Probing the crystal structure landscape by doping: 4-bromo, 4-chloro and 4-methylcinnamic acids.

PubMed

Desiraju, Gautam R; Chakraborty, Shaunak; Joseph, Sumy

2018-06-11

Accessing the data points in the crystal structure landscape of a molecule is a challenging task, either experimentally or computationally. We have charted the crystal structure landscape of 4-bromocinnamic acid (4BCA) experimentally and computationally: experimental doping is achieved with 4-methylcinnamic acid (4MCA) to obtain new crystal structures; computational doping is performed with 4-chlorocinnamic acid (4CCA) as a model system, because of the difficulties associated in parameterizing the Br-atom. The landscape of 4CCA is explored experimentally in turn, also by doping it with 4MCA, and is found to bear a close resemblance to the landscape of 4BCA, justifying the ready miscibility of these two halogenated cinnamic acids to form solid solutions without any change in crystal structure. In effect, 4MCA, 4CCA and 4BCA form a commutable group of crystal structures, which may be realized experimentally or computationally, and constitute the landscape. Unlike the results obtained by Kitaigorodskii and others, all but two of the multiple solid solutions obtained in the methyl-doping experiments take structures that are different from the hitherto observed crystal forms of the parent compounds. Even granted that the latter might be inherently polymorphic, this unusual observation provokes the suggestion that solid solution formation may be used to probe the crystal structure landscape. The influence of pi...pi interactions, weak hydrogen bonds and halogen bonds in directing the formation of these new structures is also seen. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

A top-down approach to crystal engineering of a racemic Δ2-isoxazoline.

PubMed

Lombardo, Giuseppe M; Rescifina, Antonio; Chiacchio, Ugo; Bacchi, Alessia; Punzo, Francesco

2014-02-01

The crystal structure of racemic dimethyl (4RS,5RS)-3-(4-nitrophenyl)-4,5-dihydroisoxazole-4,5-dicarboxylate, C13H12N2O7, has been determined by single-crystal X-ray diffraction. By analysing the degree of growth of the morphologically important crystal faces, a ranking of the most relevant non-covalent interactions determining the crystal structure can be inferred. The morphological information is considered with an approach opposite to the conventional one: instead of searching inside the structure for the potential key interactions and using them to calculate the crystal habit, the observed crystal morphology is used to define the preferential lines of growth of the crystal, and then this information is interpreted by means of density functional theory (DFT) calculations. Comparison with the X-ray structure confirms the validity of the strategy, thus suggesting this top-down approach to be a useful tool for crystal engineering.

Remarkable features in lattice-parameter ratios of crystals. II. Monoclinic and triclinic crystals.

PubMed

de Gelder, R; Janner, A

2005-06-01

The frequency distributions of monoclinic crystals as a function of the lattice-parameter ratios resemble the corresponding ones of orthorhombic crystals: an exponential component, with more or less pronounced sharp peaks, with in general the most important peak at the ratio value 1. In addition, the distribution as a function of the monoclinic angle beta has a sharp peak at 90 degrees and decreases sensibly at larger angles. Similar behavior is observed for the three triclinic angular parameters alpha, beta and gamma, with characteristic differences between the organic and metal-organic, bio-macromolecular and inorganic crystals, respectively. The general behavior observed for the hexagonal, tetragonal, orthorhombic, monoclinic and triclinic crystals {in the first part of this series [de Gelder & Janner (2005). Acta Cryst. B61, 287-295] and in the present case} is summarized and commented. The data involved represent 366 800 crystals, with lattice parameters taken from the Cambridge Structural Database, CSD (294 400 entries), the Protein Data Bank, PDB (18 800 entries), and the Inorganic Crystal Structure Database, ICSD (53 600 entries). A new general structural principle is suggested.

High resolution synchrotron X-radiation diffraction imaging of crystals grown in microgravity and closely related terrestrial crystals

NASA Technical Reports Server (NTRS)

Steiner, Bruce; Dobbyn, Ronald C.; Black, David; Burdette, Harold; Kuriyama, Masao; Fripp, Archibald; Simchik, Richard

1991-01-01

Irregularities in three crystals grown in space and in four terrestrial crystals grown under otherwise comparable conditions have been observed in high resolution diffraction imaging. The images provide important new clues to the nature and origins of irregularities in each crystal. For two of the materials, mercuric iodide and lead tin telluride, more than one phase (an array of non-diffracting inclusions) was observed in terrestrial samples; but the formation of these multiple phases appears to have been suppressed in directly comparable crystals grown in microgravity. The terrestrial seed crystal of triglycine sulfate displayed an unexpected layered structure, which propagated during directly comparable space growth. Terrestrial Bridgman regrowth of gallium arsenide revealed a mesoscopic structure substantially different from that of the original Czochralski material. A directly comparable crystal is to be grown shortly in space.

Generation of crystal structures using known crystal structures as analogues

PubMed Central

Cole, Jason C.; Groom, Colin R.; Read, Murray G.; Giangreco, Ilenia; McCabe, Patrick; Reilly, Anthony M.; Shields, Gregory P.

2016-01-01

This analysis attempts to answer the question of whether similar molecules crystallize in a similar manner. An analysis of structures in the Cambridge Structural Database shows that the answer is yes – sometimes they do, particularly for single-component structures. However, one does need to define what we mean by similar in both cases. Building on this observation we then demonstrate how this correlation between shape similarity and packing similarity can be used to generate potential lattices for molecules with no known crystal structure. Simple intermolecular interaction potentials can be used to minimize these potential lattices. Finally we discuss the many limitations of this approach. PMID:27484374

Crystal and molecular structure of 2,6-dibromo-3-chloro-4-fluoroaniline

NASA Astrophysics Data System (ADS)

Betz, R.

2015-12-01

The crystal and molecular structure of 2,6-dibromo-3-chloro-4-fluoroaniline is determined. The crystals are monoclinic, a = 3.8380(3), b = 13.1010(12), c = 8.0980(8) Å, β = 96.010(4)°, V = 404.94(6) Å3, Z = 2, sp. gr. P21. Classical intra- and intermolecular hydrogen bonds of the N-H··· Hal type are observed next to a series of dispersive halogen···halogen interactions in the crystal structure.

Structure of the apo form of the catabolite control protein A (CcpA) from Bacillus megaterium with a DNA-binding domain

DOE Office of Scientific and Technical Information (OSTI.GOV)

Singh, Rajesh Kumar; Palm, Gottfried J.; Panjikar, Santosh

2007-04-01

Crystal structure analysis of the apo form of catabolite control protein A reveals the three-helix bundle of the DNA-binding domain. In the crystal packing, this domain interacts with the binding site for the corepressor protein. Crystal structure determination of catabolite control protein A (CcpA) at 2.6 Å resolution reveals for the first time the structure of a full-length apo-form LacI-GalR family repressor protein. In the crystal structures of these transcription regulators, the three-helix bundle of the DNA-binding domain has only been observed in cognate DNA complexes; it has not been observed in other crystal structures owing to its mobility. Inmore » the crystal packing of apo-CcpA, the protein–protein contacts between the N-terminal three-helix bundle and the core domain consisted of interactions between the homodimers that were similar to those between the corepressor protein HPr and the CcpA N-subdomain in the ternary DNA complex. In contrast to the DNA complex, the apo-CcpA structure reveals large subdomain movements in the core, resulting in a complete loss of contacts between the N-subdomains of the homodimer.« less

An automated parallel crystallisation search for predicted crystal structures and packing motifs of carbamazepine.

PubMed

Florence, Alastair J; Johnston, Andrea; Price, Sarah L; Nowell, Harriott; Kennedy, Alan R; Shankland, Norman

2006-09-01

An automated parallel crystallisation search for physical forms of carbamazepine, covering 66 solvents and five crystallisation protocols, identified three anhydrous polymorphs (forms I-III), one hydrate and eight organic solvates, including the single-crystal structures of three previously unreported solvates (N,N-dimethylformamide (1:1); hemi-furfural; hemi-1,4-dioxane). Correlation of physical form outcome with the crystallisation conditions demonstrated that the solvent adopts a relatively nonspecific role in determining which polymorph is obtained, and that the previously reported effect of a polymer template facilitating the formation of form IV could not be reproduced by solvent crystallisation alone. In the accompanying computational search, approximately half of the energetically feasible predicted crystal structures exhibit the C=O...H--N R2(2)(8)dimer motif that is observed in the known polymorphs, with the most stable correctly corresponding to form III. Most of the other energetically feasible structures, including the global minimum, have a C=O...H--N C(4) chain hydrogen bond motif. No such chain structures were observed in this or any other previously published work, suggesting that kinetic, rather than thermodynamic, factors determine which of the energetically feasible crystal structures are observed experimentally, with the kinetics apparently favouring nucleation of crystal structures based on the CBZ-CBZ R2(2)(8) motif. (c) 2006 Wiley-Liss, Inc. and the American Pharmacists Association.

Dependence of Internal Crystal Structures of InAs Nanowires on Electrical Characteristics of Field Effect Transistors

NASA Astrophysics Data System (ADS)

Han, Sangmoon; Choi, Ilgyu; Lee, Kwanjae; Lee, Cheul-Ro; Lee, Seoung-Ki; Hwang, Jeongwoo; Chung, Dong Chul; Kim, Jin Soo

2018-02-01

We report on the dependence of internal crystal structures on the electrical properties of a catalyst-free and undoped InAs nanowire (NW) formed on a Si(111) substrate by metal-organic chemical vapor deposition. Cross-sectional transmission electron microscopy images, obtained from four different positions of a single InAs NW, indicated that the wurtzite (WZ) structure with stacking faults was observed mostly in the bottom region of the NW. Vertically along the InAs NW, the amount of stacking faults decreased and a zinc-blende (ZB) structure was observed. At the top of the NW, the ZB structure was prominently observed. The resistance and resistivity of the top region of the undoped InAs NW with the ZB structure were measured to be 121.5 kΩ and 0.19 Ω cm, respectively, which are smaller than those of the bottom region with the WZ structure, i.e., 251.8 kΩ and 0.39 Ω cm, respectively. The reduction in the resistance of the top region of the NW is attributed to the improvement in the crystal quality and the change in the ZB crystal structure. For a field effect transistor with an undoped InAs NW channel, the drain current versus drain-source voltage characteristic curves under various negative gate-source voltages were successfully observed at room temperature.

Direct observation of the ferroelectric polarization in the layered perovskite Bi{sub 4}Ti{sub 3}O{sub 12}

DOE Office of Scientific and Technical Information (OSTI.GOV)

Urushihara, Daisuke; Asaka, Toru, E-mail: asaka.toru@nitech.ac.jp; Frontier Research Institute for Materials Science, Nagoya Institute of Technology, Nagoya 466-8555

We investigated the crystal structure and ferroelectric domains of Bi{sub 4}Ti{sub 3}O{sub 12} (BTO) by means of transmission electron microscopy (TEM) and single-crystal X-ray diffractometry. From the extinction rule, we determined that the space group in the ferroelectric phase of BTO is P1a1 rather than B2cb and B1a1 which have been proposed previously. We successfully refined the crystal structure based on the space group P1a1. The 180° and 90° ferroelectric domain structures were observed by the [001]-zone dark-field TEM imaging. In the 180° domain structure, we determined that one component of the polarization vector is parallel to the a-axis. Anmore » annular bright-field scanning transmission electron microscopy (ABF-STEM) was performed for the direct observation of the crystal structures. The ABF-STEM images displayed the contrasts with respect to every atomic position in spite of the highly distorted structure of BTO. We could evaluate the tilting and distortion of the [TiO{sub 6}] octahedra relatively. Therefore, we directly observed the ferroelectric displacements of Bi and Ti ions.« less

Fe-Al alloy single-crystal thin film preparation for basic magnetic measurements

NASA Astrophysics Data System (ADS)

Abe, Tatsuya; Kawai, Tetsuroh; Futamoto, Masaaki; Ohtake, Mitsuru; Inaba, Nobuyuki

2018-04-01

Fe100-xAlx (x = 0, 4, 10, 20, 30 at. %) alloy films of 40 nm thickness are prepared on MgO(001) single-crystal substrates by varying substrate temperature from room temperature to 600 °C. Single-crystal films of (001) orientation with bcc-based disordered A2 structure are obtained for the Al content range of x = 0 - 20 at. %. An ordered phase of DO3 structure is observed in Fe70Al30 films prepared at temperatures higher than 200 °C, whereas (001) oriented single-crystal films of A2 structure are obtained when prepared at room temperature. The film surface profile does not depend much on the film composition, while the surface roughness increases with increasing substrate temperature. Island-like crystals are observed for films prepared at 600°C for all compositions. Difference in lattice spacing measured parallel and perpendicular to the substrate is noted for the single-crystal thin films and it increases with increasing Al content. The lattice strain in single-crystal film is caused possibly to accommodate the lattice mismatch with the MgO substrate. The (001)-oriented single-crystal films with A2 structure show four-fold symmetries in in-plane magnetic anisotropy with the easy magnetization axis A2[100] and the hard magnetization axis A2[110], whereas the films with DO3 ordered structure show almost isotropic magnetic properties.

Effect of the Crystal Environment on Side-Chain Conformational Dynamics in Cyanovirin-N Investigated through Crystal and Solution Molecular Dynamics Simulations

PubMed Central

Ahlstrom, Logan S.; Vorontsov, Ivan I.; Shi, Jun; Miyashita, Osamu

2017-01-01

Side chains in protein crystal structures are essential for understanding biochemical processes such as catalysis and molecular recognition. However, crystal packing could influence side-chain conformation and dynamics, thus complicating functional interpretations of available experimental structures. Here we investigate the effect of crystal packing on side-chain conformational dynamics with crystal and solution molecular dynamics simulations using Cyanovirin-N as a model system. Side-chain ensembles for solvent-exposed residues obtained from simulation largely reflect the conformations observed in the X-ray structure. This agreement is most striking for crystal-contacting residues during crystal simulation. Given the high level of correspondence between our simulations and the X-ray data, we compare side-chain ensembles in solution and crystal simulations. We observe large decreases in conformational entropy in the crystal for several long, polar and contacting residues on the protein surface. Such cases agree well with the average loss in conformational entropy per residue upon protein folding and are accompanied by a change in side-chain conformation. This finding supports the application of surface engineering to facilitate crystallization. Our simulation-based approach demonstrated here with Cyanovirin-N establishes a framework for quantitatively comparing side-chain ensembles in solution and in the crystal across a larger set of proteins to elucidate the effect of the crystal environment on protein conformations. PMID:28107510

Effect of the Crystal Environment on Side-Chain Conformational Dynamics in Cyanovirin-N Investigated through Crystal and Solution Molecular Dynamics Simulations.

PubMed

Ahlstrom, Logan S; Vorontsov, Ivan I; Shi, Jun; Miyashita, Osamu

2017-01-01

Side chains in protein crystal structures are essential for understanding biochemical processes such as catalysis and molecular recognition. However, crystal packing could influence side-chain conformation and dynamics, thus complicating functional interpretations of available experimental structures. Here we investigate the effect of crystal packing on side-chain conformational dynamics with crystal and solution molecular dynamics simulations using Cyanovirin-N as a model system. Side-chain ensembles for solvent-exposed residues obtained from simulation largely reflect the conformations observed in the X-ray structure. This agreement is most striking for crystal-contacting residues during crystal simulation. Given the high level of correspondence between our simulations and the X-ray data, we compare side-chain ensembles in solution and crystal simulations. We observe large decreases in conformational entropy in the crystal for several long, polar and contacting residues on the protein surface. Such cases agree well with the average loss in conformational entropy per residue upon protein folding and are accompanied by a change in side-chain conformation. This finding supports the application of surface engineering to facilitate crystallization. Our simulation-based approach demonstrated here with Cyanovirin-N establishes a framework for quantitatively comparing side-chain ensembles in solution and in the crystal across a larger set of proteins to elucidate the effect of the crystal environment on protein conformations.

Crystal structure of a DNA/Ba2+ G-quadruplex containing a water-mediated C-tetrad.

PubMed

Zhang, Diana; Huang, Terry; Lukeman, Philip S; Paukstelis, Paul J

2014-12-01

We have determined the 1.50 Å crystal structure of the DNA decamer, d(CCA(CNV)KGCGTGG) ((CNV)K, 3-cyanovinylcarbazole), which forms a G-quadruplex structure in the presence of Ba(2+). The structure contains several unique features including a bulged nucleotide and the first crystal structure observation of a C-tetrad. The structure reveals that water molecules mediate contacts between the divalent cations and the C-tetrad, allowing Ba(2+) ions to occupy adjacent steps in the central ion channel. One ordered Mg(2+) facilitates 3'-3' stacking of two quadruplexes in the asymmetric unit, while the bulged nucleotide mediates crystal contacts. Despite the high diffraction limit, the first four nucleotides including the (CNV)K nucleoside are disordered though they are still involved in crystal packing. This work suggests that the bulky hydrophobic groups may locally influence the formation of non-Watson-Crick structures from otherwise complementary sequences. These observations lead to the intriguing possibility that certain types of DNA damage may act as modulators of G-quadruplex formation. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

Crystal structure of a c-kit promoter quadruplex reveals the structural role of metal ions and water molecules in maintaining loop conformation.

PubMed

Wei, Dengguo; Parkinson, Gary N; Reszka, Anthony P; Neidle, Stephen

2012-05-01

We report here the 1.62 Å crystal structure of an intramolecular quadruplex DNA formed from a sequence in the promoter region of the c-kit gene. This is the first reported crystal structure of a promoter quadruplex and the first observation of localized magnesium ions in a quadruplex structure. The structure reveals that potassium and magnesium ions have an unexpected yet significant structural role in stabilizing particular quadruplex loops and grooves that is distinct from but in addition to the role of potassium ions in the ion channel at the centre of all quadruplex structures. The analysis also shows how ions cluster together with structured water molecules to stabilize the quadruplex arrangement. This particular quadruplex has been previously studied by NMR methods, and the present X-ray structure is in accord with the earlier topology assignment. However, as well as the observations of potassium and magnesium ions, the crystal structure has revealed a highly significant difference in the dimensions of the large cleft in the structure, which is a plausible target for small molecules. This difference can be understood by the stabilizing role of structured water networks.

Artistic Crystal Creations

ERIC Educational Resources Information Center

Lange, Catherine

2008-01-01

In this inquiry-based, integrative art and science activity, Grade 5-8 students use multicolored Epsom salt (magnesium sulfate) crystallizing solutions to reveal beautiful, cylindrical, 3-dimensional, needle-shaped structures. Through observations of the crystal art, students analyze factors that contribute to crystal size and formation, compare…

Confirming the Revised C-Terminal Domain of the MscL Crystal Structure

PubMed Central

Maurer, Joshua A.; Elmore, Donald E.; Clayton, Daniel; Xiong, Li; Lester, Henry A.; Dougherty, Dennis A.

2008-01-01

The structure of the C-terminal domain of the mechanosensitive channel of large conductance (MscL) has generated significant controversy. As a result, several structures have been proposed for this region: the original crystal structure (1MSL) of the Mycobacterium tuberculosis homolog (Tb), a model of the Escherichia coli homolog, and, most recently, a revised crystal structure of Tb-MscL (2OAR). To understand which of these structures represents a physiological conformation, we measured the impact of mutations to the C-terminal domain on the thermal stability of Tb-MscL using circular dichroism and performed molecular dynamics simulations of the original and the revised crystal structures of Tb-MscL. Our results imply that this region is helical and adopts an α-helical bundle conformation similar to that observed in the E. coli MscL model and the revised Tb-MscL crystal structure. PMID:18326638

Electron paramagnetic resonance study of radiation-induced paramagnetic centers in succinic anhydride single crystal

NASA Astrophysics Data System (ADS)

Caliskan, Betul; Caliskan, Ali Cengiz; Er, Emine

2017-09-01

Succinic anhydride single crystals were exposed to 60Co-gamma irradiation at room temperature. The irradiated single crystals were investigated at 125 K by Electron Paramagnetic Resonance (EPR) Spectroscopy. The investigation of EPR spectra of irradiated single crystals of succinic anhydride showed the presence of two succinic anhydride anion radicals. The anion radicals observed in gamma-irradiated succinic anhydride single crystal were created by the scission of the carbon-oxygen double bond. The structure of EPR spectra demonstrated that the hyperfine splittings arise from the same radical species. The reduction of succinic anhydride was identified which is formed by the addition of an electron to oxygen of the Csbnd O bond. The g values, the hyperfine structure constants and direction cosines of the radiation damage centers observed in succinic anhydride single crystal were obtained.

HREM study of irradiation damage in human dental enamel crystals.

PubMed

Brès, E F; Hutchison, J L; Senger, B; Voegel, J C; Frank, R M

1991-06-01

Several phenomena have been observed during the examination of human dental enamel crystals (mainly constituted by hydroxyapatite (OHAP] by high-resolution electron microscopy (HREM) at 300 and 400 keV: orientation-dependent damage in the form of mass loss from voids or uniform destruction of crystal structure, beam-induced diffusion creating outgrowths at the crystal surfaces, recrystallization of the bulk crystal and crystallization of the inorganic components of the matrix surrounding the crystals. These beam-induced crystals have the CaO structure. The phenomena observed are most likely due to various electron-crystal interaction mechanisms (ballistic knock-on damage, electronic excitations, temperature rise, etc.). In this paper, the contribution of the ballistic process to the phenomena observed is discussed. The quantitative description of the knock-on collisions rests on the McKinley-Feshbach cross-section formula. The minimum ion displacement energies which appear in this expression have been estimated on the basis of the electrostatic ion binding energies, and the covalent bond energies if required. It is shown that hydroxyl, calcium and oxygen ions can effectively be displaced by the incident 300 and 400 keV electrons. Thus, the formation of CaO crystals by the combination of calcium and oxygen ions diffusing from their initial sites inside the OHAP lattice can tentatively be explained.

Electrical properties of crystallized 30B2O3-70V2O5 glass

NASA Astrophysics Data System (ADS)

Gwoo, Donggun; Kim, Taehee; Han, Kyungseok; Choi, Wongyu; Kim, Jonghwan; Ryu, Bongki

2013-05-01

30B2O3-70V2O5 binary-system glass was prepared, and variations in structural and electrical property were examined using crystallization. While different related research studies exist, few have evaluated the variations in the structure and properties with changes in the crystallization rate. 30B2O3-70V2O5 glass was annealed in the graphite mold above the glass transition temperature for 2 h and heat-treated at each crystallization temperature for 3 h. 30B2O3-70V2O5 glass showed predominantly electronic conductive characteristic. FTIR was preferentially used for analyzing the structural changes of B-O bond after crystallization, while XRD was utilized to verify the inferred changes in the structure array (BO3 + V2O5 ↔ BO4 + 2VO2). Structural changes induced by heat treatment were confirmed by analyzing the molecular volume determined from the sample density, and conductance was measured to correlate structural and property changes. Conductivity is discussed based on the migration of vanadate ions with different valence states because of the increase in VO2 crystallinity at 130°C, which, however, was not observed at 170°C. After VO2 structures were reinforced, a 1.8-fold increase in conductance was observed (as compared to the annealed sample) after crystallization at 130°C for 3 h.

Two distinct crystallization processes in supercooled liquid

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tane, Masakazu, E-mail: mtane@sanken.osaka-u.ac.jp; Kimizuka, Hajime; Ichitsubo, Tetsu

2016-05-21

Using molecular dynamics simulations we show that two distinct crystallization processes, depending on the temperature at which crystallization occurs, appear in a supercooled liquid. As a model for glass-forming materials, an Al{sub 2}O{sub 3} model system, in which both the glass transition and crystallization from the supercooled liquid can be well reproduced, is employed. Simulations in the framework of an isothermal-isobaric ensemble indicate that the calculated time-temperature-transformation curve for the crystallization to γ(defect spinel)-Al{sub 2}O{sub 3} exhibited a typical nose shape, as experimentally observed in various glass materials. During annealing above the nose temperature, the structure of the supercooled liquidmore » does not change before the crystallization, because of the high atomic mobility (material transport). Thus, the crystallization is governed by the abrupt crystal nucleation, which results in the formation of a stable crystal structure. In contrast, during annealing below the nose temperature, the structure of the supercooled liquid gradually changes before the crystallization, and the formed crystal structure is less stable than that formed above the nose temperature, because of the restricted material transport.« less

Crystal structure of the adenosine A 2A receptor bound to an antagonist reveals a potential allosteric pocket

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sun, Bingfa; Bachhawat, Priti; Chu, Matthew Ling-Hon

The adenosine A2A receptor (A2AR) has long been implicated in cardiovascular disorders. As more selective A2AR ligands are being identified, its roles in other disorders, such as Parkinson’s disease, are starting to emerge, and A2AR antagonists are important drug candidates for nondopaminergic anti-Parkinson treatment. Here we report the crystal structure of A2A receptor bound to compound 1 (Cmpd-1), a novel A2AR/N-methyl D-aspartate receptor subtype 2B (NR2B) dual antagonist and potential anti-Parkinson candidate compound, at 3.5 Å resolution. The A2A receptor with a cytochrome b562-RIL (BRIL) fusion (A2AR–BRIL) in the intracellular loop 3 (ICL3) was crystallized in detergent micelles using vapor-phasemore » diffusion. Whereas A2AR–BRIL bound to the antagonist ZM241385 has previously been crystallized in lipidic cubic phase (LCP), structural differences in the Cmpd-1–bound A2AR–BRIL prevented formation of the lattice observed with the ZM241385–bound receptor. The crystals grew with a type II crystal lattice in contrast to the typical type I packing seen from membrane protein structures crystallized in LCP. Cmpd-1 binds in a position that overlaps with the native ligand adenosine, but its methoxyphenyl group extends to an exosite not previously observed in other A2AR structures. Structural analysis revealed that Cmpd-1 binding results in the unique conformations of two tyrosine residues, Tyr91.35 and Tyr2717.36, which are critical for the formation of the exosite. The structure reveals insights into antagonist binding that are not observed in other A2AR structures, highlighting flexibility in the binding pocket that may facilitate the development of A2AR-selective compounds for the treatment of Parkinson’s disease.« less

Computed crystal energy landscapes for understanding and predicting organic crystal structures and polymorphism.

PubMed

Price, Sarah Sally L

2009-01-20

The phenomenon of polymorphism, the ability of a molecule to adopt more than one crystal structure, is a well-established property of crystalline solids. The possible variations in physical properties between polymorphs make the reliable reproduction of a crystalline form essential for all research using organic materials, as well as quality control in manufacture. Thus, the last two decades have seen both an increase in interest in polymorphism and the availability of the computer power needed to make the computational prediction of organic crystal structures a practical possibility. In the past decade, researchers have made considerable improvements in the theoretical basis for calculating the sets of structures that are within the energy range of possible polymorphism, called crystal energy landscapes. It is common to find that a molecule has a wide variety of ways of packing with lattice energy within a few kilojoules per mole of the most stable structure. However, as we develop methods to search for and characterize "all" solid forms, it is also now usual for polymorphs and solvates to be found. Thus, the computed crystal energy landscape reflects and to an increasing extent "predicts" the emerging complexity of the solid state observed for many organic molecules. This Account will discuss the ways in which the calculation of the crystal energy landscape of a molecule can be used as a complementary technique to solid form screening for polymorphs. Current methods can predict the known crystal structure, even under "blind test" conditions, but such successes are generally restricted to those structures that are the most stable over a wide range of thermodynamic conditions. The other low-energy structures can be alternative polymorphs, which have sometimes been found in later experimental studies. Examining the computed structures reveals the various compromises between close packing, hydrogen bonding, and pi-pi stacking that can result in energetically feasible structures. Indeed, we have observed that systems with many almost equi-energetic structures that contain a common interchangeable motif correlate with a tendency to disorder and problems with control of the crystallization product. Thus, contrasting the computed crystal energy landscape with the known crystal structures of a given molecule provides a valuable complement to solid form screening, and the examination of the low-energy structures often leads to a rationalization of the forms found.

Structural properties and defects of GaN crystals grown at ultra-high pressures: A molecular dynamics simulation

NASA Astrophysics Data System (ADS)

Gao, Tinghong; Li, Yidan; Xie, Quan; Tian, Zean; Chen, Qian; Liang, Yongchao; Ren, Lei; Hu, Xuechen

2018-01-01

The growth of GaN crystals at different pressures was studied by molecular dynamics simulation employing the Stillinger-Weber potential, and their structural properties and defects were characterized using the radial distribution function, the Voronoi polyhedron index method, and a suitable visualization technology. Crystal structures formed at 0, 1, 5, 10, and 20 GPa featured an overwhelming number of <4 0 0 0> Voronoi polyhedra, whereas amorphous structures comprising numerous disordered polyhedra were produced at 50 GPa. During quenching, coherent twin boundaries were easily formed between zinc-blende and wurtzite crystal structures in GaN. Notably, point defects usually appeared at low pressure, whereas dislocations were observed at high pressure, since the simultaneous growth of two crystal grains with different crystal orientations and their boundary expansion was hindered in the latter case, resulting in the formation of a dislocation between these grains.

Crystal structure of zwitterionic bisimidazolium sulfonates

NASA Astrophysics Data System (ADS)

Kohmoto, Shigeo; Okuyama, Shinpei; Yokota, Nobuyuki; Takahashi, Masahiro; Kishikawa, Keiki; Masu, Hyuma; Azumaya, Isao

2012-05-01

Crystal structures of three zwitterionic bisimidazolium salts 1-3 in which imidazolium sulfonate moieties were connected with aromatic linkers, p-xylylene, 4,4'-dimethylenebiphenyl, and phenylene, respectively, were examined. The latter two were obtained as hydrates. An S-shaped molecular structure in which the sulfonate moiety was placed on the imidazolium ring was observed for 1. A helical array of hydrated water molecules was obtained for 2 while a linear array of hydrated water molecules was observed for 3.

Self-assembled ordered structures in thin films of HAT5 discotic liquid crystal.

PubMed

Morales, Piero; Lagerwall, Jan; Vacca, Paolo; Laschat, Sabine; Scalia, Giusy

2010-05-20

Thin films of the discotic liquid crystal hexapentyloxytriphenylene (HAT5), prepared from solution via casting or spin-coating, were investigated by atomic force microscopy and polarizing optical microscopy, revealing large-scale ordered structures substantially different from those typically observed in standard samples of the same material. Thin and very long fibrils of planar-aligned liquid crystal were found, possibly formed as a result of an intermediate lyotropic nematic state arising during the solvent evaporation process. Moreover, in sufficiently thin films the crystallization seems to be suppressed, extending the uniform order of the liquid crystal phase down to room temperature. This should be compared to the bulk situation, where the same material crystallizes into a polymorphic structure at 68 °C.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sabin, Charles; Plevka, Pavel, E-mail: pavel.plevka@ceitec.muni.cz

Molecular replacement and noncrystallographic symmetry averaging were used to detwin a data set affected by perfect hemihedral twinning. The noncrystallographic symmetry averaging of the electron-density map corrected errors in the detwinning introduced by the differences between the molecular-replacement model and the crystallized structure. Hemihedral twinning is a crystal-growth anomaly in which a specimen is composed of two crystal domains that coincide with each other in three dimensions. However, the orientations of the crystal lattices in the two domains differ in a specific way. In diffraction data collected from hemihedrally twinned crystals, each observed intensity contains contributions from both of themore » domains. With perfect hemihedral twinning, the two domains have the same volumes and the observed intensities do not contain sufficient information to detwin the data. Here, the use of molecular replacement and of noncrystallographic symmetry (NCS) averaging to detwin a 2.1 Å resolution data set for Aichi virus 1 affected by perfect hemihedral twinning is described. The NCS averaging enabled the correction of errors in the detwinning introduced by the differences between the molecular-replacement model and the crystallized structure. The procedure permitted the structure to be determined from a molecular-replacement model that had 16% sequence identity and a 1.6 Å r.m.s.d. for C{sup α} atoms in comparison to the crystallized structure. The same approach could be used to solve other data sets affected by perfect hemihedral twinning from crystals with NCS.« less

Evolution of molecular crystal optical phonons near structural phase transitions

NASA Astrophysics Data System (ADS)

Michki, Nigel; Niessen, Katherine; Xu, Mengyang; Markelz, Andrea

Molecular crystals are increasingly important photonic and electronic materials. For example organic semiconductors are lightweight compared to inorganic semiconductors and have inexpensive scale up processing with roll to roll printing. However their implementation is limited by their environmental sensitivity, in part arising from the weak intermolecular interactions of the crystal. These weak interactions result in optical phonons in the terahertz frequency range. We examine the evolution of intermolecular interactions near structural phase transitions by measuring the optical phonons as a function of temperature and crystal orientation using terahertz time-domain spectroscopy. The measured orientation dependence of the resonances provides an additional constraint for comparison of the observed spectra with the density functional calculations, enabling us to follow specific phonon modes. We observe crystal reorganization near 350 K for oxalic acid as it transforms from dihydrate to anhydrous form. We also report the first THz spectra for the molecular crystal fructose through its melting point.

High-resolution transmission electron microscopy of hexagonal and rhombohedral molybdenum disulfide crystals.

PubMed

Isshiki, T; Nishio, K; Saijo, H; Shiojiri, M; Yabuuchi, Y; Takahashi, N

1993-07-01

Natural (molybdenite) and synthesized molybdenum disulfide crystals have been studied by high-resolution transmission electron microscopy. The image simulation demonstrates that the [0001] and [0110] HRTEM images of hexagonal and rhombohedral MoS2 crystals hardly disclose their stacking sequences, and that the [2110] images can distinguish the Mo and S columns along the incident electron beam and enable one to determine not only the crystal structure but also the fault structure. Observed [0001] images of cleaved molybdenite and synthesized MoS2 crystals, however, reveal the strain field around partial dislocations limiting an extended dislocation. A cross-sectional image of a single molecular (S-Mo-S) layer cleaved from molybdenite has been observed. Synthesized MoS2 flakes which were prepared by grinding have been found to be rhombohedral crystals containing many stacking faults caused by glides between S/S layers.

Racemic crystallography of synthetic protein enantiomers used to determine the X-ray structure of plectasin by direct methods

PubMed Central

Mandal, Kalyaneswar; Pentelute, Brad L; Tereshko, Valentina; Thammavongsa, Vilasak; Schneewind, Olaf; Kossiakoff, Anthony A; Kent, Stephen B H

2009-01-01

We describe the use of racemic crystallography to determine the X-ray structure of the natural product plectasin, a potent antimicrobial protein recently isolated from fungus. The protein enantiomers l-plectasin and d-plectasin were prepared by total chemical synthesis; interestingly, l-plectasin showed the expected antimicrobial activity, while d-plectasin was devoid of such activity. The mirror image proteins were then used for racemic crystallization. Synchrotron X-ray diffraction data were collected to atomic resolution from a racemic plectasin crystal; the racemate crystallized in the achiral centrosymmetric space group with one l-plectasin molecule and one d-plectasin molecule forming the unit cell. Dimer-like intermolecular interactions between the protein enantiomers were observed, which may account for the observed extremely low solvent content (13%–15%) and more highly ordered nature of the racemic crystals. The structure of the plectasin molecule was well defined for all 40 amino acids and was generally similar to the previously determined NMR structure, suggesting minimal impact of the crystal packing on the plectasin conformation. PMID:19472324

On the Relationship Between Scintillation Anisotropy and Crystal Structure in Pure Crystalline Organic Scintillator Materials

DOE Office of Scientific and Technical Information (OSTI.GOV)

Schuster, Patricia; Feng, Patrick; Brubaker, Erik

We report the scintillation anisotropy effect for proton recoil events has been investigated in five pure organic crystalline materials: anthracene, trans-stilbene, p-terphenyl, bibenzyl, and diphenylacetylene. These measurements include characterization of the scintillation response for one hemisphere of proton recoil directions in each crystal. In addition to standard measurements of the total light output and pulse shape at each angle, the prompt and delayed light anisotropies are analyzed, allowing for investigation of the singlet and triplet molecular excitation behaviors independently. This work provides new quantitative and qualitative observations that make progress toward understanding the physical mechanisms behind the scintillation anisotropy. Thesemore » measurements show that the relationship between the prompt and delayed light anisotropies is correlated with crystal structure, as it changes between the pi-stacked crystal structure materials (anthracene and p-terphenyl) and the herringbone crystal structure materials (stilbene, bibenzyl, and diphenylacetylene). The observations are consistent with a model in which there are preferred directions of kinetic processes for the molecular excitations. Finally, these processes and the impact of their directional dependencies on the scintillation anisotropy are discussed.« less

Pseudoracemic amino acid complexes: blind predictions for flexible two-component crystals.

PubMed

Görbitz, Carl Henrik; Dalhus, Bjørn; Day, Graeme M

2010-08-14

Ab initio prediction of the crystal packing in complexes between two flexible molecules is a particularly challenging computational chemistry problem. In this work we present results of single crystal structure determinations as well as theoretical predictions for three 1 ratio 1 complexes between hydrophobic l- and d-amino acids (pseudoracemates), known from previous crystallographic work to form structures with one of two alternative hydrogen bonding arrangements. These are accurately reproduced in the theoretical predictions together with a series of patterns that have never been observed experimentally. In this bewildering forest of potential polymorphs, hydrogen bonding arrangements and molecular conformations, the theoretical predictions succeeded, for all three complexes, in finding the correct hydrogen bonding pattern. For two of the complexes, the calculations also reproduce the exact space group and side chain orientations in the best ranked predicted structure. This includes one complex for which the observed crystal packing clearly contradicted previous experience based on experimental data for a substantial number of related amino acid complexes. The results highlight the significant recent advances that have been made in computational methods for crystal structure prediction.

On the Relationship Between Scintillation Anisotropy and Crystal Structure in Pure Crystalline Organic Scintillator Materials

DOE PAGES

Schuster, Patricia; Feng, Patrick; Brubaker, Erik

2018-05-03

We report the scintillation anisotropy effect for proton recoil events has been investigated in five pure organic crystalline materials: anthracene, trans-stilbene, p-terphenyl, bibenzyl, and diphenylacetylene. These measurements include characterization of the scintillation response for one hemisphere of proton recoil directions in each crystal. In addition to standard measurements of the total light output and pulse shape at each angle, the prompt and delayed light anisotropies are analyzed, allowing for investigation of the singlet and triplet molecular excitation behaviors independently. This work provides new quantitative and qualitative observations that make progress toward understanding the physical mechanisms behind the scintillation anisotropy. Thesemore » measurements show that the relationship between the prompt and delayed light anisotropies is correlated with crystal structure, as it changes between the pi-stacked crystal structure materials (anthracene and p-terphenyl) and the herringbone crystal structure materials (stilbene, bibenzyl, and diphenylacetylene). The observations are consistent with a model in which there are preferred directions of kinetic processes for the molecular excitations. Finally, these processes and the impact of their directional dependencies on the scintillation anisotropy are discussed.« less

FCC-HCP coexistence in dense thermo-responsive microgel crystals

NASA Astrophysics Data System (ADS)

Karthickeyan, D.; Joshi, R. G.; Tata, B. V. R.

2017-06-01

Analogous to hard-sphere suspensions, monodisperse thermo-responsive poly (N-isopropyl acrylamide) (PNIPAM) microgel particles beyond a volume fraction (ϕ) of 0.5 freeze into face centered cubic (FCC)-hexagonal close packed (HCP) coexistence under as prepared conditions and into an FCC structure upon annealing. We report here FCC-HCP coexistence to be stable in dense PNIPAM microgel crystals (ϕ > 0.74) with particles in their deswollen state (referred to as osmotically compressed microgel crystals) and the FCC structure with particles in their swollen state by performing annealing studies with different cooling rates. The structure of PNIPAM microgel crystals is characterized using static light scattering technique and UV-Visible spectroscopy and dynamics by dynamic light scattering (DLS). DLS studies reveal that the particle motion is diffusive at short times in crystals with ϕ < 0.74 and sub-diffusive at short times in PNIPAM crystals with ϕ > 0.74. The observed sub-diffusive behavior at short times is due to the overlap (interpenetration) of the dangling polymer chains between the shells of neighbouring PNIPAM microgel particles. Overlap is found to disappear upon heating the crystals well above their melting temperature, Tm due to reduction in the particle size. Annealing studies confirm that the overlap of dangling polymer chains between the shells of neighbouring PNIPAM spheres is responsible for the stability of FCC-HCP coexistence observed in osmotically compressed PNIPAM microgel crystals. Results are discussed in the light of recent reports of stabilizing the HCP structure in hard sphere crystals by adding interacting polymer chains.

Real-time molecular scale observation of crystal formation.

PubMed

Schreiber, Roy E; Houben, Lothar; Wolf, Sharon G; Leitus, Gregory; Lang, Zhong-Ling; Carbó, Jorge J; Poblet, Josep M; Neumann, Ronny

2017-04-01

How molecules in solution form crystal nuclei, which then grow into large crystals, is a poorly understood phenomenon. The classical mechanism of homogeneous crystal nucleation proceeds via the spontaneous random aggregation of species from liquid or solution. However, a non-classical mechanism suggests the formation of an amorphous dense phase that reorders to form stable crystal nuclei. So far it has remained an experimental challenge to observe the formation of crystal nuclei from five to thirty molecules. Here, using polyoxometallates, we show that the formation of small crystal nuclei is observable by cryogenic transmission electron microscopy. We observe both classical and non-classical nucleation processes, depending on the identity of the cation present. The experiments verify theoretical studies that suggest non-classical nucleation is the lower of the two energy pathways. The arrangement in just a seven-molecule proto-crystal matches the order found by X-ray diffraction of a single bulk crystal, which demonstrates that the same structure was formed in each case.

A first principles prediction of the crystal structure of C6Br2ClFH2

NASA Astrophysics Data System (ADS)

Misquitta, Alston J.; Welch, Gareth W. A.; Stone, Anthony J.; Price, Sarah L.

2008-04-01

We have constructed an intermolecular potential for the 1,3-dibromo-2-chloro-5-fluorobenzene molecule from first principles using SAPT(DFT) interaction energy calculations and the Williams-Stone-Misquitta method for obtaining molecular properties in distributed form. This molecule was included in the fourth Blind Test of crystal structure prediction organised by the Cambridge Crystallographic Data Centre. Using our potential, we have predicted the crystal structure of CBrClFH and found the lowest energy solution to be in excellent agreement with the experimentally observed crystal when it was subsequently revealed.

Mechanisms of heterogeneous crystal growth in atomic systems: insights from computer simulations.

PubMed

Gulam Razul, M S; Hendry, J G; Kusalik, P G

2005-11-22

In this paper we analyze the atomic-level structure of solid/liquid interfaces of Lennard-Jones fcc systems. The 001, 011, and 111 faces are examined during steady-state growth and melting of these crystals. The mechanisms of crystallization and melting are explored using averaged configurations generated during these steady-state runs, where subsequent tagging and labeling of particles at the interface provide many insights into the detailed atomic behavior at the freezing and melting interfaces. The interfaces are generally found to be rough and we observe the structure of freezing and melting interfaces to be very similar. Large structural fluctuations with solidlike and liquidlike characteristics are apparent in both the freezing and melting interfaces. The behavior at the interface observed under either growth or melting conditions reflects a competition between ordering and disordering processes. In addition, we observe atom hopping that imparts liquidlike characteristics to the solid side of the interfaces for all three crystal faces. Solid order is observed to extend as rough, three-dimensional protuberances through the interface, particularly for the 001 and 011 faces. We are also able to reconcile our different measures for the interfacial width and address the onset of asymmetry in the growth rates at high rates of crystal growth/melting.

Transmission electron microscopy: direct observation of crystal structure in refractory ceramics.

PubMed

Shaw, T M; Thomas, G

1978-11-10

Using high-resolution multibeam interference techniques in the transmission electron microscope, images have been obtained that make possible a real-space structure analysis of a beryllium-silicon-nitrogen compound. The results illustrate the usefulness of lattice imaging in the analysis of local crystal structure in these technologically promising ceramic materials.

Evidence for monoclinic distortion in the ground state phase of underdoped La 1.95Sr 0.05CuO 4: A single crystal neutron diffraction study

DOE PAGES

Singh, Anar; Schefer, Jurg; Sura, Ravi; ...

2016-03-24

The existing controversy about the symmetry of the crystal structure of the ground state of the critical doped La 1.95Sr 0.05CuO 4 has been resolved by analyzing the single crystal neutron diffraction data collected between 5 and 730 K. We observed small but significant intensities for "forbidden" reflections given by extinction rules of the orthorhombic Bmab space group at low temperatures. A careful investigation of neutron diffraction data reveals that the crystal structure of La 1.95Sr 0.05CuO 4 at 5 K is monoclinic with B2/m (2/m 1 1) space group. The monoclinic structure emerges from the orthorhombic structure in amore » continuous way; however, the structure is stable below similar to 120K which agrees with other observed phenomena. Lastly, our results on symmetry changes are crucial for the interpretation of physical properties also in other high temperature superconductors with similar structures.« less

Evidence for monoclinic distortion in the ground state phase of underdoped La{sub 1.95}Sr{sub 0.05}CuO{sub 4}: A single crystal neutron diffraction study

DOE Office of Scientific and Technical Information (OSTI.GOV)

Singh, Anar, E-mail: singhanar@gmail.com; Schefer, Jürg; Frontzek, Matthias

2016-03-28

The existing controversy about the symmetry of the crystal structure of the ground state of the critical doped La{sub 1.95}Sr{sub 0.05}CuO{sub 4} has been resolved by analyzing the single crystal neutron diffraction data collected between 5 and 730 K. We observed small but significant intensities for “forbidden” reflections given by extinction rules of the orthorhombic Bmab space group at low temperatures. A careful investigation of neutron diffraction data reveals that the crystal structure of La{sub 1.95}Sr{sub 0.05}CuO{sub 4} at 5 K is monoclinic with B2/m (2/m 1 1) space group. The monoclinic structure emerges from the orthorhombic structure in a continuous way;more » however, the structure is stable below ∼120 K which agrees with other observed phenomena. Our results on symmetry changes are crucial for the interpretation of physical properties also in other high temperature superconductors with similar structures.« less

Structural and photoluminescence studies on europium-doped lithium tetraborate (Eu:Li2B4O7) single crystal grown by microtube Czochralski (μT-Cz) technique

NASA Astrophysics Data System (ADS)

A, Kumaresh; R, Arun Kumar; N, Ravikumar; U, Madhusoodanan; B, S. Panigrahi; K, Marimuthu; M, Anuradha

2016-05-01

Rare earth europium (Eu3+)-doped lithium tetraborate (Eu:Li2B4O7) crystal is grown from its stoichiometric melt by microtube Czochralski pulling technique (μT-Cz) for the first time. The grown crystals are subjected to powder x-ray diffraction (PXRD) analysis which reveals the tetragonal crystal structure of the crystals. UV-vis-NIR spectral analysis is carried out to study the optical characteristics of the grown crystals. The crystal is transparent in the entire visible region, and the lower cutoff is observed to be at 304 nm. The existence of BO3 and BO4 bonding structure and the molecular associations are analyzed by Fourier transform infrared (FTIR) spectroscopy. The results of excitation and emission-photoluminescence spectra of europium ion incorporated in lithium tetraborate (LTB) single crystal reveal that the observations of peaks at 258, 297, and 318 nm in the excitation spectra and peaks at 579, 591, 597, 613, and 651 nm are observed in the emission spectra. The chromaticity coordinates are calculated from the emission spectra, and the emission intensity of the grown crystal is characterized through a CIE 1931 (Commission International d’Eclairage) color chromaticity diagram. Project supported by the Department of Science and Technology-Science and Engineering Research Board (Grant No. SR/S2/LOP-0012/2011), the Government of India for Awarding Major Research Project, the University Grants Commission-Department of Atomic Research-Consortium for Scientific Research (Grant No. CSR-KN/CSR-63/2014-2015/503), and the Kalpakkam and Indore, India.

Glycine glycinium picrate—Reinvestigation of the structure and vibrational spectra

NASA Astrophysics Data System (ADS)

Ghazaryan, V. V.; Fleck, M.; Petrosyan, A. M.

2011-01-01

The crystal of diglycine picrate (glycine glycinum picrate) has been obtained from an aqueous solution containing stoichiometric quantities of the components. The species crystallizes in the monoclinic system (space group P2 1/ c). The crystal structure was determined with high accuracy, IR and Raman spectra are discussed and compared with previous results, and the molecular structure is presented. It was shown that crystals of diglycine picrate obtained from the solution containing equimolar quantities may contain picric acid as impurity, which is the reason for the previously reported observation of second harmonic generation in this centrosymmetric crystal. With this example we want to point out the risk of misinterpretation of SHG signals in general.

Cubic-to-tetragonal structural phase transition in Rb1-xCsxCaF3 solid solutions: Thermal expansion and EPR studies

NASA Astrophysics Data System (ADS)

Lahoz, F.; Villacampa, B.; Alcalá, R.; Marquina, C.; Ibarra, M. R.

1997-04-01

The influence of crystal mixing on the structural phase transitions in Rb1-xCsxCaF3 (0=0.44. This transition shows a weak first-order component in the x=0 and 0.1 samples, which is progressively smeared out for x>0.1, indicating a spatial distribution of the critical temperature in those crystals with high ionic substitution rate. In RbCaF3 , another structural phase transition was observed at 20 K with a thermal hysteresis between 20 and 40 K. This transition has not been found in any of the mixed crystals.

The control of ice crystal growth and effect on porous structure of konjac glucomannan-based aerogels.

PubMed

Ni, Xuewen; Ke, Fan; Xiao, Man; Wu, Kao; Kuang, Ying; Corke, Harold; Jiang, Fatang

2016-11-01

Konjac glucomannan (KGM)-based aerogels were prepared using a combination of sol-gel and freeze-drying methods. Preparation conditions were chosen to control ice crystal growth and aerogel structure formation. The ice crystals formed during pre-freezing were observed by low temperature polarizing microscopy, and images of aerogel pores were obtained by scanning electron microscopy. The size of ice crystals were calculated and size distribution maps were drawn, and similarly for aerogel pores. Results showed that ice crystal growth and aerogel pore sizes may be controlled by varying pre-freezing temperatures, KGM concentration and glyceryl monostearate concentration. The impact of pre-freezing temperatures on ice crystal growth was explained as combining ice crystal growth rate with nucleation rate, while the impacts of KGM and glyceryl monostearate concentration on ice crystal growth were interpreted based on their influences on sol network structure. Copyright © 2016 Elsevier B.V. All rights reserved.

Electrochemical deposition of silver crystals aboard Skylab 4

NASA Technical Reports Server (NTRS)

Grodzka, P. G.; Facemire, B. R.; Johnston, M. H.; Gates, D. W.

1976-01-01

Silver crystals were grown aboard Skylab 4 by an electro-chemical reaction and subsequently returned to earth for comparison with crystals grown at 1- and 5-g. Both the Skylab and earth-grown crystals show a variety of structures. Certain tendencies in structure dependency on gravity level, however, can be discerned. In addition, downward growing dendrite streamers; upward growing chunky crystal streamers; growth along an air/liquid interface; and ribbon, film, and fiber crystal habits were observed in experiments conducted on the ground with solutions of varying concentrations. It was also observed that the crystal structures of space and ground electro-deposited silver crystals were very similar to the structures of germanium selenide and germanium telluride crystals grown in space and on the ground by a vapor transport technique. Consideration of the data leads to the conclusions that: (1) the rate of electrochemical displacement of silver ions from a 5 percent aqueous solution by copper is predominantly diffussion controlled in space and kinetically controlled in 1- and higher-g because of augmentation of mass transport by convection; (2) downward and upward crystal streamers are the result of gravity-driven convection, the flow patterns of which can be delineated. Lateral growths along an air/liquid interface are the result of surface-tension-driven convection, the pattern of which also can be delineated; (3) electrolysis in space or low-g environments can produce either dendritic crystals with more perfect microcrystalline structures or massive, single crystals with fewer defects than those grown on ground or at higher g-levels. Ribbons or films of space-grown silicon crystals would find a ready market for electronic substrate and photocell applications. Space-grown dendritic, metal crystals present the possibility of unique catalysts. Large perfect crystals of various materials are desired for a number of electronic and optical applications; and (4) vapor transport growth of germanium selenide and germanium telluride is affected by convection mechanisms similar to the mechanisms hypothesized for the electrochemical deposition of silver crystals. Evidence and considerations leading to the preceding summaries and conclusions are presented. The implications of the findings and conclusions for technological applications are discussed, and recommendations for further experiments are presented.

Alignment of crystal orientations of the multi-domain photonic crystals in Parides sesostris wing scales

PubMed Central

Yoshioka, S.; Fujita, H.; Kinoshita, S.; Matsuhana, B.

2014-01-01

It is known that the wing scales of the emerald-patched cattleheart butterfly, Parides sesostris, contain gyroid-type photonic crystals, which produce a green structural colour. However, the photonic crystal is not a single crystal that spreads over the entire scale, but it is separated into many small domains with different crystal orientations. As a photonic crystal generally has band gaps at different frequencies depending on the direction of light propagation, it seems mysterious that the scale is observed to be uniformly green under an optical microscope despite the multi-domain structure. In this study, we have carefully investigated the structure of the wing scale and discovered that the crystal orientations of different domains are not perfectly random, but there is a preferred crystal orientation that is aligned along the surface normal of the scale. This finding suggests that there is an additional factor during the developmental process of the microstructure that regulates the crystal orientation. PMID:24352678

The Surface Structure of Ground Metal Crystals

NASA Technical Reports Server (NTRS)

Boas, W.; Schmid, E.

1944-01-01

The changes produced on metallic surfaces as a result of grinding and polishing are not as yet fully understood. Undoubtedly there is some more or less marked change in the crystal structure, at least, in the top layer. Hereby a diffusion of separated crystal particles may be involved, or, on plastic material, the formation of a layer in greatly deformed state, with possible recrystallization in certain conditions. Czochralski verified the existence of such a layer on tin micro-sections by successive observations of the texture after repeated etching; while Thomassen established, roentgenographically by means of the Debye-Scherrer method, the existence of diffused crystal fractions on the surface of ground and polished tin bars, which he had already observed after turning (on the lathe). (Thickness of this layer - 0.07 mm). Whether this layer borders direct on the undamaged base material or whether deformed intermediate layers form the transition, nothing is known. One observation ty Sachs and Shoji simply states that after the turning of an alpha-brass crystal the disturbance starting from the surface, penetrates fairly deep (approx. 1 mm) into the crystal (proof by recrystallization at 750 C).

Distortion of Local Atomic Structures in Amorphous Ge-Sb-Te Phase Change Materials

NASA Astrophysics Data System (ADS)

Hirata, A.; Ichitsubo, T.; Guan, P. F.; Fujita, T.; Chen, M. W.

2018-05-01

The local atomic structures of amorphous Ge-Sb-Te phase-change materials have yet to be clarified and the rapid crystal-amorphous phase change resulting in distinct optical contrast is not well understood. We report the direct observation of local atomic structures in amorphous Ge2Sb2Te5 using "local" reverse Monte Carlo modeling dedicated to an angstrom-beam electron diffraction analysis. The results corroborated the existence of local structures with rocksalt crystal-like topology that were greatly distorted compared to the crystal symmetry. This distortion resulted in the breaking of ideal octahedral atomic environments, thereby forming local disordered structures that basically satisfied the overall amorphous structure factor. The crystal-like distorted octahedral structures could be the main building blocks in the formation of the overall amorphous structure of Ge-Sb-Te.

X-ray transparent microfluidic chip for mesophase-based crystallization of membrane proteins and on-chip structure determination

DOE PAGES

Khvostichenko, Daria S.; Schieferstein, Jeremy M.; Pawate, Ashtamurthy S.; ...

2014-08-21

Crystallization from lipidic mesophase matrices is a promising route to diffraction-quality crystals and structures of membrane proteins. The microfluidic approach reported here eliminates two bottlenecks of the standard mesophase-based crystallization protocols: (i) manual preparation of viscous mesophases and (ii) manual harvesting of often small and fragile protein crystals. In the approach reported here, protein-loaded mesophases are formulated in an X-ray transparent microfluidic chip using only 60 nL of the protein solution per crystallization trial. The X-ray transparency of the chip enables diffraction data collection from multiple crystals residing in microfluidic wells, eliminating the normally required manual harvesting and mounting ofmore » individual crystals. In addition, we validated our approach by on-chip crystallization of photosynthetic reaction center, a membrane protein from Rhodobacter sphaeroides, followed by solving its structure to a resolution of 2.5 Å using X-ray diffraction data collected on-chip under ambient conditions. A moderate conformational change in hydrophilic chains of the protein was observed when comparing the on-chip, room temperature structure with known structures for which data were acquired under cryogenic conditions.« less

X-ray Transparent Microfluidic Chip for Mesophase-Based Crystallization of Membrane Proteins and On-Chip Structure Determination

DOE Office of Scientific and Technical Information (OSTI.GOV)

Khvostichenko, Daria S.; Schieferstein, Jeremy M.; Pawate, Ashtamurthy S.

2014-10-01

Crystallization from lipidic mesophase matrices is a promising route to diffraction-quality crystals and structures of membrane proteins. The microfluidic approach reported here eliminates two bottlenecks of the standard mesophase-based crystallization protocols: (i) manual preparation of viscous mesophases and (ii) manual harvesting of often small and fragile protein crystals. In the approach reported here, protein-loaded mesophases are formulated in an X-ray transparent microfluidic chip using only 60 nL of the protein solution per crystallization trial. The X-ray transparency of the chip enables diffraction data collection from multiple crystals residing in microfluidic wells, eliminating the normally required manual harvesting and mounting ofmore » individual crystals. We validated our approach by on-chip crystallization of photosynthetic reaction center, a membrane protein from Rhodobacter sphaeroides, followed by solving its structure to a resolution of 2.5 Å using X-ray diffraction data collected on-chip under ambient conditions. A moderate conformational change in hydrophilic chains of the protein was observed when comparing the on-chip, room temperature structure with known structures for which data were acquired under cryogenic conditions.« less

Physical and Structural Studies on the Cryo-cooling of Insulin Crystals

NASA Technical Reports Server (NTRS)

Lovelace, J.; Bellamy, H.; Snell, E. H.; Borgstahl, G.

2003-01-01

Reflection profiles were analyzed from microgravity-(mg) and earth-grown insulin crystals to measure mosaicity (h) and to reveal mosaic domain structure and composition. The effects of cryocooling on single and multi-domain crystals were compared. The effects of cryocooling on insulin structure were also re-examined. Microgravity crystals were larger, more homogeneous, and more perfect than earth crystals. Several mg crystals contained primarily a single mosaic domain with havg of 0.005deg. The earth crystals varied in quality and all contained multiple domains with havg of 0.031deg. Cryocooling caused a 43-fold increase in h for mg crystals (havg=0.217deg) and an %fold increase for earth crystals (havg=0.246deg). These results indicate that very well-ordered crystals are not completely protected from the stresses associated with cryocooling, especially when structural perturbations occur. However, there were differences in the reflection profiles. For multi-mosaic domain crystals, each domain individually broadened and separated from the other domains upon cryo-cooling. Cryo-cooling did not cause an increase in the number of domains. A crystal composed of a single domain retained this domain structure and the reflection profiles simply broadened. Therefore, an improved signal-to-noise ratio for each reflection was measured from cryo-cooled single domain crystals relative to cryo-cooled multi-domain crystals. This improved signal, along with the increase in crystal size, facilitated the measurement of the weaker high- resolution reflections. The observed broadening of reflection profiles indicates increased variation in unit cell dimensions which may be linked to cryo-cooling-associated structural changes and disorder.

Study of structural and optical properties of YAG and Nd:YAG single crystals

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kostić, S.; Lazarević, Z.Ž., E-mail: lzorica@yahoo.com; Radojević, V.

2015-03-15

Highlights: • Transparent YAG and pale pink Nd:YAG single crystals were produced by the Czochralski technique. • Growth mechanisms and shape of the liquid/solid interface and incorporation of Nd{sup 3+} were studied. • The structure of the crystals was investigated by X-ray diffraction, Raman and IR spectroscopy. • The 15 Raman and 17 IR modes were observed. • The obtained YAG and Nd:YAG single crystals were without core and of good optical quality. - Abstract: Yttrium aluminum garnet (YAG, Y{sub 3}Al{sub 5}O{sub 12}) and yttrium aluminum garnet doped with neodymium (Nd:YAG) single crystals were grown by the Czochralski technique. Themore » critical diameter and the critical rate of rotation were calculated. Suitable polishing and etching solutions were determined. As a result of our experiments, the transparent YAG and pale pink Nd:YAG single crystals were produced. The obtained crystals were studied by X-ray diffraction, Raman and IR spectroscopy. The crystal structure was confirmed by XRD. The 15 Raman and 17 IR modes were observed. The Raman and IR spectroscopy results are in accordance with X-ray diffraction analysis. The obtained YAG and Nd:YAG single crystals were without core and of good optical quality. The absence of a core was confirmed by viewing polished crystal slices. Also, it is important to emphasize that the obtained Nd:YAG single crystal has a concentration of 0.8 wt.% Nd{sup 3+} that is characteristic for laser materials.« less

Electron spin resonance of an irradiated single crystal of potassium hydrogen maleate

DOE Office of Scientific and Technical Information (OSTI.GOV)

Iwasaki, Machio; Itoh, Koichi

1963-09-15

Electron spin resonance absorptions of x-irradiated single crystals of potassium hydrogen maleate and potassium deuterium maleate were observed. Both compounds gave the same hyperfine structures, although the slightly sharper line widths were observed for the deuterium exchanged compound.

Growth, structural, optical and surface analysis of piperazinium tartrate: A NLO single crystal

NASA Astrophysics Data System (ADS)

Gupta, Apurva; Raseel Rahman M., K.; Nair, Lekha

2018-05-01

Single crystal of piperazinium tartrate (PPZT) was grown by the slow evaporation solution growth technique at room temperature. Crystallinity of grown crystal was examined by powder X-ray diffraction. High transparency and wide band gap were observed in the UV-Visible spectroscopic studies. Intense and broad emissions were observed in the blue region, as that is indicated by photoluminescence spectroscopy. The quality of the grown PPZT single crystals were analyzed by the etching studies using the water as the etchant.

Laser generation in opal-like single-crystal and heterostructure photonic crystals

NASA Astrophysics Data System (ADS)

Kuchyanov, A. S.; Plekhanov, A. I.

2016-11-01

This study describes the laser generation of a 6Zh rhodamine in artificial opals representing single-crystal and heterostructure films. The spectral and angular properties of emission and the threshold characteristics of generation are investigated. In the case where the 6Zh rhodamine was in a bulk opal, the so-called random laser generation was observed. In contrast to this, the laser generation caused by a distributed feedback inside the structure of the photonic bandgap was observed in photonic-crystal opal films.

A Maltose-Binding Protein Fusion Construct Yields a Robust Crystallography Platform for MCL1

PubMed Central

Clifton, Matthew C.; Dranow, David M.; Leed, Alison; Fulroth, Ben; Fairman, James W.; Abendroth, Jan; Atkins, Kateri A.; Wallace, Ellen; Fan, Dazhong; Xu, Guoping; Ni, Z. J.; Daniels, Doug; Van Drie, John; Wei, Guo; Burgin, Alex B.; Golub, Todd R.; Hubbard, Brian K.; Serrano-Wu, Michael H.

2015-01-01

Crystallization of a maltose-binding protein MCL1 fusion has yielded a robust crystallography platform that generated the first apo MCL1 crystal structure, as well as five ligand-bound structures. The ability to obtain fragment-bound structures advances structure-based drug design efforts that, despite considerable effort, had previously been intractable by crystallography. In the ligand-independent crystal form we identify inhibitor binding modes not observed in earlier crystallographic systems. This MBP-MCL1 construct dramatically improves the structural understanding of well-validated MCL1 ligands, and will likely catalyze the structure-based optimization of high affinity MCL1 inhibitors. PMID:25909780

Why don't we find more polymorphs?

PubMed

Price, Sarah L

2013-08-01

Crystal structure prediction (CSP) studies are not limited to being a search for the most thermodynamically stable crystal structure, but play a valuable role in understanding polymorphism, as shown by interdisciplinary studies where the crystal energy landscape has been explored experimentally and computationally. CSP usually produces more thermodynamically plausible crystal structures than known polymorphs. This article illustrates some reasons why: because (i) of approximations in the calculations, particularly the neglect of thermal effects (see §1.1); (ii) of the molecular rearrangement during nucleation and growth (see §1.2); (iii) the solid-state structures observed show dynamic or static disorder, stacking faults, other defects or are not crystalline and so represent more than one calculated structure (see §1.3); (iv) the structures are metastable relative to other molecular compositions (see §1.4); (v) the right crystallization experiment has not yet been performed (see §1.5) or (vi) cannot be performed (see §1.6) and the possibility (vii) that the polymorphs are not detected or structurally characterized (see §1.7). Thus, we can only aspire to a general predictive theory for polymorphism, as this appears to require a quantitative understanding of the kinetic factors involved in all possible multi-component crystallizations. For a specific molecule, analysis of the crystal energy landscape shows the potential complexity of its crystallization behaviour.

Isothermal Crystallization Behavior of Cocoa Butter at 17 and 20 °C with and without Limonene.

PubMed

Rigolle, Annelien; Goderis, Bart; Van Den Abeele, Koen; Foubert, Imogen

2016-05-04

Differential scanning calorimetry and real-time X-ray diffraction using synchrotron radiation were used to elucidate isothermal cocoa butter crystallization at 17 and 20 °C in the absence and presence of different limonene concentrations. At 17 °C, a three-step crystallization process was visible for pure cocoa butter, whereby first an unknown structure with long spacings between a 2L and 3L structure was formed that rapidly transformed into the more stable α structure, which in turn was converted into more stable β' crystals. At 20 °C, an α-mediated β' crystallization was observed. The addition of limonene resulted in a reduction of the amount of unstable crystals and an acceleration of polymorphic transitions. At 17 °C, the crystallization process was accelerated due to the acceleration of the formation of more stable polymorphic forms, whereas there were insufficient α crystals for an α-mediated β' nucleation at 20 °C, resulting in a slower crystallization process.

Structure, dielectric and electric properties of diisobutylammonium hydrogen sulfate crystal

NASA Astrophysics Data System (ADS)

Bednarchuk, Tamara J.; Kinzhybalo, Vasyl; Markiewicz, Ewa; Hilczer, Bożena; Pietraszko, Adam

2018-02-01

Diisobutylammonium hydrogen sulfate, a new organic-inorganic hybrid compound, was successfully synthesized and three structural phases in 298-433 K temperature range were revealed by differential scanning calorimetry and X-ray powder diffraction studies. Single crystal X-ray diffraction data were used to describe the crystal structures in each particular case. In phase III (below 336/319 K on heating/cooling) the crystal arrangement appears to be within the triclinic symmetry with P-1 space group. During heating in the 336-339 K region (and 319-337 K on cooling) the crystal exists in the phase II, characterized by monoclinic symmetry with P21/c space group. Consequently, above 339 K (during heating, and 337 K during cooling temperature sequences), i.e. in phase I the crystal exhibits orthorhombic symmetry (Cmce space group). Ferroelastic domain structure was observed in phase III. These phase boundaries (III→II and II→I) were accompanied by the presence of small anomalies, apparent in the dielectric permittivity and electric conductivity experimental data. Fast proton transport with activation energy of 0.23 eV was observed in the high temperature phase I and related to phonon assisted proton diffusion conditioned by disorder of diisobutylammonium (diba) cations, as well as by high thermal displacements of oxygen and sulfur atoms of hydrogen sulfate anion (hs).

Long Periodic Structure of a Room-Temperature Ionic Liquid by High-Pressure Small-Angle X-Ray Scattering and Wide-Angle X-Ray Scattering: 1-Decyl-3-Methylimidazolium Chloride.

PubMed

Abe, Hiroshi; Hamaya, Nozomu; Koyama, Yoshihiro; Kishimura, Hiroaki; Takekiyo, Takahiro; Yoshimura, Yukihiro; Wakabayashi, Daisuke; Funamori, Nobumasa; Matsuishi, Kiyoto

2018-04-23

The Bragg reflections of 1-decyl-3-methylimidazolium chloride ([C 10 mim][Cl]), a room-temperature ionic liquid, are observed in a lowly scattered wavevector (q) region using high-pressure (HP) small-angle X-ray scattering methods. The HP crystal of [C 10 mim][Cl] was characterized by an extremely long periodic structure. The peak position at the lowest q (1.4 nm -1 ) was different from that of the prepeak observed in the liquid state (2.3 nm -1 ). Simultaneously, Bragg reflections at high-q were detected using HP wide-angle X-ray scattering. The longest lattice constant was estimated to be 4.3 nm using structural analysis. The crystal structure of HP differed from that of the low-temperature (LT) crystal and the LT liquid crystal. With increasing pressure, Bragg reflections in the high-q component became much broader, and were accompanied by phase transition, although those in the low-q component were observed to be relatively sharp. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Metastable solidification of hypereutectic Co 2Si-CoSi composition: Microstructural studies and in-situ observations

DOE PAGES

Wang, Yeqing; Gao, Jianrong; Kolbe, Matthias; ...

2017-09-18

Metastable solidification of undercooled Co 60Si 40 melts was investigated by microstructural studies and in-situ high-energy X-ray diffraction. Five solidification paths were identified. Three of them were observed at low undercoolings, which show uncoupled and coupled growth of stable β-Co 2Si and CoSi compounds. The other paths were observed at high undercoolings, which show peritectic and primary crystallization of a metastable Co 5Si 3 compound. The β-Co 2Si and Co 5Si 3 compounds crystallize into a hexagonal crystal structure and experience solid-state decomposition. Microstructure formation depends on solidification path. The coupled and uncoupled growth of the stable compounds produces amore » regular lamellar eutectic structure and an anomalous eutectic structure, respectively. The crystallization and solid-state decomposition of the metastable Co 5Si 3 compound brings about a fine-grained two-phase mixture, which represents another type of anomalous eutectic structure. Here, the results provide proof of two rare mechanisms of anomalous eutectic formation and shed light onto metastable phase relations in the undercooled region of the Co-Si system.« less

Metastable solidification of hypereutectic Co 2Si-CoSi composition: Microstructural studies and in-situ observations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wang, Yeqing; Gao, Jianrong; Kolbe, Matthias

Metastable solidification of undercooled Co 60Si 40 melts was investigated by microstructural studies and in-situ high-energy X-ray diffraction. Five solidification paths were identified. Three of them were observed at low undercoolings, which show uncoupled and coupled growth of stable β-Co 2Si and CoSi compounds. The other paths were observed at high undercoolings, which show peritectic and primary crystallization of a metastable Co 5Si 3 compound. The β-Co 2Si and Co 5Si 3 compounds crystallize into a hexagonal crystal structure and experience solid-state decomposition. Microstructure formation depends on solidification path. The coupled and uncoupled growth of the stable compounds produces amore » regular lamellar eutectic structure and an anomalous eutectic structure, respectively. The crystallization and solid-state decomposition of the metastable Co 5Si 3 compound brings about a fine-grained two-phase mixture, which represents another type of anomalous eutectic structure. Here, the results provide proof of two rare mechanisms of anomalous eutectic formation and shed light onto metastable phase relations in the undercooled region of the Co-Si system.« less

The crystal structure of Pseudomonas aeruginosa exotoxin domain III with nicotinamide and AMP: conformational differences with the intact exotoxin.

PubMed Central

Li, M; Dyda, F; Benhar, I; Pastan, I; Davies, D R

1995-01-01

Domain III of Pseudomonas aeruginosa exotoxin A catalyses the transfer of ADP-ribose from NAD to a modified histidine residue of elongation factor 2 in eukaryotic cells, thus inactivating elongation factor 2. This domain III is inactive in the intact toxin but is active in the isolated form. We report here the 2.5-A crystal structure of this isolated domain crystallized in the presence of NAD and compare it with the corresponding structure in the intact Pseudomonas aeruginosa exotoxin A. We observe a significant conformational difference in the active site region from Arg-458 to Asp-463. Contacts with part of domain II in the intact toxin prevent the adoption of the isolated domain conformation and provide a structural explanation for the observed inactivity. Additional electron density in the active site region corresponds to separate AMP and nicotinamide and indicates that the NAD has been hydrolyzed. The structure has been compared with the catalytic domain of the diphtheria toxin, which was crystallized with ApUp. Images Fig. 1 PMID:7568123

How to assign a (3 + 1)-dimensional superspace group to an incommensurately modulated biological macromolecular crystal

PubMed Central

2017-01-01

Periodic crystal diffraction is described using a three-dimensional (3D) unit cell and 3D space-group symmetry. Incommensurately modulated crystals are a subset of aperiodic crystals that need four to six dimensions to describe the observed diffraction pattern, and they have characteristic satellite reflections that are offset from the main reflections. These satellites have a non-integral relationship to the primary lattice and require q vectors for processing. Incommensurately modulated biological macromolecular crystals have been frequently observed but so far have not been solved. The authors of this article have been spearheading an initiative to determine this type of crystal structure. The first step toward structure solution is to collect the diffraction data making sure that the satellite reflections are well separated from the main reflections. Once collected they can be integrated and then scaled with appropriate software. Then the assignment of the superspace group is needed. The most common form of modulation is in only one extra direction and can be described with a (3 + 1)D superspace group. The (3 + 1)D superspace groups for chemical crystallographers are fully described in Volume C of International Tables for Crystallography. This text includes all types of crystallographic symmetry elements found in small-molecule crystals and can be difficult for structural biologists to understand and apply to their crystals. This article provides an explanation for structural biologists that includes only the subset of biological symmetry elements and demonstrates the application to a real-life example of an incommensurately modulated protein crystal. PMID:28808437

Surface and electronic structure of Bi-Ca-Sr-Cu-O superconductors studied by LEED, UPS and XPS

NASA Astrophysics Data System (ADS)

Shen, Z.-X.; Lindberg, P. A. P.; Wells, B. O.; Lindau, I.; Spicer, W. E.; Mitzi, D. B.; Eom, C. B.; Kapitulnik, A.; Geballe, T. H.; Soukiassian, P.

