bluuebunny/crossref_metadata_2025 huggingface dataset:
Crystallographic orbits analysis of staurolite twins
Authors: Marzouki Mohamed Amine , Souvignier Bernd , Nespolo Massimo
Published: November 2015

Staurolite is an enigmatic mineral characterized by a high degree of pseudo-symmetry, which frequently occurs twinned. It gives two twins with different occurrence frequency, the 90° or Greek cross (lower frequency) and the 60° or Saint Andrews cross (higher frequency). To date no explanation has been found for their different occurrence frequency. We have analyzed the structure of staurolite in terms of the pseudo-eigensymmetry of the crystallographic orbits building this structure [1]. The union of the crystallographic orbits based on oxygen atoms has a pseudo-cubic eigensymmetry which contains the twin operations of both twins: the operations restore, with good approximation, the whole set of oxygen atoms, which justifies the high frequency of twinning of this mineral but does not discriminate between the two twins. On the other hand, a subset of the tetrahedral cations has a pseudo-eigensymmetry which contains the twin operation of the Saint Andrews cross, but not that of the Greek cross. Also, a subset of the octahedral cations has a pseudo-eigensymmetry which contains the twin operation of the Greek cross and a larger subset has an eigensymmetry which contains the twin operation of the Saint Andrews. The substructure approximately restored by the twin operation is thus more extensive for the Saint Andrews cross, which justifies its higher occurrence frequency.
Investigating the annealing dependency of Al/Si distribution in Eifel sanidine
Authors: Kähn Johannes , Többens Daniel , Hoffmann Jens-Uwe , Reehuis Manfred , Schorr Susan
Published: November 2015

Sanidine is the monoclinic high-T modification of K-rich alkalifeldspars. Annealing at T > 9000C usually causes disordering of Al/Si distribution at the two non-equivalent tetrahedral sites, but it is supposedly possible to disorder samples of sanidine from Volkesfeld/Eifel at notably lower temperatures and shorter times [1]. To investigate this behavior and compare various approaches to obtain the Al/Si distribution, samples from different Eifel locations and Madagascar have been studied. Al/Si order was determined by direct and indirect methods, including X-ray and neutron diffraction of powder and single crystal samples. Neutron powder diffraction experiments were executed at the Fine Resolution Neutron Powder Diffractometer E9, single crystal neutron diffraction at the 4-circle Diffractometer E5 and diffuse neutron scattering experiments at the Flat-Cone Diffractometer E2, all located at the Berlin Research Reactor BERII. The Al/Si distribution was determined directly, refining site occupancies by applying Rietveld analysis to powder diffraction data and XTAL for single crystal data. This approach is inapplicable when using X-ray data, due to similar atomic form factors of Al3+ and Si4+, thus indirect methods [2,3,4] were applied. X-ray powder diffraction was performed at Helmholtz Centre Berlin, single crystal X-ray diffraction was done at Ruhr-University Bochum. The obtained data was processed using Rietveld refinement and ShelXL software, respectively. It was possible to verify a dependency of decreasing Al/Si order on increasing annealing times and temperatures. Interestingly we observed different results from direct and indirect methods, regardless whether samples were untreated or annealed. Applying the direct determination method, a stronger change of Al/Si distribution during annealing was revealed. Moreover, diffuse scattering of untreated and annealed samples was detected, which may arise from hydron incorporated in the crystal lattice.
Investigation of layered double hydroxides type ZnMgAl-carbonate and derivates.
Authors: do Carmo Weberton , de Carvalho Gustavo , da Silva Juliana , Chagas Luciano , Leitão Alexandre , Diniz Renata
Published: November 2015

Layered double hydroxides (LDHs) or hydrotalite-like compounds belong to a class of synthetic two-dimensional inorganic materials with lamellar structures, where the hydroxyl-hydrated compounds are formed by chemical substitution of divalent ion of the brucite-like octahedral layers by trivalent ions [1]. The LDH are represented by the general formula, Figure a , where M2+, M3+ are divalent and trivalent cation and Am- is interlayer anion responsible by charge balancing, the range of divalent and trivalent ions (x) varies normally between 0.17 a 0.33. According Montanari and co-works [2] compounds type ZnAl-hydrotalcites (ZnAl-HT) have relevant industrial interest; however the scientific literature concerning this material as catalysts or catalyst precursor is scarce. Based on this fact, in the present communication we will present a studied on how the variation in percentage of Zinc in a ZnMgAl-HT catalyst precursor can influence the formation of mixed oxides after calcination. The ZnMgAl-HTs, Figure b , y=5, 10,15,20,25,50,75 and 100% were prepared by co-precipitation and urea method. Mg-Zn/Al mixed oxides were prepared from calcinations of hydrotalcites precursors at 5000C for 4 hours. The material synthesized were characterized by X-ray powder diffraction, the measurements were carried out in Bruker D8 DaVinci diffractometer, equipped with CuKα radiation , LynxEye linear Position Sensitive Detector, Ni-filter. Data was collect between 8 and 800in 2θ with step size of 0.020and the count time of 0.05 per step. Soller slit 2.50of divergence and 0.2 mm primary slit were used. For the ZnMgAl-HT samples the measurements were performed at different temperatures, range 25-12000C, heating rate 50C/min. It was observed differences among XRD patterns for y greater than 25% of Zn in urea method at 5000C, and for co-precipitation method just for the substitution at 50 and 75% of Zn. These results suggested that the increase in Zn percentage change the structure of calcinated samples.
NMR crystallography, diffraction and modeling of small organic molecules
Authors: Monteiro Mafra Luís Miguel
Published: November 2015

