bluuebunny/crossref_metadata_2025 huggingface dataset:
Structural insights of mediated electron transfer by P450 BM3 monooxygenase
Authors: Panneerselvam Saravanan , Shehzad Aamir , Mueller-Dieckmann Jochen , Schwaneberg Ulrich
Published: November 2015

P450 BM3 is a 119-kDa water-soluble heme monooxygenase originating from Bacillus megaterium. P450 BM3 and variants are known to oxidize structurally diverse substrates. However, the requirement for the natural cofactor, NADPH, limits cell-free applications of P450 BM3 in drug synthesis, fuelling efforts to establish alternative cofactor system. Hence, P450 BM3 variants have been generated which circumvent the requirement for NADPH, and enabled P450 BM3 to be driven with alternative electron sources. In this study, crystal structures of the P450 BM3 M7 heme domain variant (F87A, V281G, M354S) with and without cobalt (III) sepulchrate are reported. Cobalt (III) sepulchrate acts as an electron shuttle in an alternative cofactor system employing zinc dust as the electron source. The crystal structure shows a binding site for the mediator cobalt (III) sepulchrate at the entrance of the substrate access channel. The mediator occupies a position which is far from the active site and distinct from the binding of the natural redox partner (FAD/NADPH binding domain). The unusual binding position suggests that the mediator shuttles electrons to the heme-centre through new routes. Electron transfer could occur by a `through-protein' or a `substrate-relayed' pathway. The latter seems more plausible since it would ensure efficient use of electrons only in the presence of a substrate in the active site. The structural evidence also indicates that the use of a positively charged mediator is important to effectively reduce the catalytic heme domain. Understanding the mediator-monooxygenase interface opens new avenues for tailoring P450 BM3 to match application demands. Structural and molecular understanding of mediated electron transfer enables a paradigm shift from a mediator acceptance screening to a rational mediator design which considers only stability and electron transfer performance parameters.
A Novel Monovalent Cation-Stabilized Fold Mediates an Aptamer-Protein Complex
Authors: Padlan Camille , Malashkevich Vladimir , Almo Steve , Levy Matthew , Brenowitz Michael , Girvin Mark
Published: November 2015

RNA aptamers are structured single-stranded oligonucleotides selected to bind tightly and specifically to a broad spectrum of biomolecular targets. The structural stability and diverse functionality of aptamers have enabled their use as diagnostic tools, inhibitors and potential therapeutic agents. However, since very few attempts at solving atomic structures of protein-aptamer complexes have succeeded, surprisingly little is known about how aptamers specifically bind to selected regions on the surface of proteins and cells. We show that aptamers can be effectively minimized for structural analysis using chemical mapping to experimentally define the secondary structure and identify tertiary contacts within the RNA and with the target protein. Ribonuclease and SHAPE mapping were used to determine the correct predicted secondary structure of a high affinity aptamer (Lys1) selected against lysozyme (KD ~ 30 nM). A deletion variant, minE (KD ~ 20 nM), was engineered to delete a long, apparently unstructured region. The lysozyme-minE complex was determined by x-ray crystallography at a 2.0 Å resolution, yielding a seventh RNA aptamer-protein structure. Solution hydroxyl-radical footprinting confirms the binding interface observed in the crystal. Although the minE aptamer interacts with a positively charged face of lysozyme, the electrostatic contribution to the binding free energy is minimal. The minE aptamer was found to inhibit the function of lysozyme in the standard cell-wall hydrolysis assay – a surprising result since the aptamer binding site is quite far from the catalytic site, and no structural differences between free lysozyme and that in complex with the aptamer could be detected. The long term goal of this study is to develop a systematic approach to aptamer minimization and use solved structures to probe the mechanisms by which RNA aptamers bind their targets and regulate catalytic activity and/or cellular function.
Agarose Hydrogel Protects Protein Crystals From Osmotic Shock
Authors: Sugiyama Shigeru , Terai Takuya , Matsumura Hiroyoshi , Maruyama Mihoko , Takahashi Yoshinori , Yoshikawa Hiroshi , Yoshimura Masashi , Adachi Hiroaki , Takano Kazufumi , Murakami Satoshi , Inoue Tsuyoshi , Nagano Tetsuo , Mori Yusuke
Published: November 2015

High-throughput protein X-ray crystallography offers an unprecedented opportunity to facilitate drug discovery. The most reliable approach is to determine the three-dimensional (3D) structure of the protein-ligand complex by soaking the ligand in apo-crystals, but many lead compounds are not readily water-soluble. Such lead compounds must be dissolved in concentrated organic solvents such as DMSO. Therefore, to date, it has been impossible to produce crystals of protein-ligand complexes by soaking in apo-crystals, because protein crystals dissolve immediately upon soaking in concentrated organic solvents containing lead compounds. The problem arises from the influence of osmotic shock on crystal packing during soaking. We propose an approach to avoid the damage by growing protein crystals in a high-strength hydrogel(1-3). Interestingly, the hydrogel-grown crystals did not dissolve at all for more than thirty minutes in concentrated organic solvents and ionic-strength solutions such as 60% DMSO, and 5.0M lithium acetate. Their X-ray diffraction data were suitable for structure analysis. Surprisingly, some of the crystals diffracted to the highest resolution reported in the Protein Data Bank. Furthermore, the 3D structure determined from hydrogel-grown apo-avidin crystals which were transferred to a solution containing the ligand revealed a clear electron-density map of the ligand bound to the active site. This result indicates that it is possible to bind ligand compounds into hydrogel-grown apo-crystals.
Dehydration and cation replacement dramatically improve crystals of large RNAs
Authors: Ferre-D'Amare Adrian
Published: November 2015

