bluuebunny/crossref_metadata_2025 huggingface dataset:
Synthesis and Structure of novel Luminescent lanthanide organic frameworks.
Authors: Abdelbaky Mohammed S. M. , Amghouz Zakariae , Granda Santiago
Published: November 2015

Lanthanide-Organic frameworks (LnOFs) are currently attracting increasing attention due to their excellent luminescence properties, in which both Ln3+ and organic linkers can be used to give rise to luminescence materials with increased brightness and emission quantum yield [1,2]. Lithium doped MOFs are of particular interest due to the recent studies showing enhanced H2 uptake, as well as promising candidates for replacing the conventional electrode in Li-ion batteries [3,4]. Herein, novel Lithium-lanthanide frameworks based on a rigid dicarboxylic acid, formulated as [LiLn(BDC)2(H2O)·2(H2O)] (Ln = Y, Dy, Ho, Er, Yb, Y1-xEux, Y1-xTbx and H2BDC = Terephthalic acid), have been obtained as single phases under hydrothermal conditions. The crystal structures were solved by single-crystal X-ray diffraction and the bulk characterized by powder X-ray diffraction (PXRD), thermal analyses (TG-MS and DSC), vibrational spectroscopy (FTIR), scanning/transmission electron microscopy (SEM-EDX, TEM, SAED, STEM-EDX), and powder X-ray thermodiffractometry (HT-XRD). All compounds are isostructural (monoclinic P21/c, a = 11.6365(7) Å, b =16.0920(2) Å, c = 13.2243(8) Å and β = 132.23(1)° for Ln = Y [5]) and possess a 3D framework with 1D trigonal channels running along the [101] direction contain water molecules. The structure is built up of unusual four-membered rings formed by edge- and vertex-shared {LnO8} and {LiO4} polyhedra. The four-membered rings are isolated and connected to each other via carboxylate groups. Topologically, the 3D frameworks belongs to a new 2-nodal 3,10-c net with point symbol of {4.5^2}2{4^14.5^10.6^18.7.8^2}. HT-XRD reveals that the compounds undergo phase transformation upon dehydration process which is a reversible process involving a spontaneous rehydration characterized by fast kinetic. The luminescence properties of selected compounds are also studied.
New Oxomolybdenum(VI) Hybrid Materials
Authors: Ribau Amarante Tatiana , Neves Patrícia , Almeida Paz Filipe Alexandre , Valente Anabela , Pillinger Martyn , Sousa Gonçalves Isabel
Published: November 2015

The chemistry of MovIoxides is dominated by complexes containing the cis-dioxomolybdenum(VI) structural units. Many of these complexes have been investigated as epoxidation catalysts and a number of papers have been published on the effect of nitrogen donor ligands. The motivation to study these discrete, homogeneous catalysts in the form of monomeric or dimeric species stemmed from the fact that they are well-defined, single site catalysts, which usually favour high reaction activities and product selectivities. Our research group has investigated the reaction of dichlorodioxomolybdenum(VI) complexes with excess water using three distinct heating methods: hydrothermal, reflux or microwave-assisted synthesis. The main challenge was to design and prepare novel heterogeneous MovIcatalysts with the same catalytic properties and kinetics usually attained from the homogeneous counterparts. The results led to the isolation of several higher nuclearity oxomolybdenum(VI) compounds, namely the octanuclear complex [Mo8O22(OH)4(di-t-Bu-bipy)4] (di-tert-butyl-2,2'-bipyridine),[1] and the polymeric materials {[MoO3(bipy)][MoO3(H2O)]}n (2,2'-bipyridine)[2] and {[Mo3O9(pzpy)}n (2-[3(5)-pyrazolyl]pyridine).[3] These compounds where characterized by using solid-state techniques, namely elemental analyses, thermogravimetry, FT-IR, solid-state NMR, electron microscopy and powder X-ray diffraction (both from laboratory and/or synchrotron sources). The catalytic behaviour of the discrete complexes and the polymeric compounds was tested in olefin epoxidation reactions. Fundação para a Ciência e a Tecnologia (FCT, Portugal; PTDC/EQUEQU/121677/2010; PTDC/QEQ-SUP/1906/2012; SFRH/BPD/97660/2013; EXPL/CTM-NAN/0013/2013 - FCOMP-01-0124-FEDER-041282), the European Union, QREN, FEDER, COMPETE, and Associate Laboratory CICECO (PEst-C/CTM/LA0011/2013) are gratefully acknowledged for funding.
Antimicrobial complexes of Schiff base ligands and copper family metal ions
Authors: Kracht Sonja , Fromm Katharina
Published: November 2015

Schiff base complexes were extensively studied because of their catalytic properties in various fields and partly for their biological activity[1]. The utilisation of copper (II)[2] and silver (I)[3] can introduce antimicrobial properties to these structures or enhance them; thus provides new fields of applications, like in medicine. Compared to classical Schiff bases, the synthesis of dual N,N-donor Schiff bases is facile too, and the resulting product contains several coordination sides for diverse metals. Applying these unique advantages, we developed several antibacterial Schiff base metal complexes. Our ligand system is based on functionalized pyridine end-capped imine linker units which differ in the nature of the linker chain, such as ethylene glycols or alkyl chains. Substitution on the pyridine rings offer the possibility to attach oligomers or polymer chains which can work e.g. as handles. By applying, for example, mechanical force, like ultra-sonication, the metal ions can be released (Figure 1) by an external trigger and used for catalysis or in medicine, where its antimicrobial properties are required. Figure 1: Schematic illustration of controlled silver release from a ligand-polymer system by applied force (arrows).
Kinetic Assembly of a Thermally Stable Porous Coordination Network
Authors: Kitagawa Hakuba , Ohtsu Hiroyoshi , Kawano Masaki
Published: November 2015