Solid-state NMR (SSNMR) is a powerful atomic-level characterization technique able to study the local chemical environment of a nucleus in crystalline/amorphous solids. Toward a better understanding of how small molecules self-assemble in the solid-state and reorganizes to produce its hydrate/anhydrous forms, an experimental SSNMR, X-ray diffraction (XRD), and computational study of the supramolecular assemblies of selected small pharmaceuticals is presented. The effect of crystal packing on the 1H and 13C chemical shifts including nonconventional hydrogen bonds, pi···pi and CH···pi contacts, is studied through computer simulations. It will be shown that NMR chemical shifts are sensitive detectors of hydration/dehydration states in highly insoluble antibiotics.[1] Recently, SSNMR became an important gadget in the process of crystal structure solution in powders. This is a non-trivial task and using powder XRD methods alone may often lead to the wrong structure solution. In this talk, a new hybrid approach for structure determination of crystalline solids, will be presented, based on the combination of SSNMR, XRD and an ensemble of computational-assisted structure solution tools including a genetic algorithm based on evolution-inspired operators repeatedly applied to populations of possible crystal structure solutions that evolve to eventually produce the best new offspring candidates. Such methodologies are successfully applied to challenging cases involving multiple component crystals composed by flexible molecules such as a trihydrate β-lactamic antibiotic [2] and an azole-based co-crystal featuring an hydrogen bond network of α-helixes involving NH···N/CH···π intermolecular interactions. ACKNOLEDGEMENTS: Supported by Fundação para a Ciência e a Tecnologia (FCT), Portuguese National NMR Network (RNRMN), CICECO (PEst-C/CTM/LA0011/2013), FEDER, COMPETE, and University of Aveiro. FCT is greatly acknowledge for the consolidation grant IF/01401/2013.
PPM Detection Limits in PXRD by Integrating Nonlinear Optics and Synchrotron XRD
Authors: Toth Scott , Newman Justin , Schmitt Paul , Dettmar Christopher , Zhang Shijie , Taylor Lynne , Simpson Garth
Published: November 2015

SHG microscopy allows rapid and selective identification of trace chiral crystals within amorphous media, enabling targeted XRD using a 5-10 micrometer diameter "minibeam". The sensitivity of PXRD is increased substantially by reducing the background scattering contributions of amorphous material otherwise encountered with a larger beam. In addition, performing diffraction only at the locations most likely to produce diffraction greatly reduced the overall beam-time required to perform the PXRD analyses. Integration of the SHG microscope directly into a synchrotron X-ray beamline at Argonne National Laboratory recovered high spatial registry between the regions of interest identified by SHG for positioning within the X-ray beam. Using this approach, diffraction was performed on individual griseofulvin nanocrystals suspended within an amorphous polymer, corresponding to a total of ~20 fg of total crystalline material. Additional measurements for ritonavir in hydroxypropylmethylcellulose (HPMC) were also performed, in which a bulk API concentration of 100 ppm produced diffraction peaks with a signal to noise ratio of >3000. Among other applications, sensitive detection of trace crystallinity can inform the design of amorphous formulations, in which the bioavailability of active pharmaceutical ingredients (APIs) is enhanced by maintaining them in an amorphous state. However, the long-term stability of a final dosage form can be negatively impacted by spontaneous transitioning to the typically more stable crystalline forms of the APIs, such that extensive quantitative characterization of the crystallization behaviors of amorphous formulations is routinely performed.
Size dependences of transition temperatures of nanoparticles by SAXS and XRD
Authors: Kellermann Guinther , Craievich Aldo
Published: November 2015

SAXS technique alone and combined with XRD can be applied to determine the size dependences of crystal-to-liquid and liquid-to crystal transition temperatures of nanoparticles in dilute state. Since the volume of nanoparticles at the transition temperatures are expected to exhibit (weak) discontinuities, SAXS can be applied to determine the melting and freezing temperatures of nanoparticles as functions of their size. For this purpose, a set of samples, each of them with different nanoparticle size, is studied by in situ SAXS at varying temperatures. The variations in nanoparticle volume at the transitions lead to discontinuities in the 3D integral of SAXS intensity, ΔQ, in the slope of Guinier plots, ΔS, and in SAXS intensity at any q except at q=0, ΔI(q>0). Thus, the transition (melting and freezing) temperatures of a nearly monodisperse set of nanoparticles, can be derived from the discontinuities observed in the temperature dependence of V, S or I(q>0). Since the transition temperatures are strongly dependent on the size of the nanoparticles, for samples containing nanoparticles with a wide size distribution the size dependences of the melting and freezing temperatures cannot be determined by applying the method outlined above. However, in the particular case of systems consisting of a dilute set of spherical nanoparticles with a broad radius distribution, N(R), the combined use of SAXS and XRD makes it possible to determine the radius dependences of the melting and freezing temperatures, MT(R) and FT(R), respectively. This is achieved by studying a single sample in situ, along a heating/cooling cycle, and simultaneously determining the temperature dependences of the SAXS intensity pattern and the area of XRD Bragg peaks. A few applications of these procedures will be described, namely the determination of the radius dependences MT(R) and FT(R) of (i) a nearly monodisperse set of Pb nanoparticles embedded in a lead-borate glass (Gorgeski et al, 2014) and (ii) a polydisperse set of Bi nanoparticles embedded in a sodium-borate glass [Kellermann and Craievich, 2002). Other relevant structural features of Bi nanoparticles embedded in borate glass could also be derived from the analysis of the same experimental results [Kellermann and Craievich, 2008].
In Situ Materials Characterization across Atomic and Microstructure Lengthscales
Authors: Zhang Fan , Allen Andrew , Levine Lyle , Long Gabrielle , Ilavsky Jan , Hammons Joshua , Jemian Pete
Published: November 2015