1989-02-01

Single crystal and polycrystalline samples of Bi2CaSr2Cu2O8 have been studied by various surface sensitive techniques, including low energy electron diffraction (LEED), ultraviolet photoemission spectroscopy (UPS) and x-ray photoemission spectroscopy (XPS). The surface structure of the single crystals was characterized by LEED to be consistent with that of the bulk structure. Our data suggest that Bi2CaSr2Cu2O8 single crystals are very stable in the ultrahigh vacuu. No change of XPS spectra with temperature was observed. We have also studied the electronic structure of Bi2Sr2CuO6, which has a lower superconducting transition temperature Tc. Comparing the electronic structure of the two Bi-Ca-Sr-Cu-O superconductors, an important difference in the density of states near EF was observed which seems to be related to the difference in Tc.

Structure, Energetics, and Dynamics of Screw Dislocations in Even n-Alkane Crystals.

PubMed

Olson, Isabel A; Shtukenberg, Alexander G; Hakobyan, Gagik; Rohl, Andrew L; Raiteri, Paolo; Ward, Michael D; Kahr, Bart

2016-08-18

Spiral hillocks on n-alkane crystal surfaces were observed immediately after Frank recognized the importance of screw dislocations for crystal growth, yet their structures and energies in molecular crystals remain ill-defined. To illustrate the structural chemistry of screw dislocations that are responsible for plasticity in organic crystals and upon which the organic electronics and pharmaceutical industries depend, molecular dynamics was used to examine heterochiral dislocation pairs with Burgers vectors along [001] in n-hexane, n-octane, and n-decane crystals. The cores were anisotropic and elongated in the (110) slip plane, with significant local changes in molecular position, orientation, conformation, and energy. This detailed atomic level picture produced a distribution of strain consistent with linear elastic theory, giving confidence in the simulations. Dislocations with doubled Burgers vectors split into pairs with elementary displacements. These results suggest a pathway to understanding the mechanical properties and failure associated with elastic and plastic deformation in soft crystals.

Magneto-optical properties of biogenic photonic crystals in algae

DOE Office of Scientific and Technical Information (OSTI.GOV)

Iwasaka, M., E-mail: iwasaka-m@umin.ac.jp; Japan Science and Technology Agency, PRESTO, 4-1-8 Honcho, Kawaguchi 332-0012 Saitama; Mizukawa, Y.

In the present study, the effects of strong static magnetic fields on the structural colors of the cell covering crystals on a microalgae, coccolithophore, were investigated. The coccolithophore, Emiliania huxleyi, generates a precise assembly of calcite crystals called coccoliths by biomineralization. The coccoliths attached to the cells exhibited structural colors under side light illumination, and the colors underwent dynamic transitions when the magnetic fields were changed between 0 T and 5 T, probably due to diamagnetically induced changes of their inclination under the magnetic fields. The specific light-scattering property of individual coccoliths separated from the cells was also observed. Light scattering frommore » a condensed suspension of coccoliths drastically decreased when magnetic fields of more than 4 T were applied parallel to the direction of observation. The magnetically aligned cell-covering crystals of the coccolithophores exhibited the properties of both a photonic crystal and a minimum micromirror.« less

Influence of annealing temperature on optical properties of the photonic-crystal structures obtained by self-organization of colloidal microspheres of polystyrene and silica

NASA Astrophysics Data System (ADS)

Mikhnev, L. V.; Bondarenko, E. A.; Chapura, O. M.; Skomorokhov, A. A.; Kravtsov, A. A.

2018-01-01

The influence of annealing temperature on the transmission spectra of photonic crystals composed of polystyrene and silicon dioxide microspheres was studied. It was found that annealing of photonic crystals based on polystyrene and silica leads to a shift in the photonic band gap to the short-wavelength region. Based on the results of optical studies, the dependences of the structural parameters of the obtained opal-like crystals on annealing temperature were obtained. In the case of polystyrene photonic crystals, the displacement of the photonic band gap is observed in a narrow temperature range above the glass transition temperature. For SiO2 photonic crystals, it was found that the process of microspheres sintering is complex and involves three stages of structural modification.

Magnetically-induced ferroelectricity in the (ND4)2[FeCl5(D2O)] molecular compound

PubMed Central

Alberto Rodríguez-Velamazán, José; Fabelo, Óscar; Millán, Ángel; Campo, Javier; Johnson, Roger D.; Chapon, Laurent

2015-01-01

The number of magnetoelectric multiferroic materials reported to date is scarce, as magnetic structures that break inversion symmetry and induce an improper ferroelectric polarization typically arise through subtle competition between different magnetic interactions. The (NH4)2[FeCl5(H2O)] compound is a rare case where such improper ferroelectricity has been observed in a molecular material. We have used single crystal and powder neutron diffraction to obtain detailed solutions for the crystal and magnetic structures of (NH4)2[FeCl5(H2O)], from which we determined the mechanism of multiferroicity. From the crystal structure analysis, we observed an order-disorder phase transition related to the ordering of the ammonium counterion. We have determined the magnetic structure below TN, at 2 K and zero magnetic field, which corresponds to a cycloidal spin arrangement with magnetic moments contained in the ac-plane, propagating parallel to the c-axis. The observed ferroelectricity can be explained, from the obtained magnetic structure, via the inverse Dzyaloshinskii-Moriya mechanism. PMID:26417890

Shear induced structures in crystallizing cocoa butter

NASA Astrophysics Data System (ADS)

Mazzanti, Gianfranco; Guthrie, Sarah E.; Sirota, Eric B.; Marangoni, Alejandro G.; Idziak, Stefan H. J.

2004-03-01

Cocoa butter is the main structural component of chocolate and many cosmetics. It crystallizes in several polymorphs, called phases I to VI. We used Synchrotron X-ray diffraction to study the effect of shear on its crystallization. A previously unreported phase (phase X) was found and a crystallization path through phase IV under shear was observed. Samples were crystallized under shear from the melt in temperature controlled Couette cells, at final crystallization temperatures of 17.5^oC, 20^oC and 22.5^oC in Beamline X10A of NSLS. The formation of phase X was observed at low shear rates (90 s-1) and low crystallization temperature (17.5^oC), but was absent at high shear (720 s-1) and high temperature (20^oC). The d-spacing and melting point suggest that this new phase is a mixture rich on two of the three major components of cocoa butter. We also found that, contrary to previous reports, the transition from phase II to phase V can happen through the intermediate phase IV, at high shear rates and temperature.

Growth and structural characterization of single crystals of the magnetic superconductor Ru1-xSr2-yGd1+yCu2+xO8-δ (RuGd-1212) obtained by the partial melting technique

NASA Astrophysics Data System (ADS)

Yamaki, K.; Bamba, Y.; Mochiku, T.; Funahashi, S.; Matsushita, Y.; Irie, A.

2018-05-01

In this study, cubic single crystals of the magnetic superconductor Ru1-xSr2-yGd1+yCu2+xO8-δ (RuGd-1212) with typical dimensions of 100-150 μm in length were grown by the partial melting technique. Multiple 00l reflections were first observed by XRD measurements of the bulk RuGd-1212 single crystals. The resistivity of the obtained crystals was roughly estimated to be ∼24-80 mΩ cm and no superconducting transition was observed down to 4.2 K. From the XRD measurements and refinement of the crystal structure, it was apparent that the Ru and Sr sites of the single-crystal RuGd-1212 were partially substituted by Cu and Gd, respectively. Oxygen defects were found to be minor (δ ≈ 0.1). The lattice parameters a and c of the single crystals were found to be larger and smaller, respectively, than those of a polycrystalline sample.

Multiple solvent crystal structures of ribonuclease A: An assessment of the method

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dechene, Michelle; Wink, Glenna; Smith, Mychal

2010-11-12

The multiple solvent crystal structures (MSCS) method uses organic solvents to map the surfaces of proteins. It identifies binding sites and allows for a more thorough examination of protein plasticity and hydration than could be achieved by a single structure. The crystal structures of bovine pancreatic ribonuclease A (RNAse A) soaked in the following organic solvents are presented: 50% dioxane, 50% dimethylformamide, 70% dimethylsulfoxide, 70% 1,6-hexanediol, 70% isopropanol, 50% R,S,R-bisfuran alcohol, 70% t-butanol, 50% trifluoroethanol, or 1.0M trimethylamine-N-oxide. This set of structures is compared with four sets of crystal structures of RNAse A from the protein data bank (PDB) andmore » with the solution NMR structure to assess the validity of previously untested assumptions associated with MSCS analysis. Plasticity from MSCS is the same as from PDB structures obtained in the same crystal form and deviates only at crystal contacts when compared to structures from a diverse set of crystal environments. Furthermore, there is a good correlation between plasticity as observed by MSCS and the dynamic regions seen by NMR. Conserved water binding sites are identified by MSCS to be those that are conserved in the sets of structures taken from the PDB. Comparison of the MSCS structures with inhibitor-bound crystal structures of RNAse A reveals that the organic solvent molecules identify key interactions made by inhibitor molecules, highlighting ligand binding hot-spots in the active site. The present work firmly establishes the relevance of information obtained by MSCS.« less

A new crystal form of Aspergillus oryzae catechol oxidase and evaluation of copper site structures in coupled binuclear copper enzymes.

PubMed

Penttinen, Leena; Rutanen, Chiara; Saloheimo, Markku; Kruus, Kristiina; Rouvinen, Juha; Hakulinen, Nina

2018-01-01

Coupled binuclear copper (CBC) enzymes have a conserved type 3 copper site that binds molecular oxygen to oxidize various mono- and diphenolic compounds. In this study, we found a new crystal form of catechol oxidase from Aspergillus oryzae (AoCO4) and solved two new structures from two different crystals at 1.8-Å and at 2.5-Å resolutions. These structures showed different copper site forms (met/deoxy and deoxy) and also differed from the copper site observed in the previously solved structure of AoCO4. We also analysed the electron density maps of all of the 56 CBC enzyme structures available in the protein data bank (PDB) and found that many of the published structures have vague copper sites. Some of the copper sites were then re-refined to find a better fit to the observed electron density. General problems in the refinement of metalloproteins and metal centres are discussed.

Concerted ligand exchange and the roles of counter anions in the reversible structural switching of crystalline peptide metallo-macrocycles.

PubMed

Miyake, Ryosuke; Shionoya, Mitsuhiko

2014-06-02

To understand reversible structural switching in crystalline materials, we studied the mechanism of reversible crystal-to-crystal transformation of a tetranuclear Ni(II) macrocycle consisting of artificial β-dipeptides. On the basis of detailed structural analyses and thermodynamic measurements made in a comparison of pseudo-isostructural crystals (NO3 and BF4 salts), we herein discuss how ligand-exchange reactions take place in the crystal due to changes in water content and temperature. Observations of the structural transformation of NO3 salt indicated that a pseudo crystalline phase transformation takes place through concerted ligand-exchange reactions at the four Ni(II) centers of the macrocycle with hydrogen bond switching. A mechanism for this ligand exchange was supported by IR spectroscopy. Thermodynamic measurements suggested that the favorable compensation relationship of the enthalpy changes due to water uptake and structural changes are keys to the reversible structural transformation. On the basis of a comparison with the pseudo-isostructural crystals, it is apparent that the crystal packing structure and the types of counter anions are important factors for facilitating reversible ligand exchange with single crystallinity.

The strength of a calcified tissue depends in part on the molecular structure and organization of its constituent mineral crystals in their organic matrix

NASA Technical Reports Server (NTRS)

Landis, W. J.

1995-01-01

High-voltage electron-microscopic tomographic (3D) studies of the ultrastructural interaction between mineral and organic matrix in a variety of calcified tissues reveal different crystal structural and organizational features in association with their respective organic matrices. In brittle or weak pathologic or ectopic calcifications, including examples of osteogenesis imperfecta, calciphylaxis, calcergy, and dermatomyositis, hydroxyapatite crystals occur in various sizes and shapes and are oriented and aligned with respect to collagen in a manner which is distinct from that found in normal calcified tissues. A model of collagen-mineral interaction is proposed which may account for the observed crystal structures and organization. The results indicate that the ultimate strength, support, and other mechanical properties provided by a calcified tissue are dependent in part upon the molecular structure and arrangement of its constituent mineral crystals within their organic matrix.

Dark-field transmission electron microscopy of cortical bone reveals details of extrafibrillar crystals.

PubMed

Schwarcz, Henry P; McNally, Elizabeth A; Botton, Gianluigi A

2014-12-01

In a previous study we showed that most of the mineral in bone is present in the form of "mineral structures", 5-6nm-thick, elongated plates which surround and are oriented parallel to collagen fibrils. Using dark-field transmission electron microscopy, we viewed mineral structures in ion-milled sections of cortical human bone cut parallel to the collagen fibrils. Within the mineral structures we observe single crystals of apatite averaging 5.8±2.7nm in width and 28±19nm in length, their long axes oriented parallel to the fibril axis. Some appear to be composite, co-aligned crystals as thin as 2nm. From their similarity to TEM images of crystals liberated from deproteinated bone we infer that we are viewing sections through platy crystals of apatite that are assembled together to form the mineral structures. Copyright © 2014 Elsevier Inc. All rights reserved.

The strength of a calcified tissue depends in part on the molecular structure and organization of its constituent mineral crystals in their organic matrix.

PubMed

Landis, W J

1995-05-01

High-voltage electron-microscopic tomographic (3D) studies of the ultrastructural interaction between mineral and organic matrix in a variety of calcified tissues reveal different crystal structural and organizational features in association with their respective organic matrices. In brittle or weak pathologic or ectopic calcifications, including examples of osteogenesis imperfecta, calciphylaxis, calcergy, and dermatomyositis, hydroxyapatite crystals occur in various sizes and shapes and are oriented and aligned with respect to collagen in a manner which is distinct from that found in normal calcified tissues. A model of collagen-mineral interaction is proposed which may account for the observed crystal structures and organization. The results indicate that the ultimate strength, support, and other mechanical properties provided by a calcified tissue are dependent in part upon the molecular structure and arrangement of its constituent mineral crystals within their organic matrix.

Crystal structure of simple metals at high pressures

NASA Astrophysics Data System (ADS)

Degtyareva, Olga

2010-09-01

The effects of pressure on the crystal structure of simple (or sp-) elements are analysed in terms of changes in coordination number, packing density, and interatomic distances, and general rules are established. In the polyvalent elements from groups 14-17, the covalently bonded structures tend to transform to metallic phases with a gradual increase in coordination number and packing density, a behaviour normally expected under pressure. Group 1 and 2 metallic elements, however, show a reverse trend towards structures with low packing density due to intricate changes in their electronic structure. Complex crystal structures such as host-guest and incommensurately modulated structures found in these elements are given special attention in this review in an attempt to determine their role in the observed phase-transition sequences.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhao, Haishuang; Krysiak, Yaşar; Hoffmann, Kristin

The crystal structure and disorder phenomena of Al{sub 4}B{sub 2}O{sub 9}, an aluminum borate from the mullite-type family, were studied using automated diffraction tomography (ADT), a recently established method for collection and analysis of electron diffraction data. Al{sub 4}B{sub 2}O{sub 9}, prepared by sol-gel approach, crystallizes in the monoclinic space group C2/m. The ab initio structure determination based on three-dimensional electron diffraction data from single ordered crystals reveals that edge-connected AlO{sub 6} octahedra expanding along the b axis constitute the backbone. The ordered structure (A) was confirmed by TEM and HAADF-STEM images. Furthermore, disordered crystals with diffuse scattering along themore » b axis are observed. Analysis of the modulation pattern implies a mean superstructure (AAB) with a threefold b axis, where B corresponds to an A layer shifted by ½a and ½c. Diffraction patterns simulated for the AAB sequence including additional stacking disorder are in good agreement with experimental electron diffraction patterns. - Graphical abstract: Crystal structure and disorder phenomena of B-rich Al{sub 4}B{sub 2}O{sub 9} studied by automated electron diffraction tomography (ADT) and described by diffraction simulation using DISCUS. - Highlights: • Ab-initio structure solution by electron diffraction from single nanocrystals. • Detected modulation corresponding mainly to three-fold superstructure. • Diffuse diffraction streaks caused by stacking faults in disordered crystals. • Observed streaks explained by simulated electron diffraction patterns.« less

The gamut of alkoxy radicals

NASA Astrophysics Data System (ADS)

Box, Harold C.; Budzinski, Edwin E.; Freund, Harold G.

1984-12-01

It is shown that various radicals exhibiting diverse ESR and ENDOR spectral characteristics are nonetheless a closely related family of alkoxy radicals. The relationship is established by correlating the g tensor with crystal structure and by relating dihedral angles inferred from proton hyperfine couplings to dihedral angles inferred from the g tensor and crystal structure. The analysis also serves to demonstrate that an ESR absorption observed in x-irradiated single crystals of uridine 5'-monophosphate is due to an alkoxy radical.

Progress in thin-film silicon solar cells based on photonic-crystal structures

NASA Astrophysics Data System (ADS)

Ishizaki, Kenji; De Zoysa, Menaka; Tanaka, Yoshinori; Jeon, Seung-Woo; Noda, Susumu

2018-06-01

We review the recent progress in thin-film silicon solar cells with photonic crystals, where absorption enhancement is achieved by using large-area resonant effects in photonic crystals. First, a definitive guideline for enhancing light absorption in a wide wavelength range (600–1100 nm) is introduced, showing that the formation of multiple band edges utilizing higher-order modes confined in the thickness direction and the introduction of photonic superlattice structures enable significant absorption enhancement, exceeding that observed for conventional random scatterers. Subsequently, experimental evidence of this enhancement is demonstrated for a variety of thin-film Si solar cells: ∼500-nm-thick ultrathin microcrystalline silicon cells, few-µm-thick microcrystalline silicon cells, and ∼20-µm-thick thin single-crystalline silicon cells. The high short-circuit current densities and/or efficiencies observed for each cell structure confirm the effectiveness of using multiple band-edge resonant modes of photonic crystals for enhancing broadband absorption in actual solar cells.

Distribution function of random strains in an elastically anisotropic continuum and defect strengths of T m3 + impurity ions in crystals with zircon structure

NASA Astrophysics Data System (ADS)

Malkin, B. Z.; Abishev, N. M.; Baibekov, E. I.; Pytalev, D. S.; Boldyrev, K. N.; Popova, M. N.; Bettinelli, M.

2017-07-01

We construct a distribution function of the strain-tensor components induced by point defects in an elastically anisotropic continuum, which can be used to account quantitatively for many effects observed in different branches of condensed matter physics. Parameters of the derived six-dimensional generalized Lorentz distribution are expressed through the integrals computed over the array of strains. The distribution functions for the cubic diamond and elpasolite crystals and tetragonal crystals with the zircon and scheelite structures are presented. Our theoretical approach is supported by a successful modeling of specific line shapes of singlet-doublet transitions of the T m3 + ions doped into AB O4 (A =Y , Lu; B =P , V) crystals with zircon structure, observed in high-resolution optical spectra. The values of the defect strengths of impurity T m3 + ions in the oxygen surroundings, obtained as a result of this modeling, can be used in future studies of random strains in different rare-earth oxides.

Dynamical ion transfer between coupled Coulomb crystals in a double-well potential.

PubMed

Klumpp, Andrea; Zampetaki, Alexandra; Schmelcher, Peter

2017-09-01

We investigate the nonequilibrium dynamics of coupled Coulomb crystals of different sizes trapped in a double well potential. The dynamics is induced by an instantaneous quench of the potential barrier separating the two crystals. Due to the intra- and intercrystal Coulomb interactions and the asymmetric population of the potential wells, we observe a complex reordering of ions within the two crystals as well as ion transfer processes from one well to the other. The study and analysis of the latter processes constitutes the main focus of this work. In particular, we examine the dependence of the observed ion transfers on the quench amplitude performing an analysis for different crystalline configurations ranging from one-dimensional ion chains via two-dimensional zigzag chains and ring structures to three-dimensional spherical structures. Such an analysis provides us with the means to extract the general principles governing the ion transfer dynamics and we gain some insight on the structural disorder caused by the quench of the barrier height.

Single crystal structure analyses of scheelite-powellite CaW1-xMoxO4 solidsolutions and unique occurrence in Jisyakuyama skarn deposits

NASA Astrophysics Data System (ADS)

Yamashita, K.; Yoshiasa, A.; Miyazaki, H.; Tokuda, M.; Tobase, T.; Isobe, H.; Nishiyama, T.; Sugiyama, K.; Miyawaki, R.

2017-12-01

Jisyakuyama skarn deposit, Fukuchi, Fukuoka, Japan, shows a simple occurrenceformed by penetration of hot water into limestone cracks. A unique occurrence of scheelite-powellite CaW1-xMoxO4 minerals is observed in the skarn deposit. Many syntheticexperiments for scheelite-powellite solid solutions have been reported as research onfluorescent materials. In this system it is known that a complete continuous solid solution isformed even at room temperature. In this study, we have carried out the chemical analyses,crystal structural refinements and detail description of occurrence on scheelite-powelliteminerals. We have also attempted synthesis of single crystal of solid solution in a widecomposition range. The chemical compositions were determined by JEOL scanningelectron microscope and EDS, INCA system. We have performed the crystal structurerefinements of the scheelite-powellite CaW1-xMoxO4 solid solutions (x=0.0-1.0) byRIGAKU single-crystal structure analysis system RAPID. The R and S values are around0.0s and 1.03. As the result of structural refinements of natural products and many solidsolutions, we confirm that most large natural single crystals have compositions at bothendmembers, and large solid solution crystals are rare. The lattice constants, interatomicdistances and other crystallographic parameters for the solid solution change uniquely withcomposition and it was confirmed as a continuous solid solution. Single crystals of scheeliteendmember + powellite endmember + solid solution with various compositions form anaggregate in the deposit (Figure 1). Crystal shapes of powellite and scheelite arehypidiomorphic and allotriomorphic, respectively. Many solid solution crystals areaccompanied by scheelite endmember and a compositional gap is observed betweenpowellite and solid-solution crystals. The presence of several penetration solutions withsignificantly different W and Mo contents may be assumed. This research can be expectedto lead to giving restrictive conditions to elucidate the mineralization process. Figure1. Scheelite + Powellite + solid solution aggregate

Probing Zeolite Crystal Architecture and Structural Imperfections using Differently Sized Fluorescent Organic Probe Molecules.

PubMed

Hendriks, Frank C; Schmidt, Joel E; Rombouts, Jeroen A; Lammertsma, Koop; Bruijnincx, Pieter C A; Weckhuysen, Bert M

2017-05-05

A micro-spectroscopic method has been developed to probe the accessibility of zeolite crystals using a series of fluorescent 4-(4-diethylaminostyryl)-1-methylpyridinium iodide (DAMPI) probes of increasing molecular size. Staining large zeolite crystals with MFI (ZSM-5) topology and subsequent mapping of the resulting fluorescence using confocal fluorescence microscopy reveal differences in structural integrity: the 90° intergrowth sections of MFI crystals are prone to develop structural imperfections, which act as entrance routes for the probes into the zeolite crystal. Polarization-dependent measurements provide evidence for the probe molecule's alignment within the MFI zeolite pore system. The developed method was extended to BEA (Beta) crystals, showing that the previously observed hourglass pattern is a general feature of BEA crystals with this morphology. Furthermore, the probes can accurately identify at which crystal faces of BEA straight or sinusoidal pores open to the surface. The results show this method can spatially resolve the architecture-dependent internal pore structure of microporous materials, which is difficult to assess using other characterization techniques such as X-ray diffraction. © 2017 The Authors. Published by Wiley-VCH Verlag GmbH & Co. KGaA.

Importance of the DNA “bond” in programmable nanoparticle crystallization

PubMed Central

Macfarlane, Robert J.; Thaner, Ryan V.; Brown, Keith A.; Zhang, Jian; Lee, Byeongdu; Nguyen, SonBinh T.; Mirkin, Chad A.

2014-01-01

If a solution of DNA-coated nanoparticles is allowed to crystallize, the thermodynamic structure can be predicted by a set of structural design rules analogous to Pauling’s rules for ionic crystallization. The details of the crystallization process, however, have proved more difficult to characterize as they depend on a complex interplay of many factors. Here, we report that this crystallization process is dictated by the individual DNA bonds and that the effect of changing structural or environmental conditions can be understood by considering the effect of these parameters on free oligonucleotides. Specifically, we observed the reorganization of nanoparticle superlattices using time-resolved synchrotron small-angle X-ray scattering in systems with different DNA sequences, salt concentrations, and densities of DNA linkers on the surface of the nanoparticles. The agreement between bulk crystallization and the behavior of free oligonucleotides may bear important consequences for constructing novel classes of crystals and incorporating new interparticle bonds in a rational manner. PMID:25298535

Selenium Derivatization of Nucleic Acids for Crystallography

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jiang,J.; Sheng, J.; Carrasco, N.

2007-01-01

The high-resolution structure of the DNA (5'-GTGTACA-C-3') with the selenium derivatization at the 2'-position of T2 was determined via MAD and SAD phasing. The selenium-derivatized structure (1.28 {angstrom} resolution) with the 2'-Se modification in the minor groove is isomorphorous to the native structure (2.0 {angstrom}). To directly compare with the conventional bromine derivatization, we incorporated bromine into the 5-postion of T4, determined the bromine-derivatized DNA structure at 1.5 {angstrom} resolution, and found that the local backbone torsion angles and solvent hydration patterns were altered in the structure with the Br incorporation in the major groove. Furthermore, while the native andmore » Br-derivatized DNAs needed over a week to form reasonable-size crystals, we observed that the Se-derivatized DNAs grew crystals overnight with high-diffraction quality, suggesting that the Se derivatization facilitated the crystal formation. In addition, the Se-derivatized DNA sequences crystallized under a broader range of buffer conditions, and generally had a faster crystal growth rate. Our experimental results indicate that the selenium derivatization of DNAs may facilitate the determination of nucleic acid X-ray crystal structures in phasing and high-quality crystal growth. In addition, our results suggest that the Se derivatization can be an alternative to the conventional Br derivatization.« less

Domain characterization of Pb(Zn1/3Nb2/3)O3-(6%-7%)PbTiO3 single crystals using scanning electron acoustic microscopy

NASA Astrophysics Data System (ADS)

Wong, Meng Fei; Heng, Xiangxin; Zeng, Kaiyang

2008-10-01

Domain structures of [001]T and [011]T-cut Pb(Zn1/3Nb2/3)O3-(6%-7%)PbTiO3 (PZN-PT) single crystals are studied using scanning electron acoustic microscope (SEAM) technique. The observation of the orientation of domain walls agree reasonably well with the trigonometric projection of rhombohedral and orthorhombic dipoles on the (001) and (011) surfaces, respectively. After mechanical loading with microindentation, domain switching is also observed to form a hyperbolic butterfly shape and extend preferentially along four diagonal directions, i.e., ⟨110⟩ on (001) surface and ⟨111¯⟩ on (011) surface. The critical shear stress to cause domain switching for PZN-PT crystal is estimated to be approximately 49 MPa for both {110} and {111¯} planes based on theoretical analysis. Generally, the SEAM technique has been successfully demonstrated to be a valid technique for observation of domain structures in single crystal PZN-PTs.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Stauber, Mark; Yeshiva University, 2495 Amsterdam Avenue, New York, NY 10033-3312; Jakoncic, Jean

Crystallization of lysozyme with (R)-2-methyl-2, 4-pentanediol produces more ordered crystals and a higher resolution protein structure than crystallization with (S)-2-methyl-2, 4-pentanediol. The results suggest that chiral interactions with chiral additives are important in protein crystal formation. Chiral control of crystallization has ample precedent in the small-molecule world, but relatively little is known about the role of chirality in protein crystallization. In this study, lysozyme was crystallized in the presence of the chiral additive 2-methyl-2, 4-pentanediol (MPD) separately using the R and S enantiomers as well as with a racemic RS mixture. Crystals grown with (R)-MPD had the most order andmore » produced the highest resolution protein structures. This result is consistent with the observation that in the crystals grown with (R)-MPD and (RS)-MPD the crystal contacts are made by (R)-MPD, demonstrating that there is preferential interaction between lysozyme and this enantiomer. These findings suggest that chiral interactions are important in protein crystallization.« less

Formation mechanism of self-assembled polarization-dependent periodic nanostructures in β-Ga2O3

NASA Astrophysics Data System (ADS)

Nakanishi, Y.; Shimotsuma, Y.; Sakakura, M.; Shimizu, M.; Miura, K.

2018-02-01

We have successfully observed self-assembled periodic nanostructures inside Si single crystal and GaP crystal, by the femtosecond double-pulse irradiation. These results experimentally indicate that the self-assembly of the periodic nanostructures inside semiconductors triggered by ultrashort pulses irradiation are possibly associated with a direct or an indirect band gap. More recently we have also empirically classified the photoinduced bulk nanogratings into the following three types: (1) structural deficiency, (2) compressed structure, (3) partial crystallization. We have still a big question about what material properties are involved in the bulk nanograting structure formation. In this study, to expand the selectivity of the material for bulk nanograting formation, we have employed β-Ga2O3 crystals (indirect bandgap Eg 4.8 eV) as a sample for femtosecond laser irradiation. The nanograting structure inside β-Ga2O3 crystal was aligned perpendicular to the laser polarization direction. Such phenomenon is similar to the nanograting in SiO2 glass (Eg 9 eV). Moreover, to clarify the band structure, we have also investigate the photoinduced structure in Sn doped β-Ga2O3 crystals, which exhibit direct bandgap according to the first principle calculation.

The structure of XIAP BIR2: understanding the selectivity of the BIR domains

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lukacs, Christine, E-mail: cmlukacs230@gmail.com; Belunis, Charles; Crowther, Robert

2013-09-01

The high-resolution crystal structures of apo and peptide-bound XIAP BIR2 are presented and compared with BIR3 structures to understand their selectivity. This crystal system can be used to determine the structures of BIR2–inhibitor complexes. XIAP, a member of the inhibitor of apoptosis family of proteins, is a critical regulator of apoptosis. Inhibition of the BIR domain–caspase interaction is a promising approach towards treating cancer. Previous work has been directed towards inhibiting the BIR3–caspase-9 interaction, which blocks the intrinsic apoptotic pathway; selectively inhibiting the BIR2–caspase-3 interaction would also block the extrinsic pathway. The BIR2 domain of XIAP has successfully been crystallized;more » peptides and small-molecule inhibitors can be soaked into these crystals, which diffract to high resolution. Here, the BIR2 apo crystal structure and the structures of five BIR2–tetrapeptide complexes are described. The structural flexibility observed on comparing these structures, along with a comparison with XIAP BIR3, affords an understanding of the structural elements that drive selectivity between BIR2 and BIR3 and which can be used to design BIR2-selective inhibitors.« less

Influence of crystal orientation on the formation of femtosecond laser-induced periodic surface structures and lattice defects accumulation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sedao, Xxx; Garrelie, Florence, E-mail: florence.garrelie@univ-st-etienne.fr; Colombier, Jean-Philippe

2014-04-28

The influence of crystal orientation on the formation of femtosecond laser-induced periodic surface structures (LIPSS) has been investigated on a polycrystalline nickel sample. Electron Backscatter Diffraction characterization has been exploited to provide structural information within the laser spot on irradiated samples to determine the dependence of LIPSS formation and lattice defects (stacking faults, twins, dislocations) upon the crystal orientation. Significant differences are observed at low-to-medium number of laser pulses, outstandingly for (111)-oriented surface which favors lattice defects formation rather than LIPSS formation.

Synthesis and Crystal Structure of a Chalcone Derivative

NASA Astrophysics Data System (ADS)

Singh, Vikram D.; Salian, Vinutha V.; Narayana, B.; Sarojini, B. K.; Kamni; Anthal, Sumati; Kant, Rajni

2017-12-01

(2E)-3-(anthrance-9-yl)-1-(3,4-dichlorophenyl)prop-2-en-1-one [C23H14OCl2] is synthesized and its crystal structure is determined by single X-ray diffraction. There exist two molecules in the asymmetric unit. The dihedral angle between the benzene and anthracene moiety of the molecule A and B is 86.51(12)° and 76.42(13)°, respectively. No classical hydrogen bonds are observed and only van der Waals forces stabilize the crystal packing.

Characterization of Structural Defects in Wide Band-Gap Compound Materials for Semiconductor and Opto-Electronic Applications

NASA Astrophysics Data System (ADS)

Goue, Ouloide Yannick

Single crystals of binary and ternary compounds are touted to replace silicon for specialized applications in the semiconductor industry. However, the relative high density of structural defects in those crystals has hampered the performance of devices built on them. In order to enhance the performance of those devices, structurally perfect single crystals must be grown. The aim of this thesis is to investigate the interplay between crystal growth process and crystal quality as well as structural defect types and transport property. To this end, the thesis is divided into two parts. The first part provides a general review of the theory of crystal growth (chapter I), an introduction to the materials being investigated (chapter II and III) and the characterization techniques being used (chapter IV). • In chapter I, a brief description of the theory of crystal growth is provided with an eye towards the driving force behind crystal nucleation and growth along with the kinetic factors affecting crystal growth. The case of crystal growth of silicon carbide (SiC) by physical vapor transport (PVT) and chemical vapor deposition (CVD) is discussed. The Bridgman, travelling heater method (THM) and physical transport growth of cadmium zinc telluride (CZT) is also treated. In chapters II and III, we introduce the compound materials being investigated in this study. While a description of their crystal structure and properties is provided, the issues associated with their growth are discussed. In chapter IV, a description of the characterization techniques used in these studies is presented. These techniques are synchrotron X-ray topography (SXRT), transmission electron microscopy, transmission infrared microscopy (TIM), micro-Raman spectroscopy (muRS) and light microscopy. Extensive treatment of SXRT technique is also provided. In the second part, the experimental results obtained in the course of these studies are presented and discussed. These results are divided into three subsections. • The development of a new technique for the production of large and high quality silicon carbide single crystal boule is proposed. This technique herein referred to as Large Tapered Crystal (LTC) growth consists of two steps: growth of long SiC rod crystal by solvent-laser heated floating zone (Solvent-LHFZ) and lateral expansion of a seed by hot wall chemical vapor deposition (HWCVD). Solvent-LHFZ was successful as SiC rod crystals, replicating the polytype structure of the starting seed, were achieved at a growth rate varying from 4 to 100mum/hr. However, SXRT revealed the presence of an inhomogeneous strain in the grown crystal rod. This was further confirmed by SEM images, which showed the platelet-like morphology of the growth front with pockets in which iron (Fe)-rich material from the Fe solvent is trapped. It was furthermore observed that at high Fe to Si ratio (˜1.9), no growth was achieved. HWCVD enlargement was also successful as SiC boules, replicating the polytype structure of the starting seed, were achieved at growth rate of about 180mum/hr. The boules had a faceted hexagonal morphology with a strain-free surface marked by steps. Combination of SXRT, TEM and muRS revealed the presence of stacking disorder in the seed (3C, 4H and 15R-SiC) that replicated in the homoepitaxial layer. The formation of the observed stacking disorder is attributed to the low energy difference between stacking configurations on the growth surface as proposed by Takahashi and Ohtani. • The influence of structural defect type and distribution on minority carrier lifetime in 4H-SiC epilayers was investigated. Structural defect type and distribution map was obtained using SXRT, whereas minority carrier lifetime map was obtained using muPCD. Decrease in carrier lifetime observed from muPCD map was associated with specific structural defects such as low angle grain boundaries (LAGBs), stacking faults (SFs), interfacial dislocations (IDs), half loop arrays (HLAs) as well as basal plane dislocations (BPDs) pinned at TSDs. While the effect of morphological defects was mitigated, combination of defects such as microcracks, overlapping triangular defects and BPD half loops were observed to reduce carrier lifetime. Furthermore, regions of high dislocation density were associated with low carrier lifetime. • Finally, the effect of cadmium (Cd) overpressure on the quality of cadmium zinc telluride crystal ingots was investigated for two set of samples (set 1 and 2). Overall, high resistivity single crystals were achieved. Evaluation of the crystal quality by SXRT revealed that under certain Cd overpressures and growth conditions, the quality of the grown boule improved. Similarly, transmission infrared (IR) microscopy showed a correlation between the size/density and distribution of Te inclusions/precipitates and Cd overpressure. The size of Te inclusions was observed to decrease as a function of Cd overpressure as predicted from partial pressure data for stoichiometric melt. The best improvement in crystalline quality were observed for samples from set 1at a Cd reservoir of 785 °C and for set 2 samples for a Cd reservoir at 825 °C. This difference in Cd reservoir temperature for stoichiometric growth between set 1 and set 2 was attributed to other factors such as rate of cooling of Cd reservoir, rate of cooling of the crystal along with control of the melt interface. The summary of these results and the implication of this growth approach for producing high quality CZT single crystals are discussed.

Structure and crystallization of SiO2 and B2O3 doped lithium disilicate glasses from theory and experiment.

PubMed

Erlebach, Andreas; Thieme, Katrin; Sierka, Marek; Rüssel, Christian

2017-09-27

Solid solutions of SiO 2 and B 2 O 3 in Li 2 O·2SiO 2 are synthesized and characterized for the first time. Their structure and crystallization mechanisms are investigated employing a combination of simulations at the density functional theory level and experiments on the crystallization of SiO 2 and B 2 O 3 doped lithium disilicate glasses. The remarkable agreement of calculated and experimentally determined cell parameters reveals the preferential, kinetically controlled incorporation of [SiO 4 ] and [BO 4 ] at the Li + lattice sites of the Li 2 O·2SiO 2 crystal structure. While the addition of SiO 2 increases the glass viscosity resulting in lower crystal growth velocities, glasses containing B 2 O 3 show a reduction of both viscosities and crystal growth velocities. These observations could be rationalized by a change of the chemical composition of the glass matrix surrounding the precipitated crystal phase during the course of crystallization, which leads to a deceleration of the attachment of building units required for further crystal growth at the liquid-crystal interface.

SdsA polymorph isolation and improvement of their crystal quality using nonconventional crystallization techniques

DOE Office of Scientific and Technical Information (OSTI.GOV)

De la Mora, Eugenio; Flores-Hernández, Edith; Jakoncic, Jean

SdsA, a sodium dodecyl sulfate hydrolase, from Pseudomonas aeruginosa was crystallized in three different crystal polymorphs and their three-dimensional structure was determined. The different polymorphs present different crystal packing habits. One of the polymorphs suggests the existence of a tetramer, an oligomeric state not observed previously, while the crystal packing of the remaining two polymorphs obstructs the active site entrance but stabilizes flexible regions of the protein. Nonconventional crystallization methods that minimize convection, such as counterdiffusion in polyvinyl alcohol gel coupled with the influence of a 500 MHz (10.2 T) magnetic field, were necessary to isolate the poorest diffracting polymorphmore » and increase its internal order to determine its structure by X-ray diffraction. In conclusion, the results obtained show the effectiveness of nonconventional crystallographic methods to isolate different crystal polymorphs.« less

Systematic Comparison of Crystal and NMR Protein Structures Deposited in the Protein Data Bank

PubMed Central

Sikic, Kresimir; Tomic, Sanja; Carugo, Oliviero

2010-01-01

Nearly all the macromolecular three-dimensional structures deposited in Protein Data Bank were determined by either crystallographic (X-ray) or Nuclear Magnetic Resonance (NMR) spectroscopic methods. This paper reports a systematic comparison of the crystallographic and NMR results deposited in the files of the Protein Data Bank, in order to find out to which extent these information can be aggregated in bioinformatics. A non-redundant data set containing 109 NMR – X-ray structure pairs of nearly identical proteins was derived from the Protein Data Bank. A series of comparisons were performed by focusing the attention towards both global features and local details. It was observed that: (1) the RMDS values between NMR and crystal structures range from about 1.5 Å to about 2.5 Å; (2) the correlation between conformational deviations and residue type reveals that hydrophobic amino acids are more similar in crystal and NMR structures than hydrophilic amino acids; (3) the correlation between solvent accessibility of the residues and their conformational variability in solid state and in solution is relatively modest (correlation coefficient = 0.462); (4) beta strands on average match better between NMR and crystal structures than helices and loops; (5) conformational differences between loops are independent of crystal packing interactions in the solid state; (6) very seldom, side chains buried in the protein interior are observed to adopt different orientations in the solid state and in solution. PMID:21293729

Theoretical exploration of various lithium peroxide crystal structures in a Li-air battery

DOE PAGES

Lau, Kah; Qiu, Dantong; Luo, Xiangyi; ...

2015-01-14

We describe a series of metastable Li₂O₂ crystal structures involving different orientations and displacements of the O₂²⁻ peroxy ions based on the known Li₂O₂ crystal structure. Within the vicinity of the chemical potential ΔG ~ 0.20 eV/Li from the thermodynamic ground state of the Li₂O₂ crystal structure (i.e., Föppl structure), all of these newly found metastable Li₂O₂ crystal structures are found to be insulating and high-k materials, and they have a common unique signature of an O₂²⁻ O-O vibration mode (ω ~ 799–865 cm⁻¹), which is in the range of that commonly observed in Li-air battery experiments, regardless of themore » random O₂²⁻ orientations and the symmetry in the crystal lattice. From XRD patterns analysis, the commercially available Li₂O₂ powder is confirmed to be the thermodynamic ground state Föppl-like structure. However, for Li₂O₂ compounds that are grown electrochemically under the environment of Li-O₂ cells, we found that the XRD patterns alone are not sufficient for structural identification of these metastable Li₂O₂ crystalline phases due to the poor crystallinity of the sample. In addition, the commonly known Raman signal of O₂²⁻ vibration mode is also found to be insufficient to validate the possible existence of these newly predicted Li₂O₂ crystal structures, as all of them similarly share the similar O₂²⁻ vibration mode. However considering that the discharge voltage in most Li-O₂ cells are typically several tenths of an eV below the thermodynamic equilibrium for the formation of ground state Föppl structure, the formation of these metastable Li₂O₂ crystal structures appears to be thermodynamically feasible.« less

Effects of crystallization on structural and dielectric properties of thin amorphous films of (1 - x)BaTiO3-xSrTiO3 (x=0-0.5, 1.0)

NASA Astrophysics Data System (ADS)

Kawano, H.; Morii, K.; Nakayama, Y.

1993-05-01

The possibilities for fabricating solid solutions of (Ba1-x,Srx)TiO3 (x≤0.5,1.0) by crystallization of amorphous films and for improving their dielectric properties by adjusting the Sr content were investigated. Thin amorphous films were prepared from powder targets consisting of mixtures of BaTiO3 and SrTiO3 by sputtering with a neutralized Ar-ion beam. The amorphous films crystallized into (Ba1-x, Srx)TiO3 solid solutions with a cubic perovskite-type structure after annealing in air at 923 K for more than 1 h. The Debye-type dielectric relaxation was observed for the amorphous films, whereas the crystallized films showed paraelectric behavior. The relative dielectric constants were of the order of 20 for the amorphous samples, but increased greatly after crystallization to about 60-200, depending on the composition; a larger increase in the dielectric constant was observed in the higher Sr content films, in the range x≤0.5, which could be correlated with an increase in the grain size of the crystallites. The crystallization processes responsible for the difference in the grain size are discussed based on the microstructural observations.

Remote Sensing of Crystal Shapes in Ice Clouds

NASA Technical Reports Server (NTRS)

van Diedenhoven, Bastiaan

2017-01-01

Ice crystals in clouds exist in a virtually limitless variation of geometries. The most basic shapes of ice crystals are columnar or plate-like hexagonal prisms with aspect ratios determined by relative humidity and temperature. However, crystals in ice clouds generally display more complex structures owing to aggregation, riming and growth histories through varying temperature and humidity regimes. Crystal shape is relevant for cloud evolution as it affects microphysical properties such as fall speeds and aggregation efficiency. Furthermore, the scattering properties of ice crystals are affected by their general shape, as well as by microscopic features such as surface roughness, impurities and internal structure. To improve the representation of ice clouds in climate models, increased understanding of the global variation of crystal shape and how it relates to, e.g., location, cloud temperature and atmospheric state is crucial. Here, the remote sensing of ice crystal macroscale and microscale structure from airborne and space-based lidar depolarization observations and multi-directional measurements of total and polarized reflectances is reviewed. In addition, a brief overview is given of in situ and laboratory observations of ice crystal shape as well as the optical properties of ice crystals that serve as foundations for the remote sensing approaches. Lidar depolarization is generally found to increase with increasing cloud height and to vary with latitude. Although this variation is generally linked to the variation of ice crystal shape, the interpretation of the depolarization remains largely qualitative and more research is needed before quantitative conclusions about ice shape can be deduced. The angular variation of total and polarized reflectances of ice clouds has been analyzed by numerous studies in order to infer information about ice crystal shapes from them. From these studies it is apparent that pristine crystals with smooth surfaces are generally inconsistent with the data and thus crystal impurity, distortion or surface roughness is prevalent. However, conclusions about the dominating ice shapes are often inconclusive and contradictory and are highly dependent on the limited selection of shapes included in the investigations. Since ice crystal optical properties are mostly determined by the aspect ratios of the crystal components and their microscale structure, it is advised that remote sensing applications focus on the variation of these ice shape characteristics, rather than on the macroscale shape or habit. Recent studies use databases with nearly continuous ranges of crystal component aspect ratio and-or roughness levels to infer the variation of ice crystal shape from satellite and airborne remote sensing measurements. Here, the rationale and results of varying strategies for the remote sensing of ice crystal shape are reviewed. Observed systematic variations of ice crystal geometry with location, cloud height and atmospheric state suggested by the data are discussed. Finally, a prospective is given on the future of the remote sensing of ice cloud particle shapes.

REVIEW: Optics of globular photonic crystals

NASA Astrophysics Data System (ADS)

Gorelik, V. S.

2007-05-01

The results of experimental and theoretical studies of the optical properties of globular photonic crystals - new physical objects having a crystal structure with the lattice period exceeding considerably the atomic size, are presented. As globular photonic crystals, artificial opal matrices consisting of close-packed silica globules of diameter ~200 nm were used. The reflection spectra of these objects characterising the parameters of photonic bands existing in these crystals in the visible spectral region are presented. The idealised models of the energy band structure of photonic crystals investigated in the review give analytic dispersion dependences for the group velocity and the effective photon mass in a globular photonic crystal. The characteristics of secondary emission excited in globular photonic crystals by monochromatic and broadband radiation are presented. The results of investigations of single-photon-excited delayed scattering of light observed in globular photonic crystals exposed to cw UV radiation and radiation from a repetitively pulsed copper vapour laser are presented. The possibilities of using globular photonic crystals as active media for lasing in different spectral regions are considered. It is proposed to use globular photonic crystals as sensitive sensors in optoelectronic devices for molecular analysis of organic and inorganic materials by the modern methods of laser spectroscopy. The results of experimental studies of spontaneous and stimulated globular scattering of light are discussed. The conditions for observing resonance and two-photon-excited delayed scattering of light are found. The possibility of accumulation and localisation of the laser radiation energy inside a globular photonic crystal is reported.

Development of an automated large-scale protein-crystallization and monitoring system for high-throughput protein-structure analyses.

PubMed

Hiraki, Masahiko; Kato, Ryuichi; Nagai, Minoru; Satoh, Tadashi; Hirano, Satoshi; Ihara, Kentaro; Kudo, Norio; Nagae, Masamichi; Kobayashi, Masanori; Inoue, Michio; Uejima, Tamami; Oda, Shunichiro; Chavas, Leonard M G; Akutsu, Masato; Yamada, Yusuke; Kawasaki, Masato; Matsugaki, Naohiro; Igarashi, Noriyuki; Suzuki, Mamoru; Wakatsuki, Soichi

2006-09-01

Protein crystallization remains one of the bottlenecks in crystallographic analysis of macromolecules. An automated large-scale protein-crystallization system named PXS has been developed consisting of the following subsystems, which proceed in parallel under unified control software: dispensing precipitants and protein solutions, sealing crystallization plates, carrying robot, incubators, observation system and image-storage server. A sitting-drop crystallization plate specialized for PXS has also been designed and developed. PXS can set up 7680 drops for vapour diffusion per hour, which includes time for replenishing supplies such as disposable tips and crystallization plates. Images of the crystallization drops are automatically recorded according to a preprogrammed schedule and can be viewed by users remotely using web-based browser software. A number of protein crystals were successfully produced and several protein structures could be determined directly from crystals grown by PXS. In other cases, X-ray quality crystals were obtained by further optimization by manual screening based on the conditions found by PXS.

Time Dependent Structural Evolution of Porous Organic Cage CC3

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lucero, Jolie; Elsaidi, Sameh; Anderson, Ryther

Porous organic cage compounds are emerged with remarkable structural diversity and functionality that have applications in gas separation, catalysis and energy storage. Fundamental understanding of nucleation and growth of such materials have significant implications for understanding molecularly directed self-assembly phenomena. Herein we followed the structural evolution of a prototypical type of porous organic cage, CC3 as a function of synthesis time. Three distinctive crystal formation stages were identified: at short synthesis times, a rapid crystal growth stage in which amorphous agglomerates transformed into larger irregular particles was observed. At intermediate synthesis times, a decrease in crystal size over time wasmore » observed presumably due to crystal fragmentation, redissolution and/or homogeneous nucleation led. Finally, at longer synthesis times, a regrowth process was observed in which particles coalesced through Ostwald ripening leading to a continuous increase in crystal size. Molecular simulation studies, based on the construction of in silico CC3 models and simulation of XRD patterns and nitrogen isotherms, confirm the samples at different synthesis times to be a mixture of CC3α and CC3 amorphous phases. The CC3α phase is found to contract at different synthesis times, and the amorphous phase is found to essentially disappear at the longest synthesis time. Nitrogen and carbon dioxide adsorption properties of these CC3 phases were evaluated, and were highly dependent on synthesis time.« less

Cubic-to-tetragonal structural phase transition in Rb{sub 1{minus}x}Cs{sub x}CaF{sub 3} solid solutions: Thermal expansion and EPR studies

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lahoz, F.; Villacampa, B.; Alcala, R.

1997-04-01

The influence of crystal mixing on the structural phase transitions in Rb{sub 1{minus}x}Cs{sub x}CaF{sub 3} (0{lt}x{lt}1) fluoroperovskite crystals has been studied by thermal expansion and EPR measurements of Ni{sup 2+} and Ni{sup 3+} paramagnetic probes. A cubic-to-tetragonal phase transition has been detected in crystals with x=0, 0.1, 0.21, 0.27, and 0.35. The critical temperature and the tetragonal distortion decrease as x increases. No transition was observed for x{ge}0.44. This transition shows a weak first-order component in the x=0 and 0.1 samples, which is progressively smeared out for x{gt}0.1, indicating a spatial distribution of the critical temperature in those crystals withmore » high ionic substitution rate. In RbCaF{sub 3}, another structural phase transition was observed at 20 K with a thermal hysteresis between 20 and 40 K. This transition has not been found in any of the mixed crystals.« less

Synthesis and Crystal Structure of 2’-Se-modified guanosine Containing DNA

DOE Office of Scientific and Technical Information (OSTI.GOV)

Salon, J.; Sheng, J; Gan, J

Selenium modification of nucleic acids is of great importance in X-ray crystal structure determination and functional study of nucleic acids. Herein, we describe a convenient synthesis of a new building block, the 2{prime}-SeMe-modified guanosine (G{sub Se}) phosphoramidite, and report the first incorporation of the 2{prime}-Se-G moiety into DNA. The X-ray crystal structure of the 2{prime}-Se-modified octamer DNA (5{prime}-GTG{sub Se}TACAC-3{prime}) was determined at a resolution of 1.20 {angstrom}. We also found that the 2{prime}-Se modification points to the minor groove and that the modified and native structures are virtually identical. Furthermore, we observed that the 2{prime}-Se-G modification can significantly facilitate themore » crystal growth with respect to the corresponding native DNA.« less

The Crystal Structure of a Quercetin 2,3-Dioxygenase from Bacillus subtilis Suggests Modulation of Enzyme Activity by a Change in the Metal Ion at the Active Site(s)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gopal, B.; Madan, Lalima L.; Betz, Stephen F.

2010-11-10

Common structural motifs, such as the cupin domains, are found in enzymes performing different biochemical functions while retaining a similar active site configuration and structural scaffold. The soil bacterium Bacillus subtilis has 20 cupin genes (0.5% of the total genome) with up to 14% of its genes in the form of doublets, thus making it an attractive system for studying the effects of gene duplication. There are four bicupins in B. subtilis encoded by the genes yvrK, yoaN, yxaG, and ywfC. The gene products of yvrK and yoaN function as oxalate decarboxylases with a manganese ion at the active site(s),more » whereas YwfC is a bacitracin synthetase. Here we present the crystal structure of YxaG, a novel iron-containing quercetin 2,3-dioxygenase with one active site in each cupin domain. Yxag is a dimer, both in solution and in the crystal. The crystal structure shows that the coordination geometry of the Fe ion is different in the two active sites of YxaG. Replacement of the iron at the active site with other metal ions suggests modulation of enzymatic activity in accordance with the Irving-Williams observation on the stability of metal ion complexes. This observation, along with a comparison with the crystal structure of YvrK determined recently, has allowed for a detailed structure-function analysis of the active site, providing clues to the diversification of function in the bicupin family of proteins.« less

Ordered distribution of I and Cl in the low-temperature crystal structure of mutnovskite, Pb{sub 4}As{sub 2}S{sub 6}ICl: An X-ray single-crystal study

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bindi, Luca; Garavelli, Anna; Pinto, Daniela

2008-02-15

To study the temperature-dependent structural changes and to analyze the crystal chemical behavior of the halogens as a function of temperature, a crystal of the recently discovered mineral mutnovskite, ideally Pb{sub 2}AsS{sub 3}(I,Cl,Br), has been investigated by X-ray single-crystal diffraction methods at 300 and 110 K. At room temperature (RT) mutnovskite was confirmed to possess a centrosymmetric structure-type, space group Pnma, while at low temperature (110 K) it adopts a non-centrosymmetric orthorhombic structure-type, space group Pnm2{sub 1}, with a=11.5394(9) A, b=6.6732(5) A, c=9.3454(7) A, V=719.64(9) A{sup 3} and Z=2. Mutnovskite reconverts to the centrosymmetric-type upon returning to RT thus indicatingmore » that the phase transition is completely reversible in character. The refinement of the LT-structure leads to a residual factor R=0.0336 for 1827 independent observed reflections [F{sub o}>4{sigma}(F{sub o})] and 80 variables. The crystal structure of cooled mutnovskite is topologically identical to that observed at RT and the slight structural changes occurring during the phase transition Pnma{yields}Pnm2{sub 1} are mainly restricted to the coordination polyhedra around Pb. The structure solution revealed that I and Cl are ordered into two specific sites. Indeed, the unique mixed (I,Cl) position in the RT-structure (Wyckoff position 4c) transforms into two 2a Wyckoff positions in the LT-structure hosting I and Cl, respectively. - Graphical abstract: In the crystal structure of mutnovskite at 110 K the two halogens I and Cl are ordered into two specific sites and only slight changes in the coordination environment around Pb atoms occur during the phase transition Pnma{yields}Pnm2{sub 1} from the RT-structure to the LT-structure. Two kinds of layers alternating along a are present in the LT-structure: Layer I contains Cl atoms and [001] columns of Pb1 and Pb4 prisms, layer II contains I atoms and [001] columns of Pb2 and Pb3 prisms.« less

Monoclinic nanodomains in morphotropic phase boundary Pb(Mg{sub 1/3}Nb{sub 2/3})O{sub 3}–PbTiO{sub 3}

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sato, Y., E-mail: y-sato@sigma.t.u-tokyo.ac.jp; Hirayama, T.; Ikuhara, Y.

2014-02-24

Crystalline structure is a fundamental characteristic of many materials, and drastic changes in properties may accompany crystal phase transitions. A prominent example of this is the morphotropic phase boundary of (Pb(Mg{sub 1/3}Nb{sub 2/3})O{sub 3}-PbTiO{sub 3}) single crystal, a region that exhibits a high piezoelectric effect. Although the highest piezoelectricity is often attributed to a monoclinic crystal phase, formation of ferroelectric nanodomains (NDs) complicates understanding of this crystal structure. In this Letter, we report dedicated transmission electron microscopy and electron diffraction analysis to understand the crystal structure at the ND level. Splitting of diffraction spots, caused by very small lattice distortionmore » in the NDs, is important to understanding crystal structure and has been unambiguously observed. The results can be explained by monoclinic phase NDs. Combining these results with our previous findings on ND dynamics [Sato et al. Phys. Rev. Lett. 107, 187601 (2011)], monoclinic NDs can potentially make a considerable contribution to the piezoelectricity in these materials.« less

Calculation of photonic bandgap for 2D hexagonal and square structure base on hybrid polymer material

NASA Astrophysics Data System (ADS)

Hidayat, S.; Riveli, N.

2018-05-01

We have calculated 2D photonic crystal band gap using plane-wave expansion method. The studied model of structures is hexagonal lattice and square lattice of rod cylinder in air. We have simulated the dispersion relation of it structure using hybrid polymer as rod material. The parameter structures are nrod = 1.5, nhole = 1, and rrod = 0.25a, where a is lattice constant. We found the distributed feedback occurs at the edge of upper band or frequency at 0.66 (a/λ). In our experimental work, we have successfully fabricated the 2D photonic crystal from hybrid polymer incorporated with organic dye laser. The lasing characteristics ware investigated using strip-line excitation light of SHG Nd-YAG laser (λ=532 nm). The lasing wavelengths for hexagonal structure are observed at 606 nm and 621 nm for photonic crystal period of 400 nm and 410 nm, respectively. λ=532 nm). Whereas the square structure, the lasing wavelengths are observed at (588 nm ± 2) and (606 nm ± 2 nm) for grating period of 391 nm and 405 nm.

High resolution electron microscopy study of crystal growth mechanisms in chicken bone composites

NASA Astrophysics Data System (ADS)

Cuisinier, F. J. G.; Steuer, P.; Brisson, A.; Voegel, J. C.

1995-12-01

The present study describes the early stages of chicken bone crystal growth, followed by high resolution electron microscopy (HREM). We have developed an original analysis procedure to determine the crystal structure. Images were first digitalized and selected areas were fast Fourier transformed. Numerical masks were selected around the most intense spots and the filtered signal was retransformed back to real space. The filtered images were then compared to computer calculated images to identify the inorganic mineral phase. Nanometer-sized particles were observed on amorphous areas. These particles have a structure loosely related to hydroxyapatite (HA) and a specific orientation. In a more advanced situation, the nanoparticles appeared to grow in two dimensions and to form plate-like crystals. These crystals seem, in a last growth step, to fuse by their (100) faces. These experimental observations allowed us to propose a four-step model for the development and growth of chicken bone crystals. The two initial stages are the ionic adsorption onto the organic substrate followed by the nucleation of nanometer-sized particles. The two following steps, i.e. two-dimensional growth of the nanoparticles leading to the formation of needle-like crystals, and the lateral fusion of these crystals by their (100) faces, are controlled only by spatial constraints inside the extracellular organic matrix.

Effect of surface modification of cellulose nanocrystal on nonisothermal crystallization of poly(β-hydroxybutyrate) composites.

PubMed

Chen, Jianxiang; Wu, Defeng; Tam, Kam C; Pan, Keren; Zheng, Zhigong

2017-02-10

Ring-opening polymerization of l-lactide from cellulose nanocrystal (CNC) surface yielded polylactide-grafted CNC (CNC-g-PLA). The structure and chemical composition of the CNC-g-PLA were characterized by FT-IR, 1 H NMR, XPS and XRD. The crystallization behavior and lamellar structure of poly(β-hydroxybutyrate) (PHB) in the presence of pristine CNC and CNC-g-PLA were elucidated via DSC and SAXS, and Babinet's reciprocity theory was applied. Crystallization kinetics were further analyzed using Ozawa, Mo and Kissinger models. In the presence of pristine CNC, nucleation of PHB crystals led to an increase in the crystallization temperature (T c ) of PHB; while CNC-g-PLA acted as antinucleation agent, resulting in a remarkable reduction in T c of PHB. Accordingly, the composite with pristine CNC possessed a higher crystallization rate than neat PHB, while CNC-g-PLA displayed the lowest crystallization rate. However, the lamellar structure of PHB was not affected by the presence of pristine and modified CNCs, and almost identical crystallization activation energies as the neat PHB were observed, indicating that nucleation is dominant during PHB crystallization, instead of crystal growth. This study offers a promising approach of using pristine and modified CNCs to control the crystallization of biodegradable aliphatic polyesters. Copyright © 2016 Elsevier Ltd. All rights reserved.

Crystal structure, electronic structure, optical and scintillation properties of self-activated Cs 4YbI 6 [Crystal structure, optical and scintillation properties of self-activated Cs 4YbI 6

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wu, Yuntao; Chakoumakos, Bryan C.; Shi, Hongliang

A self-activated Cs 4YbI 6 single crystal was grown by the vertical Bridgman method. Crystal structure refinements verified the phase purity and the trigonal crystal system with a space group of more » $$\\bar{R}$$3 c. By using differential scanning calorimetry, the melting and crystallization points were determined to be 550 and 510 °C, respectively. Luminescence and scintillation properties were systematically studied. Upon ultraviolet light (360 nm) excitation, the Cs 4YbI 6 crystal exhibits bluish-green emission centered at 450 and 480 nm due to spin-allowed and spin-forbidden transitions of Yb 2+ activators. The lifetimes of the corresponding emission bands at room temperature are tens and hundreds of nanoseconds, respectively. X-ray excited radioluminescence spectrum is dominated by the spin-forbidden transition of Yb 2+ at 480 nm. The absolute light yield is 2700 ± 200 photons/MeV with a principal scintillation decay time of 33 ns. In conclusion, the physical explanation for the low light yield observed is proposed from experimental and theoretical insights.« less

Crystal structure, electronic structure, optical and scintillation properties of self-activated Cs 4YbI 6 [Crystal structure, optical and scintillation properties of self-activated Cs 4YbI 6

DOE PAGES

Wu, Yuntao; Chakoumakos, Bryan C.; Shi, Hongliang; ...

2018-05-14

A self-activated Cs 4YbI 6 single crystal was grown by the vertical Bridgman method. Crystal structure refinements verified the phase purity and the trigonal crystal system with a space group of more » $$\\bar{R}$$3 c. By using differential scanning calorimetry, the melting and crystallization points were determined to be 550 and 510 °C, respectively. Luminescence and scintillation properties were systematically studied. Upon ultraviolet light (360 nm) excitation, the Cs 4YbI 6 crystal exhibits bluish-green emission centered at 450 and 480 nm due to spin-allowed and spin-forbidden transitions of Yb 2+ activators. The lifetimes of the corresponding emission bands at room temperature are tens and hundreds of nanoseconds, respectively. X-ray excited radioluminescence spectrum is dominated by the spin-forbidden transition of Yb 2+ at 480 nm. The absolute light yield is 2700 ± 200 photons/MeV with a principal scintillation decay time of 33 ns. In conclusion, the physical explanation for the low light yield observed is proposed from experimental and theoretical insights.« less

Crystal structure of simple metals at high pressures

DOE Office of Scientific and Technical Information (OSTI.GOV)

Degtyareva, Olga

2010-10-22

The effects of pressure on the crystal structure of simple (or sp-) elements are analysed in terms of changes in coordination number, packing density, and interatomic distances, and general rules are established. In the polyvalent elements from groups 14-17, the covalently bonded structures tend to transform to metallic phases with a gradual increase in coordination number and packing density, a behaviour normally expected under pressure. Group 1 and 2 metallic elements, however, show a reverse trend towards structures with low packing density due to intricate changes in their electronic structure. Complex crystal structures such as host-guest and incommensurately modulated structuresmore » found in these elements are given special attention in this review in an attempt to determine their role in the observed phase-transition sequences.« less

Formation of porous crystals via viscoelastic phase separation

NASA Astrophysics Data System (ADS)

Tsurusawa, Hideyo; Russo, John; Leocmach, Mathieu; Tanaka, Hajime

2017-10-01

Viscoelastic phase separation of colloidal suspensions can be interrupted to form gels either by glass transition or by crystallization. With a new confocal microscopy protocol, we follow the entire kinetics of phase separation, from homogeneous phase to different arrested states. For the first time in experiments, our results unveil a novel crystallization pathway to sponge-like porous crystal structures. In the early stages, we show that nucleation requires a structural reorganization of the liquid phase, called stress-driven ageing. Once nucleation starts, we observe that crystallization follows three different routes: direct crystallization of the liquid phase, the Bergeron process, and Ostwald ripening. Nucleation starts inside the reorganized network, but crystals grow past it by direct condensation of the gas phase on their surface, driving liquid evaporation, and producing a network structure different from the original phase separation pattern. We argue that similar crystal-gel states can be formed in monatomic and molecular systems if the liquid phase is slow enough to induce viscoelastic phase separation, but fast enough to prevent immediate vitrification. This provides a novel pathway to form nanoporous crystals of metals and semiconductors without dealloying, which may be important for catalytic, optical, sensing, and filtration applications.

Conformational flexibility in the catalytic triad revealed by the high-resolution crystal structure of Streptomyces erythraeus trypsin in an unliganded state

PubMed Central

Blankenship, Elise; Vukoti, Krishna; Miyagi, Masaru; Lodowski, David T.

2014-01-01

With more than 500 crystal structures determined, serine proteases make up greater than one-third of all proteases structurally examined to date, making them among the best biochemically and structurally characterized enzymes. Despite the numerous crystallographic and biochemical studies of trypsin and related serine proteases, there are still considerable shortcomings in the understanding of their catalytic mechanism. Streptomyces erythraeus trypsin (SET) does not exhibit autolysis and crystallizes readily at physiological pH; hence, it is well suited for structural studies aimed at extending the understanding of the catalytic mechanism of serine proteases. While X-ray crystallographic structures of this enzyme have been reported, no coordinates have ever been made available in the Protein Data Bank. Based on this, and observations on the extreme stability and unique properties of this particular trypsin, it was decided to crystallize it and determine its structure. Here, the first sub-angstrom resolution structure of an unmodified, unliganded trypsin crystallized at physiological pH is reported. Detailed structural analysis reveals the geometry and structural rigidity of the catalytic triad in the unoccupied active site and comparison to related serine proteases provides a context for interpretation of biochemical studies of catalytic mechanism and activity. PMID:24598752

Conformational flexibility in the catalytic triad revealed by the high-resolution crystal structure of Streptomyces erythraeus trypsin in an unliganded state.

PubMed

Blankenship, Elise; Vukoti, Krishna; Miyagi, Masaru; Lodowski, David T

2014-03-01

With more than 500 crystal structures determined, serine proteases make up greater than one-third of all proteases structurally examined to date, making them among the best biochemically and structurally characterized enzymes. Despite the numerous crystallographic and biochemical studies of trypsin and related serine proteases, there are still considerable shortcomings in the understanding of their catalytic mechanism. Streptomyces erythraeus trypsin (SET) does not exhibit autolysis and crystallizes readily at physiological pH; hence, it is well suited for structural studies aimed at extending the understanding of the catalytic mechanism of serine proteases. While X-ray crystallographic structures of this enzyme have been reported, no coordinates have ever been made available in the Protein Data Bank. Based on this, and observations on the extreme stability and unique properties of this particular trypsin, it was decided to crystallize it and determine its structure. Here, the first sub-angstrom resolution structure of an unmodified, unliganded trypsin crystallized at physiological pH is reported. Detailed structural analysis reveals the geometry and structural rigidity of the catalytic triad in the unoccupied active site and comparison to related serine proteases provides a context for interpretation of biochemical studies of catalytic mechanism and activity.

Three-dimensional Bragg diffraction in growth-disordered opals

NASA Astrophysics Data System (ADS)

Baryshev, A. V.; Kaplyanskii, Alexander A.; Kosobukin, Vladimir A.; Limonov, M. F.; Samusev, K. B.; Usvyat, D. E.

2003-06-01

After artificial opals as well as opal-based infilled and inverted composites are considered to be promising representatives of photonic crystal materials. Earlier, photonic stop gaps in opals were studied mainly in transmission or specular reflection geometries corresponding to "one-dimensional" Bragg diffraction. On the contrary, this work was aimed at observing the typical patterns of optical Bragg diffraction in which phenomenon opal crystal structure acts as a three-dimensional diffraction grating. Although our experiments were performed for artificial opals possessing unavoidable imperfections a well-pronounced diffraction peaks were observed characteristic of a crystal structure. Each of the diffraction maxima reveals a photonic stop gap in the specified direction, while the spectral width of the peak is a measure of the photonic stop gap width.

The application of crystal soaking technique to study the effect of zinc and cresol on insulinotropin crystals grown from a saline solution.

PubMed

Kim, Y; Haren, A M

1995-11-01

The purpose of this study is to investigate the effect of zinc and cresol on the structure of insulinotropin crystals. Insulinotropin crystals grown from a saline solution were treated with zinc and/or m-cresol using a crystal soaking technique. The effects of these additives on the crystal structure were investigated with powder X-ray diffraction, photomicrography, and differential scanning calorimetry. The molecular interaction between insulinotropin and m-trifluorocresol in solution was also studied by 19F NMR: The data suggest that the original crystals grown from a saline solution have relatively weak lattice forces. After the addition of m-cresol to the suspension of the insulinotropin crystals, the crystals were immediately rendered amorphous. The m-cresol molecules which diffused into the crystals through solvent channels may have disturbed the lattice interactions that maintain the integrity of the crystal. In contrast, the zinc added to the suspension stabilized the crystal lattice so that the subsequent addition of m-cresol did not alter the integrity of the crystals. A marked increase in melting point (206 degrees versus 184 degrees) and heat of fusion (24.6 J/g versus 1.4 J/g) of the crystals was observed after the treatment with zinc. The solubility of the zinc treated crystals in a pH 7.1 phosphate buffered saline was 1/20 of that of the original crystals. When the insulinotropin crystals were treated with the additives using a crystal soaking method, the crystals underwent structural changes. Zinc stabilized the crystal lattice, and reduced the solubility of the peptide.

Site-discrimination by molecular imposters at dissymmetric molecular crystal surfaces

NASA Astrophysics Data System (ADS)

Poloni, Laura N.