The advantage of porous coordination network synthesis is designability by changing metal sources and ligands.[1] Therefore, not only many commercially available ligands but also newly synthesized ones were used for networking. On the other hand, most of metal sources are common reagents or stable metal moieties because they can be more predictable as a metal connector. So far, there is no report focusing on usage of labile metal sources for selective network formation. One of the promising methods to produce unique networks with such labile metal sources is kinetic control[2] because labile metal sources produce various species in solution. In this talk, we will introduce selective syntheses of thermally stable porous coordination networks using a labile Cu4I4 cubane cluster [Cu4I4(PPh3)4] (1) and a rigid tetradentate Td-symmetry ligand tetra-(4-(4-pyridyl)phenyl)methane (2) by kinetic and thermodynamic control.[3] On heating the mixture of 1 and 2 in DMSO at 453 K, a homogenous colorless solution was obtained. Rapid cooling (~20 Kmin-1) of the solution produced yellow needle crystals, {[(CuI)2(2)]·solvent}n (3a) that shows novel CuI helical chain unit, in 99% yield (Fig. A). On the other hand, slow cooling (~3 Kmin-1) produced orange block crystals, {[(Cu2I2)(2)]·solvent}n (3b) that shows rhombic Cu2I2 dimer unit, in 95% yield. Both the network crystals can keep the crystallinity up to 673 K under N2 atmosphere. In kinetic product 3a, due to the unique structure, iodides of the CuI chains facing to 1D channel, the network crystal shows chemisorption of I2 by making a covalent bond with an iodide of part of the CuI chains to form an I3– group (Fig. B). On the other hand, in thermodynamic product 3b, Cu2I2 dimer units are hindered by bridging ligand 2. That is why network crystal 3b shows only physisorption of I2, even though network has 1D channel similar to 3a.
The synthesis of lanthanide based sandwich type polyoxometalates
Authors: Kaur Amanpreet , Hundal Maninder
Published: November 2015

Polyoxometalates (POMs) have been declared as a rising field in advance inorganic chemistry, since the first polyanion was reported by Berzelius in 1826. Polyoxometalates (POMs) containing Keggin and Wells-Dawson moieties are chemically robust and can be easily modified with incorporation of different metal ions [1]. The incorporation of Ln(III) ions into polyoxometalates offers unique functionality for generation of new complexes containing luminescent, magnetic, catalytic and surface functional properties [2]. Ln(III) ions are having multiple coordination number, can link polyoxometalates into solid-state oligomers, sandwich-type and large wheel structures. Mono-lacunary or mono-vacant sandwich type clusters are obtained by removing octahedral metal atoms from POM cluster and connecting two POM units by lanthanide ions. These complexes are having interesting magnetic properties due to valence electrons in 4f and may behave like single molecular magnets, as reported in literature. These also exhibit photoluminescence properties followed by excitation of O-W ligand to metal charge transfer. In Ln-POMs, Ln ions can play important role in connecting POM units due to their high oxophilicity and coordination flexibility. Moreover, the assembly of purely inorganic POM-based frameworks occupies high potentiality for the synthesis of new porous materials which combine the thermodynamic stability of zeolites and mesoporous silicas [3]. So taking a cue from the literature, we have studied the interactions of polyoxometalate anions with different lanthanide ions like Eu(III), Nd(III), Sm(III) and Gd(III). The above mentioned Ln(III) based complexes are sandwich type, have been isolated and characterized by means of FT-IR spectroscopy, thermo gravimetric analysis (TGA) and X-ray single crystal analysis. Single-crystal X-ray diffraction analyses shows that in these POM units the Ln(III) ion(s) substitute for [WO]4+ unit(s) in the `cap' region of the tungsten-oxygen framework of the parent Keggin ion. In each cluster, sandwich structures in the asymmetric unit are linked by K(I) cation. Each potassium atom is coordinated with terminal oxygen atoms and these terminal oxygen atoms are forming bridge between Ln(III) and K(I) ions. The coordination numbers of potassium metal ions vary from 6 to 11 in different clusters. These bridging K+ ions are responsible for 3-D structure in each complex.
Molecular structure investigation by ab initio, DFT and X-ray diffraction of thiazole-derived compound
Authors: Boulakoud Manel , Chouaih Abdelkader , Hamzaoui Fodil
Published: November 2015

We report here the synthesis of Z-3-(2-Ethoxyphenyl)-2-(2-Ethoxyphenyl)-1,3-Thiazolidin-4-one compound. The crystal structure has been determined by X-ray diffraction. The compound crystallizes in the monoclinic system with space group P21/n and cell parameters: a = 9.4094(10), b = 9.3066(10), c = 20.960(2) Å, β=99.0375(10)0, V = 1812.7(3)Å3 and Z = 4. The structure has been refined to a final R = 0.05 for 2083 observed reflections. The refined structure was found to be significantly non planar. The molecule exhibits intermolecular hydrogen bond of type C–H...O, C–H...N and C–H...S. Ab initio calculations were also performed at Hartree–Fock and density functional theory levels. The full HF and DFT geometry optimization was carried out using 6-31G(d,p) basis set. The observed molecular structure is compared with that calculated by both HF and density functional theory methods. The optimized geometry of the title compound was found to be consistent structure determined by X-ray diffraction.
Mixing and Quantifying Multi-Component Materials for Pyrotechnic Applications
Authors: Blair Lisa , Coles Simon , Sinclair Ian , Vrcelj Ranko
Published: November 2015