Advanced materials exhibit complex, hierarchical, and multiscale microstructures that control their performance. Today, optimization of these microstructures requires iterative, ex situ studies using multiple independent instruments with different samples. To address many of the grand challenges facing the material research community, it is desirable to correlate material performance under realistic processing and operating conditions with in situ characterization of material structures across atomic and microstructural length scales. To meet this need, we have made progress in recent years in developing a suite of materials-measurement techniques that combines ultra-small angle X-ray scattering, small-angle X-ray scattering, X-ray diffraction, X-ray photon correlation spectroscopy, and X-ray imaging. When making use of high energy x rays from a third generation synchrotron source, this combined suite of techniques not only enables investigation of thick, complex materials under real operating/ processing conditions, but also allows robust structural characterization over 7 decades of structural and microstructural feature sizes, from sub-angstrom to millimeters. Depending on the scattering characteristics of the material, it can cover an unprecedented 11 decades in scattering intensity. This arrangement also allows the combination of measurement techniques be determined solely by the user's needs, allowing an unparalleled flexibility in addressing any set of microstructure, structure and dynamics material-measurement requirements. In this presentation, we will focus on various considerations required to make this combined technique possible, and use data from a series of in situ studies of aluminum alloys as examples to demonstrate the unique capability of this instrument. We will also discuss the potential impact that multi-bend achromat lattice, a concept being embraced by the worldwide synchrotron community, has on this technique.
Two dimensional crystallization of calcium transport regulatory complexes
Authors: Glaves John , Gorski Przemek , Trieber Catharine , Stokes David , Young Howard
Published: November 2015

Phospholamban and sarcolipin physically interact with the sarcoplasmic reticulum calcium pump (SERCA) and differentially regulate contractility in smooth, skeletal, and cardiac muscle. While mutagenesis and cross-linking studies have provided insight into the mechanism of interaction, we lack a molecular understanding of these regulatory complexes. We have compared two crystal forms of SERCA in the absence and presence of phospholamban by electron cryo-microscopy. Our previous studies with phospholamban utilized both small helical crystals [1] and large two-dimensional crystals [2], where the fundamental units of both crystal forms were found to be anti-parallel dimer ribbons of SERCA molecules. The SERCA dimer ribbons have been known for decades as a rigid assembly of calcium-free SERCA molecules induced by the addition of decavanadate. While the lattice formed by the SERCA dimer ribbons is different in the helical (p2) and two-dimensional crystals (p22121), we now show that a phospholamban oligomer interacts with SERCA in a similar manner in both crystal types. With this information, we next undertook a structural investigation of SERCA and sarcolipin in the large two-dimensional crystals. Both wild-type and a gain-of-function mutant (Asn4-to-Ala) mutant of sarcolipin were utilized. Projection maps were determined for SERCA in the presence of sarcolipin to a resolution of 8.5 Å and were most consistent with a pentameric state for sarcolipin. While both phospholamban and sarcolipin interacted with transmembrane segment M3 of SERCA, the interaction of the sarcolipin pentamer was mediated by an additional density consistent with a sarcolipin monomer.
Molecular mechanism of strigolactone perception by DWARF14
Authors: Tanokura Masaru , Miyakawa Takuya , Xue You-Lin , Nakamura Hidemitsu , Hou Feng , Qin Hui-Min , Fukui Kosuke , Shi Xuan , Ito Shinsaku , Miyauchi Yumiko , Asano Atsuko , Totsuka Naoya , Asami Tadao
Published: November 2015

