bluuebunny/crossref_metadata_2025 huggingface dataset:
Complementary XRD and XAFS Studies of Double Metal Cyanides catalysts
Authors: Jablonska Krystyna , Demchenko Iraida , Dynowska Elzbieta , Chrusciel Arkadiusz , Janik Jaroslaw
Published: November 2015

"Highly disordered materials exhibit diversity of the functional properties which are of interest of nowadays technology. The example of such materials is the group of a non-stoichiometric composite transition metal complex salts, known as double metal cyanides (DMC). These materials are used as the industrial catalysts and form an interesting family of porous molecular materials with large fraction of the amorphous phase. This fraction may be obtained by introduction to the crystalline zinc hexacyanocobaltate (III) (Zn3[Co(CN)6]2·nH2O) organic ligands of different size. Depending on the type of ligands the catalysts exhibit different levels of activity. The crystalline zinc hexacyanocobaltate exhibits only very weak catalytic properties. The others have a considerably high activity, which is their key feature. Although the said group of catalysts is successfully used and progressively developed for decades, the knowledge on the molecular nature of their particularly high activity and selectivity is modest and limited to some phenomenological hypotheses based on overall chemical premises. The attempt to formulate important for DMC catalysts relationship between the concentration of amorphous phase and their activity as well the influence of an organic ligand presence on formation of amorphous phase, suspected to be responsible for catalytic properties, will be presented. The base for this is the reliable characterization of such materials which requires application of several methods providing complementary information. The application of x-ray diffraction and absorption will be discussed and the benefit of each method will be described. Acknowledgments: Research funded in part by the Projects BSR, Science Link and Innotech K2/IN2/21/181982/NCBR/ 12(K-DMC). Financial support from the EU FP7 under the grant agreement REGPOT-CT-2013-316014 is gratefully acknowledged. Jaroslaw Janik is a Fellow of the project ""PhD Scholarships - an investment in faculty Opole province"" co-financed by the European Union under the European Social Fund."
ESRF X-rays at the service of industry
Authors: Monaco-Malbet Stéphanie , Poudevigne Emilie , Sztucki Michael , Boller Elodie , Lafford Tamzin , Mitchell Edward
Published: November 2015

The creation and tailoring of new materials are at the heart of current industry challenges. New materials must meet ever more stringent requirements of performance, whilst fitting into the modern cradle-to-grave cycle of material production, use, and recycling. The properties and function expected of materials depend heavily upon their composition and their micro- or even nano-structure. Their "ultimate" characterisation is possible down to the atomic scale using the tools and techniques of large-scale facilities such as synchrotron X-rays. The European Synchrotron Radiation Facility (ESRF) provides the ability to visualise the atomic, nano-, and macro-structure of a huge range of complex materials, often under processing or end-use conditions and in real time. This capability lends itself to an equally wide range of industrial R&D problems which, in particular, have been adopted by the healthcare industry. Beyond drug discovery and development, the ESRF is also very active in providing analysis for micro- and nano-electronics, energy and smart materials, transport, chemistry and catalysis, engineering materials, and home and body care amongst others. In Europe and worldwide, funding agencies are requesting and demanding a stronger economic return from the significant public investments made in central facilities and this is resulting a gradual but firm pressure for stronger interactions with industry. In this context, new business models are springing to life, with more partnerships, more services, and nimble small start-ups bridging the gap between the oft "ivory tower" nature of research infrastructure and the commercially driven industry world. This presentation will present and discuss the increasingly critical role of such large-scale facilities in delivering ultimate materials characterization for innovative industrial and applied R&D, looking to both the current developments and future possibilities as well as review several examples of partnerships between research and industry and the impact these partnerships have on academic research.
Structural studies of Legionella effectors
Authors: Wong Kathy , Zhang Yinglu , Kozlov Guennadi , Gehring Kalle
Published: November 2015

Legionella pneumophila is a gram-negative bacterium that causes Legionnaires' disease. It uses a Dot/Icm type IV secretion system to inject effector proteins into the host cell to manipulate host processes. Currently, about 300 Icm/Dot dependent effectors of L.pneumophila have been identified. Lpg1496 is an effector protein, which contains a conserved domain from the SidE family. To date, the middle domain and the conserved SidE domain have been crystallized and the structure solved at a resolution of 1.15Å and 2.3Å, respectively. A structural homology search using the middle domain suggested a similarity to phosphoribosylaminoimidazolesuccinocarboxamide (SAICAR) synthase, an ATPase involved in purine nucleotide synthesis. We performed 1H–15N HSQC NMR titrations to show that this domain binds ATP, ADP and AMP, with the highest binding affinity for ADP. A structural homology search using the SidE domain showed a similarity to cyclic nucleotide phosphodiesterases. To further elucidate the function of lpg1496, other fragments have been cloned, expressed, and subjected to crystallization trials. Currently, we have successfully crystallized the N-terminal domain, with crystals diffracting to <2.0Å. Obtaining the crystal structure of lpg1496 and revealing its function will not only lead to a better understanding of the virulence of L. pneumophila, but also contribute to the development of novel therapeutic treatments of Legionnaires' disease.
Insights on small-molecules inhibitors and protein-protein interactions of the T4SS
Authors: Um Nlend Ingrid , Baron Christian
Published: November 2015

