solid forms were produced by recrystallization under different conditions in order to establish the structural reference standards. The results of this study will be useful for the development of efficient quality control methods for a drug which is very important to the social health programs.
Direct evidence for 2-fold to 3-fold change of interpenetration in a MOF
Authors: Aggarwal Himanshu , Bhatt Prashant , Benzuidenhout Charl , Barbour Leonard
Published: November 2015

Single-crystal to single-crystal transformations has recently received much attention in the field of crystal engineering. Such transformations not only provide insight into the changes taking place within the crystal at the molecular level, but they also aid our understanding of the structure-property relationships. Discrete crystals have been shown to tolerate considerable dynamic behavior at the molecular level while maintaining their single-crystal character. Examples that are common in the literature include bond formation/cleavage,[1] guest uptake,[2] release or exchange as well as polymorphic phase transformations. However, there are rare examples of the structural transformations on the host framework initiated by removal of guest or change in physical conditions such as temperature or pressure. We have investigated a known doubly-interpenetrated metal organic framework with the formula [Zn2(ndc)2(bpy)] which possesses minimal porosity when activated. We have shown not only that the material converts to its triply-interpenetrated analogue upon desolvation, but that the transformation occurs in a single-crystal to single-crystal manner under ambient conditions.[3] This contribution probes the limits to which a single-crystal material can undergo structural rearrangement while still maintaining the macroscopic integrity of the crystal as a discrete entity.
Macrocyclic Boronic Ester: Porous and Host-Guest Structures Revealed by SDPD
Authors: Uekusa Hidehiro , Fujii Kotaro , Johmoto Kohei , Kikuchi Yuji , Takahagi Hiroki , Ono Kosuke , Iwasawa Nobuharu
Published: November 2015

Diboronic acid and racemic tetrol are found to form a self-assembled macrocyclic boronic ester in the presence of appropriate guest molecules[1]. In the crystal, stacking of macrocyclic ring is observed to form infinite channel structure accommodating guest molecules by supramolecular interactions. In such structure, it is important to investigate the guest uptake and release mechanism via the crystal structure determination of the guest-free apohost. However, the apohost crystal can only be obtained by guest release process by heating, which results to form powder crystals. In this study, the structure of apohost was determined by "Structure Determination from Powder X-ray Diffraction data" technique [2][3] and the structural change by guest sorption and desorption processes were investigated. The powder X-ray diffraction pattern of the toluene inclusion crystal and the apohost crystal, which was obtained by heating of the inclusion crystal, are significantly different. However, even after the guest release, the apohost structure determined from the powder X-ray diffraction data was found to retain its crystal packing with one dimensional guest free channel. Interestingly, the apohost crystal easily absorbs the toluene and other aromatic molecules when the vapor was applied, and the crystal transforms into the guest inclusion crystal. Also, such vapor application is interesting method to switch the physicochemical property of the crystal. When naphthalene vapor was applied to the apohost crystal, naphthalene inclusion crystal was readily formed, and it became fluorescent crystal. This property was switched off by heating and guest desorption. In summary, the macrocyclic boronic ester is promising compound that forms inclusion supramolecular crystal, which can be utilized as guest storage / release, separate, protect, and other physicochemical functional material.
Varying experimental conditions to study interactions in the solid state
Authors: Boldyreva Elena
Published: November 2015

Supramolecular interactions in the solid state attract much attention. Different experimental and computational approaches are used, to predict and to design crystal structures, to predict the properties based on molecular and crystal structures, to range different types of intermolecular interactions. Analysis of the crystal structures at fixed (e.g. ambient) temperature and pressure conditions is most common for experiments, whereas most DFT calculations are limited to 0 K, to minimize computational costs. At the same time, evolution of a crystal structure as a function of experimental conditions can contribute significantly to understanding the structure-forming role and relative energies of different types of intermolecular interactions in the same crystal structure and of similar interactions in a series of different but structurally or chemically related compounds. In the present invited contribution I attempt to illustrate this using several selected examples from my own practice and from the papers published by other research groups. I consider, in particular, the results of variable-temperature and variable-pressure studies of continuous lattice strain and phase transitions in small-molecule organic compounds, the results of variable-temperature and variable-pressure crystallization, the results of comparing the dissolution profiles of mono- and multi-component small-molecule organic crystals. I shall also discuss how variable-temperature and variable-pressure experimental diffraction data can assist in optimizing the calculations aimed at comparing the relative stability of polymorphs and predicting polymorph transitions. The study was supported by Russian Ministry of Science and Education and Russian Academy of Sciences.
Studying structure disorder in DL-Norvaline by single crystal diffuse scattering
Authors: Xu Jun , Linden Anthony , Bürgi Hans-Beat
Published: November 2015