The terpenoid, small-compound strigolactones (SLs) are plant hormones that regulate plant shoot branching, which is an important agronomic trait that determines crop yields. An α/β-hydrolase protein, DWARF14 (D14), has been recognized to be an essential component of plant SL signaling. Recently, it has been demonstrated that D14 interacts with a gibberellin (GA)-signaling repressor SLR1 in an SL-dependent manner [1], which suggests that SLR1 mediates crosstalk between the SL and GA signalings in the regulation of plant shoot branching. Although D14 functions in SL perception to promote the interaction with SLR1, its molecular mechanism remains unclear. Here, we report the crystal structure of D14 in the complex with 5-hydroxy-3-methylbutenolide (D-OH), which is a reaction product of SLs. The structure was solved at a 2.10-Å resolution when an SL synthetic analogue, (–)-ent-2'-epi-GR7, was soaked into D14 crystals [1]. In the complex structure, D-OH was located at a site far from the catalytic residues including H297 and appeared to function as a plug for the catalytic cavity to induce an overall hydrophobic surface with a hydrophilic patch between the two α-helices in the cap structure of D14. In the binding site, the indole amine of Trp205 formed a hydrogen bond with the oxygen atom of the C2' hydroxy group, which arose from the catalytic reaction of D14, instead of a water molecule in the structure of apo D14. In addition, the side chain of Phe245 moved 1.3 Å toward D-OH. Mutational analyses of D14 showed that the interaction between D14 and SLR1 required an enzymatic activity of D14 and the residues Trp205 and Phe245 were essential for the SL-dependent SLR1-binding of D14. These results suggest that the D14–D-OH complex mediates the interaction with SLR1 in which the D-OH-induced surface and/or structural change is crucial.
Crystal Structure analyses of dipeptidyl aminopeptidase BII fromP. mexicanaWO24.
Authors: Sakamoto Yasumitsu , Suzuki Yoshiyuki , Iizuka Ippei , Tateoka Chika , Roppongi Saori , Fujimoto Mayu , Inaka Koji , Tanaka Hiroaki , Ohta Kazunori , Okada Hirofumi , Nonaka Takamasa , Ogasawara Wataru , Tanaka Nobutada
Published: November 2015

The peptidase family S46 that contains the dipeptidyl aminopeptidase BII (DAP BII) fromPseudoxanthomonas mexicanaWO24 is the only exopeptidase family in clan PA peptidases. Our present phylogenetic and experimental studies indicated that the catalytic triad of DAP BII is composed of His 86, Asp 224 and Ser 657 and implied that unknown large helical domains involved in exopeptidase activity[1]. However, three-dimensional structure of a family S46 peptidase has not yet been reported. Thus, the crystal structure of DAP BII is essential not only to understand the catalytic mechanism of family S46 peptidases but also to clarify the structural origin of the exo-type peptidase activities of these enzymes. Recently, we have successfully crystallized the DAP BII and collected X-ray diffraction data to 2.3 Å resolution from the crystal. This crystal belonging to space groupP212121, with unit-cell parametersa= 76.55 Å,b= 130.86 Å,c= 170.87 Å[2]. Structural analysis by the multi-wavelength anomalous diffraction method is underway[3]. Here, we report the first crystallization and structural analysis of the DAP BII fromP. mexicanaWO24 as family S46 peptidase. Other enzymes that belong to this family are DPP7 and DPP11 fromPorphyromonas gingivalis, DPP11 fromPorphyromonas endodontalis(periodontal pathogen) and DPP11 fromShewanella putrefaciens(multidrug resistance associated opportunistic pathogen). These gram-negative bacterial pathogens are known to asaccharolytic. Especially,Porphyromonas gingivalisis known to utilize dipeptides, instead of free amino acids, as energy source and cellular material. Since S46 peptidases are not found in mammals, we expect our study will be useful for the discovery of specific inhibitors to S46 peptidases from these pathogens.
An insightful myosin structure reveals how actin triggers force production
Authors: Llinas Paola , Isabet Tatiana , Song Lin , Zhong Allan , Sirigu Serena , Ropars Virginie , Benisty Hannah , Sweeney H. , Houdusse Anne
Published: November 2015

Directed force production is essential for life. Allostery is at the heart of the mechanism that cellular nanomotors use to walk, pull or anchor. Such molecular motors are essential for a cell to migrate, to divide and organise the intra-cellular traffic between its compartments. The actin-based motors, myosins, are critical for many of these movements, for muscle contraction, cytokinesis and sophisticated cellular functions such as hearing. Deficit in these motors can lead to a number of human genetic disorders. Force is produced by these motors by the conversion of chemical energy derived from ATP hydrolysis into mechanical energy via the interaction with their track, the actin filament. Biophysical approaches have provided insights into the chemo-mechanical coupling in the actomyosin system. They show how three allosteric sites communicate via relatively small conformational changes in the motor domain that are coupled and amplified by a lever-arm mechanism that produce a working stroke of several nanometers. While ATP binding and hydrolysis are essential for detachment of the motor from its track and its trapping in the pre-stroke conformation, step-wise rebinding to the track triggers controlled release of hydrolysis products upon the working stroke. A reverse motor, myosin VI has been particularly intriguing and informative regarding the force production mechanism. An unpublished structural state not only reveal how trapping of the hydrolysis products stabilize the primed pre-stroke conformation, it also provides insights for the rearrangements triggered by actin to promote Pi release. This new structural state has all the expected features of the Pi release state populated upon motor re-binding to its track. This allows visualization for the first time of the structural rearrangements triggered by actin binding that are coupled to force generation and product release at the beginning of the powerstroke.
The Structure of the Yeast Mitochondrial Large Ribosomal Subunit
Authors: Brown Alan , Amunts Alexey , Bai Xiao-chen , Llácer Jose , Hussain Tanweer , Emsley Paul , Long Fei , Murshudov Garib , Scheres Sjors , Ramakrishnan Venki
Published: November 2015

Mitochondria have specialized ribosomes that have diverged from their bacterial and cytoplasmic counterparts. We have solved the structure of the yeast mitoribosomal large subunit using single-particle electron cryo-microscopy. The resolution of 3.2 Ångstroms enabled a nearly complete atomic model to be built de novo and refined, including 39 proteins, 13 of which are unique to mitochondria, as well as expansion segments of mitoribosomal RNA. The structure reveals a new exit tunnel path and architecture, unique elements of the E site and a putative membrane docking site.
Bringing Instrumentation to the Undergraduate Laboratory
Authors: Ott Holger , Noll Bruce , Phillips Scott , Ruf Michael
Published: November 2015