ABSTRACT: Bacterial T4SS are complexes, constituted of 8 to 12 conserved proteins, used by many gram-negative bacteria for the translocation of proteins and DNA-protein complexes as well as for the transportation of DNA-protein complexes across their cell envelope. T4SS are excellent model targets for the development of antivirulence drugs as it is an essential virulence factor for many bacterial pathogens, such as Brucella. Antivirulence drugs that deprive the pathogen of its essential virulence factor, the T4SS, would constitute alternatives to or enhancements of current antibiotic treatment. VirB8, a conserved assembly factor in T4SS forms dimers that are very important for T4SS function in these pathogens. Due to its multiple interactions, VirB8 is an excellent model for the analysis of assembly factors but also a possible target for drugs that could target its protein–protein interactions, which would disarm bacteria by depriving them of their essential virulence functions.
Central spike proteins of contractile ejection systems
Authors: Shneider Mikhail , Buth Sergey , Ho Brian , Basler Marek , Mekalanos John , Leiman Petr
Published: November 2015

Contractile tails of bacteriophages and related systems - R-type pyocins, the Serratia entomophila antifeeding prophage, the Photorhabdus Virulence Cassette, and the Type VI Secretion System (T6SS) - contain a special spike-shaped protein complex, which is involved in breaching the target cell envelope during infection. We have identified the genes and determined crystal structures for several spike proteins from phages, pyocins, and T6SS, and established a paradigm for their organization and function. The architecture of spike proteins is remarkably well conserved at the level of tertiary structure, but the corresponding genes and amino acid sequences have undergone huge rearrangements with domains becoming separate genes that are very far away from each other in the genome. Large bacteriophages and T6SS have the most complex spikes, in which the tip is a small protein that forms a very sharp conical extension on the spike. The membrane-attacking tip is stabilized by a buried Fe or Zn ion. The spike tip proteins belong to the PAAR (Proline-Alanine-Alanine-aRginine) repeat domain superfamily with several thousand members in the GenBank. PAAR repeat proteins from T6SS are often extended by a domain with a putative effector function (nuclease, DNases, peptidases, etc.) or by a transthyretin domain. PAAR knockout mutants of Vibrio cholerae and Acinetobacter baylyi have either reduced or completely abolished T6SS activity, showing that PAAR proteins are essential for T6SS function and can play an important role in building of the T6SS machine and/or target cell membrane piercing. The unique HMM profile of PAAR repeat proteins makes it possible to identify their orthologs in all T6SS and contractile tail phages including T4, phiKZ, P1, etc. Complete structures (including the tip protein) of phage T4 central spike and T6SS spike of Vibrio cholerae will be presented and discussed.
The role of BamA in the biogenesis of beta-barrel membrane proteins
Authors: Noinaj Nicholas , Kuszak Adam , Balusek Curtis , Gumbart JC , Lukacik Petra , Chang Hoshing , Easley Nicole , Lithgow Trevor , Buchanan Susan
Published: November 2015

Beta-barrel membrane proteins are essential for nutrient import, signaling, motility, and survival. In Gram-negative bacteria, the beta-barrel assembly machinery (BAM) complex is responsible for the biogenesis of beta-barrel outer membrane proteins (OMPs), with homologous complexes found in mitochondria and chloroplasts. Despite their essential roles, exactly how these OMPs are formed remains unknown. The BAM complex consists of a central and essential component called BamA (an OMP itself) and four lipoproteins called BamB-E. While the structure of the lipoproteins have been reported, the structure of full length BamA has been elusive. Recently though, we described the structure of BamA from two species of bacteria: Neisseria gonorrhoeae and Haemophilus ducreyi. BamA consists of a large periplasmic domain attached to a 16-strand transmembrane beta-barrel domain. Together, our crystal structures and molecule dynamics (MD) simulations revealed several structural features which gave clues to the mechanism by which BamA catalyzes beta-barrel assembly. The first is that the interior cavity is accessible in one BamA structure and conformationally closed in the other. Second, an exterior rim of the beta-barrel has a distinctly narrowed hydrophobic surface, locally destabilizing the outer membrane. Third, the beta-barrel can undergo lateral opening, suggesting a route from the interior cavity in BamA into the outer membrane. And fourth, a surface exposed exit pore positioned above the lateral opening site which may play a role in the biogenesis of extracellular loops. In this presentation, the crystal structures and MD simulations of BamA will be presented along with our work looking at the role of these four structural features in the role of BamA within the BAM complex.
Multiple approaches towards understanding the type II secretion system
Authors: Lu Connie , Park Young-un , Korotkov Konstantin , Mi Wei , Turley Stewart , Bhatt Veer , Shah Ripal , Hol Wim
Published: November 2015

