bluuebunny/crossref_metadata_2025 huggingface dataset:
Intermolecular Hydrogen and Halogen Bonds in Fluorinated Benzimidazoles
Authors: Claramunt Rosa M , Pérez-Torralba Marta , García M. Ángeles , López Concepción , Torralba M. Carmen , Torres M. Rosario , Alkorta Ibon , Elguero José
Published: November 2015

After hydrogen bonds (HB) the most studied of related weak interactions are the halogen bonds (XB). The competition between these two interactions as well as their interplay to determine the crystal packing of organic derivatives is a subject of interest. Most the studies related to XB concerns the heaviest halogen atoms, I and Br, less Cl and much less F, because the interaction energy decreases in this order. [1,2] We present here our studies on the structure of five tetrafluorinated benzazoles by X-ray crystallography and solid-state NMR, a powerful synergic mixture of techniques. The compounds are 4,5,6,7-tetrafluoro-1H-benzimidazole (1), 4,5,6,7-tetrafluoro-2-(trifluoromethyl)-1H-benzimidazole (2), 4,5,6,7-tetrafluoro-1H-benzimidazole-2(3H)-one (3), 4,5,6,7-tetrafluoro-1-methyl-1H-benzimidazole-2(3H)-one (4), and 4,5,6,7-tetrafluoro-1,3-dimethyl-1H-benzimidazole-2(3H)-one (5). As a common general feature, these compounds are quite planar due to the presence of the two aromatic rings. The existence of the methyl groups as substituent in the nitrogen atoms does not modify the planarity of the molecule. The bond distances and angles are in agreement with the expected ones for this kind of compounds. The presence of the carbonyl group induces some electronic changes in the imidazole ring that is resembled in the lengthening of the C2N3 bond distance and in a higher deviation of C2 atom from the molecular plane. Moreover, all the compounds show one or more interactions by strong linear hydrogen bonds, which lead to the formation of chains that, in some cases, can exhibit additional interactions via pi-pi and/or F···F contacts spreading out the dimensionality of the structure in the crystal. [3] The distribution of the F···F contacts in compounds 1-5 is similar to those of the literature and includes for 4,5,6,7-tetrafluoro-1H-benzimidazole-2(3H)-one (3) one of the shortest F···F distances ever reported [2.596(3) Å]. Two polymorphs of compound 4 are identified.
Supramolecular architecture of PGM-arene-amino acid complexes
Authors: Benyei Attila , Bortel Gabor , Patalenszki Janos , Buglyo Peter
Published: November 2015

Arene complexes of Platinum Group Metals (PGM) show various biological effects and there are several promising anticancer drug candidates in this class of compounds. Synergism of biological activity is foreseen when anciliary ligands such as amino acid derivatives or other bioligands are incorporated into the complexes. A series of Ru(II), Os(II), Rh(III) and Ir(III) complexes were studied and interesting kinetic/equilibrium/structural properties could be revealed [1-3]. According to our latest results presented here the N-acetylcysteine complex of the [(η6-Ar)Ru]2+ core (Ar = p-cymene) is a dimer showing bridging thiolate and chloride cordination (Figure 1, a) while a monomeric complex was formed with [S, COO–,NH2] coordination for S-methyl-cysteine when the counter ion is nitrate (Figure 1, b). With methionine an analogous compound was formed (Figure 1, c). Supramolecular analysis of the complexes indicates competing steric/Coulombic/van der Waals interactions and hydrogen bonds. X-ray diffraction and spectroscopic analysis revealed the structure of the complexes both in solution and in the solid state and also support kinetic/equilibrium findings. Acknowledgement: The research was supported by the EU and co-financed by the European Social Fund under the project ENVIKUT (TÁMOP-4.2.2.A-11/1/KONV-2012-0043). The work was supported by the Hungarian Scientific Research Fund (OTKA K76142), too. P.B. thanks members of the EU COST Action CM1105 for motivating discussions. G.B. acknowledges the support of the Bolyai János Scholarship of the Hungarian Academy of Sciences.
Comparative study between two new phthalate/imidazole Cobalt complexes
Authors: Benkanoun Aouaouche , Balegroune Fadéla , Guehria-Laidoudi Achoura , Dahaoui Slimane , Lecomte Claude
Published: November 2015