The organization of atoms and molecules into crystalline forms is ubiquitous in nature and has been critical to the development of many technologies on which modern society relies. Classical crystal growth theory can describe atomic crystal growth, however, a description of molecular crystal growth is lacking. Molecular crystals are often characterized by anisotropic intermolecular interactions and dissymmetric crystal surfaces with anisotropic growth rates along different crystallographic directions. This thesis describes combination of experimental and computational techniques to relate crystal structure to surface structure and observed growth rates. Molecular imposters, also known as tailor-made impurities, can be used to control crystal growth for practical applications such as inhibition of pathological crystals, but can also be used to understand site specificity at crystal growth surfaces. The first part of this thesis builds on previous real-time in situ atomic force microscopy (AFM) observations of dislocation-actuated growth on the morphologically significant face of hexagonal L-cystine crystals, which aggregate in vivo to form kidney stones in patients suffering from cystinuria. The inhibitory effect of various L-cystine structural mimics (a.k.a. molecular imposters) was investigated through experimental and computational methods to identify the key structural factors responsible for molecular recognition between molecular imposters and L-cystine crystal surface sites. The investigation of L-cystine crystal growth in the presence of molecular imposters through a combination of kinetic analysis using in situ AFM, morphology analysis and birefringence measurements of bulk crystals, and molecular modeling of imposter binding to energetically inequivalent surface sites revealed that different molecular imposters inhibited crystal growth by a Cabrera-Vermilyea pinning mechanism and that imposters bind to a single binding site on the dissymmetric {1000} L-cystine surfaces. Collectively, these findings identify the key structural factors responsible for molecular recognition between molecular imposters and L-cystine crystal step sites, thereby articulating a strategy for stone prevention based on molecular design. The second part of this thesis describes the crystal growth and inhibition of a P2X3 receptor antagonist, denoted as DAPSA, recently reported as a non-opioid treatment of chronic pain. The low solubility of this compound results in the formation of drug-induced renal calculi (a.k.a. xenostones). in situ AFM of the morphologically significant (011) DAPSA surface revealed dislocation-actuated growth spirals with an anisotropic morphology, behavior that can be attributed to the non-uniform rate of solute attachment to eight crystallographically unique steps of the spiral, a direct consequence of the dissymmetry of this crystal surface. Eighteen molecular imposters were selected from the screening library to systematically investigate the roles of imposter substitute position, size, and functionality on the step velocities along the eight unique crystallographic directions. A non-uniform reduction in step velocities was observed, signaling site discrimination of imposter binding that can be attributed to stereochemical recognition of the imposters at specific crystal sites. The anisotropy of growth inhibition observed in the presence of the various imposters is consistent with binding energies calculated for the thirty-two crystallographically unique kink sites on steps advancing along predominant growth directions. These results provide insight to the design of growth inhibitors for molecular crystalline solids with complex and dissymmetric surfaces, while also suggesting a strategy for formulations containing congeners that can prevent harmful crystal growth in human renal structures. The last two crystalline systems discussed in this thesis are two isomorphous crystal systems that are ideal for the study of impurity incorporation at dissymmetric surfaces because their morphology is dominated by dissymmetric {101} growth faces. Growth processes on the dissymmetric (101) surfaces of these crystalline systems were investigated using metadynamics simulations to determine the free energy of adsorption for solute and impurity attachment to different flat, stepped, and kinked (101) surface terminations. Results suggest that growth occurs via a non-Kossel crystal growth mechanism, and highlights the need for dissymmetric surface structures (i.e. steps and kinks) for a higher fidelity in the orientation of adsorbed molecules. Overall, the results presented in this thesis suggest that growth of molecular crystals, particularly at dissymmetric surfaces, is complex and requires the combination of several experimental and computational techniques to decipher the mechanisms responsible for growth phenomena. The use of molecular imposters to inhibit growth can be useful for the development of therapeutics for pathological crystals, but can also inform processes by which crystal growth occurs at complex surfaces as a result of their site selectivity.

Light emission from organic single crystals operated by electrolyte doping

NASA Astrophysics Data System (ADS)

Matsuki, Keiichiro; Sakanoue, Tomo; Yomogida, Yohei; Hotta, Shu; Takenobu, Taishi

2018-03-01

Light-emitting devices based on electrolytes, such as light-emitting electrochemical cells (LECs) and electric double-layer transistors (EDLTs), are solution-processable devices with a very simple structure. Therefore, it is necessary to apply this device structure into highly fluorescent organic materials for future printed applications. However, owing to compatibility problems between electrolytes and organic crystals, electrolyte-based single-crystal light-emitting devices have not yet been demonstrated. Here, we report on light-emitting devices based on organic single crystals and electrolytes. As the fluorescent materials, α,ω-bis(biphenylyl)terthiophene (BP3T) and 5,6,11,12-tetraphenylnaphthacene (rubrene) single crystals were selected. Using ionic liquids as electrolytes, we observed clear light emission from BP3T LECs and rubrene EDLTs.

Growth, structural, spectral, optical, and thermal studies on amino acid based new NLO single crystal: L-phenylalanine-4-nitrophenol.

PubMed

Prakash, M; Lydia Caroline, M; Geetha, D

2013-05-01

A new organic nonlinear optical single crystal, L-phenylalanine-4-nitrophenol (LPAPN) belonging to the amino acid group has been successfully grown by slow evaporation technique. The lattice parameters of the grown crystal have been determined by X-ray diffraction studies. FT-IR spectrum was recorded to identify the presence of functional group and molecular structure was confirmed by NMR spectrum. Thermal strength of the grown crystal has been studied using TG-DTA analyses. The grown crystals were found to be transparent in the entire visible region. The existence of second harmonic generation signals was observed using Nd:YAG laser with fundamental wavelength of 1064 nm. Copyright © 2013 Elsevier B.V. All rights reserved.

Crystal growth and optical properties of 4-aminobenzophenone (ABP)

NASA Astrophysics Data System (ADS)

Li, Zhengdong; Wu, Baichang; Su, Genbo; Huang, Gongfan

1997-02-01

Bulk crystals of 4-aminobenzophenone (ABP) were grown from organic solution. The crystal structure was determined by X-ray analysis. The refractive indices were determined by the method of prism minimum deviation. Some effective nonlinear-optical coefficients deff were measured. A blue second-harmonic emission with wavelengths of 433 and 460 nm were observed during laser diode pumping.

Controllable light diffraction in woodpile photonic crystals filled with liquid crystal

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ho, Chih-Hua; Zeng, Hao; Wiersma, Diederik S.

2015-01-12

An approach to switching between different patterns of light beams transmitted through the woodpile photonic crystals filled with liquid crystals is proposed. The phase transition between the nematic and isotropic liquid crystal states leads to an observable variation of the spatial pattern transmitted through the photonic structure. The transmission profiles in the nematic phase also show polarization sensibility due to refractive index dependence on the field polarization. The experimental results are consistent with a numerical calculation by Finite Difference Time Domain method.

Crystal growth, structural, optical, dielectric and thermal studies of an amino acid based organic NLO material: L-Phenylalanine L-phenylalaninium malonate

NASA Astrophysics Data System (ADS)

Prakash, M.; Geetha, D.; Lydia Caroline, M.; Ramesh, P. S.

2011-12-01

Good transparent single crystals of L-phenylalanine L-phenylalaninium malonate (LPPMA) have been grown successfully by slow evaporation technique from aqueous solution. Single crystal X-ray diffractometer was utilized to measure unit cell parameter and to confirm the crystal structure. The chemical structure of compound was established by FT-NMR technique. The vibrational modes of the molecules of elucidated from FTIR spectra. Its optical behaviour has been examined by UV-vis spectral analysis, which shows the absence of absorbance in the visible region. Thermal properties of the LPPMA crystal were carried out by thermo gravimetric analysis (TGA) and differential thermal analysis (DTA) techniques, which indicate that the material does not decompose before melting. The melting point of grown crystal was observed as 180 °C by melting point apparatus. The NLO property was confirmed by the powder technique of Kurtz and Perry. The dielectric behaviour of the sample was also studied for the first time.

Ground Based Program for the Physical Analysis of Macromolecular Crystal Growth

NASA Technical Reports Server (NTRS)

Malkin, Alexander J.

1998-01-01

During the past year we have focused on application of in situ Atomic Force Microscopy (AFM) for studies of the growth mechanisms and kinetics of crystallization for different macromolecular systems. Mechanisms of macrostep formation and their decay, which are important in understanding of defect formation, were studied on the surfaces of thaumatin, catalase, canavalin and lysozyme crystals. Experiments revealed that step bunching on crystalline surfaces occurred either due to two- or three-dimensional nucleation on the terraces of vicinal slopes or as a result of uneven step generation by complex dislocation sources. No step bunching arising from interaction of individual steps in the course of the experiment was observed. The molecular structure of the growth steps for thaumatin and lipase crystals were deduced. It was further shown that growth step advance occurs by incorporation of single protein molecules. In singular directions growth steps move by one-dimensional nucleation on step edges followed by lateral growth. One-dimensional nuclei have different sizes, less then a single unit cell, varying for different directions of step movement. There is no roughness due to thermal fluctuations, and each protein molecule which incorporated into the step remained. Growth kinetics for catalase crystals was investigated over wide supersaturation ranges. Strong directional kinetic anisotropy in the tangential step growth rates in different directions was seen. The influence of impurities on growth kinetics and cessation of macromolecular crystals was studied. Thus, for catalase, in addition to pronounced impurity effects on the kinetics of crystallization, we were also able to directly observe adsorption of some impurities. At low supersaturation we repeatedly observed filaments which formed from impurity molecules sedimenting on the surfaces. Similar filaments were observed on the surfaces of thaumatin, canavalin and STMV crystals as well, but the frequency was low compared with catalase crystallization. Cessation of growth of xylanase and lysozyme crystals was also observed and appeared to be a consequence of the formation of dense impurity adsorption layers. Attachment: "An in situ AFM investigation of catalase crystallization", "Atomic force microscopy studies of living cells: visualization of motility, division, aggregation, transformation, and apoptosis", AFM studies on mechanisms of nucleation and growth of macromolecular crystals", and "In situ atomic force microscopy studies of surface morphology, growth kinetics, defect structure and dissolution in macromolecular crystallization".

Ge K-Edge Extended X-Ray Absorption Fine Structure Study of the Local Structure of Amorphous GeTe and the Crystallization

NASA Astrophysics Data System (ADS)

Maeda, Yoshihito; Wakagi, Masatoshi

1991-01-01

The local structure and crystallization of amorphous GeTe (a-GeTe) were examined by means of Ge K-edge EXAFS. In a-GeTe, both Ge-Ge and Ge-Te bonds were observed to exist in nearest neighbors of Ge. The average coordination number around Ge is 3.7, which is close to the tetrahedral structure. A random covalent network (RCN) model seems to be suitable for the local Structure. After a-GeTe crystallizes at 129°C, the Ge-Ge bond disappears and the Ge-Te bond length increases considerably. As temperature rises, in a-GeTe the Debye-Waller factor of the Ge-Te bond increases greatly, while that of the Ge-Ge bond increases only slightly. At the crystallization, it is found that the fluctuation of the Ge-Te bond length plays a major role in the change of the local structure and bonding state around Ge.

Efficient green luminescence of terbium oxalate crystals: A case study with Judd-Ofelt theory and single crystal structure analysis and the effect of dehydration on luminescence

NASA Astrophysics Data System (ADS)

Alexander, Dinu; Joy, Monu; Thomas, Kukku; Sisira, S.; Biju, P. R.; Unnikrishnan, N. V.; Sudarsanakumar, C.; Ittyachen, M. A.; Joseph, Cyriac

2018-06-01

Design and synthesis of Lanthanide based metal organic framework is a frontier area of research owing to their structural diversity enabling specific applications. The luminescence properties of rare earths, tuned by the structural features of Ln-MOFs are investigated extensively. Rare earth oxalates which can be synthesized in a facile method, ensuring the structural features of MOFs with excellent photoluminescence characteristics deserves much attention. This work is the first time report on the single crystal structure and Judd-Ofelt (JO) theoretical analysis - their correlation with the intense and sharp green luminescence of Terbium oxalate crystals. The intense green luminescence observed for Terbium oxalate crystals for a wide range of excitation from DUV to visible region despite the luminescence limiting factors are discussed. The absence of concentration quenching and lifting up of forbidden nature of f-f transitions, allowing direct excitation of Terbium ions is analysed with the help of JO theory and single crystal structure analysis. The JO analysis predicted the asymmetry of Terbium sites, allowing the electric dipole transitions and from the JO intensity parameters, promising spectroscopic parameters - emission cross section, branching ratio, gain band width and gain coefficient of the material were calculated. The single crystal structure analysis revealed the asymmetry of Tb sites and structure of Terbium oxalate is formed by the hydrogen bonded stacking of overlapped six Terbium membered rings connected by the oxalate ligands. The molecularly thick layers thus formed on the crystal surface are imaged by the atomic force microscopy. The presence of water channels in the structure and the effect of lattice water molecules on the luminescence intensity are also investigated.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Aliev, Ziya S., E-mail: ziyasaliev@gmail.com; Institute of Physics, ANAS, H.Javid ave. 131, AZ1143 Baku; Donostia International Physics Center

Single crystals of the ternary copper compounds CuTlS and CuTlSe have been successfully grown from stoichiometric melt by using vertical Bridgman-Stockbarger method. The crystal structure of the both compounds has been determined by powder and single crystal X-Ray diffraction. They crystallize in the PbFCl structure type with two formula units in the tetragonal system, space group P4/nmm, a=3.922(2); c=8.123(6); Z=2 and a=4.087(6); c=8.195(19) Å; Z=2, respectively. The band structure of the reported compounds has been analyzed by means of full-potential linearized augmented plane-wave (FLAPW) method based on the density functional theory (DFT). Both compounds have similar band structures and aremore » narrow-gap semiconductors with indirect band gap. The resistivity measurements agree with a semiconductor behavior although anomalies are observed at low temperature. - Graphical abstract: The crystal structures of CuTl and CuTlSe are isostructural with the PbFCl-type and the superconductor LiFeAs-type tetragonal structure. The band structure calculations confirmed that they are narrow-gap semiconductors with indirect band gaps of 0.326 and 0.083 eV. The resistivity measurements, although confirming the semiconducting behavior of both compounds exhibit unusual anomalies at low temperatures. - Highlights: • Single crystals of CuTlS and CuTlSe have been successfully grown by Bridgman-Stockbarger method. • The crystal structure of the both compounds has been determined by single crystal XRD. • The band structure of the both compounds has been analyzed based on the density functional theory (DFT). • The resistivity measurements have been carried out from room temperature down to 10 K.« less

Ultrasound liquid crystal lens

NASA Astrophysics Data System (ADS)

Shimizu, Yuki; Koyama, Daisuke; Fukui, Marina; Emoto, Akira; Nakamura, Kentaro; Matsukawa, Mami

2018-04-01

A variable-focus lens using a combination of liquid crystals and ultrasound is discussed. The lens uses a technique based on ultrasound vibration to control the molecular orientation of the liquid crystal. The lens structure is simple, with no mechanical moving parts and no transparent electrodes, which is helpful for device downsizing; the structure consists of a liquid crystal layer sandwiched between two glass substrates with a piezoelectric ring. The tens-of-kHz ultrasonic resonance flexural vibration used to excite the lens generates an acoustic radiation force on the liquid crystal layer to induce changes in the molecular orientation of the liquid crystal. The orientations of the liquid crystal molecules and the optical characteristics of the lens were investigated under ultrasound excitation. Clear optical images were observed through the lens, and the focal point could be controlled using the input voltage to the piezoelectric ring to give the lens its variable-focus action.

Molecular and electronic structure of terminal and alkali metal-capped uranium(V) nitride complexes

PubMed Central

King, David M.; Cleaves, Peter A.; Wooles, Ashley J.; Gardner, Benedict M.; Chilton, Nicholas F.; Tuna, Floriana; Lewis, William; McInnes, Eric J. L.; Liddle, Stephen T.

2016-01-01

Determining the electronic structure of actinide complexes is intrinsically challenging because inter-electronic repulsion, crystal field, and spin–orbit coupling effects can be of similar magnitude. Moreover, such efforts have been hampered by the lack of structurally analogous families of complexes to study. Here we report an improved method to U≡N triple bonds, and assemble a family of uranium(V) nitrides. Along with an isoelectronic oxo, we quantify the electronic structure of this 5f1 family by magnetometry, optical and electron paramagnetic resonance (EPR) spectroscopies and modelling. Thus, we define the relative importance of the spin–orbit and crystal field interactions, and explain the experimentally observed different ground states. We find optical absorption linewidths give a potential tool to identify spin–orbit coupled states, and show measurement of UV···UV super-exchange coupling in dimers by EPR. We show that observed slow magnetic relaxation occurs via two-phonon processes, with no obvious correlation to the crystal field. PMID:27996007

Unravelling surface and interfacial structures of a metal-organic framework by transmission electron microscopy.

PubMed

Zhu, Yihan; Ciston, Jim; Zheng, Bin; Miao, Xiaohe; Czarnik, Cory; Pan, Yichang; Sougrat, Rachid; Lai, Zhiping; Hsiung, Chia-En; Yao, Kexin; Pinnau, Ingo; Pan, Ming; Han, Yu

2017-05-01

Metal-organic frameworks (MOFs) are crystalline porous materials with designable topology, porosity and functionality, having promising applications in gas storage and separation, ion conduction and catalysis. It is challenging to observe MOFs with transmission electron microscopy (TEM) due to the extreme instability of MOFs upon electron beam irradiation. Here, we use a direct-detection electron-counting camera to acquire TEM images of the MOF ZIF-8 with an ultralow dose of 4.1 electrons per square ångström to retain the structural integrity. The obtained image involves structural information transferred up to 2.1 Å, allowing the resolution of individual atomic columns of Zn and organic linkers in the framework. Furthermore, TEM reveals important local structural features of ZIF-8 crystals that cannot be identified by diffraction techniques, including armchair-type surface terminations and coherent interfaces between assembled crystals. These observations allow us to understand how ZIF-8 crystals self-assemble and the subsequent influence of interfacial cavities on mass transport of guest molecules.

Unravelling surface and interfacial structures of a metal-organic framework by transmission electron microscopy

NASA Astrophysics Data System (ADS)

Zhu, Yihan; Ciston, Jim; Zheng, Bin; Miao, Xiaohe; Czarnik, Cory; Pan, Yichang; Sougrat, Rachid; Lai, Zhiping; Hsiung, Chia-En; Yao, Kexin; Pinnau, Ingo; Pan, Ming; Han, Yu

2017-05-01

Metal-organic frameworks (MOFs) are crystalline porous materials with designable topology, porosity and functionality, having promising applications in gas storage and separation, ion conduction and catalysis. It is challenging to observe MOFs with transmission electron microscopy (TEM) due to the extreme instability of MOFs upon electron beam irradiation. Here, we use a direct-detection electron-counting camera to acquire TEM images of the MOF ZIF-8 with an ultralow dose of 4.1 electrons per square ångström to retain the structural integrity. The obtained image involves structural information transferred up to 2.1 Å, allowing the resolution of individual atomic columns of Zn and organic linkers in the framework. Furthermore, TEM reveals important local structural features of ZIF-8 crystals that cannot be identified by diffraction techniques, including armchair-type surface terminations and coherent interfaces between assembled crystals. These observations allow us to understand how ZIF-8 crystals self-assemble and the subsequent influence of interfacial cavities on mass transport of guest molecules.

Synthesis and crystal structure of the solid solution Co3(SeO3)3-x(PO3OH)x(H2O) involving crystallographic split positions of Se4+ and P5+.

PubMed

Zimmermann, Iwan; Johnsson, Mats

2013-10-21

Three new cobalt selenite hydroxo-phosphates laying in the solid solution Co3(SeO3)3-x(PO3OH)x(H2O), with x = 0.8, x = 1.0, and x = 1.2 are reported. Single crystals were obtained by hydrothermal synthesis and the crystal structure was determined by single crystal X-ray diffraction. The structure can be described as a 3D framework having selenite and hydroxo-phosphate groups protruding into channels in the crystal structure. Se(4+) and P(5+) share a split position in the structure so that either SeO3 groups having a stereochemically active lone pair or tetrahedrally coordinated PO3OH groups are present. The OH-group is thus only present when the split position is occupied by P(5+). The crystal water is coordinated to a cobalt atom and TG and IR measurements show that the water and hydroxyl groups leave the structure at unusually high temperatures (>450 °C). Magnetic susceptibility measurements show antiferromagnetic coupling below 16 K and a magnetic moment of 4.02(3) μB per Co atom was observed.

Low-resolution structure of Drosophila translin

PubMed Central

Kumar, Vinay; Gupta, Gagan D.

2012-01-01

Crystals of native Drosophila melanogaster translin diffracted to 7 Å resolution. Reductive methylation of the protein improved crystal quality. The native and methylated proteins showed similar profiles in size-exclusion chromatography analyses but the methylated protein displayed reduced DNA-binding activity. Crystals of the methylated protein diffracted to 4.2 Å resolution at BM14 of the ESRF synchrotron. Crystals with 49% solvent content belonged to monoclinic space group P21 with eight protomers in the asymmetric unit. Only 2% of low-resolution structures with similar low percentage solvent content were found in the PDB. The crystal structure, solved by molecular replacement method, refined to Rwork (Rfree) of 0.24 (0.29) with excellent stereochemistry. The crystal structure clearly shows that drosophila protein exists as an octamer, and not as a decamer as expected from gel-filtration elution profiles. The similar octameric quaternary fold in translin orthologs and in translin–TRAX complexes suggests an up-down dimer as the basic structural subunit of translin-like proteins. The drosophila oligomer displays asymmetric assembly and increased radius of gyration that accounts for the observed differences between the elution profiles of human and drosophila proteins on gel-filtration columns. This study demonstrates clearly that low-resolution X-ray structure can be useful in understanding complex biological oligomers. PMID:23650579

Growth and luminescent properties of Yb:YAG and Ca co-doped Yb:YAG ultrafast scintillation crystals

NASA Astrophysics Data System (ADS)

Zhu, Maodong; Qi, Hongji; Pan, Mingyan; Hou, Qing; Jiang, Benxue; Jin, Yaxue; Han, Hetong; Song, Zhaohui; Zhang, Hui

2018-05-01

In this work, Yb-doped Y3Al5O12 [yttrium aluminum garnet (YAG)] crystals and Ca co-doped Yb:YAG crystals were grown by the Czochralski (CZ) method. The chemical formulas of the two crystals are (Yb0.1Y0.9)3Al5O12 and (Ca0.001Yb0.1Y0.899)3Al5O12, respectively. The structural, optical and luminescent properties of the Yb:YAG and Ca, Yb:YAG crystals were investigated by X-ray rocking curve, X-ray diffraction, Raman spectra, UV-Visble-NIR absorption spectra and X-ray fluorescence. X-ray fluorescence spectrum with two emission peaks at 330 nm and 490 nm were observed in the two kinds of crystals, which would increase slightly after the annealing. Comparing to the Yb:YAG crystal, Ca co-doped Yb:YAG crystal behaved the better luminescent intensity without changing the crystal structure and vibrational modes. This indicates that by doping Ca2+ in Yb:YAG crystal may be an appropriate way to enhance the luminescent property of the scintillation crystal.

Raman study of TiO2 role in SiO2-Al2O3-MgO-TiO2-ZnO glass crystallization.

PubMed

Furić, Kresimir; Stoch, Leszek; Dutkiewicz, Jan

2005-05-01

Tough glass-ceramic material of special mechanical properties with nanosize crystal phases formed by appropriately controlled crystallization was studied by Raman spectroscopy. It was obtained by TiO2 activated crystallization of Mg-aluminosilicate glass of SiO2-Al2O3-MgO-TiO2-ZnO composition. Crystallization was preceded by a change in the TiO2 structural position and state, which is manifested by a changed color of glass from yellow into blue shortly before the glass transformation (Tg) temperature. Raman spectroscopy was applied to explain the mechanism of this process and to establish the role of TiO2 in the early stage of glass crystallization that precedes a complete crystal phase formation. The starting glasses were found in almost complete disorder, since all bands were weak, broad and dominated by a Bose band at about 90 cm-1. After the sample annealing all bands turned out better resolved and the Bose band practically disappeared, both confirming the amorphous structure reorganization process. A multiplet observed in the vicinity of 150 cm-1 we assigned to the anatase and other titania structures that can be considered prime centers of crystallization. Finally, in the closest neighborhood of the Rayleigh line the low frequency mode characterizing nanoparticles was observed. According to this band theory, the mean size of initial titania crystallites is about 10nm for all samples, but the size distribution varies within factor two among them.

Raman study of TiO 2 role in SiO 2-Al 2O 3-MgO-TiO 2-ZnO glass crystallization

NASA Astrophysics Data System (ADS)

Furić, Krešimir; Stoch, Leszek; Dutkiewicz, Jan

2005-05-01

Tough glass-ceramic material of special mechanical properties with nanosize crystal phases formed by appropriately controlled crystallization was studied by Raman spectroscopy. It was obtained by TiO 2 activated crystallization of Mg-aluminosilicate glass of SiO 2-Al 2O 3-MgO-TiO 2-ZnO composition. Crystallization was preceded by a change in the TiO 2 structural position and state, which is manifested by a changed color of glass from yellow into blue shortly before the glass transformation ( Tg) temperature. Raman spectroscopy was applied to explain the mechanism of this process and to establish the role of TiO 2 in the early stage of glass crystallization that precedes a complete crystal phase formation. The starting glasses were found in almost complete disorder, since all bands were weak, broad and dominated by a Bose band at about 90 cm -1. After the sample annealing all bands turned out better resolved and the Bose band practically disappeared, both confirming the amorphous structure reorganization process. A multiplet observed in the vicinity of 150 cm -1 we assigned to the anatase and other titania structures that can be considered prime centers of crystallization. Finally, in the closest neighborhood of the Rayleigh line the low frequency mode characterizing nanoparticles was observed. According to this band theory, the mean size of initial titania crystallites is about 10 nm for all samples, but the size distribution varies within factor two among them.

New Polymorph Form of Dexamethasone Acetate.

PubMed

Silva, Ronaldo Pedro da; Ambrósio, Mateus Felipe Schuchter; Piovesan, Luciana Almeida; Freitas, Maria Clara Ramalho; Aguiar, Daniel Lima Marques de; Horta, Bruno Araújo Cautiero; Epprecht, Eugenio Kahn; San Gil, Rosane Aguiar da Silva; Visentin, Lorenzo do Canto

2018-02-01

A new monohydrated polymorph of dexamethasone acetate was crystallized and its crystal structure characterized. The different analytical techniques used for describing its structural and vibrational properties were: single crystal and polycrystal X-ray diffraction, solid state nuclear magnetic resonance, infrared spectroscopy. A Hirshfeld surface analysis was carried out through self-arrangement cemented by H-bonds observed in this new polymorph. This new polymorph form appeared because of self-arrangement via classical hydrogen bonds around the water molecule. Copyright © 2018 American Pharmacists Association®. Published by Elsevier Inc. All rights reserved.

Structure of Bacillus halmapalus α-amylase crystallized with and without the substrate analogue acarbose and maltose

PubMed Central

Lyhne-Iversen, Louise; Hobley, Timothy J.; Kaasgaard, Svend G.; Harris, Pernille

2006-01-01

Recombinant Bacillus halmapalus α-amylase (BHA) was studied in two different crystal forms. The first crystal form was obtained by crystallization of BHA at room temperature in the presence of acarbose and maltose; data were collected at cryogenic temperature to a resolution of 1.9 Å. It was found that the crystal belonged to space group P212121, with unit-cell parameters a = 47.0, b = 73.5, c = 151.1 Å. A maltose molecule was observed and found to bind to BHA and previous reports of the binding of a nonasaccharide were confirmed. The second crystal form was obtained by pH-induced crystallization of BHA in a MES–HEPES–boric acid buffer (MHB buffer) at 303 K; the solubility of BHA in MHB has a retrograde temperature dependency and crystallization of BHA was only possible by raising the temperature to at least 298 K. Data were collected at cryogenic temperature to a resolution of 2.0 Å. The crystal belonged to space group P212121, with unit-cell parameters a = 38.6, b = 59.0, c = 209.8 Å. The structure was solved using molecular replacement. The maltose-binding site is described and the two structures are compared. No significant changes were seen in the structure upon binding of the substrates. PMID:16946462

Crystal nucleation of colloidal hard dumbbells

NASA Astrophysics Data System (ADS)

Ni, Ran; Dijkstra, Marjolein

2011-01-01

Using computer simulations, we investigate the homogeneous crystal nucleation in suspensions of colloidal hard dumbbells. The free energy barriers are determined by Monte Carlo simulations using the umbrella sampling technique. We calculate the nucleation rates for the plastic crystal and the aperiodic crystal phase using the kinetic prefactor as determined from event driven molecular dynamics simulations. We find good agreement with the nucleation rates determined from spontaneous nucleation events observed in event driven molecular dynamics simulations within error bars of one order of magnitude. We study the effect of aspect ratio of the dumbbells on the nucleation of plastic and aperiodic crystal phases, and we also determine the structure of the critical nuclei. Moreover, we find that the nucleation of the aligned close-packed crystal structure is strongly suppressed by a high free energy barrier at low supersaturations and slow dynamics at high supersaturations.

Nondestructive optical testing of the materials surface structure based on liquid crystals

NASA Astrophysics Data System (ADS)

Tomilin, M. G.; Stafeev, S. K.

2011-08-01

Thin layers of nematic liquid crystals (NLCs) may be used as recording media for visualizing structural and microrelief defects, distribution of low power physical fields and modifications of the surface. NLCs are more sensitive in comparison with cholesteric and smectic LCs having super molecular structures. The detecting properties of NLCs are based on local layers deformation, induced by surface fields and observed in polarizing microscope. The structural surface defects or physical field's distribution are dramatically change the distribution of surface tension. Surface defects recording becomes possible if NLC deformed structure is illuminated in transparent or reflective modes and observed in optical polarizing microscope and appearing image is compared with background structure. In this case one observes not the real defect but the local deformation in NLCs. The theory was developed to find out the real size of defects. The resolution of NLC layer is more than 2000 lines/mm. The fields of NLC application are solid crystals symmetry, minerals, metals, semiconductors, polymers and glasses structure inhomogeneities and optical coatings defects detecting. The efficiency of NLC method in biophotonics is illustrated by objective detecting cancer tissues character and visualizing the interaction traces of grippe viruses with antibodies. NLCs may detect solvent components structure in tea, wine and perfume giving unique information of their structure. It presents diagnostic information alternative to dyes and fluorescence methods. For the first time the structures of some juices and beverages are visualized to illustrate the unique possibilities of NLCs.

Density functional study for the bridged dinuclear center based on a high-resolution X-ray crystal structure of ba3 cytochrome c oxidase from Thermus thermophilus.

PubMed

Du, Wen-Ge Han; Noodleman, Louis

2013-12-16

Strong electron density for a peroxide type dioxygen species bridging the Fea3 and CuB dinuclear center (DNC) was observed in the high-resolution (1.8 Å) X-ray crystal structures (PDB entries 3S8G and 3S8F) of ba3 cytochrome c oxidase (CcO) from Thermus thermophilus. The crystals represent the as-isolated X-ray photoreduced CcO structures. The bridging peroxide was proposed to arise from the recombination of two radiation-produced HO(•) radicals formed either very near to or even in the space between the two metals of the DNC. It is unclear whether this peroxide species is in the O2(2-), O2(•)(-), HO2(-), or the H2O2 form and what is the detailed electronic structure and binding geometry including the DNC. In order to answer what form of this dioxygen species was observed in the DNC of the 1.8 Å X-ray CcO crystal structure (3S8G), we have applied broken-symmetry density functional theory (BS-DFT) geometric and energetic calculations (using OLYP potential) on large DNC cluster models with different Fea3-CuB oxidation and spin states and with O2(2-), O2(•)(-), HO2(-), or H2O2 in the bridging position. By comparing the DFT optimized geometries with the X-ray crystal structure (3S8G), we propose that the bridging peroxide is HO2(-). The X-ray crystal structure is likely to represent the superposition of the Fea3(2+)-(HO2(-))-CuB(+) DNC's in different states (Fe(2+) in low spin (LS), intermediate spin (IS), or high spin (HS)) with the majority species having the proton of the HO2(-) residing on the oxygen atom (O1) which is closer to the Fea3(2+) site in the Fea3(2+)-(HO-O)(-)-CuB(+) conformation. Our calculations show that the side chain of Tyr237 is likely trapped in the deprotonated Tyr237(-) anion form in the 3S8G X-ray crystal structure.

Incident flux angle induced crystal texture transformation in nanostructured molybdenum films

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chen, L.; Lu, T.-M.; Wang, G.-C.

2012-07-15

Molybdenum films were observed to undergo a dramatic change in crystal texture orientation when the incident flux angle was varied in an oblique angle sputter deposition on amorphous substrates. Reflection high-energy electron diffraction pole figure and scanning electron microscopy were used to analyze in detail the texture orientation of the films. The normal incident deposition resulted in a fiber texture film with the minimum energy (110) crystal plane parallel to the substrate surface. A (110)[110] biaxial texture was observed for the samples grown with low incident angles of less than 45 Degree-Sign , with respect to the surface normal. Onmore » the other hand, for an oblique angle deposition of larger than 60 Degree-Sign , a (111)[112] biaxial texture was observed and appeared to be consistent with a zone T structure where the geometrically fastest growth [001] direction of a crystal plays a dominant role in defining the texture. We argue that a structural transition had occurred when the incident flux was varied from near normal incidence to a large angle.« less

Designing functionality in perovskite thin films using ion implantation techniques: Assessment and insights from first-principles calculations

DOE PAGES

Sharma, Vinit K.; Herklotz, Andreas; Ward, Thomas Zac; ...

2017-09-11

Ion implantation has been widely used in the semiconductor industry for decades to selectively control electron/hole doping for device applications. Recently, experimental studies on ion implantation into more structurally and electronically complex materials have been undertaken in which defect generation has been used to control a variety of functional phenomena. Of particular interest, are recent findings demonstrating that low doses of low energy helium ions into single crystal films can be used to tailor the structural properties. These initial experimental studies have shown that crystal symmetry can be continuously controlled by applying increasingly large doses of He ions into amore » crystal. The observed changes in lattice structure were then observed to correlate with functional changes, such as metal-insulator transition temperature2 and optical bandgap3. In these preliminary experimental studies, changes to lattice expansion was proposed to be the direct result of chemical pressure originating predominantly from the implanted He applying chemical pressure at interstitial sites. However, the influence of possible secondary knock-on damage arising from the He atoms transferring energy to the lattice through nuclear-nuclear collision with the crystal lattice remains largely unaddressed. In this work, we focus on a SrRuO3 model system to provide a comprehensive examination of the impact of common defects on structural and electronic properties, obtain calculated defect formation energies, and define defect migration barriers. Our model indicates that, while interstitial He can modify the crystal properties, a dose significantly larger than those reported in experimental studies would be required. The true origin of the observed structural changes is likely the result of a combination of secondary defects created during He implantation. Of particular importance, we observe that different defect types can generate greatly varied local electronic structures and that the formation energies and migration energy barriers vary by defect type. Thus, we may have identified a new method of selectively inducing controlled defect complexes into single crystal materials. Development of this approach would have a broad impact on both our ability to probe specific defect contributions in fundamental studies and allow a new level of control over functional properties driven by specific defect complexes.« less

Unusual structural phase transition in [N(C2H5)4][N(CH3)4][ZnBr4

NASA Astrophysics Data System (ADS)

Krawczyk, Monika K.; Ingram, Adam; Cach, Ryszard; Czapla, Zbigniew; Czupiński, Olaf; Dacko, Sławomir; Staniorowski, Piotr

2018-04-01

The new hybrid organic-inorganic crystal [N(C2H5)4][N(CH3)4][ZnBr4] was grown and its physical properties and structural phase transition are presented. On the basis of thermal analysis (DSC (differential scanning calorimetry), DTA (differential thermal analysis), DTG), X-ray structural, dilatometric and dielectric studies as well as optical observation, the reversible first-order phase transition at 490/488 K on heating and cooling run, respectively, has been found. An appearance of domain structure of ferroelastic type gives evidence for an untypical lowering of crystal symmetry during the phase transition. At room temperature, the satisfying crystal structure solution was found in the tetragonal system, in the P?21m space group.

Structural studies of Pseudomonas and Chromobacterium ω-aminotransferases provide insights into their differing substrate specificity.

PubMed

Sayer, Christopher; Isupov, Michail N; Westlake, Aaron; Littlechild, Jennifer A

2013-04-01

The crystal structures and inhibitor complexes of two industrially important ω-aminotransferase enzymes from Pseudomonas aeruginosa and Chromobacterium violaceum have been determined in order to understand the differences in their substrate specificity. The two enzymes share 30% sequence identity and use the same amino acceptor, pyruvate; however, the Pseudomonas enzyme shows activity towards the amino donor β-alanine, whilst the Chromobacterium enzyme does not. Both enzymes show activity towards S-α-methylbenzylamine (MBA), with the Chromobacterium enzyme having a broader substrate range. The crystal structure of the P. aeruginosa enzyme has been solved in the holo form and with the inhibitor gabaculine bound. The C. violaceum enzyme has been solved in the apo and holo forms and with gabaculine bound. The structures of the holo forms of both enzymes are quite similar. There is little conformational difference observed between the inhibitor complex and the holoenzyme for the P. aeruginosa aminotransferase. In comparison, the crystal structure of the C. violaceum gabaculine complex shows significant structural rearrangements from the structures of both the apo and holo forms of the enzyme. It appears that the different rigidity of the protein scaffold contributes to the substrate specificity observed for the two ω-aminotransferases.

Crystal Structure of a Soluble Fragment of the Membrane Fusion Protein HlyD in a Type I Secretion System of Gram-Negative Bacteria.

PubMed

Kim, Jin-Sik; Song, Saemee; Lee, Minho; Lee, Seunghwa; Lee, Kangseok; Ha, Nam-Chul

2016-03-01

The protein toxin HlyA of Escherichia coli is exported without a periplasmic intermediate by the type I secretion system (T1SS). The T1SS is composed of an inner membrane ABC transporter HlyB, an outer-membrane channel protein TolC, and a membrane fusion protein HlyD. However, the assembly of the T1SS remains to be elucidated. In this study, we determine the crystal structure of a part of the C-terminal periplasmic domain of HlyD. The long α-helical domain consisting of three α helices and a lipoyl domain was identified in the crystal structure. Based on the HlyD structure, we modeled the hexameric assembly of HlyD with a long α-helical barrel, which formed a complex with TolC in an intermeshing cogwheel-to-cogwheel manner, as observed in tripartite RND-type drug efflux pumps. These observations provide a structural blueprint for understanding the type I secretion system in pathogenic Gram-negative bacteria. Copyright © 2016 Elsevier Ltd. All rights reserved.

Refractive index dependence of Papilio Ulysses butterfly wings reflectance spectra

NASA Astrophysics Data System (ADS)

Isnaeni, Muslimin, Ahmad Novi; Birowosuto, Muhammad Danang

2016-02-01

We have observed and utilized butterfly wings of Papilio Ulysses for refractive index sensor. We noticed this butterfly wings have photonic crystal structure, which causes blue color appearance on the wings. The photonic crystal structure, which consists of cuticle and air void, is approximated as one dimensional photonic crystal structure. This photonic crystal structure opens potential to several optical devices application, such as refractive index sensor. We have utilized small piece of Papilio Ulysses butterfly wings to characterize refractive index of several liquid base on reflectance spectrum of butterfly wings in the presence of sample liquid. For comparison, we simulated reflectance spectrum of one dimensional photonic crystal structure having material parameter based on real structure of butterfly wings. We found that reflectance spectrum peaks shifted as refractive index of sample changes. Although there is a slight difference in reflectance spectrum peaks between measured spectrum and calculated spectrum, the trend of reflectance spectrum peaks as function of sample's refractive index is the similar. We assume that during the measurement, the air void that filled by sample liquid is expanded due to liquid pressure. This change of void shape causes non-similarity between measured spectrum and calculated spectrum.

Ion irradiation-induced crystal structure changes in inverse spinel MgIn 2O 4

DOE PAGES

Tang, Ming; Valdez, James A.; Wang, Yongqiang; ...

2016-07-29

We performed 400 keV Ne and 200 keV He ion irradiations on fully inverse MgIn 2O 4 samples at cryogenic temperature (~ 77 K), in order to examine the influence of radiation-induced cation disordering on crystal structure. In the case of MgIn 2O 4 samples irradiated with Ne ions to a peak displacement damage dose of 4 displacements per atom (dpa), a spinel-to-rocksalt phase transformation was observed. Conversely, for MgIn 2O 4 samples irradiated with He ions to a peak displacement damage dose of 5 dpa, the only observed structural effect involved cation rearrangements from an inverse to a “random”more » spinel structure.« less

Boron Arsenide and Boron Phosphide for High Temperature and Luminescent Devices. [semiconductor devices - crystal growth/crystal structure

NASA Technical Reports Server (NTRS)

Chu, T. L.

1975-01-01

The crystal growth of boron arsenide and boron phosphide in the form of bulk crystals and epitaxial layers on suitable substrates is discussed. The physical, chemical, and electrical properties of the crystals and epitaxial layers are examined. Bulk crystals of boron arsenide were prepared by the chemical transport technique, and their carrier concentration and Hall mobility were measured. The growth of boron arsenide crystals from high temperature solutions was attempted without success. Bulk crystals of boron phosphide were also prepared by chemical transport and solution growth techniques. Techniques required for the fabrication of boron phosphide devices such as junction shaping, diffusion, and contact formation were investigated. Alloying techniques were developed for the formation of low-resistance ohmic contacts to boron phosphide. Four types of boron phosphide devices were fabricated: (1) metal-insulator-boron phosphide structures, (2) Schottky barriers; (3) boron phosphide-silicon carbide heterojunctions; and (4) p-n homojunctions. Easily visible red electroluminescence was observed from both epitaxial and solution grown p-n junctions.

Crystal structure and magnetic properties of '{alpha} Prime Prime -Fe{sub 16}N{sub 2}' containing residual {alpha}-Fe prepared by low-temperature ammonia nitridation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yamashita, S.; Masubuchi, Y.; Nakazawa, Y.

2012-10-15

Slight enhancement of saturation magnetization to 219 A m{sup 2} kg{sup -1} was observed from 199 A m{sup 2} kg{sup -1} for the original {alpha}-Fe on the intermediate nitrided mixture of '{alpha} Prime Prime -Fe{sub 16}N{sub 2}' with residual {alpha}-Fe among the low temperature ammonia nitridation products under 5 T magnetic field at room temperature. The value changed not linearly against the yield as had been expected. Crystal structure refinement indicated that the phase similar to {alpha} Prime Prime -Fe{sub 16}N{sub 2} had deviations on its lattice constants and positional parameters, compared to previously reported values for {alpha} Prime Primemore » -Fe{sub 16}N{sub 2}. Spin-polarized total energy calculations were performed using the projector-augmented wave method as implemented in the Vienna ab-initio simulation package (VASP) to calculate magnetic moment on the refined crystal structure of the intermediate '{alpha} Prime Prime -Fe{sub 16}N{sub 2}'. The calculations supported the observed magnetization enhancement in the intermediate nitridation product. - Graphical abstract: Crystal structural parameters slightly change in the intermediate nitrided '{alpha} Prime Prime -Fe{sub 16}N{sub 2}' from those in {alpha} Prime Prime -Fe{sub 16}N{sub 2} to show the magnetization maxima in the mixture of '{alpha} Prime Prime -Fe{sub 16}N{sub 2}' and the residual {alpha}-F. Highlights: Black-Right-Pointing-Pointer Larger magnetization was observed than the value of Fe{sub 16}N{sub 2} on its intermediate nitrided mixture with residual {alpha}-Fe. Black-Right-Pointing-Pointer The enhancement was related to the crystal structural deviation from Fe{sub 16}N{sub 2} on the intermediate nitride. Black-Right-Pointing-Pointer It was supported by spin-polarized total energy calculation using the deviated structure.« less

Inorganic bromine in organic molecular crystals: Database survey and four case studies

NASA Astrophysics Data System (ADS)

Nemec, Vinko; Lisac, Katarina; Stilinović, Vladimir; Cinčić, Dominik

2017-01-01

We present a Cambridge Structural Database and experimental study of multicomponent molecular crystals containing bromine. The CSD study covers supramolecular behaviour of bromide and tribromide anions as well as halogen bonded dibromine molecules in crystal structures of organic salts and cocrystals, and a study of the geometries and complexities in polybromide anion systems. In addition, we present four case studies of organic structures with bromide, tribromide and polybromide anions as well as the neutral dibromine molecule. These include the first observed crystal with diprotonated phenazine, a double salt of phenazinium bromide and tribromide, a cocrystal of 4-methoxypyridine with the neutral dibromine molecule as a halogen bond donor, as well as bis(4-methoxypyridine)bromonium polybromide. Structural features of the four case studies are in the most part consistent with the statistically prevalent behaviour indicated by the CSD study for given bromine species, although they do exhibit some unorthodox structural features and in that indicate possible supramolecular causes for aberrations from the statistically most abundant (and presumably most favourable) geometries.

Transverse magnetic field impact on waveguide modes of photonic crystals.

PubMed

Sylgacheva, Daria; Khokhlov, Nikolai; Kalish, Andrey; Dagesyan, Sarkis; Prokopov, Anatoly; Shaposhnikov, Alexandr; Berzhansky, Vladimir; Nur-E-Alam, Mohammad; Vasiliev, Mikhail; Alameh, Kamal; Belotelov, Vladimir

2016-08-15

This Letter presents a theoretical and experimental study of waveguide modes of one-dimensional magneto-photonic crystals magnetized in the in-plane direction. It is shown that the propagation constants of the TM waveguide modes are sensitive to the transverse magnetization and the spectrum of the transverse magneto-optical Kerr effect has resonant features at mode excitation frequencies. Two types of structures are considered: a non-magnetic photonic crystal with an additional magnetic layer on top and a magneto-photonic crystal with a magnetic layer within each period. We found that the magneto-optical non-reciprocity effect is greater in the first case: it has a magnitude of δ∼10^-4, while the second structure type demonstrates δ∼10^-5 only, due to the higher asymmetry of the claddings of the magnetic layer. Experimental observations show resonant features in the optical and magneto-optical Kerr effect spectra. The measured dispersion properties are in good agreement with the theoretical predictions. An amplitude of light intensity modulation of up to 2.5% was observed for waveguide mode excitation within the magnetic top layer of the non-magnetic photonic crystal structure. The presented theoretical approach may be utilized for the design of magneto-optical sensors and modulators requiring pre-determined spectral features.

Crystal structure and magnetism of the FexNi8-xSi3 materials, 0 ≤ x ≤ 8

NASA Astrophysics Data System (ADS)

Gallus, Simone; Haddouch, Mohammed Ait; Chikovani, Mamuka; Perßon, Jörg; Voigt, Jörg; Friese, Karen; Senyshyn, Anatoliy; Grzechnik, Andrzej

2018-02-01

The crystal structure and magnetic properties of the materials FexNi8-xSi3 with 0 ≤ x ≤ 8 have been investigated to estimate any possible magnetocaloric effect and compare it to that in known magnetocalorics. Two structural ranges could be identified in this system by X-ray and neutron diffraction. The structure of the samples with 0 ≤ x ≤ 4 is related to the trigonal structure of Ni31Si12. Doubled c lattice parameters compared to the one in Ni31Si12 are observed in the samples with x = 2 and x = 3. The average structure of Fe2Ni6Si3 has been determined by X-ray single-crystal diffraction. The compounds with the compositions 5 ≤ x ≤ 8 crystallize in cubic Fe3Si-type structure. Magnetic measurements have shown that the compound Fe3Ni5Si3 displays a phase transition close to room temperature. However, its magnetocaloric effect is much smaller than the one in the promising magnetocaloric materials.

Experimental Observation of Three-Component New Fermions in Topological Semimetal MoP

NASA Astrophysics Data System (ADS)

Lv, B. Q.; Feng, Z.-L.; Xu, Q.-N.; Ma, J.-Z.; Kong, L.-Y.; Richard, Pierre; Huang, Y.-B.; Strocov, V. N.; Fang, C.; Weng, H.-M.; Shi, Y.-G.; Qian, Tian; Ding, Hong; Paul Scherrer Institute, Swiss Light Source, CH-5232 Villigen PSI, Switzerland Team; Shanghai Synchrotron Radiation Facility, Shanghai Institute of Applied Physics Team; University of Chinese Academy of Sciences, Beijing 100190, China Team; Collaborative Innovation Center of Quantum Matter, Beijing, China Collaboration; Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China Team

Condensed matter systems can host quasiparticle excitations that are analogues to elementary particles such as Majorana, Weyl, and Dirac fermions. Recent advances in band theory have expanded the classification of fermions in crystals, and revealed crystal symmetry-protected electron excitations that have no high-energy counterparts. Here, using angle-resolved photoemission spectroscopy, we demonstrate the existence of a triply degenerate point in the electronic structure of MoP crystal, where the quasiparticle excitations are beyond the Majorana-Weyl-Dirac classification. Furthermore, we observe pairs of Weyl points in the bulk electronic structure coexisting with the new fermions, thus introducing a platform for studying the interplay between different types of fermions. We thank Binbin Fu, Nan Xu, and Xin Gao for the assistance in the ARPES experiments.

Surface structure modification of single crystal graphite after slow, highly charged ion irradiation

NASA Astrophysics Data System (ADS)

Alzaher, I.; Akcöltekin, S.; Ban-d'Etat, B.; Manil, B.; Dey, K. R.; Been, T.; Boduch, P.; Rothard, H.; Schleberger, M.; Lebius, H.

2018-04-01

Single crystal graphite was irradiated by slow, highly charged ions. The modification of the surface structure was studied by means of Low-Energy Electron Diffraction. The observed damage cross section increases with the potential energy, i.e. the charge state of the incident ion, at a constant kinetic energy. The potential energy is more efficient for the damage production than the kinetic energy by more than a factor of twenty. Comparison with earlier results hints to a strong link between early electron creation and later target atom rearrangement. With increasing ion fluence, the initially large-scale single crystal is first transformed into μ m-sized crystals, before complete amorphisation takes place.

Influence of computational domain size on the pattern formation of the phase field crystals

NASA Astrophysics Data System (ADS)

Starodumov, Ilya; Galenko, Peter; Alexandrov, Dmitri; Kropotin, Nikolai

2017-04-01

Modeling of crystallization process by the phase field crystal method (PFC) represents one of the important directions of modern computational materials science. This method makes it possible to research the formation of stable or metastable crystal structures. In this paper, we study the effect of computational domain size on the crystal pattern formation obtained as a result of computer simulation by the PFC method. In the current report, we show that if the size of a computational domain is changed, the result of modeling may be a structure in metastable phase instead of pure stable state. The authors present a possible theoretical justification for the observed effect and provide explanations on the possible modification of the PFC method to account for this phenomenon.

Real-time observation of morphological transformations in II-VI semiconducting nanobelts via environmental transmission electron microscopy

DOE PAGES

Agarwal, Rahul; Zakharov, Dmitri N.; Krook, Nadia M.; ...

2015-05-01

It has been observed that wurtzite II–VI semiconducting nanobelts transform into single-crystal, periodically branched nanostructures upon heating. The mechanism of this novel transformation has been elucidated by heating II–VI nanobelts in an environmental transmission electron microscope (ETEM) in oxidizing, reducing and inert atmospheres while observing their structural changes with high spatial resolution. The interplay of surface reconstruction of high-energy surfaces of the wurtzite phase and environment-dependent anisotropic chemical etching of certain crystal surfaces in the branching mechanism of nanobelts has been observed. Understanding of structural and chemical transformations of materials via in situ microscopy techniques and their role in designingmore » new nanostructured materials is discussed.« less

Visualization of Hyperconjugation and Subsequent Structural Distortions through 3D Printing of Crystal Structures.

PubMed

Mithila, Farha J; Oyola-Reynoso, Stephanie; Thuo, Martin M; Atkinson, Manza Bj

2016-01-01

Structural distortions due to hyperconjugation in organic molecules, like norbornenes, are well captured through X-ray crystallographic data, but are sometimes difficult to visualize especially for those applying chemical knowledge and are not chemists. Crystal structure from the Cambridge database were downloaded and converted to .stl format. The structures were then printed at the desired scale using a 3D printer. Replicas of the crystal structures were accurately reproduced in scale and any resulting distortions were clearly visible from the macroscale models. Through space interactions or effect of through space hyperconjugation was illustrated through loss of symmetry or distortions thereof. The norbornene structures exhibits distortion that cannot be observed through conventional ball and stick modelling kits. We show that 3D printed models derived from crystallographic data capture even subtle distortions in molecules. We translate such crystallographic data into scaled-up models through 3D printing.

Reliability Studies of Ceramic Capacitors.

DTIC Science & Technology

1983-07-01

increases. This case has been found to be a good approximation for single crystals with high chemical and structural purity. Shallow traps may arise as a...theory, this sudden increase may be otherwise explained. Single crystals of ZnS have been found to exhibit this vertical increase in the current...Smith and Rose observed SCLC behavior in CdS single crystals . Branwood and Tredgold 2 8 and Branwood et al. 2 9 measured BaTiO 3 single crystals and

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gentles, Robert G.; Sheriff, Steven; Beno, Brett R.

Structure based rationales for the activities of potent N-benzyl-4-heteroaryl-1-(phenylsulfonyl)piperazine-2-carboxamide inhibitors of the hepatitis C viral polymerase are described herein. These compounds bind to the hepatitis C virus non-structural protein 5B (NS5B), and co-crystal structures of select examples from this series with NS5B are reported. Comparison of co-crystal structures of a potent analog with both NS5B genotype 1a and genotype 1b provides a possible explanation for the genotype-selectivity observed with this compound class and suggests opportunities for the further optimization of the series.

Crystal Structure of Allophycocyanin from Marine Cyanobacterium Phormidium sp. A09DM

PubMed Central

Gupta, Gagan Deep; Madamwar, Datta

2015-01-01

Isolated phycobilisome (PBS) sub-assemblies have been widely subjected to X-ray crystallography analysis to obtain greater insights into the structure-function relationship of this light harvesting complex. Allophycocyanin (APC) is the phycobiliprotein always found in the PBS core complex. Phycocyanobilin (PCB) chromophores, covalently bound to conserved Cys residues of α- and β- subunits of APC, are responsible for solar energy absorption from phycocyanin and for transfer to photosynthetic apparatus. In the known APC structures, heterodimers of α- and β- subunits (known as αβ monomers) assemble as trimer or hexamer. We here for the first time report the crystal structure of APC isolated from a marine cyanobacterium (Phormidium sp. A09DM). The crystal structure has been refined against all the observed data to the resolution of 2.51 Å to Rwork (Rfree) of 0.158 (0.229) with good stereochemistry of the atomic model. The Phormidium protein exists as a trimer of αβ monomers in solution and in crystal lattice. The overall tertiary structures of α- and β- subunits, and trimeric quaternary fold of the Phormidium protein resemble the other known APC structures. Also, configuration and conformation of the two covalently bound PCB chromophores in the marine APC are same as those observed in fresh water cyanobacteria and marine red algae. More hydrophobic residues, however, constitute the environment of the chromophore bound to α-subunit of the Phormidium protein, owing mainly to amino acid substitutions in the marine protein. PMID:25923120

Crystal structure and luminescence properties of silver in AgM(PO{sub 3}){sub 3} (M = Mg, Zn, Ba) polyphosphates

DOE Office of Scientific and Technical Information (OSTI.GOV)

Belharouak, I.; Parent, C.; Tanguy, B.

1999-06-01

The relationships between the crystal structures and the luminescent properties of the AgM(PO{sub 3}){sub 3} (M = Mg, Zn, Ba) polyphosphates are reported in comparison with those of AgPO{sub 3}. The structure of the magnesium and zinc phosphates is characterized by long polyphosphates chains connected to infinite chains of [AgO{sub 6}] and [MO{sub 6}] polyhedra sharing faces. The basic structural phosphate unit in AgBa(PO{sub 3}){sub 3} is a P{sub 3}O{sub 9} ring. Silver atoms are located in distorted octahedral sites. Two types of luminescent centers have been observed. The UV emission observed in all these materials is typical of isolatedmore » Ag{sup +} ions. The visible emission observed only in the zinc phosphate is probably the result of a silver-zinc association. 16 refs., 8 figs., 3 tabs.« less

Low carrier semiconductor like behavior in Lu3Ir4Ge13 single crystal

NASA Astrophysics Data System (ADS)

Kumar, Anil; Matteppanavar, Shidaling; Thamizhavel, A.; Ramakrishnan, S.

2018-04-01

Single crystal of Lu3Ir4Ge13 crystallizing in the Yb3Rh4Sn13-type cubic crystal structure has been grown by Czochralski method in a tetra-arc furnace. In this paper we report on the crystal structure, magnetic and transport properties of Lu3Ir4Ge13. The analysis of the powder x-ray diffraction (XRD) studies revealed that Lu3Ir4Ge13 crystallizes in a cubic structure with the space group Pm-3n, no. 223. The lattice parameter was obtained from the Rietveld refinement of the room temperature XRD data which amounts to 8.904 (3) Å with low R factors. The temperature dependence of the resistivity exhibited semiconductor like behavior till 1.8 K, with a broad hump around 15 - 62 K. This hump was observed in both warming and cooling cycle with a very small hysteresis, it may be due to the existence of structural transition from high - low symmetry. The temperature dependent magnetization data shows the diamagnetic behavior with an anomaly around 70 K, which is well supported by the derivative of resistivity data.

Structural studies of bean pod mottle virus, capsid, and RNA in crystal and solution states by laser Raman spectroscopy

DOE Office of Scientific and Technical Information (OSTI.GOV)

Li, Tiansheng; Thomas, G.J. Jr.; Chen, Zhongguo

Structures of protein and RNA components of bean pod mottle virus (BPMV) have been investigated by use of laser Raman spectroscopy. Raman spectra were collected from both aqueous solutions and single crystals of BPMV capsids (top component) and virions (middle and bottom components, which package, respectively, small and large RNA molecules). Analysis of the data permits the assignment of conformation-sensitive Raman bands to viral protein and RNA constituents and observation of structural similarities and differences between solution and crystalline states of BPMV components. The Raman results show that the protein subunits of the empty capsid contain between 45% and 55%more » {beta}-strand and {beta}-turn secondary structure, in agreement with the recently determined X-ray crystal structure, and that this total {beta}-strand content undergoes a small increase with packaging of RNA. A comparison of Raman spectra of crystal and solution states of the BPMV middle component reveals only minor structural differences between the two, and these are restricted almost exclusively to Raman bands of RNA in the region of assigned phosphodiester conformation markers. Although in both the crystal and solution only C3{prime} endo/anti nucleosides are detected, the crystal exhibits a weaker 813-cm{sup {minus}1} band and strong 870-cm{sup {minus}1} band, which suggests that {approximately}8% of the nucleotides have O-P-O torsions configured differently in the crystal from that in the solution.« less

Crystallinity of tellurium capping and epitaxy of ferromagnetic topological insulator films on SrTiO 3

DOE Office of Scientific and Technical Information (OSTI.GOV)

Park, Jihwey; Soh, Yeong-Ah; Aeppli, Gabriel

2015-06-30

Thin films of topological insulators are often capped with an insulating layer since topological insulators are known to be fragile to degradation. However, capping can hinder the observation of novel transport properties of the surface states. To understand the influence of capping on the surface states, it is crucial to understand the crystal structure and the atomic arrangement at the interfaces. Here, we use x-ray diffraction to establish the crystal structure of magnetic topological insulator Cr-doped (Bi,Sb) 2Te 3 (CBST) films grown on SrTiO 3 (1 1 1) substrates with and without a Te capping layer. We find that bothmore » the film and capping layer are single crystal and that the crystal quality of the film is independent of the presence of the capping layer, but that x-rays cause sublimation of the CBST film, which is prevented by the capping layer. Our findings show that the different transport properties of capped films cannot be attributed to a lower crystal quality but to a more subtle effect such as a different electronic structure at the interface with the capping layer. Our results on the crystal structure and atomic arrangements of the topological heterostructure will enable modelling the electronic structure and design of topological heterostructures.« less

Center for Macromolecular Crystallography, University of Alabama in Birmingham

NASA Technical Reports Server (NTRS)

Navia, Manuel A.

1991-01-01

Porcine pancreatic elastase (PPE) crystals grown under microgravity conditions on mission STS-26 of the Space Shuttle Discovery were shown to diffract to considerably higher resolution than the best PPE crystals grown by us on the ground. We have now independently refined both the microgravity and ground-based data. Preliminary results of these refinements are summarized. These results show nearly a doubling of experimental diffraction data for this structure, exceeding 1.3 A resolution. Improved phase information derived from the refined structure of PPE based on this microgravity data has allowed us to interpret previously-uninterpretable electron density obtained from ground-based crystals of a complex of PPE with a chemically-reactive inhibitor. Intermediate stages in the enzyme-inhibitor reaction mechanism in the crystal can now be directly observed. Further refinement of PPE structures is in progress.

EPR study of free radical in gamma-irradiated bis(cyclopentadienyl)zirconium dichloride single crystal

NASA Astrophysics Data System (ADS)

Caliskan, Betul; Caliskan, Ali Cengiz

2017-06-01

Bis(cyclopentadienyl)zirconium dichloride (BCZD; zirconocene dichloride) single crystals were exposed to 60Co-γ irradiation at room temperature. The irradiated single crystals were investigated between 125 and 470 K by electron paramagnetic resonance spectroscopy. The spectra of the crystals were found to be temperature independent. The paramagnetic center was attributed to the cyclopentadienyl radical. The g values of the radiation damage center observed in BCZD single crystal and the hyperfine structure constants of the free electron with nearby protons were obtained.

Size-Dependent Grain-Boundary Structure with Improved Conductive and Mechanical Stabilities in Sub-10-nm Gold Crystals

NASA Astrophysics Data System (ADS)

Wang, Chunyang; Du, Kui; Song, Kepeng; Ye, Xinglong; Qi, Lu; He, Suyun; Tang, Daiming; Lu, Ning; Jin, Haijun; Li, Feng; Ye, Hengqiang

2018-05-01

Low-angle grain boundaries generally exist in the form of dislocation arrays, while high-angle grain boundaries (misorientation angle >15 ° ) exist in the form of structural units in bulk metals. Here, through in situ atomic resolution aberration corrected electron microscopy observations, we report size-dependent grain-boundary structures improving both stabilities of electrical conductivity and mechanical properties in sub-10-nm-sized gold crystals. With the diameter of a nanocrystal decreasing below 10 nm, the high-angle grain boundary in the crystal exists as an array of dislocations. This size effect may be of importance to a new generation of interconnects applications.

A Novel Coupled Resonator Photonic Crystal Design in Lithium Niobate for Electrooptic Applications

DOE PAGES

Ozturk, Birol; Yavuzcetin, Ozgur; Sridhar, Srinivas

2015-01-01

High-aspect-ratio photonic crystal air-hole fabrication on bulk Lithium Niobate (LN) substrates is extremely difficult due to its inherent resistance to etching, resulting in conical structures and high insertion losses. Here, we propose a novel coupled resonator photonic crystal (CRPC) design, combining a coupled resonator approach with that of Bragg gratings. CRPC design parameters were optimized by analytical calculations and FDTD simulations. CRPC structures with optimized parameters were fabricated and electrooptically tested on bulk LN annealed proton exchange waveguides. Low insertion loss and large electrooptic effect were observed with the fabricated devices, making the CRPC design a promising structure for electroopticmore » device applications.« less

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ma, Xiang; Zhang, Shuai; Jiao, Fang

Two-step nucleation pathways in which disordered, amorphous, or dense liquid states precede appearance of crystalline phases have been reported for a wide range of materials, but the dynamics of such pathways are poorly understood. Moreover, whether these pathways are general features of crystallizing systems or a consequence of system-specific structural details that select for direct vs two-step processes is unknown. Using atomic force microscopy to directly observe crystallization of sequence-defined polymers, we show that crystallization pathways are indeed sequence dependent. When a short hydrophobic region is added to a sequence that directly forms crystalline particles, crystallization instead follows a two-stepmore » pathway that begins with creation of disordered clusters of 10-20 molecules and is characterized by highly non-linear crystallization kinetics in which clusters transform into ordered structures that then enter the growth phase. The results shed new light on non-classical crystallization mechanisms and have implications for design of self-assembling polymer systems.« less

Chiral Asymmetric Structures in Aspartic Acid and Valine Crystals Assessed by Atomic Force Microscopy.

PubMed

Teschke, Omar; Soares, David Mendez

2016-03-29

Structures of crystallized deposits formed by the molecular self-assembly of aspartic acid and valine on silicon substrates were imaged by atomic force microscopy. Images of d- and l-aspartic acid crystal surfaces showing extended molecularly flat sheets or regions separated by single molecule thick steps are presented. Distinct orientation surfaces were imaged, which, combined with the single molecule step size, defines the geometry of the crystal. However, single molecule step growth also reveals the crystal chirality, i.e., growth orientations. The imaged ordered lattice of aspartic acid (asp) and valine (val) mostly revealed periodicities corresponding to bulk terminations, but a previously unreported molecular hexagonal lattice configuration was observed for both l-asp and l-val but not for d-asp or d-val. Atomic force microscopy can then be used to identify the different chiral forms of aspartic acid and valine crystals.

Flow induced/ refined solution crystallization of a semiconducting polymer

NASA Astrophysics Data System (ADS)

Nguyen, Ngoc A.

Organic photovoltaics, a new generation of solar cells, has gained scientific and economic interests due to the ability of solution-processing and potentially low-cost power production. Though, the low power conversion efficiency of organic/ plastic solar cells is one of the most pertinent challenges that has appealed to research communities from many different fields including materials science and engineering, electrical engineering, chemical engineering, physics and chemistry. This thesis focuses on investigating and controlling the morphology of a semi-conducting, semi-crystalline polymer formed under shear-flow. Molecular structures and processing techniques are critical factors that significantly affect the morphology formation in the plastic solar cells, thus influencing device performance. In this study, flow-induced solution crystallization of poly (3-hexylthiophene) (P3HT) in a poor solvent, 2-ethylnapthalene (2-EN) was utilized to make a paint-like, structural liquid. The polymer crystals observed in this structured paint are micrometers long, nanometers in cross section and have a structure similar to that formed under quiescent conditions. There is pi-pi stacking order along the fibril axis, while polymer chain folding occurs along the fibril width and the order of the side-chain stacking is along fibril height. It was revealed that shear-flow not only induces P3HT crystallization from solution, but also refines and perfects the P3HT crystals. Thus, a general strategy to refine the semiconducting polymer crystals from solution under shear-flow has been developed and employed by simply tuning the processing (shearing) conditions with respect to the dissolution temperature of P3HT in 2-EN. The experimental results demonstrated that shear removes defects and allows more perfect crystals to be formed. There is no glass transition temperature observed in the crystals formed using the flow-induced crystallization indicating a significantly different morphology formation in comparison to that of the pristine (as-received) P3HT. As a result, single P3HT crystals with high surface energy chain folds were analyzed and determined. Previous reported results of infinite melting enthalpy of extended chain P3HT crystals are much higher than the result discovered in this study. The findings in this study revealed that the infinite melting enthalpy of chain-folded P3HT crystals is considerably decreased due to the presence of this P3HT chain-folded surface energy. In this study, the kinetics and mechanism of P3HT crystallization under shear-flow was thoroughly investigated as well. A homogeneous nucleation of P3HT was observed that allows one dimensional fibril crystal growth. The micrometer long P3HT crystals are formed and limited by the contact time between the P3HT molecules. Furthermore, it was found that phenyl-C61-butyric acid methyl ester (PCBM) nanoparticles inhibit the crystallization of P3HT under shear. However, the shear-flow leads to nanophase agglomeration of PCBM and creates percolation of P3HT fibril crystal networks and the PCBM phase separated domains that apparently present better pathways for transporting electrons and holes. Interestingly, the structured liquid was simply applied onto substrates with a paintbrush resulting in similar device performance to those made with current techniques in which the morphology is commonly formed during application or post-processing steps. These detailed findings are given and discussed in the thesis.

Observation of a commensurate array of flux chains in tilted flux lattices in Bi-Sr-Ca-Cu-O single crystals

NASA Astrophysics Data System (ADS)

Bolle, C. A.; Gammel, P. L.; Grier, D. G.; Murray, C. A.; Bishop, D. J.; Mitzi, D. B.; Kapitulnik, A.

1991-01-01

We report the observation of a novel flux-lattice structure, a commensurate array of flux-line chains. Our experiments consist of the magnetic decoration of the flux lattices in single crystals of Ba-Sr-Ca-Cu-O where the magnetic field is applied at an angle with respect to the conducting planes. For a narrow range of angles, the equilibrium structure is one with uniformly spaced chains with a higher line density of vortices than the background lattice. Our observations are in qualitative agreement with theories which suggest that, in strongly anisotropic materials the vortices develop an attractive interaction in tilted magnetic fields.

The magnetic and crystal structures of Sr2IrO4: A neutron diffraction study

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ye, Feng; Chi, Songxue; Chakoumakos, Bryan C

2013-01-01

We report a single-crystal neutron diffraction study of the layered Sr2IrO4. This work unambigu- ously determines the magnetic and crystal structures, and reveals that the spin orientation rigidly tracks the staggered rotation of the IrO6 octahedra in Sr2IrO4. The long-range antiferromagnetic order has a canted spin configuration with an ordered moment of 0.208(3) B/Ir site within the basal plane; a detailed examination of the spin canting yields 0.202(3) and 0.049(2) B/site for the a-axis and the b-axis, respectively. It is intriguing that forbidden nuclear reflections of space group I41/acd are also observed in a wide temperature range from 4 Kmore » to 600 K, which suggests a reduced crystal structure symmetry. This neutron scattering work provides a direct, well-refined experimen- tal characterization of the magnetic and crystal structures that are crucial to the understanding of the unconventional magnetism existent in this unusual magnetic insulator.« less

Spatial frequency maps of power flow in metamaterials and photonic crystals: Investigating backward-wave modes across the electromagnetic spectrum

NASA Astrophysics Data System (ADS)

Aghanejad, Iman; Markley, Loïc

2017-11-01

We present spatial frequency maps of power flow in metamaterials and photonic crystals in order to provide insights into their electromagnetic responses and further our understanding of backward power in periodic structures. Since 2001, many different structures across the electromagnetic spectrum have been presented in the literature as exhibiting an isotropic negative effective index. Although these structures all exhibit circular or spherical equifrequency contours that resemble those of left-handed media, here we show through k -space diagrams that the distribution of power in the spatial frequency domain can vary considerably across these structures. In particular, we show that backward power arises from high-order right-handed harmonics in photonic crystals, magnetodielectric crystals, and across the layers of coupled-plasmonic-waveguide metamaterials, while arising from left-handed harmonic pairs in split-ring resonator and wire composites, plasmonic crystals, and along the layers of coupled-plasmonic-waveguide metamaterials. We also show that the fishnet structure exhibits the same left-handed harmonic pairs as the latter group. These observations allow us to categorize different metamaterials according to their spatial spectral source of backward power and identify the mechanism behind negative refraction at a given interface. Finally, we discuss how k -space maps of power flow can be used to explain the high or low transmittance of power into different metamaterial or photonic crystal structures.

Transmission electron microscopy study of the MgS–Tm{sub 2}S{sub 3} system

DOE Office of Scientific and Technical Information (OSTI.GOV)

Varadé-López, R., E-mail: rebeca.varade@ucm.es; Ávila-Brande, D., E-mail: davilabr@ucm.es; Urones-Garrote, E., E-mail: esteban.urones@pdi.ucm.es

2015-09-15

This work presents the structural–microstructural characterization of the NaCl-derivative MgS–Tm{sub 2}S{sub 3} system, which can be formulated by the expression Mg{sub (1−x)}Tm{sub (2/3)x}□{sub (1/3)x}S (□→cation vacancy). Transmission electron microscopy observations show the transition between NaCl-type and spinel-type structures when 0 ≤x≤ 0.75. The increase of Tm content in the solid solution provokes the increase of the spinel-type phase proportion, which intergrows with the NaCl-type crystals. When x≥0.75, some phases derived from NaCl-type structure through the chemical twinning at the unit cell level crystallographic operation are observed, such as CT-MgTm{sub 2}S{sub 4} and CT-MgTm{sub 4}S{sub 7}. The existence and nature ofmore » the extended defects observed along the c direction of these structures are characterized by means of Scanning-Transmission electron microscopy high-angle dark field imaging, which allows observing the presence of quasi ordered crystals with new possible complex stoichiometries at atomic resolution. - Graphical abstract: HAADF-STEM image of a disordered CT-MgYb{sub 2}S{sub 4} crystal. The disordered twin-slab sequences are marked by arrows. - Highlights: • Structural evolution of the Mg{sub (1−x)}Tm{sub (2/3)x}□{sub (1/3)x}S system was characterized by means of TEM. • The increase in Tm content provokes the transition from NaCl to spinel-type structure up to x=0.75. • Chemical twinned phases CT-MgTm{sub 2}S{sub 4} and CT-MgTm{sub 4}S{sub 7} are observed at high Tm contents. • Extended defects in CT-crystals are characterized with atomic resolution STEM-HAADF images.« less

Synthesis, growth, crystal structure, optical and third order nonlinear optical properties of quinolinium derivative single crystal: PNQI

NASA Astrophysics Data System (ADS)

Karthigha, S.; Krishnamoorthi, C.

2018-03-01

An organic quinolinium derivative nonlinear optical (NLO) crystal, 1-ethyl-2-[2-(4-nitro-phenyl)-vinyl]-quinolinium iodide (PNQI) was synthesized and successfully grown by slow evaporation solution growth technique. Formation of a crystalline compound was confirmed by single crystal X-ray diffraction. The quinolinium compound PNQI crystallizes in the triclinic crystal system with a centrosymmetric space group of P-1 symmetry. The molecular structure of PNQI was confirmed by 1H NMR and 13C NMR spectral studies. The thermal properties of the crystal have been investigated by thermogravimetric (TG) and differential scanning calorimetry (DSC) studies. The optical characteristics obtained from UV-Vis-NIR spectral data were described and the cut-off wavelength observed at 506 nm. The etching study was performed to analyse the growth features of PNQI single crystal. The third order NLO properties such as nonlinear refractive index (n2), nonlinear absorption coefficient (β) and nonlinear susceptibility (χ (3)) of the crystal were investigated using Z-scan technique at 632.8 nm of Hesbnd Ne laser.