Transport of folded proteins across membranes is a feat accomplished by few biomacromolecular machines. One of the machineries able to do so is the sophisticated type II secretion system (T2SS). It can translocate key virulence factors from the bacterial periplasm into the lumen of the gut of the human host. A prime example is the secretion of cholera toxin by Vibrio cholerae. The T2SS consists of ~12 different proteins, most of these present in multiple copies, organized into three subassemblies: (i) the Inner Membrane Platform; (ii) the Pseudopilus in the periplasm, which acts most likely as a piston pushing exoproteins through the outer membrane pore; (iii) the Outer Membrane Complex, allowing passage of ~100 kDa folded proteins. We have determined crystal structures from more than a dozen T2SS domains, yet, a full understanding of the architecture and mechanism of action of the T2SS remains a formidable challenge. Our approaches include the use of "assistant-multimers" to promote recalcitrant multimer formation and of nanobodies to overcome reluctant crystal formation. The Inner Membrane Platform is interacting with the secretion ATPase GspE which most likely needs to be hexameric for full activity. Full-length GspE co-crystallized with its major partner, the cytoplasmic domain of GspL, revealed a tremendous flexibility of this ATPase, and, most unexpectedly, also the organization of the same linear arrangement of cyto-GspL domains throughout three entirely different crystal forms. Two very different hexamers of GspE were elucidated by linking the GspE subunit to the subunit of Hcp1, which successfully acted as an "assistant hexamer", inducing hexamer formation by GspE. The dodecameric nature of the ~ 850 kDa GspD, the major component of the Outer Membrane Complex, evident in earlier electron microscopy studies, was observed in the dodecameric ring-like helix in crystals of its N-terminal domain. The contacts between GspD and the inner-membrane protein GspC will be discussed as well as the remarkably frequent occurrence of dimers of Inner Membrane Platform domains. How dimers are co-assembled with an ATPase hexamer with C6 symmetry and the Outer Membrane Complex dodecamer with C12 symmetry remains one of the many fascinating outstanding questions of the T2SS.
A reshaped approach for protein nanocrystal structure analysis from XFELs
Authors: Williams Sophie , Dilanian Ruben , Martin Andrew , Streltsov Victor , Quiney Harry
Published: November 2015

The size and quality of protein crystals are critical limiting factors in conventional X-ray crystallography structural studies. Serial femtosecond X-ray crystallography (SFX) presents new opportunities through the use of submicron and nano-scale crystal samples. SFX experiments with X-ray free-electron lasers have demonstrated success (Chapman, 2011). While new instances are arising for the study of poorly crystallizing proteins, fresh examination must also be made of their analysis. Significantly, the smallness of the crystal samples creates broad integrated intensity distributions that require careful consideration for the accurate reconstruction of high-resolution protein crystal structures. Structural imperfections are also expected to play significant roles in the formation of SFX diffraction patterns (Dilanian, 2013). We present preliminary results from a new approach for SFX data analysis. As motivation, it is observed that significant similarities lie between merged SFX data-sets and powder diffraction patterns. The merged Bragg peak-shape distributions in SFX diffraction patterns are characterised by the shape, size and disorder distributions of the large crystal sample set. Powder diffraction peak-shape distributions are formed similarly by a collection of independent scatterers of such varying characteristics. The presented method utilizes an established powder diffraction analysis tool, the Le Bail method (Le Bail, 1988), for extension and application to SFX data. It is shown here that the continuous whole-pattern fitting technique, combined with variable peak-shape functions, can be used to closely model simulated SFX patterns and to extract integrated intensities. The presented approach is posed as a new analysis method for SFX experiments in which both crystal size and structural disorder variations can be incorporated.
Improving the accuracy for Photosystem II and other XFEL structures
Authors: Sauter Nicholas , Brewster Aaron , Hattne Johan , Amin Muhamed , Kern Jan , Yano Junko , Yachandra Vittal
Published: November 2015

Femtosecond-scale XFEL pulses can produce diffraction free from radiation damage, under functional physiological conditions where reaction dynamics can be studied for systems such as photosystem II. However, it has been extremely difficult to derive accurate structure factors from the data since every shot is a still exposure from a distinct specimen. Accuracy can be improved by software methods implemented in the program cctbx.xfel, including optimal indexing and retention of data from multiple lattices, and separate determination of the resolution cutoff for individual lattices. Various techniques can produce well-conforming descriptions of the Bragg spot shape and crystal mosaicity, enabled in part by sub-pixel characterization of the detector geometry. By carefully discriminating between image pixels known to contain diffraction signal and the surrounding pixels containing only background noise, and by extending postrefinement techniques that lead to a better crystal orientation, we derive accurate structure factors with substantially fewer crystal specimen exposures. It is hoped that these developments will make it easier to measure small structure factor differences, such as those from anomalous scattering that will enable the de novo determination of macromolecular structure.
Serial femtosecond X-ray diffraction of in vivo crystals in intact yeast cells
Authors: Passon Daniel , Jakobi Arjen , Stellato Francesco , Liang Mengning , Knoops Kevin , Komadina Dana , Williams Chris , White Thomas , Bourenkov Gleb , Messerschmidt Marc , van der Klei Ida , Chapman Henry , Wilmanns Matthias
Published: November 2015

