[Fine stereo structure for natural organic molecules, a preliminary study. II. Melting point influenced by structure factors].

PubMed

Lu, Y; Zheng, Q; Lu, D; Ma, P; Chen, Y

1995-06-01

Crystal structures of two compounds from Tripterygium wilfordii Hook f. have been determined by X-ray diffraction method. Structure factors influencing melting point of solid state have been analysed. Crystal class (or space group), recrystallization solvent, force between molecules and fine changes of molecular structures will all cause melting point changes of crystal substance.

Crystal engineering of ibuprofen compounds: From molecule to crystal structure to morphology prediction by computational simulation and experimental study

NASA Astrophysics Data System (ADS)

Zhang, Min; Liang, Zuozhong; Wu, Fei; Chen, Jian-Feng; Xue, Chunyu; Zhao, Hong

2017-06-01

We selected the crystal structures of ibuprofen with seven common space groups (Cc, P21/c, P212121, P21, Pbca, Pna21, and Pbcn), which was generated from ibuprofen molecule by molecular simulation. The predicted crystal structures of ibuprofen with space group P21/c has the lowest total energy and the largest density, which is nearly indistinguishable with experimental result. In addition, the XRD patterns for predicted crystal structure are highly consistent with recrystallization from solvent of ibuprofen. That indicates that the simulation can accurately predict the crystal structure of ibuprofen from the molecule. Furthermore, based on this crystal structure, we predicted the crystal habit in vacuum using the attachment energy (AE) method and considered solvent effects in a systematic way using the modified attachment energy (MAE) model. The simulation can accurately construct a complete process from molecule to crystal structure to morphology prediction. Experimentally, we observed crystal morphologies in four different polarity solvents compounds (ethanol, acetonitrile, ethyl acetate, and toluene). We found that the aspect ratio decreases of crystal habits in this ibuprofen system were found to vary with increasing solvent relative polarity. Besides, the modified crystal morphologies are in good agreement with the observed experimental morphologies. Finally, this work may guide computer-aided design of the desirable crystal morphology.

Prediction and theoretical characterization of p-type organic semiconductor crystals for field-effect transistor applications.

PubMed

Atahan-Evrenk, Sule; Aspuru-Guzik, Alán

2014-01-01

The theoretical prediction and characterization of the solid-state structure of organic semiconductors has tremendous potential for the discovery of new high performance materials. To date, the theoretical analysis mostly relied on the availability of crystal structures obtained through X-ray diffraction. However, the theoretical prediction of the crystal structures of organic semiconductor molecules remains a challenge. This review highlights some of the recent advances in the determination of structure-property relationships of the known organic semiconductor single-crystals and summarizes a few available studies on the prediction of the crystal structures of p-type organic semiconductors for transistor applications.

Synthesis, crystal structure, NLO and Hirshfeld surface analysis of 1,2,3-triazolyl chalcone single crystal

NASA Astrophysics Data System (ADS)

Shruthi, C.; Ravindrachary, V.; Guruswamy, B.; Lokanath, N. K.; Kumara, Karthik; Goveas, Janet

2018-05-01

Needle shaped brown coloured single crystal of the title compound was grown by slow evaporation technique using methanol as solvent. The grown crystal was characterized using FT-IR, Single crystal XRD, UV-visible and NLO studies. Crystal structure was confirmed by FT-IR study and the functional groups were identified. XRD study reveals that the crystal belongs to orthorhombic crystal system with pnaa space group and the corresponding cell parameters were calculated. UV-visible spectrum shows that the crystal is transparent in the entire visible region and absorption takes place in the UV-range. NLO efficiency of the crystal obtained 0.66 times that of urea was determined by SHG test. The intermolecular interaction and percentage contribution of each individual atom in the crystal lattice was quantized using Hirshfeld surface and 2D finger print analysis.

Crystals of Janus colloids at various interaction ranges

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

Preisler, Z.; Soft Condensed Matter, Debye Institute for Nanomaterials Science, Utrecht University, Princetonplein 5, 3584 CC Utrecht; Vissers, T.