Preparation of well-ordered crystals of large RNAs remains a daunting experimental challenge. This probably reflects the relatively undifferentiated molecular surface of folded RNAs (dominated by a regular array of phosphates), the comparatively low free energy of RNA tertiary structure stabilization, and the resulting tendency of RNAs to be conformationally polydisperse. We have found empirically that dehydration and exchange of counterions, can dramatically improve the diffraction properties of some RNA crystals. Two examples from our work are crystals of the glmS ribozyme-riboswitch [1] and of the ternary complex of a T-box riboswitch, its cognate tRNA and an RNA binding protein [2]. Untreated, flash-frozen crystals of the glmS ribozyme diffracted synchrotron X-rays to 3.3 Å resolution. Upon controlled dehydration by soaking into solutions with higher osmolarity, the unit cell contracted by approximately 10%, and diffraction data could be collected that extended to 1.7 Å resolution. Untreated crystals of the T-box ternary complex diffracted X-rays only to 8 Å resolution. A combination of controlled dehydration and exchange of the magnesium an lithium ions needed for crystal growth with strontium (a soft divalent cation), dramatically extended the diffraction limit, allowing the structure to be solved by SAD at 3.2 Å resolution. Because it is a polyanion, RNA is heavily hydrated and surrounded by a diffuse cloud of counterions. It can also site-specifically bind to partially or wholly desolvated metal ions. Hydration and ion binding not only control RNA folding, but also modulate crystallogenesis. Therefore, controlled dehydration and cation exchange are post-crystallization treatments that should be routinely explored for RNA. This work was supported in part by the Intramural Program of the National Heart, Lung and Blood Institute.
The use of Gold Nanoparticles as additives in Protein Crystallization
Authors: Ribeiro Diana , Kulakova Alina , Quaresma Pedro , Pereira Eulália , Bonifácio Cecília , Romão Maria João , Franco Ricardo , Carvalho Ana Luísa
Published: November 2015

Gold nanoparticles (AuNPs) exhibit unique properties that have made them a very attractive material for application in biological assays [1]. Given the potentially interesting interactions between AuNPs and biological macromolecules, we investigated AuNPs-induced protein crystal growth [2]. Differently functionalized AuNPs were tested as additives in co-crystallization studies with model proteins (hen egg white lysozyme (HEWL), ribonuclease A (RNase A) and proteinase K) as well as with case studies where there were problems in obtaining well-diffracting crystals. Trials were performed considering different crystallization drawbacks, from total absence of crystals to improvement of crystal morphology, size, twinning and number of crystals per drop. Improvement of some of these factors was observed in the cases of HEWL, RNase A, phenylalanine hydroxylase (PAH), myoglobin, native aldehyde oxidase (AOH) and human albumin. In these proteins, the presence of the AuNPs promoted an increase in the size and/or better crystal morphology. From the systematic trials and subsequent observations, it can be concluded that the introduction of AuNPs should definitely be considered in crystal optimization trials to improve previously determined crystallization conditions. Acknowledgments The work was supported by the Portuguese Science and Technology Foundation (FCT-MEC) through grants PTDC/CTM-NAN/112241/2009 to RF, PEst-C/EQB/LA0006/2011 and PEst-C/EQB/LA0006/2013 (to Associate Lab REQUIMTE).
Femtosecond Nanocrystallography and Characterization of Photosystem II
Authors: Kupitz Christopher , Basu Shibom , Grotjohann Ingo , Fromme Raimund , Wang Dingjie , James Dan , Spence John , Weierstall Uwe , Fromme Petra
Published: November 2015

Membrane proteins are extremely difficult to crystallize, however they are highly important proteins for cellular function. Photosystem I, one of the most complex membrane proteins solved to date took more than a decade to have a structure solved to molecular resolution. Large, well-ordered crystal growth is one of the major bottlenecks in structural determination by x-ray crystallography, due to the difficulty of making the "perfect" crystal. The development of femtosecond nanocrystallography, which uses a stream of fully hydrated nanocrystals to collect diffraction snapshots, effectively reduces this bottleneck[1] Photosystem II changed our biosphere via splitting water and evolving oxygen 2.5 billion years ago. Using femtosecond nanocrystallography we are developing a time-resolved femtosecond crystallography method [2] to unravel the mechanism of water splitting by determining the conformational changes that take place during the oxygen evolution process. Multiple crystallization techniques were originally developed in order to make the nanocrystals necessary for femtosecond nanocrystallography. For Photosystem II nano/microcrystals a free interface diffusion method, is used to increase yield over traditional methods. These crystals are then characterized by three different methods before being used for collecting diff raction data. The three methods currently used are optical microscopy, dynamic light scattering (DLS), and Second Order Nonlinear Imaging of Chiral Crystals (SONICC).
Promises and pitfalls of In-situ diffraction
Authors: Holton James
Published: November 2015