Homogenous Nucleation and Crystal Growth in a Model Liquid from Direct Energy Landscape Sampling Simulation

NASA Astrophysics Data System (ADS)

Walter, Nathan; Zhang, Yang

Nucleation and crystal growth are understood to be activated processes involving the crossing of free-energy barriers. Attempts to capture the entire crystallization process over long timescales with molecular dynamic simulations have met major obstacles because of molecular dynamics' temporal constraints. Herein, we circumvent this temporal limitation by using a brutal-force, metadynamics-like, adaptive basin-climbing algorithm and directly sample the free-energy landscape of a model liquid Argon. The algorithm biases the system to evolve from an amorphous liquid like structure towards an FCC crystal through inherent structure, and then traces back the energy barriers. Consequently, the sampled timescale is macroscopically long. We observe that the formation of a crystal involves two processes, each with a unique temperature-dependent energy barrier. One barrier corresponds to the crystal nucleus formation; the other barrier corresponds to the crystal growth. We find the two processes dominate in different temperature regimes. Compared to other computation techniques, our method requires no assumptions about the shape or chemical potential of the critical crystal nucleus. The success of this method is encouraging for studying the crystallization of more complex

Time crystals: a review

NASA Astrophysics Data System (ADS)

Sacha, Krzysztof; Zakrzewski, Jakub

2018-01-01

Time crystals are time-periodic self-organized structures postulated by Frank Wilczek in 2012. While the original concept was strongly criticized, it stimulated at the same time an intensive research leading to propositions and experimental verifications of discrete (or Floquet) time crystals—the structures that appear in the time domain due to spontaneous breaking of discrete time translation symmetry. The struggle to observe discrete time crystals is reviewed here together with propositions that generalize this concept introducing condensed matter like physics in the time domain. We shall also revisit the original Wilczek’s idea and review strategies aimed at spontaneous breaking of continuous time translation symmetry.

Crystal growth, structural, optical, dielectric and thermal studies of an amino acid based organic NLO material: L-phenylalanine L-phenylalaninium malonate.

PubMed

Prakash, M; Geetha, D; Caroline, M Lydia; Ramesh, P S

2011-12-01

Good transparent single crystals of L-phenylalanine L-phenylalaninium malonate (LPPMA) have been grown successfully by slow evaporation technique from aqueous solution. Single crystal X-ray diffractometer was utilized to measure unit cell parameter and to confirm the crystal structure. The chemical structure of compound was established by FT-NMR technique. The vibrational modes of the molecules of elucidated from FTIR spectra. Its optical behaviour has been examined by UV-vis spectral analysis, which shows the absence of absorbance in the visible region. Thermal properties of the LPPMA crystal were carried out by thermo gravimetric analysis (TGA) and differential thermal analysis (DTA) techniques, which indicate that the material does not decompose before melting. The melting point of grown crystal was observed as 180°C by melting point apparatus. The NLO property was confirmed by the powder technique of Kurtz and Perry. The dielectric behaviour of the sample was also studied for the first time. Copyright © 2011 Elsevier B.V. All rights reserved.

Structural transformation of crystallized debranched cassava starch during dual hydrothermal treatment in relation to enzyme digestibility.

PubMed

Boonna, Sureeporn; Tongta, Sunanta

2018-07-01

Structural transformation of crystallized debranched cassava starch prepared by temperature cycling (TC) treatment and then subjected to annealing (ANN), heat-moisture treatment (HMT) and dual hydrothermal treatments of ANN and HMT was investigated. The relative crystallinity, lateral crystal size, melting temperature and resistant starch (RS) content increased for all hydrothermally treated samples, but the slowly digestible starch (SDS) content decreased. The RS content followed the order: HMT → ANN > HMT > ANN → HMT > ANN > TC, respectively. The HMT → ANN sample showed a larger lateral crystal size with more homogeneity, whereas the ANN → HMT sample had a smaller lateral crystal size with a higher melting temperature. After cooking at 50% moisture, the increased RS content of samples was observed, particularly for the ANN → HMT sample. These results suggest that structural changes of crystallized debranched starch during hydrothermal treatments depend on initial crystalline characteristics and treatment sequences, influencing thermal stability, enzyme digestibility, and cooking stability. Copyright © 2018 Elsevier Ltd. All rights reserved.

Vibrational and structural investigation of SOUL protein single crystals by using micro-Raman spectroscopy

NASA Astrophysics Data System (ADS)

Rossi, Barbara; Giarola, Marco; Mariotto, Gino; Ambrosi, Emmanuele; Monaco, Hugo L.

2010-05-01

Protein SOUL is a new member of the recently discovered putative heme-binding protein family called SOUL/HEBP and, to date, no structural information exists for this protein. Here, micro-Raman spectroscopy is used to study the vibrational properties of single crystals obtained from recombinant protein SOUL by means of two different optimization routes. This spectroscopic approach offers the valuable advantage of the in-situ collection of experimental data from protein crystals, placed onto a hanging-drop plate, under the same conditions used to grow the crystals. By focusing on the regions of amides I and III bands, some secondary structure characteristic features have been recognized. Moreover, some side-chain marker bands were observed in the Raman spectra of SOUL crystals and the unambiguous assignment of these peaks inferred by comparing the experimental Raman spectra of pure amino acids and their Raman intensities computed using quantum chemical calculations. Our comparative analysis allows to get a deeper understanding of the side-chain environments and of the interactions involving these specific amino acids in the two different SOUL crystals.

On beam shaping of the field radiated by a line source coupled to finite or infinite photonic crystals.

PubMed

Ceccuzzi, Silvio; Jandieri, Vakhtang; Baccarelli, Paolo; Ponti, Cristina; Schettini, Giuseppe

2016-04-01

Comparison of the beam-shaping effect of a field radiated by a line source, when an ideal infinite structure constituted by two photonic crystals and an actual finite one are considered, has been carried out by means of two different methods. The lattice sums technique combined with the generalized reflection matrix method is used to rigorously investigate the radiation from the infinite photonic crystals, whereas radiation from crystals composed of a finite number of rods along the layers is analyzed using the cylindrical-wave approach. A directive radiation is observed with the line source embedded in the structure. With an increased separation distance between the crystals, a significant edge diffraction appears that provides the main radiation mechanism in the finite layout. Suitable absorbers are implemented to reduce the above-mentioned diffraction and the reflections at the boundaries, thus obtaining good agreement between radiation patterns of a localized line source coupled to finite and infinite photonic crystals, when the number of periods of the finite structure is properly chosen.

A new crystal form of a hyperthermophilic endocellulase

PubMed Central

Kataoka, Misumi; Ishikawa, Kazuhiko

2014-01-01

The hyperthermophilic glycoside hydrolase family endocellulase 12 from the archaeon Pyrococcus furiosus (EGPf; Gene ID PF0854; EC 3.2.1.4) catalyzes the hydrolytic cleavage of the β-1,4-glucosidic linkage in β-glucan in lignocellulose biomass. A crystal of EGPf was previously prepared at pH 9.0 and its structure was determined at an atomic resolution of 1.07 Å. This article reports the crystallization of EGPf at the more physiologically relevant pH of 5.5. Structure determination showed that this new crystal form has the symmetry of space group C2. Two molecules of the enzyme are observed in the asymmetric unit. Crystal packing is weak at pH 5.5 owing to two flexible interfaces between symmetry-related molecules. Comparison of the EGPf structures obtained at pH 9.0 and pH 5.5 reveals a significant conformational difference at the active centre and in the surface loops. The interfaces in the vicinity of the flexible surface loops impact the quality of the EGPf crystal. PMID:25005081

Mass Spectrometry Imaging of Drug Related Crystal-Like Structures in Formalin-Fixed Frozen and Paraffin-Embedded Rabbit Kidney Tissue Sections

NASA Astrophysics Data System (ADS)

Bruinen, Anne L.; van Oevelen, Cateau; Eijkel, Gert B.; Van Heerden, Marjolein; Cuyckens, Filip; Heeren, Ron M. A.

2016-01-01

A multimodal mass spectrometry imaging (MSI) based approach was used to characterize the molecular content of crystal-like structures in a frozen and paraffin embedded piece of a formalin-fixed rabbit kidney. Matrix assisted laser desorption/ionization time-of-flight (MALDI-TOF) imaging and desorption electrospray ionization (DESI) mass spectrometry imaging were combined to analyze the frozen and paraffin embedded sample without further preparation steps to remove the paraffin. The investigated rabbit kidney was part of a study on a drug compound in development, in which severe renal toxicity was observed in dosed rabbits. Histological examination of the kidney showed tubular degeneration with precipitation of crystal-like structures in the cortex, which were assumed to cause the renal toxicity. The MS imaging approach was used to find out whether the crystal-like structures were composed of the drug compound, metabolites, or an endogenous compound as a reaction to the drug administration. The generated MALDI-MSI data were analyzed using principal component analysis. In combination with the MS/MS results, this way of data processing demonstrates that the crystal structures were mainly composed of metabolites and relatively little parent drug.

Reversible structure manipulation by tuning carrier concentration in metastable Cu 2S

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tao, Jing; Chen, Jingyi; Li, Jun

Harnessing a material’s functionality in applications and for fundamental studies often requires direct manipulation of its crystal symmetry. Here, we manipulate the crystal structure of Cu 2S nanoparticles in a controlled and reversible fashion via variation of the electron dose rate, observed by transmission electron microscopy. Our control method is in contrast to conventional chemical doping, which is irreversible and often introduces unwanted lattice distortions. Our study sheds light on the much-debated question of whether a change in electronic structure can facilitate a change of crystal symmetry, or whether vice versa is always the case. Finally, we show that amore » minimal perturbation to the electronic degree of freedom can drive the structural phase transition in Cu 2S, hence resolving this dilemma.« less

The crystal and magnetic structures of Sr 2LaFe 3O 8

NASA Astrophysics Data System (ADS)

Battle, P. D.; Gibb, T. C.; Lightfoot, P.

1990-02-01

The crystal and magnetic structures of the anion-deficient perovskite Sr 2LaFe 3O 8 (space group Pmma, a = 5.5095(1), b = 11.8845(5), c = 5.6028(1)AÅ) have been refined from X-ray and neutron powder diffraction data collected at room temperature. The crystal structure consists of layers of octahedral (O) and tetrahedral (T) iron-oxygen polyhedra arranged in the stacking sequence … OOTOOT … perpendicular to theyˆaxis of the unit cell. The magnetic structure is that of a G-type antiferromagnet with ordered magnetic moments of 3.77(5) and 3.15(11) μ B at the octahedral and tetrahedral sites, respectively. The low moment at the tetrahedral site is consistent with the observed disorder and magnetic anisotropy.

Reversible structure manipulation by tuning carrier concentration in metastable Cu 2S

DOE PAGES

Tao, Jing; Chen, Jingyi; Li, Jun; ...

2017-08-30

Harnessing a material’s functionality in applications and for fundamental studies often requires direct manipulation of its crystal symmetry. Here, we manipulate the crystal structure of Cu 2S nanoparticles in a controlled and reversible fashion via variation of the electron dose rate, observed by transmission electron microscopy. Our control method is in contrast to conventional chemical doping, which is irreversible and often introduces unwanted lattice distortions. Our study sheds light on the much-debated question of whether a change in electronic structure can facilitate a change of crystal symmetry, or whether vice versa is always the case. Finally, we show that amore » minimal perturbation to the electronic degree of freedom can drive the structural phase transition in Cu 2S, hence resolving this dilemma.« less

Note: Rigid holder to host and bend a crystal for multiple volume reflection of a particle beam

DOE Office of Scientific and Technical Information (OSTI.GOV)

Carassiti, V.; Melchiorri, M.; Dalpiaz, P.

2010-06-15

A holder to lodge and bend a silicon crystal to excite multivolume reflection of a high-energy particle beam has been designed and fabricated. A mechanically robust and stable structure fastens a crystal at best condition for experiments. The holder has allowed the observation of 12-time repeated volume reflection with very high efficiency. We detail the most important features behind the construction of the holder together with the characterization of the crystal being bent by the holder.

Coexistence of twisted and untwisted crystals: An impurity/structural order model with implications for agate patterns

USGS Publications Warehouse

Comer, J.; Ortoleva, P.

2007-01-01

Coexistence of twisted and untwisted crystals is explained via a model that accounts for the coupling of the entropic and energetic effects of impurities and a supra-lattice-scale structural order parameter. It is shown that twisted impure crystals can be in equilibrium with untwisted purer ones. The model explains how coexistence can occur in agates and other systems under hydrostatic stress. The model implies that untwisted crystals grown under one set of conditions could undergo a phase separation that, when accompanied by an imposed compositional gradient, leads to commonly observed, alternating bands of twisted and untwisted crystals and, when occurring in the absence of an external gradient, mossy patterns of crystal texture can emerge. This phenomenon is not related to anisotropic applied stress. Rather coexistence is a consequence of a compositional segregation/twist phase transition. Since twist coexistence is a compositional equilibrium, it arises from the exchange between bulk phases; hence, the detailed nature of the atomic structure within an interface between twisted and untwisted zones is not relevant. The approach places crystal-twist phenomena within the theory of order/disorder phase transitions.

Disappearing Enantiomorphs: Single Handedness in Racemate Crystals.

PubMed

Parschau, Manfred; Ernst, Karl-Heinz

2015-11-23

Although crystallization is the most important method for the separation of enantiomers of chiral molecules in the chemical industry, the chiral recognition involved in this process is poorly understood at the molecular level. We report on the initial steps in the formation of layered racemate crystals from a racemic mixture, as observed by STM at submolecular resolution. Grown on a copper single-crystal surface, the chiral hydrocarbon heptahelicene formed chiral racemic lattice structures within the first layer. In the second layer, enantiomerically pure domains were observed, underneath which the first layer contained exclusively the other enantiomer. Hence, the system changed from a 2D racemate into a 3D racemate with enantiomerically pure layers after exceeding monolayer-saturation coverage. A chiral bias in form of a small enantiomeric excess suppressed the crystallization of one double-layer enantiomorph so that the pure minor enantiomer crystallized only in the second layer. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Structure, dynamics and bifurcations of discrete solitons in trapped ion crystals

NASA Astrophysics Data System (ADS)

Landa, H.; Reznik, B.; Brox, J.; Mielenz, M.; Schaetz, T.

2013-09-01

We study discrete solitons (kinks) accessible in the state-of-the-art trapped ion experiments, considering zigzag crystals and quasi-three-dimensional configurations, both theoretically and experimentally. We first extend the theoretical understanding of different phenomena predicted and recently experimentally observed in the structure and dynamics of these topological excitations. Employing tools from topological degree theory, we analyze bifurcations of crystal configurations in dependence on the trapping parameters, and investigate the formation of kink configurations and the transformations of kinks between different structures. This allows us to accurately define and calculate the effective potential experienced by solitons within the Wigner crystal, and study how this (so-called Peierls-Nabarro) potential gets modified to a non-periodic globally trapping potential in certain parameter regimes. The kinks' rest mass (energy) and spectrum of modes are computed and the dynamics of linear and nonlinear kink oscillations are analyzed. We also present novel, experimentally observed, configurations of kinks incorporating a large-mass defect realized by an embedded molecular ion, and of pairs of interacting kinks stable for long times, offering the perspective for exploring and exploiting complex collective nonlinear excitations, controllable on the quantum level.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zheligovskaya, E. A., E-mail: lmm@phyche.ac.ru

Structural mechanisms are proposed for experimentally observed phase transitions between crystalline modifications of aqueous ice, Ih and II, as well as II and Ic. It is known that the Ih–II transition occurs with the conservation of large structural units (hexagonal channels) common for these ices. It is shown that the Ih → II transition may occur with the conservation of 5/6 of all hydrogen bonds in crystal, including all hydrogen bonds in the retained channels (3/4 of the total number of bonds in crystal) and 1/3 of the bonds between these channels (1/12 of the total number). The transformation ofmore » other hydrogen bonds between the retained channels leads to the occurrence of proton order in ice II. A structural mechanism is proposed to explain the transformation of single crystals of ice Ih either into single crystals of ice II or into crystalline twins of ice II with c axes rotated by 180° with respect to each other, which is often observed at the Ih → II transition. It is established that up to 7/12 of all hydrogen bonds are retained at the irreversible cooperative II → Ic transition.« less

Genome Pool Strategy for Structural Coverage of Protein Families

PubMed Central

Jaroszewski, Lukasz; Slabinski, Lukasz; Wooley, John; Deacon, Ashley M.; Lesley, Scott A.; Wilson, Ian. A.; Godzik, Adam

2010-01-01

As noticed by generations of structural biologists, closely homologous proteins may have substantially different crystallization properties and propensities. These observations can be used to systematically introduce additional dimensionality into crystallization trials by targeting homologous proteins from multiple genomes in a “genome pool” strategy. Through extensive use of our recently introduced “crystallization feasibility score” (Slabinski et al., 2007a), we can explain that the genome pool strategy works well because the crystallization feasibility scores are surprisingly broad within families of homologous proteins, with most families containing a range of optimal to very difficult targets. We also show that some families can be regarded as relatively “easy”, where a significant number of proteins are predicted to have optimal crystallization features, and others are “very difficult”, where almost none are predicted to result in a crystal structure. Thus, the outcome of such variable distributions of such crystallizability' preferences leads to uneven structural coverage of known families, with “easier” or “optimal” families having several times more solved structures than “very difficult” ones. Nevertheless, this latter category can be successfully targeted by increasing the number of genomes that are used to select targets from a given family. On average, adding 10 new genomes to the “genome pool” provides more promising targets for 7 “very difficult” families. In contrast, our crystallization feasibility score does not indicate that any specific microbial genomes can be readily classified as “easier” or “very difficult” with respect to providing suitable candidates for crystallization and structure determination. Finally, our analyses show that specific physicochemical properties of the protein sequence favor successful outcomes for structure determination and, hence, the group of proteins with known 3D structures is systematically different from the general pool of known proteins. We, therefore, assess the structural consequences of these differences in protein sequence and protein biophysical properties. PMID:19000818

Structure of free radicals in irradiated acetyl-L-leucine single crystals at 77 K

DOE Office of Scientific and Technical Information (OSTI.GOV)

Almanov, G.A.; Bogdanchikov, G.A.; Usov, O.M.

1988-09-01

By using the EPR method, two types of radicals are observed, which are formed in acetyl-L-leucine single crystals irradiated at 77K. These are alkyl type radicals (CH/sub 3/)/sub 2/CCH/sub 2/CH(NHCOCH/sub 3/)COOH and peptide group radicals. When the crystals are defrozen to room temperatures, the radicals of the second type disappear without formation of paramagnetic particles. Two possible structures of the peptide group radicals were studied by the INDO method. On defreezing to room temperature, the alkyl group radical is retained, while the peptide radical disappears without formation of paramagnetic particles. For the protonated form of the anion-radical, a better agreementmore » is observed between the theoretically calculated and the experimentally obtained HFI constants. The quantum chemical analysis of the possible structures of the peptide group radicals indicates that the formation of the protonated form of the anion-radical is energetically favorable.« less

Direct observation of hierarchical nucleation of martensite and size-dependent superelasticity in shape memory alloys.

PubMed

Liu, Lifeng; Ding, Xiangdong; Li, Ju; Lookman, Turab; Sun, Jun

2014-02-21

Martensitic transformation usually creates hierarchical internal structures beyond mere change of the atomic crystal structure. Multi-stage nucleation is thus required, where nucleation (level-1) of the underlying atomic crystal lattice does not have to be immediately followed by the nucleation of higher-order superstructures (level-2 and above), such as polysynthetic laths. Using in situ transmission electron microscopy (TEM), we directly observe the nucleation of the level-2 superstructure in a Cu-Al-Ni single crystal under compression, with critical super-nuclei size L2c around 500 nm. When the sample size D decreases below L2c, the superelasticity behavior changes from a flat stress plateau to a continuously rising stress-strain curve. Such size dependence definitely would impact the application of shape memory alloys in miniaturized MEMS/NEMS devices.

The perfection and defect structure of organic hourglass inclusion K 2SO 4 crystals

NASA Astrophysics Data System (ADS)

Vetter, William M.; Totsuka, Hirono; Dudley, Michael; Kahr, Bart

2002-06-01

Hourglass inclusion crystals of K 2SO 4 were grown from aqueous solutions containing the dye acid fuchsin, and studied by synchrotron white-beam X-ray topography and reciprocal space mapping. Both self-nucleated and larger, seeded dye-included crystals were prepared, as well as comparable undoped crystals. While the dye modified the crystals' habit strongly, X-ray topographs showed it had no influence on their dislocation configurations, which were typical for solution-grown crystals. No kinematical contrast arising from the presence of the dye was observed that indicated dye-induced strain in the crystal lattice. Growth sector boundaries were visible in the dyed crystals but not in undoped crystals, implying there was a slightly higher lattice mismatch across growth sector boundaries in the dye-included crystals. Reciprocal space maps of small areas on an hourglass inclusion crystal within either a dye-included growth sector or an undoped growth sector showed single peaks with the same perfect crystal rocking curve width and no dilatation or tilt of the host lattice resulting from the dye's presence. These results showed hourglass inclusion crystals can be grown in which the presence of the dye disturbs the crystalline structure of the host salt minimally, and that hourglass inclusions have the nature of a solid solution.

Transmission electron microscopy study of crystal growth, solid solution, and defect formation: Hollandite and synthetic tremolite

NASA Astrophysics Data System (ADS)

Bozhilov, Krassimir Nikolov

Transmission electron microscopy was applied to study the crystal growth, origin of microstructures, and composition of hollandite and synthetic tremolite. The nonequilibrium shape of hollandite crystals, with reentrant angles between prismatic faces, is interpreted to be due to a multistage growth process and the development of lamellar defects that affect the growth rates of the F-faces. The process of crystal growth can be divided into three phases: (1) development of a core of intergrown romanechite and hollandite structures, (2) topotactic transformation of romanechite to hollandite and development of a lamellar microstructure, and (3) extensive overgrowth of hollandite with a high density of chain multiplicity faults, which alters the shapes of the crystals. The products from time-series of hydrothermal tremolite synthesis experiments from an oxide mixture and by recrystallization from diopside, enstatite, quartz, and water have been characterized. The crystallization starts with rapid, metastable formation of pyroxene and Mg-enriched amphibole. Chain multiplicity faults are low in density. The observed Mg enrichment is due primarily to solid solution involving the magnesio-cummingtonite component, which reaches up to 24 mol% in the initial, metastable growth stage. In products from the final stages of the experiments, the magnesio-cummingtonite component in tremolite varies between 7 and 13 mol%. Formation of monoclinic primitive tremolite is also observed. Experimental recrystallization of pyroxenes to amphibole takes place by a complex, multistage mechanism. The product amphibole crystals have low chain-multiplicity fault densities, which in general are not strongly correlated with variations in the Ca/Mg ratio. The yield of tremolitic amphibole is limited by the sluggishness of diopside hydration and dissolution and the formation of persistent, metastable solid solutions rich in the magnesio-cummingtonite component. Distance Least Squares refinements and lattice energy calculations for magnesio-cummingtonite/tremolite solid solutions reproduce the reduction of symmetry that occurs with reduction of the M4 cation size, as observed in natural amphiboles. Tremolitic amphibole with more than 20% magnesio-cummingtonite component in solid solution favors a primitive monoclinic structure. The intermediate compositions show significant structural distortions, which supports other observations suggesting that such intermediate compositions are unstable.

SEMICONDUCTOR MATERIALS: Chemical etching of a GaSb crystal incorporated with Mn grown by the Bridgman method under microgravity conditions

NASA Astrophysics Data System (ADS)

Xiaofeng, Chen; Nuofu, Chen; Jinliang, Wu; Xiulan, Zhang; Chunlin, Chai; Yude, Yu

2009-08-01

A GaSb crystal incorporated with Mn has been grown by the Bridgman method on the Polizon facility onboard the FOTON-M3 spacecraft. Structural defects and growth striations have been successfully revealed by the chemical etching method. By calculating various parameters of the convection, the striation patterns can be explained, and the critical value of the Taylor number, which characterizes the convective condition of the rotating magnetic field induced azimuthal flow, was shown. The stresses generated during crystal growth can be reflected by the observations of etch pit distribution and other structural defects. Suggestions for improving the space experiment to improve the quality of the crystal are given.

Structural differences between single crystal and polycrystalline UBe 13

DOE Office of Scientific and Technical Information (OSTI.GOV)

Volz, Heather Michelle; Vogel, Sven C.; Smith, Alice Iulia

Here, we report on observations of structural and chemical differences between samples of UBe 13 that were synthesised using two different methods. Unexplained discrepancies in properties between samples with differing synthesis had previously been found in this heavy fermion superconductor. A polycrystalline UBe13 sample was made by arc-melting the constituents. Single crystals were grown using an aluminium flux and had a consistently slightly larger lattice parameter than the polycrystals, which merited further study. Neutron diffraction data were collected at the Lujan Center at LANSCE on the HIPPO diffractometer. Aluminium was detected by inductively coupled plasma mass spectrometry (ICP-MS) in themore » flux-grown single crystal (0.803 wt%), and small amounts (~0.2 wt%) of thorium were detected in the UBe 13 polycrystalline sample. In order to probe the implications of the presence of Al, calculations by spin-polarised DFT-GGA+U show that the incorporation of Al onto the 96i site (the lowest symmetry site in the structure) is energetically more favourable than on other sites. In general, the trends calculated by DFT for bond lengths and lattice parameter increases are consistent with bond lengths experimentally observed by neutron diffraction, but specific percentage changes with aluminium incorporation may be obscured by the unexpected thorium in the polycrystalline sample. The aggregate of our initial observations suggests that incorporation of aluminium from the flux into single crystal UBe 13 is significant.« less

Structural differences between single crystal and polycrystalline UBe 13

DOE PAGES

Volz, Heather Michelle; Vogel, Sven C.; Smith, Alice Iulia; ...

2018-05-16

Here, we report on observations of structural and chemical differences between samples of UBe 13 that were synthesised using two different methods. Unexplained discrepancies in properties between samples with differing synthesis had previously been found in this heavy fermion superconductor. A polycrystalline UBe13 sample was made by arc-melting the constituents. Single crystals were grown using an aluminium flux and had a consistently slightly larger lattice parameter than the polycrystals, which merited further study. Neutron diffraction data were collected at the Lujan Center at LANSCE on the HIPPO diffractometer. Aluminium was detected by inductively coupled plasma mass spectrometry (ICP-MS) in themore » flux-grown single crystal (0.803 wt%), and small amounts (~0.2 wt%) of thorium were detected in the UBe 13 polycrystalline sample. In order to probe the implications of the presence of Al, calculations by spin-polarised DFT-GGA+U show that the incorporation of Al onto the 96i site (the lowest symmetry site in the structure) is energetically more favourable than on other sites. In general, the trends calculated by DFT for bond lengths and lattice parameter increases are consistent with bond lengths experimentally observed by neutron diffraction, but specific percentage changes with aluminium incorporation may be obscured by the unexpected thorium in the polycrystalline sample. The aggregate of our initial observations suggests that incorporation of aluminium from the flux into single crystal UBe 13 is significant.« less

Structural studies of Pseudomonas and Chromobacterium ω-aminotransferases provide insights into their differing substrate specificity

PubMed Central

Sayer, Christopher; Isupov, Michail N.; Westlake, Aaron; Littlechild, Jennifer A.

2013-01-01

The crystal structures and inhibitor complexes of two industrially important ω-aminotransferase enzymes from Pseudomonas aeruginosa and Chromobacterium violaceum have been determined in order to understand the differences in their substrate specificity. The two enzymes share 30% sequence identity and use the same amino acceptor, pyruvate; however, the Pseudomonas enzyme shows activity towards the amino donor β-alanine, whilst the Chromobacterium enzyme does not. Both enzymes show activity towards S-α-methylbenzylamine (MBA), with the Chromobacterium enzyme having a broader substrate range. The crystal structure of the P. aeruginosa enzyme has been solved in the holo form and with the inhibitor gabaculine bound. The C. violaceum enzyme has been solved in the apo and holo forms and with gabaculine bound. The structures of the holo forms of both enzymes are quite similar. There is little conformational difference observed between the inhibitor complex and the holoenzyme for the P. aeruginosa aminotransferase. In comparison, the crystal structure of the C. violaceum gabaculine complex shows significant structural rearrangements from the structures of both the apo and holo forms of the enzyme. It appears that the different rigidity of the protein scaffold contributes to the substrate specificity observed for the two ω-­aminotransferases. PMID:23519665

Structure of N-acetyl-[beta]-D-glucosaminidase (GcnA) from the Endocarditis Pathogen Streptococcus gordonii and its Complex with the Mechanism-based Inhibitor NAG-thiazoline

DOE Office of Scientific and Technical Information (OSTI.GOV)

Langley, David B.; Harty, Derek W.S.; Jacques, Nicholas A.

2008-09-17

The crystal structure of GcnA, an N-acetyl-{beta}-D-glucosaminidase from Streptococcus gordonii, was solved by multiple wavelength anomalous dispersion phasing using crystals of selenomethionine-substituted protein. GcnA is a homodimer with subunits each comprised of three domains. The structure of the C-terminal {alpha}-helical domain has not been observed previously and forms a large dimerization interface. The fold of the N-terminal domain is observed in all structurally related glycosidases although its function is unknown. The central domain has a canonical ({beta}/{alpha}){sub 8} TIM-barrel fold which harbours the active site. The primary sequence and structure of this central domain identifies the enzyme as a familymore » 20 glycosidase. Key residues implicated in catalysis have different conformations in two different crystal forms, which probably represent active and inactive conformations of the enzyme. The catalytic mechanism for this class of glycoside hydrolase, where the substrate rather than the enzyme provides the cleavage-inducing nucleophile, has been confirmed by the structure of GcnA complexed with a putative reaction intermediate analogue, N-acetyl-{beta}-D-glucosamine-thiazoline. The catalytic mechanism is discussed in light of these and other family 20 structures.« less

Growth and structural, optical, and electrical properties of zincite crystals

NASA Astrophysics Data System (ADS)

Kaurova, I. A.; Kuz'micheva, G. M.; Rybakov, V. B.

2013-03-01

An X-ray diffraction study of ZnO crystals grown by the hydrothermal method has revealed reflections that give grounds to assign them to the sp. gr. P3 rather than to P63 mc. The distribution of Zn1, Zn2, O1, and O2 over structural positions, along with vacancies and incorporated zinc atoms, explains the dissymmetrization observed in terms of the kinetic (growth) phase transition of the order-disorder type, which is caused by ordering Zn and O atoms over structural positions. The color of crystals of refined compositions (Zn0.975□0.025)Zn i(0.015)(O0.990□0.010) (green) and (Zn0.965□0.035)Zn i(0.035)O (bright green) is related to different oxygen contents, which is confirmed by the results of electron probe X-ray microanalysis and absorption spectroscopy. The degree of the structural quality of crystals, their resistivity, and activation energy are also related to oxygen vacancies.

Valence-band and core-level photoemission study of single-crystal Bi2CaSr2Cu2O8 superconductors

NASA Astrophysics Data System (ADS)

Shen, Z.-X.; Lindberg, P. A. P.; Wells, B. O.; Mitzi, D. B.; Lindau, I.; Spicer, W. E.; Kapitulnik, A.

1988-12-01

High-quality single crystals of Bi2CaSr2Cu2O8 superconductors have been prepared and cleaved in ultrahigh vacuum. Low-energy electron diffraction measurements show that the surface structure is consistent with the bulk crystal structure. Ultraviolet photoemission and x-ray photoemission experiments were performed on these well-characterized sample surfaces. The valence-band and the core-level spectra obtained from the single-crystal surfaces are in agreement with spectra recorded from polycrystalline samples, justifying earlier results from polycrystalline samples. Cu satellites are observed both in the valence band and Cu 2p core level, signaling the strong correlation among the Cu 3d electrons. The O 1s core-level data exhibit a sharp, single peak at 529-eV binding energy without any clear satellite structures.

Mechanisms for pressure-induced crystal-crystal transition, amorphization, and devitrification of SnI{sub 4}

DOE Office of Scientific and Technical Information (OSTI.GOV)

Liu, H.; Tse, J. S., E-mail: john.tse@usask.ca; Hu, M. Y.

2015-10-28

The pressure-induced amorphization and subsequent recrystallization of SnI{sub 4} have been investigated using first principles molecular dynamics calculations together with high-pressure {sup 119}Sn nuclear resonant inelastic x-ray scattering measurements. Above ∼8 GPa, we observe a transformation from an ambient crystalline phase to an intermediate crystal structure and a subsequent recrystallization into a cubic phase at ∼64 GPa. The crystalline-to-amorphous transition was identified on the basis of elastic compatibility criteria. The measured tin vibrational density of states shows large amplitude librations of SnI{sub 4} under ambient conditions. Although high pressure structures of SnI{sub 4} were thought to be determined by randommore » packing of equal-sized spheres, we detected electron charge transfer in each phase. This charge transfer results in a crystal structure packing determined by larger than expected iodine atoms.« less

Mechanisms for pressure-induced crystal-crystal transition, amorphization, and devitrification of Snl 4

DOE PAGES

Liu, Hanyu; Tse, John S.; Hu, Michael Y.; ...

2015-10-27

The pressure-induced amorphization and subsequent recrystallization of SnI 4 have been investigated using first principles molecular dynamics calculations together with high-pressure 119Sn nuclear resonant inelastic x-ray scattering measurements. Above ~8 GPa, we observe a transformation from an ambient crystalline phase to an intermediate crystal structure and a subsequent recrystallization into a cubic phase at ~64 GPa. The crystalline-to-amorphous transition was identified on the basis of elastic compatibility criteria. The measured tin vibrational density of states shows large amplitude librations of SnI 4 under ambient conditions. Although high pressure structures of SnI 4 were thought to be determined by random packingmore » of equal-sized spheres, we detected electron charge transfer in each phase. As a result, this charge transfer results in a crystal structure packing determined by larger than expected iodine atoms. (C) 2015 AIP Publishing LLC.« less

Control of morphology and crystal purity of InP nanowires by variation of phosphine flux during selective area MOMBE

NASA Astrophysics Data System (ADS)

Kelrich, A.; Dubrovskii, V. G.; Calahorra, Y.; Cohen, S.; Ritter, D.

2015-02-01

We present experimental results showing how the growth rate, morphology and crystal structure of Au-catalyzed InP nanowires (NWs) fabricated by selective area metal organic molecular beam epitaxy can be tuned by the growth parameters: temperature and phosphine flux. The InP NWs with 20-65 nm diameters are grown at temperatures of 420 and 480 °C with the PH3 flow varying from 1 to 9 sccm. The NW tapering is suppressed at a higher temperature, while pure wurtzite crystal structure is preferred at higher phosphine flows. Therefore, by combining high temperature and high phosphine flux, we are able to fabricate non-tapered and stacking fault-free InP NWs with the quality that other methods rarely achieve. We also develop a model for NW growth and crystal structure which explains fairly well the observed experimental tendencies.

Mechanisms for pressure-induced crystal-crystal transition, amorphization, and devitrification of SnI4.

PubMed

Liu, H; Tse, J S; Hu, M Y; Bi, W; Zhao, J; Alp, E E; Pasternak, M; Taylor, R D; Lashley, J C

2015-10-28

The pressure-induced amorphization and subsequent recrystallization of SnI4 have been investigated using first principles molecular dynamics calculations together with high-pressure (119)Sn nuclear resonant inelastic x-ray scattering measurements. Above ∼8 GPa, we observe a transformation from an ambient crystalline phase to an intermediate crystal structure and a subsequent recrystallization into a cubic phase at ∼64 GPa. The crystalline-to-amorphous transition was identified on the basis of elastic compatibility criteria. The measured tin vibrational density of states shows large amplitude librations of SnI4 under ambient conditions. Although high pressure structures of SnI4 were thought to be determined by random packing of equal-sized spheres, we detected electron charge transfer in each phase. This charge transfer results in a crystal structure packing determined by larger than expected iodine atoms.

Crystal Structure and Ferroelectric Properties of ε-Ga2O3 Films Grown on (0001)-Sapphire.

PubMed

Mezzadri, Francesco; Calestani, Gianluca; Boschi, Francesco; Delmonte, Davide; Bosi, Matteo; Fornari, Roberto

2016-11-21

The crystal structure and ferroelectric properties of ε-Ga 2 O 3 deposited by low-temperature MOCVD on (0001)-sapphire were investigated by single-crystal X-ray diffraction and the dynamic hysteresis measurement technique. A thorough investigation of this relatively unknown polymorph of Ga 2 O 3 showed that it is composed of layers of both octahedrally and tetrahedrally coordinated Ga 3+ sites, which appear to be occupied with a 66% probability. The refinement of the crystal structure in the noncentrosymmetric space group P6 3 mc pointed out the presence of uncompensated electrical dipoles suggesting ferroelectric properties, which were finally demonstrated by independent measurements of the ferroelectric hysteresis. A clear epitaxial relation is observed with respect to the c-oriented sapphire substrate, with the Ga 2 O 3 [10-10] direction being parallel to the Al 2 O 3 direction [11-20], yielding a lattice mismatch of about 4.1%.

Fano resonance in anodic aluminum oxide based photonic crystals.

PubMed

Shang, Guo Liang; Fei, Guang Tao; Zhang, Yao; Yan, Peng; Xu, Shao Hui; Ouyang, Hao Miao; Zhang, Li De

2014-01-08

Anodic aluminum oxide based photonic crystals with periodic porous structure have been prepared using voltage compensation method. The as-prepared sample showed an ultra-narrow photonic bandgap. Asymmetric line-shape profiles of the photonic bandgaps have been observed, which is attributed to Fano resonance between the photonic bandgap state of photonic crystal and continuum scattering state of porous structure. And the exhibited Fano resonance shows more clearly when the sample is saturated ethanol gas than air-filled. Further theoretical analysis by transfer matrix method verified these results. These findings provide a better understanding on the nature of photonic bandgaps of photonic crystals made up of porous materials, in which the porous structures not only exist as layers of effective-refractive-index material providing Bragg scattering, but also provide a continuum light scattering state to interact with Bragg scattering state to show an asymmetric line-shape profile.

The MORPHEUS II protein crystallization screen

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gorrec, Fabrice, E-mail: fgorrec@mrc-lmb.cam.ac.uk

2015-06-27

MORPHEUS II is a 96-condition initial crystallization screen formulated de novo. The screen incorporates reagents selected from the Protein Data Bank to yield crystals that are not observed in traditional conditions. In addition, the formulation facilitates the optimization and cryoprotection of crystals. High-quality macromolecular crystals are a prerequisite for the process of protein structure determination by X-ray diffraction. Unfortunately, the relative yield of diffraction-quality crystals from crystallization experiments is often very low. In this context, innovative crystallization screen formulations are continuously being developed. In the past, MORPHEUS, a screen in which each condition integrates a mix of additives selected frommore » the Protein Data Bank, a cryoprotectant and a buffer system, was developed. Here, MORPHEUS II, a follow-up to the original 96-condition initial screen, is described. Reagents were selected to yield crystals when none might be observed in traditional initial screens. Besides, the screen includes heavy atoms for experimental phasing and small polyols to ensure the cryoprotection of crystals. The suitability of the resulting novel conditions is shown by the crystallization of a broad variety of protein samples and their efficiency is compared with commercially available conditions.« less

Quasi 2D electronic states with high spin-polarization in centrosymmetric MoS2 bulk crystals

NASA Astrophysics Data System (ADS)

Gehlmann, Mathias; Aguilera, Irene; Bihlmayer, Gustav; Młyńczak, Ewa; Eschbach, Markus; Döring, Sven; Gospodarič, Pika; Cramm, Stefan; Kardynał, Beata; Plucinski, Lukasz; Blügel, Stefan; Schneider, Claus M.

2016-06-01

Time reversal dictates that nonmagnetic, centrosymmetric crystals cannot be spin-polarized as a whole. However, it has been recently shown that the electronic structure in these crystals can in fact show regions of high spin-polarization, as long as it is probed locally in real and in reciprocal space. In this article we present the first observation of this type of compensated polarization in MoS2 bulk crystals. Using spin- and angle-resolved photoemission spectroscopy (ARPES), we directly observed a spin-polarization of more than 65% for distinct valleys in the electronic band structure. By additionally evaluating the probing depth of our method, we find that these valence band states at the point in the Brillouin zone are close to fully polarized for the individual atomic trilayers of MoS2, which is confirmed by our density functional theory calculations. Furthermore, we show that this spin-layer locking leads to the observation of highly spin-polarized bands in ARPES since these states are almost completely confined within two dimensions. Our findings prove that these highly desired properties of MoS2 can be accessed without thinning it down to the monolayer limit.

Carboplatin binding to histidine

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tanley, Simon W. M.; Diederichs, Kay; Kroon-Batenburg, Loes M. J.

An X-ray crystal structure showing the binding of purely carboplatin to histidine in a model protein has finally been obtained. This required extensive crystallization trials and various novel crystal structure analyses. Carboplatin is a second-generation platinum anticancer agent used for the treatment of a variety of cancers. Previous X-ray crystallographic studies of carboplatin binding to histidine (in hen egg-white lysozyme; HEWL) showed the partial conversion of carboplatin to cisplatin owing to the high NaCl concentration used in the crystallization conditions. HEWL co-crystallizations with carboplatin in NaBr conditions have now been carried out to confirm whether carboplatin converts to the brominemore » form and whether this takes place in a similar way to the partial conversion of carboplatin to cisplatin observed previously in NaCl conditions. Here, it is reported that a partial chemical transformation takes place but to a transplatin form. Thus, to attempt to resolve purely carboplatin binding at histidine, this study utilized co-crystallization of HEWL with carboplatin without NaCl to eliminate the partial chemical conversion of carboplatin. Tetragonal HEWL crystals co-crystallized with carboplatin were successfully obtained in four different conditions, each at a different pH value. The structural results obtained show carboplatin bound to either one or both of the N atoms of His15 of HEWL, and this particular variation was dependent on the concentration of anions in the crystallization mixture and the elapsed time, as well as the pH used. The structural details of the bound carboplatin molecule also differed between them. Overall, the most detailed crystal structure showed the majority of the carboplatin atoms bound to the platinum centre; however, the four-carbon ring structure of the cyclobutanedicarboxylate moiety (CBDC) remained elusive. The potential impact of the results for the administration of carboplatin as an anticancer agent are described.« less

The complex metal-rich boride Ti1+xRh2-x+yIr3-yB3 (x=0.68, y=1.06) with a new structure type containing B4 zigzag fragments: Synthesis, crystal chemistry and theoretical calculations

NASA Astrophysics Data System (ADS)

Goerens, Christian; Fokwa, Boniface P. T.

2012-08-01

Polycrystalline samples and single crystals of the new complex boride Ti1+xRh2-x+yIr3-yB3 (x=0.68; y=1.06) were synthesized by arc-melting the elements in a water-cooled copper crucible under an argon atmosphere and characterized by X-Ray diffraction as well as EDX measurements. The crystal structure was refined on the basis of single crystal data. The new phase, which represents a new structure type containing trans zigzag B4 fragments as well as isolated boron atoms crystallizes in the orthorhombic space group Pbam (Nr. 55) with the lattice parameters a=8.620(1) Å, b=14.995(2) Å and c=3.234(1) Å. First-principles density functional theory calculations using the Vienna ab-initio simulation package (VASP) were performed on an appropriate structural model (using a supercell approach) and the experimental crystallographic data could be reproduced accurately. Based on this model, the density of states and crystal orbital Hamilton population (for bonding analysis) were calculated, using the linear muffin-tin orbital atomic sphere approximation (LMTO-ASA) method. According to these calculations, this metal-rich compound should be metallic, as expected. Furthermore, very strong boron-boron interactions are observed in the trans zigzag B4 fragment, which induce a clear differentiation of two types of metal-boron contacts with different strength. The observed three-dimensional metal-metal interaction is in good agreement with the predicted metallic behavior.

Investigation on bandgap, diffraction, interference, and refraction effects of photonic crystal structure in GaN/InGaN LEDs for light extraction.

PubMed

Patra, Saroj Kanta; Adhikari, Sonachand; Pal, Suchandan

2014-06-20

In this paper, we have made a clear differentiation among bandgap, diffraction, interference, and refraction effects in photonic crystal structures (PhCs). For observing bandgap, diffraction, and refraction effects, PhCs are considered on the top p-GaN surface of light emitting diodes (LEDs), whereas for interference effect, hole type PhCs are considered to be embedded within n-GaN layer of LED. From analysis, it is observed that at a particular lattice periodicity, for which bandgap lies within the wavelength of interest shows a significant light extraction due to inhibition of guided mode. Beyond a certain periodicity, diffraction effect starts dominating and light extraction improves further. The interference effect is observed in embedded photonic crystal LEDs, where depth of etching supports constructive interference of outward light waves. We have also shed light on refraction effects exhibited by the PhCs and whether negative refraction properties of PhCs may be useful in case of LED light extraction.

Nanoparticles in liquid crystals, and liquid crystals in nanoparticles

NASA Astrophysics Data System (ADS)

de Pablo, Juan

2015-03-01

Liquid crystals are remarkably sensitive to interfacial interactions. Small perturbations at a liquid crystal interface, for example, can be propagated over relatively long length scales, thereby providing the basis for a wide range of applications that rely on amplification of molecular events into macroscopic observables. Our recent research efforts have focused on the reverse phenomenon; that is, we have sought to manipulate the interfacial assembly of nanoparticles or the organization of surface active molecules by controlling the structure of a liquid crystal. This presentation will consist of a review of the basic principles that are responsible for liquid crystal-mediated interactions, followed by demonstrations of those principles in the context of two types of systems. In the first, a liquid crystal is used to direct the assembly of nanoparticles; through a combination of molecular and continuum models, it is found that minute changes in interfacial energy and particle size lead to liquid-crystal induced attractions that can span multiple orders of magnitude. Theoretical predictions are confirmed by experimental observations, which also suggest that LC-mediated assembly provides an effective means for fabrication of plasmonic devices. In the second type of system, the structure of a liquid crystal is controlled by confinement in submicron droplets. The morphology of the liquid crystal in a drop depends on a delicate balance between bulk and interfacial contributions to the free energy; that balance can be easily perturbed by adsorption of analytes or nanoparticles at the interface, thereby providing the basis for development of hierarchical assembly of responsive, anisotropic materials. Theoretical predictions also indicate that the three-dimensional order of a liquid crystal can be projected onto a two-dimensional interface, and give rise to novel nanostructures that are not found in simple isotropic fluids.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Davaasuren, Bambar; Dashjav, Enkhtsetseg; Kreiner, Guido

The carboferrates RE{sub 15}[Fe{sub 8}C{sub 25}] (RE=Dy, Ho) were prepared from mixtures of the elements by arc-melting followed with subsequent annealing at 1373 K. The crystal structures were determined from single crystal X-ray diffraction data and revealed an isotypic relationship to Er{sub 15}[Fe{sub 8}C{sub 25}] (hP48, P321). The main feature of the crystal structure is given by Fe{sub 6} cluster units characterized by covalent Fe–Fe bonding interactions. {sup 57}Fe Mössbauer spectra of Dy{sub 15}[Fe{sub 8}C{sub 25}] were fitted by three subspectra with relative spectral weights of about 3:3:2 which is in general agreement with the crystal structure. Below 50 K,more » an onset of magnetic hyperfine fields at the three iron sites is observed which is supposed to be caused by dipolar fields arising from neighboring, slowly relaxing Dy magnetic moments. - Graphical abstract: Fe{sub 6}-cluster in the crystal structure of RE{sub 15}[Fe{sub 8}C{sub 25}], RE=Dy, Ho. - Highlights: • New carboferrates RE{sub 15}[Fe{sub 8}C{sub 25}] with RE=Dy, Ho have been synthesized. • The crystal structures were refined using single crystal X-ray data. • An orientational relationship between Fe{sub 6}-clusters and Fe in γ-Fe is outlined. • {sup 57}Fe Mössbauer spectra are in agreement with structural data from X-rays. • Magnetic hyperfine fields below 50 K are explained by dipolar fields from Dy atoms.« less

Crystal structure and physical properties of a novel Kondo antiferromagnet: U3Ru4Al12

NASA Astrophysics Data System (ADS)

Pasturel, M; Tougait, O; Potel, M; Roisnel, T; Wochowski, K; Noël, H; Troć, R

2009-03-01

A novel ternary compound U3Ru4Al12 has been identified in the U-Ru-Al ternary diagram. Single-crystal x-ray diffraction indicates a hexagonal Gd3Ru4Al12-type structure for this uranium-based intermetallic. While this structure type usually induces geometrically a spin-glass behaviour, an antiferromagnetic ordering is observed at TN = 8.4 K in the present case. The reduced effective magnetic moment of U atoms (μeff = 2.6 µB) can be explained by Kondo-like interactions and crystal field effects that have been identified by a logarithmic temperature dependence of the electrical resistivity, negative values of the magnetoresistivity and particular shape of the Seebeck coefficient.

Acoustic band gaps of the woodpile sonic crystal with the simple cubic lattice

NASA Astrophysics Data System (ADS)

Wu, Liang-Yu; Chen, Lien-Wen

2011-02-01

This study theoretically and experimentally investigates the acoustic band gap of a three-dimensional woodpile sonic crystal. Such crystals are built by blocks or rods that are orthogonally stacked together. The adjacent layers are perpendicular to each other. The woodpile structure is embedded in air background. Their band structures and transmission spectra are calculated using the finite element method with a periodic boundary condition. The dependence of the band gap on the width of the stacked rods is discussed. The deaf bands in the band structure are observed by comparing with the calculated transmission spectra. The experimental transmission spectra for the Γ-X and Γ-X' directions are also presented. The calculated results are compared with the experimental results.

Mesoscale martensitic transformation in single crystals of topological defects

PubMed Central

Martínez-González, José A.; Ramírez-Hernández, Abelardo; Zhou, Ye; Sadati, Monirosadat; Zhang, Rui; Nealey, Paul F.; de Pablo, Juan J.

2017-01-01

Liquid-crystal blue phases (BPs) are highly ordered at two levels. Molecules exhibit orientational order at nanometer length scales, while chirality leads to ordered arrays of double-twisted cylinders over micrometer scales. Past studies of polycrystalline BPs were challenged by the existence of grain boundaries between randomly oriented crystalline nanodomains. Here, the nucleation of BPs is controlled with precision by relying on chemically nanopatterned surfaces, leading to macroscopic single-crystal BP specimens where the dynamics of mesocrystal formation can be directly observed. Theory and experiments show that transitions between two BPs having a different network structure proceed through local reorganization of the crystalline array, without diffusion of the double-twisted cylinders. In solid crystals, martensitic transformations between crystal structures involve the concerted motion of a few atoms, without diffusion. The transformation between BPs, where crystal features arise in the submicron regime, is found to be martensitic in nature when one considers the collective behavior of the double-twist cylinders. Single-crystal BPs are shown to offer fertile grounds for the study of directed crystal nucleation and the controlled growth of soft matter. PMID:28874557

DOE Office of Scientific and Technical Information (OSTI.GOV)

Li, Xiao; Martínez-González, José A.; Hernández-Ortiz, Juan P.

Liquid crystal blue phases (BPs) are highly ordered at two levels. Molecules exhibit orientational order at nanometer length scales, while chirality leads to ordered arrays of doubletwisted cylinders over micrometer scales. Past studies of polycrystalline BPs were challenged by grain boundaries between randomly oriented crystalline nanodomains. Here, the nucleation of BPs is controlled with considerable precision by relying on chemically nano-patterned surfaces, leading to macroscopic single-crystal BP specimens where the dynamics of meso-crystal formation can be directly observed. Theory and experiments show that transitions between two BPs having a different network structure proceed through local re-organization of the crystalline array,more » without diffusion of the double twisted cylinders. In solid crystals, martensitic transformations between crystal structures involve the concerted motion of a few atoms, without diffusion. The transformation between BPs, where crystal features arise in the sub-micron regime, is found to be martensitic in nature, with the diffusion-less feature associated to the collective behavior of the double twist cylinders. Single-crystal BPs are shown to offer fertile grounds for the study of directed crystal-nucleation and the controlled growth of soft matter.« less

Crystal structures and mutagenesis of PPP-family ser/thr protein phosphatases elucidate the selectivity of cantharidin and novel norcantharidin-based inhibitors of PP5C.

PubMed

Chattopadhyay, Debasish; Swingle, Mark R; Salter, Edward A; Wood, Eric; D'Arcy, Brandon; Zivanov, Catherine; Abney, Kevin; Musiyenko, Alla; Rusin, Scott F; Kettenbach, Arminja; Yet, Larry; Schroeder, Chad E; Golden, Jennifer E; Dunham, Wade H; Gingras, Anne-Claude; Banerjee, Surajit; Forbes, David; Wierzbicki, Andrzej; Honkanen, Richard E

2016-06-01

Cantharidin is a natural toxin and an active constituent in a traditional Chinese medicine used to treat tumors. Cantharidin acts as a semi-selective inhibitor of PPP-family ser/thr protein phosphatases. Despite sharing a common catalytic mechanism and marked structural similarity with PP1C, PP2AC and PP5C, human PP4C was found to be insensitive to the inhibitory activity of cantharidin. To explore the molecular basis for this selectivity, we synthesized and tested novel C5/C6-derivatives designed from quantum-based modeling of the interactions revealed in the co-crystal structures of PP5C in complex with cantharidin. Structure-activity relationship studies and analysis of high-resolution (1.25Å) PP5C-inhibitor co-crystal structures reveal close contacts between the inhibitor bridgehead oxygen and both a catalytic metal ion and a non-catalytic phenylalanine residue, the latter of which is substituted by tryptophan in PP4C. Quantum chemistry calculations predicted that steric clashes with the bulkier tryptophan side chain in PP4C would force all cantharidin-based inhibitors into an unfavorable binding mode, disrupting the strong coordination of active site metal ions observed in the PP5C co-crystal structures, thereby rendering PP4C insensitive to the inhibitors. This prediction was confirmed by inhibition studies employing native human PP4C. Mutation of PP5C (F446W) and PP1C (F257W), to mimic the PP4C active site, resulted in markedly suppressed sensitivity to cantharidin. These observations provide insight into the structural basis for the natural selectivity of cantharidin and provide an avenue for PP4C deselection. The novel crystal structures also provide insight into interactions that provide increased selectivity of the C5/C6 modifications for PP5C versus other PPP-family phosphatases. Copyright © 2016 Elsevier Inc. All rights reserved.

Structures and phase transitions of the A7PSe6 (A = ag, Cu) argyrodite-type ionic conductors. III. alpha-Cu7PSe6

PubMed

Gaudin; Petricek; Boucher; Taulelle; Evain

2000-12-01

The crystal structure of the third polymorph of the Cu(7)PSe(6) argyrodite compound, alpha-Cu(7)PSe(6), heptacopper phosphorus hexaselenide, is determined by means of single-crystal diffraction from twinned crystals and X-ray powder diffraction, with the help of extensive NMR measurements. In the low-temperature form, i.e. below the last phase transition, alpha-Cu(7)PSe(6) crystallizes in orthorhombic symmetry, space group Pna2(1), with a = 14.3179 (4), b = 7.1112 (2), c = 10.1023 (3) A, V = 1028.590 (9) A(3) (deduced from powder data, T = 173 K) and Z = 4. Taking into account a twinning by reticular merohedry, the refinement of the alpha-Cu(7)PSe(6) structure leads to the residual factors R = 0.0466 and wR = 0.0486 for 127 parameters and 3714 observed, independent reflections (single-crystal data, T = 173 K). A full localization of the Cu(+)d(10) element is reached with one twofold-, one threefold- and five fourfold-coordinated Cu atoms. The observation of two phase transitions for Cu(7)PSe(6), to be compared with only one for Ag(7)PSe(6), is attributed to the d(10) element stability in a low coordination environment, copper being less prone to lower coordination sites than silver, especially at low temperature.

Phase behavior of binary and polydisperse suspensions of compressible microgels controlled by selective particle deswelling

NASA Astrophysics Data System (ADS)

Scotti, A.; Gasser, U.; Herman, E. S.; Han, Jun; Menzel, A.; Lyon, L. A.; Fernandez-Nieves, A.

2017-09-01

We investigate the phase behavior of suspensions of poly(N -isopropylacrylamide) (pNIPAM) microgels with either bimodal or polydisperse size distribution. We observe a shift of the fluid-crystal transition to higher concentrations depending on the polydispersity or the fraction of large particles in suspension. Crystallization is observed up to polydispersities as high as 18.5%, and up to a number fraction of large particles of 29% in bidisperse suspensions. The crystal structure is random hexagonal close-packed as in monodisperse pNIPAM microgel suspensions. We explain our experimental results by considering the effect of bound counterions. Above a critical particle concentration, these cause deswelling of the largest microgels, which are the softest, changing the size distribution of the suspension and enabling crystal formation in conditions where incompressible particles would not crystallize.

High-resolution electron microscopy and its applications.

PubMed

Li, F H

1987-12-01

A review of research on high-resolution electron microscopy (HREM) carried out at the Institute of Physics, the Chinese Academy of Sciences, is presented. Apart from the direct observation of crystal and quasicrystal defects for some alloys, oxides, minerals, etc., and the structure determination for some minute crystals, an approximate image-contrast theory named pseudo-weak-phase object approximation (PWPOA), which shows the image contrast change with crystal thickness, is described. Within the framework of PWPOA, the image contrast of lithium ions in the crystal of R-Li2Ti3O7 has been observed. The usefulness of diffraction analysis techniques such as the direct method and Patterson method in HREM is discussed. Image deconvolution and resolution enhancement for weak-phase objects by use of the direct method are illustrated. In addition, preliminary results of image restoration for thick crystals are given.

Single crystals of the 96 K superconductor (Hg,Cu)Ba2CuO4+δ: Growth, structure and magnetism

NASA Astrophysics Data System (ADS)

Pelloquin, D.; Hardy, V.; Maignan, A.; Raveau, B.

1997-02-01

Single crystals of the 1201 (n = 1) (Hg,Cu)Ba2CuO4+δ mercury based cuprate have been grown by using a simple process without dry box. The as-synthesized crystals exhibit constant Tc(onset) of 96 K with sharp superconducting transitions. The electron microscopy coupled with EDX analyses evidence a ``1201''-type structure while a mercury deficiency is observed balanced by an excess of copper. The structural refinements based on single-crystal X-ray diffraction data confirm the electron deficiency on the Hg site (0,0,0) and show a splitting of the latter along the c axis correlated to the partial substitution of Cu for Hg. This structural study leads to the following formula Hg0.84Cu0.16Ba2CuO4.19. The magnetic study of a large crystal (1.1 × 0.38 × 0.065 mm3) shows that the (Hg,Cu)-1201 crystals exhibit an irreversibility line higher than that of the 1201 Hg0.8Bi0.2Ba2CuO4+δ crystal (Tc = 75 K). From the reversible magnetization, a λab(0) = 2470 Å value can be extrapolated. Using a 3D-2D decoupling formula, we obtain γ = 29 for the electronic anisotropy of this phase.

Structural and optical effects induced by gamma irradiation on NdPO{sub 4}: X-ray diffraction, spectroscopic and luminescence study

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sadhasivam, S.; Rajesh, N.P., E-mail: rajeshnp@hotmail.com

2016-02-15

Highlights: • Inorganic NdPO{sub 4} crystal was grown first time using potassium polyphosphate (K{sub 6}P{sub 4}O{sub 13}) flux. • NdPO{sub 4} crystal is insoluble in water, non-hygroscopic and high radiation resistance favoring for actinides host. • Actinide immobilization can be made at 1273 K. • High yield of 1061 nm photon emission. - Abstract: Rare earth orthophosphate (NdPO{sub 4}) monazite single crystals were grown using high temperature flux growth method employing K{sub 6}P{sub 4}O{sub 13} (K{sub 6}) as molten solvent. Their structural parameters were studied using single crystal X-ray diffraction (XRD) method. The grown crystals were examined by SEM andmore » EDX techniques for their homogeniousity and inclusion in the crystals. The influence of gamma irradiation in structural and optical absorption properties were studied by the powder XRD, FTIR and reflectance spectroscopy. The effect of gamma irradiation on luminescence properties was recorded. No significant structural change is observed up to 150 kGy gamma dose. The gamma ray induced charge trap in the crystal was saturated to 40 kGy dose. The luminescence intensity decreases with an increase in the irradiation. The emission of luminescence intensity stabilizes above 40 kGy gamma dose.« less

Crystal pathologies in macromolecular crystallography.

PubMed

Dauter, Zbigniew; Jaskólski, Mariusz

Macromolecules, such as proteins or nucleic acids, form crystals with a large volume fraction of water, ~50% on average. Apart from typical physical defects and rather trivial poor quality problems, macromolecular crystals, as essentially any crystals, can also suffer from several kinds of pathologies, in which everything seems to be perfect, except that from the structural point of view the interpretation may be very difficult, sometimes even impossible. A frequent nuisance is pseudosymmetry, or non-crystallographic symmetry (NCS), which is particularly nasty when it has translational character. Lattice-translocation defects, also called order-disorder twinning (OD-twinning), occur when molecules are packed regularly in layers but the layers are stacked (without rotation) in two (or more) discrete modes, with a unique translocation vector. Crystal twinning arises when twin domains have different orientations, incompatible with the symmetry of the crystal structure. There are also crystals in which the periodic (lattice) order is broken or absent altogether. When the strict short-range translational order from one unit cell to the next is lost but the long-range order is restored by a periodic modulation, we have a modulated crystal structure. In quasicrystals (not observed for macromolecules yet), the periodic order (in 3D space) is lost completely and the diffraction pattern (which is still discrete) cannot be even indexed using three hkl indices. In addition, there are other physical defects and phenomena (such as high mosaicity, diffraction anisotropy, diffuse scattering, etc.) which make diffraction data processing and structure solution difficult or even impossible.

The Crystal Structure of GXGD Membrane Protease FlaK

DOE Office of Scientific and Technical Information (OSTI.GOV)

J Hu; Y Xue; S Lee

2011-12-31

The GXGD proteases are polytopic membrane proteins with catalytic activities against membrane-spanning substrates that require a pair of aspartyl residues. Representative members of the family include preflagellin peptidase, type 4 prepilin peptidase, presenilin and signal peptide peptidase. Many GXGD proteases are important in medicine. For example, type 4 prepilin peptidase may contribute to bacterial pathogenesis, and mutations in presenilin are associated with Alzheimer's disease. As yet, there is no atomic-resolution structure in this protease family. Here we report the crystal structure of FlaK, a preflagellin peptidase from Methanococcus maripaludis, solved at 3.6 {angstrom} resolution. The structure contains six transmembrane helices.more » The GXGD motif and a short transmembrane helix, helix 4, are positioned at the centre, surrounded by other transmembrane helices. The crystal structure indicates that the protease must undergo conformational changes to bring the GXGD motif and a second essential aspartyl residue from transmembrane helix 1 into close proximity for catalysis. A comparison of the crystal structure with models of presenilin derived from biochemical analysis reveals three common transmembrane segments that are similarly arranged around the active site. This observation reinforces the idea that the prokaryotic and human proteases are evolutionarily related. The crystal structure presented here provides a framework for understanding the mechanism of the GXGD proteases, and may facilitate the rational design of inhibitors that target specific members of the family.« less

The crystal structure of GXGD membrane protease FlaK

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hu, Jian; Xue, Yi; Lee, Sangwon

2011-09-20

The GXGD proteases are polytopic membrane proteins with catalytic activities against membrane-spanning substrates that require a pair of aspartyl residues. Representative members of the family include preflagellin peptidase, type 4 prepilin peptidase, presenilin and signal peptide peptidase. Many GXGD proteases are important in medicine. For example, type 4 prepilin peptidase may contribute to bacterial pathogenesis, and mutations in presenilin are associated with Alzheimer's disease. As yet, there is no atomic-resolution structure in this protease family. Here we report the crystal structure of FlaK, a preflagellin peptidase from Methanococcus maripaludis, solved at 3.6 {angstrom} resolution. The structure contains six transmembrane helices.more » The GXGD motif and a short transmembrane helix, helix 4, are positioned at the centre, surrounded by other transmembrane helices. The crystal structure indicates that the protease must undergo conformational changes to bring the GXGD motif and a second essential aspartyl residue from transmembrane helix 1 into close proximity for catalysis. A comparison of the crystal structure with models of presenilin derived from biochemical analysis reveals three common transmembrane segments that are similarly arranged around the active site. This observation reinforces the idea that the prokaryotic and human proteases are evolutionarily related. The crystal structure presented here provides a framework for understanding the mechanism of the GXGD proteases, and may facilitate the rational design of inhibitors that target specific members of the family.« less

Direct Band Gap Wurtzite Gallium Phosphide Nanowires

PubMed Central

2013-01-01

The main challenge for light-emitting diodes is to increase the efficiency in the green part of the spectrum. Gallium phosphide (GaP) with the normal cubic crystal structure has an indirect band gap, which severely limits the green emission efficiency. Band structure calculations have predicted a direct band gap for wurtzite GaP. Here, we report the fabrication of GaP nanowires with pure hexagonal crystal structure and demonstrate the direct nature of the band gap. We observe strong photoluminescence at a wavelength of 594 nm with short lifetime, typical for a direct band gap. Furthermore, by incorporation of aluminum or arsenic in the GaP nanowires, the emitted wavelength is tuned across an important range of the visible light spectrum (555–690 nm). This approach of crystal structure engineering enables new pathways to tailor materials properties enhancing the functionality. PMID:23464761

Temperature-dependent dielectric functions and interband critical points of sulfur-rich TlIn(S1-xSex)2 layered solid solution crystals

NASA Astrophysics Data System (ADS)

Gomonnai, O. O.; Gordan, O.; Guranich, P. P.; Slivka, A. G.; Gomonnai, A. V.; Zahn, D. R. T.

2017-12-01

Real and imaginary parts of the dielectric function of TlIn(S1-xSex)2 (x = 0.05, 0.08, 0.25) single crystals were determined in the spectral range from 1 to 5 eV within a temperature interval 140-293 K from spectroscopic ellipsometry measurements. The energies of interband transitions (critical points) of the TlIn(S1-xSex)2 crystals were obtained from the second derivative of the real and imaginary parts of dielectric function. Structural phase transitions are behind the observed change of electronic band structure.

Structural insights into the mycobacteria transcription initiation complex from analysis of X-ray crystal structures

DOE PAGES

Hubin, Elizabeth A.; Lilic, Mirjana; Darst, Seth A.; ...

2017-07-13

The mycobacteria RNA polymerase (RNAP) is a target for antimicrobials against tuberculosis, motivating structure/function studies. Here we report a 3.2 Å-resolution crystal structure of a Mycobacterium smegmatis (Msm) open promoter complex (RPo), along with structural analysis of the Msm RPo and a previously reported 2.76 Å-resolution crystal structure of an Msm transcription initiation complex with a promoter DNA fragment. We observe the interaction of the Msm RNAP α-subunit C-terminal domain (αCTD) with DNA, and we provide evidence that the a CTD may play a role in Mtb transcription regulation. Here, our results reveal the structure of an Actinobacteria-unique insert ofmore » the RNAP β' subunit. Finally, our analysis reveals the disposition of the N-terminal segment of Msm σ A, which may comprise an intrinsically disordered protein domain unique to mycobacteria. The clade-specific features of the mycobacteria RNAP provide clues to the profound instability of mycobacteria RPo compared with E. coli.« less

Structural insights into the mycobacteria transcription initiation complex from analysis of X-ray crystal structures

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hubin, Elizabeth A.; Lilic, Mirjana; Darst, Seth A.

The mycobacteria RNA polymerase (RNAP) is a target for antimicrobials against tuberculosis, motivating structure/function studies. Here we report a 3.2 Å-resolution crystal structure of a Mycobacterium smegmatis (Msm) open promoter complex (RPo), along with structural analysis of the Msm RPo and a previously reported 2.76 Å-resolution crystal structure of an Msm transcription initiation complex with a promoter DNA fragment. We observe the interaction of the Msm RNAP α-subunit C-terminal domain (αCTD) with DNA, and we provide evidence that the αCTD may play a role in Mtb transcription regulation. Our results reveal the structure of an Actinobacteria-unique insert of the RNAPmore » β' subunit. Finally, our analysis reveals the disposition of the N-terminal segment of Msm σA, which may comprise an intrinsically disordered protein domain unique to mycobacteria. The clade-specific features of the mycobacteria RNAP provide clues to the profound instability of mycobacteria RPo compared with E. coli.« less

Structural insights into the mycobacteria transcription initiation complex from analysis of X-ray crystal structures

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hubin, Elizabeth A.; Lilic, Mirjana; Darst, Seth A.

The mycobacteria RNA polymerase (RNAP) is a target for antimicrobials against tuberculosis, motivating structure/function studies. Here we report a 3.2 Å-resolution crystal structure of a Mycobacterium smegmatis (Msm) open promoter complex (RPo), along with structural analysis of the Msm RPo and a previously reported 2.76 Å-resolution crystal structure of an Msm transcription initiation complex with a promoter DNA fragment. We observe the interaction of the Msm RNAP α-subunit C-terminal domain (αCTD) with DNA, and we provide evidence that the a CTD may play a role in Mtb transcription regulation. Here, our results reveal the structure of an Actinobacteria-unique insert ofmore » the RNAP β' subunit. Finally, our analysis reveals the disposition of the N-terminal segment of Msm σ A, which may comprise an intrinsically disordered protein domain unique to mycobacteria. The clade-specific features of the mycobacteria RNAP provide clues to the profound instability of mycobacteria RPo compared with E. coli.« less

Colloidal crystals with diamond symmetry at optical lengthscales

NASA Astrophysics Data System (ADS)

Wang, Yifan; Jenkins, Ian C.; McGinley, James T.; Sinno, Talid; Crocker, John C.

2017-02-01

Future optical materials promise to do for photonics what semiconductors did for electronics, but the challenge has long been in creating the structure they require--a regular, three-dimensional array of transparent microspheres arranged like the atoms in a diamond crystal. Here we demonstrate a simple approach for spontaneously growing double-diamond (or B32) crystals that contain a suitable diamond structure, using DNA to direct the self-assembly process. While diamond symmetry crystals have been grown from much smaller nanoparticles, none of those previous methods suffice for the larger particles needed for photonic applications, whose size must be comparable to the wavelength of visible light. Intriguingly, the crystals we observe do not readily form in previously validated simulations; nor have they been predicted theoretically. This finding suggests that other unexpected microstructures may be accessible using this approach and bodes well for future efforts to inexpensively mass-produce metamaterials for an array of photonic applications.

Face-Dependent Solvent Adsorption: A Comparative Study on the Interfaces of HMX Crystal with Three Solvents.

PubMed

Liu, Yingzhe; Lai, Weipeng; Ma, Yiding; Yu, Tao; Kang, Ying; Ge, Zhongxue

2017-07-27

To understand the crystal-solvent interfacial interactions on the molecular scale, the interfaces between three solvents, that is, acetone, γ-butyrolactone, and cyclohexanone, and three growth faces of 1,3,5,7-tetranitro-1,3,5,7-tetrazocane (HMX) crystal have been investigated with the aid of theoretical chemistry. The results show that the structural features of crystal faces play a critical role in the energetic, structural, and dynamic properties at the interfaces. For each solvent, the same change trend of some properties among the three faces of HMX crystal is observed, including adsorption affinity, local mass density, and solvent diffusion. For example, the rate of solvent diffusion at the three faces ranks as (011) > (110) > (020) regardless of solvent species. This can be attributed to the similar adsorption sites for solvent incorporation at the same face, which are concentrated at the cavities formed by surficial HMX molecules.

Structural transition and enhanced phase transition properties of Se doped Ge2Sb2Te5 alloys

NASA Astrophysics Data System (ADS)

Vinod, E. M.; Ramesh, K.; Sangunni, K. S.

2015-01-01

Amorphous Ge2Sb2Te5 (GST) alloy, upon heating crystallize to a metastable NaCl structure around 150°C and then to a stable hexagonal structure at high temperatures (>=250°C). It has been generally understood that the phase change takes place between amorphous and the metastable NaCl structure and not between the amorphous and the stable hexagonal phase. In the present work, it is observed that the thermally evaporated (GST)1-xSex thin films (0 <= x <= 0.50) crystallize directly to the stable hexagonal structure for x >= 0.10, when annealed at temperatures >= 150°C. The intermediate NaCl structure has been observed only for x < 0.10. Chemically ordered network of GST is largely modified for x >= 0.10. Resistance, thermal stability and threshold voltage of the films are found to increase with the increase of Se. The contrast in electrical resistivity between the amorphous and crystalline phases is about 6 orders of magnitude. The increase in Se shifts the absorption edge to lower wavelength and the band gap widens from 0.63 to 1.05 eV. Higher resistance ratio, higher crystallization temperature, direct transition to the stable phase indicate that (GST)1-xSex films are better candidates for phase change memory applications.

Transition from two-dimensional photonic crystals to dielectric metasurfaces in the optical diffraction with a fine structure

PubMed Central

Rybin, Mikhail V.; Samusev, Kirill B.; Lukashenko, Stanislav Yu.; Kivshar, Yuri S.; Limonov, Mikhail F.