This multidisciplinary research is looking at the relationship between components of a pyrotechnic product and how manufacturing, in particular the mixing method employed, affects its macroscopic structure and properties. For pyrotechnics to produce the desired effect the ingredients must be intimately mixed, however, the present physical mixing approach can lead to inconsistencies in performance between batches. X-ray computed tomography (CT) was used to investigate the distribution of components in a pyrotechnic mixture. Near-neighbour distances between particles were calculated and used to assess the homogeneity of the mixtures and the efficiency of combustion. Another strand of this research to overcome batch inconsistencies was by chemically binding pyrotechnic ingredients rather than physically mixing them together. One method of achieving this was through incorporating two or more components within the same crystalline lattice. This may be achieved through co-crystallisation or coordination in functional frameworks, thereby reducing the number of components in a physical mixture and minimising the variation between batches. Pang et al. have investigated using MOFs (metal-organic frameworks) to stabilise energetic materials [1]. The research presented here uses MOFs to bring together fuels and oxidisers into one framework to create a MOFirework. Numerous linkers and metal centres were investigated to build up a structural family to correlate structure with pyrotechnic function (e.g. changing burn colour; Sr = red, Ba = green). Both powder and single crystal X-ray diffraction were used to characterise the products. Differential scanning calorimetry was used to look at the thermal profiles to investigate their possible uses as pyrotechnics. Lastly, a burn test was carried out to determine their pyrotechnic effect (e.g. gas, smoke, gas, light, heat, colour, and sound) and quantitatively link this to structure.
Synthesis, magneto-structural features and thermal behavior of a new MOF
Authors: Aliouane Khadidja , Benmerad Belkacem , Rahahlia Narimène , Kherfi Hamza , Guehria-Laïdoudi Achoura , Dahaoui Slimane , Lecomte Claude
Published: November 2015

By applying soft synthesis conditions, in presence of a mixture that contains malonic acid, (3 mmol), lanthanide salt CeCl3.7H2O (1 mmol), alkaline-earth hydroxide Ca(OH)2 (1 mmol), and at pH below 4, we have obtained single crystals of a novel rare-earth complex which includes the dianion [L2-], {[Ce2(C3H2O4)3(H2O)3].2H2O}.The given formula was deduced from the single crystal structure analysis. The asymmetric unit corresponds to chemical formula (Figure 1). This novel polymeric compound is a three-dimensional MOF, built up from cross-linked infinite chains of one-edge-shared CeO7(H2O)3 and CeO9 polyhedrons embedding solvent molecules. Each crystallographically different metal is connected to two neighbouring ones, through four μ2-oxo bridges, to form repeat four-membered typical Ce/O/Ce/O rings. The three independant ligands show different conformations of their end functional groups: syn-syn, syn-anti, anti-anti, giving explanation for the concomitant magnetic interactions and interesting magneto-structural data. These studies are still in progress. The TG curve shows five successive weight losses. The material begins losing weight directly upon starting the thermal gravimetric experiments. It is one of the more unstable lanthanide malonates known. The correlative thermal behaviour data and X-Ray structural sub-features of the novel Ce(III)-based MOF obtained, brought out the great supramolecular effects: decarboxylation process, crystalline, and thermal stabilities are much more related to the specific infinite hydrogen patterns, than the size, shape, and embedding capability of voids accommodated in the 3D packing.
Structural Studies of Iron(III) Complexes with N4O2 Coordination Sphere
Authors: Fuentealba Mauricio , Gonzalez Deborah , Artigas Vania
Published: November 2015

The Spin-Crossover (SCO) phenomenon implicates a switchable between a low-spin (LS) diamagnetic state, which is stable at low temperatures and a paramagnetic high-spin state (HS), which is stable at higher temperatures. This transition is generated by an external perturbation such as temperature, pressure or light. In general, the switching process in solid-state systems is controlled by cooperative intermolecular interactions. The correlation of structure with physical properties is crucial to the identification of these interactions and ultimately the understanding of the complex processes that control the SCO phenomenon[1]. With the aim of developing new SCO materials, we carried out the syntheses and crystal structure analysis of seven iron(III) complexes, mixing 5-bromo-salicylaldehyde or 5-chloro-salicylaldehyde and ethylendiamine with iron(III) chloride and/or ammonium hexafluorophosphate solutions by slow diffusion or reflux in methanol or 2-propanol (figure 1). The crystal structures show the iron(III) centre is hexacoordinated (FeN4O2) and the coordination polyhedron can be described as a distorted octahedron formed by the 4 N atoms of the ethylenediamine fragment and 2 hydroxyl O atoms from the salicylaldehyde fragment, this distortion was evaluated at 120 and 298 K, the major distortion were observed in complexes [2]+ PF6–· MeOH, [2]+ PF6–·iPrOH and [1]+ PF6–·MeOH, which is characteristic in HS states, while the complexes [2]+ Cl–·iPrOH, [1]+ PF6–·iPrOH [2]+ and [2]+ClO4–, shows a minor distortion according to LS states. On the other hand, [1]+ClO4– is a SCO complex with a typical geometry for both spin states at 120 K (LS) and 298 K (HS). Finally, we studied the intermolecular interactions using Crystal Explorer Software[2] between the iron complexes, the counterion and/or the solvate molecule, for instance, in the [2]+PF6–·MeOH complex, the most remarkable feature observed are Br···Br intermolecular interactions (figure 2). ACKNOWLEDGMENTS: FONDECYT N01130640, FONDEQUIP EQM120095 and Beca CONICYT folio 21130944
Heterogeneous catalitic activity of Novel Indium MOFs
Authors: Aguirre-Diaz Lina , Iglesias Marta , Snejko Natalia , Gutierrez-Puebla Enrique , Monge Maria
Published: November 2015