We investigate the effect of interaction range on the phase behaviour of Janus particles with a Kern-Frenkel potential. Specifically, we study interaction ranges Δ = 0.1σ, 0.3σ, 0.4σ, 0.5σ with σ the particle diameter, and use variable box shape simulations to predict crystal structures. We found that changing the interaction range beyond 0.2σ drastically increases the variety of possible crystal structures. In addition to close-packed structures, we find body-centered tetragonal and AA-stacked hexagonal crystals, as well as several lamellar crystals. For long interaction ranges and low temperatures, we also observe an extremely large number of metastable structures which compete withmore » the thermodynamically stable ones. These competing structures hinder the detection of the lowest-energy crystal structures, and are also likely to interfere with the spontaneous formation of the ground-state structure. Finally, we determine the gas-liquid coexistence curves for several interaction ranges, and observe that these are metastable with respect to crystallization.« less

Crystal growth, spectral, structural and optical studies of π-conjugated stilbazolium crystal: 4-bromobenzaldehyde-4'-N'-methylstilbazolium tosylate.

PubMed

Krishna Kumar, M; Sudhahar, S; Bhagavannarayana, G; Mohan Kumar, R

2014-05-05

Nonlinear optical (NLO) organic compound, 4-bromobenzaldehyde-4'-N'-methylstilbazolium tosylate was synthesized by reflux method. The formation of molecular complex was confirmed from (1)H NMR, FT-IR and FT-Raman spectral analyses. The single crystals were grown by slow evaporation solution growth method and the crystal structure and atomic packing of grown crystal was identified. The morphology and growth axis of grown crystal were determined. The crystal perfection was analyzed using high resolution X-ray diffraction study on (001) plane. Thermal stability, decomposition stages and melting point of the grown crystal were analyzed. The optical absorption coefficient (α) and energy band gap (E(g)) of the crystal were determined using UV-visible absorption studies. Second harmonic generation efficiency of the grown crystal was examined by Kurtz powder method with different particle size using 1064 nm laser. Laser induced damage threshold study was carried out for the grown crystal using Nd:YAG laser. Copyright © 2014 Elsevier B.V. All rights reserved.

Synthesis, growth, structural, spectroscopic and optical studies of a semiorganic NLO crystal: zinc guanidinium phosphate.

PubMed

Suvitha, A; Murugakoothan, P

2012-02-01

The semi-organic nonlinear optical (NLO) crystal, zinc guanidinium phosphate (ZGuP) has been grown through synthesis between zinc sulphate, guanidine carbonate and orthophosphoric acid from its aqueous solution by slow solvent evaporation technique. Solubility of the synthesized material has been determined for various temperatures using water as solvent. The grown crystal has been characterized by powder X-ray diffraction to confirm the crystal structure. Investigation has been carried out to assign the vibrational frequencies of the grown crystals by Fourier transform infrared spectroscopy technique. (1)H and (13)C FT-NMR have been recorded to elucidate the molecular structure. The optical absorption study confirms the suitability of the crystal for device applications. The second harmonic generation (SHG) efficiency of ZGuP is found to be 1.825 times that of potassium dihydrogen phosphate (KDP). Thermal behavior of the grown crystals has been studied by thermogravimetric and differential thermal analysis. The mechanical properties of the grown crystals have been studied using Vickers microhardness tester. Copyright © 2011 Elsevier B.V. All rights reserved.

Deducing 2D crystal structure at the liquid/solid interface with atomic resolution: a combined STM and SFG study.

PubMed

McClelland, Arthur A; Ahn, Seokhoon; Matzger, Adam J; Chen, Zhan

2009-11-17

Sum frequency generation vibrational spectroscopy (SFG) has been applied to study two-dimensional (2D) crystals formed by an isophthalic acid diester on the surface of highly oriented pyrolytic graphite, providing complementary measurements to scanning tunneling microscopy (STM) and computational modeling. SFG results indicate that both aromatic and C=O groups in the 2D crystal tilt from the surface. This study demonstrates that a combination of SFG and STM techniques can be used to gain a more complete picture of 2D crystal structure, and it is necessary to consider solvent-2D crystal interactions and dynamics in the computer models to achieve an accurate representation of interfacial structure.

Studies on the syntheses, structural Characterization, antimicrobial of the CO-CRYSTAL 1,10-phenanthrolin-1-IUM(1,10-phenH+)-caffeine(caf)-hexafluorophosphate

NASA Astrophysics Data System (ADS)

El Hamdani, H.; El Amane, M.; Duhayon, C.