2016-01-01

We study experimentally a fine structure of the optical Laue diffraction from two-dimensional periodic photonic lattices. The periodic photonic lattices with the C4v square symmetry, orthogonal C2v symmetry, and hexagonal C6v symmetry are composed of submicron dielectric elements fabricated by the direct laser writing technique. We observe surprisingly strong optical diffraction from a finite number of elements that provides an excellent tool to determine not only the symmetry but also exact number of particles in the finite-length structure and the sample shape. Using different samples with orthogonal C2v symmetry and varying the lattice spacing, we observe experimentally a transition between the regime of multi-order diffraction, being typical for photonic crystals to the regime where only the zero-order diffraction can be observed, being is a clear fingerprint of dielectric metasurfaces characterized by effective parameters. PMID:27491952

Does Z' equal 1 or 2? Enhanced powder NMR crystallography verification of a disordered room temperature crystal structure of a p38 inhibitor for chronic obstructive pulmonary disease.

PubMed

Widdifield, Cory M; Nilsson Lill, Sten O; Broo, Anders; Lindkvist, Maria; Pettersen, Anna; Svensk Ankarberg, Anna; Aldred, Peter; Schantz, Staffan; Emsley, Lyndon

2017-06-28

The crystal structure of the Form A polymorph of N-cyclopropyl-3-fluoro-4-methyl-5-[3-[[1-[2-[2-(methylamino)ethoxy]phenyl]cyclopropyl]amino]-2-oxo-pyrazin-1-yl]benzamide (i.e., AZD7624), determined using single-crystal X-ray diffraction (scXRD) at 100 K, contains two molecules in the asymmetric unit (Z' = 2) and has regions of local static disorder. This substance has been in phase IIa drug development trials for the treatment of chronic obstructive pulmonary disease, a disease which affects over 300 million people and contributes to nearly 3 million deaths annually. While attempting to verify the crystal structure using nuclear magnetic resonance crystallography (NMRX), we measured 13 C solid-state NMR (SSNMR) spectra at 295 K that appeared consistent with Z' = 1 rather than Z' = 2. To understand this surprising observation, we used multinuclear SSNMR ( 1 H, 13 C, 15 N), gauge-including projector augmented-wave density functional theory (GIPAW DFT) calculations, crystal structure prediction (CSP), and powder XRD (pXRD) to determine the room temperature crystal structure. Due to the large size of AZD7624 (ca. 500 amu, 54 distinct 13 C environments for Z' = 2), static disorder at 100 K, and (as we show) dynamic disorder at ambient temperatures, NMR spectral assignment was a challenge. We introduce a method to enhance confidence in NMR assignments by comparing experimental 13 C isotropic chemical shifts against site-specific DFT-calculated shift distributions established using CSP-generated crystal structures. The assignment and room temperature NMRX structure determination process also included measurements of 13 C shift tensors and the observation of residual dipolar coupling between 13 C and 14 N. CSP generated ca. 90 reasonable candidate structures (Z' = 1 and Z' = 2), which when coupled with GIPAW DFT results, room temperature pXRD, and the assigned SSNMR data, establish Z' = 2 at room temperature. We find that the polymorphic Form A of AZD7624 is maintained at room temperature, although dynamic disorder is present on the NMR timescale. Of the CSP-generated structures, 2 are found to be fully consistent with the SSNMR and pXRD data; within this pair, they are found to be structurally very similar (RMSD 16 = 0.30 Å). We establish that the CSP structure in best agreement with the NMR data possesses the highest degree of structural similarity with the scXRD-determined structure (RMSD 16 = 0.17 Å), and has the lowest DFT-calculated energy amongst all CSP-generated structures with Z' = 2.

Validation of molecular crystal structures from powder diffraction data with dispersion-corrected density functional theory (DFT-D).

PubMed

van de Streek, Jacco; Neumann, Marcus A

2014-12-01

In 2010 we energy-minimized 225 high-quality single-crystal (SX) structures with dispersion-corrected density functional theory (DFT-D) to establish a quantitative benchmark. For the current paper, 215 organic crystal structures determined from X-ray powder diffraction (XRPD) data and published in an IUCr journal were energy-minimized with DFT-D and compared to the SX benchmark. The on average slightly less accurate atomic coordinates of XRPD structures do lead to systematically higher root mean square Cartesian displacement (RMSCD) values upon energy minimization than for SX structures, but the RMSCD value is still a good indicator for the detection of structures that deserve a closer look. The upper RMSCD limit for a correct structure must be increased from 0.25 Å for SX structures to 0.35 Å for XRPD structures; the grey area must be extended from 0.30 to 0.40 Å. Based on the energy minimizations, three structures are re-refined to give more precise atomic coordinates. For six structures our calculations provide the missing positions for the H atoms, for five structures they provide corrected positions for some H atoms. Seven crystal structures showed a minor error for a non-H atom. For five structures the energy minimizations suggest a higher space-group symmetry. For the 225 SX structures, the only deviations observed upon energy minimization were three minor H-atom related issues. Preferred orientation is the most important cause of problems. A preferred-orientation correction is the only correction where the experimental data are modified to fit the model. We conclude that molecular crystal structures determined from powder diffraction data that are published in IUCr journals are of high quality, with less than 4% containing an error in a non-H atom.

Validation of molecular crystal structures from powder diffraction data with dispersion-corrected density functional theory (DFT-D)

PubMed Central

van de Streek, Jacco; Neumann, Marcus A.

2014-01-01

In 2010 we energy-minimized 225 high-quality single-crystal (SX) structures with dispersion-corrected density functional theory (DFT-D) to establish a quantitative benchmark. For the current paper, 215 organic crystal structures determined from X-ray powder diffraction (XRPD) data and published in an IUCr journal were energy-minimized with DFT-D and compared to the SX benchmark. The on average slightly less accurate atomic coordinates of XRPD structures do lead to systematically higher root mean square Cartesian displacement (RMSCD) values upon energy minimization than for SX structures, but the RMSCD value is still a good indicator for the detection of structures that deserve a closer look. The upper RMSCD limit for a correct structure must be increased from 0.25 Å for SX structures to 0.35 Å for XRPD structures; the grey area must be extended from 0.30 to 0.40 Å. Based on the energy minimizations, three structures are re-refined to give more precise atomic coordinates. For six structures our calculations provide the missing positions for the H atoms, for five structures they provide corrected positions for some H atoms. Seven crystal structures showed a minor error for a non-H atom. For five structures the energy minimizations suggest a higher space-group symmetry. For the 225 SX structures, the only deviations observed upon energy minimization were three minor H-atom related issues. Preferred orientation is the most important cause of problems. A preferred-orientation correction is the only correction where the experimental data are modified to fit the model. We conclude that molecular crystal structures determined from powder diffraction data that are published in IUCr journals are of high quality, with less than 4% containing an error in a non-H atom. PMID:25449625

Structure of human thymidylate synthase under low-salt conditions.

PubMed

Lovelace, Leslie L; Minor, Wladek; Lebioda, Lukasz

2005-05-01

Human thymidylate synthase, a target in cancer chemotherapy, was crystallized from PEG 3350 with 30 mM ammonium sulfate (AS) in the crystallization medium. The crystals are isomorphous with the high-salt crystals ( approximately 2.0 M AS) and the structure has been solved and refined (R = 22.6%, R(free) = 24.3%) at 1.8 A resolution. The high- and low-AS-concentration structures are quite similar, with loop 181-197 is in the inactive conformation. Also, residues 95-106 and 129-135 (eukaryotic inserts region) show high mobility as assessed by poor electron density and high values of crystallographic temperature factors (residues 1-25 and 108-129 are disordered in both structures). The high mobility of this region may reflect the situation at physiological ionic strength. Of the four sulfate ions observed bound at 2.0 M AS, only two are present at 30 mM AS. The inactive conformation appears to be stabilized by the side chain of Val3 or a leucine residue from the disordered regions. The low-salt conditions of these crystals should be much more suitable for the study of thymidylate synthase inhibitors, especially those that utilize sulfate-binding sites to stabilize the inactive conformation of loop 181-197.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rashin, Alexander A., E-mail: alexander-rashin@hotmail.com; Iowa State University, 112 Office and Lab Bldg, Ames, IA 50011-3020; Domagalski, Marcin J.

Conformational differences between myoglobin structures are studied. Most structural differences in whale myoglobin beyond the uncertainty threshold can be correlated with a few specific structural factors. There are always exceptions and a search for additional factors is needed. The results might have serious implications for biological insights from conformational differences. Validation of general ideas about the origins of conformational differences in proteins is critical in order to arrive at meaningful functional insights. Here, principal component analysis (PCA) and distance difference matrices are used to validate some such ideas about the conformational differences between 291 myoglobin structures from sperm whale, horsemore » and pig. Almost all of the horse and pig structures form compact PCA clusters with only minor coordinate differences and outliers that are easily explained. The 222 whale structures form a few dense clusters with multiple outliers. A few whale outliers with a prominent distortion of the GH loop are very similar to the cluster of horse structures, which all have a similar GH-loop distortion apparently owing to intermolecular crystal lattice hydrogen bonds to the GH loop from residues near the distal histidine His64. The variations of the GH-loop coordinates in the whale structures are likely to be owing to the observed alternative intermolecular crystal lattice bond, with the change to the GH loop distorting bonds correlated with the binding of specific ‘unusual’ ligands. Such an alternative intermolecular bond is not observed in horse myoglobins, obliterating any correlation with the ligands. Intermolecular bonds do not usually cause significant coordinate differences and cannot be validated as their universal cause. Most of the native-like whale myoglobin structure outliers can be correlated with a few specific factors. However, these factors do not always lead to coordinate differences beyond the previously determined uncertainty thresholds. The binding of unusual ligands by myoglobin, leading to crystal-induced distortions, suggests that some of the conformational differences between the apo and holo structures might not be ‘functionally important’ but rather artifacts caused by the binding of ‘unusual’ substrate analogs. The causes of P6 symmetry in myoglobin crystals and the relationship between crystal and solution structures are also discussed.« less

Single crystal growth and characterization of kagomé-lattice shandites Co3Sn2-xInxS2

NASA Astrophysics Data System (ADS)

Kassem, Mohamed A.; Tabata, Yoshikazu; Waki, Takeshi; Nakamura, Hiroyuki

2015-09-01

Single crystals of the shandite-type half metallic ferromagnet Co3Sn2S2, and its In-substituted compounds, Co3Sn2-xInxS2 (0

Non-triglyceride components modulate the fat crystal network of palm kernel oil and coconut oil.

PubMed

Chai, Xiuhang; Meng, Zong; Jiang, Jiang; Cao, Peirang; Liang, Xinyu; Piatko, Michael; Campbell, Shawn; Lo, Seong Koon; Liu, Yuanfa

2018-03-01

PKO and CNO are composed of 97-98% triacylglycerols and 2-3% minor non-triglyceride components (FFA, DAG and MAG). Triglycerides were separated from minor components by chromatographic method. The lipid composition, thermal properties, polymorphism, isothermal crystallization behavior, nanostructure and microstructure of PKO, PKO-TAG, CNO and CNO-TAG were evaluated. Removal of minor components had no effect on lipid composition and equilibrium solid fat contents. However, presence of minor components did increase the slip melting point and promoted the onset of crystallization from DSC crystallization profiles. The thickness of the nanoscale crystals increased with no polymorphic transformation after removing the minor components. Crystallization kinetics revealed that minor components decreased crystal growth rate with higher t 1/2 . Sharp changes in the values of the Avrami constant k and exponent n were observed for all fats around 10°C. Increases in n around 10°C indicated a change from one-dimensional to multi-dimensional growth . From the results of polarized light micrographs, the transformation from the coarser crystal structure to tiny crystal structure occurred in microstructure networks at the action of minor components. Copyright © 2017 Elsevier Ltd. All rights reserved.

The transmission spectrum of sound through a phononic crystal subjected to liquid flow

NASA Astrophysics Data System (ADS)

Declercq, Nico F.; Chehami, Lynda; Moiseyenko, Rayisa P.

2018-01-01

The influence of liquid-flow up to 7 mm/s is examined on transmission spectra of phononic crystals, revealing a potential use for slow liquid-flow measurement techniques. It is known that transmission of ultrasound through a phononic crystal is determined by its periodicity and depends on the material characteristics of the crystal's constituents. Here, the crystal consists of metal rods with the space in between filled with water. Previous studies have assumed still water in the crystal, and here, we consider flowing liquid. First, the crystal bandgaps are investigated in still water, and the results of transmission experiments are compared with theoretical band structures obtained with the finite element method. Then, changes in transmission spectra are investigated for different speeds of liquid flow. Two situations are investigated: a crystal is placed with a principal symmetry axis in the flow direction ( ΓX) and then at an angle ( ΓM). The good stability of the bandgap structure of the transmission spectrum for both directions is observed, which may be of importance for the application of phononic crystals as acoustic filters in an environment of flowing liquid. Minor transmission amplitude changes on the other hand reveal a possibility for slow liquid flow measurements.

Shear-induced partial translational ordering of a colloidal solid

NASA Astrophysics Data System (ADS)

Ackerson, B. J.; Clark, N. A.

1984-08-01

Highly charged submicrometer plastic spheres suspended in water at low ionic strength will order spontaneously into bcc crystals or polycrystals. A simple linear shear orients and disorders these crystals by forcing (110) planes to stack normal to the shear gradient and to slide relative to each other with a <111> direction parallel to the solvent flow. In this paper we analyze in detail the disordering and flow processes occurring beyond the intrinsic elastic limit of the bcc crystal. We are led to a model in which the flow of a colloidal crystal is interpreted as a fundamentally different process from that found in atomic crystals. In the colloidal crystal the coupling of particle motion to the background fluid forces a homogeneous flow, where every layer is in motion relative to its neighboring layers. In contrast, the plastic flow in an atomic solid is defect mediated flow. At the lowest applied stress, the local bcc order in the colloidal crystal exhibits shear strains both parallel and perpendicular to the direction of the applied stress. The magnitude of these deformations is estimated using the configurational energy for bcc and distorted bcc crystals, assuming a screened Coulomb pair interaction between colloidal particles. As the applied stress is increased, the intrinsic elastic limit of the crystal is exceeded and the crystal begins to flow with adjacent layers executing an oscillatory path governed by the balance of viscous and screened Coulomb forces. The path takes the structure from the bcc1 and bcc2 twins observed at zero shear to a distorted two-dimensional hcp structure at moderate shear rates, with a loss of interlayer registration as the shear is increased. This theoretical model is consistent with other experimental observations, as well.

Structures of the Mycobacterium tuberculosis GlpX protein (class II fructose-1,6-bisphosphatase): implications for the active oligomeric state, catalytic mechanism and citrate inhibition

DOE PAGES

Wolf, Nina M.; Gutka, Hiten J.; Movahedzadeh, Farahnaz; ...

2018-04-03

The crystal structures of native class II fructose-1,6-bisphosphatase (FBPaseII) from Mycobacterium tuberculosis at 2.6 Å resolution and two active-site protein variants are presented. The variants were complexed with the reaction product fructose 6-phosphate (F6P). The Thr84Ala mutant is inactive, while the Thr84Ser mutant has a lower catalytic activity. The structures reveal the presence of a 222 tetramer, similar to those described for fructose-1,6/sedoheptulose-1,7-bisphosphatase from Synechocystis (strain 6803) as well as the equivalent enzyme from Thermosynechococcus elongatus . This homotetramer corresponds to a homologous oligomer that is present but not described in the crystal structure of FBPaseII from Escherichia coli and ismore » probably conserved in all FBPaseIIs. The constellation of amino-acid residues in the active site of FBPaseII from M. tuberculosis ( Mt FBPaseII) is conserved and is analogous to that described previously for the E. coli enzyme. Moreover, the structure of the active site of the partially active (Thr84Ser) variant and the analysis of the kinetics are consistent with the previously proposed catalytic mechanism. The presence of metabolites in the crystallization medium (for example citrate and malonate) and in the corresponding crystal structures of Mt FBPaseII, combined with their observed inhibitory effect, could suggest the existence of an uncharacterized inhibition of this class of enzymes besides the allosteric inhibition by adenosine monophosphate observed for the Synechocystis enzyme. The structural and functional insights derived from the structure of Mt FBPaseII will provide critical information for the design of lead inhibitors, which will be used to validate this target for future chemical intervention.« less

Structures of the Mycobacterium tuberculosis GlpX protein (class II fructose-1,6-bisphosphatase): implications for the active oligomeric state, catalytic mechanism and citrate inhibition

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wolf, Nina M.; Gutka, Hiten J.; Movahedzadeh, Farahnaz

The crystal structures of native class II fructose-1,6-bisphosphatase (FBPaseII) from Mycobacterium tuberculosis at 2.6 Å resolution and two active-site protein variants are presented. The variants were complexed with the reaction product fructose 6-phosphate (F6P). The Thr84Ala mutant is inactive, while the Thr84Ser mutant has a lower catalytic activity. The structures reveal the presence of a 222 tetramer, similar to those described for fructose-1,6/sedoheptulose-1,7-bisphosphatase from Synechocystis (strain 6803) as well as the equivalent enzyme from Thermosynechococcus elongatus . This homotetramer corresponds to a homologous oligomer that is present but not described in the crystal structure of FBPaseII from Escherichia coli and ismore » probably conserved in all FBPaseIIs. The constellation of amino-acid residues in the active site of FBPaseII from M. tuberculosis ( Mt FBPaseII) is conserved and is analogous to that described previously for the E. coli enzyme. Moreover, the structure of the active site of the partially active (Thr84Ser) variant and the analysis of the kinetics are consistent with the previously proposed catalytic mechanism. The presence of metabolites in the crystallization medium (for example citrate and malonate) and in the corresponding crystal structures of Mt FBPaseII, combined with their observed inhibitory effect, could suggest the existence of an uncharacterized inhibition of this class of enzymes besides the allosteric inhibition by adenosine monophosphate observed for the Synechocystis enzyme. The structural and functional insights derived from the structure of Mt FBPaseII will provide critical information for the design of lead inhibitors, which will be used to validate this target for future chemical intervention.« less

Synthesis and crystal structure of a new aluminum-silicon-nitride phosphor containing boron, Ba5B2Al4Si32N52:Eu

NASA Astrophysics Data System (ADS)

Yoshimura, Fumitaka; Yamane, Hisanori; Nagasako, Makoto

2017-07-01

Single crystals of Ba5B2Al4Si32N52:Eu were grown on the wall of a boron nitride crucible by heating a starting mixture of binary nitrides at 2050 °C and a N2 pressure of 0.85 MPa. The fundamental reflections of X-ray diffraction (XRD) for the crystals were indexed with triclinic cell parameters, a=9.7879(11) Å, b=9.7920(11) Å, c=12.7226(15) Å, α=96.074(4)°, β=112.330(3)°, and γ=94.080(4)°. Streak lines were observed between the fundamental reflections in the direction of the c* axis in the oscillation XRD images and selected area electron diffraction (SAED) patterns, indicating stacking faults in the structure. The atomic images of stacking faults with a slip system of (0 0 1)[-1 1 0]/3, and displacement of a Ba atom layer with (0 0 1)[-1 -1 0]/6 were observed with a scanning transmission electron microscope (STEM). The models of the basic (normal-stacking) structure with space group P1 and local structures of the stacking faults are herein presented. The single crystals emitted blue light with a peak wavelength of 472 nm and a full width at half maximum of 78 nm under 365 nm excitation.

Shock Induced Chemistry: Application and Development of Ultrafast Nonlinear Probes of the Energy Dynamics of Molecules in Solids

DTIC Science & Technology

1988-01-01

crystal and in a mixed crystal. The mixed crystal data was taken with resonance enhancement by the pentacene .. ... 7 Accesiw, r)re 0IE r)) NiS cR4~ IE~) D...observations as well as their implications about the nature of the coupling of a localized defect to the bulk modes of the crystal have been analyzed [7...matter systems, in addition to phonon induced fluctuations of local mechanical properties, there can be much slower timescale structural evolution

XANES study of Fe-implanted strontium titanate

NASA Astrophysics Data System (ADS)

Lobacheva, O.; Goncharova, L. V.; Chavarha, M.; Sham, T. K.

2014-03-01

Properties of strontium titanate SrTiO3 (STO) depend to a great extent on the substitutional dopants and defects of crystal structure. The ion beam implantation method was used for doping STO (001) crystals with Fe at different doses. Implanted samples were then annealed at 350°C in oxygen to induce recrystallization and remove oxygen vacancies produced during ion implantation process. The effect of Fe doping and post-implantation annealing was studied by X-ray Absorption Near Edge Spectroscopy (XANES) method and Superconducting Quantum Interference Device (SQUID). XANES allowed to monitor the change in structure of STO crystals and in the local environment of Fe following the implantation and annealing steps. SQUID measurements revealed correlation between magnetic moment and Fe implantation dose. Ferromagnetic hysteresis was observed on selected Fe-implanted STO at 5 K. The observed magnetic properties can be correlated with the several Fe oxide phases in addition to the presence of O/Ti vacancies.

Experimental demonstration of two-dimensional hybrid waveguide-integrated plasmonic crystals on silicon-on-insulator platform

NASA Astrophysics Data System (ADS)

Ren, Guanghui; Yudistira, Didit; Nguyen, Thach G.; Khodasevych, Iryna; Schoenhardt, Steffen; Berean, Kyle J.; Hamm, Joachim M.; Hess, Ortwin; Mitchell, Arnan

2017-07-01

Nanoscale plasmonic structures can offer unique functionality due to extreme sub-wavelength optical confinement, but the realization of complex plasmonic circuits is hampered by high propagation losses. Hybrid approaches can potentially overcome this limitation, but only few practical approaches based on either single or few element arrays of nanoantennas on dielectric nanowire have been experimentally demonstrated. In this paper, we demonstrate a two dimensional hybrid photonic plasmonic crystal interfaced with a standard silicon photonic platform. Off resonance, we observe low loss propagation through our structure, while on resonance we observe strong propagation suppression and intense concentration of light into a dense lattice of nanoscale hot-spots on the surface providing clear evidence of a hybrid photonic plasmonic crystal bandgap. This fully integrated approach is compatible with established silicon-on-insulator (SOI) fabrication techniques and constitutes a significant step toward harnessing plasmonic functionality within SOI photonic circuits.

High-Pressure Structural Response of an Insensitive Energetic Crystal: Dihydroxylammonium 5,5'-Bistetrazole-1,1'-diolate (TKX-50)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dreger, Zbigniew A.; Stash, Adam I.; Yu, Zhi-Gang

2017-03-06

The structural response of a novel, insensitive energetic crystal—dihydroxylammonium 5,5'-bistetrazole-1,1'-diolate (TKX-50)—was examined under high pressure. Using synchrotron single-crystal X-ray diffraction measurements, details of molecular, intermolecular, and crystal changes were determined to ~10 GPa to understand its structural stability. The experimental results showed that TKX-50 exhibits highly anisotropic compression and significantly lower volume compressibility than currently known energetic crystals. These results are found to be in general agreement with our previous predictions from the DFT calculations. Additionally, the experimental data revealed anomalous compression—an expansion of the unit cell along the a axis (negative linear compressibility, NLC) upon compression to ~3 GPa.more » The structural analyses demonstrated that this unusual effect, the first such observation in an energetic crystal, is a consequence of the highly anisotropic response of 3D motifs, comprised of two parallel anions [(C 2N 8O 2) 2–] linked with two cations [(NH 3OH) +] through four strong hydrogen bonds. The present results demonstrate that the structural stability of TKX-50 is controlled by the strong and highly anisotropic intermolecular interactions, and these may contribute to its shock insensitivity.« less

High-pressure structural response of an insensitive energetic crystal: Dihydroxylammonium 5,5'-bistetrazole-1,1'-diolate (TKX-50)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dreger, Zbigniew A.; Stash, Adam I.; Yu, Zhi -Gang

The structural response of a novel, insensitive energetic crystal—dihydroxylammonium 5,5'-bistetrazole-1,1'-diolate (TKX-50)—was examined under high pressure. Using synchrotron single-crystal X-ray diffraction measurements, details of molecular, intermolecular, and crystal changes were determined to ~10 GPa to understand its structural stability. The experimental results showed that TKX-50 exhibits highly anisotropic compression and significantly lower volume compressibility than currently known energetic crystals. These results are found to be in general agreement with our previous predictions from the DFT calculations. Additionally, the experimental data revealed anomalous compression—an expansion of the unit cell along the a axis (negative linear compressibility, NLC) upon compression to ~3 GPa.more » The structural analyses demonstrated that this unusual effect, the first such observation in an energetic crystal, is a consequence of the highly anisotropic response of 3D motifs, comprised of two parallel anions [(C 2N 8O 2) 2–] linked with two cations [(NH 3OH) +] through four strong hydrogen bonds. Finally, the present results demonstrate that the structural stability of TKX-50 is controlled by the strong and highly anisotropic intermolecular interactions, and these may contribute to its shock insensitivity.« less

High-pressure structural response of an insensitive energetic crystal: Dihydroxylammonium 5,5'-bistetrazole-1,1'-diolate (TKX-50)

DOE PAGES

Dreger, Zbigniew A.; Stash, Adam I.; Yu, Zhi -Gang; ...

2017-02-28

The structural response of a novel, insensitive energetic crystal—dihydroxylammonium 5,5'-bistetrazole-1,1'-diolate (TKX-50)—was examined under high pressure. Using synchrotron single-crystal X-ray diffraction measurements, details of molecular, intermolecular, and crystal changes were determined to ~10 GPa to understand its structural stability. The experimental results showed that TKX-50 exhibits highly anisotropic compression and significantly lower volume compressibility than currently known energetic crystals. These results are found to be in general agreement with our previous predictions from the DFT calculations. Additionally, the experimental data revealed anomalous compression—an expansion of the unit cell along the a axis (negative linear compressibility, NLC) upon compression to ~3 GPa.more » The structural analyses demonstrated that this unusual effect, the first such observation in an energetic crystal, is a consequence of the highly anisotropic response of 3D motifs, comprised of two parallel anions [(C 2N 8O 2) 2–] linked with two cations [(NH 3OH) +] through four strong hydrogen bonds. Finally, the present results demonstrate that the structural stability of TKX-50 is controlled by the strong and highly anisotropic intermolecular interactions, and these may contribute to its shock insensitivity.« less

Some observations on rutherfordine

USGS Publications Warehouse

Clark, Joan R.; Christ, C.L.

1956-01-01

The optical properties of rutherfordine, UO2CO3, previously determined on microscopic crystals, have been redetermined on considerably larger crystals; and the relations among the indices of refraction, the morphology, and the crystal structure have been examined. Rutherfordine is orthorhombic, biaxial positive, with α = 1.715, β = 1.730, γ = 1.795, 2V = 53° (calc.); X = b, Y = c (elongation, Z = a. The crystal structure of UO2CO 3 consists of layers of carbonate groups parallel to (010) with linear (O-U-O) ions normal to the layers. The indices β and γ correspond to vibration directions parallel to layers; the unexpectedly large difference in value between β and γ is ascribed to the optical anisotropy of the uranium-oxygen bonding in the layer. Indexed X-ray powder data are given.

Direct imaging of isofrequency contours in photonic structures

DOE PAGES

Regan, E. C.; Igarashi, Y.; Zhen, B.; ...

2016-11-25

The isofrequency contours of a photonic crystal are important for predicting and understanding exotic optical phenomena that are not apparent from high-symmetry band structure visualizations. We demonstrate a method to directly visualize the isofrequency contours of high-quality photonic crystal slabs that show quantitatively good agreement with numerical results throughout the visible spectrum. Our technique relies on resonance-enhanced photon scattering from generic fabrication disorder and surface roughness, so it can be applied to general photonic and plasmonic crystals or even quasi-crystals. We also present an analytical model of the scattering process, which explains the observation of isofrequency contours in our technique.more » Furthermore, the isofrequency contours provide information about the characteristics of the disorder and therefore serve as a feedback tool to improve fabrication processes.« less

Astronaut Scott Parazynski works with PCG experiment on middeck

NASA Image and Video Library

1994-11-14

STS066-13-029 (3-14 Nov 1994) --- On the Space Shuttle Atlantis' mid-deck, astronaut Scott E. Parazynski, mission specialist, works at one of two areas onboard the Shuttle which support the Protein Crystal Growth (PCG) experiment. This particular section is called the Vapor Diffusion Apparatus (VDA), housed in a Single Locker Thermal Enclosure (STES). Together with the Crystal Observation System, housed in the Thermal Enclosure System (COS/TES) the VDA represents the continuing research into the structures of proteins and other macromolecules such as viruses. In addition to using the microgravity of space to grow high-quality protein crystals for structural analyses, the experiments are expected to help develop technologies and methods to improve the protein crystallization process on Earth as well as in space.

Viral capsomere structure, surface processes and growth kinetics in the crystallization of macromolecular crystals visualized by in situ atomic force microscopy

NASA Astrophysics Data System (ADS)

Malkin, A. J.; Kuznetsov, Yu. G.; McPherson, A.

2001-11-01

In situ atomic force microscopy (AFM) was used to investigate surface evolution during the growth of single crystals of turnip yellow mosaic virus (TYMV), cucumber mosaic virus (CMV) and glucose isomerase. Growth of these crystals proceeded by two-dimensional (2D) nucleation. For glucose isomerase, from supersaturation dependencies of tangential step rates and critical step length, the kinetic coefficients of the steps and the surface free energy of the step edge were calculated for different crystallographic directions. The molecular structure of the step edges, the adsorption of individual virus particles and their aggregates, and the initial stages of formation of 2D nuclei on the surfaces of TYMV and CMV crystals were recorded. The surfaces of individual TYMV virions within crystals were visualized, and hexameric and pentameric capsomers of the T=3 capsids were clearly resolved. This, so far as we are aware, is the first direct visualization of the capsomere structure of a virus by AFM. In the course of recording the in situ development of the TYMV crystals, a profound restructuring of the surface arrangement was observed. This transformation was highly cooperative in nature, but the transitions were unambiguous and readily explicable in terms of an organized loss of classes of virus particles from specific lattice positions.

Two-step crystal growth mechanism during crystallization of an undercooled Ni50Al50 alloy

NASA Astrophysics Data System (ADS)

An, Simin; Li, Jiahao; Li, Yang; Li, Shunning; Wang, Qi; Liu, Baixin

2016-08-01

Crystallization processes are always accompanied by the emergence of multiple intermediate states, of which the structures and transition dynamics are far from clarity, since it is difficult to experimentally observe the microscopic pathway. To insight the structural evolution and the crystallization dynamics, we perform large-scale molecular dynamics simulations to investigate the time-dependent crystallization behavior of the NiAl intermetallic upon rapid solidification. The simulation results reveal that the crystallization process occurs via a two-step growth mechanism, involving the formation of initial non-equilibrium long range order (NLRO) regions and of the subsequent equilibrium long range order (ELRO) regions. The formation of the NLRO regions makes the grains rather inhomogeneous, while the rearrangement of the NLRO regions into the ELRO regions makes the grains more ordered and compact. This two-step growth mechanism is actually controlled by the evolution of the coordination polyhedra, which are characterized predominantly by the transformation from five-fold symmetry to four-fold and six-fold symmetry. From liquids to NLRO and further to ELRO, the five-fold symmetry of these polyhedra gradually fades, and finally vanishes when B2 structure is distributed throughout the grain bulk. The energy decrease along the pathway further implies the reliability of the proposed crystallization processes.

Analyzing multistep homogeneous nucleation in vapor-to-solid transitions using molecular dynamics simulations

NASA Astrophysics Data System (ADS)

Tanaka, Kyoko K.; Diemand, Jürg; Tanaka, Hidekazu; Angélil, Raymond

2017-08-01

In this paper, we present multistep homogeneous nucleations in vapor-to-solid transitions as revealed by molecular dynamics simulations on Lennard-Jones molecules, where liquidlike clusters are created and crystallized. During a long, direct N V E (constant volume, energy, and number of molecules) involving the integration of (1.9 -15 )× 106 molecules in up to 200 million steps (=4.3 μ s ), crystallization in many large, supercooled nanoclusters is observed once the liquid clusters grow to a certain size (˜800 molecules for the case of T ≃0.5 ɛ /k ). In the simulations, we discovered an interesting process associated with crystallization: the solid clusters lost 2-5 % of their mass during crystallization at low temperatures below their melting temperatures. Although the crystallized clusters were heated by latent heat, they were stabilized by cooling due to evaporation. The clusters crystallized quickly and completely except at surface layers. However, they did not have stable crystal structures, rather they had metastable structures such as icosahedral, decahedral, face-centered-cubic-rich (fcc-rich), and hexagonal-close-packed-rich (hcp-rich). Several kinds of cluster structures coexisted in the same size range of ˜1000 -5000 molecules. Our results imply that multistep nucleation is a common first stage of condensation from vapor to solid.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Stauber, Mark; Jakoncic, Jean; Berger, Jacob

Chiral control of crystallization has ample precedent in the small-molecule world, but relatively little is known about the role of chirality in protein crystallization. In this study, lysozyme was crystallized in the presence of the chiral additive 2-methyl-2,4-pentanediol (MPD) separately using the R and S enantiomers as well as with a racemic RS mixture. Crystals grown with ( R)-MPD had the most order and produced the highest resolution protein structures. This result is consistent with the observation that in the crystals grown with ( R)-MPD and ( RS)-MPD the crystal contacts are made by ( R)-MPD, demonstrating that there ismore » preferential interaction between lysozyme and this enantiomer. These findings suggest that chiral interactions are important in protein crystallization.« less

Crystalline perfection and optical studies of L-Histidinium dihydrogen phosphate orthophosphoric acid (LHDP) single crystals

NASA Astrophysics Data System (ADS)

Ittyachan, Reena; Arunkumar, A.; Bhagavannarayana, G.

2015-10-01

Single crystals of L-Histidinium dihydrogenphosphate orthophosphoric acid (LHDP) were grown by slow evaporation solution growth technique. The grown crystals were confirmed by single crystal X-ray diffraction techniques. The HRXRD rocking curve measurements revealed the crystalline perfection of grown crystal and the absence of structural grain boundaries. The lower optical cut-off wavelength for this crystal was observed at 240 nm. The third order nonlinear refractive index (n2), nonlinear absorption coefficient (β) and susceptibility (χ(3)) were calculated by Z-scan studies using Nd: YAG laser as a source. The single shot laser damage threshold of grown crystal was measured to be 6.286 GW/cm2 using Nd: YAG laser.

Crystal structure of low-symmetry rondorfite

NASA Astrophysics Data System (ADS)

Rastsvetaeva, R. K.; Zadov, A. E.; Chukanov, N. V.

2008-03-01

The crystal structure of an aluminum-rich variety of the mineral rondorfite with the composition Ca16[Mg2(Si7Al)(O31OH)]Cl4 from the skarns of the Verkhne-Chegemskoe plateau (the Kabardino-Balkarian Republic, the Northern Caucasus Region, Russia) was solved in the triclinic space group with the unit-cell parameters a = 15.100(2) Å, b = 15.110(2) Å, c = 15.092(2) Å, α = 90.06(1)°, β = 90.01(1)°, γ = 89.93(1)°, Z = 4, sp. gr. P1. The structural model consisting of 248 independent atoms was determined by the phase-correction method and refined to R = 3.8% with anisotropic displacement parameters based on all 7156 independent reflections with 7156 F > 3σ( F). The crystal structure is based on pentamers consisting of four Si tetrahedra linked by the central Mg tetrahedron. The structure can formally be refined in the cubic space group ( a = 15.105 Å, sp. gr. Fd overline 3 , seven independent positions) with anisotropic displacement parameters to R = 2.74% based on 579 reflections with F > 3σ( F) without accounting for more than 1000 observed reflections, which are inconsistent with the cubic symmetry of the crystal structure.

Crystallization of lysozyme with ( R)-, ( S)- and ( RS)-2-methyl-2,4-pentanediol

DOE PAGES

Stauber, Mark; Jakoncic, Jean; Berger, Jacob; ...

2015-03-01

Chiral control of crystallization has ample precedent in the small-molecule world, but relatively little is known about the role of chirality in protein crystallization. In this study, lysozyme was crystallized in the presence of the chiral additive 2-methyl-2,4-pentanediol (MPD) separately using the R and S enantiomers as well as with a racemic RS mixture. Crystals grown with ( R)-MPD had the most order and produced the highest resolution protein structures. This result is consistent with the observation that in the crystals grown with ( R)-MPD and ( RS)-MPD the crystal contacts are made by ( R)-MPD, demonstrating that there ismore » preferential interaction between lysozyme and this enantiomer. These findings suggest that chiral interactions are important in protein crystallization.« less

High-speed observation of ZnO microspherical crystals produced by laser ablation (Conference Presentation)

NASA Astrophysics Data System (ADS)

Nakamura, Daisuke; Tasaki, Ryohei; Fujiwara, Yuki; Nagasaki, Fumiaki; Higashihata, Mitsuhiro; Ikenoue, Hiroshi; Okada, Tatsuo

2017-03-01

ZnO nano/microstructures have attracted much attention as building blocks for optoelectronic devices because of their high crystalline quality and unique structures. We have succeeded in synthesizing ZnO microspherical crystals by a simple atmospheric laser ablation method, and demonstrated ultraviolet whispering-gallery-mode lasing from the spheres. In the microsphere synthesis process, molten droplets formed into spherical shapes by surface tension, and crystalized during ejection from the ablation spot. In this study, we observed the generation of ZnO microspheres by high-speed camera. Now we are trying to control and manipulate the microspheres using a vortex beam.

Defect types and room-temperature ferromagnetism in undoped rutile TiO2 single crystals

NASA Astrophysics Data System (ADS)

Li, Dong-Xiang; Qin, Xiu-Bo; Zheng, Li-Rong; Li, Yu-Xiao; Cao, Xing-Zhong; Li, Zhuo-Xin; Yang, Jing; Wang, Bao-Yi

2013-03-01

Room-temperature ferromagnetism has been experimentally observed in annealed rutile TiO2 single crystals when a magnetic field is applied parallel to the sample plane. By combining X-ray absorption near the edge structure spectrum and positron annihilation lifetime spectroscopy, Ti3+—VO defect complexes (or clusters) have been identified in annealed crystals at a high vacuum. We elucidate that the unpaired 3d electrons in Ti3+ ions provide the observed room-temperature ferromagnetism. In addition, excess oxygen ions in the TiO2 lattice could induce a number of Ti vacancies which obviously increase magnetic moments.

Packing interface energetics in different crystal forms of the λ Cro dimer.

PubMed

Ahlstrom, Logan S; Miyashita, Osamu

2014-07-01

Variation among crystal structures of the λ Cro dimer highlights conformational flexibility. The structures range from a wild type closed to a mutant fully open conformation, but it is unclear if each represents a stable solution state or if one may be the result of crystal packing. Here we use molecular dynamics (MD) simulation to investigate the energetics of crystal packing interfaces and the influence of site-directed mutagenesis on them in order to examine the effect of crystal packing on wild type and mutant Cro dimer conformation. Replica exchange MD of mutant Cro in solution shows that the observed conformational differences between the wild type and mutant protein are not the direct consequence of mutation. Instead, simulation of Cro in different crystal environments reveals that mutation affects the stability of crystal forms. Molecular Mechanics Poisson-Boltzmann Surface Area binding energy calculations reveal the detailed energetics of packing interfaces. Packing interfaces can have diverse properties in strength, energetic components, and some are stronger than the biological dimer interface. Further analysis shows that mutation can strengthen packing interfaces by as much as ∼5 kcal/mol in either crystal environment. Thus, in the case of Cro, mutation provides an additional energetic contribution during crystal formation that may stabilize a fully open higher energy state. Moreover, the effect of mutation in the lattice can extend to packing interfaces not involving mutation sites. Our results provide insight into possible models for the effect of crystallization on Cro conformational dynamics and emphasize careful consideration of protein crystal structures. © 2013 Wiley Periodicals, Inc.

Packing Interface Energetics in Different Crystal Forms of the λ Cro Dimer

PubMed Central

Ahlstrom, Logan S.; Miyashita, Osamu

2014-01-01

Variation among crystal structures of the λ Cro dimer highlights conformational flexibility. The structures range from a wild type closed to a mutant fully open conformation, but it is unclear if each represents a stable solution state or if one may be the result of crystal packing. Here we use molecular dynamics (MD) simulation to investigate the energetics of crystal packing interfaces and the influence of site-directed mutagenesis on them, in order to examine the effect of crystal packing on wild type and mutant Cro dimer conformation. Replica exchange MD of mutant Cro in solution shows that the observed conformational differences between the wild type and mutant protein are not the direct consequence of mutation. Instead, simulation of Cro in different crystal environments reveals that mutation affects the stability of crystal forms. Molecular Mechanics Poisson-Boltzmann Surface Area binding energy calculations reveal the detailed energetics of packing interfaces. Packing interfaces can have diverse properties in strength, energetic components, and some are stronger than the biological dimer interface. Further analysis shows that mutation can strengthen packing interfaces by as much as ~5 kcal/mol in either crystal environment. Thus, in the case of Cro, mutation provides an additional energetic contribution during crystal formation that may stabilize a fully open higher energy state. Moreover, the effect of mutation in the lattice can extend to packing interfaces not involving mutation sites. Our results provide insight into possible models for the effect of crystallization on Cro conformational dynamics and emphasize careful consideration of protein crystal structures. PMID:24218107

Synthesis, crystal structure, and magnetic properties of two-dimensional divalent metal glutarate/dipyridylamine coordination polymers, with a single crystal-to-single crystal transformation in the copper derivative

DOE Office of Scientific and Technical Information (OSTI.GOV)

Montney, Matthew R.; Supkowski, Ronald M.; Staples, Richard J.

Hydrothermal reaction of divalent metal chlorides with glutaric acid and 4,4'-dipyridylamine (dpa) has afforded an isostructural family of coordination polymers with formulation [M(glu)(dpa)]{sub n} (M=Co (1), Ni (2), Cu (3); glu=glutarate). Square pyramidal coordination is seen in 1-3, with semi-ligation of a sixth donor to produce a '5+1' extended coordination sphere. Neighboring metal atoms are linked into 1D [M(glu)]{sub n} neutral chains through chelating/monodentate bridging glutarate moieties with a syn-anti binding mode, and semi-chelation of the pendant carboxylate oxygen. These chains further connect into 2D layers through dipodal dpa ligands. Neighboring layers stack into the pseudo 3D crystal structure ofmore » 1-3 through supramolecular hydrogen bonding between dpa amine units and the semi-chelated glutarate oxygen atoms. The variable temperature magnetic behavior of 1-3 was explored and modeled as infinite 1D Heisenberg chains. Notably, complex 3 undergoes a thermally induced single crystal-to-single crystal transformation between centric and acentric space groups, with a conformationally disordered unilayer structure at 293 K and an ordered bilayer structure at 173 K. All materials were further characterized via infrared spectroscopy and elemental and thermogravimetric analyses. - Graphical abstract: The coordination polymers [M(glu)(dpa)]{sub n} (M=Co (1), Ni (2), Cu (3); glu=glutarate, dpa=4,4'-dipyridylamine) exhibit 2D layer structures based on 1D [M(glu)]{sub n} chains linked through dpa tethers. Antiferromagnetic coupling is observed for 2 and 3, while ferromagnetism is predominant in 1. Compound 3 undergoes a thermally induced single crystal-to-single crystal transformation from an acentric to a centrosymmetric space group.« less

The Crystal Structure of Micro- and Nanopowders of ZnS Studied by EPR of Mn2+ and XRD.

PubMed

Nosenko, Valentyna; Vorona, Igor; Grachev, Valentyn; Ishchenko, Stanislav; Baran, Nikolai; Becherikov, Yurii; Zhuk, Anton; Polishchuk, Yuliya; Kladko, Vasyl; Selishchev, Alexander

2016-12-01

The crystal structure of micro- and nanopowders of ZnS doped with different impurities was analyzed by the electron paramagnetic resonance (EPR) of Mn 2+ and XRD methods. The powders of ZnS:Cu, ZnS:Mn, ZnS:Co, and ZnS:Eu with the particle sizes of 5-7 μm, 50-200 nm, 7-10 μm, and 5-7 nm, respectively, were studied. Manganese was incorporated in the crystal lattice of all the samples as uncontrolled impurity or by doping. The Mn 2+ ions were used as EPR structural probes. It is found that the ZnS:Cu has the cubic structure, the ZnS:Mn has the hexagonal structure with a rhombic distortion, the ZnS:Co is the mixture of the cubic and hexagonal phases in the ratio of 1:10, and the ZnS:Eu has the cubic structure and a distorted cubic structure with stacking defects in the ratio 3:1. The EPR technique is shown to be a powerful tool in the determination of the crystal structure for mixed-polytype ZnS powders and powders with small nanoparticles. It allows observation of the stacking defects, which is revealed in the XRD spectra.

Resonant Coherent Excitation of Hydrogen-Like Ar Ions to the n =: 3 States

NASA Astrophysics Data System (ADS)

Azuma, T.; Ito, T.; Takabayashi, Y.; Komaki, K.; Yamazaki, Y.; Yamazaki, Y.; Takada, E.; Murakami, T.

We have succeeded in observing resonant coherent excitaion (RCE) of 1s electrons to the n = 3 states in 390 MeV/u hydrogen-like Ar17+ ions planar channeled in a silicon crystal through measurements of the charge-state distribution of ions transmitting the crystal. Furthermore, we directly confirmed RCE to the n = 3 states by observing the enhancement of the de-excitation X-rays, i.e., Kβ X-rays under the resonance condition. The resonance profiles of the charge-state distribution as functions of the incident angle to the crystal, which uniquely relates with the transition energy, have a characteristic structure consisting of several peaks. Compared with the profile of RCE to the n = 2 states, the present profiles show a large peak shift from the j = 1/2 and 3/2 levels in vacuum, and the profiles are much wider than those expected from the Stark-split level structure of the n = 3 manifolds due to the position- (distance from the channel center in the planar channel) dependent strong static field in the crystal.

Spatially Resolved Imaging on Photocarrier Generations and Band Alignments at Perovskite/PbI2 Heterointerfaces of Perovskite Solar Cells by Light-Modulated Scanning Tunneling Microscopy.

PubMed

Shih, Min-Chuan; Li, Shao-Sian; Hsieh, Cheng-Hua; Wang, Ying-Chiao; Yang, Hung-Duen; Chiu, Ya-Ping; Chang, Chia-Seng; Chen, Chun-Wei

2017-02-08

The presence of the PbI 2 passivation layers at perovskite crystal grains has been found to considerably affect the charge carrier transport behaviors and device performance of perovskite solar cells. This work demonstrates the application of a novel light-modulated scanning tunneling microscopy (LM-STM) technique to reveal the interfacial electronic structures at the heterointerfaces between CH 3 NH 3 PbI 3 perovskite crystals and PbI 2 passivation layers of individual perovskite grains under light illumination. Most importantly, this technique enabled the first observation of spatially resolved mapping images of photoinduced interfacial band bending of valence bands and conduction bands and the photogenerated electron and hole carriers at the heterointerfaces of perovskite crystal grains. By systematically exploring the interfacial electronic structures of individual perovskite grains, enhanced charge separation and reduced back recombination were observed when an optimal design of interfacial PbI 2 passivation layers consisting of a thickness less than 20 nm at perovskite crystal grains was applied.

New investigations of the guanine trichloro cuprate(II) complex crystal

NASA Astrophysics Data System (ADS)

Fabijanić, Ivana; Matković-Čalogović, Dubravka; Pilepić, Viktor; Ivanišević, Irena; Mohaček-Grošev, Vlasta; Sanković, Krešimir

2017-01-01

Crystals of the guanine trichloro cuprate(II) complex, (HGua)2[Cu2Cl6]·2H2O (HGua = protonated guanine), were prepared and analysed by spectroscopic (IR, Raman) and computational methods. A new single-crystal X-ray diffraction analysis was conducted to obtain data with lower standard uncertainties than those in the previously published structure. Raman and IR spectroscopy and quantum-mechanical analysis gave us new insight into the vibrational states of the (HGua)2[Cu2Cl6]·2H2O crystal. The vibrational spectra of the crystal were assigned by performing a normal coordinate analysis for a free dimer with a centre of inversion as the only symmetry element. The stretching vibration observed at 279 cm-1 in the infrared spectrum corresponds to the N-Cu bond. The noncovalent interaction (NCI) plots and quantum theory of atoms in molecules (QTAIM) analysis of the electron density obtained from periodic DFT calculations elucidated the interactions that exist within the crystal structure. Closed-shell ionic attractions, as well as weak and medium strength hydrogen bonds, prevailed in the crystal packing.

Growth and characterization of pure and Ca2+ doped MnHg(SCN)4 single crystals

NASA Astrophysics Data System (ADS)

Latha, C.; Mahadevan, C. K.; Guo, Li; Liu, Jinghe

2018-05-01

Manganese-mercury thiocyanate, MnHg(SCN)4, crystal is considered to be an important organometallic nonlinear optical (NLO) material exhibiting higher thermal stability and second harmonic generation (SHG) efficiency. In order to understand the effect of Ca2+ as an impurity on the physicochemical properties, we have grown pure and Ca2+ doped (with a concentration of 1 mol%) MnHg(SCN)4 single crystals by the free evaporation of solvent method and characterized structurally, chemically, optically and electrically by adopting the available standard methods. Results obtained indicate that Ca2+ doping increases significantly the optical transmittance, SHG efficiency, and DC electrical conductivity and decreases the dielectric loss factor (improves the crystal quality), and AC electrical conductivity without distorting the crystal structure. Also, the low dielectric constant (εr) values observed for both the pure and doped crystals considered at near ambient temperatures indicate the possibility of using these crystals not only as potential NLO materials (useful in the photonics industry) but also as promising low εr value dielectric materials (useful in the microelectronics industry).

Effect of modification of isotactic polypropylene by additives of polyamide 6/66 on structural characteristics of composites

NASA Astrophysics Data System (ADS)

Vorontsov, N. V.; Popov, A. A.; Margolin, A. L.

2017-12-01

Changes in the supramolecular structure of polymer composites based on isotactic polypropylene (PP) and polyamide 6/66 (PA) are studied depending on the PP : PA ratio. Temperatures and enthalpies of melting and crystallization of both PP and PA and their composites are determined depending on the composition of the mixtures. It was shown that the initial melting point of a composite does not change with increasing PA content in the blends. The crystallization temperature of the mixtures is shown to increase with the addition of PA and becomes much higher than the crystallization temperatures of both PP and PA. The observed effect can be due to a strong interaction between the PP and PA molecules, thus decreasing the molecular mobility and increasing the crystallization temperature. The crystallization and melting of PP-PA mixtures are found to proceed at the close temperatures, although the crystallization and melting temperatures of pure PP and pure PA differ widely. The melting and crystallization enthalpies decrease with increasing PA concentration in the mixtures, which indicates a decrease in the degree of crystallinity of the composite.

Crystal morphology modification by the addition of tailor-made stereocontrolled poly(N-isopropyl acrylamide).

PubMed

Munk, Tommy; Baldursdottir, Stefania; Hietala, Sami; Rades, Thomas; Kapp, Sebastian; Nuopponen, Markus; Kalliomäki, Katriina; Tenhu, Heikki; Rantanen, Jukka

2012-07-02

The use of additives in crystallization of pharmaceuticals is known to influence the particulate properties critically affecting downstream processing and the final product performance. Desired functionality can be build into these materials, e.g. via optimized synthesis of a polymeric additive. One such additive is the thermosensitive polymer poly(N-isopropyl acrylamide) (PNIPAM). The use of PNIPAM as a crystallization additive provides a possibility to affect viscosity at separation temperatures and nucleation and growth rates at higher temperatures. In this study, novel PNIPAM derivatives consisting of both isotactic-rich and atactic blocks were used as additives in evaporative crystallization of a model compound, nitrofurantoin (NF). Special attention was paid to possible interactions between NF and PNIPAM and the aggregation state of PNIPAM as a function of temperature and solvent composition. Optical light microscopy and Raman and FTIR spectroscopy were used to investigate the structure of the NF crystals and possible interaction with PNIPAM. A drastic change in the growth mechanism of nitrofurantoin crystals as monohydrate form II (NFMH-II) was observed in the presence of PNIPAM; the morphology of crystals changed from needle to dendritic shape. Additionally, the amphiphilic nature of PNIPAM increased the solubility of nitrofurantoin in water. PNIPAMs with varying molecular weights and stereoregularities resulted in similar changes in the crystal habit of the drug regardless of whether the polymer was aggregated or not. However, with increased additive concentration slower nucleation and growth rates of the crystals were observed. Heating of the crystallization medium resulted in phase separation of the PNIPAM. The phase separation had an influence on the achieved crystal morphology resulting in fewer, visually larger and more irregular dendritic crystals. No proof of hydrogen bond formation between PNIPAM and NF was observed, and the suggested mechanism for the observed dendritic morphology is related to the steric hindrance phenomenon. PNIPAM can be used as a crystallization additive with an obvious effect on the growth of NF crystals.

Acemetacin cocrystal structures by powder X-ray diffraction.

PubMed

Bolla, Geetha; Chernyshev, Vladimir; Nangia, Ashwini

2017-05-01

Cocrystals of acemetacin drug (ACM) with nicotinamide (NAM), p -aminobenzoic acid (PABA), valerolactam (VLM) and 2-pyridone (2HP) were prepared by melt crystallization and their X-ray crystal structures determined by high-resolution powder X-ray diffraction. The powerful technique of structure determination from powder data (SDPD) provided details of molecular packing and hydrogen bonding in pharmaceutical cocrystals of acemetacin. ACM-NAM occurs in anhydrate and hydrate forms, whereas the other structures crystallized in a single crystalline form. The carboxylic acid group of ACM forms theacid-amide dimer three-point synthon R 3 2 (9) R 2 2 (8) R 3 2 (9) with three different syn amides (VLM, 2HP and caprolactam). The conformations of the ACM molecule observed in the crystal structures differ mainly in the mutual orientation of chlorobenzene fragment and the neighboring methyl group, being anti (type I) or syn (type II). ACM hydrate, ACM-NAM, ACM-NAM-hydrate and the piperazine salt of ACM exhibit the type I conformation, whereas ACM polymorphs and other cocrystals adopt the ACM type II conformation. Hydrogen-bond interactions in all the crystal structures were quantified by calculating their molecular electrostatic potential (MEP) surfaces. Hirshfeld surface analysis of the cocrystal surfaces shows that about 50% of the contribution is due to a combination of strong and weak O⋯H, N⋯H, Cl⋯H and C⋯H interactions. The physicochemical properties of these cocrystals are under study.

Acemetacin cocrystal structures by powder X-ray diffraction

PubMed Central

Bolla, Geetha

2017-01-01

Cocrystals of acemetacin drug (ACM) with nicotinamide (NAM), p-aminobenzoic acid (PABA), valerolactam (VLM) and 2-pyridone (2HP) were prepared by melt crystallization and their X-ray crystal structures determined by high-resolution powder X-ray diffraction. The powerful technique of structure determination from powder data (SDPD) provided details of molecular packing and hydrogen bonding in pharmaceutical cocrystals of acemetacin. ACM–NAM occurs in anhydrate and hydrate forms, whereas the other structures crystallized in a single crystalline form. The carboxylic acid group of ACM forms theacid–amide dimer three-point synthon R 3 2(9)R 2 2(8)R 3 2(9) with three different syn amides (VLM, 2HP and caprolactam). The conformations of the ACM molecule observed in the crystal structures differ mainly in the mutual orientation of chlorobenzene fragment and the neighboring methyl group, being anti (type I) or syn (type II). ACM hydrate, ACM—NAM, ACM–NAM-hydrate and the piperazine salt of ACM exhibit the type I conformation, whereas ACM polymorphs and other cocrystals adopt the ACM type II conformation. Hydrogen-bond interactions in all the crystal structures were quantified by calculating their molecular electrostatic potential (MEP) surfaces. Hirshfeld surface analysis of the cocrystal surfaces shows that about 50% of the contribution is due to a combination of strong and weak O⋯H, N⋯H, Cl⋯H and C⋯H interactions. The physicochemical properties of these cocrystals are under study. PMID:28512568

Crystal faces of anhydrite (CaSO 4) and their preferential dissolution in aqueous solutions studied with AFM

NASA Astrophysics Data System (ADS)

Shindo, H.; Kaise, M.; Kondoh, H.; Nishihara, C.; Nozoye, H.

Structures of cleaved surfaces of anhydrite were studied with atomic force microscopy (AFM) before and after partial dissolution in aqueous solutions of NH 4Cl and NaHSO 4. Two crystal faces showed atom-resolved images just after cleavage, (100) and (010), of which the former was roughened by the dissolution, while step structures were developed on the latter. After dissolution, steplines ran along the a- and c-axes on the (010) face, while they ran in directions inclined to these axes before. It was revealed that the arrangement of dipoles is a key factor in determining stabilities of step structures on crystal faces. On the terraces, the arrangement of oxygen atoms of the sulfate groups and calcium ions were clearly observed.

Tautomeric and ionisation forms of dopamine and tyramine in the solid state

NASA Astrophysics Data System (ADS)

Cruickshank, Laura; Kennedy, Alan R.; Shankland, Norman

2013-11-01

Crystallisation of the phenylethylamine neurotransmitter dopamine from basic aqueous solution yielded the 3-phenoxide Zwitterionic tautomer, despite this being a minority form in the solution state. In the crystal structure, dopamine has a dimeric [OCCOH]2 hydrogen bonded catechol motif that expands through Nsbnd H⋯O interactions to give a 2-dimensional sheet of classical hydrogen bonds. These sheets are further interconnected by Nsbnd H⋯π interactions. The structurally related base tyramine crystallises under similar conditions as a hemihydrate with all four possible species of tyramine present (cationic, anionic, Zwitterionic and neutral) in the crystal structure. Single crystal X-ray diffraction studies at 121 and 293 K showed dynamic hydrogen atom disorder for the phenol/phenoxide group, suggesting that the tyramine speciation observed arises from a solid-state process.

Crystal engineering: co-crystals of cinnamic acid derivatives with a pyridyl derivative co-crystallizer.

PubMed

Lorenzo, Daniel A; Forrest, Sebastian J K; Sparkes, Hazel A

2016-02-01

A number of hydrogen-bonded co-crystals, consisting of a cinnamic acid derivative and a pyridyl co-crystallizer, have been synthesized and their properties investigated by X-ray diffraction. Samples were prepared by recrystallization or solvent drop grinding of trans-cinnamic acid (1), 4-methylcinnamic acid (2), 4-methoxy cinnamic acid (3) or 3,4-methoxy cinnamic acid (4), with 4,4-dipyridyl (A), iso-nicotinamide (B) or nicotinamide (C). The X-ray single-crystal structures of seven novel co-crystals, obtained through recrystallization, are examined and the hydrogen-bonding interactions discussed. Consistent hydrogen-bonding motifs were observed for samples prepared when using 4,4-dipyridyl (A) or iso-nicotinamide (B) as the co-crystallizing agent. Powder X-ray diffraction analysis of the samples prepared by solvent drop grinding suggests the formation of ten co-crystals.

X-Ray Structure of the Human Calreticulin Globular Domain Reveals a Peptide-Binding Area and Suggests a Multi-Molecular Mechanism

PubMed Central

Chouquet, Anne; Païdassi, Helena; Ling, Wai Li; Frachet, Philippe; Houen, Gunnar; Arlaud, Gérard J.; Gaboriaud, Christine

2011-01-01

In the endoplasmic reticulum, calreticulin acts as a chaperone and a Ca2+-signalling protein. At the cell surface, it mediates numerous important biological effects. The crystal structure of the human calreticulin globular domain was solved at 1.55 Å resolution. Interactions of the flexible N-terminal extension with the edge of the lectin site are consistently observed, revealing a hitherto unidentified peptide-binding site. A calreticulin molecular zipper, observed in all crystal lattices, could further extend this site by creating a binding cavity lined by hydrophobic residues. These data thus provide a first structural insight into the lectin-independent binding properties of calreticulin and suggest new working hypotheses, including that of a multi-molecular mechanism. PMID:21423620

Electronic and structural aspects of spin transitions observed by optical microscopy. The case of [Fe(ptz)6](BF4)2.

PubMed

Chong, Christian; Mishra, Haritosh; Boukheddaden, Kamel; Denise, Stéphane; Bouchez, Guillaume; Collet, Eric; Ameline, Jean-Claude; Naik, Anil D; Garcia, Yann; Varret, François

2010-02-11

The colorimetric analysis of images recorded with an optical microscope during the onset of the spin crossover transformation allows monitoring separately the involved electronic and structural aspects, through the separation of resonant absorption and scattering effects. Complementary information can also be obtained by using the polarized modes of the microscope. These potentialities are illustrated by the observation of [Fe(ptz)(6)](BF(4))(2) single crystals during the onset of the thermal transitions in the 110-140 K range. We characterized the interplay between the electronic (HS <--> LS) and structural (order <--> disorder) transformations. Elastic stresses and mechanical effects (hopping, self-cleavage) generated by the volume change upon electronic transition are also illustrated, with their impact on the photoswitching properties of the crystals.

Crystal structure and equation of state of Fe-Si alloys at super-Earth core conditions

PubMed Central

Fratanduono, Dayne E.; Coppari, Federica; Newman, Matthew G.; Duffy, Thomas S.

2018-01-01

The high-pressure behavior of Fe alloys governs the interior structure and dynamics of super-Earths, rocky extrasolar planets that could be as much as 10 times more massive than Earth. In experiments reaching up to 1300 GPa, we combine laser-driven dynamic ramp compression with in situ x-ray diffraction to study the effect of composition on the crystal structure and density of Fe-Si alloys, a potential constituent of super-Earth cores. We find that Fe-Si alloy with 7 weight % (wt %) Si adopts the hexagonal close-packed structure over the measured pressure range, whereas Fe-15wt%Si is observed in a body-centered cubic structure. This study represents the first experimental determination of the density and crystal structure of Fe-Si alloys at pressures corresponding to the center of a ~3–Earth mass terrestrial planet. Our results allow for direct determination of the effects of light elements on core radius, density, and pressures for these planets. PMID:29707632

Crystal structure and equation of state of Fe-Si alloys at super-Earth core conditions

DOE PAGES

Wicks, June K.; Smith, Raymond F.; Fratanduono, Dayne E.; ...

2018-04-25

In this paper, the high-pressure behavior of Fe alloys governs the interior structure and dynamics of super-Earths, rocky extrasolar planets that could be as much as ten times more massive than Earth. In experiments reaching up to 1300 GPa, we combine laser-driven dynamic ramp compression with in situ X-ray diffraction to study the effect of composition on the crystal structure and density of Fe-Si alloys, a potential constituent of super-Earth cores. We find that Fe-7wt.%Si adopts the hexagonal close packed (hcp) structure over the measured pressure range, whereas Fe-15wt.%Si is observed in a body-centered cubic (bcc) structure. This study representsmore » the first experimental determination of the density and crystal structure of Fe-Si alloys at pressures corresponding to the center of a ~3 Earth-mass terrestrial planet. Our results allow for direct determination of the effects of light elements on core radius, density, and pressures for such planets.« less

Crystal structure and equation of state of Fe-Si alloys at super-Earth core conditions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wicks, June K.; Smith, Raymond F.; Fratanduono, Dayne E.

In this paper, the high-pressure behavior of Fe alloys governs the interior structure and dynamics of super-Earths, rocky extrasolar planets that could be as much as ten times more massive than Earth. In experiments reaching up to 1300 GPa, we combine laser-driven dynamic ramp compression with in situ X-ray diffraction to study the effect of composition on the crystal structure and density of Fe-Si alloys, a potential constituent of super-Earth cores. We find that Fe-7wt.%Si adopts the hexagonal close packed (hcp) structure over the measured pressure range, whereas Fe-15wt.%Si is observed in a body-centered cubic (bcc) structure. This study representsmore » the first experimental determination of the density and crystal structure of Fe-Si alloys at pressures corresponding to the center of a ~3 Earth-mass terrestrial planet. Our results allow for direct determination of the effects of light elements on core radius, density, and pressures for such planets.« less

Filtering properties of Thue-Morse nano-photonic crystals containing high-temperature superconductor

NASA Astrophysics Data System (ADS)

Talebzadeh, Robabeh; Bavaghar, Mehrdad

2018-05-01

In this paper, we introduced new design of quasi-periodic layered structures by choosing order two of ternary Thue-Morse structure. We considered Superconductor-dielectric photonic crystal with mirror symmetric as (ABSSAB)N(BASSBA)N composed of two kinds of nano-scale dielectric layers (A and B) and high-temperature superconductor layers where N is the number of period. This structure is assumed to be the free space. By using the transfer matrix method and the two fluid model, we theoretically study the transmission spectrum of ternary Thue-Morse superconducting photonic crystals with mirror symmetry and introduce this structure as a narrow optical filter. We showed that transmission peak so-called defect mode appears itself inside the transmission spectrum of suggested structure as same as defective layered structure. Also, we analyzed the influence of various related parameters such as the operating temperature of superconductor layer on position of defect mode. The redshift of defect mode with increasing the operating temperature was observed.

The influence of additives on the crystal habit of gibbsite

NASA Astrophysics Data System (ADS)

Seyssiecq, Isabelle; Veesler, Stéphane; Pèpe, Gérard; Boistelle, Roland

1999-01-01

Crystallization of gibbsite (Al(OH) 3) is an important stage of the Bayer process, production of alumina from bauxite ores. In both pure or industrial supersaturated sodium aluminate solutions, gibbsite crystals are always agglomerated. In the present paper, we present results of a study concerning the influence of different polycarboxylic acids as crystal habit modifier for gibbsite. In pure solution, agglomerated hexagonal plates are observed. Whereas acicular and tabular morphologies are found in the presence of different additives. These results are discussed referring to the crystallographic structure of gibbsite. It is found that only oxygen atoms are present on gibbsite surface. This observation leads us to propose an additive way of acting by formation of a molecular complex between the growth unit and the carboxylic groups of the additive.

Thick strings, the liquid crystal blue phase, and cosmological large-scale structure

NASA Technical Reports Server (NTRS)

Luo, Xiaochun; Schramm, David N.

1992-01-01

A phenomenological model based on the liquid crystal blue phase is proposed as a model for a late-time cosmological phase transition. Topological defects, in particular thick strings and/or domain walls, are presented as seeds for structure formation. It is shown that the observed large-scale structure, including quasi-periodic wall structure, can be well fitted in the model without violating the microwave background isotropy bound or the limits from induced gravitational waves and the millisecond pulsar timing. Furthermore, such late-time transitions can produce objects such as quasars at high redshifts. The model appears to work with either cold or hot dark matter.

Crystal growth and dislocation etch pits observation of chalcopyrite CdSiP2

NASA Astrophysics Data System (ADS)

He, Zhiyu; Zhao, Beijun; Zhu, Shifu; Chen, Baojun; Huang, Wei; Lin, Li; Feng, Bo

2018-01-01

CdSiP2 is the only crystal that can offer Non-critical Phase Matching (NCPM) for a 1064 nm pumped optical parametric oscillation (OPO) with idler output in the 6 μm range. In this paper, a large, crack-free CdSiP2 single crystal measuring 18 mm in diameter and 65 mm in length was successfully grown by the Vertical Bridgman method (MVB) with an explosion-proof quartz ampoule. The results of lattice parameters, element composition and IR transmittance of the as-grown crystal characterized by X-ray diffraction (XRD), energy dispersive X-ray spectrometer (EDS) and Fourier transformation infrared spectrometer (FTIR) showed the as grown crystal crystallized well and the absorption coefficients at 4878 cm-1 and 2500 cm-1 were 0.14 cm-1 and 0.06 cm-1. Moreover, a new etchant composed of Br2, HCl, HNO3, CH3OH and H2O (1:800:800:400:400 in volume ratio) was prepared and the dislocation etch pits on oriented faces of as-grown CdSiP2 crystal were observed for the first time. It is found the etch pits are in rectangular structure on the (1 0 1) face, but in trigonal pyramid structure on (3 1 2) face. According to the quantities of the etch pits, the average densities of dislocation were evaluated to be 2.28 × 105/cm2 and 1.4 × 105/cm2, respectively.

Effect of Partial Crystallization on the Structural and Luminescence Properties of Er3+-Doped Phosphate Glasses

PubMed Central

Lopez-Iscoa, Pablo; Salminen, Turkka; Hakkarainen, Teemu; Petit, Laeticia; Janner, Davide; Boetti, Nadia G.; Lastusaari, Mika; Pugliese, Diego; Paturi, Petriina; Milanese, Daniel

2017-01-01

Er-doped phosphate glass ceramics were fabricated by melt-quenching technique followed by a heat treatment. The effect of the crystallization on the structural and luminescence properties of phosphate glasses containing Al2O3, TiO2, and ZnO was investigated. The morphological and structural properties of the glass ceramics were characterized by Field Emission-Scanning Electron Microscopy (FE-SEM), X-ray Diffraction (XRD), and micro-Raman spectroscopy. Additionally, the luminescence spectra and the lifetime values were measured in order to study the influence of the crystallization on the spectroscopic properties of the glasses. The volume ratio between the crystal and the glassy phases increased along with the duration of the heat treatment. The crystallization of the glass ceramics was confirmed by the presence of sharp peaks in the XRD patterns and different crystal phases were identified depending on the glass composition. Sr(PO3)2 crystals were found to precipitate in all the investigated glasses. As evidenced by the spectroscopic properties, the site of the Er3+ ions was not strongly affected by the heat treatment except for the fully crystallized glass ceramic which does not contain Al2O3, TiO2, and ZnO. An increase of the lifetime was also observed after the heat treatment of this glass. Therefore, we suspect that the Er3+ ions are incorporated in the precipitated crystals only in this glass ceramic. PMID:28772833

Crystal grain growth at the α -uranium phase transformation in praseodymium

NASA Astrophysics Data System (ADS)

Cunningham, Nicholas C.; Velisavljevic, Nenad; Vohra, Yogesh K.

2005-01-01

Structural phase transformations under pressure are examined in praseodymium metal for the range 0-40GPa at ambient temperature. Pressure was generated with a diamond-anvil cell, and data were collected using high-resolution synchrotron x-ray diffraction and the image plate technique. The structural sequence double hexagonal close packed (dhcp)→face centered cubic (fcc)→distorted-fcc (d-fcc)→ α -uranium (α-U) is observed with increasing pressure. Rietveld refinement of all crystallographic phases provided confirmation of the hR24 structure for the d-fcc phase while the previously reported monoclinic phase between the d-fcc and the α-U phase was not confirmed. We observe dramatic crystal grain growth during the volume collapse concurrent with the symmetry-lowering transition to the α-U structure. No preferred orientation axis is observed, and the formation process for these large grains is expected to be via a nucleation and growth mechanism. An analogous effect in rare earth metal cerium suggests that the grain growth during transformation to the α-U structure is a common occurrence in f -electron metals at high pressures.

Crystal structure of the FLT3 kinase domain bound to the inhibitor quizartinib (AC220)

DOE PAGES

Zorn, Julie A.; Wang, Qi; Fujimura, Eric; ...

2015-04-02

More than 30% of acute myeloid leukemia (AML) patients possess activating mutations in the receptor tyrosine kinase FMS-like tyrosine kinase 3 or FLT3. A small-molecule inhibitor of FLT3 (known as quizartinib or AC220) that is currently in clinical trials appears promising for the treatment of AML. Here, we report the co-crystal structure of the kinase domain of FLT3 in complex with quizartinib. FLT3 with quizartinib bound adopts an “Abl-like” inactive conformation with the activation loop stabilized in the “DFG-out” orientation and folded back onto the kinase domain. This conformation is similar to that observed for the uncomplexed intracellular domain ofmore » FLT3 as well as for related receptor tyrosine kinases, except for a localized induced fit in the activation loop. The co-crystal structure reveals the interactions between quizartinib and the active site of FLT3 that are key for achieving its high potency against both wild-type FLT3 as well as a FLT3 variant observed in many AML patients. This co-complex further provides a structural rationale for quizartinib-resistance mutations.« less

The oxygenating constituent of 3,6-diketocamphane monooxygenase from the CAM plasmid of Pseudomonas putida: the first crystal structure of a type II Baeyer–Villiger monooxygenase

DOE Office of Scientific and Technical Information (OSTI.GOV)

Isupov, Michail N.; Schröder, Ewald; Gibson, Robert P.