Generally, group IIIA metal-based polycarboxylates are less studied, compared with those of transition or rare earth metals. However, In-MOFs have received recently much attention due to their interesting network topologies, which are mainly owing to the variety of coordination modes (6, 7 or 8) in indium MOFs with O- and N-donor ligands. [1]. Some of In-MOFs exhibit an exceptional gas absorption, fluorescent, ion-exchange properties, and can be used as heterogeneous Lewis acid catalysts in various organic transformations. The high relevance of Indium materials in catalytic studies for important organic reactions led to development of indium MOFs. [2-3] Here we report the solvothermal synthesis, structural characterization, topological analysis and catalytic studies of six new indium-based MOFs using 5-(4-carboxy-2-nitrophenoxy)isophtalic acid (H3popha) together with N-donor ancillary ligands (Figure 1). The three indium compounds showing 3D networks are the following: [In8(OH)6(popha)6(H2O)4]·xH2O (1), [In2(popha)2(4,4-bipy)2] (2) and [In3(OH)3(popha)2(4,4'-bipy)2]·xH2O (3). Meanwhile, compounds with a 2D network have a composition [In(popha)(1,10-phen)]·xH2O (4), [In(popha)(1,10-phen)]·xH2O (5) and [In(popha)(2,2'-bipy)]·xH2O (6). The catalytic study performed using indium compounds 1-6 as catalysts in a Lewis acidity promoted organic reaction, allows for establishing a connection between the corresponding MOF network dimensionality and its catalytic behavior.
Mapping topology and structural disorder in [M(CN)2]- coordination polymers
Authors: Hill Joshua , Thompson Amber , Goodwin Andrew
Published: November 2015

Dicyanometallate coordination polymers show a number of desirable properties: piezoelectricity, record-breaking negative thermal expansion (NTE) and negative linear compressibility (NLC), vapochromism, and luminescence. Despite this, the rules governing the structural trends arising from the use of this roughly 10 Å linker, [M(CN)2]- where M = Cu, Ag, or Au, are relatively poorly explored. This talk is concerned both with mapping the composition–connectivity relationship in these systems and understanding the role of guest cation size/shape mismatch. We show that using guest cations that would be a poor fit for the void-space in commonly adopted topologies can lead to two structural phenomena exemplified in compounds reported here. Firstly, the adoption of unusual topologies, such as 5-connected frameworks e.g.[Bu4N]0.5Cd[Ag(CN)2]2.5 and secondly, correlated structural disorder as seen in molecular perovskite analogues [Bu4N]M'[Au(CN)2]3 where M' = Cd, Mn, Fe.
New platforms for gas separations and storage, chemical sensing, and catalysis
Authors: Zaworotko Michael , Perry John
Published: November 2015

"Over the past two decades Metal-Organic Materials (MOMs), as exemplified by porous coordination polymers, discrete metal-organic polyhedra and metal-organic frameworks, have experienced tremendous growth in both the number of research papers and their impact. MOMs are receiving such attention thanks to their modular nature which affords them the potential to offer game-changing solutions for several important technological problems. MOMs can exhibit permanent porosity and many of their most anticipated applications, such as gas storage (carbon dioxide sequestration, natural gas, and hydrogen storage for energy applications), chemical separations, chemical sensing, catalysis, and drug delivery, involve the uptake or encapsulation of guests. Further, as they can often be obtained in a crystalline form, MOMs are also well suited to act as platforms materials for probing structure-property relationships. This presentation will survey several promising new MOM platforms that are being pursued by our research group and will address their performance with respect to carbon dioxide capture and sequestration, natural gas storage, and catalysis. Additionally, we will place these results in the context of the ""2-step"" crystal engineering principles that guided our research into the rational design of these high-performance materials (see Figure)."
Neutron crystal structure of human FPPS complexed with risedronate
Authors: Yokoyama Takeshi , Ostermann Andreas , Mizuguchi Mineyuki , Niimura Nobuo , Schrader Tobias , Tanaka Ichiro
Published: November 2015