Diffraction methods are the most important methods to study the three-dimensional arrangement of matter at the atomic level. Real materials are often not perfectly ordered and the resulting diffraction pattern may contain a weak continuous or structured background known as diffuse scattering, in addition to sharp Bragg peaks. Our motivation is to analyse diffuse scattering in order to learn about the Short Range Order (SRO) of disordered crystals and improve the tools to model disorder phenomena. We are now investigating the SRO in DL-Norvaline which crystallizes in three known temperature-dependent phases. At least two of them (beta-phase space group C2/c above -700C, alpha-phase P21/c around -900C) show disordered average structures in which the alkyl side chain adopts several conformations [1]. The scattering data were collected using synchrotron radiation and a noise-free Pilatus pixel detector at the ESRF BM01A station. The diffraction pattern of the β-phase shows diffuse streaks parallel to a reciprocal lattice axis and diffuse clouds around low angle reflections [2] (Fig. 1). These features result from static and dynamic disorder. The diffuse streaks indicate disorder amongst stacks of layers of molecules, while the diffuse clouds arise from thermal motion. The modelling of the disorder involves the use of the Monte Carlo and differential evolution algorithms embedded in ZODS [3]. Our progress with model development will be presented.
Modelling diffuse scattering of the disordered crystal structure of Na2SiF6
Authors: Stronks Erik , Bürgi Hans-Beat , Linden Anthony , Kroon-Batenburg Loes
Published: November 2015

Many crystalline materials are not perfectly ordered, but are disordered to a smaller or larger extent. The properties of such materials are often related to the nature of the disorder. In diffraction experiments, disorder is observable as diffuse scattering. In routine X-ray structure determinations, only Bragg reflections are considered, leading to average crystal structure models. Methods to derive the average structure from the Bragg reflections are very well established, whereas diffuse scattering is rarely accounted for and mostly ignored. Our attempts at modelling the disordered structure of crystalline sodium fluorosilicate will be presented. Although the average crystal structure is known [1], there is some uncertainty about the true space group [2]. Na2SiF6assumes a crystalline morphology that resembles that of ice and is therefore known as an ice–analog material [3]. In the average crystal structure (in space group P321), the asymmetric unit contains two ordered sodium cations (both sitting on a two-fold axis) and two disordered SiF62-anions (one sitting on a 3-fold axis and the other on a 32 site). Each anion can occupy two alternative sites in the unit cell, related by a non-crystallographic mirror plane at z = ¼. The occupation is mutually exclusive for both anions. Diffuse scattering can be observed as planes perpendicular to l in the hnl and nkl precession images where these diffuse planes can be found at integer l. For l odd, the diffuse scattering is more intense. Also there are diffuse clouds of intensity around certain Bragg peaks. In the hkn planes, diffuse streaks are visible parallel to a*, b*, and a* - b*, while some Bragg peaks have diffuse clouds of intensity around them. The pattern of streaks and clouds evolves when going to higher order planes. In the figure below, the hk1 precession image is illustrated. The observed diffuse scattering features will be interpreted in terms of structural models obtained by Monte Carlo simulations.
Electron density, d-p hybridization and dipole moment of PbTiO3 and BaTiO3
Authors: Yamanaka Takamitsu , Nakamoto Yuki , Ahart Muhtar , Mao Ho , Hemley Russell
Published: November 2015

Present experiment first reveals electron density (ED) distributions and split atomic displacements of ferroelectrics PbTiO3 (PTO) and BaTiO3 (BTO) by high-resolution x-ray single crystal diffraction study under high pressures using maximum entropy method (MEM). Diffraction measurements were carried out using a four-circle diffractometer installed at BL-10A Photon Factory, KEK, Japan. *** ED observed by FMEM(h) illustrates the d-p pai-bond resulting from the hybridization of Ti 3d and O 2p orbitals. The split atom distribution is generated from the dynamical disorder (static time and space average) due to the thermal vibration of atoms in the [001] direction of these crystal structures. The split distributions of Ti and O are clearly disclosed in the tetragonal ferroelectric PTO and BTO. The ferroelectric pseudo-particle occupies double-well potential. The feature disappears in the cubic paraelectric phase and electron density is more localized with increasing pressure in the cubic phase. *** Effective charges of atoms in PTO and BTO are evaluated from the least-squares refinement based on diffraction intensities. Using the pseudopotential model, inner-core electrons are frozen with bonding effects, but only valence electron clouds are deformed due to coordination and thermal vibration of atoms. The pressure dependence of the dipole moment (l) is calculated by the effective charge (q) and atomic deformation Δr. The dipole moment of ferroelectric materials is derived from the spontaneous polarization Ps (= ρ l = ρNΔr). Pressure dependences of dipole moments of PTO and BTO are first experimentally determined by observed effective charge q and Δr from their structure refinements. The dipole moment of PTO is much larger than BTO, which implies the difference in the dielectricity of these ferroelectrics. The result is consistent with the dielectric measurement.
Neutron Diffractions in Pulsed High Magnetic Fields
Authors: Nojiri Hiroyuki , Narumi Yasuo
Published: November 2015