Peroxisomes are membrane-enclosed organelles in eukaryotic cells with important roles in lipid metabolism and the scavenging of reactive oxygen species. Peroxisomes are capable of carrying an unusually high load of proteins, which under appropriate nutrient conditions results in the in situ crystallization of peroxisomal proteins in several yeast species and vertebrate hepatocytes [1,2]. In the methylotrophic yeast H.polymorpha, the predominant peroxisomal protein alcohol/methanol oxidase (AO) oligomerizes into octameric assemblies with a molecular mass of 600 kDa that spontaneously form 200-500 nm crystallites within peroxisomes [1]. We exposed H.polymorpha cell suspensions containing peroxisome-confined AO crystallites to femtosecond X-ray pulses at the Coherent X-ray Imaging (CXI) experimental endstation at the Linac Coherent Light Source. Peak detection routines mining the resulting scattering profiles identified >5000 Bragg-sampled diffraction patterns, providing the proof of concept that background scattering from the cells does not deteriorate the signal-to-noise ratio to an extent precluding observation of diffraction from individual AO crystallites. Summation patterns assembled from the individual frames match low-resolution powder diffraction patterns from concentrated suspensions of purified peroxisomes collected at the P14 beamline at the PETRAIII synchrotron, confirming that the observed diffraction mainly results from Bragg scattering of peroxisomal crystallites. To the best of our knowledge our data are the first to report room temperature X-ray diffraction from functional protein crystals in their native cellular environment. Currently the maximum resolution achieved in the diffraction patterns is limited to 20-15 Å. Future work will need to address improved sample preparation protocols in order to assess whether diffraction to a resolution sufficient to permit structure solution can be obtained. Protein crystal formation in vivo has been observed under physiological or pathological conditions in a number of other systems [3]. We hope that our results will help to establish serial femtosecond X-ray diffraction (SFX) as a method for structural characterization of cellular structures with crystalline content and provide a proof of concept for using in situ crystallization of proteins as a means to generate nanocrystalline samples for SFX.
Crystal structure of rhodopsin bound to arrestin by femtosecond X-ray laser
Authors: Xu H. Eric
Published: November 2015

G protein-coupled receptors (GPCRs) signal primarily through G proteins or arrestins. Arrestin binding to GPCRs blocks G protein interaction and redirects signaling to numerous G protein-independent pathways. One structure of a GPCR bound to a G protein was solved, but the structure of a GPCR-arrestin complex has remained unknown despite its central role in GPCR biology. Here we report the crystal structure of a constitutively active form of human rhodopsin bound to a pre-activated form of the mouse visual arrestin, determined by serial femtosecond X-ray laser crystallography. The structure reveals that arrestin binding induces large and unexpected conformational changes at both the extracellular and intracellular sides of rhodopsin. Arrestin also undergoes dramatic rearrangements from its inactive well-ordered β-sheet structure into a more flexible molten globule-type state, allowing a snake-like movement of the first 77 arrestin residues that shortens its central crest finger loop by seven residues to accommodate the concave surface of rhodopsin. This structure provides a basis for understanding GPCR-mediated arrestin-biased signaling, reveals a new paradigm of signal transduction by a molten globule, and demonstrates the extraordinary power of X-ray lasers for advancing the frontiers of structural biology.
Studies of NH--N Hydrogen Bond Chains in Imidazoles by Neutron Diffraction
Authors: Williams Ian , Zhou Yan , Zhang Yuxin , Sung Herman , Edwards Alison
Published: November 2015

Crystals of imidazole compounds typically organize themselves with NH---N hydrogen bonded 1D chains in the absence of other hydrogen bond donor or acceptor groups. The 'synthon' is robust, but can vary considerably in length, which is related to the pKa and the linearity of the hydrogen bond. For symmetric imidazoles with effectively perfect pKa matching of the two N atoms, this implies that many crystals may exhibit statistical disorder of the hydrogen positions. However X-ray studies alone cannot readily distinguish the true extent of this, since unlike carboxylic acid analogues, even fully ordered systems show little difference in the N(1)-C(2) and N(3)=C(2) bond lengths of the imidazole ring. Despite their fundamental nature, surprisingly few neutron studies have been carried out on such NH---N systems and only the parent compound imidazole itself has been examined in depth.[1,2] Herein we report the extension of this to a range of other imidazoles and benzimidazoles. In particular 2-methylbenzimidazole [3] and 2-ethylbenzimidazole are ideal candidates to allow study of bent and linear, ordered and disordered hydrogen bond chains in this family of compounds. Neutron data were collected at low temperature on these and other compounds, using specimens of around cubic 1mm on KOALA Laue neutron diffractometer at the Bragg Institute, Australia. The results support the general findings of related single crystal X-ray studies. However the N-H positions are obtained with good accuracy and correlations of covalent N-H to intermolecular H--N can be made. They also confirm that essentially full ordering of hydrogen bond chains in crystals such as 2-Ethylbenzimidazole (shown in Figure) is possible, with only a single 'negative peak' for the proton position found along the N---N vector. This may have positive implications for the development of such crystals as molecular ferroelectrics. The authors are grateful for an award of beam-time by ANSTO (Proposal 2765).
'Uncertainty' region of acid-base ΔpKa: Salt versus co-crystal formation
Authors: Ramon Gaelle , Davies Kate , Nassimbeni Luigi
Published: November 2015