Nitrogen-containing bisphosphonates (N-BPs), such as risedronate and zoledronate, are currently used as clinical drug for bone-resorption diseases and are potent inhibitor of farnesyl pyrophosphate synthase (FPPS). The potential of N-BPs as antitumor agents has also been suggested by the several in vitro and in vivo preclinical studies. However, BP drugs limit their therapeutic use to bone-related diseases, because BPs are highly charged and water soluble molecules. X-ray crystallographic analyses of FPPS with N-BPs have revealed that N-BPs bind to FPPS with three magnesium ions and several water molecules. In order to develop a novel FPPS inhibitor, the hydrogen-bond networks formed by FPPS, BPs and water molecules are necessary to be elucidated. To understand the structural characteristics of N-BPs bound to FPPS, including hydrogen atoms and hydration by water, neutron diffraction studies were initiated using BIODIFF at the Heinz Maier-Leibnitz Zentrum (MLZ). FPPS-risedronate complex crystals of approximate dimensions 2.8 × 2.5 × 1.5 mm (~ 3.5 mm3) were obtained by repeated macro-seeding. Monochromatic neutron diffraction data were collected to 2.4 Å resolution with 98.4% overall completeness and 10.7% Rmerge. As a result of X-ray/neutron joint refinment, R and Rfree values for the neutron data were 19.6 and 23.3%, respectively. This neutron structure clearly reveals the protonation state of risedronate, hydration in the inhibitor-binding region. Furthermore, the amide H/D exchange analysis showed that there is a highly rigid region which regulate the structural change upon the binding of the ligands. Here we will discuss the detailed hydrogen-bond network and the protonation state of FPPS and risedronate.
High-resolution neutron structure analyses of porcine pancreatic elastase
Authors: Tamada Taro , Kinoshita Takayoshi , Yamada Mitsugu , Kurihara Kazuo , Tada Toshiji , Kuroki Ryota
Published: November 2015

Elastase is a serine protease classified in the chymotrypsin family, and is attractive target for studies of structure based drug design (SBDD). The structural information including hydrogen positions and hydration will help us to further elucidate the catalytic mechanism of serine protease. To obtain such structural information, we performed the neutron structure analyses of porcine pancreatic elastase (PPE) with and without its inhibitor using diffraction data obtained at a BIX-3 diffractometer in the research reactor JRR-3. The PPE structure in complex with a peptidic inhibitor, which was used to mimic the tetrahedral intermediate state, was determined to 1.65 Å resolution [1]. His57, Asp102, and Ser195 (chymotrypsin numbering) compose the "catalytic triad" conserved in the active site of serine protease. The complex structure determined by neutron crystallography shows that the hydrogen bond between His57 and Asp102 is essentially short but conventional hydrogen bond, not a low-barrier hydrogen bond. In addition, this neutron structure clearly shows that the oxygen of oxopropyl group of the inhibitor is present as an oxygen anion rather than a hydroxyl group, supporting the role of the oxyanion hole in stabilizing the intermediate in catalysis. The neutron structure of PPE without inhibitor determined to 1.9 Å resolution shows that a water molecule and hydroxyl group of Ser195 block to two backbone amides of Gly193 and Ser195, which form oxyanion hole, respectively. This structural information allows us to understand the role of resting state upon the catalytic reaction. Furthermore, the structural change of the active site residues including hydration structure obtained from the comparison between structures with and without inhibitor may help designing potent inhibitors by SBDD.
Monoclinic HEWL derivative structure at 0.75 Å resolution
Authors: Pompidor Guillaume , Cianci Michele , Schneider Thomas
Published: November 2015

Tris-dipicolinate lanthanide complex, Na3.[Ln(DPA)3], where DPA stands for pyridine-2,6 dicarboxylate, has been proven to be especially interesting to produce derivative crystals with high phasing power [1]. The lanthanide complex can act as a cross-linking agent, which binds at the interface between protein molecules, leading to a supramolecular interaction at the crystal scale [2]. In the case of hen egg-white lysozyme (HEWL), derivative crystals obtained by co-crystallization with Yb(DPA)33-belong to the space group C2, in similar crystallization conditions that normally lead to the tetragonal form P43212. Data were collected on a derivative crystal up to a resolution of 0.75 Å at the EMBL beamline P13 at PETRA III at DESY (Hamburg, Germany). Taking advantage of the high the resolution and the strong anomalous signal of the Yb3+(f″ = 5.2 e-at 17 keV), the structure was solved by both SAD and ab initio methods. Data collection, experimentally phased electron density maps and the structure, especially with respect to the vicinity of the lanthanide binding sites, will be discussed.
Structure and mechanism of LGK: insights into the bioconversion of levoglucosan
Authors: Bacik John , Broom-Peltz Brian , Jarboe Laura , Mark Brian , Michalczyk Ryszard , Fisher Zoe , Unkefer Clifford
Published: November 2015

Lignocellulosic biomass is an abundant source of carbohydrates that can be used for the production of biofuels. Additional processing of biomass-derived sugars arises from the fact that the most abundant sugar product from biomass pyrolysis is the unusual anhydro-ring containing sugar, levoglucosan (LG). LG does not fall within the native substrate range of commonly used biocatalysts such as Escherichia coli and Saccharomyces cerevisiae. However, LG can be further converted to glucose-6-phosphate through the activity of the sugar kinase known as levoglucosan kinase (LGK), which has been isolated from a variety of fungal sources. Integration of recombinant LGK from Lipomyces starkeyi into an engineered ethanologenic Escherichia coli strain has been shown to allow for the utilization of LG as the sole carbon source for ethanol production [1]. However, challenges associated with effective utilization of LG include a high Km of LGK for LG, and the relatively low activity of LGK at physiological pH. In addition to the practical applications of LGK for biofuel production, the enzyme is an exceptional target for structural and mechanistic studies since it appears to possess dual hydrolase and kinase functionality. In order to gain a better understanding of the structure and mechanism of LGK, we have crystallized and determined several high-resolution X-ray structures of Lipomyces starkeyi LGK bound to reaction substrates and products. We have also recently collected low-resolution neutron diffraction for an LGK crystal, and further optimization of LGK crystals is currently underway to improve crystal size and diffraction. Neutron diffraction will reveal the protonation states of key residues in the active site of LGK and provide highly detailed information about hydrogen bonds, including water-bonding interactions. The rational design of new LGK constructs will be used to improve applications of this enzyme towards levoglucosan derived biofuel production.
Crambin - record in crystallographic resolution for a biological macromolecule
Authors: Kallio Johanna , Lamzin Victor
Published: November 2015