The main strategy for preparing novel multifunctional materials is based on self-assembly method which employs polydentate organic ligands containing N- or O-donor as building blocks. In this context, those ligands like imidazole or carboxylate groups are of special interest due to their good coordination ability and diverse coordination modes [1]. As a part of our investigations of extended structures with mixed ligands, new complexes [Co(Hipht)2(Im)2(H2O)2] and [Co(Tpht)(Im)3(H2O)2].H2O were obtained by direct method, then characterized by IR spectroscopy, TG/ATD and X-ray crystallography. In the compound [Co(Hipht)2(Im)2(H2O)2], CoII is located on a symmetry center, surrounded by two aqua ligands, two hydrogeno-isophthalate ligands and two imidazole molecules, where all ligands adopt monodentate mode. The complex's geometry consist of two intermolecular N-H...O bonds (2,157 Å and 2,630 Å) formed by one H atom of imidazole ligand and oxygen atoms of acid molecules evolving along two directions, giving rise to R24 (16) synthons. The interplanar distance of 3,718 Å between two parallel imidazole rings reveals the existence of Π-Π interactions. In the [Co(Tpht)(Im)3(H2O)2].H2O [2], the Co cation exhibits an octahedral coordination sphere, with two aqua, three N-coordinated imidazole ligands and one terephthalato dianion. The three independent imidazole groups and the single terephtalate dianion, all unidentate participate respectively as donor and acceptor in strong to moderate hydrogen bonds, and allow the recognition of supramolecular dimensionality. The backbone of the architecture is the helical hydrogen-bonded ladder running along b axis, composed of alternating R44(10) and R33(8) heterosynthons, which are developed in bicyclic sheets. Non covalent interactions play a significant role in this class of materials [3], in fact, extended hydrogen bonds networks associated to Π-Π interactions lead to 3D supramolecular architecture for the two complexes.
Exploiting weak supramolecular interactions to assemble organic cage materials
Authors: Chong Samantha , Hasell Tom , Culshaw Jamie , Little Marc , Schmidtmann Marc , Holden Daniel , Chen Linjiang , Jelfs Kim , Cooper Andrew
Published: November 2015

Intensive research into microporous materials has been driven by potential applications in areas such as catalysis, gas separation, storage, and sensing. Recently, a new class of purely organic molecular cage materials has emerged, which can exhibit significant porosity arising from the internal molecular cavity as well as extrinsic porosity from packing in the crystal structure [1]. Unlike extended frameworks, porous molecular materials lack strongly directional interactions to drive their assembly, complicating the crystal engineering possible for isoreticular metal-organic frameworks [2], for example. Our work has focused on covalent imine-linked cages, which exhibit diverse crystal chemistry. The connectivity of the pore network is derived from the cage packing: Therefore, the crystal structure directly affects the observed porosity. The imine cages synthesised so far lack strongly hydrogen bonding groups. Thus, the solid state supramolecular assembly of cage molecules is governed by the aggregate of weak interactions, such as van der Waals forces. By identifying robust `tectons', that is, regularly occurring supramolecular motifs, progress toward designing the crystal structure and therefore controlling the physical properties of organic cage materials becomes possible. Here, we report exploiting robust supramolecular motifs, comprising either cage modules or host and guest molecules to gain control over the porosity of the bulk material. We demonstrate how formation of a desired void network topology can be driven by hosting a specific guest in preferred sites which maximise weak host-guest interactions [3]. Subsequent guest removal can produce stable polymorphs, one of which exhibited double the Brunauer-Emmett-Teller surface area with respect to the originally observed polymorph. We also examine how the interaction between gas phase guests and cage host is important in the application of porous organic cages in rare gas separation.
3D-ΔPDF: a routine method for analyzing diffuse scattering from single crystals.
Authors: Simonov Arkadiy , Weber Thomas
Published: November 2015

With the recent advances in x-ray area detectors, high quality diffuse scattering became readily available. This allows to investigate local order in single crystals and provides invaluable information about real structures of disordered crystals, e.g. stacking probabilities, or structural dynamics. Recently, a new method called Three Dimensional Difference Pair Distribution Function (3D-ΔPDF) analysis was introduced [1]. It provides direct access to the short range order correlations and allows to investigate the diffuse scattering of both static and dynamic origin in a unified fashion . The method is similar to the powder PDF, but availability of three dimensional diffraction data provides several key differences. Firstly, it allows elimination of Bragg peaks and refinement of diffuse scattering alone which conveniently separates the investigation of average structure from investigation of ordering. Secondly, due to reduced overlap of PDF signals, the correlation coefficients at very long interatomic vectors become accessible. The 3D-ΔPDF analysis can be performed in the newly developed program Yell [2]. The program supports all types of correlations and contains a fast FFT-based method for diffuse scattering calculation, and the constraints of arbitrary arithmetic expressions.
Diffuse scattering and phase transitions in aperiodic inclusion compounds
Authors: Rabiller Philippe , Toudic Bertrand , Guérin Laurent , Mariette Céline , Hollingsworth Mark
Published: November 2015

Small molecules, such as urea, thiourea, perhydrotriphenylene can be co-crystallised with long-chain hydrocarbon molecules to form inclusion compounds. The guest chains are confined to narrow, approximately cylindrical, channels created by the host small-molecule lattice. The stoichiometry and the conformations of the chains included inside the channels are function of internal interactions such as intra-chain interaction, but also of overall co-operative properties of the resulting three dimensionally ordered single crystal. These intergrowth compounds may form incommensurate composite crystals. A prototype example of such uniaxial intergrowth aperiodic crystals is n-alkane (CnH2n+2)/urea (CO(NH2)2). In these supra-molecular systems, urea molecules are connected by H-bonds and form helical ribbons, which repeat every six urea molecules to form a series of linear, hexagonal tunnels that can accommodate linear alkanes. Because the channels (~0.53 nm) are larger than the hydrocarbon chains, guests are held loosely and can undergo substantial motions. A significant amount of diffuse scattering of the first and second kinds can be depicted in scattering experiments, static or dynamic. These materials undergo a large variety of continuous or weakly first order structural phase transitions when changing the alkane molecule length and giving place to large pre-transitional effects. The talk will give an overview of the diffuse scattering in these compounds and will focus on connection with aperiodicity.
Superconductivity Mechanism in the Modulated Quantum Well of YBCO Structure
Authors: Nguyen Van Tri
Published: November 2015