The hydrogen bond is a very important interaction which demonstrates a wide variety in strength and shape and can be held as the central point in the crystal engineering process of a great number of compounds. In the formation of salts versus co-crystals, pH control is necessary in order to obtain one form or the other. In the pharmaceutical industry which is actively developing Active Pharmaceutical Ingredients (APIs) with desirable properties, such consideration is of major concern. In 2012, Cruz-Cabeza[1] carried out a survey of over 6 000 structures and found a linear relationship between ΔpKa and the probability of proton transfer for the pKa range of -1 to +4. The cross-over point was determined to be at ΔpKa = 1.3. Beyond this point the probability to obtain a salt rather than a co-crystal is higher than 50%. Parallel to this work, Gilli & Gilli[2] have built a sliding rule which predicts the strength of a Donor – Acceptor hydrogen bond based on the ΔpKa of the system. Their device predicts the formation of salts if ΔpKa > 3, and co-crystals when ΔpKa < -3. In their paper, Gilli & Gilli point out that the interval of ΔpKa matching should be shifted by 1.5 units when interpreting crystal structures,[3] which agrees with the findings of Cruz-Cabeza. In this work we discuss the bonding of 22 structures made up of acid-base pairs which either form salts or co-crystals. A series of five substituted benzoic acids with 10 substituted pyridines and quinolines have been crystallized so that their ΔpKa, defined as pKa(base) – pKa(acid), spans the range -1.14 to +4.16. This covers the `uncertainty' region for the formation of salt versus co-crystals. Although most of our results confirmed that structure formation of co-crystal versus salt parts at ΔpKa ≍ 2, we report here a structure that does not follow the general rule and serves as a cautionary tale.
Decoding conformational polymorphism in organic substances
Authors: Orlando Ahmed , Loconte Laura , Ortoleva Emanuele , Gatti Carlo , Lo Presti Leonardo
Published: November 2015

Different polymorphs have different intensive physical properties and it is still impossible to predict from scratch if a change in the crystallization conditions will result in different crystal structures or not. In this contribution, possible correlations are highlighted among charge density features, molecular conformation and interaction energetics in the two known polymorphic forms of (DTC)[1,2], an isothiazole β-sultamic derivative. A tentative rationale is provided for the relative stability of the two forms on the basis of their different self-recognition patterns. Both polymorphs crystallize in the same P21/n space group and show very different non-covalent networks of weak C-H–X (X = N,O,π) interactions due to the dissimilar conformation of the asymmetric units (ASU). Accurate multi-temperature (100 K ≤ T ≤ 298 K) single-crystal X-Ray diffraction experiments were carried out and the evolution of crystal packing and self-recognition energetics were monitored through periodic quantum-mechanical calculations at fixed geometries. Preliminary results show that dispersive/repulsive and electrostatic non-covalent interactions dominate the crystal packing in both polymorphs. At T=100 K the form A have a tighter packing, as it shows a greater propensity in being involved in H bonds than B (see the Hirshfeld surface fingerprint plots[3] of forms A -left- and B -right- here reported). This reflects in greater density, whereas the estimated DFT cohesive energies of the two forms are similar. DTC has enough molecular flexibility to access various favourable arrangements during the nucleation, as the interconversion between the A and B conformers in the gas phase takes place with a very small activation energy. The possible role of the solvent in favouring either of the two observed conformations is discussed.
Structural Study of Ferroelectric Phase in Acid–Base Supramolecule
Authors: Nakao Akiko , Kumai Reiji , Horiuchi Sachio , Tokura Yoshinori , Ohhara Takashi , Hanashima Takayasu , Munakata Koji , Kiyanagi Ryoji , Kawasaki Takuro , Oikawa Kenichi , Kaneko Koji , Mamura Itaru
Published: November 2015

Supramolecular ferroelectric cocrystal of phenazine (Phz) with chloranilic acid (H2ca), which exhibits three successive phase transitions, have been characterized by the interplay between their structural transformations and solid-state acid–base (proton transfer) reactions (Figure) [1]. This material undergoes a ferroelectric phase (FE-I phase) transition of displacive-type at 253 K followed by successive phase transitions to the lattice modulated phases with incommensurate periodicities and with commensurate 2-fold periodicity (FE-II phase) at lower temperature [2]. To elucidate the origin of the ferroelectricity in the FE-I phase, it is crucial to study the crystal structure using single crystals. The synchrotron x-ray diffraction experiment was carried out on the imaging-plate diffractometer at BL-8A of Photon Factory in KEK. Superstructure reflections with the modulation wave vector q=(1/2 1/2 1/2) were clearly observed below 103 K. Considering the preserved 2/m Laue symmetry, the lattice can be transformed to a C-centered monoclinic lattice, which is related by (-2a, -2b, a + c) or (2a, -2b, -a - c) with the FE-I structure. Although the lattice distortion and the intensities of the superlattice reflections are consistent with the 2/m Laue symmetry, the space group C1 is deduced from the polar nature and a subgroup symmetry of the FE-I structure. Moreover, we performed single-crystal neutron diffraction experiments at SENJU of MLF/J-PARC in order to determine the displacement of the hydrogen atom. The crystal structure analysis at 10 K was carried out using the reflections measured in a half-sphere of reciprocal space at d > 0.4. The structure analysis was performed on the basis of the space group C1, where four Phz and four H2ca become crystallographically inequivalent. Finally, all the structural parameters including all hydrogen atoms were successfully refined. In the FE-II phase, the neutral and ionic molecules alternately align along the π-molecular stack.
Crystal structures of di- and tri-hydrochlorides of 1,4,7-triazaheptane
Authors: Watanabe Kiyotaka , Hihara Goro , Miyamae Hiroshi
Published: November 2015