A couple of years ago a study was presented that set the record for the highest X-ray crystallographic resolution for a biological macromolecule [1]. The structure of the small protein crambin was determined to 0.48 Å resolution - this almost doubled the amount of available experimental data. Crambin is a small protein consisting of 46 amino acids belonging to the thionin family. Although the protein and its structure has long been known, it lacks any obvious enzymatic activity and has a hard-to-guess biological function. The protein crystallizes readily and serves as an excellent specimen for exploring the limits of resolution of the diffraction. The results demonstrated the possibilities that can be offered by a high-energy synchrotron source. The structure refined with Refmac, Shelxl and Mopro revealed a wealth of details. Bonding electron density became visible along the main chain. However, no fundamental additional structural features could be detected in comparison to the previously collected data set to 0.54 Å resolution. The availability of extremely high-resolution data is certainly of great help to drive further software development and methods for data interpretation. The question will always remain as to what the true limits are in terms of what can be seen in a biological macromolecule. Here we will present the results of our recent efforts in interpretation of such ultra-high resolution data.
Ultra-high resolution structure of high-potential iron-sulfur protein
Authors: Hirano Yu , Takeda Kazuki , Kurihara Kazuo , Tamada Taro , Miki Kunio
Published: November 2015

It is important for understanding the electron transfer reaction to include the information about valence shell electrons and hydrogen atoms into crystal structure refinement. High-potential iron-sulfur protein (HiPIP) possesses a Fe4S4 cluster which exhibits +2/+3 redox states and acts as an electron carrier from cytochrome bc1 complex to the reaction center complex in photosynthetic purple bacteria. We have reported the X-ray crystal structure of HiPIP from Thermochtomatium tepidum at 0.72 Å resolution (1). Recently, we have successfully collected 0.48 Å resolution data of HiPIP using high-energy X-rays (31 keV) in BL41XU beamline of SPring-8. We performed multipolar refinement with the MoPro program (2) to consider valence shell electrons in the structure refinement of HiPIP. Refinement of multipolar parameters was applied to atoms of single conformational residues, water molecules with two hydrogen atoms, and the Fe4S4 cluster. After multipolar refinement, the deformation map clearly displays the distribution of valence shell electrons such as lone-pair electrons of carbonyl oxygen atoms, bonding electrons in aromatic rings, and d-orbital electrons of Fe atoms in the Fe4S4 cluster. The deformation map also indicates electrostatic interactions between the S atoms of Fe4S4-(Cys-Sγ)4 and protein environment. In addition, we performed preliminary neutron diffraction experiment at iBIX beamline of Japan Proton Accelerator Research Complex (J-PARC) and observed diffraction spots up to 1.17 Å resolution using HiPIP crystal with the size of 2.3 mm3. In the multipolar refinement, the positions of hydrogen atoms were fixed to the standard bond distances derived from neutron crystal structures of small molecules and atomic displacement parameters of hydrogen atoms were constrained to 1.2 or 1.5 fold of their root atoms. Therefore, a high resolution neutron structure of HiPIP will improve the results obtained from the multipolar refinement.
Structural flexibility revealed by ultra-high resolution data
Authors: Dauter Zbigniew
Published: November 2015

Not many macromolecular crystals diffract X-rays to ultra-high resolution, defined usually as higher than 0.8 Å, and in the Protein Data Bank there are currently 43 such submissions. These structures range in size from antibiotics of about a hundred atoms to proteins with more than 3,000 independent atoms in the asymmetric unit of the crystal cell. The unprecedented data resolution reveals a great wealth of structural details, which cannot be visualized by analyses at lower resolution. The accuracy of the refined stereochemical and geometrical parameters is then comparable with values typical for small-molecular crystallography and exceeds the accuracy of the library of the standard restraint target values, routinely used in refinement of proteins and nucleotides. Somewhat unexpectedly, the very high resolution diffraction does not necessarily relates to extreme stability of the crystallized molecules, so that the obtained electron density maps reveal significant parts of the atomic models existing in multiple conformations, slightly differing from each other. For example, about 1/3 of the protein chain in the 0.65 Å structure of lysozyme [1] and majority of phosphate groups in the 0.75 Å structure of Z-DNA dodecamer [2] could be modeled in double conformations.
Quasicrystal approximants solved by Rotation Electron Diffraction (RED)
Authors: Hovmöller Sven , SINGH Devinder , Wan Wei , Yun Yifeng , Grushko Benjamin , Zou Xiaodong
Published: November 2015