The ultimate test of any crystallization experiment is how well the crystals (if any) diffract x-rays. In particular, we would like this diffraction data to be as free from caveats as possible, so that we know one condition really does produce better crystals than another, and not that we had a great crystal somewhere, but it was messed up in the harvesting and cryo-preservation process. So why doesn't everyone do in-situ diffraction? The reason is because of background. The principle impediment to observing weak high-resolution spots is that they get lost in the background scattering, so every effort must be made to minimize it. Unfortunately, plastic, water, oil, amorphous protein and protein crystal all generate a similar number of background x-rays per unit thickness. This is because they are all made of similarly light elements (oxygen, carbon, nitrogen) and have similar densities (0.9 to 1.2 g/cm^3). There is no such thing as a "low background" material, and everything the main beam touches on its way in, through and out of whatever is holding the crystal generates background. This is why loop mounts are so popular: the total path of the x-rays through non-crystalline stuff in a typical loop mount is generally not much thicker than the crystal, and reducing this thickness further has diminishing returns because the background is now dominated by that from disorder in the crystal lattice itself. So, why not make ultra-thin in-situ trays? Not only are thin walls difficult to manufacture cheaply, but they also dry out a lot faster, which is problematic for growing the crystals in the first place. The future success of in-situ diffraction requires trays that are not only thin-walled and low-permeability, but cheap.
X-Ray Single Crystal Structural Analysis of Magnetically Oriented Microcrystals
Authors: Tsuboi Chiaki , Aburaya Kazuki , Higuchi Shingo , Kimura Fumiko , Maeyama Masataka , Kimura Tsunehisa
Published: November 2015

We have developed magnetically oriented microcrystal array (MOMA) technique that enables single crystal X-ray diffraction analyses from microcrystalline powder. In this method, microcrystals suspended in a UV-curable monomer matrix are there-dimensionally aligned by special rotating magnetic field, followed by consolidation of the matrix by photopolymerization. From thus achieved MOMAs, we have been succeeded in crystal structure analysis for some substances [1, 2]. Though MOMA method is an effective technique, it has some problems as follows: in a MOMA, the alignment is deteriorated during the consolidation process. In addition, the sample microcrystals cannot be recovered from a MOMA. To overcome these problems, we performed an in-situ X-ray diffraction measurement using a three-dimensional magnetically oriented microcrystal suspension (3D MOMS) of L-alanine. An experimental setting of the in-situ X-ray measurement of MOMS is schematically shown in the figure. L-alanine microcrystal suspension was poured into a glass capillary and placed on the rotating unit equipped with a pair of neodymium magnets. Rotating X-ray chopper with 10°-slits was placed between the collimator and the suspension. By using this chopper, it was possible to expose the X-ray only when the rotating MOMS makes a specific direction with respect to the impinging X-ray. This has the same effect as the omega oscillation in conventional single crystal measurement. A total of 22 XRD images of 10° increments from 0° to 220° were obtained. The data set was processed by using conventional software to obtain three-dimensional molecular structure of L-alanine. The structure is in good agreement with that reported for the single crystal. R1 and wR2 were 6.53 and 17.4 %, respectively. RMSD value between the determined molecular structure and the reported one was 0.0045 Å. From this result, we conclude that this method can be effective and practical to be used widely for crystal structure analyses.
X-Ray Diffraction from Magnetically Oriented Microcrystal Suspension
Authors: Aburaya Kazuaki , Tsuboi Chiaki , Kimura Fumiko , Matsumoto Kenji , Maeyama Masataka , Kimura Tsunehisa
Published: November 2015

A three dimensionally magnetically oriented microcrystal array (3D-MOMA) is attractive to determination of a crystal structure as well as a molecular structure because it does not require a single crystal with sufficient size and quality for diffraction studies. We have developed a novel method to fabricate 3D-MOMA and determined several crystal structures using the 3D-MOMAs[1],[2]. However, the structure determination through MOMA requires a solidification treatment with UV curable monomer prior to X-ray diffraction experiment. We have developed a new X-ray diffractometer equipped with a magnetic field generator, which makes it possible to collect diffraction data without the solidification treatment. In this poster, we describe X-ray diffraction analyses of a magnetically oriented microcrystal suspension (MOMS) of L-alanine without the solidification treatment. A suspension of L-alanine microcrystals was poured in a glass capillary and rotated at a constant speed in a magnetic circuit attached in the X-ray diffractometer. Then, diffraction images were collected every 60 seconds. In the initial phase, the diffraction pattern showed a broad shape similar to that from a powder sample. As time goes on, diffraction patterns have gradually changed to single-crystal like patterns. After 2 hours, the shape of diffraction spots became as sharp as that of a single crystal. This observation shows that the microcrystals are oriented in the same direction. Owing to the improvement of the magnetic circuit and X-ray diffractometer, the quality of the diffraction has been greatly improved compared to that reported previously[3]. Further details of the analyses will be shown in the poster.
Crystallinity fitting using cellulose crystallite models
Authors: Ahvenainen Patrik , Serimaa Ritva
Published: November 2015