Four protonated 1,4,8,11-tetraazacyclotetradecane has been characterized as nitrates to show expanded ring structure due to charge repulsion[1]. However, linier polyamine, 1,4,7-triazaheptane (diethylentriamine=dien) gave di-hydrochloride(1) and tri-hydrochloride(2) and their single crystal structures were examined. In the compound 1, the terminal N atoms are protonated as expected but the dien takes U-shaped conformation with forming double H-bond to a Cl- ion at the terminals and the central nitrogen forms another H-bond to the other Cl- ion, as shown in the figure. The dien takes linear conformation in the compound 2 as expected.
Towards continuous crystallisation of layered and disordered solid forms
Authors: Klapwijk Anneke , Thomas Lynne , Wilson Chick
Published: November 2015

Crystallisation is a vital step in the manufacture of many pharmaceuticals and fine chemicals, producing solids in a form ideal for downstream processes. Unlike others, these industries have not kept pace with advances in continuous production and for centuries industrial crystallisation has operated as a batch process, relying heavily on stirred tank reactors which bring batch to batch variations and limited control over particle attributes. Continuous crystallisation can offer improved product quality, less waste and access to new products more efficiently. One such particle attribute is the presence of molecular disorder in crystalline materials where different ratios of disordered components may show different physical properties [1]. However, disorder can be difficult to control and characterise so has not to date been widely exploited for achieving optimised properties. Multi-component crystallisation can be used to encourage orientational disorder and layering within the crystal lattice by appropriate choice of co-former and by utilising the principles of crystal engineering. The research being presented aims to systematically study disordered and layered materials. Systems that exhibit these characteristics will be discussed structurally, together with results from transferring production of these materials from evaporative to cooling crystallisation, frequently a key first step in achieving crystallisation in a continuous flow environment. In addition, the structural attributes of the particles produced will be correlated with different physical properties such as solubility and compressibility [2].
Pharmaceutical Drug Polymorphism: A Case Study of Three Novel Drugs
Authors: Kant Rajni
Published: November 2015

Polymorphism is more widespread in pharmaceutical solids, with estimates of 30-50% in drug-like molecules, compared to 4-5% polymorphic crystals in the Cambridge Structural Database (Nangia, 2007). Most of the drug molecules are formulated and marketed in crystalline form and many of these are highly functionalized and can self-organize in several ways in the solid state with nearly the same lattice energies. Though a lot of work is going on in the field of pharmaceutical drug polymorphism and its possible application in the field of crystal engineering, yet there are difficulties in getting polymorphs of many important molecules. The present work deals with a comparative crystallographic study on the existing polymorphic forms of three medicinally important molecules, Aspirin, Paracetamol and Norfloxacin which are known to have a wide spectrum of medicinal activities. Broadly, the present study accounts for the following observations: (i) Choice of the solvent system, its purity and its reaction mechanism with solute under ideal condition of growth/crystallization. (ii) The interaction of grown material with X-rays should be very healthy in the sense that maximum number of planes in a given crystal should diffract the incoming X-ray beam. This aspect is once again related to quality single crystal growth. Fairly good interaction of a compound with X-rays leads to better refined structure, yielding a very high level of confidence between the chemical and computed structure. (iii) Analysis of a molecule's ability to exhibit biological activities by employing some suitable empirical and clinical modes. (iv) Most of physical properties of a grown material depend on how the molecules have been packed in the unit cell and how the derived knowledge of intra and intermolecular interactions is applied for engineering a crystal of choice.
Affirmative polymorph generation of annulenes by using CH/O interactions
Authors: Hisaki Ichiro , Tohnai Norimitsu , Miyata Mikiji
Published: November 2015

CH/O interaction is recognized as a weak hydrogen bond with less directionality, compared with a strong hydrogen bond such as that between carboxylic acids. Therefore, the interaction does not seem to be suitable for precise design of crystal structures. In connection with this, however, we emphasized that the CH/O interaction, particularly that provided by methyl ester group, can utilize for affirmative generation of polymorphs of cyclic pi conjugated molecules. Since functionality of solid state materials based on pi conjugated molecules is crucially affected by their molecular arrangements, polymorphs are exactly appropriate systems to reveal the superstructure-dependent properties of such the materials, and therefore, affirmative preparation of polymorphs of pi conjugated molecules is challenging. Herein, we describe formation, crystallographic characterization, and superstructure-dependent properties of polymorphs of methyl ester functionalized dehydrobenzoannulenes (DBAs), a family of cyclic conjugated molecules consisted of benzene rings and acetylene units. We synthesized five DBA derivatives 1-5 with two types of annulene cores (octadehydrodibenzo[12]annulene and octadehydrotribenzo[14]annulene cores) and different number and position of methyl ester groups (Scheme1). These derivatives exhibit two to five polymorphic crystals with physical properties strongly depending with their supramolecular structures.[1-3] We believe that the present polymorph generation is exactly provided by rotationally flexible conformations of the ester groups and versatile ways of directionally tolerant CH/O interactions of the ester groups.
Specific energy contributions associated with competing hydrogen bond motifs
Authors: Gelbrich Thomas , Griesser Ulrich
Published: November 2015