We have developed single crystal electron diffraction for powder-sized samples, i.e. < 0.1μm in all dimensions. Complete 3D electron diffraction is collected by Rotation Electron Diffraction (RED) in about one hour. Data processing takes another hour. The crystal structures are solved by standard crystallographic techniques. X-ray crystallography requires crystals several micrometers big. For nanometer sized crystals, electron diffraction and electron microscopy (EM) are the only possibilities. Modern transmission EMs are equipped with the two things that are necessary for turning them into automatic single crystal diffractometers; they have CCD cameras and all lenses and the sample stage are computer-controlled. Two methods have been developed for collecting complete (except for a missing cone) 3D electron diffraction data; the Rotation Electron Diffraction (RED) [1] and Automated Electron Diffraction Tomography (ADT) by Kolb et al. [2]. Because of the very strong interaction between electrons and matter, an electron diffraction pattern with visible spots is obtained in one second from a submicron sized crystal in the EM. By collecting 1000-2000 electron diffraction patterns, a complete 3D data set is obtained. The geometry in RED is analogous to the rotation method in X-ray crystallography; the sample is rotated continuously along one rotation axis. The data processing results in a list of typically over 1000 reflections with h,k,l and Intensity. The unit cell is typically obtained correctly to within 1%. Space group determination is done as in X-ray crystallography from systematically absent reflections, but special care must be taken because occasionally multiple electron diffraction can give rise to very strong forbidden reflections. At +/-60° tilt with 0.1° steps, a complete data collection will be some 1200 frames. With one second exposures this takes about one hour. There is no need to align the crystal orientation. The reciprocal lattice can be rotated and displayed at any direction of view. Sections such as hk0, hk1, hk2, h0l and so on can easily be cut out and displayed. We have solved over 50 crystal structures by RED in one year. These include the most complex zeolites ever solved and quasicrystal approximants, such as the pseudo-decagonal approximants PD2 [3] and PD1 in AlCoNi. Observed and calculated sections of reciprocal space (cut at 1.0Å) are shown in Fig. 1. Notice the 10-fold symmetry of strong reflections.
Biomolecular systems under pressure
Authors: Katrusiak Andrzej , Aniola Michalina , Dziubek Kamil , Ostrowska Kinga , Patyk Ewa
Published: November 2015

Biological systems are often regarded as the ultimate goal of all knowledge in this respect that they can provide the clue for understanding the origin of life and the means for improving the life conditions and healthcare. Hence the interest in high-pressure behavior of organic and biomolecular systems. Such simple organic systems were among the first structural studies at high pressure at all. They included chloroform by Roger Fourme in 1968 [1] and benzene by Piermarini et al. in 1969, still with the use of photographic technique. The efficient studies on bio-macromolecular crystals had to wait for several decades till synchrotron radiation became more accessible and Roger Fourme again stood in the avant-garde of these studies [2]. At the turn of centuries his innovations in the laboratory equipment and experimental setup let him exploring high-pressure conformations of proteins, viral capsids and the double-helix molecular architecture in nucleic acids. These directions of high-pressure studies are continued for simple and macromolecular systems of biological importance. Recently new surprising facts were revealed about the compression of urea, sucrose, and other organic compounds, as well as of macromolecular crystals. Sugars are the main energy carriers for animals as well as building blocks in the living tissue, they are also ideal models for studying pressure-induced changes of OH···O and CH···O interactions. Different types of transformations occur in compressed urea, the first organic compound synthesized in laboratory. Hen egg-white lysozyme was investigated at moderate pressure in a beryllium vessel and the compression of both tetragonal and orthorhombic modifications were measured to 1.0 GPa in a DAC; the high-pressure structure of the tetragonal form was determined and refined at still higher pressure by Fourme et al. [3] Can high pressure provide information about the remarkable polymorphism of lysozyme?
Crystallographic Studies of Proteins Under High Pressure Conditions
Authors: Gruner Sol
Published: November 2015

High pressures encountered in the biosphere (i.e., at the bottom of the oceans) have extraordinary effects on biological molecules and assemblies. These include pressure denaturation of proteins, as well as dramatic changes in protein monomer-multimer association, substrate binding, membrane ion transport, transcription/translation of DNA & RNA, virus infectivity, enzyme kinetics, and conformational states of proteins. Yet practically all the biomolecules involved are highly incompressible. The challenge is to understand how pressure affects structure and to elucidate the relevant physical mechanisms for the observed effects even though the volume changes are very small. X-ray crystallography of proteins under high pressure conditions will be described. It is seen that the key point is not the magnitude of the structural changes, but rather the way differential compressibility of different parts of the protein affect functionality.
About precipitates in boron doped Si investigated by dynamical X-ray diffraction
Authors: Will Johannes , Gröschel Alexander , Spiecker Erdmann , Magerl Andreas
Published: November 2015