Cellulose is the most abundant biopolymer on Earth and hence it has enormous potential as a source of renewable energy. The nanoscale properties of cellulose are also import for the wood and papermaking industries. The atomic level structure of naturally occurring cellulose Iβ allomorph is well known [1] and this atomistic model is employed in this study for the cellulose unit cell structure. The cellulose crystallinity cannot be measured directly with scattering methods, but the crystallinity of the sample can be estimated by fitting models of crystalline and amorphous contributions to the sample intensity profile. The crystallinity fitting can be enhanced by improving the cellulose fitting model or the amorphous model. We focus on the cellulose crystallite model. The nanoscale level organization of crystalline cellulose in different plant materials is less well established that the unit cell structure of cellulose Iβ. Information on the texture of the sample is obtained efficiently by measuring the sample with a two-dimensional detector. The two-dimensional diffraction pattern can be used to obtain a wealth of information in one measurement, including the crystallite size, crystallite orientation and the crystallinity of the sample. The small size of cellulose crystallites in the wood cell wall limits the information obtainable from the diffraction pattern as the diffraction peaks widen and overlap. The overlapping of certain diffraction peaks can be studied at least qualitatively by computing the diffraction patterns from crystallite models of varying dimensions. Different models for cellulose crystallite have been suggested in the literature, such as the 36 chain model [2]. We investigate how the crystallinity fitting is influenced by the selected cellulose crystallite model and evaluate the suitability of different models to experimental X-ray scattering data of plant material, wood and highly crystalline cellulose.
Determination of crystal size distribution by two-dimensional X-ray diffraction
Authors: Rodriguez-Navarro Alejandro , Kudłacz Krzysztof
Published: November 2015

Polycrystalline materials properties and behaviour are ultimately determined by their crystallinity, phase composition and microstructure (i.e., crystal size, preferential orientation). Two-dimensional (2D) diffraction patterns collected with an area detector (i.e., CDD), available in modern X-ray diffractometers, contain detailed information about all these important material characteristics. Furthermore, recent advances in detector technologies permits the collection of high resolution diffraction patterns in which the microstructure of the material can be directly imaged. If the size of beam relative to the crystal size in the sample is adequately choosen, the diffraction pattern produced will have spotty rings in which the spots are the diffracted images of individual grains. The resolution of the image is mainly dependent on the characteristics of the X-ray beam (i.e., diameter, angular divergence), which can be modulated by X-ray optics, sample to detector distance, the pixel size of the detector and the sharpness of the point spread function. From these patterns, the crystal size distribution of different crystalline phases present in the sample can be independently determined using specialized software capable of extracting and combining the information contained in these patterns. This technique is applicable to materials with crystal sizes ranging from submicron to mm sizes and is complementary to techniques based on peak profile analyses (i.e., Scherrer method) which are applicable only to nanocrystalline materials. Finally, given the high sensitivity of current detectors, crystal size evolution can be followed in real-time to study important transformation processes such as crystallization, annealing, etc. The use of 2D X-ray diffraction as applied to microstructure characterization will be illustrated through several examples.
Synthesis and Gas Storages of Mesoporous Aluminium Metal-Organic Frameworks
Authors: Lin Chia-Her
Published: November 2015

Two mesoporous metal-organic framework of [Al(OH)(SDC)] (CYCU-3) and [Al(OH)(SDC)] (CYCU-4), (H2SDC = 4,4'-stilbenedicarboxylic acid) were synthesized between Al(III) ions and H2SDC under solvothermal reactions. The two crystals have same formula with different topology as supramolecular isomerisms and form 3D mesoporous frameworks in which carboxylate oxygen on each terminus of the ligand forms AlO6 octahedra by cornered-sharing to come into 1D inorganic chain. Further gas sorption measurements also exhibit highly porous properties and uptake capacities of H2 (8.22 and 7.36 mmol/g at 77 K and 1 atm) and CO2 (1.54 and 1.66 mmol/g at 298 K and 1 atm; 2.83 and 2.65 mmol/g CO2 at 273 K and 1 atm). As verified by N2 sorption measurements, the CYCU-3 exhibits the largest pore volume (1.39 cm3g–1) and the largest open channels (3.0 nm) in the system of Al-MOFs reported to date. The CYCU-4 has about 2.1 nm open channels and large pore volume of 1.20 cm3g–1.
Development of Phosphonate Monoesters Building Units in Metal-Organic Frameworks
Authors: Gelfand Benjamin , Lin Jian-Bin , Shimizu George
Published: November 2015