The first crystal structure of a type II Baeyer–Villiger monooxygenase reveals a different ring orientation of its FMN cofactor compared with other related bacterial luciferase-family enzymes. The three-dimensional structures of the native enzyme and the FMN complex of the overexpressed form of the oxygenating component of the type II Baeyer–Villiger 3,6-diketocamphane monooxygenase have been determined to 1.9 Å resolution. The structure of this dimeric FMN-dependent enzyme, which is encoded on the large CAM plasmid of Pseudomonas putida, has been solved by a combination of multiple anomalous dispersion from a bromine crystal soak and molecular replacement using a bacterial luciferase model.more » The orientation of the isoalloxazine ring of the FMN cofactor in the active site of this TIM-barrel fold enzyme differs significantly from that previously observed in enzymes of the bacterial luciferase-like superfamily. The Ala77 residue is in a cis conformation and forms a β-bulge at the C-terminus of β-strand 3, which is a feature observed in many proteins of this superfamily.« less

Translation effects on vertical Bridgman growth and optical, mechanical and surface analysis of 2-phenylphenol single crystal

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sadhasivam, S., E-mail: sadha.phy1@gmail.com; Perumal, Rajesh Narayana

2-phenylphenol optical crystals were grown in cone ampoules using vertical Bridgman technique. Single crystal of 2-phenylphenol with 150 mm length has been grown. The inclination on the conical part of the ampoule reduces the growth defects in the 2-phenylphenol single crystal. The lattice parameters and structure studied using single crystal X-ray diffraction method. 2-phenylphenol single crystal belongs to orthorhombic space group Fdd2. The micro translation rate affects crystal growth of 2-phenylphenol crystal was studied. The translation rate dependent defects present in the crystal were investigated by transmittance, indentation and etching characterizations. The dislocation induced indentation crack lengths variations were studied. Etchmore » pits and striations observed for the selective etchants furnish significant information on growth aspects and degree of defect present in the crystal.« less

Fabrication and characterization of poly(L-lactic acid) gels induced by fibrous complex crystallization with solvents

DOE Office of Scientific and Technical Information (OSTI.GOV)

Matsuda, Yasuhiro; Fukatsu, Akinobu; Wang, Yangyang

2014-01-01

Complex crystal induced gelation of poly(L-lactic acid) (PLLA) solutions was studied for a series of solvents, including N,N-dimethylformamide (DMF). By cooling the solutions prepared at elevated temperatures, PLLA gels were produced in solvents that induced complex crystals ( -crystals) with PLLA. Fibrous structure of PLLA in the gel with DMF was observed by polarizing optical microscopy, field emission electron microscopy, and atomic force microscopy. Upon heating, the crystal form of PLLA in the DMF gel changed from -crystal to a-crystal, the major crystal form in common untreated PLLA films, but the morphology and high elastic modulus of the gel remainedmore » until the a-crystal dissolved at higher temperature. In addition, a solvent exchanging method was developed, which allowed PLLA gels to be prepared in other useful solvents that do not induce -crystals without losing the morphology and mechanical properties.« less

Gaia: automated quality assessment of protein structure models.

PubMed

Kota, Pradeep; Ding, Feng; Ramachandran, Srinivas; Dokholyan, Nikolay V

2011-08-15

Increasing use of structural modeling for understanding structure-function relationships in proteins has led to the need to ensure that the protein models being used are of acceptable quality. Quality of a given protein structure can be assessed by comparing various intrinsic structural properties of the protein to those observed in high-resolution protein structures. In this study, we present tools to compare a given structure to high-resolution crystal structures. We assess packing by calculating the total void volume, the percentage of unsatisfied hydrogen bonds, the number of steric clashes and the scaling of the accessible surface area. We assess covalent geometry by determining bond lengths, angles, dihedrals and rotamers. The statistical parameters for the above measures, obtained from high-resolution crystal structures enable us to provide a quality-score that points to specific areas where a given protein structural model needs improvement. We provide these tools that appraise protein structures in the form of a web server Gaia (http://chiron.dokhlab.org). Gaia evaluates the packing and covalent geometry of a given protein structure and provides quantitative comparison of the given structure to high-resolution crystal structures. dokh@unc.edu Supplementary data are available at Bioinformatics online.

Two Active Site Divalent Ions in the Crystal Structure of the Hammerhead Ribozyme Bound to a Transition State Analogue.

PubMed

Mir, Aamir; Golden, Barbara L

2016-02-02

The crystal structure of the hammerhead ribozyme bound to the pentavalent transition state analogue vanadate reveals significant rearrangements relative to the previously determined structures. The active site contracts, bringing G10.1 closer to the cleavage site and repositioning a divalent metal ion such that it could, ultimately, interact directly with the scissile phosphate. This ion could also position a water molecule to serve as a general acid in the cleavage reaction. A second divalent ion is observed coordinated to O6 of G12. This metal ion is well-placed to help tune the pKA of G12. On the basis of this crystal structure as well as a wealth of biochemical studies, we propose a mechanism in which G12 serves as the general base and a magnesium-bound water serves as a general acid.

Crystal Structures of the Receiver Domain of the Response Regulator PhoP from Escherichia coli in the Absence and Presence of the Phosphoryl Analog Beryllofluoride▿

PubMed Central

Bachhawat, Priti; Stock, Ann M.

2007-01-01

The response regulator PhoP is part of the PhoQ/PhoP two-component system involved in responses to depletion of extracellular Mg2+. Here, we report the crystal structures of the receiver domain of Escherichia coli PhoP determined in the absence and presence of the phosphoryl analog beryllofluoride. In the presence of beryllofluoride, the active receiver domain forms a twofold symmetric dimer similar to that seen in structures of other regulatory domains from the OmpR/PhoB family, providing further evidence that members of this family utilize a common mode of dimerization in the active state. In the absence of activating agents, the PhoP receiver domain crystallizes with a similar structure, consistent with the previous observation that high concentrations can promote an active state of PhoP independent of phosphorylation. PMID:17545283

Two active site divalent ions in the crystal structure of the hammerhead ribozyme bound to a transition state analogue

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mir, Aamir; Golden, Barbara L.

2015-11-09

The crystal structure of the hammerhead ribozyme bound to the pentavalent transition state analogue vanadate reveals significant rearrangements relative to the previously determined structures. The active site contracts, bringing G10.1 closer to the cleavage site and repositioning a divalent metal ion such that it could, ultimately, interact directly with the scissile phosphate. This ion could also position a water molecule to serve as a general acid in the cleavage reaction. A second divalent ion is observed coordinated to O6 of G12. This metal ion is well-placed to help tune the p K A of G12. Finally, on the basis ofmore » this crystal structure as well as a wealth of biochemical studies, in this paper we propose a mechanism in which G12 serves as the general base and a magnesium-bound water serves as a general acid.« less

Crystal structure of the vitamin B3 transporter PnuC, a full-length SWEET homolog.

PubMed

Jaehme, Michael; Guskov, Albert; Slotboom, Dirk Jan

2014-11-01

PnuC transporters catalyze cellular uptake of the NAD+ precursor nicotinamide riboside (NR) and belong to a large superfamily that includes the SWEET sugar transporters. We present a crystal structure of Neisseria mucosa PnuC, which adopts a highly symmetrical fold with 3+1+3 membrane topology not previously observed in any protein. The high symmetry of PnuC with a single NR bound in the center suggests a simple alternating-access translocation mechanism.

Quantum Chemical and Physicochemical Studies of Oximes (Prophylactics against and Reactivators of Phosphorylated AChE).

DTIC Science & Technology

1984-10-25

crystal structure of nicotinic acid ,. and we used the ether bridge from the crystal structure of dimethyl ether. We are investigating various rotamers...observations were made: - The titration curve (after the subtraction of the blank curve) shows only one titrable group, i.e. the oxime moiety. - The...subtraction of the blank curve, shows two titrable groups, i.e. the two oxime moieties. The results are as follows: Temperature Conditions PKa pK2

Solid iron-hydrogen alloys under high pressure by first principles

NASA Astrophysics Data System (ADS)

Umemoto, K.; Hirose, K.

2016-12-01

Hydrogen and iron are two of major constituents of the Earth and planetary interiors. The crystal structure of solid FeHx is one of the most fundamental information in order to understand properties of planetary cores. It is well known that FeH takes closed-packed structures: dhcp, hcp, and fcc. Recently, hydrogen-rich phases, FeH2 and FeH3, were experimentally synthesized [1]. Although a tetragonal structure of FeH2 was proposed, it could not explain experimental observations, energetic stability and compression curve. Here we propose a new crystal structure of FeH2. The symmetry of the new structure is completely identical to that in originally proposed one, but the hydrogen sublattice which cannot be directly determined by XRD experiments is different. It will be demonstrated by first principles that the new structure can be fully consistent with experimental observations. [1] C. M. Pépin, A. Dewaele, G. Geneste, P. Loubeyre, and M. Mezouar, Phys. Rev. Lett. 113, 265504 (2014).

Machine learning for the structure-energy-property landscapes of molecular crystals.

PubMed

Musil, Félix; De, Sandip; Yang, Jack; Campbell, Joshua E; Day, Graeme M; Ceriotti, Michele

2018-02-07

Molecular crystals play an important role in several fields of science and technology. They frequently crystallize in different polymorphs with substantially different physical properties. To help guide the synthesis of candidate materials, atomic-scale modelling can be used to enumerate the stable polymorphs and to predict their properties, as well as to propose heuristic rules to rationalize the correlations between crystal structure and materials properties. Here we show how a recently-developed machine-learning (ML) framework can be used to achieve inexpensive and accurate predictions of the stability and properties of polymorphs, and a data-driven classification that is less biased and more flexible than typical heuristic rules. We discuss, as examples, the lattice energy and property landscapes of pentacene and two azapentacene isomers that are of interest as organic semiconductor materials. We show that we can estimate force field or DFT lattice energies with sub-kJ mol -1 accuracy, using only a few hundred reference configurations, and reduce by a factor of ten the computational effort needed to predict charge mobility in the crystal structures. The automatic structural classification of the polymorphs reveals a more detailed picture of molecular packing than that provided by conventional heuristics, and helps disentangle the role of hydrogen bonded and π-stacking interactions in determining molecular self-assembly. This observation demonstrates that ML is not just a black-box scheme to interpolate between reference calculations, but can also be used as a tool to gain intuitive insights into structure-property relations in molecular crystal engineering.

Nano-optical functionality based on local photoisomerization in photochromic single crystal

NASA Astrophysics Data System (ADS)

Nakagomi, Ryo; Uchiyama, Kazuharu; Kubota, Satoru; Hatano, Eri; Uchida, Kingo; Naruse, Makoto; Hori, Hirokazu

2018-01-01

Towards the construction of functional devices and systems using optical near-field processes, we demonstrate the multivalent features in the path-branching phenomena in a photochromic single crystal observed in optical phase change between colorless (1o) and blue-colored (1c) phases that transmits in subwavelength scale over a macroscopic spatial range associated with local mechanical distortions induced. To observe the near-field optical processes of transmission path branching, we have developed a top-to-bottom double-probe scanning near-field optical microscope capable of nanometer-scale correlation measurements by two individually position-controlled probes that face each other sandwiching the photochromic material. We have experimentally confirmed that a local near-field optical excitation applied to one side of the photochromic crystal by a probe tip resulted in characteristic structures of subwavelength scale around 100 nm or less that are observed by the other probe tip located on the opposite side. The structures are different from those resulting from far-field excitations that are quantitively evaluated by autocorrelations. The results suggest that the mechanical distortion caused by the local phase change in the photochromic crystal suppresses the phase change of the neighboring molecules. This new type of optical-near-field-induced local photoisomerization has the potential to allow the construction of functional devices with multivalent properties for natural intelligence.

Crystal structure, matrix-isolation FTIR, and UV-induced conformational isomerization of 3-quinolinecarboxaldehyde.

PubMed

Kuş, Nihal; Henriques, Marta Sofia; Paixão, José António; Lapinski, Leszek; Fausto, Rui

2014-09-25

The crystal structure of 3-quinolinecarboxaldehyde (3QC) has been solved, and the compound has been shown to crystallize in the space group P21/c (monoclinic) with a = 6.306(4), b = 18.551(11), c = 6.999(4) Å, β = 106.111(13)°, and Z = 4. The crystals were found to exhibit pseudomerohedral twinning with a twin law corresponding to a two-fold rotation around the monoclinic (100) reciprocal lattice axis (or [4 0 1] in direct space). Individual molecules adopt the syn conformation in the crystal, with the oxygen atom of the aldehyde substituent directed toward the same side of the ring nitrogen atom. In the gas phase, the compound exists in two nearly isoenergetic conformers (syn and anti), which could be successfully trapped in solid argon at 10 K, and their infrared spectra are registered and interpreted. Upon in situ irradiation of matrix-isolated 3QC with UV light (λ > 315 nm), significant reduction of the population of the less stable anti conformer was observed, while that of the conformational ground state (syn conformer) increased, indicating occurrence of the anti → syn isomerization. Upon irradiation at higher energy (λ > 235 nm), the syn → anti reverse photoreaction was observed. Interpretation of the structural, spectroscopic, and photochemical experimental data received support from quantum chemical theoretical results obtained at both DFT/B3LYP (including TD-DFT investigation of excited states) and MP2 levels, using the 6-311++G(d,p) basis set.

Influence of molecular electronic properties on the IR spectra of dimeric hydrogen bond systems: polarized spectra of 2-hydroxybenzothiazole and 2-mercaptobenzothiazole crystals

NASA Astrophysics Data System (ADS)

Flakus, Henryk T.; Miros, Artur; Jones, Peter G.

2002-01-01

We have studied the polarized IR spectra of the hydrogen-bonded molecular crystals of 2-hydroxybenzothiazole (HBT) and 2-mercaptobenzothiazole (MBT). The crystal structure of 2-hydroxybenzothiazole was determined by X-ray diffraction. The polarized spectra of the crystals were measured, in the frequency ranges of the νN-H and νN-D bands, at room temperature, and at 77 K. In both systems an extremely strong H/D isotopic effect in the spectra was observed, involving reduction of the well-developed νN-H band fine structure to a single prominent νN-D line only. The two νN-H bands were also shown to exhibit almost identical properties, band shapes, temperature and dichroic properties included. The spectra were quantitatively reconstituted, along with the strong isotopic effect, when calculated using the 'strong-coupling' theory, assuming the centrosymmetric dimers of HBT or MBT to be the structural units responsible for the crystalline spectral properties. The similarity of the spectra of the two crystalline systems was considered to be a result of longer-distance couplings between the proton vibrations in the dimers, via the aromatic ring electrons. When investigating the 'residual' νN-H band shapes for crystals isotopically diluted by deuterium, we observed some 'self-organization' effects in the spectra, indicating the energetically favored presence of two identical hydrogen isotopes in each hydrogen bond dimer.

Pauli structures arising from confined particles interacting via a statistical potential

NASA Astrophysics Data System (ADS)

Batle, Josep; Ciftja, Orion; Farouk, Ahmed; Alkhambashi, Majid; Abdalla, Soliman

2017-09-01

There have been suggestions that the Pauli exclusion principle alone can lead a non-interacting (free) system of identical fermions to form crystalline structures dubbed Pauli crystals. Single-shot imaging experiments for the case of ultra-cold systems of free spin-polarized fermionic atoms in a two-dimensional harmonic trap appear to show geometric arrangements that cannot be characterized as Wigner crystals. This work explores this idea and considers a well-known approach that enables one to treat a quantum system of free fermions as a system of classical particles interacting with a statistical interaction potential. The model under consideration, though classical in nature, incorporates the quantum statistics by endowing the classical particles with an effective interaction potential. The reasonable expectation is that possible Pauli crystal features seen in experiments may manifest in this model that captures the correct quantum statistics as a first order correction. We use the Monte Carlo simulated annealing method to obtain the most stable configurations of finite two-dimensional systems of confined particles that interact with an appropriate statistical repulsion potential. We consider both an isotropic harmonic and a hard-wall confinement potential. Despite minor differences, the most stable configurations observed in our model correspond to the reported Pauli crystals in single-shot imaging experiments of free spin-polarized fermions in a harmonic trap. The crystalline configurations observed appear to be different from the expected classical Wigner crystal structures that would emerge should the confined classical particles had interacted with a pair-wise Coulomb repulsion.

Growth, crystalline perfection, spectral and optical characterization of a novel optical material: l-tryptophan p-nitrophenol trisolvate single crystal.

PubMed

Sivakumar, N; Srividya, J; Mohana, J; Anbalagan, G

2015-03-15

l-tryptophan p-nitrophenol trisolvate (LTPN), an organic nonlinear optical material was synthesized using ethanol-water mixed solvent and the crystals were grown by a slow solvent evaporation method. The crystal structure and morphology were studied by single crystal X-ray diffraction analysis. The crystalline perfection of the LTPN crystal was analyzed by high-resolution X-ray diffraction study. The molecular structure of the crystal was confirmed by observing the various characteristic functional groups of the material using vibrational spectroscopy. The cut-off wavelength, optical transmission, refractive index and band gap energy were determined using UV-visible data. The variation of refractive index with wavelength shows the normal behavior. The second harmonic generation of the crystal was confirmed and the efficiency was measured using Kurtz Perry powder method. Single and multiple shot methods were employed to measure surface laser damage of the crystal. The photoluminescence spectral study revealed that the emission may be associated with the radiative recombination of trapped electrons and holes. Microhardness measurements revealed that LTPN belongs to a soft material category. Copyright © 2014 Elsevier B.V. All rights reserved.

Electronic structures and abnormal phonon behaviors of cobalt-modified Na0.5Bi0.5TiO3-6%BaTiO3 single crystals

NASA Astrophysics Data System (ADS)

Huang, T.; Zhang, P.; Xu, L. P.; Chen, C.; Zhang, J. Z.; Hu, Z. G.; Luo, H. S.; Chu, J. H.

2016-10-01

Optical properties, electronic structures, and structural variations of x wt% cobalt (Co) doped Na0.5Bi0.5TiO3-6%BaTiO3 (x=0%, 0.5%, 0.8%) single crystals have been studied by temperature-dependent optical ellipsometry and Raman spectra from 250 to 650 K. Based on the temperature evolution of electronic transitions (Ecp1 and Ecp2) and the phonon modes involving Ti-O vibrations, two critical temperature points exhibit an increasing trend with Co dopants, which are related to structural variations for ferroelectric to anti-ferroelectric, and anti-ferroelectric to paraelectric transition, respectively. Additionally, distinguishing abnormal phonon behaviors can be observed from Raman spectra for the crystal of x=0.5% and 0.8%, which show reverse frequency shift of the modes involving Ti-O vibration. It can be ascribed to different relative concentration of Co2+ and Co3+ in the crystals, which has been confirmed by X-ray Photoelectron Spectroscopy data.

Crystal growth, electronic structure and optical properties of Sr2Mg(BO3)2

NASA Astrophysics Data System (ADS)

Lv, Xianshun; Wei, Lei; Wang, Xuping; Xu, Jianhua; Yu, Huajian; Hu, Yanyan; Zhang, Huadi; Zhang, Cong; Wang, Jiyang; Li, Qinggang

2018-02-01

Single crystals of Sr2Mg(BO3)2 (SMBO) were grown by Kyropoulos method. X-ray powder diffraction (XRD) analysis, transmission spectrum, thermal properties, band structure, density of states and charge distribution as well as Raman spectra of SMBO were described. The as-grown SMBO crystals show wide transparency range with UV cut-off below 180 nm. A direct band gap of 4.66 eV was obtained from the calculated electronic structure results. The calculated band structure and density of states results indicated the top valence band is determined by O 2p states whereas the low conduction band mainly consists of Sr 5s states. Twelve Raman peaks were observed in the experimental spectrum, fewer than the number predicted by the site group analysis. Raman peaks of SMBO were assigned combining first-principle calculation and site group analysis results. The strongest peak at 917 cm-1 in the experimental spectrum is assigned to symmetric stretching mode A1‧(ν1) of free BO3 units. SMBO is a potential Raman crystal which can be used in deep UV laser frequency conversion.

Synthesis of liquid crystal silane-functionalized gold nanoparticles and their effects on the optical and electro-optic properties of a structurally related nematic liquid crystal.

PubMed

Mirzaei, Javad; Urbanski, Martin; Kitzerow, Heinz-S; Hegmann, Torsten

2014-05-19

Chemically and thermally robust liquid crystal silane-functionalized gold nanoparticles (i.e. AuNP1-AuNP3) were synthesized through silane conjugation. Colloidal dispersions of these particles with mesogenic ligands that are structurally identical (as in AuNP1, AuNP2) or compatible (as in AuNP3) with molecules of the nematic liquid crystal (N-LC) host showed superior colloidal stability and dispersibility. The thermal, optical, and electro-optic behaviors of the N-LC composites at different concentrations of each gold nanoparticle were investigated. All dispersions showed lower values for the rotational viscosity and elastic constant, but only AuNP3 with a dissimilar structure between the nanoparticle ligand and the host displayed the most drastic thermal effects and overall strongest impact on the electro-optic properties of the host. The observed results were explained considering both the structure and the density of the surface ligands of each gold nanoparticle. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Electronic and structural ground state of heavy alkali metals at high pressure

DOE PAGES

Fabbris, G.; Lim, J.; Veiga, L. S. I.; ...

2015-02-17

Here, alkali metals display unexpected properties at high pressure, including emergence of low symmetry crystal structures, that appear to occur due to enhanced electronic correlations among the otherwise nearly-free conduction electrons. We investigate the high pressure electronic and structural ground state of K, Rb, and Cs using x-ray absorption spectroscopy and x-ray diffraction measurements together with ab initio theoretical calculations. The sequence of phase transitions under pressure observed at low temperature is similar in all three heavy alkalis except for the absence of the oC84 phase in Cs. Both the experimental and theoretical results point to pressure-enhanced localization of themore » valence electrons characterized by pseudo-gap formation near the Fermi level and strong spd hybridization. Although the crystal structures predicted to host magnetic order in K are not observed, the localization process appears to drive these alkalis closer to a strongly correlated electron state.« less

Superconductivity versus structural phase transition in the closely related Bi 2Rh 3.5S 2 and Bi 2Rh 3S 2

DOE PAGES

Kaluarachchi, Udhara S.; Xie, Weiwei; Lin, Qisheng; ...

2015-05-19

Single crystals of Bi 2Rh 3S 2 and Bi 2Rh 3.5S 2 were synthesized by solution growth, and the crystal structures and thermodynamic and transport properties of both compounds were studied. In the case of Bi 2Rh 3S 2, a structural first-order transition at around 165 K is identified by single-crystal diffraction experiments, with clear signatures visible in resistivity, magnetization, and specific heat data. No superconducting transition for Bi 2Rh 3S 2 was observed down to 0.5 K. In contrast, no structural phase transition at high temperature was observed for Bi 2Rh 3.5S 2; however, bulk superconductivity with a criticalmore » temperature, T c ≈ 1.7 K, was observed. The Sommerfeld coefficient γ and the Debye temperature (Θ D) were found to be 9.41 mJ mol –1K –2 and 209 K, respectively, for Bi 2Rh 3S 2, and 22 mJ mol –1K –2 and 196 K, respectively, for Bi 2Rh 3.5S 2. As a result, the study of the specific heat in the superconducting state of Bi 2Rh 3.5S 2 suggests that Bi 2Rh 3.5S 2 is a weakly coupled, BCS superconductor.« less

Direct observation of nanowire growth and decomposition.

PubMed

Rackauskas, Simas; Shandakov, Sergey D; Jiang, Hua; Wagner, Jakob B; Nasibulin, Albert G

2017-09-26

Fundamental concepts of the crystal formation suggest that the growth and decomposition are determined by simultaneous embedding and removal of the atoms. Apparently, by changing the crystal formation conditions one can switch the regimes from the growth to decomposition. To the best of our knowledge, so far this has been only postulated, but never observed at the atomic level. By means of in situ environmental transmission electron microscopy we monitored and examined the atomic layer transformation at the conditions of the crystal growth and its decomposition using CuO nanowires selected as a model object. The atomic layer growth/decomposition was studied by varying an O 2 partial pressure. Three distinct regimes of the atomic layer evolution were experimentally observed: growth, transition and decomposition. The transition regime, at which atomic layer growth/decomposition switch takes place, is characterised by random nucleation of the atomic layers on the growing {111} surface. The decomposition starts on the side of the nanowire by removing the atomic layers without altering the overall crystal structure, which besides the fundamental importance offers new possibilities for the nanowire manipulation. Understanding of the crystal growth kinetics and nucleation at the atomic level is essential for the precise control of 1D crystal formation.

Crystal Structures of T Cell Receptor (Beta) Chains Related to Rheumatoid Arthritis

DOE Office of Scientific and Technical Information (OSTI.GOV)

Li,H.; van Vranken, S.; Zhao, Y.

The crystal structures of the V{beta}17+ {beta} chains of two human T cell receptors (TCRs), originally derived from the synovial fluid (SF4) and tissue (C5-1) of a patient with rheumatoid arthritis (RA), have been determined in native (SF4) and mutant (C5-1{sub F104{yields}Y/C187{yields}S}) forms, respectively. These TCR {beta} chains form homo-dimers in solution and in crystals. Structural comparison reveals that the main-chain conformations in the CDR regions of the C5-1 and SF4 V{beta}17 closely resemble those of a V{beta}17 JM22 in a bound form; however, the CDR3 region shows different conformations among these three V{beta}17 structures. At the side-chain level, conformationalmore » differences were observed at the CDR2 regions between our two ligand-free forms and the bound JM22 form. Other significant differences were observed at the V{beta} regions 8-12, 40-44, and 82-88 between C5-1/SF4 and JM22 V{beta}17, implying that there is considerable variability in the structures of very similar {beta} chains. Structural alignments also reveal a considerable variation in the V{beta}-C{beta} associations, and this may affect ligand recognition. The crystal structures also provide insights into the structure basis of T cell recognition of Mycoplasma arthritidis mitogen (MAM), a superantigen that may be implicated in the development of human RA. Structural comparisons of the V{beta} domains of known TCR structures indicate that there are significant similarities among V{beta} regions that are MAM-reactive, whereas there appear to be significant structural differences among those V{beta} regions that lack MAM-reactivity. It further reveals that CDR2 and framework region (FR) 3 are likely to account for the binding of TCR to MAM.« less

Dehydration process in NaCl solutions under various external electric fields

NASA Astrophysics Data System (ADS)

Kadota, Kazunori; Shimosaka, Atsuko; Shirakawa, Yoshiyuki; Hidaka, Jusuke

2007-06-01

Ionic motions at solid-liquid interface in supersaturated NaCl solutions have been investigated by molecular dynamics (MD) simulation for understanding crystal growth processes. The density profile in the vicinity of the interfaces between NaCl(100) and the supersaturated NaCl solution was calculated. Diffusion coefficients of water molecules in the solution were estimated as a function of distance from the crystal interface. It turned out that the structure and dynamics of the solution in the interfaces was different from those of bulk solution owing to electric fields depending on the surface charge. Therefore, the electric field was applied to the supersaturated solutions and dehydration phenomenon occurring in the process of the crystal growth was discussed. As the electric field increased, it was observed that the Na+ keeping strongly hydration structure broke out by the electric force. In supersaturated concentration, the solution structure is significantly different from that of dilution and has a complicated structure with hydration ions and clusters of NaCl. If the electric fields were applied to the solutions, the breakout of hydration structure was not affected with increasing the supersaturated ratio. This reason is that the cluster structures are destroyed by the electric force. The situation depends on the electric field or crystal surface structure.

Structural studies of Pseudomonas and Chromobacterium ω-aminotransferases provide insights into their differing substrate specificity

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sayer, Christopher; Isupov, Michail N.; Westlake, Aaron

2013-04-01

The X-ray structures of two ω-aminotransferases from P. aeruginosa and C. violaceum in complex with an inhibitor offer the first detailed insight into the structural basis of the substrate specificity of these industrially important enzymes. The crystal structures and inhibitor complexes of two industrially important ω-aminotransferase enzymes from Pseudomonas aeruginosa and Chromobacterium violaceum have been determined in order to understand the differences in their substrate specificity. The two enzymes share 30% sequence identity and use the same amino acceptor, pyruvate; however, the Pseudomonas enzyme shows activity towards the amino donor β-alanine, whilst the Chromobacterium enzyme does not. Both enzymes showmore » activity towards S-α-methylbenzylamine (MBA), with the Chromobacterium enzyme having a broader substrate range. The crystal structure of the P. aeruginosa enzyme has been solved in the holo form and with the inhibitor gabaculine bound. The C. violaceum enzyme has been solved in the apo and holo forms and with gabaculine bound. The structures of the holo forms of both enzymes are quite similar. There is little conformational difference observed between the inhibitor complex and the holoenzyme for the P. aeruginosa aminotransferase. In comparison, the crystal structure of the C. violaceum gabaculine complex shows significant structural rearrangements from the structures of both the apo and holo forms of the enzyme. It appears that the different rigidity of the protein scaffold contributes to the substrate specificity observed for the two ω-aminotransferases.« less

Disparate HDV ribozyme crystal structures represent intermediates on a rugged free-energy landscape

PubMed Central

Sripathi, Kamali N.; Tay, Wendy W.; Banáš, Pavel; Otyepka, Michal; Šponer, Jiří; Walter, Nils G.

2014-01-01

The hepatitis delta virus (HDV) ribozyme is a member of the class of small, self-cleaving catalytic RNAs found in a wide range of genomes from HDV to human. Both pre- and post-catalysis (precursor and product) crystal structures of the cis-acting genomic HDV ribozyme have been determined. These structures, together with extensive solution probing, have suggested that a significant conformational change accompanies catalysis. A recent crystal structure of a trans-acting precursor, obtained at low pH and by molecular replacement from the previous product conformation, conforms to the product, raising the possibility that it represents an activated conformer past the conformational change. Here, using fluorescence resonance energy transfer (FRET), we discovered that cleavage of this ribozyme at physiological pH is accompanied by a structural lengthening in magnitude comparable to previous trans-acting HDV ribozymes. Conformational heterogeneity observed by FRET in solution appears to have been removed upon crystallization. Analysis of a total of 1.8 µsec of molecular dynamics (MD) simulations showed that the crystallographically unresolved cleavage site conformation is likely correctly modeled after the hammerhead ribozyme, but that crystal contacts and the removal of several 2′-oxygens near the scissile phosphate compromise catalytic in-line fitness. A cis-acting version of the ribozyme exhibits a more dynamic active site, while a G-1 residue upstream of the scissile phosphate favors poor fitness, allowing us to rationalize corresponding changes in catalytic activity. Based on these data, we propose that the available crystal structures of the HDV ribozyme represent intermediates on an overall rugged RNA folding free-energy landscape. PMID:24854621

High pressure phase transitions in the rare earth metal erbium to 151 GPa.

PubMed

Samudrala, Gopi K; Thomas, Sarah A; Montgomery, Jeffrey M; Vohra, Yogesh K

2011-08-10

High pressure x-ray diffraction studies have been performed on the heavy rare earth metal erbium (Er) in a diamond anvil cell at room temperature to a pressure of 151 GPa and Er has been compressed to 40% of its initial volume. The rare earth crystal structure sequence hcp → Sm type → dhcp → distorted fcc (hcp: hexagonal close packed; fcc: face centered cubic; dhcp: double hcp) is observed in Er below 58 GPa. We have carried out Rietveld refinement of crystal structures in the pressure range between 58 GPa and 151 GPa. We have examined various crystal structures that have been proposed for the distorted fcc (dfcc) phase and the post-dfcc phase in rare earth metals. We find that the hexagonal hR 24 structure is the best fit between 58 and 118 GPa. Above 118 GPa, a structural transformation from hR 24 phase to a monoclinic C 2/m phase is observed with a volume change of - 1.9%. We have also established a clear trend for the pressure at which a post-dfcc phase is formed in rare earth metals and show that there is a monotonic increase in this pressure with the filling of 4f shell.

High pressure phase transitions in the rare earth metal erbium to 151 GPa

NASA Astrophysics Data System (ADS)

Samudrala, Gopi K.; Thomas, Sarah A.; Montgomery, Jeffrey M.; Vohra, Yogesh K.

2011-08-01

High pressure x-ray diffraction studies have been performed on the heavy rare earth metal erbium (Er) in a diamond anvil cell at room temperature to a pressure of 151 GPa and Er has been compressed to 40% of its initial volume. The rare earth crystal structure sequence {hcp} \\to {Sm}~ {type} \\to {dhcp} \\to {distorted} fcc (hcp: hexagonal close packed; fcc: face centered cubic; dhcp: double hcp) is observed in Er below 58 GPa. We have carried out Rietveld refinement of crystal structures in the pressure range between 58 GPa and 151 GPa. We have examined various crystal structures that have been proposed for the distorted fcc (dfcc) phase and the post-dfcc phase in rare earth metals. We find that the hexagonal hR 24 structure is the best fit between 58 and 118 GPa. Above 118 GPa, a structural transformation from hR 24 phase to a monoclinic C 2/m phase is observed with a volume change of - 1.9%. We have also established a clear trend for the pressure at which a post-dfcc phase is formed in rare earth metals and show that there is a monotonic increase in this pressure with the filling of 4f shell.

Polymorphic polytypic transition induced in crystals by interaction of spirals and 2D growth mechanisms

NASA Astrophysics Data System (ADS)

Aquilano, Dino; Veesler, Stéphane; Astier, Jean Pierre; Pastero, Linda

2003-01-01

The relationship between crystal polymorphism and polytypism can be revealed by surface patterns through the interlacing of the growth spirals. Simple high-symmetry structures as SiC, ZnS, CdI2 and more complex low-symmetry layered structures as n-paraffins, n-alcohols and micas are concerned with polymorphic-polytypic transition. In this paper, we will show for the first time, through in situ AFM observations and X-ray diffractometry, that a protein polymorph (P2 12 12 1α-amylase) locally changes, during growth, to a monoclinic P2 1 polytype, thanks to the screw dislocation activity. The interplay between spiral steps and 2D nuclei of the polytypes coexisting in the same crystalline individual allows to foresee the consequences on the crystal quality. The discussion is extended to other mineral and biological molecules and a new general rule is proposed to explain the interactions between surface patterns and the bulk crystal structure.

Observing in space and time the ephemeral nucleation of liquid-to-crystal phase transitions.

PubMed

Yoo, Byung-Kuk; Kwon, Oh-Hoon; Liu, Haihua; Tang, Jau; Zewail, Ahmed H

2015-10-19

The phase transition of crystalline ordering is a general phenomenon, but its evolution in space and time requires microscopic probes for visualization. Here we report direct imaging of the transformation of amorphous titanium dioxide nanofilm, from the liquid state, passing through the nucleation step and finally to the ordered crystal phase. Single-pulse transient diffraction profiles at different times provide the structural transformation and the specific degree of crystallinity (η) in the evolution process. It is found that the temporal behaviour of η exhibits unique 'two-step' dynamics, with a robust 'plateau' that extends over a microsecond; the rate constants vary by two orders of magnitude. Such behaviour reflects the presence of intermediate structure(s) that are the precursor of the ordered crystal state. Theoretically, we extend the well-known Johnson-Mehl-Avrami-Kolmogorov equation, which describes the isothermal process with a stretched-exponential function, but here over the range of times covering the melt-to-crystal transformation.

Effect of severe plastic deformation on the structure and crystal-lattice distortions in the Ni3(Al, X) ( X = Ti, Nb) intermetallic compound

NASA Astrophysics Data System (ADS)

Kazantseva, N. V.; Pilyugin, V. P.; Danilov, S. E.; Kolosov, V. Yu.

2015-05-01

A systematic combined study of crystal lattice distortions caused by doping and by severe plastic deformation (SPD) of Ti- and Nb-doped Ni3Al intermetallic compound has been carried out using methods of X-ray diffraction, electron microscopy, and electrical-resistance measurements. The degree of imperfection of the alloys has been estimated based on the results obtained by all three methods. The degree of structural perfection of niobium-doped crystals was found to be higher than in the case of Ti doping. The character of stresses (tensile stresses after doping; and compressive stresses after SPD) in the crystal lattice has been established and their values have been calculated. A significant increase in the density of dislocations, point defects, and lattice curvature has been found after SPD. A nanocrystalline structure is formed in these alloys, but no complete disordering of the intermetallic phase is observed.

Synthesis, crystal structure and electrical properties of N,N-dimethylanilinium trichloridostannate (II): (C8H12N)SnCl3

NASA Astrophysics Data System (ADS)

Chouaib, H.; Kamoun, S.; Costa, L. C.; Graça, M. P. F.

2015-12-01

A new (C8H12N)SnCl3 crystal of the general formula AMX3 was grown by soft chemistry method. X-ray study shows that the crystal crystallized in a monoclinic system with the space group P21/a. The structure was solved by Patterson method and refined to a final value of R = 0.0304 for 1157 independent observed reflections. The cohesion and the stability of the atomic arrangement result from the N-H … Cl hydrogen bonds between (C8H12N)+ cations and isolated (SnCl3)- anions. At high temperature this compound exhibits a structural phase transition at 340 K. This transition has been characterized by differential scanning calorimetric and impedance spectroscopy. The impedance data were well fitted to an Rp//CPE equivalent electrical circuit model. The close values of activation energies, obtained from the thermal behavior of the conductivity and the relaxation time confirm the presence of a hopping transport mechanism.

Crystal Structure of a Four-Layer Aggregate of Engineered TMV CP Implies the Importance of Terminal Residues for Oligomer Assembly

PubMed Central

Li, Xiangyang; Song, Baoan; Chen, Xi; Wang, Zhenchao; Zeng, Mengjiao; Yu, Dandan; Hu, Deyu; Chen, Zhuo; Jin, Linhong; Yang, Song; Yang, Caiguang; Chen, Baoen

2013-01-01

Background Crystal structures of the tobacco mosaic virus (TMV) coat protein (CP) in its helical and disk conformations have previously been determined at the atomic level. For the helical structure, interactions of proteins and nucleic acids in the main chains were clearly observed; however, the conformation of residues at the C-terminus was flexible and disordered. For the four-layer aggregate disk structure, interactions of the main chain residues could only be observed through water–mediated hydrogen bonding with protein residues. In this study, the effects of the C-terminal peptides on the interactions of TMV CP were investigated by crystal structure determination. Methodology/Principal Findings The crystal structure of a genetically engineered TMV CP was resolved at 3.06 Å. For the genetically engineered TMV CP, a six-histidine (His) tag was introduced at the N-terminus, and the C-terminal residues 155 to 158 were truncated (N-His-TMV CP19). Overall, N-His-TMV CP19 protein self-assembled into the four-layer aggregate form. The conformations of residues Gln36, Thr59, Asp115 and Arg134 were carefully analyzed in the high radius and low radius regions of N-His-TMV CP19, which were found to be significantly different from those observed previously for the helical and four-layer aggregate forms. In addition, the aggregation of the N-His-TMV CP19 layers was found to primarily be mediated through direct hydrogen-bonding. Notably, this engineered protein also can package RNA effectively and assemble into an infectious virus particle. Conclusion The terminal sequence of amino acids influences the conformation and interactions of the four-layer aggregate. Direct protein–protein interactions are observed in the major overlap region when residues Gly155 to Thr158 at the C-terminus are truncated. This engineered TMV CP is reassembled by direct protein–protein interaction and maintains the normal function of the four-layer aggregate of TMV CP in the presence of RNA. PMID:24223721

Structure determination of uracil-DNA N-glycosylase from Deinococcus radiodurans in complex with DNA.

PubMed

Pedersen, Hege Lynum; Johnson, Kenneth A; McVey, Colin E; Leiros, Ingar; Moe, Elin

2015-10-01

Uracil-DNA N-glycosylase (UNG) is a DNA-repair enzyme in the base-excision repair (BER) pathway which removes uracil from DNA. Here, the crystal structure of UNG from the extremophilic bacterium Deinococcus radiodurans (DrUNG) in complex with DNA is reported at a resolution of 1.35 Å. Prior to the crystallization experiments, the affinity between DrUNG and different DNA oligonucleotides was tested by electrophoretic mobility shift assays (EMSAs). As a result of this analysis, two 16 nt double-stranded DNAs were chosen for the co-crystallization experiments, one of which (16 nt AU) resulted in well diffracting crystals. The DNA in the co-crystal structure contained an abasic site (substrate product) flipped into the active site of the enzyme, with no uracil in the active-site pocket. Despite the high resolution, it was not possible to fit all of the terminal nucleotides of the DNA complex into electron density owing to disorder caused by a lack of stabilizing interactions. However, the DNA which was in contact with the enzyme, close to the active site, was well ordered and allowed detailed analysis of the enzyme-DNA interaction. The complex revealed that the interaction between DrUNG and DNA is similar to that in the previously determined crystal structure of human UNG (hUNG) in complex with DNA [Slupphaug et al. (1996). Nature (London), 384, 87-92]. Substitutions in a (here defined) variable part of the leucine loop result in a shorter loop (eight residues instead of nine) in DrUNG compared with hUNG; regardless of this, it seems to fulfil its role and generate a stabilizing force with the minor groove upon flipping out of the damaged base into the active site. The structure also provides a rationale for the previously observed high catalytic efficiency of DrUNG caused by high substrate affinity by demonstrating an increased number of long-range electrostatic interactions between the enzyme and the DNA. Interestingly, specific interactions between residues in the N-terminus of a symmetry-related molecule and the complementary DNA strand facing away from the active site were also observed which seem to stabilize the enzyme-DNA complex. However, the significance of this observation remains to be investigated. The results provide new insights into the current knowledge about DNA damage recognition and repair by uracil-DNA glycosylases.

Effect of Water Vapor, Temperature, and Rapid Annealing on Formamidinium Lead Triiodide Perovskite Crystallization

DOE Office of Scientific and Technical Information (OSTI.GOV)

Aguiar, Jeffery A.; Wozny, Sarah; Alkurd, Nooraldeen R.

Perovskite-based solar cells are one of the emerging candidates for radically lower cost photovoltaics. Herein, we report on the synthesis and crystallization of organic-inorganic formamidinium lead triiodide perovskite films under controlled atmospheric and environmental conditions. Using in situ (scanning) transmission electron microscopy, we make observations of the crystallization process of these materials in nitrogen and oxygen gas with and without the presence of water vapor. Complementary planar samples were also fabricated in the presence of water vapor and characterized by in situ X-ray diffraction. Direct observations of the material structure and final morphology indicate that the exposure to water vapormore » results in a porous film that is metastable, regardless of the presence of argon, nitrogen, or oxygen. However, the optimal crystallization temperature of 175 degrees C is unperturbed across conditions. Rapid modulation about the annealing temperature of 175 degrees C in +/-25 degrees C steps (150-200 degrees C) promotes crystallization and significantly improves the film morphology by overcoming the presence of impregnated water trapped in the material. Following this processing protocol, we demonstrate substantial growth to micron-size grains via observation inside of an environmentally controlled transmission electron microscope. Adapting this insight from our in situ microscopy, we are able to provide an informed materials protocol to control the structure and morphology of these organic-inorganic semiconductors, which is readily applicable to benchtop device growth strategies.« less

Effect of Water Vapor, Temperature, and Rapid Annealing on Formamidinium Lead Triiodide Perovskite Crystallization

DOE Office of Scientific and Technical Information (OSTI.GOV)

Aguiar, Jeffery A.; Wozny, Sarah; Alkurd, Nooraldeen R.

Perovskite-based solar cells are one of the emerging candidates for radically lower cost photovoltaics. Herein, we report on the synthesis and crystallization of organic-inorganic formamidinium lead triiodide perovskite films under controlled atmospheric and environmental conditions. Using in situ (scanning) transmission electron microscopy, we make observations of the crystallization process of these materials in nitrogen and oxygen gas with and without the presence of water vapor. Complementary planar samples were also fabricated in the presence of water vapor and characterized by in situ X-ray diffraction. Direct observations of the material structure and final morphology indicate that the exposure to water vapormore » results in a porous film that is metastable, regardless of the presence of argon, nitrogen, or oxygen. However, the optimal crystallization temperature of 175 °C is unperturbed across conditions. Rapid modulation about the annealing temperature of 175 °C in ±25 °C steps (150-200 °C) promotes crystallization and significantly improves the film morphology by overcoming the presence of impregnated water trapped in the material. Following this processing protocol, we demonstrate substantial growth to micron-size grains via observation inside of an environmentally controlled transmission electron microscope. Adapting this insight from our in situ microscopy, we are able to provide an informed materials protocol to control the structure and morphology of these organic-inorganic semiconductors, which is readily applicable to benchtop device growth strategies.« less

Vortex lattice structures in YNi{sub 2}B{sub 2}C

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yethiraj, M.; Paul, D.M.; Tomy, C.V.

The authors observe a flux lattice with square symmetry in the superconductor YNi{sub 2}B{sub 2}C when the applied field is parallel to the c-axis of the crystal. A square lattice observed previously in the isostructural magnetic analog ErNi{sub 2}B{sub 2}C was attributed to the interaction between magnetic order in that system and the flux lattice. Since the Y-based compound does not order magnetically, it is clear that the structure of the flux lattice is unrelated to magnetic order. In fact, they show that the flux lines have a square cross-section when the applied field is parallel to the c-axis ofmore » the crystal, since the measured penetration depth along the 100 crystal direction is larger than the penetration depth along the 110 by approximately 60%. This is the likely reason for the square symmetry of the lattice. Although they find considerable disorder in the arrangement of the flux lines at 2.5T, no melting of the vortex lattice was observed.« less

Vortex lattice structures in YNi{sub 2}B{sub 2}C

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yethiraj, M.; Paul, D.M.; Tomy, C.V.

We observe a flux lattice with square symmetry in the superconductor YNi{sub 2}B{sub 2}C when the applied field is parallel to the c-axis of the crystal. A square lattice observed previously in the isostructural magnetic analog ErNi{sub 2}B{sub 2}C was attributed to the interaction between magnetic order in that system and the flux lattice. Since the Y-based compound does not order magnetically, it is clear that the structure of the flux lattice is unrelated to magnetic order. In fact, we show that the flux lines have a square cross-section when the applied field is parallel to the c-axis of themore » crystal, since the measured penetration depth along the 110 crystal direction is smaller than the penetration depth along the 100 by approximately 30%. This causes the square symmetry of the lattice. Although we find considerable disorder in the arrangement of the flux lines at 2.5T, no melting of the vortex lattice was observed.« less

Interfacial magnetic coupling in hetero-structure of Fe/double-perovskite NdBaMn2O6 single crystal

NASA Astrophysics Data System (ADS)

Lin, W. C.; Tsai, C. L.; Ogawa, K.; Yamada, S.; Gandhi, Ashish C.; Lin, J. G.

2018-04-01

The interfacial magnetic coupling between metallic Fe and the double-perovskite NdBaMn2O6 single crystal was investigated in the heterostructure of 4-nm Pd/10-nm Fe/NdBaMn2O6. A considerable magnetic coupling effect was observed in the temperature range coincident with the magnetic phase transition of NdBaMn2O6. When the temperature was elevated above 270 K, NdBaMn2O6 transformed from a state of antiferromagnetic fluctuating domains to a superparamagnetism-like (ferromagnetic fluctuation) state with high magnetic susceptibility. Concurrently, the interfacial magnetic coupling between the Fe layer and the NdBaMn2O6 crystal was observed, as indicated by the considerable squareness reduction and coercivity enhancement in the Fe layer. Moreover, the presence of the Fe layer changed the magnetic structure of NdBaMn2O6 from conventional 4-fold symmetry to 2-fold symmetry. These observations offer applicable insights into the mutual magnetic interaction in the heterostructures of metallic ferromagnetism/perovskite materials.

Defect-mediated phonon dynamics in TaS2 and WSe2

PubMed Central

Cremons, Daniel R.; Plemmons, Dayne A.; Flannigan, David J.

2017-01-01

We report correlative crystallographic and morphological studies of defect-dependent phonon dynamics in single flakes of 1T-TaS2 and 2H-WSe2 using selected-area diffraction and bright-field imaging in an ultrafast electron microscope. In both materials, we observe in-plane speed-of-sound acoustic-phonon wave trains, the dynamics of which (i.e., emergence, propagation, and interference) are strongly dependent upon discrete interfacial features (e.g., vacuum/crystal and crystal/crystal interfaces). In TaS2, we observe cross-propagating in-plane acoustic-phonon wave trains of differing frequencies that undergo coherent interference approximately 200 ps after initial emergence from distinct interfacial regions. With ultrafast bright-field imaging, the properties of the interfering wave trains are observed to correspond to the beat frequency of the individual oscillations, while intensity oscillations of Bragg spots generated from selected areas within the region of interest match well with the real-space dynamics. In WSe2, distinct acoustic-phonon dynamics are observed emanating and propagating away from structurally dissimilar morphological discontinuities (vacuum/crystal interface and crystal terrace), and results of ultrafast selected-area diffraction reveal thickness-dependent phonon frequencies. The overall observed dynamics are well-described using finite element analysis and time-dependent linear-elastic continuum mechanics. PMID:28503630

DOE Office of Scientific and Technical Information (OSTI.GOV)

Thiruselvam, Viswanathan; Sivaraman, Padavattan; Kumarevel, Thirumananseri, E-mail: kumarevel.thirumananseri@riken.jp

Highlights: • Crystal structure of ferritin was determined. • Endogenously expressed iron’s were identified. • Binuclear iron sites were observed at A and B active sites. - Abstract: Ferritin is an iron regulatory protein. It is responsible for storage and detoxification of excess iron thereby it regulates iron level in the body. Here we report the crystal structure of ferritin with two endogenously expressed Fe atoms binding in both the sites. The protein was purified and characterized by MALDI-TOF and N-terminal amino acid sequencing. The crystal belongs to I4 space group and it diffracted up to 2.5 Å. The structuralmore » analysis suggested that it crystallizes as hexamer and confirmed that it happened to be the first report of endogenously expressed Fe ions incorporated in both the A and B sites, situated in between the helices.« less

Temperature-dependent μ-Raman investigation of struvite crystals.

PubMed

Prywer, Jolanta; Kasprowicz, D; Runka, T

2016-04-05

The effect of temperature on the vibrational properties of struvite crystals grown from silica gels was systematically studied by μ-Raman spectroscopy. The time-dependent Raman spectra recorded in the process of long time annealing of struvite crystal at 353 K do not indicate structural changes in the struvite crystal with the time of annealing. The temperature-dependent Raman spectra recorded in the range 298-423 K reveal a phase transition in struvite at about 368 K. Above this characteristic temperature, some of bands assigned to vibrations of the PO4 and NH4 tetrahedra and water molecules observed in the Raman spectra in low temperatures (orthorhombic phase) change their spectral parameters or disappear, which indicates a transition to a higher symmetry structure of struvite in the range of high temperatures. Copyright © 2016 Elsevier B.V. All rights reserved.

The crystal structure of the regulatory domain of the human sodium-driven chloride/bicarbonate exchanger.

PubMed

Alvadia, Carolina M; Sommer, Theis; Bjerregaard-Andersen, Kaare; Damkier, Helle Hasager; Montrasio, Michele; Aalkjaer, Christian; Morth, J Preben

2017-09-21

The sodium-driven chloride/bicarbonate exchanger (NDCBE) is essential for maintaining homeostatic pH in neurons. The crystal structure at 2.8 Å resolution of the regulatory N-terminal domain of human NDCBE represents the first crystal structure of an electroneutral sodium-bicarbonate cotransporter. The crystal structure forms an equivalent dimeric interface as observed for the cytoplasmic domain of Band 3, and thus establishes that the consensus motif VTVLP is the key minimal dimerization motif. The VTVLP motif is highly conserved and likely to be the physiologically relevant interface for all other members of the SLC4 family. A novel conserved Zn 2+ -binding motif present in the N-terminal domain of NDCBE is identified and characterized in vitro. Cellular studies confirm the Zn 2+ dependent transport of two electroneutral bicarbonate transporters, NCBE and NBCn1. The Zn 2+ site is mapped to a cluster of histidines close to the conserved ETARWLKFEE motif and likely plays a role in the regulation of this important motif. The combined structural and bioinformatics analysis provides a model that predicts with additional confidence the physiologically relevant interface between the cytoplasmic domain and the transmembrane domain.

Structure and properties of fullerene molecular crystals with linear-scaling van der Waals density functional theory

NASA Astrophysics Data System (ADS)

Mostofi, Arash; Andrinopoulos, Lampros; Hine, Nicholas

2014-03-01

Fullerene molecular crystals are of technological promise for their use in heterojunction photovoltaic cells. An improved theoretical understanding of their structure and properties would be a step towards the rational design of new devices. Simulations based on density-functional theory (DFT) are invaluable for developing such insight, but standard semi-local functionals do not capture the important inter-molecular van der Waals (vdW) interactions in fullerene crystals. Furthermore the computational cost associated with the large unit cells needed are at the limit or beyond the capabilities of traditional DFT methods. In this work we overcome these limitations by using our implementation of a number of vdW-DFs in the ONETEP linear-scaling DFT code to study the structural properties of C60 molecular crystals. Powder neutron diffraction shows that the low-temperature Pa-3 phase is orientationally ordered with individual C60 units rotated around the [111] direction. We fully explore the energy landscape associated with the rotation angle and find two stable structures that are energetically very close, one of which corresponds to the experimentally observed structure. We further consider the effect of orientational disorder in very large supercells of thousands of atoms.

Structural characterization of polymorphs and molecular complexes of finasteride

NASA Astrophysics Data System (ADS)

Wawrzycka, Irena; Stȩpniak, Krystyna; Matyjaszczyk, Sławomir; Kozioł, Anna E.; Lis, Tadeusz; Abboud, Khalil A.

1999-01-01

The molecular structure of finasteride, 17 β-( N-tert-butylcarbamoyl)-4-aza-5 α-androst-1-en-3-one, and structures of three related crystalline forms have been determined by X-ray analysis. The rigid steroid skeleton of the molecule adopts a half-chair/chair/chair/half-chair conformation. Two peptide groups, one cyclic (lactam) in the ring A and a second being a part of the substituent at C17, are the main factors influencing intermolecular contacts. Different hydrogen-bond interactions of these hydrophilic groups are observed in the crystal structures. An infinite ribbon of finasteride molecules is formed between lactam groups in the orthorhombic homomolecular crystal ( 1) obtained from an ethanol solution. The linear molecular complex finasteride-acetic acid ( 1a) is connected by hydrogen bonds between the lactam of finasteride and the carboxyl group of acetic acid. The crystallization from an ethyl acetate solution gives a complex structure of bis-finasteride monohydrate ethyl acetate clathrate ( 1b) with guest molecule disordered in channels. Crystals of a second (monoclinic) finasteride polymorph ( 2) were obtained during thermal decomposition of 1a, and sublimation of 1, 1a and 1b. Two polymorphic forms show different IR spectra.

[Structure of crambin in solution, crystal and in the trajectories of molecular dynamics simulations].

PubMed

Abaturov, L V; Nosova, N G

2013-01-01

The mechanisms of the three-dimensional crambin structure alterations in the crystalline environments and in the trajectories of the molecular dynamics simulations in the vacuum and crystal surroundings have been analyzed. In the crystalline state and in the solution the partial regrouping of remote intramolecular packing contacts, involved in the formation and stabilization of the tertiary structure of the crambin molecule, occurs in NMR structures. In the crystalline state it is initiated by the formation of the intermolecular contacts, the conformational influence of its appearance is distributed over the structure. The changes of the conformations and positions of the residues of the loop segments, where the intermolecular contacts of the crystal surroundings are preferably concentrated, are most observable. Under the influence of these contacts the principal change of the regular secondary structure of crambin is taking place: extension of the two-strand beta structure to the three-strand structure with the participation of the single last residue N46 of the C-terminal loop. In comparison with the C-terminal loop the more profound changes are observed in the conformation and the atomic positions of the backbone atoms and in the solvent accessibility of the residues of the interhelical loop. In the solution of the ensemble of the 8 NMR structures relative accessibility to the solvent differs more noticeably also in the region of the loop segments and rather markedly in the interhelical loop. In the crambin cryogenic crystal structures the positions of the atoms of the backbone and/or side chain of 14-18 of 46 residues are discretely disordered. The disorganizations of at least 8 of 14 residues occur directly in the regions of the intermolecular contacts and another 5 residues are disordered indirectly through the intramolecular contacts with the residues of the intermolecular contacts. Upon the molecular dynamics simulation in the vacuum surrounding as in the solution of the crystalline structure of crambin the essential changes of the backbone conformation are caused by the intermolecular contacts absence, but partly masked by the structure changes owing to the nonpolar H atoms absence on the simulated structure. The intermolecular contact absence is partly manifested upon the molecular dynamics simulation of the crambin crystal with one protein molecule. Compared to the crystal structure the lengths of the interpeptide hydrogen bonds and other interresidue contacts in an average solution NMR structure are somewhat shorter and accordingly the energy of the interpeptide hydrogen bonds is better. This length shortening can occur at the stage of the refinement of the NMR structures of the crambin and other proteins by its energy minimizations in the vacuum surroundings and not exist in the solution protein structures.

X-ray structural investigation of nonsymmetrically and symmetrically alkylated [1]benzothieno[3,2-b]benzothiophene derivatives in bulk and thin films.

PubMed

Gbabode, Gabin; Dohr, Michael; Niebel, Claude; Balandier, Jean-Yves; Ruzié, Christian; Négrier, Philippe; Mondieig, Denise; Geerts, Yves H; Resel, Roland; Sferrazza, Michele

2014-08-27

A detailed structural study of the bulk and thin film phases observed for two potential high-performance organic semiconductors has been carried out. The molecules are based on [1]benzothieno[3,2-b]benzothiophene (BTBT) as conjugated core and octyl side groups, which are anchored either symmetrically at both sides of the BTBT core (C8-BTBT-C8) or nonsymmetrically at one side only (C8-BTBT). Thin films of different thickness (8-85 nm) have been prepared by spin-coating for both systems and analyzed by combining specular and grazing incidence X-ray diffraction. In the case of C8-BTBT-C8, the known crystal structure obtained from single-crystal investigations is observed within all thin films, down to a film thickness of 9 nm. In the case of C8-BTBT, the crystal structure of the bulk phase has been determined from X-ray powder diffraction data with a consistent matching of experimental and calculated X-ray diffraction patterns (Rwp = 5.8%). The packing arrangement of C8-BTBT is similar to that of C8-BTBT-C8, that is, consisting of a lamellar structure with molecules arranged in a "herringbone" fashion, yet with lamellae composed of two head-to-head (or tail-to-tail as the structure is periodic) superimposed molecules instead of only one molecule for C8-BTBT-C8. As for C8-BTBT-C8, we demonstrate that the same phase is observed in bulk and thin films for C8-BTBT whatever the film thickness investigated.

The molecular and crystal structure of dextrans: a combined electron and X-ray diffraction study. II. A low temperature, hydrated polymorph.

PubMed

Guizard, C; Chanzy, H; Sarko, A

1985-06-05

The crystal and molecular structure of a dextran hydrate has been determined through combined electron and X-ray diffraction analysis, aided by stereochemical model refinement. A total of 65 hk0 electron diffraction intensities were measured on frozen single crystals held at the temperature of liquid nitrogen, to a resolution limit of 1.6 A. The X-ray intensities were measured from powder patterns recorded from collections of the single crystals. The structure crystallizes in a monoclinic unit cell with parameters a = 25.71 A, b = 10.21 A, c (chain axis) = 7.76 A and beta = 91.3 degrees. The space group is P2(1) with b axis unique. The unit cell contains six chains and eight water molecules, with three chains of the same polarity and four water molecules constituting the asymmetric unit. Along the chain direction the asymmetric unit is a dimer residue; however, the individual glucopyranose residues are very nearly related by a molecular 2-fold screw axis. The conformation of the chain is very similar to that in the anhydrous structure, but the chain packing differs in the two structures in that the rotational positions of the chains about the helix axes (the chain setting angles) are considerably different. The chains still pack in the form of sheets that are separated by water molecules. The difference in the chain setting angles between the anhydrous and hydrate structures corresponds to the angle between like unit cell axes observed in the diffraction diagrams recorded from hybrid crystals containing both polymorphs. Despite some beam damage effects, the structure was determined to a satisfactory degree of agreement, with the residuals R''(electron diffraction) = 0.258 and R(X-ray) = 0.127.

Observations of cavity polaritons in one-dimensional photonic crystals containing a liquid-crystalline semiconductor based on perylene bisimide units

NASA Astrophysics Data System (ADS)

Sakata, T.; Suzuki, M.; Yamamoto, T.; Nakanishi, S.; Funahashi, M.; Tsurumachi, N.

2017-10-01

We investigated the optical transmission properties of one-dimensional photonic crystal (1D-PC) microcavity structures containing the liquid-crystalline (LC) perylene tetracarboxylic bisimide (PTCBI) derivative. We fabricated the microcavity structures for this study by two different methods and observed the cavity polaritons successfully in both samples. For one sample, since the PTCBI molecules were aligned in the cavity layer of the 1D-PC by utilizing a friction transfer method, vacuum Rabi splitting energy was strongly dependent on the polarization of the incident light produced by the peculiar optical features of the LC organic semiconductor. For the other sample, we did not utilize the friction transfer method and did not observe such polarization dependence. However, we did observe a relatively large Rabi splitting energy of 187 meV, probably due to the improvement of optical confinement effect.

Magneto-photonic crystal optical sensors with sensitive covers

NASA Astrophysics Data System (ADS)

Dissanayake, Neluka; Levy, Miguel; Chakravarty, A.; Heiden, P. A.; Chen, N.; Fratello, V. J.

2011-08-01

We report on a magneto-photonic crystal on-chip optical sensor for specific analyte detection with polypyrrole and gold nano particles as modified photonic crystal waveguide cover layers. The reaction of the active sensor material with various analytes modifies the electronic structure of the sensor layer causing changes in its refractive index and a strong transduction signal. Magneto-photonic crystal enhanced polarization rotation sensitive to the nature of the cover layer detects the index modification upon analyte adsorption. A high degree of selectivity and sensitivity are observed for aqueous ammonia and methanol with polypyrrole and for thiolated-gold- with gold-nanoparticles covers.

A photoluminescence, thermoluminescence and electron paramagnetic resonance study of EFG grown europium doped lithium fluoride (LiF) crystals

NASA Astrophysics Data System (ADS)

Seth, Pooja; Swati, G.; Haranath, D.; Rao, S. M. D.; Aggarwal, Shruti

2018-07-01

Europium (Eu) doped LiF crystals have been grown by the Edge-defined film fed growth (EFG) technique. The designing and installation of the furnace used for the growth of the crystals have been discussed in detail. In the present study, Eu (Eu2O3) has been doped in LiF in different concentration (0.02-0.2 wt %). X-ray diffractometry (XRD) and Energy Dispersive X-ray (EDX) spectroscopy confirms the incorporation of Eu in LiF. The influence of Eu on LiF has been investigated through photoluminescence (PL), thermoluminescence (TL) and electron paramagnetic resonance (EPR) in as-grown and annealed crystals. PL emission spectra shows the presence of both Eu3+ and Eu2+ form in the as-grown crystals which is confirmed by EPR results. Whereas, in annealed crystals, Eu is present predominantly as Eu2+ form. This suggests that growing crystals at high temperature (∼900 °C) in argon gas atmosphere through EFG technique favours the reduction of Eu3+ → Eu2+. This reduction phenomenon has been explained on the basis of charge compensation model. TL study of the LiF: Eu (0.02-0.2 wt %) crystals has been done after irradiation with Co60 gamma rays. In this study, it has been observed that the TL intensity as well as glow curve structure of LiF: Eu crystals are a strong function of Eu concentration. The maximum TL is observed at Eu concentration of 0.05 wt% at which a well defined glow curve structure with a prominent peak at 185 °C and a small peak at 253 °C. Beyond this concentration (0.05 wt %), TL intensity decreases due to aggregation of defects in the host. The peak at 185 °C in LiF: Eu (0.05 wt %) is certainly due to the presence of Eu2+ associated defects which is also supported by the PL spectra. It has been observed that Eu doping have a key role in creation of more defect levels which lead to the increased number of electron and hole traps. Further, trapping parameters are analysed using glow curve deconvolution method to have an insight study of TL phenomena. Further, TL glow curve structure of as-grown and annealed crystal are distinct which may be attributed to the nature of defect traps formed inside the LiF.

Growth and characterization of a novel nonlinear optical borate crystal - Yttrium calcium borate (YCB)

NASA Astrophysics Data System (ADS)

Arun Kumar, R.; Arivanandhan, M.; Dhanasekaran, R.; Hayakawa, Y.

2013-06-01

A new nonlinear optical single crystal yttrium calcium borate Y2CaB10O19 (YCB) was grown for the first time from its melt. The starting materials were prepared by the solid-state reaction method. The melting point of the synthesized material was identified to be 967 °C. YCB crystal exhibits monoclinic crystal structure with the space group C2. The crystalline perfection of the grown YCB crystal was found to be good. From the UV-VIS-NIR studies, the lower cutoff wavelength of the crystal occurs below 200 nm. The functional groups of the grown crystal were assigned using the FTIR data. The second harmonic generation (SHG) of the YCB crystal was observed using a Nd:YAG laser with a fundamental wavelength of 1064 nm. The laser damage threshold value of the YCB crystal was found to be very high - 10.5 GW/cm2.

Effect of L-Valine on the growth and characterization of Sodium Acid Phthalate (SAP) single crystals.

PubMed

Nirmala, L Ruby; Thomas Joseph Prakash, J

2013-06-01

Undoped and amino acid doped good quality single crystals of Sodium Acid Phthalate crystals (SAP) were grown by slow evaporation solution growth technique which are semiorganic in nature. The effect of amino acid (L-Valine) dopant on the growth and the properties of SAP single crystal was investigated. The single crystal X-ray diffraction studies and FT-IR studies were carried out to identify the crystal structure and the presence of functional groups in undoped and L-Valine doped SAP crystals. The transparent nature of the grown crystal was observed using UV-Visible spectrum. The thermal decomposition of the doped SAP crystals was investigated by thermo gravimetric analysis (TGA) and differential thermal analysis (DTA). The enhancement in the NLO property of the undoped and L-Valine doped SAP crystals using KDP crystal as a reference was studied using SHG measurements. Vickers micro hardness measurements are used for the study of mechanical strength of the grown crystals. Copyright © 2013 Elsevier B.V. All rights reserved.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kaluarachchi, Udhara S.; Xie, Weiwei; Lin, Qisheng

Single crystals of Bi 2Rh 3S 2 and Bi 2Rh 3.5S 2 were synthesized by solution growth, and the crystal structures and thermodynamic and transport properties of both compounds were studied. In the case of Bi 2Rh 3S 2, a structural first-order transition at around 165 K is identified by single-crystal diffraction experiments, with clear signatures visible in resistivity, magnetization, and specific heat data. No superconducting transition for Bi 2Rh 3S 2 was observed down to 0.5 K. In contrast, no structural phase transition at high temperature was observed for Bi 2Rh 3.5S 2; however, bulk superconductivity with a criticalmore » temperature, T c ≈ 1.7 K, was observed. The Sommerfeld coefficient γ and the Debye temperature (Θ D) were found to be 9.41 mJ mol –1K –2 and 209 K, respectively, for Bi 2Rh 3S 2, and 22 mJ mol –1K –2 and 196 K, respectively, for Bi 2Rh 3.5S 2. As a result, the study of the specific heat in the superconducting state of Bi 2Rh 3.5S 2 suggests that Bi 2Rh 3.5S 2 is a weakly coupled, BCS superconductor.« less

Observation of Intermolecular Hydrogen Bonding Interactions in Biosynthesized and Biodegradable Poly [(R)-3-hydroxybutyrate- co-(R)-3-hydroxyhexanoate] in Chloroform and 1,1,1,3,3,3-Hexafluoro-2-propanol (HFIP).

PubMed

Sobieski, Brian J; Noda, Isao; Rabolt, John F; Chase, D Bruce

2017-10-01

In this work, we describe polymer-solvent interactions in biosynthesized and biodegradable poly[(R)-3-hydroxybutyrate- co-(R)-3-hydroxyhexanoate] (PHBHx) and the atactic homopolymer, poly(3-hydroxybutyrate) (a-PHB), which were studied both as neat polymers and in solutions of chloroform and 1,1,1,3,3,3-hexafluoro-2-propanol (HFIP). Specifically, infrared frequency shifts of the carbonyl band were observed in semi-crystalline PHBHx, but not in a-PHB, because it cannot form the helical conformation required for crystallization. The carbonyl band of PHBHx exhibited the high frequency associated with amorphous structure in chloroform and the lower frequency traditionally attributed to the helical crystalline structure in HFIP. The same results were obtained for a-PHB, demonstrating that the helical structure is not required for a lower frequency carbonyl-stretching mode. It is proposed that the band shift is due to hydrogen bonding between the carbonyl and hydroxyl hydrogen in HFIP. Therefore, the carbonyl frequency observed upon crystallization is most likely due to hydrogen bonding between the carbonyl and methyl hydrogen of the neighboring polymer chain in the crystal lattice as previously suggested.

Crystal structure and substrate specificity of the [beta]-ketoacyl-acyl carrier protein synthase III (FabH) from Staphylococcus aureus

DOE Office of Scientific and Technical Information (OSTI.GOV)

Qiu, Xiayang; Choudhry, Anthony E.; Janson, Cheryl A.

{beta}-Ketoacyl-ACP synthase III (FabH), an essential enzyme for bacterial viability, catalyzes the initiation of fatty acid elongation by condensing malonyl-ACP with acetyl-CoA. We have determined the crystal structure of FabH from Staphylococcus aureus, a Gram-positive human pathogen, to 2 {angstrom} resolution. Although the overall structure of S. aureus FabH is similar to that of Escherichia coli FabH, the primer binding pocket in S. aureus FabH is significantly larger than that present in E. coli FabH. The structural differences, which agree with kinetic parameters, provide explanation for the observed varying substrate specificity for E. coli and S. aureus FabH. The rankmore » order of activity of S. aureus FabH with various acyl-CoA primers was as follows: isobutyryl- > hexanoyl- > butyryl- > isovaleryl- >> acetyl-CoA. The availability of crystal structure may aid in designing potent, selective inhibitors of S. aureus FabH.« less

Local Structural Investigations, Defect Formation, and Ionic Conductivity of the Lithium Ionic Conductor Li 4 P 2 S 6

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dietrich, Christian; Sadowski, Marcel; Sicolo, Sabrina

Glassy, glass–ceramic, and crystalline lithium thiophosphates have attracted interest in their use as solid electrolytes in all-solid-state batteries. Despite similar structural motifs, including PS 4 3–, P 2S 6 4–, and P 2S 7 4– polyhedra, these materials exhibit a wide range of possible compositions, crystal structures, and ionic conductivities. Here, we present a combined approach of Bragg diffraction, pair distribution function analysis, Raman spectroscopy, and 31P magic angle spinning nuclear magnetic resonance spectroscopy to study the underlying crystal structure of Li 4P 2S 6. In this work, we show that the material crystallizes in a planar structural arrangement asmore » a glass ceramic composite, explaining the observed relatively low ionic conductivity, depending on the fraction of glass content. Calculations based on density functional theory provide an understanding of occurring diffusion pathways and ionic conductivity of this Li + ionic conductor.« less

Water polygons in high-resolution protein crystal structures.

PubMed

Lee, Jonas; Kim, Sung-Hou

2009-07-01

We have analyzed the interstitial water (ISW) structures in 1500 protein crystal structures deposited in the Protein Data Bank that have greater than 1.5 A resolution with less than 90% sequence similarity with each other. We observed varieties of polygonal water structures composed of three to eight water molecules. These polygons may represent the time- and space-averaged structures of "stable" water oligomers present in liquid water, and their presence as well as relative population may be relevant in understanding physical properties of liquid water at a given temperature. On an average, 13% of ISWs are localized enough to be visible by X-ray diffraction. Of those, averages of 78% are water molecules in the first water layer on the protein surface. Of the localized ISWs beyond the first layer, almost half of them form water polygons such as trigons, tetragons, as well as expected pentagons, hexagons, higher polygons, partial dodecahedrons, and disordered networks. Most of the octagons and nanogons are formed by fusion of smaller polygons. The trigons are most commonly observed. We suggest that our observation provides an experimental basis for including these water polygon structures in correlating and predicting various water properties in liquid state.

Water polygons in high-resolution protein crystal structures

PubMed Central

Lee, Jonas; Kim, Sung-Hou

2009-01-01

We have analyzed the interstitial water (ISW) structures in 1500 protein crystal structures deposited in the Protein Data Bank that have greater than 1.5 Å resolution with less than 90% sequence similarity with each other. We observed varieties of polygonal water structures composed of three to eight water molecules. These polygons may represent the time- and space-averaged structures of “stable” water oligomers present in liquid water, and their presence as well as relative population may be relevant in understanding physical properties of liquid water at a given temperature. On an average, 13% of ISWs are localized enough to be visible by X-ray diffraction. Of those, averages of 78% are water molecules in the first water layer on the protein surface. Of the localized ISWs beyond the first layer, almost half of them form water polygons such as trigons, tetragons, as well as expected pentagons, hexagons, higher polygons, partial dodecahedrons, and disordered networks. Most of the octagons and nanogons are formed by fusion of smaller polygons. The trigons are most commonly observed. We suggest that our observation provides an experimental basis for including these water polygon structures in correlating and predicting various water properties in liquid state. PMID:19551896

Sun protection enhancement of titanium dioxide crystals by the use of carnauba wax nanoparticles: the synergistic interaction between organic and inorganic sunscreens at nanoscale.