Efforts to bring crystallography into undergraduate laboratories are often hampered by one principal factor: the available funding. The acquisition of instrumentation has always been the stumbling block to establishing a program of crystallography in the undergraduate curriculum. With the introduction of Bruker's D8 QUEST ECO line of diffractometers, new opportunities arise. The ECO line is an all air-cooled set of instrumentation that lowers initial cost, operating cost, and environmental footprint. The system is configured with molybdenum radiation, and, for the first time in a low-cost instrument, with copper radiation. While molybdenum radiation has long been the dominant wavelength, copper allows access to absolute configuration of light-atom molecules. These instruments are fully capable research instruments, allowing for the demonstration and training of the complete experiment, from crystal selection, to selection of experimental parameters, data collection, and structure solution and refinement. Various levels of automation are available to match the needs and abilities of the students, making these instruments versatile through the entire undergraduate program. The transition from this entry-level system to high-end research instrumentation is transparent and undergraduate students will be well prepared for the next steps in their careers.
Two Reversible Phase Transitions in the Fluorophosphate (NH4)2PO3F·(NH4)NO3
Authors: Weil Matthias , Häusler Thomas
Published: November 2015

Fluorophosphates have multiple applications, e.g. as wood preservatives, as corrosion inhibitors or as toothpaste additives [1]. Fluorophosphates contain the tetrahedral anion PO3F2- that is characterized by three P-O bonds of similar length (ca. 1.51 Å) and one considerably longer P-F bond (ca. 1.60 Å). In the course of systematic crystal growth experiments of new fluorophosphates, we have isolated the double salt (NH4)2PO3F·(NH4)NO3. Temperature-dependent X-ray diffraction studies on polycrystalline and single-crystalline samples revealed two reversible phase transitions. The room-temperature polymorph I (space group P21/n) transforms at ca. 170 K into the intermediate polymorph II (space group P-1) that in turn transforms at ca. 140 K into the low-temperature polymorph III (space group P21/n). The driving force of the phase transitions I->II and II->III is a tilting of the nitrate groups within the structure relative to the other building blocks. The two phase transitions are accompanied by an increase of the unit cell volume on cooling. The three-dimensional structural set-up in the three polymorphs of (NH4)2PO3F·(NH4)NO3 is dominated by an intricate N-H...O hydrogen-bonding system between ammonium donor groups and nitrate and fluorophosphates acceptor groups. It is interesting to note that hydrogen-bonding of the type N-H...F plays a minor role.
Energetic Cocrystals – Structural Studies of Nitrotriazolone Salts & Cocrystals
Authors: Lloyd Hayleigh , Pulham Colin , Coster Paul , Henderson Craig , Williamson David , Jardine Andy
Published: November 2015

Developments in energetic materials are currently focused on the requirements for safer, yet still powerful materials for uses within mining, munitions and rocket propulsion systems One strategy that can be used to achieve these desirable properties is to synthesise new molecules, but this is both time-consuming and resource-intensive. Instead, another strategy is to crystallise energetic molecules with other molecules to form salts or cocrystals. This approach has been used extensively within the pharmaceutical industry in order to enhance desirable properties, e.g. solubility and bioavailability. To date, however, there has been very little research on the cocrystallisation of energetic materials. Examples include trinitrotoluene (TNT) with pyrene, naphthalene, and CL-20. To start this design process, the relationships between the types and strengths of interactions within a crystal structure and materials properties need to be established. Once these structure-property relationships have been established, the engineering of new and improved energetic materials can be achieved. The main focus of this work is on the energetic material 3-nitro-1,2,4-triazol-5-one (NTO) and the characterisation of a selection of new salts and cocrystals. NTO is an insensitive high explosive that has a similar performance to the more widely used explosive, RDX, yet is more stable, less prone to accidental detonation, and more soluble in water. Its high solubility in water is a major issue, as NTO is biologically active and represents a potential risk to the environment. There are only a few known salts of NTO and no published cocrystals, so the design and preparation of the first NTO cocrystals is a key objective. A selection of crystal structures of salts and cocrystals of NTO with nitrogen-rich aromatic systems has been obtained and the results are presented here. Interesting trends between pKa, functional groups, and intermolecular interactions have been observed.
Bioactive molecules modelised by numerical simulation:molecules against Escherichia Coli
Authors: Kakou Yao Rita , Abodou Tenon Jules , Abou Akoun
Published: November 2015

The work exposed in this paper joins in the research of medecine by means of the modelling by digital simulation (method in silico). This method allows to plan the biological activities of new molecules and to design others more active than existing molecules against a given infection . The generated and validated models are used here in the research for molecules potentially more active against Escherichia coli which causes diarrheic infections at the human beings. Here, we report works the synthesis of our works of structural determination, of forecast of biological activity and conception of molecules bioactive again Eschericha coli.
Liquid-liquid solvent extraction of rare earths: a crystallographic analysis.
Authors: Jacobs Jeroen , Binnemans Koen , Van Meervelt Luc
Published: November 2015