The use of predictable coordination geometries and the development of new ligands has allowed supramolecular chemists to design a plethora of new materials. Among these are metal-organic frameworks (MOFs), which are composed of ligands coordinating to metal atoms or clusters to generate a framework with potential porosity. MOFs exemplify supramolecular design strategy as their extended structure and tunable properties allow them to be applied for various applications.1 To date, many MOFs utilize carboxylates as the coordinating group since they have well studied coordination geometries and thus predictable framework topologies. Though there are examples of carboxylate-based MOFs possessing water stability, most do not possess this key feature, hindering their application in industrial settings. Phosphonate monoesters (PMEs) have been investigated as a means to impart water stability to a MOF by kinetically shielding the linker-metal bond with the ester moiety.2 Unfortunately, phosphonate monoesters have relatively unexplored coordination geometries, with most studies focusing on chlodronic acid and its derivatives, which do not typically form porous materials. In an attempt to establish building units based on PMEs, 1,4-benzenediphosphonate monoester ligands have been synthesized, coordinated to Cu(II), and characterized. It was found that while the methyl and ethyl analogues form similar 3-D structures with poor water stability,3 the isopropyl analogue forms a layered material possessing water stability. The isopropyl analogue contains chains of Cu-PME, with the isopropyl esters lying directly above and below the Cu atoms, kinetically shielding this bond from water. This water stable building unit was predicted to generate a porous framework with non-linear ligands. To test this hypothesis, 1,3,5-benzenetriphosphonate monoisopropyl ester was synthesized and coordinated to Cu(II). Unfortunately, no single crystal of sufficient quality has been produced, though a predicted and refined structure matches well to various characterization techniques. As predicted, this material is porous and does not degrade in harsh humid conditions (353K and 90% relative humidity).
Correlated defects in group 4 metal-organic frameworks
Authors: Cliffe Matthew , Wan Wei , Zou Xiaodong , Coudert François-Xavier , Goodwin Andrew
Published: November 2015

The importance of defects for inorganic functional framework materials is well established, being crucial for properties from relaxor ferroelectricity to superconductivity. The corresponding study of defects in metal-organic frameworks (MOFs) is still however in its infancy. Recent studies have established that ligand-absence defects can be controllably introduced into frameworks and that these defects can drastically improve the material properties, but have so far shown no evidence of correlation between defects. Much of this research has focussed on UiO-66, a zirconium dicarboxylate MOF that was amongst the first very stable MOFs to be discovered.[1] As a result of its stability, it and its derivatives have been investigated for a wide range of properties including photo- and Brønsted acid catalysis, sensing and gas sorption properties. The ability to introduce defects has been demonstrated to substantially enhance both the sorption and catalytic properties of UiO-66.[2][3] We have demonstrated, using a combination of powder X-ray diffraction, total scattering and electron diffraction measurements, that UiO-66 can be engineered, under the appropriate synthetic conditions, to accommodate correlated defect nanodomains. These correlations offer exciting opportunities for manipulating the physical properties, including mass transport, chemical activity and mechanical flexibility.
Designing Proton Conducting Metal Organic Frameworks
Authors: Shimizu George , Gelfand Benjamin
Published: November 2015

Metal organic frameworks (MOFs) or porous coordination polymers (PCPs) represent a tunable molecular scaffolding that can be adjusted for a breadth of applications. This presentation will concern our efforts towards tailoring MOFs towards making new proton conductors ultimately for fuel cells. A major hurdle in these technologies is an electrolyte capable of conducting protons above 100°C. Higher operating temperatures will enhance electrode kinetics and decrease electrode poisoning among several critical operational benefits. In contrast to the macromolecular approaches typically employed towards these electrolytes, we have used a MOF strategy to generate crystalline networks with acidic pores. These MOFs present options to address higher temperature conduction,1 conduction over 10-2 Scm-1,2 and water stability.3 The emphasis in the talk will concern routes to designing these systems and subsequent challenges in their characterization.
Theoretical Equilibrium Morphology and Twin Energy of Monoclinic Hydroxyapatite
Authors: Pastero Linda , Cámara Fernando , Bruno Marco , Rubbo Marco , Aquilano Dino
Published: November 2015

Microsized hydroxyapatite (HAp), we synthesized under mild hydrothermal conditions, shows both monoclinic and hexagonal polymorphs made by rod-shaped single crystals along with simple and multiple twins. The theoretical morphology, obtained through the Hartman-Perdok analysis on the P21/c polymorph, allowed to predict the stable surfaces of the main {hkl} forms. Their surface energies have been evaluated, at 0 K, by ab initio quantum-mechanical calculations. The resulting HAp equilibrium shape (ES) [1] is dominated by a pseudo-hexagonal prism formed by the the {001}, {100} and {-102} forms (having close energy values), all developing around the OH channels of the structure. The basal {010} form truncates the pseudo-hexagonal prism perpendicularly to the OH channels, while three other less important prisms {012}, {110} and {11-2}, lying in between the pseudo-hexagonal prism and the basal pinacoid, enter the ES. A simple kinetic model based on 2D nucleation is proposed to explain the morphology of the single crystals [1]. Assuming [2, 3] that the simplest twin law for the monoclinic phase is generated by a threefold rotation about the 21axis, we found that the three original composition planes (OCP) of the twin coincide with the faces of the {001}, {100} and {-102} forms. For each OCP there are two different surface terminations, according to whether the frontier between parent (P) and twinned (T) crystals intercepts (or not) the centers of mass of PO4and Ca ions and of the O atoms of the OH groups. We examined, as an example, the two kinds of interfaces for the twin (100)P/(001)T. The calculated twin energies result to be very close and low (3.3 and 4.2 erg cm-2), when compared to the value of the HAp surface energy in the [010] zone (≍ 1500 erg cm-2). This means that the probability of formation of a 2D-nucleus oriented in twin position on all the [010] zone is practically equivalent to that needed to generate a normally oriented 2D nucleus in the same zone
Neutron Diffraction Investigation on the Symmetrical Hydrogen Bond in K3H(SO4)2
Authors: Oh In-Hwan , Sohn Yoo-Jung , Meven Martin , Heger Gernot
Published: November 2015