PubMed

Villalobos-Hernández, J R; Müller-Goymann, C C

2006-09-28

Carnauba wax is partially composed of cinnamates. The rational combination of cinnamates and titanium dioxide has shown a synergistic effect to improve the sun protection factor (SPF) of cosmetic preparations. However, the mechanism of this interaction has not been fully understood. In this study, an ethanolic extract of the carnauba wax and an ethanolic solution of a typical cinnamate derivative, ethylcinnamate, were prepared and their UV absorption and SPF either alone or in the presence of titanium dioxide were compared. The titanium dioxide crystals and the cinnamates solutions were also distributed into a matrix composed of saturated fatty acids to emulate the structure of the crystallized carnauba wax. SPF, differential scanning calorimetry (DSC) and X-ray studies of these matrices were performed. Additionally, carnauba wax nanosuspensions containing titanium dioxide either in the lipid phase or in the aqueous phase were prepared to evaluate their SPFs and their physical structure. Strong UV absorption was observed in diluted suspensions of titanium dioxide after the addition of cinnamates. The saturated fatty acid matrices probably favored the adsorption of the cinnamates at the surface of titanium dioxide crystals, which was reflected by an increase in the SPF. No modification of the crystal structure of the fatty acid matrices was observed after the addition of cinnamates or titanium dioxide. The distribution of the titanium dioxide inside the lipid phase of the nanosuspensions was more effective to reach higher SPFs than that at the aqueous phase. The close contact between the carnauba wax and the titanium dioxide crystals after the high-pressure homogenization process was confirmed by transmission electron microscopy (TEM).

Structural variations of single and tandem mismatches in RNA duplexes: a joint MD simulation and crystal structure database analysis.

PubMed

Halder, Sukanya; Bhattacharyya, Dhananjay

2012-10-04

Internal loops within RNA duplex regions are formed by single or tandem basepairing mismatches with flanking canonical Watson-Crick basepairs on both sides. They are the most common motif observed in RNA secondary structures and play integral functional and structural roles. In this report, we have studied the structural features of 1 × 1, 2 × 2, and 3 × 3 internal loops using all-atom molecular dynamics (MD) simulation technique with explicit solvent model. As MD simulation is intricately dependent on the choice of force-field and these are often rather approximate, we have used both the most popular force-fields for nucleic acids-CHARMM27 and AMBER94-for a comparative analysis. We find that tandem noncanonical basepairs forming 2 × 2 and 3 × 3 internal loops are considerably more stable than the single mismatches forming 1 × 1 internal loops, irrespective of the force field. We have also analyzed crystal structure database to study the conservation of these helical fragments in the corresponding sets of RNA structures. We observe that the nature of stability in MD simulations mimic their fluctuating natures in crystal data sets also, probably indicating reliable natures of both the force fields to reproduce experimental results. We also notice significant structural changes in the wobble G:U basepairs present in these double helical stretches, leading to a biphasic stability for these wobble pairs to release the deformational strains introduced by internal loops within duplex regions.

Superprism effect in a metal-clad terahertz photonic crystal slab.

PubMed

Prasad, Tushar; Colvin, Vicki L; Jian, Zhongping; Mittleman, Daniel M

2007-03-15

We report an experimental demonstration of the superprism effect in a photonic crystal slab at terahertz frequencies. For a 10% frequency variation around 0.28 THz, the refraction angle at the output facet of a wedge-shaped photonic crystal varies by about 15 degrees. A comparison with the predictions of a band structure calculation demonstrates that a three-dimensional treatment, accurately modeling the finite slab thickness and the metallic boundary conditions, is required for even a qualitative agreement with the experimental observations.

Crystal growth of carbonate apatite using a CaCO3 flux.

PubMed

Suetsugu, Y; Tanaka, J

1999-09-01

Single crystals of carbonate apatite were grown using a CaCO3 flux under an Ar gas pressure of 55 MPa. The crystals obtained were observed by scanning electron microscopy, optical microscopy and X-ray diffraction. Electron probe microanalyses and thermal analyses were performed. CO3 ions in planar triangle form replaced both OH sites and PO4 tetrahedral sites in the apatite structure: in particular, the OH sites were perfectly substituted by CO3 ions using this method.

Protein Crystal Growth (PCG) experiment aboard mission STS-66

NASA Technical Reports Server (NTRS)

2000-01-01

On the Space Shuttle Orbiter Atlantis' middeck, Astronaut Joseph R. Tarner, mission specialist, works at an area amidst several lockers which support the Protein Crystal Growth (PCG) experiment during the STS-66 mission. This particular section is called the Crystal Observation System, housed in the Thermal Enclosure System (COS/TES). Together with the Vapor Diffusion Apparatus (VDA), housed in Single Locker Thermal Enclosure (SLTES), the COS/TES represents the continuing research into the structure of proteins and other macromolecules such as viruses.

Ray trace visualization of negative refraction of light in two-dimensional air-bridged silicon photonic crystal slabs at 1.55 microm.

PubMed

Gan, Lin; Liu, Ya-Zhao; Li, Jiang-Yan; Zhang, Ze-Bo; Zhang, Dao-Zhong; Li, Zhi-Yuan

2009-06-08

We demonstrate design, fabrication, and ray trace observation of negative refraction of near-infrared light in a two-dimensional square lattice of air holes etched into an air-bridged silicon slab. Special surface morphologies are designed to reduce the impedance mismatch when light refracts from a homogeneous silicon slab into the photonic crystal slab. We clearly observed negative refraction of infrared light for TE-like modes in a broad wavelength range by using scanning near-field optical microscopy technology. The experimental results are in good agreement with finite-difference time-domain simulations. The results indicate the designed photonic crystal structure can serve as polarization beam splitter.

Structural investigation of cooperite (PtS) crystals

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rozhdestvina, V. I., E-mail: veronika@ascnet.ru; Udovenko, A. A.; Rubanov, S. V.

2016-03-15

The single-crystal structure of cooperite, a natural platinum sulfide PtS, is studied by X-ray diffraction supported by high-resolution scanning transmission electron microscopy and X-ray spectrum microanalysis. It is found that, in addition to the main reflections corresponding to the known tetragonal cell (a = 3.47 and c = 6.11 Å; space group P4{sub 2}/mmc), many weak reflections with intensities I ≤ 60σ(I) are clearly observed. These reflections fit the tetragonal cell (space group I4/mmm) with doubled parameters. In structures with small (P4{sub 2}/mmc) and large (I4/mmm) cells, the S atoms occupy statistically two special positions. It is shown that themore » chemical composition of the cooperite crystals deviates from the stoichiometric composition: sulfur-deficient specimens predominate.« less

Structure and functionality of nanostructured triacylglycerol crystal networks.

PubMed

Ramel, Pere R; Co, Edmund D; Acevedo, Nuria C; Marangoni, Alejandro G

2016-10-01

In this review, recent advances in the characterization of the nanoscale structure of fat crystal networks are outlined. The effect of different factors on the properties of crystalline nanoplatelets (CNPs) is comprehensively described. These are discussed together with the observed changes in polymorphism and micro- or mesostructural properties so as to have a complete understanding of the influence of different internal and external factors on the material properties of fats. The relationship between the nanostructure and the material properties of fats (i.e., oil binding capacity and rheology) is also described. Characterization of the nanostructure of fats has provided a new dimension to the analysis of fat crystal networks and opportunities for nanoengineering that could result in innovations in the food industry with regards to processing and structuring fatty materials. Copyright © 2016 Elsevier B.V. All rights reserved.

Enzyme catalysis captured using multiple structures from one crystal at varying temperatures.

PubMed

Horrell, Sam; Kekilli, Demet; Sen, Kakali; Owen, Robin L; Dworkowski, Florian S N; Antonyuk, Svetlana V; Keal, Thomas W; Yong, Chin W; Eady, Robert R; Hasnain, S Samar; Strange, Richard W; Hough, Michael A

2018-05-01

High-resolution crystal structures of enzymes in relevant redox states have transformed our understanding of enzyme catalysis. Recent developments have demonstrated that X-rays can be used, via the generation of solvated electrons, to drive reactions in crystals at cryogenic temperatures (100 K) to generate 'structural movies' of enzyme reactions. However, a serious limitation at these temperatures is that protein conformational motion can be significantly supressed. Here, the recently developed MSOX (multiple serial structures from one crystal) approach has been applied to nitrite-bound copper nitrite reductase at room temperature and at 190 K, close to the glass transition. During both series of multiple structures, nitrite was initially observed in a 'top-hat' geometry, which was rapidly transformed to a 'side-on' configuration before conversion to side-on NO, followed by dissociation of NO and substitution by water to reform the resting state. Density functional theory calculations indicate that the top-hat orientation corresponds to the oxidized type 2 copper site, while the side-on orientation is consistent with the reduced state. It is demonstrated that substrate-to-product conversion within the crystal occurs at a lower radiation dose at 190 K, allowing more of the enzyme catalytic cycle to be captured at high resolution than in the previous 100 K experiment. At room temperature the reaction was very rapid, but it remained possible to generate and characterize several structural states. These experiments open up the possibility of obtaining MSOX structural movies at multiple temperatures (MSOX-VT), providing an unparallelled level of structural information during catalysis for redox enzymes.

Development of modal layering in granites: a case study from the Carna Pluton, Connemara, Ireland

NASA Astrophysics Data System (ADS)

McKenzie, Kirsty; McCarthy, William; Hunt, Emma

2016-04-01

Modal layering in igneous rocks uniquely record dynamic processes operating in magma chambers and also host a large proportion of Earth's strategic mineral deposits. This research investigates the origin of biotite modal layering and primary pseudo-sedimentary structures in felsic magmas, by using a combination of Crystal Size Distribution (CSD) analysis and Electron Probe Microanalysis (EPMA) to determine the mechanisms responsible for the development of these structures in the Carna Pluton, Connemara, Ireland. The Carna Pluton is a composite granodiorite intrusion and is one of five plutons comprising the Galway Granite Complex (425 - 380 Ma). Prominent 30 cm thick modal layers are defined by sharp basal contacts to a biotite-rich (20%) granite, which grades upward over 10 cm into biotite-poor, alkali-feldspar megacrystic granite. The layering strikes parallel to, and dips 30-60° N toward the external pluton contact. Pseudo-sedimentary structures (cross-bedding, flame structures, slumping and crystal graded bedding) are observed within these layers. Petrographic observations indicate the layers contain euhedral biotite and fresh undeformed quartz and feldspar. Throughout the pluton, alkali-feldspar phenocrysts define a foliation that is sub-parallel to the strike of biotite modal layers. Together these observations indicate that the intrusion's concentric foliation, biotite layers and associated structures formed in the magmatic state and due to a complex interaction between magma flow and crystallisation processes. Biotite CSDs (>250 crystals per sample) were determined for nine samples across three biotite-rich layers in a single unit. Preliminary CSD results suggest biotite within basal contacts accumulated via fractional crystallisation within an upward-growing crystal pile, likely reflecting the yield strength of the magma as a limiting factor to gravitational settling of biotite. This is supported by the abrupt decrease in mean biotite crystal size across the contact, compared to the biotite crystals in the megacrystic granite below. CSD results provide additional evidence for in-situ textural coarsening of biotite. This study proposes a new model for the crystallisation dynamics of the Carna Pluton. During emplacement, 2 - 5 cm alkali-feldspar megacrysts were aligned and fractional crystallisation was the primary mechanism driving the formation of biotite modal layers. Pseudo-sedimentary structures are interpreted to have formed due to the entrainment of biotite crystals within a necessarily highly fluid magma chamber. However, this interpretation is difficult to reconcile with the high viscosities commonly associated with granitic melts. To test this hypothesis, ongoing EPMA analysis on biotite F content and Fe/(Fe+Mg) ratios will assess whether the magma viscosity could have been low enough to produce these features via flow processes; or whether expansion of the pluton and tilting of planar primary magmatic layers, prior to solidification, could be responsible.

Structural characterization of framework-gas interactions in the metal-organic framework Co2(dobdc) by in situ single-crystal X-ray diffraction.

PubMed

Gonzalez, Miguel I; Mason, Jarad A; Bloch, Eric D; Teat, Simon J; Gagnon, Kevin J; Morrison, Gregory Y; Queen, Wendy L; Long, Jeffrey R

2017-06-01

The crystallographic characterization of framework-guest interactions in metal-organic frameworks allows the location of guest binding sites and provides meaningful information on the nature of these interactions, enabling the correlation of structure with adsorption behavior. Here, techniques developed for in situ single-crystal X-ray diffraction experiments on porous crystals have enabled the direct observation of CO, CH 4 , N 2 , O 2 , Ar, and P 4 adsorption in Co 2 (dobdc) (dobdc 4- = 2,5-dioxido-1,4-benzenedicarboxylate), a metal-organic framework bearing coordinatively unsaturated cobalt(ii) sites. All these molecules exhibit such weak interactions with the high-spin cobalt(ii) sites in the framework that no analogous molecular structures exist, demonstrating the utility of metal-organic frameworks as crystalline matrices for the isolation and structural determination of unstable species. Notably, the Co-CH 4 and Co-Ar interactions observed in Co 2 (dobdc) represent, to the best of our knowledge, the first single-crystal structure determination of a metal-CH 4 interaction and the first crystallographically characterized metal-Ar interaction. Analysis of low-pressure gas adsorption isotherms confirms that these gases exhibit mainly physisorptive interactions with the cobalt(ii) sites in Co 2 (dobdc), with differential enthalpies of adsorption as weak as -17(1) kJ mol -1 (for Ar). Moreover, the structures of Co 2 (dobdc)·3.8N 2 , Co 2 (dobdc)·5.9O 2 , and Co 2 (dobdc)·2.0Ar reveal the location of secondary (N 2 , O 2 , and Ar) and tertiary (O 2 ) binding sites in Co 2 (dobdc), while high-pressure CO 2 , CO, CH 4 , N 2 , and Ar adsorption isotherms show that these binding sites become more relevant at elevated pressures.

X-ray diffraction of solid tin to 1.2 TPa

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lazicki, A.; Rygg, J. R.; Coppari, F.

2015-08-12

In this study, we report direct in situ measurements of the crystal structure of tin between 0.12 and 1.2 TPa, the highest stress at which a crystal structure has ever been observed. Using angle-dispersive powder x-ray diffraction, we find that dynamically compressed Sn transforms to the body-centered-cubic (bcc) structure previously identified by ambient-temperature quasistatic-compression studies and by zero-kelvin density-functional theory predictions between 0.06 and 0.16 TPa. However, we observe no evidence for the hexagonal close-packed (hcp) phase found by those studies to be stable above 0.16 TPa. Instead, our results are consistent with bcc up to 1.2 TPa. We conjecturemore » that at high temperature bcc is stabilized relative to hcp due to differences in vibrational free energy.« less

Laboratory Investigation of the Growth and Crystal Structure of Nitric Acid Hydrates by Transmission Electron Microscopy (TEM)

NASA Technical Reports Server (NTRS)

Blake, David F.; Chang, Sherwood (Technical Monitor)

1994-01-01

A great deal of recent laboratory work has focussed on the characterization of the nitric acid hydrates, thought to be present in type I Polar Stratospheric Clouds (PSCs). Phase relationships and vapor pressure measurements (1-3) and infrared characterizations (4-5) have been made. However, the observed properties of crystalline solids (composition, melting point, vapor pressure, surface reactivity, thermodynamic stability, extent of solid solution with other components, etc.) are controlled by their crystal structure. The only means of unequivocal structural identification for crystalline solids is diffraction (using electrons, X-rays, neutrons, etc.). Other observed properties of crystalline solids, such as their infrared spectra, their vapor pressure as a function of temperature, etc. yield only indirect information about what phases are present, their relative proportions, or whether they are crystalline or amorphous.

Structure of periodic crystals and quasicrystals in ultrathin films of Ba-Ti-O

DOE PAGES

Cockayne, Eric; Mihalkovič, Marek; Henley, Christopher L.

2016-01-07

Here, we model the remarkable thin-film Ba-Ti-O structures formed by heat treatment of an initial perovskite BaTiO 3 thin film on a Pt(111) surface. All structures contain a rumpled Ti-O network with all Ti threefold coordinated with O, and with Ba occupying the larger. mainly Ti 7O 7, pores. The quasicrystal structue is a simple decoration of three types of tiles: square, triangle and 30° rhombus, with edge lengths 6.85 Å, joined edge-to-edge in a quasicrystalline pattern; observed periodic crystals in ultrathin film Ba-Ti-O are built from these and other tiles. Simulated STM images reproduce the patterns seen experimentally, andmore » identify the bright protrusions as Ba atoms. The models are consistent with all experimental observations.« less

Alternating twist structures formed by electroconvection in the nematic phase of an achiral bent-core molecule.

PubMed

Tanaka, Shingo; Dhara, Surajit; Sadashiva, B K; Shimbo, Yoshio; Takanishi, Yoichi; Araoka, Fumito; Ishikawa, Ken; Takezoe, Hideo

2008-04-01

We report an unusual electroconvection in the nematic phase of a bent-core liquid crystal. In a voltage-frequency diagram, two frequency regions exhibiting prewavy stripe patterns were found, as reported by Wiant We found that these stripes never show extinction dark when cells were rotated under crossed polarizers. Based on the color interchange in between neighboring stripes by the rotation of the cells or an analyzer, twisted molecular orientation is suggested; i.e., the directors are alternately twisted from the top to the bottom surfaces with a pretilt angle in adjacent stripes, which is an analogue of the twisted (splayed) structure observed in surface-stabilized ferroelectric liquid crystal cells. The transmittance spectra calculated using the 4x4 matrix method from the model structure are consistent with the experimental observation.

Structure-mechanical property correlations in mechanochromic luminescent crystals of boron difluoride dibenzoylmethane derivatives.

PubMed

Krishna, Gamidi Rama; Devarapalli, Ramesh; Prusty, Rajesh; Liu, Tiandong; Fraser, Cassandra L; Ramamurty, Upadrasta; Reddy, Chilla Malla

2015-11-01

The structure and mechanical properties of crystalline materials of three boron difluoride dibenzoylmethane (BF2dbm) derivatives were investigated to examine the correlation, if any, among mechanochromic luminescence (ML) behaviour, solid-state structure, and the mechanical behaviour of single crystals. Qualitative mechanical deformation tests show that the crystals of BF2dbm( (t) Bu)2 can be bent permanently, whereas those of BF2dbm(OMe)2 exhibit an inhomogeneous shearing mode of deformation, and finally BF2dbmOMe crystals are brittle. Quantitative mechanical analysis by nano-indentation on the major facets of the crystals shows that BF2dbm( (t) Bu)2 is soft and compliant with low values of elastic modulus, E, and hardness, H, confirming its superior suceptibility for plastic deformation, which is attributed to the presence of a multitude of slip systems in the crystal structure. In contrast, both BF2dbm(OMe)2 and BF2dbmOMe are considerably stiffer and harder with comparable E and H, which are rationalized through analysis of the structural attributes such as the intermolecular interactions, slip systems and their relative orientation with respect to the indentation direction. As expected from the qualitative mechanical behaviour, prominent ML was observed in BF2dbm( (t) Bu)2, whereas BF2dbm(OMe)2 exhibits only a moderate ML and BF2dbmOMe shows no detectable ML, all examined under identical conditions. These results confirm that the extent of ML in crystalline organic solid-state fluorophore materials can be correlated positively with the extent of plasticity (low recovery). In turn, they offer opportunities to design new and improved efficient ML materials using crystal engineering principles.

Anisotropic lattice softening near the structural phase transition in the thermosalient crystal 1,2,4,5-tetrabromobenzene.

PubMed

Zakharov, Boris A; Michalchuk, Adam A L; Morrison, Carole A; Boldyreva, Elena V

2018-03-28

The thermosalient effect (crystal jumping on heating) attracts much attention as both an intriguing academic phenomenon and in relation to its potential for the development of molecular actuators but its mechanism remains unclear. 1,2,4,5-Tetrabromobenzene (TBB) is one of the most extensively studied thermosalient compounds that has been shown previously to undergo a phase transition on heating, accompanied by crystal jumping and cracking. The difference in the crystal structures and intermolecular interaction energies of the low- and high-temperature phases is, however, too small to account for the large stress that arises over the course of the transformation. The energy is released spontaneously, and crystals jump across distances that exceed the crystal size by orders of magnitude. In the present work, the anisotropy of lattice strain is followed across the phase transition by single-crystal X-ray diffraction, focusing on the structural evolution from 273 to 343 K. A pronounced lattice softening is observed close to the transition point, with the structure becoming more rigid immediately after the phase transition. The diffraction studies are further supported by theoretical analysis of pairwise intermolecular energies and zone-centre lattice vibrations. Only three modes are found to monotonically soften up to the phase transition, with complex behaviour exhibited by the remaining lattice modes. The thermosalient effect is delayed with respect to the structural transformation itself. This can originate from the martensitic mechanism of the transformation, and the accumulation of stress associated with vibrational switching across the phase transition. The finding of this study sheds more light on the nature of the thermosalient effect in 1,2,4,5-tetrabromobenzene and can be applicable also to other thermosalient compounds.

Zr 2Ir 6B with an eightfold superstructure of the cubic perovskite-like boride ZrIr 3B 0.5: Synthesis, crystal structure and bonding analysis

NASA Astrophysics Data System (ADS)

Hermus, Martin; Fokwa, Boniface P. T.

2010-04-01

Single phase powder samples and single crystals of Zr 2Ir 6B were successfully synthesized by arc-melting the elements in a water-cooled copper crucible under an argon atmosphere. Superstructure reflections were observed both on powder and on single crystal diffraction data, leading to an eightfold superstructure of ZrIr 3B x phase. The new phase, which has a metallic luster, crystallizes in space group Fm3¯m (no. 225) with the lattice parameters a=7.9903(4) Å, V=510.14(4) Å 3. Its crystal structure was refined on the basis of powder as well as single crystal data. The single crystal refinement converged to R1=0.0239 and w R2=0.0624 for all 88 unique reflections and 6 parameters. Zr 2Ir 6B is isotypic to Ti 2Rh 6B and its structure can be described as a defect double perovskite, A2BB' O6, where the A site is occupied by zirconium, the B site by boron, the O site by iridium but the B' site is vacant, leading to the formation of empty and boron-filled octahedral Ir 6 clusters. According to the result of tight-binding electronic structure calculations, Ir-B and Ir-Zr interactions are mainly responsible for the structural stability of the phase. According to COHP bonding analysis, the strongest bonding occurs for the Ir-B contacts, and the Ir-Ir bonding within the empty clusters is two times stronger than that in the BIr 6 octahedra.

In-situ Crystallization of Highly Volatile Commercial Mold Flux Using an Isolated Observation System in the Confocal Laser Scanning Microscope

NASA Astrophysics Data System (ADS)

Park, Jun-Yong; Ryu, Jae Wook; Sohn, Il

2014-08-01

The in situ crystallization behavior of highly volatile commercial mold fluxes for medium carbon steels was investigated using the confocal laser scanning microscope (CLSM) equipped with an optimized isolated observation system. The highly volatile compounds of the mold flux were suppressed during heating allowing direct observation in the CLSM. Cooling rates of 25, 50, 100, 400, and 800 K/min were incorporated and continuous cooling transformation (CCT) diagrams of 4 different commercial mold fluxes for medium carbon steels were developed. Identification of the crystalline phase was conducted with XRD and SEM-EDS analysis. A cuspidine crystalline was observed in all samples at various cooling rates. With higher basicity, CaF2, and NaF, the crystallization of the fluxes was enhanced according to the CCT diagram. As the slag structure becomes depolymerized, the diffusion rate of the cathodic ions seems to increase.

Structural, thermal and optical properties of a semiorganic nonlinear optical single crystal: glycine zinc sulphate.

PubMed

Balakrishnan, T; Ramamurthi, K

2007-10-01

Glycine zinc sulphate salt was synthesized and the solubility and metastable zonewidth were estimated from the aqueous solution. Single crystals of glycine zinc sulphate were grown by solvent evaporation method from aqueous solution. Grown crystals were characterized by X-ray diffraction and FT-IR spectral analyses. The range and percentage of optical transmission was ascertained by recording UV-vis-NIR spectrum. Thermal properties of the crystal were investigated by thermogravimetric analysis. Microhardness study was carried out on (01-1) face of the grown crystal. Its powder second harmonic generation efficiency was measured using Nd:YAG laser and the value was observed to be 0.7 times that of potassium dihydrogen orthophosphate.

Structural basis for antibody recognition in the receptor-binding domains of toxins A and B from Clostridium difficile.

PubMed

Murase, Tomohiko; Eugenio, Luiz; Schorr, Melissa; Hussack, Greg; Tanha, Jamshid; Kitova, Elena N; Klassen, John S; Ng, Kenneth K S

2014-01-24

Clostridium difficile infection is a serious and highly prevalent nosocomial disease in which the two large, Rho-glucosylating toxins TcdA and TcdB are the main virulence factors. We report for the first time crystal structures revealing how neutralizing and non-neutralizing single-domain antibodies (sdAbs) recognize the receptor-binding domains (RBDs) of TcdA and TcdB. Surprisingly, the complexes formed by two neutralizing antibodies recognizing TcdA do not show direct interference with the previously identified carbohydrate-binding sites, suggesting that neutralization of toxin activity may be mediated by mechanisms distinct from steric blockage of receptor binding. A camelid sdAb complex also reveals the molecular structure of the TcdB RBD for the first time, facilitating the crystallization of a strongly negatively charged protein fragment that has resisted previous attempts at crystallization and structure determination. Electrospray ionization mass spectrometry measurements confirm the stoichiometries of sdAbs observed in the crystal structures. These studies indicate how key epitopes in the RBDs from TcdA and TcdB are recognized by sdAbs, providing molecular insights into toxin structure and function and providing for the first time a basis for the design of highly specific toxin-specific therapeutic and diagnostic agents.

Structural Basis for Antibody Recognition in the Receptor-binding Domains of Toxins A and B from Clostridium difficile*

PubMed Central

Murase, Tomohiko; Eugenio, Luiz; Schorr, Melissa; Hussack, Greg; Tanha, Jamshid; Kitova, Elena N.; Klassen, John S.; Ng, Kenneth K. S.

2014-01-01

Clostridium difficile infection is a serious and highly prevalent nosocomial disease in which the two large, Rho-glucosylating toxins TcdA and TcdB are the main virulence factors. We report for the first time crystal structures revealing how neutralizing and non-neutralizing single-domain antibodies (sdAbs) recognize the receptor-binding domains (RBDs) of TcdA and TcdB. Surprisingly, the complexes formed by two neutralizing antibodies recognizing TcdA do not show direct interference with the previously identified carbohydrate-binding sites, suggesting that neutralization of toxin activity may be mediated by mechanisms distinct from steric blockage of receptor binding. A camelid sdAb complex also reveals the molecular structure of the TcdB RBD for the first time, facilitating the crystallization of a strongly negatively charged protein fragment that has resisted previous attempts at crystallization and structure determination. Electrospray ionization mass spectrometry measurements confirm the stoichiometries of sdAbs observed in the crystal structures. These studies indicate how key epitopes in the RBDs from TcdA and TcdB are recognized by sdAbs, providing molecular insights into toxin structure and function and providing for the first time a basis for the design of highly specific toxin-specific therapeutic and diagnostic agents. PMID:24311789

Crystal structures of 2,3,8,9,14,15-hexa-methyl-5,6,11,12,17,18-hexa-aza-tri-naphthyl-ene and 2,3,8,9,14,15-hexa-phenyl-5,6,11,12,17,18-hexa-za-tri-naphthyl-ene di-chloro-methane disolvate.

PubMed

Fangmann, Pia; Schmidtmann, Marc; Beckhaus, Rüdiger

2018-02-01

The crystal structures of two substituted HATN (hexa-aza-tri-naphthyl-ene) derivatives, namely 2,3,8,9,14,15-hexa-methyl- and 2,3,8,9,14,15-hexa-phenyl-5,6,11,12,17,18- hexa-zatri-naphthyl-ene (HATNMe 6 and HATNPh 6 ), are reported. Whereas the structure of the methyl-substituted derivative (HATNMe 6 ) contains no solvent mol-ecules (C 30 H 24 N 6 ), the hexa-phenyl-substituted structure (HATNPh 6 ) contains two mol-ecules of di-chloro-methane (C 60 H 36 N 6 ·2CH 2 Cl 2 ). This class of planar bridging ligands is known for its electron-deficient systems and its ability to form π-π stacking inter-actions. Indeed, in both crystal structures strong π-π stacking inter-actions are observed, but with different packing features. The di-chloro-methane mol-ecules in the crystal structure of HATNPh 6 are situated in the voids and are involved in C-H⋯N contacts to the nitro-gen atoms of the pyrazine units.

Synthesis, structural and optical characterization of APbX{sub 3} (A=methylammonium, dimethylammonium, trimethylammonium; X=I, Br, Cl) hybrid organic-inorganic materials

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mancini, Alessandro; Quadrelli, Paolo; Amoroso, Giuseppe

2016-08-15

In this paper we report the synthesis, the crystal structure and the optical response of APbX{sub 3} (A=MA, DMA, and TMA; X=I, Br) hybrid organic-inorganic materials including some new phases. We observe that as the cation group increases in size, the optical absorption edge shifts to higher energies with energy steps which are systematic and independent on the anion. A linear correlation between the optical bad gap and the tolerance factor has been shown for the series of samples investigated. - Graphical abstract: The crystal structure and the optical response of the two series of hybrid organic-inorganic materials APbX{sub 3}more » (A=MA, DMA, and TMA; X=I, Br), which include some new phases, are reported. A dependence of crystal structure and band-gap with tolerance factor is shown. Display Omitted - Highlights: • DMAPbI{sub 3}, TMAPbI{sub 3} and TMAPbBr{sub 3} are reported as new hybrid organic-inorganic compounds. • Crystal structure and optical properties as a function of the number of methyl groups are provided. • Correlation between structure and optical properties are given as a function of tolerance factor.« less

Photonic-magnonic crystals: Multifunctional periodic structures for magnonic and photonic applications

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kłos, J. W., E-mail: klos@amu.edu.pl; Krawczyk, M.; Dadoenkova, Yu. S.

2014-05-07

We investigate the properties of a photonic-magnonic crystal, a complex multifunctional one-dimensional structure with magnonic and photonic band gaps in the GHz and PHz frequency ranges for spin waves and light, respectively. The system consists of periodically distributed dielectric magnetic slabs of yttrium iron garnet and nonmagnetic spacers with an internal structure of alternating TiO{sub 2} and SiO{sub 2} layers which form finite-size dielectric photonic crystals. We show that the spin-wave coupling between the magnetic layers, and thus the formation of the magnonic band structure, necessitates a nonzero in-plane component of the spin-wave wave vector. A more complex structure perceivedmore » by light is evidenced by the photonic miniband structure and the transmission spectra in which we have observed transmission peaks related to the repetition of the magnetic slabs in the frequency ranges corresponding to the photonic band gaps of the TiO{sub 2}/SiO{sub 2} stack. Moreover, we show that these modes split to very high sharp (a few THz wide) subpeaks in the transmittance spectra. The proposed novel multifunctional artificial crystals can have interesting applications and be used for creating common resonant cavities for spin waves and light to enhance the mutual influence between them.« less

Crystal growth, structural, optical, spectral and thermal studies of tris( L-phenylalanine) L-phenylalaninium nitrate: A new organic nonlinear optical material

NASA Astrophysics Data System (ADS)

Prakash, M.; Geetha, D.; Lydia Caroline, M.

2011-10-01

Tris( L-phenylalanine) L-phenylalaninium nitrate, C 9H 12NO 2+·NO 3-·3C 9H 11NO 2 (TPLPN), a new organic nonlinear optical material was grown from aqueous solution by slow evaporation solution growth at room temperature. The grown crystals were subjected to powder X-ray diffraction and single crystal X-ray diffraction studies to confirm the crystalline nature and crystal structure. The modes of vibration of different molecular groups present in TPLPN have been identified by FTIR spectral analysis. The presence of hydrogen and carbon in the grown crystal were confirmed by using proton and carbon nuclear magnetic resonance (NMR) spectral analyses. The optical transmission spectral study establishes good transmitting ability of the crystal in the entire visible region. The thermogravimetric (TG) and differential thermal analyses (DTA) were carried out to understand the thermal stability of the sample. The nonlinear optical property of the compound observed using Kurtz powder second harmonic generation test assets the suitability of the grown material for the frequency conversion of laser radiation of Nd:YAG.

Crystal structure and habit of dirithromycin acetone solvate: A combined experimental and simulative study

NASA Astrophysics Data System (ADS)

Yi, Qinhua; Chen, Jianfeng; Le, Yuan; Wang, Jiexin; Xue, Chunyu; Zhao, Hong

2013-06-01

Dirithromycin (DIR) was crystallized from acetone solvent in the form of an acetone solvate. Its crystal structure belongs to monoclinic, space group P21, with the unit cell parameters a=14.688(3) Å, b=11.6120(12) Å, c=14.9129(12) Å, β=94.794(10)°, and Z=2. Results of X-ray diffraction (XRD) and thermogravimetry-differential scanning calorimetry (TG-DSC) indicated that the solvent molecules could enter the crystal lattice and thus the solvate is formed. The molecular dynamics (MD) simulation method was applied to study the solvent effect. It revealed that the relative growth rates of the main crystal habit faces changed a lot, which made the most morphologically important habit face shift from (001) face to (100) face due to polar groups or atoms exposure and hence a large solvent interaction. The prism habit predicted by a modified attachment energy (AE) model agreed well with the observed experimental morphology grown from the acetone solution. This prediction method may help for a solvent selection to improve the morphology in the drug crystallization process.

Multiple pathways of crystal nucleation in an extremely supersaturated aqueous potassium dihydrogen phosphate (KDP) solution droplet

PubMed Central

Lee, Sooheyong; Wi, Haeng Sub; Jo, Wonhyuk; Cho, Yong Chan; Lee, Hyun Hwi; Jeong, Se-Young; Kim, Yong-Il; Lee, Geun Woo

2016-01-01

Solution studies have proposed that crystal nucleation can take more complex pathways than previously expected in classical nucleation theory, such as formation of prenucleation clusters or densified amorphous/liquid phases. These findings show that it is possible to separate fluctuations in the different order parameters governing crystal nucleation, that is, density and structure. However, a direct observation of the multipathways from aqueous solutions remains a great challenge because heterogeneous nucleation sites, such as container walls, can prevent these paths. Here, we demonstrate the existence of multiple pathways of nucleation in highly supersaturated aqueous KH2PO4 (KDP) solution using the combination of a containerless device (electrostatic levitation), and in situ micro-Raman and synchrotron X-ray scattering. Specifically, we find that, at an unprecedentedly deep level of supersaturation, a high-concentration KDP solution first transforms into a metastable crystal before reaching stability at room temperature. However, a low-concentration solution, with different local structures, directly transforms into the stable crystal phase. These apparent multiple pathways of crystallization depend on the degree of supersaturation. PMID:27791068

Multiple pathways of crystal nucleation in an extremely supersaturated aqueous potassium dihydrogen phosphate (KDP) solution droplet.

PubMed

Lee, Sooheyong; Wi, Haeng Sub; Jo, Wonhyuk; Cho, Yong Chan; Lee, Hyun Hwi; Jeong, Se-Young; Kim, Yong-Il; Lee, Geun Woo

2016-11-29

Solution studies have proposed that crystal nucleation can take more complex pathways than previously expected in classical nucleation theory, such as formation of prenucleation clusters or densified amorphous/liquid phases. These findings show that it is possible to separate fluctuations in the different order parameters governing crystal nucleation, that is, density and structure. However, a direct observation of the multipathways from aqueous solutions remains a great challenge because heterogeneous nucleation sites, such as container walls, can prevent these paths. Here, we demonstrate the existence of multiple pathways of nucleation in highly supersaturated aqueous KH 2 PO 4 (KDP) solution using the combination of a containerless device (electrostatic levitation), and in situ micro-Raman and synchrotron X-ray scattering. Specifically, we find that, at an unprecedentedly deep level of supersaturation, a high-concentration KDP solution first transforms into a metastable crystal before reaching stability at room temperature. However, a low-concentration solution, with different local structures, directly transforms into the stable crystal phase. These apparent multiple pathways of crystallization depend on the degree of supersaturation.

Nonreciprocity of spin waves in magnonic crystals created by surface acoustic waves in structures with yttrium iron garnet

NASA Astrophysics Data System (ADS)

Kryshtal, R. G.; Medved, A. V.

2015-12-01

Experimental results of investigations of nonreciprocity for surface magnetostatic spin waves (SMSW) in the magnonic crystal created by surface acoustic waves (SAW) in yttrium iron garnet films on a gallium gadolinium garnet substrate as without metallization and with aluminum films with different electrical conductivities (thicknesses) are presented. In structures without metallization, the frequency of magnonic gaps is dependent on mutual directions of propagation of the SAW and SMSW, showing nonreciprocal properties for SMSW in SAW - magnonic crystals even with the symmetrical dispersion characteristic. In metalized SAW - magnonic crystals the shift of the magnonic band gaps frequencies at the inversion of the biasing magnetic field was observed. The frequencies of magnonic band gaps as functions of SAW frequency are presented. Measured dependencies, showing the decrease of magnonic gaps frequency and the expansion of the magnonic band gap width with the decreasing of the metal film conductivity are given. Such nonreciprocal properties of the SAW - magnonic crystals are promising for signal processing in the GHz range.

Temperature driven structural-memory-effects in carbon nanotubes filled with Fe3C nano crystals

NASA Astrophysics Data System (ADS)

Boi, Filippo S.; Zhang, Xiaotian; Corrias, Anna

2018-02-01

We report the observation of novel temperature-driven structural-memory-effects in carbon nanotubes (CNTs) filled with Fe3C nano-crystals. These structural-transitions were measured by means of temperature (T) dependent x-ray diffraction (XRD) in the T-range from 298 K to 12 K. A clear reversible 2θ-shift in the 002-peak of the graphitic-CNTs-walls is found with the decrease of the temperature. As determined by Rietveld refinement, such 2θ-shift translates in a not previously reported decrease in the value of the CNT graphitic c-axis with the decrease of the temperature (from 298 K to 12 K). Also, a clear reversible 2θ-shift in the 031 and 131 diffraction-peaks of Fe3C is observed within the same T-range. Rietveld refinements confirm the existence of such memory-effect and also reveal a gradual decrease of the 010-axis of Fe3C with the decrease of the temperature. These observations imply that the observed structural-memory-effect is a characteristic of CNTs when Fe3C is the encapsulated ferromagnet. The generality of such memory-effects was further confirmed by additional measurements performed on other types of CNTs characterized by continuous Fe3C-filling. XRD measurements in the T-range from 298 K to 673 K revealed also an unusual reversible decrease of the Fe3C-peak intensities with the increase of the temperature. These observations can have important implications on the magnetic data recording applications of these nanostructures by helping in better understanding the unusual temperature-dependent magnetic instabilities of iron-based nano-crystals which have been recently reported in literature.

Epitaxial BiFeO3 thin films fabricated by chemical solution deposition

NASA Astrophysics Data System (ADS)

Singh, S. K.; Kim, Y. K.; Funakubo, H.; Ishiwara, H.

2006-04-01

Epitaxial BiFeO3 (BFO) thin films were fabricated on (001)-, (110)-, and (111)-oriented single-crystal SrRuO3(SRO )/SrTiO3(STO) structures by chemical solution deposition. X-ray diffraction indicates the formation of an epitaxial single-phase perovskite structure and pole figure measurement confirms the cube-on-cube epitaxial relationship of BFO ‖SRO‖STO. Chemical-solution-deposited BFO films have a rhombohedral structure with lattice parameter of 0.395nm, which is the same structure as that of a bulk single crystal. The remanent polarization of approximately 50μC/cm2 was observed in BFO (001) thin films at 80K.

Robust diamond-like Fe-Si network in the zero-strain Na xFeSiO 4 cathode

DOE PAGES

Ye, Zhuo; Zhao, Xin; Li, Shouding; ...

2016-07-14

Sodium orthosilicates Na 2 MSiO 4 ( M denotes transition metals) have attracted much attention due to the possibility of exchanging two electrons per formula unit. In this work, we report a group of sodium iron orthosilicates Na 2FeSiO 4. Their crystal structures are characterized by a diamond-like Fe-Si network. The Fe-Si network is quite robust against the charge/discharge process, which explains the high structural stability observed in experiment. Furthermore, using the density functional theory within the GGA + U framework and X-ray diffraction studies, the crystal structures and structural stabilities during the sodium extraction/re-insertion process are systematically investigated.

Proton-Induced Conductivity Enhancement in AlGaN/GaN HEMT Devices

NASA Astrophysics Data System (ADS)

Lee, In Hak; Lee, Chul; Choi, Byoung Ki; Yun, Yeseul; Chang, Young Jun; Jang, Seung Yup

2018-04-01

We investigated the influence of proton irradiation on the AlGaN/GaN high-electron-mobility transistor (HEMT) devices. Unlike previous studies on the degradation behavior upon proton irradiation, we observed improvements in their electrical conductivity and carrier concentration of up to 25% for the optimal condition. As we increased the proton dose, the carrier concentration and the mobility showed a gradual increase and decrease, respectively. From the photoluminescence measurements, we observed a reduction in the near-band-edge peak of GaN ( 366 nm), which correlate on the observed electrical properties. However, neither the Raman nor the X-ray diffraction analysis showed any changes, implying a negligible influence of protons on the crystal structures. We demonstrated that high-energy proton irradiation could be utilized to modify the transport properties of HEMT devices without damaging their crystal structures.

Dissertation Award in Nuclear Physics Recipient: Astromaterials in Neutron Stars

NASA Astrophysics Data System (ADS)

Caplan, Matthew E.

2017-09-01

Stars freeze. As they age and cool white dwarfs and neutron stars crystallize, with remarkable materials forming in their interiors. These `astromaterials' have structures similar to terrestrial crystalline solids and liquid crystals, though they are over a trillion times denser. Notably, because their material properties affect the observable properties of the star, astromaterials must be understood to interpret observations of neutron stars. Thus, astromaterial science can be thought of as an interdisciplinary field, using techniques from material science to study nuclear physics systems with astrophysical relevance. In this talk, I will discuss recent results from simulations of astromaterials and how we use these results to interpret observations of neutron stars in X-ray binaries. In addition, I will discuss how nuclear pasta, in neutron stars, forms structures remarkably similar to biophysical membranes seen in living organisms.

Real-time observation of the isothermal crystallization kinetics in a deeply supercooled liquid

NASA Astrophysics Data System (ADS)

Zanatta, M.; Cormier, L.; Hennet, L.; Petrillo, C.; Sacchetti, F.

2017-03-01

Below the melting temperature Tm, crystals are the stable phase of typical elemental or molecular systems. However, cooling down a liquid below Tm, crystallization is anything but inevitable. The liquid can be supercooled, eventually forming a glass below the glass transition temperature Tg. Despite their long lifetimes and the presence of strong barriers that produces an apparent stability, supercooled liquids and glasses remain intrinsically a metastable state and thermodynamically unstable towards the crystal. Here we investigated the isothermal crystallization kinetics of the prototypical strong glassformer GeO2 in the deep supercooled liquid at 1100 K, about half-way between Tm and Tg. The crystallization process has been observed through time-resolved neutron diffraction for about three days. Data show a continuous reorganization of the amorphous structure towards the alpha-quartz phase with the final material composed by crystalline domains plunged into a low-density, residual amorphous matrix. A quantitative analysis of the diffraction patterns allows determining the time evolution of the relative fractions of crystal and amorphous, that was interpreted through an empirical model for the crystallization kinetics. This approach provides a very good description of the experimental data and identifies a predator-prey-like mechanism between crystal and amorphous, where the density variation acts as a blocking barrier.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Brandao, T.; Robinson, H; Johnson, S

Catalysis by the Yersinia protein-tyrosine phosphatase YopH is significantly impaired by the mutation of the conserved Trp354 residue to Phe. Though not a catalytic residue, this Trp is a hinge residue in a conserved flexible loop (the WPD-loop) that must close during catalysis. To learn why this seemingly conservative mutation reduces catalysis by 2 orders of magnitude, we have solved high-resolution crystal structures for the W354F YopH in the absence and in the presence of tungstate and vanadate. Oxyanion binding to the P-loop in W354F is analogous to that observed in the native enzyme. However, the WPD-loop in the presencemore » of oxyanions assumes a half-closed conformation, in contrast to the fully closed state observed in structures of the native enzyme. This observation provides an explanation for the impaired general acid catalysis observed in kinetic experiments with Trp mutants. A 1.4 Angstroms structure of the W354F mutant obtained in the presence of vanadate reveals an unusual divanadate species with a cyclic [VO]2 core, which has precedent in small molecules but has not been previously reported in a protein crystal structure.« less

Growth, structural, optical, thermal and mechanical properties of cytosinium hydrogen selenite: A novel nonlinear optical single crystal

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jaikumar, P.; Sathiskumar, S.; Balakrishnan, T., E-mail: balacrystalgrowth@gmail.com

Highlights: • Growth of bulk single crystals of cytosinium hydrogen selenite (CHS) is reported. • Dielectric constant of CHS is measured as a function of Frequency and temperature. • Lower cut off value of UV–vis-NIR spectrum of CHS crystal is observed at 210 nm. • Meyer’s index value of CHS crystal calculated identifies it as a soft material. • Powder SHG efficiency of CHS is about 1.5 times that of KDP crystal. - Abstract: A novel nonlinear optical single crystal of cytosinium hydrogen selenite was grown from aqueous solution of cytosinium hydrogen selenite by slow solvent evaporation method at roommore » temperature. The structural properties of grown crystal have been studied by single crystal and powder X-ray diffraction analysis. Presence of various functional groups was identified from Fourier transform infrared spectroscopy. The optical transmittance and absorbance spectra were recorded by UV–vis-NIR spectrometer and the grown crystal possesses good transparency in the entire visible region. The dielectric constant and dielectric loss of the crystal were calculated as a function of frequency at different temperatures. The mechanical strength of the cytosinium hydrogen selenite crystal was estimated using Vicker’s microhardness tester. Etch patterns of the cytosinium hydrogen selenite crystal were obtained using distilled water as etchant for different etching time. Second harmonic generation efficiency tested using Nd:YAG laser is about 1.5 times that of KDP.« less

Iridescence from photonic crystals and its suppression in butterfly scales

PubMed Central

Poladian, Leon; Wickham, Shelley; Lee, Kwan; Large, Maryanne C.J.

2008-01-01

Regular three-dimensional periodic structures have been observed in the scales of over half a dozen butterfly species. We compare several of these structures: we calculate their photonic bandgap properties; measure the angular variation of the reflection spectra; and relate the observed iridescence (or its suppression) to the structures. We compare the mechanisms for iridescence suppression in different species and conclude with some speculations about form, function, development and evolution. PMID:18980932

Effect of high pressure microfluidization on the crystallization behavior of palm stearin - palm olein blends.

PubMed

Han, Lijuan; Li, Lin; Li, Bing; Zhao, Lei; Liu, Guoqin; Liu, Xinqi; Wang, Xuede

2014-04-24

Moderate and high microfluidization pressures (60 and 120 MPa) and different treatment times (once and twice) were used to investigate the effect of high-pressure microfluidization (HPM) treatment on the crystallization behavior and physical properties of binary mixtures of palm stearin (PS) and palm olein (PO). The polarized light microscopy (PLM), texture analyzer, X-ray diffraction (XRD) and differential scanning calorimetry (DSC) techniques were applied to analyze the changes in crystal network structure, hardness, polymorphism and thermal property of the control and treated blends. PLM results showed that HPM caused significant reductions in maximum crystal diameter in all treated blends, and thus led to changes in the crystal network structure, and finally caused higher hardness in than the control blends. The XRD study demonstrated that HPM altered crystalline polymorphism. The HPM-treated blends showed a predominance of the more stable β' form, which is of more interest for food applications, while the control blend had more α- and β-form. This result was further confirmed by DSC observations. These changes in crystallization behavior indicated that HPM treatment was more likely to modify the crystallization processes and nucleation mechanisms.

Growth, Faraday and inverse Faraday characteristics of Tb₂Ti₂O₇ crystal.

PubMed

Guo, Feiyun; Sun, Yilin; Yang, Xiongsheng; Chen, Xin; Zhao, Bin; Zhuang, Naifeng; Chen, Jianzhong

2016-03-21

Tb₂Ti₂O₇ (TTO) single crystal with dimensions of 20 × 20 × 16 mm³ was grown by the Czochralski method. Rietveld structure refinement of X-ray diffraction (XRD) data confirms that the compound crystallizes in the cubic system with pyrochlore structure. Transmission spectra, Magnetic circular dichroism (MCD) spectra, Faraday and inverse Faraday characteristics of TTO crystal have been measured and analyzed in detail. The results demonstrate that TTO crystal has high transmittance at 700-1400 nm waveband and a larger Verdat constant than that of TGG reported. Magnetic circular dichroism (MCD) spectra showed that the 4f→4f transitions of Tb³⁺ have significant contributions to the magneto-optical activity (MOA). In the time-resolved pump-probe spectroscopy, the rotation signals of the probe beam based on the inverse Faraday effect in magneto-optical crystal were observed at zero time delay, the full width at half maximum of the rotation and ellipticity signals can be as fast as ~500 fs, which indicates that TTO crystal can be a promising material for ultrafast all-optical magnetic switching.

Phase transitions in mixed gas hydrates: experimental observations versus calculated data.

PubMed

Schicks, Judith M; Naumann, Rudolf; Erzinger, Jörg; Hester, Keith C; Koh, Carolyn A; Sloan, E Dendy

2006-06-15

This paper presents the phase behavior of multicomponent gas hydrate systems formed from primarily methane with small amounts of ethane and propane. Experimental conditions were typically in a pressure range between 1 and 6 MPa, and the temperature range was between 260 and 290 K. These multicomponent systems have been investigated using a variety of techniques including microscopic observations, Raman spectroscopy, and X-ray diffraction. These techniques, used in combination, allowed for measurement of the hydrate structure and composition, while observing the morphology of the hydrate crystals measured. The hydrate formed immediately below the three-phase line (V-L --> V-L-H) and contained crystals that were both light and dark in appearance. The light crystals, which visually were a single solid phase, showed a spectroscopic indication for the presence of occluded free gas in the hydrate. In contrast, the dark crystals were measured to be structure II (sII) without the presence of these occluded phases. Along with hydrate measurements near the decomposition line, an unexpected transformation process was visually observed at P-T-conditions in the stability field of the hydrates. Larger crystallites transformed into a foamy solid upon cooling over this transition line (between 5 and 10 K below the decomposition temperature). Below the transition line, a mixture of sI and sII was detected. This is the first time that these multicomponent systems have been investigated at these pressure and temperature conditions using both visual and spectroscopic techniques. These techniques enabled us to observe and measure the unexpected transformation process showing coexistence of different gas hydrate phases.

One dimensional coordination polymers: Synthesis, crystal structures and spectroscopic properties

NASA Astrophysics Data System (ADS)

Karaağaç, Dursun; Kürkçüoğlu, Güneş Süheyla; Şenyel, Mustafa; Şahin, Onur

2016-11-01

Two new one dimensional (1D) cyanide complexes, namely [M(4-aepy)2(H2O)2][Pt(CN)4], (4-aepy = 4-(2-aminoethyl)pyridine M = Cu(II) (1) or Zn(II) (2)), have been synthesized and characterized by vibrational (FT-IR and Raman) spectroscopy, single crystal X-ray diffraction, thermal and elemental analyses techniques. The crystallographic analyses reveal that 1 and 2 are isomorphous and isostructural, and crystallize in the monoclinic system and C2 space group. The Pt(II) ions are coordinated by four cyanide-carbon atoms in the square-planar geometry and the [Pt(CN)4]2- ions act as a counter ion. The M(II) ions display an N4O2 coordination sphere with a distorted octahedral geometry, the nitrogen donors belonging to four molecules of the organic 4-aepy that act as unidentate ligands and two oxygen atoms from aqua ligands. The crystal structures of 1 and 2 are similar each other and linked via intermolecular hydrogen bonding, Pt⋯π interactions to form 3D supramolecular network. Vibration assignments of all the observed bands are given and the spectral features also supported to the crystal structures of the complexes.

Structural and magnetic investigations of single-crystalline neodymium zirconate pyrochlore Nd2Zr2O7

NASA Astrophysics Data System (ADS)

Hatnean, M. Ciomaga; Lees, M. R.; Petrenko, O. A.; Keeble, D. S.; Balakrishnan, G.; Gutmann, M. J.; Klekovkina, V. V.; Malkin, B. Z.

2015-05-01

We report structural and magnetic properties studies of large high-quality single crystals of the frustrated magnet Nd2Zr2O7 . Powder x-ray diffraction analysis confirms that Nd2Zr2O7 adopts the pyrochlore structure. Room-temperature x-ray diffraction and time-of-flight neutron-scattering experiments show that the crystals are stoichiometric in composition with no measurable site disorder. The temperature dependence of the magnetic susceptibility shows no magnetic ordering at temperatures down to 0.5 K. Fits to the magnetic susceptibility data using a Curie-Weiss law reveal a ferromagnetic coupling between the Nd moments. Magnetization versus field measurements show a local Ising anisotropy along the <111 > axes of the Nd3 + ions in the ground state. Specific heat versus temperature measurements in zero applied magnetic field indicate the presence of a thermal anomaly below T ˜7 K, but no evidence of magnetic ordering is observed down to 0.5 K. The experimental temperature dependence of the single-crystal bulk dc susceptibility and isothermal magnetization are analyzed using crystal field theory and the crystal field parameters and exchange coupling constants determined.

Cluster self-organization of nanotubes in a nematic phase: The percolation behavior and appearance of optical singularities

NASA Astrophysics Data System (ADS)

Ponevchinsky, V. V.; Goncharuk, A. I.; Vasil'Ev, V. I.; Lebovka, N. I.; Soskin, M. S.

2010-03-01

The structural features, as well as the optical and electrophysical properties of a 5CB nematic liquid crystal with additions of multilayer carbon nanotubes, have been investigated in the concentration range C = 0.0025-0.1 wt %. The self-aggregation of nanotubes into clusters with a fractal structure occurs in the liquid crystal. At 0.025 wt %, the clusters are merged, initiating the percolation transition of the composite to a state with a high electric conductivity. The strong interaction of 5CB molecules with the surface of nanotube clusters is responsible for the formation of micron surface liquid crystal layers with an irregular field of elastic stresses and a complex structure of birefringence. They are easily observed in a polarization microscope and visualize directly invisible submicron nanotube aggregates. Their transverse size increases when an electric field is applied to the liquid crystal cell. Two mechanisms of the generation of optical singularities in the passing laser beam have been revealed. Optical vortices appear in the speckle fields of laser radiation scattered at the indented boundaries of the nanotube clusters, whereas the birefringence of the beam in surface liquid-crystal layers is accompanied by the appearance of polarization C points.

Solid state structural investigations of the bis(chalcone) compound with single crystal X-ray crystallography, DFT, gamma-ray spectroscopy and chemical spectroscopy methods

NASA Astrophysics Data System (ADS)

Yakalı, Gül; Biçer, Abdullah; Eke, Canel; Cin, Günseli Turgut

2018-04-01

A bis(chalcone), (2E,6E)-2,6-bis((E)-3phenylallidene)cyclohexanone, was characterized by 1H NMR, 13C NMR, FTIR, UV-Vis spectroscopy, gamma-ray spectroscopy and single crystal X- ray structural analysis. The optimized molecular structure of the compound is calculated using DFT/B3LYP with 6-31G (d,p) level. The calculated geometrical parameters are in good agreement with the experimental data obtained from our reported X-ray structure. The powder and single crystal compounds were gama-irradiated using clinical electron linear accelerator and 60Co gamma-ray source, respectively. Spectral studies (1H NMR, 13C NMR, FTIR and UV-Vis) of powder chalcone compound were also investigated before and after irradiation. Depending on the irradiation notable changes were observed in spectral features powder sample. Single crystal X-ray diffraction investigation shows that both unirradiated and irradiated single crystal samples crystallizes in a orthorhombic crystal system in the centrosymmetric space group Pbcn and exhibits an C-H..O intramolecular and intermolecular hydrogen bonds. The crystal packing is stabilised by strong intermolecular bifurcate C-H..O hydrogen bonds and π…π stacking interactions. The asymmetric unit of the title compound contains one-half of a molecule. The other half of the molecule is generated with (1-x,y,-3/2-z) symmetry operator. The molecule is almost planar due to having π conjugated system of chalcones. However, irradiated single crystal compound showed significant changes lattice parameters, crystal volume and density. According to results of gamma-ray spectroscopy, radioactive elements of powder compound which are 123Sb(n,g),124Sb,57Fe(g,p),56Mn, 55Mn(g,n), and 54Mn were determined using photoactivation analysis. However, the most intensive gamma-ray energy signals are 124Sb.

Polymorphism in molecular solids: an extraordinary system of red, orange, and yellow crystals.

PubMed

Yu, Lian

2010-09-21

Diamond and graphite are polymorphs of each other: they have the same composition but different structures and properties. Many other substances exhibit polymorphism: inorganic and organic, natural and manmade. Polymorphs are encountered in studies of crystallization, phase transition, materials synthesis, and biomineralization and in the manufacture of specialty chemicals. Polymorphs can provide valuable insights into crystal packing and structure-property relationships. 5-Methyl-2-[(2-nitrophenyl)amino]-3-thiophenecarbonitrile, known as ROY for its red, orange, and yellow crystals, has seven polymorphs with solved structures, the largest number in the Cambridge Structural Database. First synthesized by medicinal chemists, ROY has attracted attention from solid-state chemists because it demonstrates the remarkable diversity possible in organic solids. Many structures of ROY polymorphs and their thermodynamic properties are known, making ROY an important model system for testing computational models. Though not the most polymorphic substance on record, ROY is extraordinary in that many of its polymorphs can crystallize simultaneously from the same liquid and are kinetically stable under the same conditions. Studies of ROY polymorphs have revealed a new crystallization mechanism that invalidates the common view that nucleation defines the polymorph of crystallization. A slow-nucleating polymorph can still dominate the product if it grows rapidly and nucleates on another polymorph. Studies of ROY have also helped understand a new, surprisingly fast mode of crystal growth in organic liquids cooled to the glass transition temperature. This growth mode exists only for those polymorphs that have more isotropic, and perhaps more liquid-like, packing. The rich polymorphism of ROY results from a combination of favorable thermodynamics and kinetics. Not only must there be many polymorphs of comparable energies or free energies, many polymorphs must be kinetically stable and crystallize at comparable rates to be observed. This system demonstrates the unique insights that polymorphism provides into solid-state structures and properties, as well as the inadequacy of our current understanding of the phenomenon. Despite many studies of ROY, it is still impossible to predict the next molecule that is equally or more polymorphic. ROY is a lucky gift from medicinal chemists.

Growth, structural, optical, thermal and dielectric properties of lanthanum chloride—thiourea—L tartaric acid coordinated complex

NASA Astrophysics Data System (ADS)

Slathia, Goldy; Bamzai, K. K.

2017-11-01

Lanthanum chloride—thiourea—l tartaric acid coordinated complex was grown in the form of single crystal by slow evaporation of supersaturated solutions at room temperature. This coordinated complex crystallizes in orthorhombic crystal system having space group P nma. The crystallinity and purity was tested by powder x-ray diffraction. Fourier transform infra red and Raman spectroscopy analysis provide the evidences on structure and mode of coordination. The scanning electron microscopy (SEM) analysis shows the morphology evolution as brought by the increase in composition of lanthanum chloride. The band transitions due to C=O and C=S chromophores remain active in grown complexes and are recorded in the UV-vis optical spectrum. The thermal effects such as dehydration, melting and decomposition were observed by the thermogravimetric and differential thermo analytical (TGA/DTA) analysis. Electrical properties were studied by dielectric analysis in frequency range 100-30 MHz at various temperatures. Increase in values of dielectric constant was observed with change in lanthanum concentration in the coordinated complex.

Nanoscale Cu{sub 2}O films: Radio-frequency magnetron sputtering and structural and optical studies

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kudryashov, D. A., E-mail: kudryashovda@apbau.ru; Gudovskikh, A. S.; Babichev, A. V.

2017-01-15

Nanoscale copper (I) oxide layers are formed by magnetron-assisted sputtering onto glassy and silicon substrates in an oxygen-free environment at room temperature, and the structural and optical properties of the layers are studied. It is shown that copper oxide formed on a silicon substrate exhibits a lower degree of disorder than that formed on a glassy substrate, which is supported by the observation of a higher intensity and a smaller half-width of reflections in the diffraction pattern. The highest intensity of reflections in the diffraction pattern is observed for Cu{sub 2}O films grown on silicon at a magnetron power ofmore » 150 W. The absorption and transmittance spectra of these Cu{sub 2}O films are in agreement with the well-known spectra of bulk crystals. In the Raman spectra of the films, phonons inherent in the crystal lattice of cubic Cu{sub 2}O crystals are identified.« less

Synthesis and characterization of a BaGdF5:Tb glass ceramic as a nanocomposite scintillator for x-ray imaging.

PubMed

Lee, Gyuhyon; Struebing, Christian; Wagner, Brent; Summers, Christopher; Ding, Yong; Bryant, Alex; Thadhani, Naresh; Shedlock, Daniel; Star-Lack, Josh; Kang, Zhitao

2016-05-20

Transparent glass ceramics with embedded light-emitting nanocrystals show great potential as low-cost nanocomposite scintillators in comparison to single crystal and transparent ceramic scintillators. In this study, cubic structure BaGdF5:Tb nanocrystals embedded in an aluminosilicate glass matrix are reported for potential high performance MeV imaging applications. Scintillator samples with systematically varied compositions were prepared by a simple conventional melt-quenching method followed by annealing. Optical, structural and scintillation properties were characterized to guide the design and optimization of selected material systems, aiming at the development of a system with higher crystal volume and larger crystal size for improved luminosity. It is observed that enhanced scintillation performance was achieved by tuning the glass matrix composition and using GdF3 in the raw materials, which served as a nucleation agent. A 26% improvement in light output was observed from a BaGdF5:Tb glass ceramic with addition of GdF3.

The MORPHEUS II protein crystallization screen

PubMed Central

Gorrec, Fabrice

2015-01-01

High-quality macromolecular crystals are a prerequisite for the process of protein structure determination by X-ray diffraction. Unfortunately, the relative yield of diffraction-quality crystals from crystallization experiments is often very low. In this context, innovative crystallization screen formulations are continuously being developed. In the past, MORPHEUS, a screen in which each condition integrates a mix of additives selected from the Protein Data Bank, a cryoprotectant and a buffer system, was developed. Here, MORPHEUS II, a follow-up to the original 96-condition initial screen, is described. Reagents were selected to yield crystals when none might be observed in traditional initial screens. Besides, the screen includes heavy atoms for experimental phasing and small polyols to ensure the cryoprotection of crystals. The suitability of the resulting novel conditions is shown by the crystallization of a broad variety of protein samples and their efficiency is compared with commercially available conditions. PMID:26144227

The MORPHEUS II protein crystallization screen.

PubMed

Gorrec, Fabrice

2015-07-01

High-quality macromolecular crystals are a prerequisite for the process of protein structure determination by X-ray diffraction. Unfortunately, the relative yield of diffraction-quality crystals from crystallization experiments is often very low. In this context, innovative crystallization screen formulations are continuously being developed. In the past, MORPHEUS, a screen in which each condition integrates a mix of additives selected from the Protein Data Bank, a cryoprotectant and a buffer system, was developed. Here, MORPHEUS II, a follow-up to the original 96-condition initial screen, is described. Reagents were selected to yield crystals when none might be observed in traditional initial screens. Besides, the screen includes heavy atoms for experimental phasing and small polyols to ensure the cryoprotection of crystals. The suitability of the resulting novel conditions is shown by the crystallization of a broad variety of protein samples and their efficiency is compared with commercially available conditions.

Role of local assembly in the hierarchical crystallization of associating colloidal hard hemispheres

NASA Astrophysics Data System (ADS)

Lei, Qun-li; Hadinoto, Kunn; Ni, Ran

2017-10-01

Hierarchical self-assembly consisting of local associations of simple building blocks for the formation of complex structures widely exists in nature, while the essential role of local assembly remains unknown. In this work, by using computer simulations, we study a simple model system consisting of associating colloidal hemispheres crystallizing into face-centered-cubic crystals comprised of spherical dimers of hemispheres, focusing on the effect of dimer formation on the hierarchical crystallization. We found that besides assisting the crystal nucleation because of increasing the symmetry of building blocks, the association between hemispheres can also induce both reentrant melting and reentrant crystallization depending on the range of interaction. Especially when the interaction is highly sticky, we observe a novel reentrant crystallization of identical crystals, which melt only in a certain temperature range. This offers another axis in fabricating responsive crystalline materials by tuning the fluctuation of local association.

Conformational variety for the ansa chain of rifamycins: Comparison of observed crystal structures and molecular dynamics simulations

NASA Astrophysics Data System (ADS)

Bacchi, Alessia; Pelizzi, Giancarlo

1999-07-01

The antibiotic activity (via inhibition of DNA-dependent RNA polymerase, DDRP) of rifamycins has been correlated to the conformation of the ansa chain, which can be described by means of 17 torsion angles defined along the ansa backbone. It has been shown that favourable or unfavourable conformations of the ansa chain in rifamycin crystals are generally diagnostic of activity or inactivity against isolated DDRP. The principles of structure correlation suggest that the torsional variety observed in rifamycin crystals should mimic the dynamic flexibility of the ansa chain in solution. Twenty-six crystal structures of rifamycins are grouped into two classes (active and non-active). For each class the variance of the 17 ansa backbone torsion angles is analysed. Active compounds show a well-defined common pattern, while non-active molecules are more scattered, mainly due to steric constraints forcing the molecules into unfavourable conformations. The experimental distributions of torsion angles are compared to the torsional freedom of the ansa chain simulated by molecular dynamics calculations performed at different temperatures and conditions on rifamycin S and rifamycin O, which represent a typical active and a typical sterically constrained molecule, respectively. It is shown that the torsional variety found in the crystalline state samples the dynamic behaviour of the ansa chain for active compounds. The methods of circular statistics are illustrated to describe torsion angle distributions.

Anisotropic physical properties of single-crystal U2Rh2Sn in high magnetic fields

NASA Astrophysics Data System (ADS)

Prokeš, K.; Gorbunov, D. I.; Reehuis, M.; Klemke, B.; Gukasov, A.; Uhlířová, K.; Fabrèges, X.; Skourski, Y.; Yokaichiya, F.; Hartwig, S.; Andreev, A. V.

2017-05-01

We report on the crystal and magnetic structures, magnetic, transport, and thermal properties of U2Rh2Sn single crystals studied in part in high magnetic fields up to 58 T. The material adopts a U3Si2 -related tetragonal crystal structure and orders antiferromagnetically below TN=25 K. The antiferromagnetic structure is characterized by a propagation vector k =(00 1/2 ) . The magnetism in U2Rh2Sn is found to be associated mainly with 5 f states. However, both unpolarized and polarized neutron experiments reveal at low temperatures in zero field non-negligible magnetic moments also on Rh sites. U moments of 0.50(2) μB are directed along the tetragonal axis while Rh moments of 0.06(4) μB form a noncollinear arrangement confined to the basal plane. The response to applied magnetic field is highly anisotropic. Above ˜15 K the easy magnetization direction is along the tetragonal axis. At lower temperatures, however, a stronger response is found perpendicular to the c axis. While for the a axis no magnetic phase transition is observed up to 58 T, for the field applied at 1.8 K along the tetragonal axis we observe above 22.5 T a field-polarized state. A magnetic phase diagram for the field applied along the c axis is presented.

Time lapse microscopy of temperature control during self-assembly of 3D DNA crystals

NASA Astrophysics Data System (ADS)

Conn, Fiona W.; Jong, Michael Alexander; Tan, Andre; Tseng, Robert; Park, Eunice; Ohayon, Yoel P.; Sha, Ruojie; Mao, Chengde; Seeman, Nadrian C.

2017-10-01

DNA nanostructures are created by exploiting the high fidelity base-pairing interactions of double-stranded branched DNA molecules. These structures present a convenient medium for the self-assembly of macroscopic 3D crystals. In some self-assemblies in this system, crystals can be formed by lowering the temperature, and they can be dissolved by raising it. The ability to monitor the formation and melting of these crystals yields information that can be used to monitor crystal formation and growth. Here, we describe the development of an inexpensive tool that enables direct observation of the crystal growth process as a function of both time and temperature. Using the hanging-drop crystallization of the well-characterized 2-turn DNA tensegrity triangle motif for our model system, its response to temperature has been characterized visually.

Disparate HDV ribozyme crystal structures represent intermediates on a rugged free-energy landscape.

PubMed

Sripathi, Kamali N; Tay, Wendy W; Banáš, Pavel; Otyepka, Michal; Šponer, Jiří; Walter, Nils G

2014-07-01

The hepatitis delta virus (HDV) ribozyme is a member of the class of small, self-cleaving catalytic RNAs found in a wide range of genomes from HDV to human. Both pre- and post-catalysis (precursor and product) crystal structures of the cis-acting genomic HDV ribozyme have been determined. These structures, together with extensive solution probing, have suggested that a significant conformational change accompanies catalysis. A recent crystal structure of a trans-acting precursor, obtained at low pH and by molecular replacement from the previous product conformation, conforms to the product, raising the possibility that it represents an activated conformer past the conformational change. Here, using fluorescence resonance energy transfer (FRET), we discovered that cleavage of this ribozyme at physiological pH is accompanied by a structural lengthening in magnitude comparable to previous trans-acting HDV ribozymes. Conformational heterogeneity observed by FRET in solution appears to have been removed upon crystallization. Analysis of a total of 1.8 µsec of molecular dynamics (MD) simulations showed that the crystallographically unresolved cleavage site conformation is likely correctly modeled after the hammerhead ribozyme, but that crystal contacts and the removal of several 2'-oxygens near the scissile phosphate compromise catalytic in-line fitness. A cis-acting version of the ribozyme exhibits a more dynamic active site, while a G-1 residue upstream of the scissile phosphate favors poor fitness, allowing us to rationalize corresponding changes in catalytic activity. Based on these data, we propose that the available crystal structures of the HDV ribozyme represent intermediates on an overall rugged RNA folding free-energy landscape. © 2014 Sripathi et al.; Published by Cold Spring Harbor Laboratory Press for the RNA Society.

Symmetry Groups of the Austenite Lattice and Construction of Self-Accommodation Complexes of Martensite Crystals in Alloys with the Shape-Memory Effect

NASA Astrophysics Data System (ADS)

Khundjua, A. G.; Ptitsin, A. G.; Brovkina, E. A.

2018-01-01

The internal structure of experimentally observed self-accommodation complexes of martensite crystals, which is determined by the system of twinning planes, is studied in this work. The direct correlation of the construction type of the complexes with the subgroups of the austenite lattice symmetry group is shown.

Low temperature structural transformation in T[Ni(CN){sub 4}].xpyz with x=1,2; T=Mn,Co,Ni,Zn,Cd; pyz=pyrazine

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rodriguez-Hernandez, J.; Instituto de Ciencia y Tecnologia de Materiales, Universidad de La Habana; Lemus-Santana, A.A.

2010-01-15

The materials under study are pillared solids T[Ni(CN){sub 4}].xpyz with one and two (x=1,2) pyrazine (pyz) molecules and where T=Mn, Co, Ni, Zn, Cd. Stimulated by their structural features and potential role as prototype of porous solids for hydrogen storage, the structural stability under cryogenic conditions for this series of pillared solids was studied. At low temperature, in the 100-200 K range, the occurrence of a reversible structural transformation was found. For T=Mn, Co, Zn, Cd, with x=2, the structural transformation was observed to occur around 185 K, and the low temperature phase crystallizes with a monoclinic unit cell (spacemore » group Pc). This structure change results from certain charge redistribution on cooling within the involved ligands. For T=Ni with x=1, both the low and high temperature phases crystallize with unit cells of tetragonal symmetry, within the same space group but with a different unit cell volume. In this case the structure change is observed around 120 K. Above that temperature the rotational states for the pyrazine molecule are thermally excited and all the pyrazine molecules in the structure become equivalent. Under this condition the material structure is described using a smaller structural unit. The structural study using X-ray powder diffraction data was complemented with calorimetric and Raman spectroscopy measurements. For the low temperature phases the crystal structures were solved from Patterson methods and then refined using the Rietveld method. - Graphical abstract: Low temperature ordered structure for pyrazine in T[Ni(CN){sub 4}].pyz.« less

Ice cream structure modification by ice-binding proteins.

PubMed

Kaleda, Aleksei; Tsanev, Robert; Klesment, Tiina; Vilu, Raivo; Laos, Katrin

2018-04-25

Ice-binding proteins (IBPs), also known as antifreeze proteins, were added to ice cream to investigate their effect on structure and texture. Ice recrystallization inhibition was assessed in the ice cream mixes using a novel accelerated microscope assay and the ice cream microstructure was studied using an ice crystal dispersion method. It was found that adding recombinantly produced fish type III IBPs at a concentration 3 mg·L -1 made ice cream hard and crystalline with improved shape preservation during melting. Ice creams made with IBPs (both from winter rye, and type III IBP) had aggregates of ice crystals that entrapped pockets of the ice cream mixture in a rigid network. Larger individual ice crystals and no entrapment in control ice creams was observed. Based on these results a model of ice crystals aggregates formation in the presence of IBPs was proposed. Copyright © 2017 Elsevier Ltd. All rights reserved.