The modulated structure by high pressure and the superconductivity of YBCO compounds have been revealed over two decades [1]. However, their nature & mechanism are not yet sufficiently known. Continuing the achieved results [2-3], the present paper aims to evidence how the Quantum Electron-Magnetic Phenomenon, namely the Super-Exchange Interaction of the "active electrons", i.e. the hybridized odd electrons from the Cu ions in the Cu-Y-Cu nanolayer as a Nanowaveguide (NWG), conditions the Superconductivity of YBCO. The 1st key: The nanostructure is of Quantum nature. The active electrons behavior as the Quasi-Free Electrons (QFEs) waving in the Quantum Well (NWG), where they can be favored to a strong Super-Exchange Interaction. Thereby, two types of the spin coupled pairs can be spontaneously formed in the NWG, where just the singlet pairs will play the role of the superconducting Cooper pairs. For studying these nanoeffects, ESR can offer an especially efficacious contribution. The 2nd key: On the basis of the consequences of the Pauli principle, the singlet pair only persists if its QFE cloud overlapping path length L = nλ/2, where λ is the de Broglie wavelength of QFE conditioned by the Nanodimension of the NWG (Fig.1, left). This electron waving status corresponds to an ideal metallic phase occurring in the NWG. The 3rd key: The spin coupling brings about a temperature depending Spin Gap of the QFEs in the NWG. Just this Spin Gaps causes the superconductivity with the phase transition characteristics (Fig.1, right) that exactly and surprisingly correspond with the experimental.
SAD experiment using the wavelength of 2.7 Å or longer
Authors: Matsugaki Naohiro , Yamada Yusuke , Hiraki Masahiko , Liebschner Dorothee , Watanabe Nobuhisa , Yao Min , Shinoda Akira , Kato Koji , Tanaka Isao , Senda Toshiya
Published: November 2015

Single-wavelength anomalous dispersion (SAD) experiment with light atoms as anomalous scatterers has been carried out using longer wavelengths up to 2.3 Å. We have been developing a synchrotron beamline dedicated to the SAD experiments where wavelengths longer than 2.7 Å are available to enhance weak anomalous signals. Larger background noise due to the longer wavelength, which is one of the major problems in the experiment, is reduced by introducing a standing helium chamber surrounding both the whole diffractometer and the X-ray detector. The system allows to perform experiments with normal and long waveldngths under the same environment. Helium cold stream is fed into the chamber at the sample position and reused after removing contaminants to keep the temperature of the stream at 30 K or below economically. Capillary-top-mount method [1] was improved to further reduce the background noise and to accommodate with smaller or needle-shape crystals. Several results on de-novo structural solutions with sulfur-SAD phasing will be reported in addition to the current performance of the beamline and its future plan.
Combined XRD and EXAFS characterization of UiO-66 and functionalized UiO-67 MOFs
Authors: Borfecchia Elisa , Øyen Sigurd , Lomachenko Kirill , Bouchevreau Boris , Chiari Elisa , Agostini Giovanni , Gianolio Diego , Bordiga Silvia , Lillerud Karl-Petter , Lamberti Carlo
Published: November 2015

The recently discovered UiO-66 (UiO-67) class of isostructural metallorganic frameworks (MOFs) are obtained connecting Zr6O4(OH)4 inorganic cornerstones with 1,4-benzene-dicarboxylate (4,4′ biphenyl-dicarboxylate) as linker resulting in a cubic framework [1]. This family of MOFs has attracted great interest because of its remarkable stability at high temperatures, high pressures and in presence of different solvents, acids and bases [2]. Industrial applications in the fields of catalysis, H2 storage, gas purification and, for the isostructural Hf form, interim radioactive waste scavenging. For these potentialities UiO-66 is one of the very few MOFs that have already been successfully commercialized. In this presentation we will show how the synergic refinement of XRPD and EXAFS data resulted in the structural determination of UiO-66/67 [1-3] and we will report new combined synchrotron radiation single crystal XRD and EXAFS data allowing the structure determination of new metal-functionalized UiO-67 of potential high industrial impact because aimed in heterogenization of homogeneous catalytic reactions.
Biochemical and structural characterization of TraE from the plasmid pKM101
Authors: Casu Bastien , Smart Jonathan , Smith Mark , Sygusch Jurgen , Baron Christian
Published: November 2015