In frustrated magnets, varieties of exotic states appear under high magnetic fields. Examples are found as complex magnetic phase diagram in multi-ferroics, a quantum phase transition in strongly correlated 5f intermetallics and quantum magnetic plateau in low-dimensional magnets. The most important basis to understand such exotic phases is the determination of their magnetic structures. Neutron diffraction is the unique and the direct method for this purpose. However, experiments in strong magnetic fields have been quite limited for technical difficulties. We have developed the techniques to combine pulsed high magnetic fields with neutron diffractions. The use of pulsed magnets have broken the technical limit of 17.5 T achieved by superconducting magnets and enabled us to access the extremely high magnetic fields of 30-40 T. At present, we have four different lines of pulsed magnet devices for practical experiments as follows. 1. Compact potable 30 T horizontal solenoid magnet system combined with an orange cryostat, 2. Compact 40 T horizontal solenoid with a custom cryostat, 3. Compact 25 T vertical split-pair magnet with a custom cryostat, 4. Middle size horizontal 50 T solenoid magnet with a custom cryostat. The temperature as low as 1.7 K is possible for all of those systems. The compact 30 T system is used in ILL, SNS, ISIS and JRR3. Upgraded 40 T version is installed in ISIS and ILL. The split-pair and the middle size system are used in J-PARC. In reactor sources, a very week magnetic peak can be detected for low background. A continuous field variation of the peak intensity is monitored by means of time-resolved technique. In spallation sources, multiple Bragg-peaks are captured by using the white beam Laue method. It is very useful to trace the change of magnetic wave vectors. We report the overview of the recent activities examining magnetic phase diagrams of multi-ferroic compounds and URu2Si2 with a multi-step meta-magnetic transition.
Native SAD Structure Solution from Merohedrally Twinned Data
Authors: Weinert Tobias , Waltersperger Sandro , Olieric Vincent , Basilico Federica , Cecatiello Valentina , Pasqualato Sebastiano , Wang Meitian
Published: November 2015

Up until now, comparatively few structures were solved by native SAD. Recent advances in multi crystal averaging [1] have shown that native SAD can be applied to an increasing number of cases. Though theoretically possible [2], successful structure solutions from twinned data have not been reported yet. Here, we report the structure solution of the human Centromere protein M from a merohedrally twinned crystal with a twinning fraction of 0.45 in the space group P3. The data were collected at the bending magnet beamline X06DA at the Swiss Light Source, which is equipped with the in-house developed multi-axis goniometer PRIGo and the PILATUS 2M detector. A highly redundant 2.2 Å dataset was collected in a number of different crystal orientations. A substructure solution could only be obtained after 50000 SHELXD [3] tries. Automatic model building after phasing and density modification resulted in a model with the majority of residues built correctly. We will present this particularly difficult case together with other more routine cases, all solved with the same experimental setup and at the beamline X06DA.
Initial phases from phosphate SAD in the direct methods determination of RNA
Authors: Mooers Blaine , Doukov Tzanko , McKay Tina , Venkataramany Akila , Mooers Victoria
Published: November 2015

Atomic resolution diffraction data from crystals of double-stranded RNAs can often resist automated structure determination by ab initio methods including charge flipping and traditional direct methods. Often it is possible to obtain quick success at direct methods structure determination by supplying the positions of one or more heavier atoms, which are used to calculate a starting set of phase angles. Long wavelength radiation such as that near the iron K absorption edge can be used to measure the weak anomalous diffraction data from phosphorous atoms in the RNA backbones. These anomalous diffraction data can be used to locate the positions of some of the phosphorous atoms. Next, the phosphorous positions can be used to provide initial phases for direct methods structure determination with atomic resolution diffraction data collected with shorter wavelength radiation. We tested this hybrid approach with two double-stranded RNAs, one with 31 unique phosphates and a second with 44 unique phosphates. We used a combination of programs including those in the CCP4, SHELX, and Sir program suites. We varied the number of sweeps of images collected at the iron edge to find the minimum number (and hence minimum exposure) required to find enough of the phosphate substructure for success at direct methods with the native data before collecting atomic resolution diffraction data with the short wavelength radiation. Our results suggest that diffraction data could be collected at these two wavelengths from a single crystal to avoid problems with non-isomorphism.
The Long-Wavelength MX Beamline I23 at Diamond Light Source
Authors: Wagner Armin , Duman Ramona , Mykhaylyk Vitaliy
Published: November 2015