2018-03-01

Co-crystal of 1,10-phenanthrolin-1-ium-caffeine-hexafluorophosphate was synthesized, studied by FTIR, 1H, 13C NMR, DSC and X-ray structure and crystallized in the monoclinic space group C2/c. The unit cell parameters are a = 19.3761 (3), b = 17.9548 (3), c = 13.8074 (3) with β = 117.8132 (10). The final R value is 0.069 for 29,522 measured reflections. The co-crystal structure analysis indicate the 1,10-phenanthroline is protonated by one nitrogen atom and formed the 1,10-phenanthrolin-1-ium cation, which is stabilized by hydrogen bonds N+-H…Odbnd C interaction with carbonyl and imidazol ring in caffeine molecule. The intermolecular hydrogen bonds: Csbnd H...O, Csbnd H...N, Nsbnd H...O, Csbnd H...F and intramolecular hydrogen bond: C1sbnd H12...O14, together play a vital role in stabilizing the structure of co-crystal. The X-ray structural analysis confirm the assignments of the structure from infrared, 1H, 13C NMR, spectroscopic data DSC and molar conductivity analysis. The antimicrobial activity of the co-crystal was studied.

Macromolecular Crystallization in Microgravity

NASA Technical Reports Server (NTRS)

Snell, Edward H.; Helliwell, John R.

2004-01-01

The key concepts that attracted crystal growers, macromolecular or solid state, to microgravity research is that density difference fluid flows and sedimentation of the growing crystals are greatly reduced. Thus, defects and flaws in the crystals can be reduced, even eliminated, and crystal volume can be increased. Macromolecular crystallography differs from the field of crystalline semiconductors. For the latter, crystals are harnessed for their electrical behaviors. A crystal of a biological macromolecule is used instead for diffraction experiments (X-ray or neutron) to determine the three-dimensional structure of the macromolecule. The better the internal order of the crystal of a biological macromolecule then the more molecular structure detail that can be extracted. This structural information that enables an understanding of how the molecule functions. This knowledge is changing the biological and chemical sciences with major potential in understanding disease pathologies. Macromolecular structural crystallography in general is a remarkable field where physics, biology, chemistry, and mathematics meet to enable insight to the basic fundamentals of life. In this review, we examine the use of microgravity as an environment to grow macromolecular crystals. We describe the crystallization procedures used on the ground, how the resulting crystals are studied and the knowledge obtained from those crystals. We address the features desired in an ordered crystal and the techniques used to evaluate those features in detail. We then introduce the microgravity environment, the techniques to access that environment, and the theory and evidence behind the use of microgravity for crystallization experiments. We describe how ground-based laboratory techniques have been adapted to microgravity flights and look at some of the methods used to analyze the resulting data. Several case studies illustrate the physical crystal quality improvements and the macromolecular structural advances. Finally, limitations and alternatives to microgravity and future directions for this research are covered.

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.

[Crystal structure of SMU.2055 protein from Streptococcus mutans and its small molecule inhibitors design and selection].

PubMed

Xiaodan, Chen; Xiurong, Zhan; Xinyu, Wu; Chunyan, Zhao; Wanghong, Zhao

2015-04-01

The aim of this study is to analyze the three-dimensional crystal structure of SMU.2055 protein, a putative acetyltransferase from the major caries pathogen Streptococcus mutans (S. mutans). The design and selection of the structure-based small molecule inhibitors are also studied. The three-dimensional crystal structure of SMU.2055 protein was obtained by structural genomics research methods of gene cloning and expression, protein purification with Ni²⁺-chelating affinity chromatography, crystal screening, and X-ray diffraction data collection. An inhibitor virtual model matching with its target protein structure was set up using computer-aided drug design methods, virtual screening and fine docking, and Libdock and Autodock procedures. The crystal of SMU.2055 protein was obtained, and its three-dimensional crystal structure was analyzed. This crystal was diffracted to a resolution of 0.23 nm. It belongs to orthorhombic space group C222(1), with unit cell parameters of a = 9.20 nm, b = 9.46 nm, and c = 19.39 nm. The asymmetric unit contained four molecules, with a solvent content of 56.7%. Moreover, five small molecule compounds, whose structure matched with that of the target protein in high degree, were designed and selected. Protein crystallography research of S. mutans SMU.2055 helps to understand the structures and functions of proteins from S. mutans at the atomic level. These five compounds may be considered as effective inhibitors to SMU.2055. The virtual model of small molecule inhibitors we built will lay a foundation to the anticaries research based on the crystal structure of proteins.

Identifying, studying and making good use of macromolecular crystals

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

Calero, Guillermo; Cohen, Aina E.; Luft, Joseph R.