Thickness-dependent Pendellösung oscillations as described in the dynamical theory of diffraction are highly sensitive to strain fields from defects in a host crystal. Based on this, we present a novel approach to determine the precipitation kinetics of oxygen in silicon (Si) at the early stages of clustering at high temperatures. We present in-situ measurements up to 11000C performed with the characteristic Kα1-line at 59.31 keV. The extracted static Debye-Waller factors are evaluated as a function of annealing time within a diffusion limited model of growing spherical precipitates. We investigated moderately p- ([B] ≍ 1015 1/cm3) and highly p+ ([B] ≍ 1018 1/cm3) boron doped Czochralski Si crystals at different nucleation and growth temperatures to determine the nucleation and precipitation kinetics as well as the long time precipitation behavior. At 6500C the diffusion constant found is enhanced compared to the extrapolated value for normal diffusion [1], and it is one order of magnitude lower compared to SIMS data [2]. However, it is close to the value obtained from dislocation unlocking experiments [3]. Moreover, the nucleation rates in p+ material are enhanced at 4500C and 7800C compared to the p- samples. The acceleration at 4500C can be explained with boron enhanced oxygen dimer diffusion, whereas the nucleation rate at 7800C is much too high to be accounted for by the enhanced oxygen dimer diffusivity alone. An analysis of the misfit strain yields a platelet morphology of the precipitates with a higher aspect ratio in the p- than in the p+ case. The long time precipitation behavior at 9000C shows a second growth regime of comparable amplitude in both materials. This can be interpreted as Ostwald ripening and gives access to the surface energy of the precipitates.
Formation of γ-Fe2O3 in hydrothermal synthesis: In situ total scattering studies
Authors: Jensen Kirsten , Andersen Henrik , Tyrsted Christoffer , Bøjesen Espen , Lock Nina , Billinge Simon , Iversen Bo , Christensen Mogens
Published: November 2015

The properties of metal oxide nanoparticles are highly dependent on particle characteristics such as size, crystallinity, and structural defects. To obtain particles with tailormade properties, it is crucial to understand the mechanisms that govern these characteristics during material synthesis. For this purpose, in situ studies of particle synthesis have proven powerful.[1] Here, in situ Total Scattering (TS) combined with in situ PXRD studies of the hydrothermal synthesis of γ-Fe2O3 (maghemite) from ammonium iron citrate will be presented. In situ TS with Pair Distribution Function (PDF) analysis has recently shown to be an efficient tool for understanding the fundamental chemical processes in particle crystallization.[2,3] The full γ-Fe2O3 crystallization process from ionic complexes over nanoclusters to crystalline particles is followed and material formation mechanisms are suggested. The study shows that the local atomic structure of the precursor solution is similar to that of the crystalline coordination polymer [Fe(H2citrate)(H2O)]n where corner sharing [FeO6] octahedra are linked by citrate. As hydrothermal treatment of the solution is initiated, clusters of edge sharing [FeO6] units form. Tetrahedrally coordinated iron subsequently appears in the structure and as the synthesis continues, the clusters slowly assemble into nanocrystalline maghemite. The primary transformation from amorphous clusters to nanocrystallites takes place by condensation of the large clusters along corner sharing tetrahedral iron units. The crystallization process is related to large changes in the local structure as the interatomic distances in the clusters change dramatically with cluster growth. The local atomic structure is size dependent, and particles below 6 nm are highly disordered. Whole Powder Pattern Modelling of the PXRD data shows that the final crystallite size (<10 nm) is dependent on synthesis temperature and that the size distribution of the particles broadens with synthesis time.
Simultaneous infrared spectroscopy and X-ray PDF measurements
Authors: Chupas Peter , Chapman Karena , Beyer Kevin , Borkiewicz Olaf , Zhao Haiyan
Published: November 2015

Combining insights from diffuse reflection infrared Fourier transform spectroscopy (DRIFTS) and X-ray pair distribution function (PDF) analysis has the potential to provide deeper insight into complex materials systems under reactive conditions, including heterogeneous catalysts and host-guest systems. We have developed instrumentation and non-ambient reaction cells that enable combined PDF-IR studies without compromise to either measurement. Through careful selection of the IR spectrometer and optics, the IR instrument and reaction cell were adapted to allow angular dispersive X-ray measurements without change to the active IR components, resulting in IR data that are entirely uncompromised. The associated PDF and diffraction data are shown to be of comparable quality and resolution to standard geometry PDF/diffraction measurements. We have demonstrated this approach through the study of desorption of coordinated and non-coordinated guests from the nanoporous Prussian blue analogue MnII3[CoIII(CN)6]2(H2O)6·x{H2O}. The combined data shows how the release of guests from different sites is coupled to structural relaxation of the framework. We will also discus recent results where we have extended the approach to the study of zeolite catalysts.
From atoms to electrodes: Mesoscale effects in electrochemical conversion
Authors: Wiaderek Kamila , Borkiewicz Olaf , Pereira Nathalie , Ilavsky Jan , Amatucci Glenn , Chupas Peter , Chapman Karena
Published: November 2015

Batteries are complex multicomponent devices wherein mesoscale phenomena–the nanoscale structure and chemistry of different components, and interactions thereof–drive functionality and performance. For example, electron/ion transport within the composite electrodes relies on bi-continuous nanostructuring to form electrically and ionicly conductive paths. Electrochemical conversion of different salts of a given metal yields a common and ostensibly identical product: the zero valent metal. For example, maximal lithiation of iron-based electrodes produces metallic iron nanoparticles for oxide, fluoride, and oxyfluoride electrodes alike. Accordingly, these provide an opportunity to explore the coupling of nanostructure development and anion chemistry, and correlate these with electrochemical performance. We combine synchrotron-based small angle X-ray scattering (SAXS) and pair distribution function (PDF) measurements to probe metallic iron formed by electrochemical conversion of different iron compounds across multiple length-scales and decouple the influence of anion chemistry and reaction temperature on the atomic structure and nanoscale morphology.