In all organisms, secretion systems mediate the passage of macromolecules across cellular membranes. The bacterial type IV secretion system (T4SS) family can be divided into three functional groups. First, as typified by the Brucella suis system, T4SSs deliver effector macromolecules into eukaryotic cells during the course of infection. Second, in some Gram-negative bacteria, such as in Helicobacter pylori (ComB system), T4SSs mediate DNA uptake from and release into the extracellular environment. Thirdly, as in the IncN plasmid pKM101, T4SSs can mediate the conjugative transfer of plasmid DNA or transposons into a wide range of bacterial species. This conjugation phenomenon contributes to the spread of antibiotic resistance genes among pathogenic bacteria, leading to the emergence of multidrug-resistant pathogenic strains. TraE of the IncN plasmid pKM101 belongs to the VirB8 family of proteins, an essential component of most T4SSs that form functional dimmers in the T4SS core. Here, we present the X-ray crystallographic structure of the periplasmic domain of TraE at 2.4 Å resolution. The structure shows many similarities to the known VirB8-like protein structures from Brucella suis [1] and Agrobacterium tumefaciens [2]. However, the nature and the number of residues implicated in the dimerization interface differ considerably from those in the TraE structure [2]. Similar to other VirB8 homologs we have shown by analytical gel filtration that there is a concentration dependant equilibrium between monomeric and dimeric forms of TraE. Moreover, using a bacterial two-hybrid assay, in vivo dimerization has been demonstrated with full-length TraE and key residues for dimerization were identified by site-directed mutagenesis. Our work adds novel insights into the growing body of knowledge on VirB8-like proteins and it will inform future strategies aimed at developing inhibitors of TraE protein interactions and of plasmid transfer.
Automated grid-based XFEL diffraction studies of single macromolecular crystals
Authors: Soltis S , Cohen Aina , Lemke Henrik , McPhillips Scott , Peters John , Song Jinhu , Stout C , Tsai Yingssu , Keable Stephen , Chen Ying
Published: November 2015

A major challenge of structural investigations of metalloproteins at synchrotrons is the damaging effects of radiation exposure. Even small X-ray doses can reduce or initiate reactions at metal centers modifying the active site. For example, in-situ visible absorption spectroscopy measurements have demonstrated that the heme/copper active site in oxidized ba3 cytochrome oxidase (ba3) is compromised during a single X-ray diffraction exposure. The use of ultrashort X-ray pulses at LCLS provides a means to measure high resolution diffraction before these damage processes occur. To this end, experiments were conducted at LCLS using large multiple crystals (> 50 µm) of ba3, hydrogenase and myoglobin. Crystals were mounted in `grids' or loops and flash frozen. The grids hold up to 75 crystals in known locations and are compatible with the Stanford Automounter used to exchange them. Following a semi-automated grid alignment procedure, a fully automated routine was used to position each crystal and collect a series of diffraction images and the Blu-Ice/DCS control system that coordinated with the LCLS EPICS system and XPP DAQ software. Single femtosecond X-ray pulses produced a `damage free' still diffraction image from each crystal. To provide additional information about crystal orientation, a series of pseudo-oscillation images were collected +/- 5.5 degrees spanning the orientation of the still image. For each one degree oscillation image the crystal was exposed to 120 attenuated X-ray pulses. A hard X-ray spectrometer was used to measure the energy spectrum of each individual X-ray pulse. The details and results of these experiments will be presented.
Assembling nanotubes with cyclic peptoids
Authors: Tedesco Consiglia , Izzo Irene , De Riccardis Francesco , Vaughan Gavin , Brunelli Michela , Fitch Andrew , Barboour Leonard
Published: November 2015

Cyclic alpha-peptoids hold the attention of both synthetic and supramolecular chemists for their biostability and potential diversity but also for their elegant and intriguing architectures.[1] Peptoids differ from peptides in the side chains, which are shifted by one position along the peptide backbone to the nitrogen atom to give N-substituted oligoglycine. The lack of the amide proton prevents the formation of NH···OC hydrogen bonds and weaker interactions, as CH···OC hydrogen bonds and CH-pi interactions, play a key role. Inter-annular CH···OC hydrogen bonds can provide face to face or side by side arrangement of macrocycles mimicking beta-sheet secondary structure in proteins.[2] In particular, the role of side chains in the solid state assembly of peptoid macrocycles will be discussed to show how they can promote the formation of a peptoid nanotube by acting as pillars, extending vertically with respect to the macrocycle planes. [3] Examples of the solid state assembly of free and metallated cyclic peptoids will be reported to show their extreme versatility as building blocks for designing new materials, with novel chemical properties and defined biological activities. In particular the first crystal structure of a recently synthesized novel cyclic alpha-peptoid, containing open channels with a radius of approximately 7 Å, will be discussed as a case of the successful engineering of cyclopeptoid crystals. In figure it is shown the channel void surface as seen along the a axis (0.0003 au, CrystalExplorer 3.1). The results of recent variable temperature high resolution XRPD measurements performed at ESRF beamline ID31 will be also reported to highlight the unusual thermal stability of this class of compounds and how the mobility of the side chains may be exploited to prepare new functional materials. EU FP7-People- IRSES grant number 319011 is gratefully acknowledged.
Porous peptide frameworks generated by stacking non-self-complementary β-sheets
Authors: Soldatov Dmitriy , Yazdani Abdolreza , Crewson Julia , Fillion Travis , Smith Aaron , Ignacio Melissa
Published: November 2015