2014-07-25

As technology advances, the crystal volume that can be used to collect useful X-ray diffraction data decreases. The technologies available to detect and study growing crystals beyond the optical resolution limit and methods to successfully place the crystal into the X-ray beam are discussed. Structural biology has contributed tremendous knowledge to the understanding of life on the molecular scale. The Protein Data Bank, a depository of this structural knowledge, currently contains over 100 000 protein structures, with the majority stemming from X-ray crystallography. As the name might suggest, crystallography requires crystals. As detectors become more sensitive and X-ray sources moremore » intense, the notion of a crystal is gradually changing from one large enough to embellish expensive jewellery to objects that have external dimensions of the order of the wavelength of visible light. Identifying these crystals is a prerequisite to their study. This paper discusses developments in identifying these crystals during crystallization screening and distinguishing them from other potential outcomes. The practical aspects of ensuring that once a crystal is identified it can then be positioned in the X-ray beam for data collection are also addressed.« less

Identifying, studying and making good use of macromolecular crystals

PubMed Central

Calero, Guillermo; Cohen, Aina E.; Luft, Joseph R.; Newman, Janet; Snell, Edward H.

2014-01-01

Structural biology has contributed tremendous knowledge to the understanding of life on the molecular scale. The Protein Data Bank, a depository of this structural knowledge, currently contains over 100 000 protein structures, with the majority stemming from X-ray crystallography. As the name might suggest, crystallography requires crystals. As detectors become more sensitive and X-ray sources more intense, the notion of a crystal is gradually changing from one large enough to embellish expensive jewellery to objects that have external dimensions of the order of the wavelength of visible light. Identifying these crystals is a prerequisite to their study. This paper discusses developments in identifying these crystals during crystallization screening and distinguishing them from other potential outcomes. The practical aspects of ensuring that once a crystal is identified it can then be positioned in the X-ray beam for data collection are also addressed. PMID:25084371

Synthesis, crystal growth, structural, thermal, optical and mechanical properties of solution grown 4-methylpyridinium 4-hydroxybenzoate single crystal.

PubMed

Sudhahar, S; Krishna Kumar, M; Sornamurthy, B M; Mohan Kumar, R

2014-01-24

Organic nonlinear optical material, 4-methylpyridinium 4-hydroxybenzoate (4MPHB) was synthesized and single crystal was grown by slow evaporation solution growth method. Single crystal and powder X-ray diffraction analyses confirm the structure and crystalline perfection of 4MPHB crystal. Infrared, Raman and NMR spectroscopy techniques were used to elucidate the functional groups present in the compound. TG-DTA analysis was carried out in nitrogen atmosphere to study the decomposition stages, endothermic and exothermic reactions. UV-visible and Photoluminescence spectra were recorded for the grown crystal to estimate the transmittance and band gap energy respectively. Linear refractive index, birefringence, and SHG efficiency of the grown crystal were studied. Laser induced surface damage threshold and mechanical properties of grown crystal were studied to assess the suitability of the grown crystals for device applications. Copyright © 2013 Elsevier B.V. All rights reserved.

Structural, optical, mechanical and dielectric studies of pure and doped L-Prolinium trichloroacetate single crystals.

PubMed

Renuka, N; Ramesh Babu, R; Vijayan, N; Vasanthakumar, Geetha; Krishna, Anuj; Ramamurthi, K

2015-02-25

In the present work, pure and metal substituted L-Prolinium trichloroacetate (LPTCA) single crystals were grown by slow evaporation method. The grown crystals were subjected to single crystal X-ray diffraction (XRD), powder X-ray diffraction, FTIR, UV-Visible-NIR, hardness, photoluminescence and dielectric studies. The dopant concentration in the crystals was measured by inductively coupled plasma (ICP) analysis. Single crystal X-ray diffraction studies of the pure and metal substituted LPTCA revealed that the grown crystals belong to the trigonal system. Ni(2+) and Co(2+) doping slightly altered the lattice parameters of LPTCA without affecting the basic structure of the crystal. FTIR spectral analysis confirms the presence of various functional groups in the grown crystals. The mechanical behavior of pure and doped crystals was analyzed by Vickers's microhardness test. The optical transmittance, dielectric and photoluminescence properties of the pure and doped crystals were analyzed. Copyright © 2014 Elsevier B.V. All rights reserved.