Liquid-liquid solvent extraction has become the primary research topic for separating mixtures of rare-earths. [1] Current research on this topic focuses on extraction processes involving ionic liquids as basic extracting agents. In the aqueous phase, the rare-earth is coordinated by the anionic entities of the ionic liquid, forming an anionic complex. The large organic cation of the ionic liquid neutralizes the complex (ion-pair complex) and migrates the entity to an organic phase. The choice of these agents is solely based on the calculation of thermodynamical extraction parameters, whilst structural information about these compounds is rare or even non-existent. Our research focuses on obtaining structural information via crystallography on the above-mentioned molecules and relating the interactions between anion and cation to the stability of the complexes. A difference in stability between the anionic complex and cation can give a different extractability. Different rare-earth chloride salts were dissolved in an aqueous phase, containing ionic liquids with β-diketonate anions and 1-alkyl-3-methylimidazolium cations. After the extraction, crystals of the formed compounds are grown from the organic phase and measured. Current results show us that an intermolecular non-classical C-H ... O hydrogen bond is persistent across the different molecules, whilst small interactions between the cation side chain and halogens on the β-diketonate add extra stability to the crystal structure. Structures formed with 2-thenolytrifluoroactylacetonate anions have no intention to form side chain interactions, leaving the alkyl chain of the 1-alkyl-3-methylimidazolium in a void, whilst structures formed with hexafluoroacetylactonate have strong side chain interactions, which leads to a better packing. The different solubility of both compounds can be related to the different interactions and stability in the crystal structure.
Co-crystals and inclusion compounds of leucyl-containing dipeptides
Authors: Ignacio Melissa , Smith Aaron , Soldatov Dmitriy
Published: November 2015

Short peptides are ecologically friendly and non-toxic molecules, so they can be safely utilized in green chemistry processes or incorporated in pharmaceuticals and food additives. It has been shown that some dipeptides can form crystals that incorporate other molecules through intermolecular hydrogen bonding and van der Waals interactions[1]. The utilization of such dipeptides for solid state organic synthesis or storage and stabilization of bioactive molecules would be of great practical interest, but the principles that define the successful combinations are not clear. In order to identify what factors lead to complementary pairs of a dipeptide and a second component, a series of leucine-containing dipeptides was screened against 40 organic solvents and solids. Direct or solvent-assisted grinding was used followed by PXRD analysis. It was found that each dipeptide was able to form new phases with some of the utilized reactive and bioactive molecules. The Figure illustrates three experimental powder patterns in the 5-35 2θ degree range. The dipeptide leucyl-valine (1) and the second component 5-acetylsalicylamide (2) combine to form a new crystalline phase (3). After screening was complete, a series of crystallizations was performed and several crystals comprised of both a dipeptide and another molecule have been isolated and studied. A number of structural motifs were observed, although a layered architecture with the second component included in the interlayer space prevailed.
Structural Diversity of MOFs Constructed by Tricarboxylate Ligand
Authors: Han Jie , Zhao Xiao-Li
Published: November 2015

Considerable progress has been made in the construction of metal-organic frameworks (MOFs) recently[1]. Due to the close relationship between the structures of MOFs and their properties, tuning structures by rational design through the judicious choice of metal ions, bridging organic ligands and reaction conditions becomes very attractive[2]. Three-dimensional pillar-layer architecture of [Co3L2(bpe)4]·2DMF·2(H2O)] (complex 1, Fig 1a), honeycomb-like channels of [Zn2L(OH)(bpe)]·5.5(H2O)] (complex 2,Fig 1b), and chain-like structure of [Zn2(HL)2(bpy)2(H2O)])2]·(bpy)·6(H2O)] (complex 3, Fig 1c) (HL3>=5-(4-carboxybenzoylamino-isophthalic acid), bpe = 1,2-bis(4-pyridyl)ethane and bpy = 4,4'-bipyridine and) have been synthesized and characterized by single X-ray crystallography(Figure 1). Complex 1 features a three-dimensional (3D) pillar-layer architecture generated from bpe-pillared M-L3-layers. Complex 2 is a 3D structure with 4- and 6-coordinated Zn2+in the centrosymmetric tetranuclear Zn4(µ3OH)2(COO)6(bpe)4SBU. Complex 3 is 2D structure. The [Zn(HL)(bpy)(H2O)] chains are connected each other by hydrogen bonding, with free bpy and guest water molecules accommodated in.
Structure of (E)-N-((5-Nitrothiophen-2-YL)Methylene)-3-(Trifluoromethyl)Aniline
Authors: Deveci Özlem , Gümüş Sümeyye , Agˇar Erbil
Published: November 2015