In this work, we present a structure investigation on K3H(SO4)2 by single crystal neutron diffraction. Letovicite with a chemical composition (NH4)3H(SO4)2 belongs to a large family of M3(H,D)(XO4)2 compounds, where M = K+, Rb+, (NH4)+, Cs+, Tl+ and X = Se6+ and S6+. This compound crystallizes in the monoclinic space group A2/a with a = 9.789(7) Å, b = 5.6815(9) Å, c = 14.703(2) Å and β = 103.03(4)0at 300K. At 2.3K, the lattice parameters are a = 9.687(20) Å, b = 5.648(13) Å, c = 14.613(9) Å and β = 103.23(14)0. Data at 2.3K were measured up to (sinθ/λ) = 0.807Å-1 with the single crystal neutron diffractormeter HEiDi at the FRM-II, Germany. H/D shows a dynamic disorder at high temperature, which can be related to very high proton conductivity. In letovicite, two types of disorder related with hydrogen atoms are reported [1]. Although letovicite shows various phase transitions owing to the proton ordering at low temperature, K3H(SO4)2, without the possibility of an orientational disorder of NH4+, undergoes no phase transition at low temperature. At room temperature, the title compound is isostructural to lectovicite, and has an inversion center in the middle of the SO4-H-SO4 dimer. The bond length, 2.483(3) Å, and bond angle, 1800, support the hypothesis that the disordered proton shows a double-well potential, if the distance between the oxygen atoms of the hydrogen bond Ro-o are longer than a critical bond length rc(2.47 Å for protons and 2.40 Å for deuterons) [2]. However, it is not easy to determine if the hydrogen bond is a low-barrier hydrogen bond (LBHB) or centered hydrogen bond (centered HB). Based on an analysis of the anisotropic parameters, the bond lengths and elongation of the hydrogen atom toward the two oxygen atoms by neutron single crystal diffraction experiments at 300K and 2.3K, it seems that the hydrogen bond in the title compound can be classified as a centered hydrogen bond or intermediate form between a cigar-like shape and the disk-like shape [3].
Structure and H position of tetragonal hydrogarnet derived from CaGeO3garnet
Authors: Nakatsuka Akihiko , Matsutomi Hiroki , Fujiwara Keiko , Nakayama Noriaki , Ohtaka Osamu , Sugiyama Kazumasa
Published: November 2015

Hydrogarnets, represented by hydrogrossular, are produced by the replacement of (ZO4)4- in garnets by (H4O4)4- (Z: tetrahedral cation) and the vacancies of tetrahedral cations are created by this replacement. Most of reported hydrogarnets crystallizes with cubic symmetry (space group Ia-3d). To our knowledge, Ca3Mn2[SiO4]2.07[H4O4]0.93 with space group I41/acd (tetragonal) [1] has been only reported as a low-symmetry hydrogarnet. In the cubic hydrogarnets, all O atoms are crystallographically equivalent, whereas in low-symmetric one, they can be located at non-equivalent sites. Therefore, the investigation of low-symmetry hydrogarnes is important to gain knowledge of the site preference of H atoms. Recently, we have successfully synthesized the single crystal of a new low-symmetry hydrogarnet CaGe0.924O3H0.304 (= Ca3(CaGe)[GeO4]2.696[H4O4]0.304) with tetragonal space group I41/a, at 3 GPa and 1273 K under the presence of H2O component. This tetragonal hydrogarnet is produced by the partial replacement of (GeO4)4- in high-pressure CaGeO3 garnet, Ca3(CaGe)[GeO4]3, by (H4O4)4-. In the present study, we report the single crystal X-ray diffraction study of this hydrogarnet at 98 and 298 K. In the structure refinement at 298 K, the occupancy parameters resulted in 0.393(2) for tetrahedral Z2(Ge) site, coordinated only by O6 atoms, and showed no significant deviation from 1.0 for the remaining cation sites. The bond valence sums of each atom except O6 atom agree with the valences of occupied atoms, whereas that of O6 atom are 1.50, deviating largely from oxygen valence. Thus, the substitution of OH groups for O atoms in the present sample occurs only at O6 site, which indicates that O6 is the most preferential site for the OH substitution. The position of H atom will be examined from the residual electron density distributions at a low temperature of 98 K, and the hydrogen bonding in the crystal structure will be discussed.
Detailed single crystal studies on silicates using neutron diffraction
Authors: Meven Martin , Gatta G.
Published: November 2015

Up to now minerals of the silicate family are an interesting and versatile topic of research. Different members of the epidote, lithium tourmaline and beryl groups with very different structural features were studied on the single crystal diffractometer HEIDI at the hot source of the Heinz Maier-Leibnitz Zentrum in Garching (MLZ) in the recent past. The combination of neutron and X-ray diffraction in combination with other methods revealed for each of the studied minerals valuable information about their structural details. Epidote, an important mineral for metamorphic or magmatic petrology was studied with neutrons at room temperature and at 1070 K. The results confirm the high structural stability with no dehydration and only slight thermal expansion [1]. A combined study with x-ray and neutron diffraction on the complex boro-cyclo-silicate elbaite give insight to the displacement regime and H and O order and disorder respectively [2]. Combined single crystal diffraction with x-rays at room temperature and with neutrons at 2.3 K on pezzottaite, an obverse/reverse twin of the beryl family reveals a complex displacement regime with possible partial H2O replacement [3].
Synthesis and characterisation of (La,Pr) monazite solid solution series
Authors: Hirsch Antje , Neumann Andreas , Wätjen Anja , Heuser Julia , Thust Anja , Peters Lars , Roth Georg
Published: November 2015