The Effect of Acidity Coefficient on Crystallization Behavior of Blast Furnace Slag Fibers

NASA Astrophysics Data System (ADS)

Tian, Tie-Lei; Zhang, Yu-Zhu; Xing, Hong-wei; Li, Jie; Zhang, Zun-Qian

2018-01-01

The chemical structure of mineral wool fiber was investigated by using Fourier Transform Infrared Spectroscopy (FTIR). Next, the glass transition temperature and the crystallization temperature of the fibers were studied. Finally, the crystallization kinetics of fiber was studied. The results show that the chemical bond structure of fibers gets more random with the increase of acidity coefficient. The crystallization phases of the fibers are mainly melilites, and also a few anorthites and diopsides. The growth mechanism of the crystals is three dimensional. The fibers with acidity coefficient of 1.2 exhibit the best thermal stability and is hard to crystallize as it has the maximum aviation energy of crystallization kinetics.

Crystal growth of enzymes in low gravity (L-5)

NASA Technical Reports Server (NTRS)

Morita, Yuhei

1993-01-01

Recent developments in protein engineering have expanded the possibilities of studies of enzymes and other proteins. Now such studies are not limited to the elucidation of the relationship between the structure and function of the protein. They also aim at the production of proteins with new and practical functions, based on results obtained during investigation of structure and function. For continuing research in this field, investigation of the tertiary structure of proteins is important. X-ray diffraction of single crystals of protein is usually used for this purpose. The main difficulty is the preparation of the crystals. The theme of the research is to prepare such crystals at very low gravity, with the main purpose being to obtain large single crystals of proteins suitable for x-ray diffraction studies.

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.

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.

Structural, mechanical, electrical and optical properties of a new lithium boro phthalate NLO crystal synthesized by a slow evaporation method

NASA Astrophysics Data System (ADS)

Mohanraj, K.; Balasubramanian, D.; Jhansi, N.

2017-11-01

A new non-linear optical (NLO) single crystal of lithium boro phthalate (LiBP) was grown by slow solvent evaporation technique. The powder sample was subjected to powder X-ray diffraction (PXRD) to find its crystalline nature and the crystal structure of the grown crystal was determined using single crystal X-ray (SXRD) diffraction analysis. The Fourier Transform Infrared (FTIR) spectrum was recorded for grown crystal to identify the various functional groups present in the compound. The mechanical property of the LiBP single crystal was studied using Vickers microhardness tester. The dielectric constant and dielectric loss measurements were carried out for the grown crystal at various temperatures. The grown crystal was subjected to UV-Visible Spectral Studies to analyze the linear optical behavior of the grown crystal. The Kurtz-Perry Powder technique was employed to measure the Second Harmonic Generation efficiency of the grown crystal.

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.

Solvent effects on the crystal growth structure and morphology of the pharmaceutical dirithromycin

NASA Astrophysics Data System (ADS)

Wang, Yuan; Liang, Zuozhong

2017-12-01

Solvent effects on the crystal structure and morphology of pharmaceutical dirithromycin molecules were systematically investigated using both experimental crystallization and theoretical simulation. Dirithromycin is one of the new generation of macrolide antibiotics with two polymorphic forms (Form I and Form II) and many solvate forms. Herein, six solvates of the dirithromycin, including acetonitrile, acetonitrile/water, acetone, 1-propanol, N,N-dimethylformamide (DMF) and cyclohexane, were studied. Experimentally, we crystallized the dirithromycin molecules in different solvents by the solvent evaporating method and measured the crystal structures with the X-ray diffraction (XRD). We compared these crystal structures of dirithromycin solvates and analyzed the solvent property-determined structure evolution. The solvents have a strong interaction with the dirithromycin molecule due to the formation of inter-molecular interactions (such as the hydrogen bonding and close contacts (sum of vdW radii)). Theoretically, we calculated the ideal crystal habit based on the solvated structures with the attachment growth (AE) model. The predicted morphologies and aspect ratios of dirithromycin solvates agree well with the experimental results. This work could be helpful to better understand the structure and morphology evolution of solvates controlled by solvents and guide the crystallization of active pharmaceutical ingredients in the pharmaceutical industry.

Crystal growth, structure analysis and characterisation of 2 - (1, 3 - dioxoisoindolin - 2 - yl) acetic acid single crystal

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

Sankari, R. Siva, E-mail: sivasankari.sh@act.edu.in; Perumal, Rajesh Narayana

2014-04-24

Single crystal of dielectric material 2 - (1, 3 - dioxoisoindolin - 2 - yl) acetic acid has been grown by slow evaporation solution growth method. The grown crystal was harvested in 25 days. The crystal structure was analyzed by Single crystal X - ray diffraction. UV-vis-NIR analysis was performed to examine the optical property of the grown crystal. The thermal property of the grown crystal was studied by thermogravimetric analysis (TGA) and differential thermal analysis (DTA). The dielectric measurements were carried out and the dielectric constant was calculated and plotted at all frequencies.