"One of major approaches in the design of cavity space in the solids utilizes non-self-complementary molecules[1]. The irregular shape of the molecules and/or specific directionality of potential H-bonds prevent close packing of the molecules and yields various architectures hosting a second component, from inclusion compounds and co-crystals to complex non-crystalline patterns in biology. The strategy of non-self-complementary molecules has been extended in our studies to 2D supramolecular polymers based on short peptides[2]. The formation of the peptide layer with a desired overall geometry is controlled by strong, charge-assisted H-bonds (arrows in the Figure) in a β-sheet-like network as well as the segregation of hydrophobic amino acid residues into the interlayer space. The H-bonds add stability to the whole architecture while the hydrophobic groups keep the stacking layers at a distance that generates a cavity space available to a second component (encircled ""G"" in the Figure). A wide range of inclusions and co-crystals have been prepared in our group based on a series of dipeptides and higher peptide oligomers. For example, the incorporation of various organic solvents and bioactive molecules have been demonstrated for leucyl-alanine and similar dipeptides: alcohols, amides, phenols, pyridines, polyols, vitamins, scents and flavors. The crystal structure studies reveal a surprisingly persistent structural motif that can be used for engineering of crystalline materials with a specific property. We believe this type of peptide matrix may be utilized in the solid state organic synthesis [3] as reactive molecules of the second component can be oriented in a predictable way with respect to each other. "
Ultra short H-bond in potassium monobasic 1,4-butodioxybis(4'-benzoic) acid
Authors: Oliveira Willian , Botelho Lilian , Ronconi Celia , Pinheiro Carlos
Published: November 2015

Hydrogen bonds have been exhaustively investigated in order to understand their role in intermolecular interactions [1]. The importance of the hydrogen bonds follows from their particular role in the molecular association thanks to their variable strength and geometry. Indeed depending on the chemical nature of the donor/acceptor as well as on the physical parameters such as temperature and pressure, hydrogen bonds can give rise to directional and/or to hydrophilic like interactions which play a crucial role both in stabilizing static structures and in mediating dynamic biological processes. Among the hydrogen bonds the less common ones are the strongest (and shortest) ones, characterized by donor–acceptor interatomic distances shorter than 2.6 Å with D–H...A angle close to 180° [2]. Most of the short hydrogen bonds observed and reported so far are intramolecular interactions, nevertheless, both the bridging as well as the coordination of the metal ions by carboxylate groups and oxalate anions can provide the possibility of short interactions [3]. During the refinement of the structure of the potassium-monodeprotonated salt of 1,4-butodioxybis(4'-benzoic) acid it was observed a high electron density maxima over the mirror symmetry element. This electron density indicates a hydrogen atom doing an ultra short intermolecular hydrogen bond (2.4846(1) Å) between the deprotonated and non-deprotonated carboxylic acid groups. The seven fold coordinate potassium atom ties the organic moieties pushing the hydrogen atom closer to the deprotonated and negatively charged, carboxylate oxygen atom. The hydrogen atomic displacement parameter suggests, however, a possible positional disorder, which could be interpreted both as symmetrical O–H–O or asymmetrical O–H...O interaction.
Hierarchical model of molecular crystals
Authors: Madura Izabela
Published: November 2015

Spatial arrangement of molecules in molecular crystals depends on properties of molecules building up the crystal, and in particular on the nature of interactions occurring between them. The knowledge about primary and subsequent interactions building up the 3D structure seems to be important in many aspects, just to mention crystal engineering and crystallization processes. If the only interactions between molecules are isotropic van der Waals interactions, the observed structure will resemble a close-packing arrangement. The presence of any directional interactions leads, in accordance to Kitaigorodsky's principles,[1] to the symmetry breaking of the close-packing structure, and resulting crystal exhibits hierarchical organization. The presentation will discuss consequences of directional intermolecular interactions and their impact on generation and organization of successive levels of the hierarchical architecture in crystals. The strategy for identification, analysis and hierarchization of weak intermolecular interactions will also be presented. Selected examples will serve to illustrate usefulness of the proposed model for the discussion on molecular symmetry, supramolecular synthons' equivalency, polymorphism, isomorphism or packing.
Charge density analysis of paracetamol, acetotoluidine and methacetin
Authors: Druzhbin Dmitry , Drebushchak Tatiana , Boldyreva Elena
Published: November 2015

Paracetamol (p-hydroxyacetanilide, Pbca), acetotoluidine (p-methylacetanilide, P21/c) and methacetin (p-methoxyacetanilide, Pbca) contain acetamide group included in molecular fragments, which play an important role in many drugs and proteins. As all of them are derivatives of acetanilide used in medicine, and due to the presence of the amide bond, their charge density analysis is important for better understanding amide infinite peptide chains. Thus, comparing the data obtained for paracetamol with acetotoluidine and with methacetin charge density data can provide deeper insight into NH···O bonding. Another point of interest is the possibility of methyl group rotation that remains to be ambiguous in these acetanilide molecule based compounds. In the present study we have attempted to elucidate these problems using precise X-ray diffraction at 100K with subsequent charge density topological analysis. All charge density refinements were based on the Hansen and Coppens multipolar atom model. The topologies of the inter- and intramolecular interactions are carefully analyzed for compounds. The atomic charges, bond orders, and the electrostatic energy in molecules are discussed. The topological characteristics in the critical point of the NH···O bond of paracetamol, acetotoluidine and methacetin are shown in the table below. In contrast to similarity in NH···O bonds for all studied compounds, intermolecular interactions between the double bonded oxygen atom and the hydrogen of dimer's methyl group are different. In acetotoluidine and methacetin the (3, –1) critical points with the same topological characteristics were detected between these atoms. In comparison to them, paracetamol with disordered methyl group [1, 2] has no such point. That can be related to the absence of the methyl group disorder in acetotoluidine and methacetin.
Molecular complexes of cyclohexanehexacarboxylic acid with aza-donors
Authors: Biswas Sharmita , Pedireddi V.
Published: November 2015