The semi-classical density sums (SCDS-Pixel) method [1] was used to study the intermolecular interaction energies in six polymorphs of phenobarbital, a model system for the barbiturate class of compounds.[2] Barbiturates display a rigid pyrimidinetrione ring whose two N–H and three C=O functions can be employed in H-bonding. The ensuing intermolecular N–H···O=C interactions result in a small set of standard H-bonded chain, layer and framework motifs.[3] Even though the average number of N–H···O=C bonds per molecule is always two, the standard barbiturate H-bond motifs differ in the number of intermolecular two-point and one-point N–H···O=C connections per molecule, i.e. (1; 0), (½; 1), (0; 2). For each polymorph (I, II, III, V, VI, X), cumulated Pixel energies, E(n), were calculated for the first n (n = 1, 2, 3, ...) interactions associated with the highest individual contributions to the lattice energy. The obtained sets of E(n) values were compared to one another to establish the differences associated with the formation of the alternate N–H···O=C motifs. Those polymorphs whose N–H···O bonded structures are dominated by two-point connections have superior E(n) values for small clusters of molecules (low n). However, this advantage diminishes gradually if larger clusters of molecules are considered and is completely compensated at n = 8. This indicates that crystal packing on the basis of one-point connection N–H···O=C motifs is viable only because the latter enable the formation of more advantageous weaker interactions which are dominated by dispersion forces. This case illustrates that an assessment of competing H-bond motifs cannot be restricted to just those molecules that are directly involved in H-bond interactions. Rather, the complete crystal packing has to be taken into account. [Figure: Evolution of the difference between E(n) (form V; one-point connections) and E(n)' (form III; two-point connections) with n].
Crystal structure and hydrogen bonded network of new cadmium hybrid complex
Authors: Bouchene Rafika , Bouacida Sofiane
Published: November 2015

Cadmium complexes exhibit extensive potential applications in many fields, such as magnetism materials, biological active materials, optical device and catalysis materials [1]. The reported compound [Tetrakis(5-amino-3-carboxy-1H-1,2,4-triazol-4-ium) hexachloridocadmate (II) tetrahydrate (1) ] was prepared as part of our ongoing investigations of hydrogen-bonding interactions in the crystal structures of metal-protonated N-aromatic heterocyclic hybrid frameworks [2]. 5-Amino-1H-1,2,4-triazole-3-carboxylic acid arises as a promising ligand which can be employed in the preparation of coordination compounds as a consequence of its multiple buildings sites and its basic nitrogen capable of associating with a proton H+ in acid solution [3]. The single-crystal X-ray structure analysis revealed that (1) crystallizes in the monoclinic P-1 space group, the Cd(II) atom is located at a crystallographic inversion centre. The latter ion is octahedrally coordinated by six chloride anions, Due to the presence of a considerable number of proton donors and acceptors, the crystal structure is rich in hydrogen bonding interactions which led to the formation of discrete cation layers spaced by hexachloridocadmate anions. Examination of the cation-anion interactions reveals that N–H...Cl hydrogen bonding are the major packing interactions, It appears that the layered structure results from the octahedral [CdCl6]2- anions along with its ability to form hydrogen bonds in different directions, intermolecular hydrogen bonding interactions between the chloride atom and oxygen atoms of water molecules interconnect the layers into a three-dimensional framework.
Hydrogen bonding in melamine compounds of amino acids
Authors: Ghouari Nasreddine , Benali-Cherif Nourreedine
Published: November 2015

The theme of this work is part of the study of intermolecular interactions that hold the crystal structures of hybrid compounds based sulphuric acid, nitric acid, Melamine, Diethylamine, L-(+) - glutamic acid, DL-2-amino butyric acid. The aim of this work is to enlarge our laboratory researches [1-3] and methods in synthesis of new hybrid compounds consisting in organic cation(s) and mineral anion(s). We have obtained single crystals of a few samples after several trials and we plan to synthesize and characterize these crystals by X-ray diffraction, FTIR and Raman. The crystals structures allow us to study the 3D network hydrogen bonding, electron density and collect several other informations useful in FTIR and Raman studies of these hybrid compounds.
Order as revealed by coherent diffraction
Authors: Ravy Sylvain
Published: November 2015

We are generally taught that a crystal is disordered if its diffraction pattern consists in Bragg reflections and diffuse scattering. However, more insight in the diffraction theory shows that a crystal can be perfectly ordered and still exhibit diffuse scattering. This is the case of the Rudin-Shapiro sequence, whose pair correlation function is similar to a random sequence one. In this paper, we show that this is true only for the infinite sequence. Indeed, finite crystals exhibit speckles patterns which can be measured by coherent diffraction. With the help of the Rudin-Shapiro sequence, we demonstrate that the intensity distribution of such patterns contains information on high order correlation functions, which are irrelevant in infinite crystal diffuse scattering pattern. This surprising result indicates that the concept of order should be revisited in the light of coherent beams.
Magnetic Option in Jana2006: A Unified Approach by Shubnikov (Super)space Groups
Authors: Petricek Vaclav , Dusek Michal
Published: November 2015