Structural properties of a family of hydrogen-bonded co-crystals formed between gemfibrozil and hydroxy derivatives of t-butylamine, determined directly from powder X-ray diffraction data

NASA Astrophysics Data System (ADS)

Cheung, Eugene Y.; David, Sarah E.; Harris, Kenneth D. M.; Conway, Barbara R.; Timmins, Peter

2007-03-01

We report the formation and structural properties of co-crystals containing gemfibrozil and hydroxy derivatives of t-butylamine H 2NC(CH 3) 3-n(CH 2OH) n, with n=0, 1, 2 and 3. In each case, a 1:1 co-crystal is formed, with transfer of a proton from the carboxylic acid group of gemfibrozil to the amino group of the t-butylamine derivative. All of the co-crystal materials prepared are polycrystalline powders, and do not contain single crystals of suitable size and/or quality for single crystal X-ray diffraction studies. Structure determination of these materials has been carried out directly from powder X-ray diffraction data, using the direct-space Genetic Algorithm technique for structure solution followed by Rietveld refinement. The structural chemistry of this series of co-crystal materials reveals well-defined structural trends within the first three members of the family ( n=0, 1, 2), but significantly contrasting structural properties for the member with n=3.

A scanning electron microscopy study of the macro-crystalline structure of 2-(2,4-dinitrobenzyl) pyridine

NASA Technical Reports Server (NTRS)

Ware, Jacqueline; Hammond, Ernest C., Jr.

1989-01-01

The compound, 2-(2,4-dinitrobenzyl) pyridine, was synthesized in the laboratory; an introductory level electron microscopy study of the macro-crystalline structure was conducted using the scanning electron microscope (SEM). The structure of these crystals was compared with the macrostructure of the crystal of 2-(2,4-dinitrobenzyl) pyridinium bromide, the hydrobromic salt of the compound which was also synthesized in the laboratory. A scanning electron microscopy crystal study was combined with a study of the principle of the electron microscope.

Correlation of Intermolecular Acyl Transfer Reactivity with Noncovalent Lattice Interactions in Molecular Crystals: Toward Prediction of Reactivity of Organic Molecules in the Solid State.

PubMed

Krishnaswamy, Shobhana; Shashidhar, Mysore S

2018-04-06

Intermolecular acyl transfer reactivity in several molecular crystals was studied, and the outcome of the reactivity was analyzed in the light of structural information obtained from the crystals of the reactants. Minor changes in the molecular structure resulted in significant variations in the noncovalent interactions and packing of molecules in the crystal lattice, which drastically affected the facility of the intermolecular acyl transfer reactivity in these crystals. Analysis of the reactivity vs crystal structure data revealed dependence of the reactivity on electrophile···nucleophile interactions and C-H···π interactions between the reacting molecules. The presence of these noncovalent interactions augmented the acyl transfer reactivity, while their absence hindered the reactivity of the molecules in the crystal. The validity of these correlations allows the prediction of intermolecular acyl transfer reactivity in crystals and co-crystals of unknown reactivity. This crystal structure-reactivity correlation parallels the molecular structure-reactivity correlation in solution-state reactions, widely accepted as organic functional group transformations, and sets the stage for the development of a similar approach for reactions in the solid state.

Structural, quantum chemical, vibrational and thermal studies of a hydrogen bonded zwitterionic co-crystal (nicotinic acid: pyrogallol)

NASA Astrophysics Data System (ADS)

Prabha, E. Arockia Jeya Yasmi; Kumar, S. Suresh; Athimoolam, S.; Sridhar, B.

2017-02-01

In the present work, a new co-crystal of nicotinic acid with pyrogallol (NICPY) has been grown in the zwitterionic form and the corresponding structural, vibrational, thermal, solubility and anti-cancer characteristics have been reported. The single crystal X-ray diffraction analysis confirms that the structural molecular packing of the crystal stabilized through N-H⋯O and O-H⋯O hydrogen bond. The stabilization energy of the hydrogen bond motifs were calculated in the solid state. Vibrational spectral studies such as Fourier transform-infrared (FT-IR) and FT-Raman were adopted to understand the zwitterionic co-crystalline nature of the compound, which has been compared with theoretically calculated vibrational frequencies. The thermal stability of the grown co-crystal was analyzed by TG/DTA study. The solubility of the NICPY co-crystal was investigated in water at different temperature and compared with that of the nicotinic acid, which is the parent compound of NICPY co-crystal. The grown crystals were treated with human cervical cancer cell line (HeLa) to analyze the cytotoxicity of NICPY crystals and compared with the parent compound, which shows that NICPY has moderate activity against human cervical cancer cell line.