Monazite type ceramics are considered as potential ceramic storage materials for high level nuclear waste. Natural monazite is a host for radioactive elements like U and Th without becoming metamict due to radiation damage. Monazites are also known for their chemical flexibility and thermal stability. In this context, a solid solution series of (La,Pr)PO4 was synthesised as powders and single crystals and characterised by PXRD (Powder X-Ray Diffraction analysis), EMPA (Electron Microprobe Analysis), TGA (Thermal Gravimetric Analysis) and DSC (Differential Scanning Calorimetry). La and Pr were used as inactive surrogates for the minor actinides Am, Cm and Np, which represent major challenges in nuclear waste management due to their long half-life and high radiotoxicity. The powder samples were prepared following the protocol of [1]. Ln2O3 were mixed with NH4H2PO4 in excess. Powders were ground, pressed, and heated for one day at 12500C in air. X-Ray laboratory and synchrotron data showed that all samples were single phase. A decrease in the lattice parameters and volume with increasing Pr content was observed as expected due to the smaller radius of Pr3+ with respect to La3+ in nine fold coordination. The monoclinic angle β showed a linear increase. Using EMPA, the composition of all samples was determined. The average deviation from the nominal composition was calculated to be about 4 mol% which covers both, sample inhomogeneity and, more importantly, experimental challenges due to grain shape and porosity. In TGA and DSC curves, similar behaviour for all samples was observed, except for the Pr end member. This unsolved issue is currently under investigation. Complementary IR and Raman spectroscopic data showed the expected linear trends [2]. This behaviour was also reported for LnPO4 (Ln = La-Gd) [3]. The author gratefully thanks the BMBF (02 NUK 021E) for financial funding.
Crystallographic characterization of eggshells as scaffolds for bone regeneration
Authors: García-Garduño Margarita , Vargas-Ulloa Laura , Hernández-Padrón Genoveva
Published: November 2015

The aim of this work was to characterize six different eggshell types as future osseous regeneration scaffolds. The study design was cross-sectional observational. The study was conducted in the Laboratory of Materials and the chemical analysis in the Faculty of Chemistry, UNAM, Mexico. Fifty samples of fresh eggs were obtained, 10 from each species (hen, turkey, duck, dove and quail). Square-shaped pieces of about 2 x 2 cm were obtained from the eggshells by means of a high-speed handpiece with a # 701 carbide bur. From the total of eggshell pieces, the ones coming from fresh eggs were included, and the ones showing signs of fracture or spots were excluded. Their morphology was analyzed with a low vacuum scanning electron microscope (JEOL 5200), with an accelerating voltage of 20 kV. The chemical elemental analysis was performed with an EDAX energy dispersive spectrometer (EDS) and the chemical composition was determined by means of a Siemens diffractometer. All of the eggshells were constituted by calcium carbonates, and their outer structure was less porous than the inner one, sometimes with granules and cuticles firmly attached to the inner surface of the eggshell. The eggshell major chemical components were mainly: oxygen, calcium, phosphorous, magnesium, sulfur and carbon. There are no significant quantities of sulfur (S) in the turkey and quail eggshells. These kinds of eggshells have not been tested yet as a scaffold, but it is expected that they may be used soon in bone regeneration once the organic part is removed. Eggshells are largely waste material. The authors anknowledge the technical support to Chem. Rafael Ivan Puente Lee
Atomic Motion in Crystals from Neutron Diffraction Experiments
Authors: Chakoumakos Bryan
Published: November 2015

Static or dynamic disorder in crystals causes a decrease in the Bragg peak intensity, and given sufficient number of Bragg peaks over an extended Q-range, atomic displacement parameters (ADPs) can be refined that quantify the intensity reduction due to the mean square displacements of atoms about their average positions. It is becoming increasingly apparent that ADPs constitute equally important structural information as atom positions and site occupancies. Unusual, yet accurately determined, ADPs can provide telltale clues to interesting physical phenomena, e.g., approach of phase transitions, glass-like thermal conductivity, pathways for high ionic conductivity, and a variety positional disorders. Consequently, the demand for high quality ADPs is increasing, owing in part to our desire to understand and tune physical properties of technological materials. Temperature dependent neutron diffraction using single-crystals is perhaps the best possible method to determine precise individual ADPs, yet the number of these studies is surprisingly limited owing to the paucity of neutron sources and dedicated single-crystal neutron diffractometers. ADPs exhibit various temperature dependent behaviors, and can range from harmonic to anharmonic. Examples from work completed and ongoing at Oak Ridge National Laboratory (stephanite, triphylite, amblygonite, petalite, brucite, filled-skutterudites, gas clathrate hydrates, etc.) as well as previously published work will be reviewed with the aim to generalize insights and recommendations. Research conducted at ORNL's High Flux Isotope Reactor and Spallation Neutron Source was sponsored by the Scientific User Facilities Division, Office of Basic Energy Sciences, U.S. Department of Energy.
Disorder in a natural ixiolite: high resolution studies at 293 K and 120 K.
Authors: Almeida Leandro , Miquita Douglas , Rodrigues Bernardo
Published: November 2015