The Schiff base compound, C12H7N2O2F3S, has been synthesized and characterized by IR, UV-Vis, 1H-NMR, 13C-NMR and single-crystal X-ray diffraction (XRD) and elemental analysis. The compound, an Ortep-3 [1] view of which is shown in Fig. 1, crystallizes in the monoclinic space group P-1 with a= 7.5700(11) Å, b= 12.8280(16) Å, c= 13.0170(16) Å, α= 89.295(10)o, β= 88.691(11)o, γ= 82.246(11)o and Z=4 in the unit cell. The molecular structure is stabilized by C-H...O and C-H...F intramolecular hydrogen bonds and molecules are linked through intermolecular C-H...O and C-H...F type hydrogen bonds and C-H...Cg (π-ring) interaction. The molecular geometry from X-ray determination of the title compound in the ground state has been compared using the Hartre-Fock (HF) and density functional theory (DFT/B3LYP) [2] with 6-31G(d) [3] basis set. The results of the optimized molecular structure are exhibited and compared with the experimental X-ray diffraction. To determine conformational flexibility, molecular energy profile of the title compound was obtained by B3LYP with the 6-31G(d) basis set calculations with respect to selected degree of torsional freedom, which was varied from –1800to +1800in steps of 100. In addition, molecular electrostatic potential (MEP) distribution and frontier molecular orbitals (FMOs) properties of the title molecule were investigated by theoretical calculations at the B3LYP/6-31G (d) level. Figure 1. Ortep 3 diagram of the title compound. Displacement ellipsoids are drawn at the 30% probability level and H atoms are shown as small spheres of arbitrary radii.
Novel solid forms of the analgesic drug ethenzamide
Authors: Choquesillo-Lazarte Duane , Verdugo-Escamilla Cristóbal , García-Ruiz Juan Manuel
Published: November 2015

The interest in multicomponent solid forms has increased in the last years within the pharmaceutical industry and also the solid-state community due to the possibility of obtaining materials with new properties [1]. Crystallization strategies, supported by solvent- and solid-based techniques, have also received attention in the search and development of methodologies for the screening of multicomponent crystals. In this work, ethenzamide, an anti-inflammatory and analgesic drug, was selected as a model drug to develop cocrystals on the basis of the synthon types using a series of phenolic coformers. Ethenzamide cocrystals and cocrystal solvates have been reported recently [2,3]. Liquid Assisted Grinding (LAG) and solution methods were used as synthetic tools. Attempts to produce cocrystals by LAG and Reaction Crystallization led to the formation of polycrystalline material. The solids obtained were then characterized by powder X-ray diffraction (PXRD), FT-IR and Raman spectroscopy. Recrystallization by slow solvent evaporation was carried out when the above-referred techniques strongly suggest the formation of a new solid form. The structure of five new multicomponent solids has been determined by single crystal X-ray diffraction. Additional stability studies have been performed at controlled relative humidity conditions and followed by PXRD.
A novel layered aluminophosphate with corner-sharing AlO6chains
Authors: Cámara Fernando , Pastero Linda , Arletti Rossella , Cagnoni Monica
Published: November 2015

The synthesis, Raman spectroscopy and crystal structure of a novel layered aluminophosphate is described. The new phase was derived by the sol-gel method starting from a modified low hydrothermal ALPO4-34 zeolite synthesis procedure[1].The structure was solved by direct methods using single-crystal X-ray diffraction. The synthesized layered material, with composition [AlPO3(OH)F(H2O)]-(H9C4ON), crystallizes in the monoclinic space group P21/a with a = 9.2282(5) Å, b = 6.9152(4) Å, c = 14.4615(9) Å, β = 101.57(1)0. Layered aluminophosphates with AlO6polyhedra have been previously described [2], although in these compounds Al octahedral share edges. The novel compound has corner sharing AlO4F(H2O) chains along [010], where fluorine is at the shared apex, four oxygen atoms are shared with PO4tetrahedra and the fifth oxygen is a H2O group. This kind of aluminophosphate chains is found in nature in tancoite [3]. Chains are linked along [100] through corner sharing with a PO4group of the adjacent chain plus hydrogen bonding of the H2O group. Layers are stacked along c* through hydrogen bonding with a double layer of morpholine (H9C4ON) molecules. The chemical stability field of the novel materialis strongly dependent from the fluorine/aluminum ratio of the starting gel. At lower fluorine concentrations only ALPO4-34 and/or AlPO4(berlinite) are stable depending on the morpholine content. Crystals growth morphology depends on the supersaturation conditions of the starting gel: at low concentrations crystals are well developed hexagonal like plate shaped and are very thin. At higher concentrations they show a more elongated morphology. A treatment with H2CO3leads to a complete morpholine removal, as shown by in situ Raman spectroscopy. Powder X-ray diffraction reveals that after morpholine extraction, the material diffract still coherently in two dimensions while a strong broadening is shown for basal planes.
Control of a thermosalient phase transition by solid solutions
Authors: Nauha Elisa , Lusi Matteo , Naumov Pance
Published: November 2015

Thermosalient crystals that exhibit macro-scale motion upon phase transition could be useful as actuators that are capable of converting thermal energy into motion or mechanical work in macroscopic devices.[1] The application capability of these miniature actuators for energy conversion depends on the temperature range and dynamics of transition. While the thermo-mechanical performance cannot be systematically varied with a pure molecular crystal, solid solutions could present a way to intentionally tune both the dynamics and the temperature of the transition in a continuous manner (Figure 1). To verify this hypothesis, Zn(2,2'-bpy)Br2,[2] was selected as a thermosalient material which could form solid solutions (or mixed complexes) with Zn(2,2'-bpy)Cl2. Only one form (isomorphous to one of the two Zn(2,2'-bpy)Br2forms) has been reported for the chloride.[3] The results indicate that indeed, the two complexes form solid solutions in varying ratios. The mixed crystals undergo the same phase transformation as the pure Zn(2,2'-bpy)Br2at a Cl/Br-ratio-dependent temperature. The temperature and dynamics of the thermosalient phenomenon correlates with the Cl/Br-ratio.
Structure, electric and magnetic properties of Pb(V1-xMx)O3, M=Ti, Fe compounds
Authors: Bordet Pierre , Colin Claire , Darie Céline , Okos Alexandru , Pop Aurel
Published: November 2015