Synthesis, growth, structural characterization, Hirshfeld analysis and nonlinear optical studies of a methyl substituted chalcone

NASA Astrophysics Data System (ADS)

Prabhu, Shobha R.; Jayarama, A.; Chandrasekharan, K.; Upadhyaya, V.; Ng, Seik Weng

2017-05-01

A new chalcone compound (2E)-3-(3-methylphenyl)-1-(4-nitrophenyl)prop-2-en-1-one (3MPNP) with molecular formula C16H13NO3 has been synthesized and crystallized by slow solvent evaporation technique. The Fourier transform infrared, Fourier transform Raman and nuclear magnetic resonance techniques were used for structural characterization. UV-visible absorption studies were carried out to study the transparency of the crystal in the visible region. Differential scanning calorimetry study shows thermal stability of crystals up to temperature 122 °C. Single crystal X-ray diffraction and powder X-ray diffraction techniques were used to study crystal structure and cell parameters. The Hirshfeld surface and 2-D fingerprint analysis were performed to study the nature of interactions and their quantitative contributions towards the crystal packing. The third order non-linear optical properties have been studied using single beam Z-scan technique and the results show that the material is a potential candidate for optical device applications such as optical limiters and optical switches.

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.

Investigation of selected structural parameters in Fe 95Si 5 amorphous alloy during crystallization process

NASA Astrophysics Data System (ADS)

Fronczyk, Adam

2007-04-01

In this study, we report on a crystallization behavior of the Fe 95Si 5 metallic glasses using a differential scanning cabrimetry (DSC), and X-ray diffraction. The paper presents the results of experimental investigation of Fe 95Si 5 amorphous alloy, subjected to the crystallizing process by the isothermal annealing. The objective of the experiment was to determine changes in the structural parameters during crystallization process of the examined alloy. Crystalline diameter and the lattice constant of the crystallizing phase were used as parameters to evaluate structural changes in material.

Study of the growth and pyroelectric properties of TGS crystals doped with aniline-family dipolar molecules

NASA Astrophysics Data System (ADS)

Zhang, Kecong; Song, Jiancheng; Wang, Min; Fang, Changshui; Lu, Mengkai

1987-04-01

TGS crystals doped with aniline-family dipolar molecules (aniline, 2-aminobenzoic acid, 3-aminobenzoic acid, 3-aminobenzene-sulphonic acid, 4-aminobenzenesulphonic acid and 4-nitroraniline) have been grown by the slow-cooling solution method. The influence of these dopants on the growth habits, crystal morphology pyroelectric properties, and structure parameters of TGS crystals has been systematically investigated. The effects of the domain structure of the seed crystal on the pyroelectric properties of the doped crystals have been studied. It is found that the spontaneous polarization (P), pyroelectric coefficient (lambda), and internal bias field of the doped crystals are slightly higher than those of the pure TGS, and the larger the dipole moment of the dopant molecule, the higher the P and lambda of the doped TGS crystal.

Hirshfeld surface analyses and crystal structures of supramolecular self-assembly thiourea derivatives directed by non-covalent interactions

NASA Astrophysics Data System (ADS)

Gumus, Ilkay; Solmaz, Ummuhan; Binzet, Gun; Keskin, Ebru; Arslan, Birdal; Arslan, Hakan

2018-04-01

The novel N-(bis(3,5-dimethoxybenzyl)carbamothioyl)-4-R-benzamide (R: H, Cl, CH3 and OCH3) compounds have been synthesized and characterized by FT-IR, 1H NMR and 13C NMR spectroscopy. Their crystal structures were also determined by single-crystal X-ray diffraction studies. Hirshfeld surfaces analysis and their associated two dimensional fingerprint plots of compounds were used as theoretical approach to assess driving force for crystal structure formation via the intermolecular interactions in the crystal lattices of synthesized compounds. The study of X-ray single crystal diffraction and Hirshfeld surfaces analysis of the prepared compounds shows that hydrogen bonding and other weaker interactions such as Nsbnd H⋯S, weak Csbnd H⋯S, Csbnd H⋯O, Csbnd H⋯N and Csbnd H···π intermolecular interactions and π-π stacking, among molecules of synthesized compounds participate in a cooperative way to stabilize the supramolecular structures.