Hydrogen bond mediated molecular complexes of cyclohexane-1,2,3,4,5,6-hexacarboxylic acid (1) with aza-donors distinguished by positional isomerism like 4,4'-bipyridine (a), 2,2'-bipyridine (b), trans-1,2-bis(4-pyridyl)ethylene (c), trans-1,2-bis(2-pyridyl)ethylene (d), 4,7-phenanthroline (e) and 1,10-phenanthroline (f) have been prepared either from a solvent mixture of methanol-water or from DMSO by solvent evaporation method. All the complexes crystallized as hydrates with different molecular ratios of 1, aza-donor and water. Detailed structural analyses of these molecular complexes have been investigated by single crystal X-ray diffraction. Structural diversity was found in the landscape of these molecular complexes depending upon the flexibility and positional isomerism of organic spacers (aza-donors) as well. Both intra and inter molecular hydrogen bonds played an important role in the formation of supramolecular architectures. Intramolecular O-H...O hydrogen bonds are present in the acid molecule due to the favourable orientation of -COOH groups in the chair form of the cyclohexane ring. In basic recognition pattern of each complex, it has been noted that acid molecules interact with aza-donors as well as water molecules through O-H...N and O-H...O hydrogen bonds, respectively. Different topological patterns like sheets, tapes, ribbons and host-guest networks have been observed in three dimensional arrangements. Inclusion of water molecules in each molecular adduct indicates the importance of water molecules to stabilise the molecular ensembles of 1 and the corresponding aza-donors. Presence of water molecules in the crystal lattices was also supported by thermogravimetric analysis (TGA).
Photochemical Reactions of Hydrogen-bonded Coordination Polymers
Authors: Vittal Jagadese
Published: November 2015

Crystallization is a kinetic phenomenon and the experimental conditions like solvents, concentration, pH, temperature and time have greater influence on the nature of products in the synthesis of coordination network structures. During crystallization, the solvents and ligands bind to the metal ions reversibly and hence, the least soluble polymer will crystallize first, independent of the metal-ligand ratio used in the crystallization. The kinetic products quite often contain solvents bonded to the metal ions. The removal of these coordinated solvents is likely to transform the kinetically formed coordination polymers (CPs) into thermodynamically stable products. In these structural conversions, supramolecular interactions play a major role. Such structural transformations as well as [2+2] cycloaddition reactions have been demonstrated in many coordination polymeric network structures aided by the directional hydrogen bonding interactions. A number of structural transformations involving the loss of solvent molecules and use of photodimerization reactions in the solid state will be presented in this talk.
The structure of the full icosahedral group
Authors: Lee Dong-il , Lee Jeong-Yup
Published: November 2015

We consider the full icosahedral group, which is the Coxeter group of type H_3. The Coxeter groups appear naturally in geometry and algebra. In 1935, the finite Coxeter groups were classified by Coxeter in terms of Coxeter-Dynkin diagrams. We remark that the affine extensions of the Coxeter groups of types H are related to quasicrystals with tenfold symmetry. Our approach to understanding the structure of Coxeter groups is the noncommutative Groebner basis theory, which is called the Groebner-Shirshov basis theory. By completing the relations coming from a presentation of the Coxeter group, we find a Groebner-Shirshov basis to obtain a set of standard monomials. Especially, for the Coxeter group of type H_3, its Groebner-Shirshov basis and the corresponding standard monomials are constructed. Thus, we understand the algebra structure of the group algebra C[H_3], which is not commutative.
Dynamical Spectrum and Diffraction
Authors: Sadun Lorenzo
Published: November 2015

The diffraction spectrum of a point pattern is very closely related to the dynamical spectrum of an associated dynamical system. This dynamical spectrum is invariant under topological conjugacy and measurable conjugacy, and in particular under a large class of shape deformations. Using measure theory and topology, we construct a pure-point diffractive set, with finite local complexity, that is not a Meyer set. This provides a counterexample to a famous conjecture of Lagarias.
Atomic-scale imaging and spectroscopy of defects in low-dimensional materials
Authors: Suenaga Kazu
Published: November 2015

Atomic defects or edge structures are of great importance for any kind of low-dimensional materials, since the interrupted periodicities strongly affect their physical and/or chemical properties. Studies of point defects in mono-layered materials have become very popular among scientists. Vacancies and topological defects in graphene are routinely examined at atomic level. Defects and edge structures in hexagonal boron nitride (h-BN) and WS2 nano-ribbons are also a hot topic among physicists. Here we describe TEM and spatially resolved EELS studies of various single-layered materials with the interrupted periodicities. Atomic defects and edge structures can be unambiguously identified with the elemental assignment. The monovacancy analysis in h-BN single-layer and the alloying and doping behaviors of MoS2/WS2 single-layers will be presented.
In-situ diffraction experiments at the Photon Factory MX beamlines
Authors: Yamada Yusuke , Matsugaki Naohiro , Hiraki Masahiko , Kato Ryuichi , Senda Toshiya
Published: November 2015