The concept of Shubnikov (magnetic) symmetry becomes frequently used for description, solution and refinement of magnetic structures. Its growing importance is connected with the ease of application to various classes of magnetic structures having the translation periodicity identical, commensurate or incommensurate with the nuclear one. Recently generalized superspace approach [1] for incommensurately modulated magnetic structures allows for combination of nuclear and magnetic modulations. This unified description helps fully understand e.g. multiferroic phases. The program Jana2006 (http://jana.fzu.cz) combines the concept of Shubnikov (super)space groups with the representational analysis based on the decomposition of the magnetic configuration space into basis modes, which transform according to different physically irreducible representations (irreps) of the space group of the paramagnetic phase [2]. Moreover, Jana2006 can launch the recently developed program ISODISTORT [3] to obtain similar but more general analysis. The generalized symmetry concept facilitates data processing where symmetry related reflections for single crystal data can be merged and the list of generated reflections for powder data can be reduced to independent ones. Another benefit concerns calculation of magnetic structure factors, stability of refinement and logical way to describe twin domains. Unlike in the Fullproff program [6], Jana2006 can combine the nuclear and magnetic scattering internally without necessity to introduce two phases. It can also calculate magnetic structures with modulated parent phase where the modulation appears before the magnetic phase transition. The lecture shows manifold possibilities how to refine modulated magnetic structures from various experiments. Several recently solved magnetic structures will be presented.
Superspace symmetry and phenomenology of incommensurate type-II multiferroics
Authors: Ribeiro J. L.
Published: November 2015

The recent upsurge of research work on multiferroic materials has made clear the need for a comprehensive knowledge of the constraints imposed by symmetry on the magnetic structure and tensor properties of incommensurate magnetic phases. That knowledge can be provided by the magnetic superspace formalism in a simple and robust manner. In this communication I will briefly review some of the basic concepts of this formalism pertaining to magnetic systems. Several practical examples will be given in order to illustrate how the assignment of a magnetic superspace group to a given phase is, in general , more restrictive and wide-ranging than the simple assignment of the order parameter irreducible representation. The direct connection between symmetry and phenomenology, which naturally arises via Landau theory, will then be used in order to illustrate how several complex phase diagrams of type-II magneto-electric multiferroics can be interpreted, and how the magnetically induced ferroelectric states can be anticipated on the basis of general symmetry considerations.
The atomic structure of defects in graphene
Authors: Warner Jamie , Robertson Alex
Published: November 2015

Defects in graphene influence its electronic, magnetic, chemical and mechanical properties. It is therefore important to have a detailed understanding of their exact atomic structure in order to accurately predict their behaviour. In this talk I will present a summary of research on resolving the atomic structure of vacancy defects in graphene, single atom dopants covalently bonded in the lattice, and their transition dynamics. By using aberration-corrected transmission electron microscopy, combined with monochromation of the electron source to reduce chromatic aberration effects, sub-Angstrom spatial resolution at a low accelerating voltage of 80 kV is achieved. Methods have been developed to introduce defects into the lattice of graphene with 10 nm spatial accuracy within the electron microscope using a controlled focussed beam. This enables the study of defect structures with unprecedented clarity and accuracy whilst in a low-pressure vacuum environment. Atomic models determined from TEM imaging are compared with DFT calculated atomic models to gain deeper insights into the C-C bond lengths and the relationship between electronic charge density distribution and bond lengths.
Crystallographic studies through HRTEM and XRD of MoS2nanostructures
Authors: Rivera-Muñoz Eric , Huirache-Acuña Rafael , Millán-Malo Beatriz , Nava Rufino , Pawelec Barbara , Loricera Cristina
Published: November 2015

Mesoporous and silica-based SBA-15 and SBA-16 materials were used as supports of novel nanostructured ternary Co(Ni)-Mo-W hydrodesulphurization (HDS) catalysts. These materials have shown a high catalytic activity in HDS of dibenzothiophene (DBT) reactions, even much higher compared with commercial catalysts. An exploration was made on the structure of both the supports as well as on tri-metallic sulfide HDS catalysts. The sulfided catalysts were tested in the HDS of DBT performed in a batch reactor at 623 K and total pressure of 3.1 MPa. The calcined and fresh sulfide catalysts were characterized by a variety of techniques, such as N2 adsorption-desorption isotherms, Temperature-Programmed Desorption (TPD) of NH3, X-ray Diffraction (XRD) and High Resolution Transmission Electron Microscopy (HRTEM). It has been found that both the morphology of the supports as its modification with varying amounts of phosphorus affect the catalytic activity of these nanostructured materials in HDS of DBT reactions. Furthermore, the nanostructures which correspond to the tri-metallic sulfided catalysts exhibit a typical morphology of MoS2 – 2H structure. The present work shows the microstructural study of these nanostructured materials, carried out from HRTEM images and XRD analysis. Both techniques, X–ray Diffractometry and High Resolution Transmission Electron Microscopy, play a fundamental role in the characterization of the microstructure of HDS catalytic nanomaterials, as well as in understanding the various phenomena involved, starting from the synthesis process unto the final performance of those materials.