Cocrystals of caffeine with formylphenoxyaliphatic acids: Syntheses, structural characterization, and biological activity

NASA Astrophysics Data System (ADS)

Suresh Kumar, G. S.; Seethalakshmi, P. G.; Bhuvanesh, N.; Kumaresan, S.

2013-02-01

Three organic cocrystals namely, caffeine:p-formylphenoxyacetic acid [(caf)(p-fpaa)] (1) caffeine:o-formylphenoxyacetic acid monohydrate [(caf)(o-fpaa)]H2O (2) and caffeine:p-formylphenoxypropionic acid [(caf)(p-fppa)] (3) were synthesized and studied by FT-IR, NMR, and single crystal XRD studies. The crystal system of cocrystal [(caf)(p-fpaa)] (1) is monoclinic with space group P21/n and Z = 16, that of cocrystal [(caf)(o-fpaa)]H2O (2) is triclinic with space group P - 1 and Z = 2, and that of cocrystal [(caf)(p-fppa)] (3) is monoclinic with space group P21/c and Z = 4. The imidazole-carboxylic acid synthon is observed in all the three cocrystals. The intermolecular hydrogen bonds, Osbnd H···N and π-π interactions together play a major role in stabilizing the crystal structure of all the three cocrystals. The biological activities of crystals 1-3 were studied.

Synthesis and structure identification of 2-amino-4, 6- dimethyl pyrimidine with gallic acid and pimelic acid

NASA Astrophysics Data System (ADS)

Mekala, R.; Jagdish, P.; Mathammal, R.

2018-07-01

Reaction of 2-amino-4, 6- dimethyl pyrimidine with carboxylic acid such as gallic acid and pimelic acid, yielded a salt and co-crystal, respectively. The new crystal forms were obtained from slow evaporation technique. The crystal structure and hydrogen bond interaction of the two crystals were determined by single X-ray diffraction analysis. Inter molecular interactions of the compounds were investigated using the 3D Hirshfeld surfaces and the associated 2D fingerprint plots. The functional groups were identified by the FTIR, FT-Raman spectral studies. The presence of carbon and hydrogen in the two samples were identified by the 1H and 13C NMR analysis. The excited energy was observed using UV-Visible spectral analysis. The fluorescence spectra revealed the emission state of the two samples. The thermal behaviour and stability of the two compounds were evaluated by the TGA-DSC analysis.

Control of the conformations of ion Coulomb crystals in a Penning trap

PubMed Central

Mavadia, Sandeep; Goodwin, Joseph F.; Stutter, Graham; Bharadia, Shailen; Crick, Daniel R.; Segal, Daniel M.; Thompson, Richard C.

2013-01-01

Laser-cooled atomic ions form ordered structures in radiofrequency ion traps and in Penning traps. Here we demonstrate in a Penning trap the creation and manipulation of a wide variety of ion Coulomb crystals formed from small numbers of ions. The configuration can be changed from a linear string, through intermediate geometries, to a planar structure. The transition from a linear string to a zigzag geometry is observed for the first time in a Penning trap. The conformations of the crystals are set by the applied trap potential and the laser parameters, and agree with simulations. These simulations indicate that the rotation frequency of a small crystal is mainly determined by the laser parameters, independent of the number of ions and the axial confinement strength. This system has potential applications for quantum simulation, quantum information processing and tests of fundamental physics models from quantum field theory to cosmology. PMID:24096901

Co-crystal and crystal: Supramolecular arrangement obtained from 4-aminosalicylic acid, bpa ligand and cobalt ion

NASA Astrophysics Data System (ADS)

Garcia, Humberto C.; Cunha, Ronaldo T.; Diniz, Renata; de Oliveira, Luiz Fernando C.

2012-02-01

In this study, the synthesis, spectroscopic properties (infrared and Raman) and crystal structures of two new compounds co-crystal and crystal named HASbpa (1) and [Co(bpa)(H2O)4]AS2ṡ4H2O (2) have been reported, where bpa is trans-1,2-bis(4-pyridyl)ethane, HAS is 4-aminosalicylic acid and AS- is aminosalicylate anion. The crystalline arrangement of the compound 1 exhibits a triclinic system with space group P1¯. The formation of a structure known as co-crystal, composed by building blocks in their neutral form; being the first work of this type involving the HAS and nitrogen ligand as bpa. For compound 2, a monoclinic system was observed with P21/c space group. The crystalline arrangement of the structure consisted of a covalent one-dimensional cationic [Co(bpa)(H2O)4]2+ chain, which interacts by hydrogen bonding, π-stacking and electrostatic interactions with aminosalicylate anions and water molecules that were trapped in the crystal. These interactions form supramolecular cavities denominated as pseudo honeycombs. For compound 1, the infrared spectrum revealed the presence of bands at 1643 and 1601 cm-1 assigned to the stretching mode of CO [ν(CO)] and CC/CN groups [ν(CC/CN)]. For the Raman spectrum, these same modes appear around 1644 and 1602 cm-1 related to HAS and bpa blocks, respectively. For compound 2, the largest displacement of the bands compared to free ligand suggested the formation of covalent bonds between bpa ligand and metallic site and loss of the proton in HAS molecule. In the infrared spectrum we can observe the presence of bands around 1635 and 1618 cm-1 attributed to the stretching ν(COO-) and ν(CC/CN), for the Raman spectrum these same modes appear around 1631 and 1619 cm-1 related to AS- and bpa ligand respectively.

Role of crystal arrangement on the mechanical performance of enamel.

PubMed

An, Bingbing; Wang, Raorao; Zhang, Dongsheng

2012-10-01

The superior mechanical properties of enamel, such as excellent penetration and crack resistance, are believed to be related to the unique microscopic structure. In this study, the effects of hydroxyapatite (HAP) crystallite orientation on the mechanical behavior of enamel have been investigated through a series of multiscale numerical simulations. A micromechanical model, which considers the HAP crystal arrangement in enamel prisms, the hierarchical structure of HAP crystals and the inelastic mechanical behavior of protein, has been developed. Numerical simulations revealed that, under compressive loading, plastic deformation progression took place in enamel prisms, which is responsible for the experimentally observed post-yield strain hardening. By comparing the mechanical responses for the uniform and non-uniform arrangement of HAP crystals within enamel prisms, it was found that the stiffness for the two cases was identical, while much greater energy dissipation was observed in the enamel with the non-uniform arrangement. Based on these results, we propose an important mechanism whereby the non-uniform arrangement of crystals in enamel rods enhances energy dissipation while maintaining sufficient stiffness to promote fracture toughness, mitigation of fracture and resistance to penetration deformation. Further simulations indicated that the non-uniform arrangement of the HAP crystals is a key factor responsible for the unique mechanical behavior of enamel, while the change in the nanostructure of nanocomposites could dictate the Young's modulus and yield strength of the biocomposite. Copyright © 2012 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

Crystal structure of human tooth enamel studied by neutron diffraction

NASA Astrophysics Data System (ADS)

Ouladdiaf, Bachir; Rodriguez-Carvajal, Juan; Goutaudier, Christelle; Ouladdiaf, Selma; Grosgogeat, Brigitte; Pradelle, Nelly; Colon, Pierre

2015-02-01

Crystal structure of human tooth enamel was investigated using high-resolution neutron powder diffraction. Excellent agreement between observed and refined patterns is obtained, using the hexagonal hydroxyapatite model for the tooth enamel, where a large hydroxyl deficiency ˜70% is found in the 4e site. Rietveld refinements method combined with the difference Fourier maps have revealed, however, that the hydroxyl ions are not only disordered along the c-axis but also within the basal plane. Additional H ions located at the 6h site and forming HPO42- anions were found.

Nucleic acid binding drugs. Part XIII. Molecular motion in a drug-nucleic acid model system: thermal motion analysis of a proflavine-dinucleoside crystal structure.

PubMed Central

Aggarwal, A K; Neidle, S

1985-01-01

The high-resolution crystal structure of the intercalation complex between proflavine and cytidylyl-3',5'-guanosine (CpG) has been studied by thermalmotion analysis. This has provided information on the translational and librational motions of individual groups in the complex. Many of these motions are similar to, though of larger magnitude than in uncomplexed dinucleosides. Pronounced librational effects were observed along the base pairs and in the plane of the drug chromophore. PMID:4034394

Multi-wavelength laser emission in dye-doped photonic liquid crystals.

PubMed

Wang, Chun-Ta; Lin, Tsung-Hsien

2008-10-27

Multi-wavelength lasing in a dye-doped cholesteric liquid crystal (CLC) cell is demonstrated. By adding oversaturated chiral dopant, the multi-photonic band CLC structure can be obtained with non-uniform chiral solubility. Under appropriate excitation, multi-wavelength lasing can be achieved with a multi-photonic band edge CLC structure. The number of lasing wavelengths can be controlled under various temperature processes. Nine wavelength CLC lasings were observed simultaneously. The wavelength range covers around 600-675nm. Furthermore, reversible tuning of multi-wavelength lasing was achieved by controlling CLC device temperature.

Crystal structure and superconducting properties of KSr2Nb3O10

NASA Astrophysics Data System (ADS)

Kawaguchi, T.; Horigane, K.; Itoh, Y.; Kobayashi, K.; Horie, R.; Kambe, T.; Akimitsu, J.

2018-05-01

We performed X-ray diffraction (XRD) and DC magnetic susceptibility measurements to elucidate the crystal structure and superconducting properties of KSr2Nb3O10. From the diffraction pattern indexing, it was found that KSr2Nb3O10 crystallizes with monoclinic symmetry, space group P21/m(11). We succeeded in preparing high temperature (HT) and low temperature (LT) phases of KSr2Nb3O10 powder samples synthesized by a conventional solid state reaction and an ion-exchange reaction, respectively. Superconductivity was observed at 4 K by Li intercalation and it was found that the superconducting volume fraction of the LT phase ( 1.4%) is clearly larger than that of the HT phase (0.07%).

Effects of dry etching processes on exciton and polariton characteristics in ZnTe

NASA Astrophysics Data System (ADS)

Sun, J. H.; Xie, W. B.; Shen, W. Z.; Ogawa, H.; Guo, Q. X.

2003-12-01

We have employed temperature-dependent reflection spectra to study the effects of reactive ion etching (RIE) on the exciton and polariton characteristics in ZnTe crystals exposed to CH4/H2 gases under different rf plasma powers. Classic exciton-polariton theory has been used to calculate the reflection spectra. By comparing with an as-grown ZnTe crystal and the temperature-dependent behavior, we are able to identify the excitons and RIE-induced polariton structures in these dry etched ZnTe crystals. An increase of the rf plasma power will lead to an increase of defect density in the surface damage layers, resulting in a decrease of the photon energies of the observed exciton and polariton structures.

High pressure synthesis, crystal growth and magnetic properties of TiOF

NASA Astrophysics Data System (ADS)

Cumby, J.; Burchell, M. B.; Attfield, J. P.

2018-06-01

Polycrystalline samples of TiOF have been prepared at 1300 °C and 8 GPa, with small single crystals grown at the same conditions. The crystal structure remains tetragonal rutile-type down to at least 90 K (space group P42/mnm, a = 4.6533 (2) Å and c = 3.0143 (2) Å at 90 K) and the Ti(O,F)6 octahedra are slightly compressed, consistent with Jahn-Teller distortion of 3d1 Ti3+. Diffuse scattering reveals disordered structural correlations that may arise from local cis-order of oxide anions driven by covalency. TiOF is paramagnetic down to 5 K and observation of a small paramagnetic moment and a substantial Pauli term indicates that the d-electrons are partially delocalised.

Containerless processing of single crystals in low-G environment

NASA Technical Reports Server (NTRS)

Walter, H. U.

1974-01-01

Experiments on containerless crystal growth from the melt were conducted during Skylab missions SL3 and SL4 (Skylab Experiment M-560). Six samples of InSb were processed, one of them heavily doped with selenium. The concept of the experiment is discussed and related to general crystal growth methods and their merits as techniques for containerless processing in space. The morphology of the crystals obtained is explained in terms of volume changes associated with solidification and wetting conditions during solidification. All samples exhibit extremely well developed growth facets. Analysis by X-ray topographical methods and chemical etching shows that the crystals are of high structural perfection. Average dislocation density as revealed by etching is of the order of 100 per sq cm; no dislocation clusters could be observed in the space-grown samples. A sequence of striations that is observed in the first half of the selenium-doped sample is explained as being caused by periodic surface breakdown.

Photonic crystals possessing multiple Weyl points and the experimental observation of robust surface states

PubMed Central

Chen, Wen-Jie; Xiao, Meng; Chan, C. T.

2016-01-01

Weyl points, as monopoles of Berry curvature in momentum space, have captured much attention recently in various branches of physics. Realizing topological materials that exhibit such nodal points is challenging and indeed, Weyl points have been found experimentally in transition metal arsenide and phosphide and gyroid photonic crystal whose structure is complex. If realizing even the simplest type of single Weyl nodes with a topological charge of 1 is difficult, then making a real crystal carrying higher topological charges may seem more challenging. Here we design, and fabricate using planar fabrication technology, a photonic crystal possessing single Weyl points (including type-II nodes) and multiple Weyl points with topological charges of 2 and 3. We characterize this photonic crystal and find nontrivial 2D bulk band gaps for a fixed kz and the associated surface modes. The robustness of these surface states against kz-preserving scattering is experimentally observed for the first time. PMID:27703140

Conformational influence of the ribose 2'-hydroxyl group: crystal structures of DNA-RNA chimeric duplexes

NASA Technical Reports Server (NTRS)

Egli, M.; Usman, N.; Rich, A.

1993-01-01

We have crystallized three double-helical DNA-RNA chimeric duplexes and determined their structures by X-ray crystallography at resolutions between 2 and 2.25 A. The two self-complementary duplexes [r(G)d(CGTATACGC)]2 and [d(GCGT)r(A)d(TACGC)]2, as well as the Okazaki fragment d(GGGTATACGC).r(GCG)d(TATACCC), were found to adopt A-type conformations. The crystal structures are non-isomorphous, and the crystallographic environments for the three chimeras are different. A number of intramolecular interactions of the ribose 2'-hydroxyl groups contribute to the stabilization of the A-conformation. Hydrogen bonds between 2'-hydroxyls and 5'-oxygens or phosphate oxygens, in addition to the previously observed hydrogen bonds to 1'-oxygens of adjacent riboses and deoxyriboses, are observed in the DNA-RNA chimeric duplexes. The crystalline chimeric duplexes do not show a transition between the DNA A- and B-conformations. CD spectra suggest that the Okazaki fragment assumes an A-conformation in solution as well. In this molecule the three RNA residues may therefore lock the complete decamer in the A-conformation. Crystals of an all-DNA strand with the same sequence as the self-complementary chimeras show a morphology which is different from those of the chimera crystals. Moreover, the oligonucleotide does not match any of the sequence characteristics of DNAs usually adopting the A-conformation in the crystalline state (e.g., octamers with short alternating stretches of purines and pyrimidines). In DNA-RNA chimeric duplexes, it is therefore possible that a single RNA residue can drive the conformational equilibrium toward the A-conformation.

Polymorphism in R-tamsulosin (an alpha blocker): The unexpected manifestation of a sulfonamide⋯o-diethoxybenzene heterosynthon

NASA Astrophysics Data System (ADS)

Nanubolu, Jagadeesh Babu; Sridhar, Balasubramanian; Ravikumar, Krishnan

2014-12-01

A two point Nsbnd H⋯O dimer or an infinite catemer are the most preferred motifs/synthons for sulfonamide structures. Such synthons are known to be so robust that they are only disrupted in the presence of highly activated O acceptors such as pyridine-N-oxide and sulfoxide. We demonstrate in this article that a multi-point synthon offered by much weaker ethoxy O and amine N acceptors can however strongly compete and disrupt the robust sulfonamide homosynthons. This has been illustrated with the synthon analysis in three polymorphic crystal structures of R-tamsulosin, an active drug used in the treatment of Benign Prostatic Hyperplasia (BPH) and its hydrochloride salt. These crystalline solids are characterized by Single crystal X-ray diffraction (SC-XRD), powder X-ray diffraction (PXRD), Fourier Transform Infrared (FT-IR) and Raman spectroscopy. Forms I, II of the free base and hydrochloride salt crystallize in the monoclinic P21, C2, and P21 space groups respectively with two molecules in the asymmetric unit (Z‧ = 2), whereas, form III of freebase crystallize in the orthorhombic P212121 space group with Z‧ = 1. Remarkably, all four crystal structures contain a totally unexpected sulfonamide⋯o-diethoxybenzene heterosynthon. The multi-point motifs observed in polymorphs are relatively stronger than those in the hydrochloride salt because of the gauche conformation of the tamsulosin linker chain which renders an additional hydrogen bond interaction with amine N acceptor, and resemble the crown ether sulfonamide recognition pattern. Observation of this new heterosynthon offers potential scope in the design of pharmaceutical cocrystals for sulfonamide bearing drug molecules. The present study also presents a detailed hydrogen bond motif analysis in 310 primary sulfonamide structures culled from the latest version of Cambridge Structural Database (CSD). The role of various competing groups is discussed in the context of understanding the most recurring sulfonamide homo and heterosynthons.

The prediction of crystal structure by merging knowledge methods with first principles quantum mechanics

NASA Astrophysics Data System (ADS)

Ceder, Gerbrand

2007-03-01

The prediction of structure is a key problem in computational materials science that forms the platform on which rational materials design can be performed. Finding structure by traditional optimization methods on quantum mechanical energy models is not possible due to the complexity and high dimensionality of the coordinate space. An unusual, but efficient solution to this problem can be obtained by merging ideas from heuristic and ab initio methods: In the same way that scientist build empirical rules by observation of experimental trends, we have developed machine learning approaches that extract knowledge from a large set of experimental information and a database of over 15,000 first principles computations, and used these to rapidly direct accurate quantum mechanical techniques to the lowest energy crystal structure of a material. Knowledge is captured in a Bayesian probability network that relates the probability to find a particular crystal structure at a given composition to structure and energy information at other compositions. We show that this approach is highly efficient in finding the ground states of binary metallic alloys and can be easily generalized to more complex systems.

Oxygen trapped by rare earth tetrahedral clusters in Nd4FeOS6: Crystal structure, electronic structure, and magnetic properties

NASA Astrophysics Data System (ADS)

Lin, Qisheng; Taufour, Valentin; Zhang, Yuemei; Wood, Max; Drtina, Thomas; Bud'ko, Sergey L.; Canfield, Paul C.; Miller, Gordon J.

2015-09-01

Single crystals of Nd4FeOS6 were grown from an Fe-S eutectic solution. Single crystal X-ray diffraction analysis revealed a Nd4MnOSe6-type structure (P63mc, a=9.2693(1) Å, c=6.6650(1)Å, V=495.94(1) Å3, Z=2), featuring parallel chains of face-sharing [FeS6×1/2]4- trigonal antiprisms and interlinked [Nd4OS3]4+ cubane-like clusters. Oxygen atoms were found to be trapped by Nd4 clusters in the [Nd4OS3]4+ chains. Structural differences among Nd4MnOSe6-type Nd4FeOS6 and the related La3CuSiS7- and Pr8CoGa3-type structures have been described. Magnetic susceptibility measurements on Nd4FeOS6 suggested the dominance of antiferromagnetic interactions at low temperature, but no magnetic ordering down to 2 K was observed. Spin-polarized electronic structure calculations revealed magnetic frustration with dominant antiferromagnetic interactions.

Structural and functional characterization of the CAP domain of pathogen-related yeast 1 (Pry1) protein

NASA Astrophysics Data System (ADS)

Darwiche, Rabih; Kelleher, Alan; Hudspeth, Elissa M.; Schneiter, Roger; Asojo, Oluwatoyin A.

2016-06-01

The production, crystal structure, and functional characterization of the C-terminal cysteine-rich secretory protein/antigen 5/pathogenesis related-1 (CAP) domain of pathogen-related yeast protein-1 (Pry1) from Saccharomyces cerevisiae is presented. The CAP domain of Pry1 (Pry1CAP) is functional in vivo as its expression restores cholesterol export to yeast mutants lacking endogenous Pry1 and Pry2. Recombinant Pry1CAP forms dimers in solution, is sufficient for in vitro cholesterol binding, and has comparable binding properties as full-length Pry1. Two crystal structures of Pry1CAP are reported, one with Mg2+ coordinated to the conserved CAP tetrad (His208, Glu215, Glu233 and His250) in spacegroup I41 and the other without divalent cations in spacegroup P6122. The latter structure contains four 1,4-dioxane molecules from the crystallization solution, one of which sits in the cholesterol binding site. Both structures reveal that the divalent cation and cholesterol binding sites are connected upon dimerization, providing a structural basis for the observed Mg2+-dependent sterol binding by Pry1.

Multicomponent hydrogen-bonding organic solids constructed from 6-hydroxy-2-naphthoic acid and N-heterocycles: Synthesis, structural characterization and synthon discussion

NASA Astrophysics Data System (ADS)

Zong, Yingxia; Shao, Hui; Pang, Yanyan; Wang, Debao; Liu, Kang; Wang, Lei

2016-07-01

Seven novel multicomponent crystals involving various substituted organic amine molecules and 6-hydroxy-2-naphthoic acid were prepared and characterized by using single crystal X-ray diffraction, infrared and thermogravimetric analyses (TGA). Crystal structures with 1,4-bis(imidazol) butane (L1) 1, 1,4-bis(imidazol-1-ylmethyl)benzene (L2) 2, 1-phenyl piperazine 3, 2-amino-4-hydroxy-6-methyl pyrimidine 4, 4,4'-bipyridine 5, 5,5'-dimethyl-2,2'-dipyridine 6, 2-amino-4,6-dimethyl pyrimidine 7 were determined. Among the seven molecular complexes, total proton transfer from 6-hydroxy-2-naphthoic acid to coformer has occurred in crystals 1-4, while the remaining were cocrystals. X-ray single-crystal structures of these complexes reveal that strong hydrogen bonding O-H···O/N-H···O/O-H···N and weak C-H···O/C-H···π/π···π intermolecular interactions direct the packing modes of molecular crystals together. The analysis of supramolecular synthons in the present structures shows that some classical supramolecular synthons like pyridine-carboxylic acid heterosynthon R22 (7) and aminopyridine-carboxylic acid heterosynthon R22 (8), are again observed in constructing the hydrogen-bonding networks in this paper. Besides, we noticed that water molecules act as a significant hydrogen-bonding connector in constructing supramolecular architectures of 3, 4, 6, and 7.

Magnetic and magnetostrictive behavior of Dy 3+ doped CoFe 2O 4 single crystals grown by flux method

NASA Astrophysics Data System (ADS)

Kambale, Rahul C.; Song, K. M.; Won, C. J.; Lee, K. D.; Hur, N.

2012-02-01

We studied the effect of Dy 3+ content on the magnetic properties of cobalt ferrite single crystal. The single crystals of CoFe 1.9Dy 0.1O 4 were grown by the flux method using Na 2B 4O 7.10 H 2O (Borax) as a solvent (flux). The black and shiny single crystals were obtained as a product. The X-ray diffraction analysis at room temperature confirmed the spinel cubic structure with lattice constant a=8.42 Å of the single crystals. The compositional analysis endorses the presence of constituents Co, Fe and Dy elements after sintering at 1300 °C within the final structure. The magnetic hysteresis measurements at various temperatures viz. 10 K, 100 K, 200 K and 300 K reveal the soft ferrimagnetic nature of the single crystal than that of for pure CoFe 2O 4. The observed saturation magnetization ( Ms) and coercivity ( Hc) are found to be lower than that of pure CoFe 2O 4 single crystal. The magnetostriction ( λ) measurement was carried out along the [001] direction. The magnetic measurements lead to conclude that the present single crystals can be used for magneto-optic recording media.

Bioinspired fabrication of hierarchically structured, pH-tunable photonic crystals with unique transition.

PubMed

Yang, Qingqing; Zhu, Shenmin; Peng, Wenhong; Yin, Chao; Wang, Wanlin; Gu, Jiajun; Zhang, Wang; Ma, Jun; Deng, Tao; Feng, Chuanliang; Zhang, Di

2013-06-25

We herein report a new class of photonic crystals with hierarchical structures, which are of color tunability over pH. The materials were fabricated through the deposition of polymethylacrylic acid (PMAA) onto a Morpho butterfly wing template by using a surface bonding and polymerization route. The amine groups of chitosan in Morpho butterfly wings provide reaction sites for the MAA monomer, resulting in hydrogen bonding between the template and MAA. Subsequent polymerization results in PMAA layers coating homogenously on the hierarchical photonic structures of the biotemplate. The pH-induced color change was detected by reflectance spectra as well as optical observation. A distinct U transition with pH was observed, demonstrating PMAA content-dependent properties. The appearance of the unique U transition results from electrostatic interaction between the -NH3(+) of chitosan and the -COO(-) groups of PMAA formed, leading to a special blue-shifted point at the pH value of the U transition, and the ionization of the two functional groups in the alkali and acid environment separately, resulting in a red shift. This work sets up a strategy for the design and fabrication of tunable photonic crystals with hierarchical structures, which provides a route for combining functional polymers with biotemplates for wide potential use in many fields.

Effect of Li and NH4 doping on the crystal perfection, second harmonic generation efficiency and laser damage threshold of potassium pentaborate crystals

NASA Astrophysics Data System (ADS)

Vigneshwaran, A. N.; Kalainathan, S.; Raja, C. Ramachandra

2018-03-01

Potassium pentaborate (KB5) is an excellent nonlinear optical material especially in the UV region. In this work, Li and NH4 doped KB5 crystals were grown using slow evaporation solution growth method. The incorporation of dopant has been confirmed and analysed by Energy dispersive X-ray analysis (EDAX), Inductively coupled plasma (ICP) analysis and Raman spectroscopy. The crystalline perfection of pure and doped KB5 crystals was studied by High resolution X-ray diffraction (HRXRD) analysis. Structural grain boundaries were observed in doped crystals. Second harmonic generation was confirmed for pure and doped crystals and output values revealed the enhancement of SHG efficiency in doped crystals. Resistance against laser damage was carried out using 1064 nm Nd-YAG laser of pulse width 10 ns. The laser damage threshold value is increased in Li doped crystal and decreased in NH4 doped crystal when compared to pure KB5 crystal.

Interaction of Tenebrio Molitor Antifreeze Protein with Ice Crystal: Insights from Molecular Dynamics Simulations.

PubMed

Ramya, L; Ramakrishnan, Vigneshwar

2016-07-01

Antifreeze proteins (AFP) observed in cold-adapting organisms bind to ice crystals and prevent further ice growth. However, the molecular mechanism of AFP-ice binding and AFP-inhibited ice growth remains unclear. Here we report the interaction of the insect antifreeze protein (Tenebrio molitor, TmAFP) with ice crystal by molecular dynamics simulation studies. Two sets of simulations were carried out at 263 K by placing the protein near the primary prism plane (PP) and basal plane (BL) of the ice crystal. To delineate the effect of temperatures, both the PP and BL simulations were carried out at 253 K as well. The analyses revealed that the protein interacts strongly with the ice crystal in BL simulation than in PP simulation both at 263 K and 253 K. Further, it was observed that the interactions are primarily mediated through the interface waters. We also observed that as the temperature decreases, the interaction between the protein and the ice increases which can be attributed to the decreased flexibility and the increased structuring of the protein at low temperature. In essence, our study has shed light on the interaction mechanism between the TmAFP antifreeze protein and the ice crystal. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

X-Ray Diffraction and Imaging Study of Imperfections of Crystallized Lysozyme with Coherent X-Rays

NASA Technical Reports Server (NTRS)

Hu, Zheng-Wei; Chu, Y. S.; Lai, B.; Cai, Z.; Thomas, B. R.; Chernov, A. A.

2003-01-01

Phase-sensitive x-ray diffraction imaging and high angular-resolution diffraction combined with phase contrast radiographic imaging are employed to characterize defects and perfection of a uniformly grown tetragonal lysozyme crystal in symmetric Laue case. The fill width at half-maximum (FWHM) of a 4 4 0 rocking curve measured from the original crystal is approximately 16.7 arcseconds, and defects, which include point defects, line defects, and microscopic domains, have been clearly observed in the diffraction images of the crystal. The observed line defects carry distinct dislocation features running approximately along the <110> growth front, and they have been found to originate mostly at a central growth area and occasionally at outer growth regions. Individual point defects trapped at a crystal nucleus are resolved in the images of high sensitivity to defects. Slow dehydration has led to the broadening of the 4 4 0 rocking curve by a factor of approximately 2.4. A significant change of the defect structure and configuration with drying has been revealed, which suggests the dehydration induced migration and evolution of dislocations and lattice rearrangements to reduce overall strain energy. The sufficient details of the observed defects shed light upon perfection, nucleation and growth, and properties of protein crystals.

Smectic C chevrons in nanocylinders

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lefort, R., E-mail: ronan.lefort@univ-rennes1.fr; Morineau, D.; Jean, F.

2014-11-17

The structure of an achiral smectic-C liquid crystal confined in nanocylinders with a planar surface anchoring is studied by small angle neutron scattering. We observe an invariant alignment of the nematic director with the pore axis, that promotes an original chevron structure with revolution symmetry.

Crystal Structure of Bfr A from Mycobacterium tuberculosis: Incorporation of Selenomethionine Results in Cleavage and Demetallation of Haem

PubMed Central

Gupta, Vibha; Gupta, Rakesh K.; Khare, Garima; Salunke, Dinakar M.; Tyagi, Anil K.

2009-01-01

Emergence of tuberculosis as a global health threat has necessitated an urgent search for new antitubercular drugs entailing determination of 3-dimensional structures of a large number of mycobacterial proteins for structure-based drug design. The essential requirement of ferritins/bacterioferritins (proteins involved in iron storage and homeostasis) for the survival of several prokaryotic pathogens makes these proteins very attractive targets for structure determination and inhibitor design. Bacterioferritins (Bfrs) differ from ferritins in that they have additional noncovalently bound haem groups. The physiological role of haem in Bfrs is not very clear but studies indicate that the haem group is involved in mediating release of iron from Bfr by facilitating reduction of the iron core. To further enhance our understanding, we have determined the crystal structure of the selenomethionyl analog of bacterioferritin A (SeMet-BfrA) from Mycobacterium tuberculosis (Mtb). Unexpectedly, electron density observed in the crystals of SeMet-BfrA analogous to haem location in bacterioferritins, shows a demetallated and degraded product of haem. This unanticipated observation is a consequence of the altered spatial electronic environment around the axial ligands of haem (in lieu of Met52 modification to SeMet52). Furthermore, the structure of Mtb SeMet-BfrA displays a possible lost protein interaction with haem propionates due to formation of a salt bridge between Arg53-Glu57, which appears to be unique to Mtb BfrA, resulting in slight modulation of haem binding pocket in this organism. The crystal structure of Mtb SeMet-BfrA provides novel leads to physiological function of haem in Bfrs. If validated as a drug target, it may also serve as a scaffold for designing specific inhibitors. In addition, this study provides evidence against the general belief that a selenium derivative of a protein represents its true physiological native structure. PMID:19946376

Twin density of aragonite in molluscan shells characterized using X-ray diffraction and transmission electron microscopy

NASA Astrophysics Data System (ADS)

Kogure, Toshihiro; Suzuki, Michio; Kim, Hyejin; Mukai, Hiroki; Checa, Antonio G.; Sasaki, Takenori; Nagasawa, Hiromichi

2014-07-01

{110} twin density in aragonites constituting various microstructures of molluscan shells has been characterized using X-ray diffraction (XRD) and transmission electron microscopy (TEM), to find the factors that determine the density in the shells. Several aragonite crystals of geological origin were also investigated for comparison. The twin density is strongly dependent on the microstructures and species of the shells. The nacreous structure has a very low twin density regardless of the shell classes. On the other hand, the twin density in the crossed-lamellar (CL) structure has large variation among classes or subclasses, which is mainly related to the crystallographic direction of the constituting aragonite fibers. TEM observation suggests two types of twin structures in aragonite crystals with dense {110} twins: rather regulated polysynthetic twins with parallel twin planes, and unregulated polycyclic ones with two or three directions for the twin planes. The former is probably characteristic in the CL structures of specific subclasses of Gastropoda. The latter type is probably related to the crystal boundaries dominated by (hk0) interfaces in the microstructures with preferred orientation of the c-axis, and the twin density is mainly correlated to the crystal size in the microstructures.

Dual curved photonic crystal ring resonator based channel drop filter using two-dimensional photonic crystal structure

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chhipa, Mayur Kumar, E-mail: mayurchhipa1@gmail.com; Dusad, Lalit Kumar

In this paper channel drop filter (CDF) is designed using dual curved photonic crystal ring resonator (PCRR). The photonic band gap (PBG) is calculated by plane wave expansion (PWE) method and the photonic crystal (PhC) based on two dimensional (2D) square lattice periodic arrays of silicon (Si) rods in air structure have been investigated using finite difference time domain (FDTD) method. The number of rods in Z and X directions is 21 and 20 respectively with lattice constant 0.540 nm and rod radius r = 0.1 µm. The channel drop filter has been optimized for telecommunication wavelengths λ = 1.591 µm with refractivemore » indices 3.533. In the designed structure further analysis is also done by changing whole rods refractive index and it has been observed that this filter may be used for filtering several other channels also. The designed structure is useful for CWDM systems. This device may serve as a key component in photonic integrated circuits. The device is ultra compact with the overall size around 123 µm{sup 2}.« less

Holographic fabrication of 3D photonic crystals through interference of multi-beams with 4 + 1, 5 + 1 and 6 + 1 configurations.

PubMed

George, D; Lutkenhaus, J; Lowell, D; Moazzezi, M; Adewole, M; Philipose, U; Zhang, H; Poole, Z L; Chen, K P; Lin, Y

2014-09-22

In this paper, we are able to fabricate 3D photonic crystals or quasi-crystals through single beam and single optical element based holographic lithography. The reflective optical elements are used to generate multiple side beams with s-polarization and one central beam with circular polarization which in turn are used for interference based holographic lithography without the need of any other bulk optics. These optical elements have been used to fabricate 3D photonic crystals with 4, 5 or 6-fold symmetry. A good agreement has been observed between fabricated holographic structures and simulated interference patterns.

Structural disorder and elementary magnetic properties of triangular lattice ErMgGaO 4 single crystals

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cevallos, F. Alex; Stolze, Karoline; Cava, Robert J.

The single crystal growth, structure, and basic magnetic properties of ErMgGaO 4 are reported. The structure consists of triangular layers of magnetic ErO 6 octahedra separated by a double layer of randomly occupied non-magnetic (Ga,Mg)O 5 bipyramids. The Er atoms are positionally disordered. Magnetic measurements parallel and perpendicular to the c axis of a single crystal reveal dominantly antiferromagnetic interactions, with a small degree of magnetic anisotropy. A weighted average of the directional data suggests an antiferromagnetic Curie Weiss temperature of approximately -30 K. Below 10 K the temperature dependences of the inverse susceptibilities in the in-plane and perpendicular-to planemore » directions are parallel, indicative of an isotropic magnetic moment at low temperatures. In conclusion, no sign of magnetic ordering is observed above 1.8 K, suggesting that ErMgGaO 4 is a geometrically frustrated magnet.« less

A liquid-liquid transition in supercooled aqueous solution related to the HDA-LDA transition

NASA Astrophysics Data System (ADS)

Woutersen, Sander; Ensing, Bernd; Hilbers, Michiel; Zhao, Zuofeng; Angell, C. Austen

2018-03-01

Simulations and theory suggest that the thermodynamic anomalies of water may be related to a phase transition between two supercooled liquid states, but so far this phase transition has not been observed experimentally because of preemptive ice crystallization. We used calorimetry, infrared spectroscopy, and molecular dynamics simulations to investigate a water-rich hydrazinium trifluoroacetate solution in which the local hydrogen bond structure surrounding a water molecule resembles that in neat water at elevated pressure, but which does not crystallize upon cooling. Instead, this solution underwent a sharp, reversible phase transition between two homogeneous liquid states. The hydrogen-bond structures of these two states are similar to those established for high- and low-density amorphous (HDA and LDA) water. Such structural similarity supports theories that predict a similar sharp transition in pure water under pressure if ice crystallization could be suppressed.

Structural disorder and elementary magnetic properties of triangular lattice ErMgGaO 4 single crystals

DOE PAGES

Cevallos, F. Alex; Stolze, Karoline; Cava, Robert J.

2018-03-23

The single crystal growth, structure, and basic magnetic properties of ErMgGaO 4 are reported. The structure consists of triangular layers of magnetic ErO 6 octahedra separated by a double layer of randomly occupied non-magnetic (Ga,Mg)O 5 bipyramids. The Er atoms are positionally disordered. Magnetic measurements parallel and perpendicular to the c axis of a single crystal reveal dominantly antiferromagnetic interactions, with a small degree of magnetic anisotropy. A weighted average of the directional data suggests an antiferromagnetic Curie Weiss temperature of approximately -30 K. Below 10 K the temperature dependences of the inverse susceptibilities in the in-plane and perpendicular-to planemore » directions are parallel, indicative of an isotropic magnetic moment at low temperatures. In conclusion, no sign of magnetic ordering is observed above 1.8 K, suggesting that ErMgGaO 4 is a geometrically frustrated magnet.« less

Micromechanical models for the stiffness and strength of UHMWPE macrofibrils

NASA Astrophysics Data System (ADS)

Dong, Hai; Wang, Zheliang; O'Connor, Thomas C.; Azoug, Aurelie; Robbins, Mark O.; Nguyen, Thao D.

2018-07-01

Ultrahigh molecular weight polyethylene (UHMWPE) fibers have a complex hierarchical structure that at the micron-scale is composed of oriented chain crystals, lamellar crystals, and amorphous domains organized into macrofibrils. We developed a computational micromechanical modeling study of the effects of the morphological structure and constituent material properties on the deformation mechanisms, stiffness and strength of the UHMWPE macrofibrils. Specifically, we developed four representative volume elements, which differed in the arrangement and orientation of the lamellar crystals, to describe the various macrofibrillar microstructures observed in recent experiments. The stiffness and strength of the crystals were determined from molecular dynamic simulations of a pure PE crystal. A finite deformation crystal plasticity model was used to describe the crystals and an isotropic viscoplastic model was used for the amorphous phase. The results show that yielding in UHMWPE macrofibrils under axial tension is dominated by the slip in the oriented crystals, while yielding under transverse compression and shear is dominated by slips in both the oriented and lamellar crystals. The results also show that the axial modulus and strength are mainly determined by the volume fraction of the oriented crystals and are insensitive to the arrangements of the lamellar crystals when the modulus of the amorphous phase is significantly smaller than that of the crystals. In contrast, the arrangement and size of the lamellar crystals have a significant effect on the stiffness and strength under transverse compression and shear. These findings can provide a guide for new materials and processing design to improve the properties of UHMWPE fibers by controlling the macrofibrillar morphologies.

Local Structure and Anisotropy in the Amorphous Precursor= to Ba-Hexaferrite Thin Films

NASA Astrophysics Data System (ADS)

Snyder, J. E.; Harris, V. G.; Koon, N. C.; Sui, X.; Kryder, M. H.

1996-03-01

Ba-hexaferrite thin-films for recording media applications are commonly fabricated by a two-step process: sputter-deposition of an amorphous precursor, followed by annealing to crystallize the BaFe_12O_19 phase. The magnetic anisotropy of the crystalline films can be either in-plane or perpendicular, depending on the sputtering process used in the first step. However, conventional characterization techniques (x-ray diffraction and TEM) have been unable to observe any structure in the amorphous precursor films. In this study, such films are investigated by PD-EXAFS (polarization-dependent extended x-ray absorption fine structure). An anisotropic local ordered structure is observed around both Fe and Ba atoms in the "amorphous" films. This anisotropic local structure appears to determine the orientation of the fast-growing basal plane directions during crystallization, and thus the directions of the c-axes and the magnetic anisotropy. Results suggest that the structure of the amorphous films consists of networks made up of units of Fe atoms surrounded by their O nearest neighbors, that are connected together. Ba atoms appear to fit into in-between spaces as network-modifiers.

Self-assembly modes of glycyrrhetinic acid esters in view of the crystal packing of related triterpene molecules.

PubMed

Langer, Dominik; Wicher, Barbara; Szczołko, Wojciech; Gdaniec, Maria; Tykarska, Ewa

2016-08-01

The crystal structures of three ester derivatives of glycyrrhetinic acid (GE) are reported. X-ray crystallography revealed that despite differences in the size of the ester substituents (ethyl, isopropyl and 2-morpholinoethyl) the scheme of molecular self-assembly is similar in all three cases but differs significantly from that observed in other known GE esters. According to our analysis, the two basic patterns of self-assembly of GE esters observed in their unsolvated crystals correspond to two distinct orientations of the ester groups relative to the triterpene backbone. Moreover, comparison of the self-assembly modes of GE esters in their unsolvated forms with the supramolecular organization of GE and carbenoxolone in their solvated crystals revealed that ester substituents replace solvent molecules hydrogen bonded to the COOH group at the triterpene skeleton, resulting in similar packing arrangements of these compounds.

The undercooling of liquids

NASA Technical Reports Server (NTRS)

Turnbull, D.

1984-01-01

The formation by melt quenching of such metastable structures as glassy or microcrystalline solids and highly supersaturated solutions is made possible by the extreme resistance of most melts to homophase crystal nucleation at deep undercooling. This nucleation resistance contrasts sharply with the very low kinetic resistance to the movement of crystal-melt interfaces, once formed, in metals and other fluid systems at even minute undercooling. The methods of nucleation study which have proven especially effective in bypassing nucleation by heterophase impurities thereby exposing the high resistance of melts to homophase nucleation may be summarized as follows: observation of the crystallization behavior of dispersed small droplets; drop tube experiments in which liquid drops solidify, under containerless conditions, during their fall in the tube; and observation of the crystallization of bulk specimens immersed in fluxes chosen to dissolve or otherwise deactivate (e.g., by wetting) heterophase nucleants. This method has proven to be remarkably effective in deactivating such nucleants in certain pure metals.

Segregation of liquid crystal mixtures in topological defects

DOE PAGES

Rahimi, Mohammad; Ramezani-Dakhel, Hadi; Zhang, Rui; ...

2017-04-28

The structure and physical properties of liquid crystal (LC) mixtures are a function of composition, and small changes can have pronounced effects on observables, such as phase-transition temperatures. Traditionally, LC mixtures have been assumed to be compositionally homogenous. The results of chemically detailed simulations presented here show that this is not the case; pronounced deviations of the local order from that observed in the bulk at defects and interfaces lead to significant compositional segregation effects. More specifically, two disclination lines are stabilized in this work by introducing into a nematic liquid crystal mixture a cylindrical body that exhibits perpendicular anchoring.more » Here, it is found that the local composition deviates considerably from that of the bulk at the interface with the cylinder and in the defects, thereby suggesting new assembly and synthetic strategies that may capitalize on the unusual molecular environment provided by liquid crystal mixtures.« less

Mims electron-nuclear double resonance in LiYF4:Ce3+ crystal

NASA Astrophysics Data System (ADS)

Gafurov, M.; Mamin, G.; Kurkin, I.; Orlinskii, S.

2018-05-01

We report the observation of the pulsed electron-nuclear double resonance (ENDOR) spectra from 19F and 7Li nuclei on impurity Ce3+ ions in LiYF4 crystal. The resolved structure from the nearby and remote nuclei in spectra is observed. The outcome shows that LiYF4:Ce3+ system can be exploited as a convenient matrix for performing spin manipulations and adjusting quantum computation protocols while ENDOR technique is usable for the investigation of electron-nuclear interaction with all the nuclei of the system.

Crystallography of Magnetite Plaquettes and their Significance as Asymmetric Catalysts for the Synthesis of Chiral Organics in Carbonaceous Chondrites

NASA Technical Reports Server (NTRS)

Chan, Q. H. S.; Zolensky, M. E.

2015-01-01

We have previously observed the magnetite plaquettes in carbonaceous chondrites using scanning electron microscope (SEM) imaging, examined the crystal orientation of the polished surfaces of magnetite plaquettes in CI Orgueil using electron backscattered diffraction (EBSD) analysis, and concluded that these magnetite plaquettes are likely naturally asymmetric materials. In this study, we expanded our EBSD observation to other magnetite plaquettes in Orgueil, and further examined the internal structure of these remarkable crystals with the use of X-ray computed microtomography.

Plasma parameters and structures of the X4 flare of 19 May 1984 as observed by SMM-XRP.

NASA Astrophysics Data System (ADS)

Schmelz, J. T.; Saba, J. L. R.; Strong, K. T.

The eruption of a large flare on the east limb of the Sun was observed by the X-ray Polychromator (XRP) on board the Solar Maximum Mission (SMM) on 19 May 1984. The XRP Flat Crystal Spectrometer (FCS) made polychromatic soft X-ray images during the preflare, flare and postflare phases. The XRP Bent Crystal Spectrometer (BCS) provided information on the temperature and dynamics of the hot (Te > 8×106K) coronal plasma from spectra integrated spatially over the whole region.

Ce3 - xMgxCo9 : Transformation of a Pauli Paramagnet into a Strong Permanent Magnet

NASA Astrophysics Data System (ADS)

Lamichhane, Tej N.; Taufour, Valentin; Palasyuk, Andriy; Lin, Qisheng; Bud'ko, Sergey L.; Canfield, Paul C.

2018-02-01

We report on the synthesis of single-crystal and polycrystalline samples of Ce3 -xMgxCo9 solid solution (0 ≤x ≲1.4 ) and characterization of their structural and magnetic properties. The crystal structure remains rhombohedral in the whole composition range and Mg partially replaces Ce in the 6 c site of the CeCo3 structure. Ferromagnetism is induced by Mg substitutions starting as low as x =0.18 and reaching a Curie temperature as high as 450 K for x =1.35 . Measurements on single crystals with x =1.34 and TC=440 K indicate an axial magnetic anisotropy with an anisotropy field of 6 T and a magnetization of 6 μB/f .u . at 300 K. Coercicity is observed in the polycrystalline samples consistent with the observed axial magnetic anisotropy. Our discovery of ferromagnetism with large axial magnetic anisotropy induced by substituting a rare-earth element by Mg is a very promising result in the search of inexpensive permanent-magnet materials and suggests that other nonmagnetic phases, similar to CeCo3 , may also conceal nearby ferromagnetic phases.

Ce 3 - x Mg x Co 9 : Transformation of a Pauli Paramagnet into a Strong Permanent Magnet

DOE PAGES

Lamichhane, Tej N.; Taufour, Valentin; Palasyuk, Andriy; ...

2018-02-23

In this article we report on the synthesis of single-crystal and polycrystalline samples of Ce 3-xMg xCo 9 solid solution (0 ≤ x ≲ 1.4) and characterization of their structural and magnetic properties. The crystal structure remains rhombohedral in the whole composition range and Mg partially replaces Ce in the 6c site of the CeCo 3 structure. Ferromagnetism is induced by Mg substitutions starting as low as x = 0.18 and reaching a Curie temperature as high as 450 K for x = 1.35 . Measurements on single crystals with x = 1.34 and T C = 440 K indicatemore » an axial magnetic anisotropy with an anisotropy field of 6 T and a magnetization of 6 μ B/f.u. at 300 K. Coercicity is observed in the polycrystalline samples consistent with the observed axial magnetic anisotropy. Our discovery of ferromagnetism with large axial magnetic anisotropy induced by substituting a rare-earth element by Mg is a very promising result in the search of inexpensive permanent-magnet materials and suggests that other nonmagnetic phases, similar to CeCo 3, may also conceal nearby ferromagnetic phases.« less

Ce 3 - x Mg x Co 9 : Transformation of a Pauli Paramagnet into a Strong Permanent Magnet

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lamichhane, Tej N.; Taufour, Valentin; Palasyuk, Andriy

In this article we report on the synthesis of single-crystal and polycrystalline samples of Ce 3-xMg xCo 9 solid solution (0 ≤ x ≲ 1.4) and characterization of their structural and magnetic properties. The crystal structure remains rhombohedral in the whole composition range and Mg partially replaces Ce in the 6c site of the CeCo 3 structure. Ferromagnetism is induced by Mg substitutions starting as low as x = 0.18 and reaching a Curie temperature as high as 450 K for x = 1.35 . Measurements on single crystals with x = 1.34 and T C = 440 K indicatemore » an axial magnetic anisotropy with an anisotropy field of 6 T and a magnetization of 6 μ B/f.u. at 300 K. Coercicity is observed in the polycrystalline samples consistent with the observed axial magnetic anisotropy. Our discovery of ferromagnetism with large axial magnetic anisotropy induced by substituting a rare-earth element by Mg is a very promising result in the search of inexpensive permanent-magnet materials and suggests that other nonmagnetic phases, similar to CeCo 3, may also conceal nearby ferromagnetic phases.« less

Electromagnetic-field amplification in finite one-dimensional photonic crystals

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gorelik, V. S.; Kapaev, V. V., E-mail: kapaev@sci.lebedev.ru

2016-09-15

The electromagnetic-field distribution in a finite one-dimensional photonic crystal is studied using the numerical solution of Maxwell’s equations by the transfer-matrix method. The dependence of the transmission coefficient T on the period d (or the wavelength λ) has the characteristic form with M–1 (M is the number of periods in the structure) maxima with T = 1 in the allowed band of an infinite crystal and zero values in the forbidden band. The field-modulus distribution E(x) in the structure for parameters that correspond to the transmission maxima closest to the boundaries of forbidden bands has maxima at the center ofmore » the structure; the value at the maximum considerably exceeds the incident-field strength. For the number of periods M ~ 50, more than an order of magnitude increase in the field amplification is observed. The numerical results are interpreted with an analytic theory constructed by representing the solution in the form of a linear combination of counterpropagating Floquet modes in a periodic structure.« less

Crystal structure of the μ-opioid receptor bound to a morphinan antagonist

PubMed Central

Manglik, Aashish; Kruse, Andrew C.; Kobilka, Tong Sun; Thian, Foon Sun; Mathiesen, Jesper M.; Sunahara, Roger K.; Pardo, Leonardo; Weis, William I.; Kobilka, Brian K.; Granier, Sébastien

2012-01-01

Summary Opium is one of the world’s oldest drugs, and its derivatives morphine and codeine are among the most used clinical drugs to relieve severe pain. These prototypical opioids produce analgesia as well as many of their undesirable side effects (sedation, apnea and dependence) by binding to and activating the G-protein-coupled μ-opioid receptor (μOR) in the central nervous system. Here we describe the 2.8 Å crystal structure of the μOR in complex with an irreversible morphinan antagonist. Compared to the buried binding pocket observed in most GPCRs published to date, the morphinan ligand binds deeply within a large solvent-exposed pocket. Of particular interest, the μOR crystallizes as a two-fold symmetric dimer through a four-helix bundle motif formed by transmembrane segments 5 and 6. These high-resolution insights into opioid receptor structure will enable the application of structure-based approaches to develop better drugs for the management of pain and addiction. PMID:22437502

Crystal structure refinement of ReSi1.75 with an ordered arrangement of silicon vacancies

NASA Astrophysics Data System (ADS)

Harada, Shunta; Hoshikawa, Hiroaki; Kuwabara, Kosuke; Tanaka, Katsushi; Okunishi, Eiji; Inui, Haruyuki

2011-08-01

The crystal structure and microstructure of ReSi1.75 were investigated by synchrotron X-ray diffraction combined with scanning transmission electron microscopy. ReSi1.75 contains an ordered arrangement of vacancies in Si sites in the underlying tetragonal C11b lattice of the MoSi2-type and the crystal structure is monoclinic with the space group Cm. Atomic positions of Si atoms near vacancies are considerably displaced from the corresponding positions in the parent C11b structure, and they exhibit anomalously large local thermal vibration accompanied by large values of atomic displacement parameter. There are four differently-oriented domains with two of them being related to each other by the 90° rotation about the c-axis of the underlying C11b lattice and the other two being their respective twins. The habit planes for domain boundaries observed experimentally are consistent with those predicted with ferroelastic theory.

Crystal structure of (Mo,W){sub 9}O{sub 25}, homologue of the Mo{sub 4}O{sub 11} (Orthorhombic)-type structure

DOE Office of Scientific and Technical Information (OSTI.GOV)

D`Yachenko, O.G.; Tabachenko, V.V.; Sundberg, M.

The structure of Mo{sub 7.6}W{sub 1.4}O{sup 25} has been determined from single crystal X-ray data. The symmetry is monoclinic with lattice parameters a = 5.448(1), b = 27.639(8), c = 6.739 (1) {angstrom}, {beta} = 90.180(9){degrees}, and space group P2{sub 1}/n. The refinement led to R = 0.046 for 2060 observed unique reflections. The Mo:W ratio was confirmed by microanalysis. The (Mo, W){sub 9}O{sub 25} structure is built up of cornersharing distorted MO{sub 6} octahedra in slabs of ReO{sub 3}-type, cut parallel to (211) and seven octahedra wide along two subcell axes. The slabs appear alternatively in mirrored orientations. Themore » slabs are mutually linked by corner sharing of fairly regular MoO{sub 4} tetrahedra so that five-sided tunnels are formed. High-resolution electron microscopy images showed well-ordered crystal fragments.« less

Neutron diffraction study of antiferromagnetic ErNi3Ga9 in magnetic fields

NASA Astrophysics Data System (ADS)

Ninomiya, Hiroki; Sato, Takaaki; Matsumoto, Yuji; Moyoshi, Taketo; Nakao, Akiko; Ohishi, Kazuki; Kousaka, Yusuke; Akimitsu, Jun; Inoue, Katsuya; Ohara, Shigeo

2018-05-01

We report specific heat, magnetization, magnetoresistance, and neutron diffraction measurements of single crystals of ErNi3Ga9. This compound crystalizes in a chiral structure with space group R 32 . The erbium ions form a two-dimensional honeycomb structure. ErNi3Ga9 displays antiferromagnetic order below 6.4 K. We determined that the magnetic structure is slightly amplitude-modulated as well as antiferromagnetic with q = (0 , 0 , 0.5) . The magnetic properties are described by an Ising-like model in which the magnetic moment is always along the c-axis owing to the large uniaxial anisotropy caused by the crystalline electric field effect in the low temperature region. When the magnetic field is applied along the c-axis, a metamagnetic transition is observed around 12 kOe at 2 K. ErNi3Ga9 possesses crystal chirality, but the antisymmetric magnetic interaction, the so-called Dzyaloshinskii-Moriya (DM) interaction, does not contribute to the magnetic structure, because the magnetic moments are parallel to the DM-vector.

Structure of the human DNA-repair protein RAD52 containing surface mutations.

PubMed

Saotome, Mika; Saito, Kengo; Onodera, Keiichi; Kurumizaka, Hitoshi; Kagawa, Wataru

2016-08-01

The Rad52 protein is a eukaryotic single-strand DNA-annealing protein that is involved in the homologous recombinational repair of DNA double-strand breaks. The isolated N-terminal half of the human RAD52 protein (RAD52(1-212)) forms an undecameric ring structure with a surface that is mostly positively charged. In the present study, it was found that RAD52(1-212) containing alanine mutations of the charged surface residues (Lys102, Lys133 and Glu202) is highly amenable to crystallization. The structure of the mutant RAD52(1-212) was solved at 2.4 Å resolution. The structure revealed an association between the symmetry-related RAD52(1-212) rings, in which a partially unfolded, C-terminal region of RAD52 extended into the DNA-binding groove of the neighbouring ring in the crystal. The alanine mutations probably reduced the surface entropy of the RAD52(1-212) ring and stabilized the ring-ring association observed in the crystal.

Synthesis, spectral, structural prediction and computational studies of octylcarbazole ornamented 3-phenothiazinal

NASA Astrophysics Data System (ADS)

Karuppasamy, Ayyanar; Udhaya kumar, Chandran; Karthikeyan, Subramanian; Velayutham Pillai, Muthiah Pillai; Ramalingan, Chennan

2017-11-01

A novel conjugated octylcarbazole ornamented 3-phenothiazinal, 10-(9-octyl-9H-carbazol-3-yl)-10H-phenothiazine-3-carbaldehyde (OCPTC) was synthesized and fully characterized by 1H-NMR, 13C-NMR, elemental and single crystal XRD analyses. The optimized geometrical structure, vibrational frequencies and NMR have been computed with M06-2X method using 6-31+G(d,p) basis set. Total electronic energies and HOMO-LUMO energy gaps in gas phase are discussed. The geometrical parameters of the title compound obtained from single crystal XRD studies have been found in accord with the calculated (DFT) values. The experimental and theoretical FT-IR and NMR results of the title molecule have been investigated. The experimentally observed vibrational frequencies have been compared with the calculated ones, which are in good agreement with each other. Single crystal X-ray structural analysis of OCPTC, evidences the ''butterfly conformation'' of phenothiazine ring with nearly perpendicular orientation of the carbazole structural motif to the phenothiazine moiety.

Crystal Structure and Proteomics Analysis of Empty Virus-like Particles of Cowpea Mosaic Virus

PubMed Central

Huynh, Nhung T.; Hesketh, Emma L.; Saxena, Pooja; Meshcheriakova, Yulia; Ku, You-Chan; Hoang, Linh T.; Johnson, John E.; Ranson, Neil A.; Lomonossoff, George P.; Reddy, Vijay S.

2016-01-01

SUMMARY Empty virus-like particles (eVLPs) of Cowpea mosaic virus (CPMV) are currently being utilized as reagents in various biomedical and nanotechnology applications. Here, we report the crystal structure of CPMV eVLPs determined using X-ray crystallography at 2.3 Å resolution and compare it with previously reported cryo-electron microscopy (cryo-EM) of eVLPs and virion crystal structures. Although the X-ray and cryo-EM structures of eVLPs are mostly similar, there exist significant differences at the C terminus of the small (S) subunit. The intact C terminus of the S subunit plays a critical role in enabling the efficient assembly of CPMV virions and eVLPs, but undergoes proteolysis after particle formation. In addition, we report the results of mass spectrometry-based proteomics analysis of coat protein subunits from CPMV eVLPs and virions that identify the C termini of S subunits undergo proteolytic cleavages at multiple sites instead of a single cleavage site as previously observed. PMID:27021160

Molecular Dynamics Study on Nucleation Behavior and Lamellar Mergence of Polyethylene Globule Crystallization

NASA Astrophysics Data System (ADS)

Yang, Xiaozhen; Wang, Simiao

2012-02-01

The site order parameter (SOP) has been adopted to analyze various order structure formation and distribution during the crystallization of a multi-chain polyethylene globule simulated by molecular dynamics. We found that the nucleation relies on crystallinity fluctuation with increase of amplitude, and the baby nucleus in the fluctuation suddenly appears with different shape and increasing size. In the growth stage, a number of lamellar mergence was observed and their selective behaviors were suggested to be related to the orientation difference between the merging lamellae. We obtained that SOP distribution of all atoms in the system during crystallization appears with two peaks: one for the amorphous phase and the other for the crystalline phase. Mesomorphic structures with medium orders locate between the two peaks as an order promotion pathway. Obtained data show that the medium order structure fluctuates at the growth front and does not always be available; the medium order structure existing at the front is not always good for developing. It is possibly caused by chain entanglement.

Synthesis and temperature dependent Raman studies of large crystalline faces topological GeBi4Te7 single crystal

NASA Astrophysics Data System (ADS)

Mal, Priyanath; Bera, G.; Turpu, G. R.; Srivastava, Sunil K.; Das, Pradip

2018-05-01

We present a study of structural and vibrational properties of topological insulator GeBi4Te7. Modified Bridgeman technique is employed to synthesize the single crystal with relatively large crystalline faces. Sharp (0 0 l) reflection confirms the high crystallinity of the single crystal. We have performed temperature dependent Raman measurement for both parallel and perpendicular to crystallographic c axis geometry. In parallel configuration we have observed seven Raman modes whereas in perpendicular geometry only four of these are identified. Appearance and disappearance of Raman modes having different intensities for parallel and perpendicular to c measurement attribute to the mode polarization. Progressive blue shift is observed with lowering temperature, reflects the increase in internal stress.

Opal-based photonic crystal with double photonic bandgap structure

NASA Astrophysics Data System (ADS)

Romanov, S. G.; Yates, H. M.; Pemble, M. E.; DeLa Rue, R. M.

2000-09-01

The interior surfaces of one part of a piece of artificial opal have been coated with GaP so that the remaining part of the opal crystal remains empty, thus forming a photonic heterostructure. Two Bragg resonances have been observed in the optical transmission and reflectance spectra. These two resonances were found to behave differently with changes in the polarization of the incident light and the angle of propagation of the light with respect to the (111) planes of opal. Depolarization of the light was observed to occur most effectively at frequencies within the stop-bands, apparently due to the re-coupling of the propagating electromagnetic wave to a different system of eigenmodes when it crosses the interface separating two parts of the double photonic crystal.

The three-dimensional structure of diaminopimelate decarboxylase from Mycobacterium tuberculosis reveals a tetrameric enzyme organisation.

PubMed

Weyand, Simone; Kefala, Georgia; Svergun, Dmitri I; Weiss, Manfred S

2009-09-01

The three-dimensional structure of the enzyme diaminopimelate decarboxylase from Mycobacterium tuberculosis has been determined in a new crystal form and refined to a resolution of 2.33 A. The monoclinic crystals contain one tetramer exhibiting D(2)-symmetry in the asymmetric unit. The tetramer exhibits a donut-like structure with a hollow interior. All four active sites are accessible only from the interior of the tetrameric assembly. Small-angle X-ray scattering indicates that in solution the predominant oligomeric species of the protein is a dimer, but also that higher oligomers exist at higher protein concentrations. The observed scattering data are best explained by assuming a dimer-tetramer equilibrium with about 7% tetramers present in solution. Consequently, at the elevated protein concentrations in the crowded environment inside the cell the observed tetramer may constitute the biologically relevant functional unit of the enzyme.

Crystal Structure of the Catalytic Domain of Drosophila [beta]1,4-Galactosyltransferase-7

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ramakrishnan, Boopathy; Qasba, Pradman K.

2010-11-03

The {beta}1,4-galactosyltransferase-7 ({beta}4Gal-T7) enzyme, one of seven members of the {beta}4Gal-T family, transfers in the presence of manganese Gal from UDP-Gal to an acceptor sugar (xylose) that is attached to a side chain hydroxyl group of Ser/Thr residues of proteoglycan proteins. It exhibits the least protein sequence similarity with the other family members, including the well studied family member {beta}4Gal-T1, which, in the presence of manganese, transfers Gal from UDP-Gal to GlcNAc. We report here the crystal structure of the catalytic domain of {beta}4Gal-T7 from Drosophila in the presence of manganese and UDP at 1.81 {angstrom} resolution. In the crystalmore » structure, a new manganese ion-binding motif (HXH) has been observed. Superposition of the crystal structures of {beta}4Gal-T7 and {beta}4Gal-T1 shows that the catalytic pocket and the substrate-binding sites in these proteins are similar. Compared with GlcNAc, xylose has a hydroxyl group (instead of an N-acetyl group) at C2 and lacks the CH{sub 2}OH group at C5; thus, these protein structures show significant differences in their acceptor-binding site. Modeling of xylose in the acceptor-binding site of the {beta}4Gal-T7 crystal structure shows that the aromatic side chain of Tyr{sup 177} interacts strongly with the C5 atom of xylose, causing steric hindrance to any additional group at C5. Because Drosophila Cd7 has a 73% protein sequence similarity to human Cd7, the present crystal structure offers a structure-based explanation for the mutations in human Cd7 that have been linked to Ehlers-Danlos syndrome.« less

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bugaris, Daniel E.; Malliakas, Christos D.; Han, Fei

A new polymorph of the RE 2Ru 3Ge 5 (RE = Pr, Sm, Dy) compounds has been grown as single crystals via an indium flux. These compounds crystallize in tetragonal space group P4/mnc with the Sc 2Fe 3Si 5-type structure, having lattice parameters a = 11.020(2) Å and c = 5.853(1) Å for RE = Pr, a = 10.982(2) Å and c = 5.777(1) Å for RE = Sm, and a = 10.927(2) Å and c = 5.697(1) Å for RE = Dy. These materials exhibit a structural transition at low temperature, which is attributed to an apparent charge densitymore » wave (CDW). Both the high-temperature average crystal structure and the low-temperature incommensurately modulated crystal structure (for Sm 2Ru 3Ge 5 as a representative) have been solved. The charge density wave order is manifested by periodic distortions of the onedimensional zigzag Ge chains. From X-ray diffraction, charge transport (electrical resistivity, Hall effect, magnetoresistance), magnetic measurements, and heat capacity, the ordering temperatures (T CDW) observed in the Pr and Sm analogues are ~200 and ~175 K, respectively. The charge transport measurement results indicate an electronic state transition happening simultaneously with the CDW transition. X-ray absorption near-edge spectroscopy (XANES) and electronic band structure results are also reported.« less

Conformational Changes and Substrate Recognition in Pseudomonas aeruginosa d-Arginine Dehydrogenase

DOE Office of Scientific and Technical Information (OSTI.GOV)

Fu, Guoxing; Yuan, Hongling; Li, Congran

2010-11-15

DADH catalyzes the flavin-dependent oxidative deamination of D-amino acids to the corresponding {alpha}-keto acids and ammonia. Here we report the first X-ray crystal structures of DADH at 1.06 {angstrom} resolution and its complexes with iminoarginine (DADH{sub red}/iminoarginine) and iminohistidine (DADH{sub red}/iminohistidine) at 1.30 {angstrom} resolution. The DADH crystal structure comprises an unliganded conformation and a product-bound conformation, which is almost identical to the DADH{sub red}/iminoarginine crystal structure. The active site of DADH was partially occupied with iminoarginine product (30% occupancy) that interacts with Tyr53 in the minor conformation of a surface loop. This flexible loop forms an 'active site lid',more » similar to those seen in other enzymes, and may play an essential role in substrate recognition. The guanidinium side chain of iminoarginine forms a hydrogen bond interaction with the hydroxyl of Thr50 and an ionic interaction with Glu87. In the structure of DADH in complex with iminohistidine, two alternate conformations were observed for iminohistidine where the imidazole groups formed hydrogen bond interactions with the side chains of His48 and Thr50 and either Glu87 or Gln336. The different interactions and very distinct binding modes observed for iminoarginine and iminohistidine are consistent with the 1000-fold difference in k{sub cat}/K{sub m} values for D-arginine and D-histidine. Comparison of the kinetic data for the activity of DADH on different D-amino acids and the crystal structures in complex with iminoarginine and iminohistidine establishes that this enzyme is characterized by relatively broad substrate specificity, being able to oxidize positively charged and large hydrophobic D-amino acids bound within a flask-like cavity.« less

Structural Properties, Order–Disorder Phenomena, and Phase Stability of Orotic Acid Crystal Forms

PubMed Central

2016-01-01

Orotic acid (OTA) is reported to exist in the anhydrous (AH), monohydrate (Hy1), and dimethyl sulfoxide monosolvate (SDMSO) forms. In this study we investigate the (de)hydration/desolvation behavior, aiming at an understanding of the elusive structural features of anhydrous OTA by a combination of experimental and computational techniques, namely, thermal analytical methods, gravimetric moisture (de)sorption studies, water activity measurements, X-ray powder diffraction, spectroscopy (vibrational, solid-state NMR), crystal energy landscape, and chemical shift calculations. The Hy1 is a highly stable hydrate, which dissociates above 135 °C and loses only a small part of the water when stored over desiccants (25 °C) for more than one year. In Hy1, orotic acid and water molecules are linked by strong hydrogen bonds in nearly perfectly planar arranged stacked layers. The layers are spaced by 3.1 Å and not linked via hydrogen bonds. Upon dehydration the X-ray powder diffraction and solid-state NMR peaks become broader, indicating some disorder in the anhydrous form. The Hy1 stacking reflection (122) is maintained, suggesting that the OTA molecules are still arranged in stacked layers in the dehydration product. Desolvation of SDMSO, a nonlayer structure, results in the same AH phase as observed upon dehydrating Hy1. Depending on the desolvation conditions, different levels of order–disorder of layers present in anhydrous OTA are observed, which is also suggested by the computed low energy crystal structures. These structures provide models for stacking faults as intergrowth of different layers is possible. The variability in anhydrate crystals is of practical concern as it affects the moisture dependent stability of AH with respect to hydration. PMID:26741914

Prediction of Ordered Water Molecules in Protein Binding Sites from Molecular Dynamics Simulations: The Impact of Ligand Binding on Hydration Networks.

PubMed

Rudling, Axel; Orro, Adolfo; Carlsson, Jens

2018-02-26

Water plays a major role in ligand binding and is attracting increasing attention in structure-based drug design. Water molecules can make large contributions to binding affinity by bridging protein-ligand interactions or by being displaced upon complex formation, but these phenomena are challenging to model at the molecular level. Herein, networks of ordered water molecules in protein binding sites were analyzed by clustering of molecular dynamics (MD) simulation trajectories. Locations of ordered waters (hydration sites) were first identified from simulations of high resolution crystal structures of 13 protein-ligand complexes. The MD-derived hydration sites reproduced 73% of the binding site water molecules observed in the crystal structures. If the simulations were repeated without the cocrystallized ligands, a majority (58%) of the crystal waters in the binding sites were still predicted. In addition, comparison of the hydration sites obtained from simulations carried out in the absence of ligands to those identified for the complexes revealed that the networks of ordered water molecules were preserved to a large extent, suggesting that the locations of waters in a protein-ligand interface are mainly dictated by the protein. Analysis of >1000 crystal structures showed that hydration sites bridged protein-ligand interactions in complexes with different ligands, and those with high MD-derived occupancies were more likely to correspond to experimentally observed ordered water molecules. The results demonstrate that ordered water molecules relevant for modeling of protein-ligand complexes can be identified from MD simulations. Our findings could contribute to development of improved methods for structure-based virtual screening and lead optimization.

Antiferromagnetism in the van der Waals layered spin-lozenge semiconductor CrTe 3

DOE PAGES

McGuire, Michael A.; Garlea, V. Ovidiu; KC, Santosh; ...

2017-04-14

We have investigated the crystallographic, magnetic, and transport properties of the van der Waals bonded, layered compound CrTe 3 on single-crystal and polycrystalline materials. Furthermore, the crystal structure contains layers made up of lozenge-shaped Cr 4 tetramers. Electrical resistivity measurements show the crystals to be semiconducting, with a temperature dependence consistent with a band gap of 0.3 eV. The magnetic susceptibility exhibits a broad maximum near 300 K characteristic of low dimensional magnetic systems. Weak anomalies are observed in the susceptibility and heat capacity near 55 K, and single-crystal neutron diffraction reveals the onset of long-range antiferromagnetic order at thismore » temperature. Strongly dispersive spin waves are observed in the ordered state. Significant magnetoelastic coupling is indicated by the anomalous temperature dependence of the lattice parameters and is evident in structural optimization in van der Waals density functional theory calculations for different magnetic configurations. The cleavability of the compound is apparent from its handling and is confirmed by first-principles calculations, which predict a cleavage energy 0.5 J / m 2 , similar to graphite. Based on our results, CrTe 3 is identified as a promising compound for studies of low dimensional magnetism in bulk crystals as well as magnetic order in monolayer materials and van der Waals heterostructures.« less

Antiferromagnetism in the van der Waals layered spin-lozenge semiconductor CrTe 3

DOE Office of Scientific and Technical Information (OSTI.GOV)

McGuire, Michael A.; Garlea, V. Ovidiu; KC, Santosh

We have investigated the crystallographic, magnetic, and transport properties of the van der Waals bonded, layered compound CrTe 3 on single-crystal and polycrystalline materials. Furthermore, the crystal structure contains layers made up of lozenge-shaped Cr 4 tetramers. Electrical resistivity measurements show the crystals to be semiconducting, with a temperature dependence consistent with a band gap of 0.3 eV. The magnetic susceptibility exhibits a broad maximum near 300 K characteristic of low dimensional magnetic systems. Weak anomalies are observed in the susceptibility and heat capacity near 55 K, and single-crystal neutron diffraction reveals the onset of long-range antiferromagnetic order at thismore » temperature. Strongly dispersive spin waves are observed in the ordered state. Significant magnetoelastic coupling is indicated by the anomalous temperature dependence of the lattice parameters and is evident in structural optimization in van der Waals density functional theory calculations for different magnetic configurations. The cleavability of the compound is apparent from its handling and is confirmed by first-principles calculations, which predict a cleavage energy 0.5 J / m 2 , similar to graphite. Based on our results, CrTe 3 is identified as a promising compound for studies of low dimensional magnetism in bulk crystals as well as magnetic order in monolayer materials and van der Waals heterostructures.« less