The long-wavelength macromolecular crystallography (MX) beamline I23 at Diamond Light Source will be the first dedicated beamline for long-wavelength phasing experiments from macromolecular crystals. By exploiting the weak anomalous differences from sulfur or phosphorous present in proteins or RNA/DNA molecules the crystallographic phase problem can be experimentally solved by anomalous diffraction methods based on their intrinsic signal without labeling the crystals with additional anomalous scatterers. Additionally, anomalous contrast can be used to unambiguously identify biologically important ions such as Ca2+, K+ or Cl-. The beamline will operate in a core wavelength range from 1.5 to 4 Å, offering a complementary setup to the suite of already five existing MX beamlines at Diamond. To minimize absorption effects, the complete beamline including sample, goniometer and detector will be operated in vacuum. An X-ray tomography setup will be integrated into the experimental end station to determine the crystal shape and size as a basis for an analytical absorption correction. A large curved Pilatus 12M detector will allow access to diffraction data up to 2theta =1100° (figure 1). Sample cooling is realized by a conductive path from a pulse tube cryo-cooler through the kappa goniometer. The beamline is currently in its construction phase with first users being expected in summer 2014. The challenges of in-vacuum long-wavelength macromolecular crystallography and the opportunities by extending the wavelength range towards the sulfur and phosphorous K-absorption edges will be discussed and an overview on the current status of the project will be given.
Softer but stronger? Sulfur SAD with low energy X-rays of 2.7 Å
Authors: Liebschner Dorothee , Matsugaki Naohiro , Senda Miki , Yamada Yusuke , Senda Toshiya
Published: November 2015

Single wavelength anomalous diffraction (SAD) is a powerful experimental phasing technique used in macromolecular crystallography (MX). SAD is based on the absorption of X-rays by heavy atoms, which can be either incorporated into the protein (crystal) or naturally present in the structure, such as sulfur or metal ions. In particular, sulfur seems to be an attractive candidate for phasing, because most proteins contain a considerable number of S atoms. However, the K-absorption edge of sulfur is around 5.1 Å wavelength (2.4 keV), which is far from the optimal wavelength of most MX-beamlines at synchrotrons. Therefore, phasing experiments have to be performed further away from the absorption edge, which results in weaker anomalous signal. This explains why S-SAD was not commonly used for a long time, although its feasibility was illustrated by the ground-breaking study by Hendrickson and Teeter [1]. Recent developments in instrumentation, software and methodology made it possible to measure intensities more accurately, and, as a consequence, S-SAD has lately obtained more and more attention [2]. The beamline BL-1A at Photon factory (KEK, Japan) is designed to take full advantage of a long wavelength X-ray beam at around 3 Å to further enhance anomalous signals. We performed S-SAD experiments at BL-1A using two different wavelengths (1.9 Å and 2.7 Å) and compared their phasing capabilities. This methodological study was performed with ferredoxin reductase crystals of various sizes. In order to guarantee statistical validity and to exclude the influence of a particular sample, we repeated the comparison with several crystals. The novelty in the approach consists in using very long wavelengths (2.7 Å), not fully exploited in the literature so far. According to our study, the 2.7 Å wavelength shows - despite strong absorption effects of the diffracted X-rays - more successful phasing results than at 1.9 Å.
Adventures in Phasing: Flavivirus NS1 solved by low resolution native S-SAD
Authors: Akey David , Brown William , Konwerski Jamie , Ogata Craig , Kuhn Richard , Smith Janet
Published: November 2015