Crystallization trial is one of the most important but time-consuming steps in macromolecular crystallography. Once a crystal appears in a certain crystallization condition, the crystal is typically harvested from the crystallization drop, soaked into a cryoprotection buffer, flash-cooled with a liquid nitrogen or cold gas flow and finally evaluated its diffraction quality by an X-ray beam. During these long process, crystal may be damaged and the result from the diffraction experiment does not necessarily reflect a nature of the crystal. On in-situ diffraction experiment, where a crystal in a crystallization drop is directly irradiated to an X-ray beam, a diffraction image from a crystal without any external factors such as harvesting and cryoprotection and, as a result, a nature of crystal can be evaluated quickly. In the Photon Factory, a new table-top diffractometer for in-situ diffraction experiments has been developed. It consists of XYZ translation stages with a plate handler, on-axis viewing system with a large numeric aperture and a plate rack where ten crystallization plates can be placed. These components sit on a common plate and it is placed on the existing diffractometer table in the beamline endstation. The CCD detector with a large active area and a pixel array detector with a small active area are used for acquiring diffraction images from crystals. Dedicated control software and user interface were also developed. Since 2014, user operation of the new diffractometer was started and in-situ diffraction experiments were mainly performed for evaluations of crystallization plates from a large crystallization screening project in our facility. BL-17A [1], one of micro-focus beamlines at the Photon Factory, is planned to be upgraded in March 2015. With this upgrade, a new diffractometer, which has a capability to handle a crystallization plate, will be installed so that diffraction data sets from crystals in crystallization drop can be collected.
Structural Biology Knowledgebase: An Integrated Resource for Modern Biologists
Authors: Gabanyi Margaret , Adams Paul , Chen Li , DePietro Paul , Gifford Lida , Haas Juergen , Minor Wladek , McLaughlin William , Schwede Torsten , Tao Yi-Ping , Westbrook John , Zimmerman Matthew , Berman Helen
Published: November 2015

"The Structural Biology Knowledgebase (SBKB, http://sbkb.org) was established as a data aggregator to facilitate research design and analysis for a wide variety of biological systems. It serves as a single resource that integrates structure, sequence, and functional annotations plus technical information regarding protein production and structure determination. Researchers can search the SBKB by sequence, PDB ID or UniProt accession code, and receive an up-to-the-minute list of matching 3D experimental structures from the Protein Data Bank, pre-built theoretical models from the Protein Model Portal, annotations from 100+ open biological resources, structural genomics target histories and protocols from TargetTrack, and ready-to-use DNA clones from DNASU. It also possible to find structures according to functional relevance (KB-Rank tool), or find related technologies and publications from the PSI Technology and Publications Portals, respectively. Interactive tools such as real-time theoretical modeling and biophysical parameter prediction also enhance understanding of proteins that are not yet well characterized. Experimentally-focused ""hubs"" collect links to helpful tools and resources for the areas of Structural Targets; Structure, Sequence and Function; Homology Models, Methods and Technologies, and Membrane Proteins. In partnership with the Nature Publishing Group, latest research highlights and articles on specific biological systems are written monthly to share the impact of structural biology. This presentation will demonstrate how the SBKB turns data into knowledge and enables further research. SBKB is funded by a grant from the National Institute of General Medical Sciences of the National Institutes of Health (U01 GM093324)."
An unusual metal ion configuration in a viral DNA-packaging nuclease active site
Authors: Zhao Haiyan , Christensen Theodore , Lin Zihan , Lynn Annie , Tang Liang
Published: November 2015

Nucleic acid metabolism is fundamental to many biological processes. A large class of enzymes such as RNase H, reverse transcriptase, retroviral integrase, topoisomerase, DNA and RNA polymerase, transposase, Holliday-junction resolvase, RNAi slicer Argonaute, and viral DNA-packaging terminase, utilize a common two-metal-ion catalytic mechanism for cleavage or synthesis of nucleic acid chains. Here we report an unusual metal-ion cluster in the active site of the nuclease domain of a viral DNA-packaging terminase unveiled by X-ray structures up to 1.38 Angstrom resolution. Two Mg2+ ions are situated in a coupled octahedral coordination system with liganding oxygen atoms from aspartic acid residues as well as water molecules. The two Mg2+ ions are located within a strikingly short distance of ~2.5 Å, which is unusual given the 1.6 Å atomic radius of Mg2+ and is shorter than previously observed metal-metal distances in metallocluster-containing enzymes or other biological systems. This provides the structural basis for distinguishing Mg2+ from other metal ions such as Ca2+ which are well known to support binding of the nucleic acid substrate but not support catalysis. Such an ultra-short distance between two metal-ions may be essential for generation of a highly positive niche, leading to nucleophilic attack at the phosphodiester bond of DNA. These results have defined the precise chemical configuration of the active site in nucleases using two-metal-ion catalytic mechanism. Moreover, assembly of this two-metal-ion cluster in the viral DNA-packaging terminase is mediated by an adjacent Lys residue, likely serving as a regulatory mechanism for activation of the nuclease activity of the terminase during packaging of viral genome.
Weak interaction of an inhibitor in the 20S proteasome
Authors: Murakami Takuto , Yamaguchi Hiroshi , Bahrudin Udin , Kita Akiko , Hisatome Ichiro , Saeki Yasushi , Tanaka Keiji , Unno Masaki , Morimoto Yukio
Published: November 2015