It is well known that ferroelectricity and magnetic order are considered as hardly compatible in perovskite compounds. In this respect, PbVO3 is quite interesting: it is isostructural to ferroelectric PbTiO3 (P4mm) and contains V4+ spin ½ cations [1]. However, previous studies have failed to observe magnetic order in PbVO3, which was attributed either to a 2D magnetic behaviour or to magnetic frustration on a square lattice [2]. We present here the study of the substitution of V4+ by Fe3+ or Ti4+ cations, aiming at a better understanding of the relations between structural, magnetic and electric properties. PbVO3 single crystals and powders of substituted compounds were prepared at 6GPa , 9500C in belt and Conac type systems. A single crystal diffraction experiment confirmed the proposed structure for PbVO3, evidencing merohedral twinning related to ferroelectric domains also observed by SEM. For the Ti substitution, a complete Pb(V4+ 1-x Ti4+ x)O3 solid solution is observed for x = 0 to 1, while the Fe substitution stops at x=0.5 due to heterovalent cation replacement, the formula being Pb(V4+ 1-2x V5+ x Fe3+ x)O3. The cation oxidation states were checked by XANES (FAME-ESRF). The structures were studied by joint refinements of NPD (D1B-ILL) and XPD (Laboratory and ID31-ESRF) data, yielding the coordinations of V and M cations and the spontaneous polarization using a point charge model. A decrease of tetragonality, domain size along the c-axis and polarization is observed with increasing substitution. For the Ti series, the magnetic behaviour progressively changes from 2D to Curie-Weiss with increasing x. In the case of Fe, a broad peak in magnetic susceptibility is observed, at temperatures increasing from 12K to 30K for x going from 0.1 to 0.5. This was checked as due to a spin glass behaviour. No sign of magnetic order was observed by NPD. At the same time, a broad, frequency dependent anomaly of the dielectric constant is observed, reminiscent of a relaxor behaviour.
Crystal Chemistry and Physics of Perovskites with Small Cations at the A Site
Authors: Belik Alexei , Yi Wei , Liang Qifeng , Matsushita Yoshitaka , Tanaka Masahiko , Terada Noriki , Suzuki Hiroyuki , Tsujii Naohito , Sobolev Alexey , Presnyakov Igor
Published: November 2015

Synthesis, crystal chemistry, and physics of perovskites with small cations at the A site are an emerging field in perovskite science. Properties of ABO3 perovskites with small cations at the A site (A = Sc and In; B = transition metals) will be reported. ScBO3 and InBO3 perovskites extend the corresponding families of perovskites with A = Y, La-Lu, and Bi and exhibit larger structural distortions. As a result of large distortions, they show, in many cases, distinct structural and magnetic properties. It is manifested in B-site-ordered monoclinic structures of ScMnO3 [Inorg. Chem. 52 (2013) 9692] and `InMnO3' [Angew. Chem.: Inter. Ed. 49 (2010) 7723]; an unusual superstructure of ScRhO3 and InRhO3 [Inorg. Chem. 52 (2013) 12005]; two magnetic transitions in ScCrO3 and InCrO3 with very close transition temperatures [Chem. Mater. 24 (2012) 2197]; and antiferromagnetic ground states and multiferroic properties of Sc2NiMnO6 and In2NiMnO6 [Inorg. Chem. 52 (2013) 14108]. Features of such perovskites, such as, transition metal doping into the A site, (Sc1-xBx)BO3, will be discussed. Special attention will be given to new spin-driven multiferroics Sc2NiMnO6 and In2NiMnO6.
Molecular recognition enrichment rules in crystals and protein/ligand complexes
Authors: Jelsch Christian , Guillot Benoit , Ejsmont Krzysztof
Published: November 2015

To analyze the propensity of chemical species to interact with each other, we have developed the concept of enrichment ratios. The ratios are derived from the decomposition of the contact surface between pairs of interacting chemical species. The actual contacts are compared with those computed as if all types of contacts had the same probability to form. As expected, several polar contacts, which can be hydrogen bonds and show electrostatic complementarity, show enrichment values larger than unity. Among other results, O···O and N···N contacts are impoverished while H···H interactions appear very slightly disfavored. We have also investigated the directionality and stereochemistry of hydrogen bonds with an oxygen acceptor including in the Cambridge Structural Database [1]. The results obtained through this survey are correlated with the charge density of these different chemical groups. The electron density of these different oxygen atoms types show striking dissimilarities in the electron lone pairs configuration. As previously observed, the directional attraction of hydrogen bond donors towards the lone pairs is much more pronounced for strong H-bonds. Van der Waals and solvent accessible surfaces are widely used representations in protein modelling and drug design. We propose in the software MoproViewer [2] a revisited definition of the molecular surface based on flattened atoms when strong hydrogen bonding is possible. These stereochemical relationships found in molecular recognition within crystal structures of small compounds have implications in drug design and were investigated in some protein/ligand cases. Finally protein/ligand electrostatic calculations are compared using two different charge density models: multipoles vs spherical dummy charges on bonds and lone pairs[3].