We used native sulfur-SAD phasing to determine a novel structure of significant health importance, the flaviviruses non-structural protein 1 (NS1). Flaviviruses cause many diseases including dengue and West Nile fever. NS1 functions in both genome replication and immune system evasion. Full length, glycosylated NS1 was expressed in insect cells and crystallized. Due to difficulties with protein expression SeMet phasing was not practical, and we embarked on an effort to use sulfur-SAD phasing. To optimize the probability of observing the estimated 1.5% S-anomalous signal, we used inverse beam protocol at 7.1 keV with 50wedges and 0.50oscillations. Crystals typically diffracted to ~3.0 Å. Pairwise comparisons of anomalous correlation coefficient (AnomCC) and Rmerge in the highest intensity (low resolution) bins were used to decide which crystals to include in the final data set. Crystals which when compared to other crystals consistently had AnomCC < 0, or Rmerge > 7.5% in the low resolution bin were excluded. Data from 18 of 28 crystals were combined to generate a data set with ~100 fold anomalous multiplicity. The final data set was of high quality by I/σI and CC1/2 metrics with a positive AnomCC to ~5.4 Å. Sulfur sites were found with SHELXD using data to 5.2 Å. Phases calculated to 4.5 Å by SHELXE and extended to 3.0 Å with DM were of sufficient quality to autobuild ~75% of the final model. The NS1 structure was complete with the exception of one 20-residue internal loop, and glycosylation was observed at expected sites. Although Rmerge values were high for the combined data (30% overall, 9% low-res, 900% hi-res), model building and refinement proceeded smoothly, supporting the notion that Rmerge is a poor indicator of data quality for purposes of refinement and may also be a poor indicator for purposes of phasing. The effects of data multiplicity and resolution on S-site determination, phase calculation and phase extension were investigated.
ProMOL: Improved approaches to identification of the function of proteins
Authors: Bernstein Herbert , Craig Paul , Bangura Abdul , Grier Alexander , Osipovitch Mikhail , Kovuri Venkata , McKay Talia , Hart Kaitlin , Tedla-Boyd Weinishet , Dodge Greg , Hartung Amanda
Published: November 2015

The goal of this project is to improve and extend best practices in the algorithmic and biochemical identification of the function of proteins, and to make these resources available to the life science education and research communities. In the earlier phases of this project we developed the ProMOL plugin for PyMOL, a tool used to explore the catalytic site structural homologies between proteins of known function and those for which functions are not yet known, and we have applied it to examine more than 3000 structures in the Protein Data Bank for which functions are not yet known. Although catalytic site structural homology alone is not sufficient to define the function of a protein, it provides one mechanism which, when combined with other structural and sequence motifs, can suggest candidates for experimental verification. In addition, similar, non-catalytic structural motifs can be indicative of non-catalytic functions. The motif library is being extended to include NMR structures, metal ions, and non-catalytic motifs. A database of results has been established. The combination of in-silico characterization and wet-lab characterization has proven to be a suitable task for undergraduate biochemistry students and partnerships to embed this work in undergraduate curricula are being established.
Small-angle scattering simulations for suspensions of nanocrystals
Authors: Schmiele Martin , Gehrer Simone , Unruh Tobias
Published: November 2015

Suspensions of nanocrystals which possess large lattice spacings d(hkl) and only a small number of unit cells along the direction of the reciprocal lattice vector G(hkl) can feature broadened Bragg peaks in small-angle scattering (SAS) patterns. The scattering from molecules located at the interface between the nanocrystals and the dispersion medium which stabilize and functionalize the nanocrystals can interfere with the scattering of the nanocrystals and affect the shape and position of their Bragg peaks. This allows to study how these molecules arrange on the surface of the nanocyrstals. As an example we study suspensions of lecithin stabilized β-tripalmitin nanocrystals which adopt a platelet-like shape. Their SAS patterns exhibit a broadened 001 Bragg peak (cf. SAXS curves in the graphical abstract). With the x-ray and neutron powder pattern simulation analysis (XNPPSA) we have demonstrated that the SAXS and SANS patterns of dilute tripalmitin (3 wt%) suspensions can be simultaneously reproduced on an absolute scale [1,2]. Thereby, powder averaged SAS diffractograms are computed for an ensemble of nanocrystals which are embedded in a dispersion medium. The crystallographic structure of the nanocrystals (CIF-file) and their geometry are taken into account and the amphiphilic lecithin molecules which cover the nanocrystals are modelled with two shells (cf. model in the right inset). From the analysis of the fitted shell thicknesses and scattering length densities it turns out that the lecithin molecules arrange rather flatly and densely packed on the surface of the nanocyrstals. Moreover, the XNPPSA method allows a reliable determination of the thickness distribution of the nanocrystals with molecular resolution [1,2]. With rising tripalmitin concentration the platelets form self-assembled stack-like structures [1,3] and finally nematic liquid-crystalline domains. The XNPPSA allows to investigate the structure and amount of such stacks in the suspensions.