Proteasomes are the multicatalytic protein complexes with huge molecular weight. It is well known that the ubiquitin proteasome system plays an important role in regulated proteolysis. The 26S proteasome is composed of two 19S regulating components and a 20S proteasome. The 20S proteasome forms barrel shape and is composed of four rings, α- and β-rings; each ring contains highly homological seven α-subunits (1~7) and seven β-subunits (1~7), N-terminal tails of α-ring subunit form a gate to facilitate substrate entry. Each of 1, 2 and 5 β–subunit has different enzyme activity; 1 is caspase-, 2 tryptic- and 5 chymotryptic- like activity, respectively. We found a new protease inhibitor compound-A, which interacts weakly against proteasome. In order to elucidate the binding mode of the compound-A to proteasome, structure determination of the 20S proteosme complexed with compound-A was carried out. Isolated and concentrated 20S proteasome was co-crystallized with compound-A. Sitting drop vapor diffusion method was applied using 0.1M MES-NaOH (pH 6.5), 35% MPD, 50 mM magnesium acetate as a reservoir solution and 10 mg/ml proteasome and 20 mM compound-A as a sample solution. Crystals are isomorphous with the previous report [1]. Diffraction images were recorded at 100 K by using ADSC Quantum 210r CCD detector at NW12A of Photon Factory, Tsukuba, Japan. Initial phases were determined by molecular replacement method using the structure of the yeast 20S proteasome [1RYP] as a starting model and the structure model with a ligand was refined by using Refmac5 in CCP4 program package with an R value of 16.5% at 2.85 Å. The electron densities have been observed at the active site as mentioned above in the β-ring. Binding site of compound-A is closed to Tyr170 and Thr1 of the β5 subunit. The compound-A binds weakly to their residues by hydrogen bondings. It is quite different from the binding mode of the known potent proteasome inhibitor bortezomib [2].
A novel six-coordinated ferric ion binding mode of TtFbpA
Authors: Wang Shipeng , Ogata Misaki , Horita Shoichiro , Ohtsuka Jun , Nagata Koji , Tanokura Masaru
Published: November 2015

Iron is an essential element for the growth and survival of nearly all living organisms. However, it is difficult for most organisms to get enough iron from the environment, because of the extremely low solubility of ferric ion. One of the strategies for iron acquisition is to use the ATP-binding cassette (ABC) transport system. In Gram-negative bacteria, a typical iron uptake ABC transporter consists of a ferric ion-binding protein (Fbp) located in periplasm (FbpA), two transmembrane proteins that form a pathway for ferric ions (FbpB), and two peripheral ATP-binding proteins located at the cytoplasm side of the inner membrane (FbpC). TtFbpA is a ferric ion-binding protein of a putative iron uptake ABC transporter from Thermus thermophilus HB8. Here we report the crystal structures of the apo-form and ferric ion-bound form of TtFbpA at 1.8-Å and 1.7-Å resolutions, respectively [1]. The crystal structure of the ferric ion-bound TtFbpA shows that a ferric ion binds to a specific site of TtFbpA to form a six-coordinated complex by three tyrosine residues, two bicarbonates and a water molecule, revealing a novel mode of coordination to a ferric ion. Another crystal structure of ferric ion-bound TtFbpA reported earlier showed the bound ferric ion is five-coordinated by three tyrosine residues and a carbonate bound in the bidentate manner [2]. The different modes of the coordination would probably result from the different pHs used for crystallization: pH 5.5 (six-coordinated) vs. pH 7.5 (five-coordinated). The Gram negative bacterium T. thermophilus HB8 can live in a wide pH range of 3.4–9.6. We propose that TtFbpA, a periplasmic protein of T. thermophilus HB8, can act as a ferric ion-binding protein over the wide pH range by taking at least two different coordination manners to a ferric ion depending on pH. This is the first example of a periplasmic ferric iron-binding protein that can coordinate a ferric ion via multiple types of coordination complex formation.
Structural studies of myo-inositol kinase
Authors: Nagata Ryuhei , Fujihashi Masahiro , Sato Takaaki , Atomi Haruyuki , Miki Kunio
Published: November 2015

The TK2285 protein from a hyperthermopilic archaeon Thermococcus kodakarensis is a myo-inositol kinase. Only two myo-inositol kinases have been identified so far. One is the TK2285 protein and the other is an enzyme from Zea mays. Both of them synthesize myo-inositol monophosphate that shows enantiomerism. Because it is too difficult to discriminate enantiomers by NMR or chromatography analysis, it has not been identified which of the six hydroxyls is phosphorylated by these enzymes. Also, little is known about the substrate recognition of myo-inositol kinase, since only the unliganded crystal structure of TK2285 has been reported. In order to reveal the substrate-binding mechanism of myo-inositol kinase and identify the phosphorylated hydroxyl group of the product, we determined the crystal structures of TK2285 as the substrate-complex and the product-complex. The substrate-complex of TK2285 was prepared by using the TK2285, myo-inositol and AMP-PCP, and the products-complex was prepared by incubating the TK2285 with myo-inositol and ATP. The substrate-complex structure showed that all of the six hydroxyls of myo-inositol interacted with TK2285. This coincides with the fact that the Km value for myo-inositol is 100-1000 fold lower than those for other sugars. Also 3-hydroxyl group of myo-inositol, which the gamma-phosphate of AMP-PCP was nearest to, was thought to be phosphorylated by this enzyme. This was proved by the product-complex structure that had ADP and myo-inositol 3-phosphate. Site-directed mutagenesis and structure comparison with TK2285 homologs also provided information about the substrate-binding mechanism of myo-inositol kinase.