Grice, Ferguson and Hawthorne [1] describes the ixiolite of Bernic Lake, Manitoba, Canada. According to these authors, the ixiolite is part of the Ixiolite-Tantalite-Wodgnite system and crystallizes in space group Pbcn, with general formula MO2, in a α-PbO2structure type. The structure of the mineral ixiolite from Volta Grande pegmatite, in Brazil, is herein described from high resolution (0.5 Å) X-ray diffraction data using MoKα radiation. This mineral has formula MO2, with M = Fe, Mn, Nb or Ta. Data were collected at 293 K and at 120 K from a well formed crystal (0.6 x 0.4 x 0.3 mm). 49868 and 32294 reflections were collected at 293 K and at 120 K, respectively. The structure of the ixiolite was well solved in both temperatures: at 293 K the mineral crystalizes in the space group Cmcm, and the structure was refined to R(F2)=0.0476, from 728 independent reflections. At 120 K, the mineral crystalizes in space group Pbcn, and the structure was refined to R(F2)= 0.0537 from 1357 independent observations. It is interesting to notice that the different space groups of the herein described ixiolite at 120 K (Pbcn) and at 293 K (Cmcm) is related to the different occupations of oxygen sites, as expected from the high mobility of oxygen atoms.
Connectivity and formula-generating functions for sheet-silicate minerals
Authors: Hawthorne Frank
Published: November 2015

Silicate sheets may be described by two-dimensional nets in which the vertices of the net are occupied by tetrahedra, and the edges of the net represent linkages between tetrahedra. A plane net must contain 3-connected vertices, but not all vertices need to be 3-connected. Simple silicate structures may thus be generated from simple 3-connected plane nets (e.g. 63, 4.82, 4.6.8, (4.6.8)2(6.82)1, etc.). More complicated silicate nets may be generated by various "building operations": (1) Insertion: insertion of 2- and 4-connected vertices into 3-connected plane nets; (2) Repetition: generation of double (or triple) nets by topological symmetry operations that retain transitivity at the junction between the repeated elements. Diversity is also introduced within the sheets of tetrahedra by [1] adjacent apical tetrahedron vertices pointing in the same or different directions, and [2] by folding of the sheets. For simple structures, net type strongly affects the stoichiometry of the resultant structure as the unit cells of the various nets are of different sizes (and shapes), although the stoichiometry may also be affected by non-tetrahedral components. Building operations strongly affect the stoichiometry of the resultant sheet, and this effect may be quantified. We define a formula-generating function F(k,l,...) that generates the formula of a sheet with specific topological features denoted by the indices k,l,... . A simple 3-connected net results in sheets of the form (T2O5)n where n denotes the number of (T2O5)n in the unit cell of the underlying net (for 63, n = 1; for 4.82, n = 2; for (4.6.8)2(6.82)1, n = 3, etc). Plane nets with k 3-connected vertices and l inserted 2-connected vertices result in sheets of the form [T(k+l) O(2.5k+3l)], where (...) are subscripted. Single- and double-sheet structures may be generated from the function F(k,l) = T(N{k+l}) O(N{3k+2.5l}-n{N-1}) where N = 1 and 2 for single- and double-sheets, respectively, and (...) are subscripted.
Single Crystal Solid-State NMR of Magnetically Oriented Powder
Authors: Kusumi Ryosuke , Kimura Fumiko , Kimura Tsunehisa
Published: November 2015

Solid-state NMR spectroscopy is one of the most widely used methods for investigating crystal structures, along with the X-ray and neutron diffraction methods. Solid-state NMR can provide structural information including isotropic chemical shift, dipolar and quadrupolar couplings, spin diffusion, and chemical shift tensor. Among these, the chemical shift tensor is of particular significance because the electronic environment around a nucleus is directly reflected on the chemical shift tensor. However, full information of the chemical shift tensor, including principal values and axes, is difficult to obtain experimentally because a large single crystal is required for the measurement. On the other hand, we have proposed the use of a magnetically oriented microcrystal array (MOMA) as an alternative to a single crystal.[1,2] A MOMA is a composite in which microcrystals are aligned three-dimensionally, prepared by using a time-dependent magnetic field. We recently demonstrated that the13C chemical shift tensors of L-alanine crystal can be completely determined by application of the standard procedure in the single-crystal rotation method to a MOMA of L-alanine microcrystals,[3] as shown in Figure 1. The L-alanine MOMA produces sharp resonance peaks without resolution enhancement by magic angle spinning (MAS). In addition, we observed that the positions of the13C resonance peaks vary systematically as a function of the angle ψ that is the sample-rotation angle about the axis inclined by the magic angle with respect to the NMR magnetic field. From the ψ-dependence of the chemical shifts,13C chemical shift tensor was completely determined. We confirmed that the combination of MOMA with the single-crystal rotation method can be applied to other nuclei such as31P and15N. These results clearly show that the MOMA method is a powerful tool for obtaining full information of the chemical shift tensor from a microcrystalline powder without MAS.