Synthesis, growth, structural, thermal and optical studies of pyrrolidinium-2-carboxylate-4-nitrophenol single crystals.

PubMed

Swarna Sowmya, N; Sampathkrishnan, S; Vidyalakshmi, Y; Sudhahar, S; Mohan Kumar, R

2015-06-15

Organic nonlinear optical material, pyrrolidinium-2-carboxylate-4-nitrophenol (PCN) was synthesized and single crystals were grown by slow evaporation solution growth method. Single crystal X-ray diffraction analysis confirmed the structure and lattice parameters of PCN crystals. Infrared, Raman and NMR spectral analyses were used to elucidate the functional groups present in the compound. The thermal behavior of synthesized compound was studied by thermogravimetric and differential scanning calorimetry (TG-DSC) analyses. The photoluminescence property was studied by exciting the crystal at 360 nm. The relative second harmonic generation (SHG) efficiency of grown crystal was estimated by using Nd:YAG laser with fundamental wavelength of 1,064 nm. Copyright © 2015 Elsevier B.V. All rights reserved.

Study and analysis of filtering characteristics of 1D photonic crystal

NASA Astrophysics Data System (ADS)

Juyal, Rohan; Suthar, Bhuvneshwer; Kumar, Arun

2018-05-01

Propagation of electromagnetic wave have been studied and analyzed through 1D photonic crystal. 1D photonic band gap material with low and high refractive index material has been chosen for this study. Band structure and reflectivity of this 1D structure has been calculated using transmission matrix method (TMM). Study and analysis of the band structure and reflectivity of this structure shows that this structure may work as an optical filter.

Synthesis and structural study of 4-(2-chlorophenyl)-2-ethoxy-5,6,7,8,9,10-hexahydrocycloocta[B]pyridine-3-carbonitrile

NASA Astrophysics Data System (ADS)

Fathima, K. Saiadali; Vasumathi, M.; Anitha, K.

2016-05-01

The novel organic material C20H21ClN2O was synthesized by One-Pot synthesis method and the single crystals were grown by slow evaporation solution growth technique. The crystal structure was elucidated by subjecting the grown crystals to the single crystal x-ray diffraction analysis and was refined by full matrix least-squares method to R=0.039 for 2746 reflections. Crystal system of the grown crystal was found to be monoclinic with the space group P21/a and a=9.196(4) Å, b=13.449(4) Å, c=14.818(4) Å, β= 101.542(3)°, V=1795.6(11) Å3 and Z=4. In this crystal structure, cyclooctanone prefers to reside in a chair-boat conformation. The structure is stabilized by attractive molecular force such as CH/π interaction called hydrophobic interaction.

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.

Clathrate Structure Determination by Combining Crystal Structure Prediction with Computational and Experimental 129Xe NMR Spectroscopy

PubMed Central

Selent, Marcin; Nyman, Jonas; Roukala, Juho; Ilczyszyn, Marek; Oilunkaniemi, Raija; Bygrave, Peter J.; Laitinen, Risto; Jokisaari, Jukka

2017-01-01

Abstract An approach is presented for the structure determination of clathrates using NMR spectroscopy of enclathrated xenon to select from a set of predicted crystal structures. Crystal structure prediction methods have been used to generate an ensemble of putative structures of o‐ and m‐fluorophenol, whose previously unknown clathrate structures have been studied by 129Xe NMR spectroscopy. The high sensitivity of the 129Xe chemical shift tensor to the chemical environment and shape of the crystalline cavity makes it ideal as a probe for porous materials. The experimental powder NMR spectra can be used to directly confirm or reject hypothetical crystal structures generated by computational prediction, whose chemical shift tensors have been simulated using density functional theory. For each fluorophenol isomer one predicted crystal structure was found, whose measured and computed chemical shift tensors agree within experimental and computational error margins and these are thus proposed as the true fluorophenol xenon clathrate structures. PMID:28111848

Powder diffraction and crystal structure prediction identify four new coumarin polymorphs

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

Shtukenberg, Alexander G.; Zhu, Qiang; Carter, Damien J.

Coumarin, a simple, commodity chemical isolated from beans in 1820, has, to date, only yielded one solid state structure. Here, we report a rich polymorphism of coumarin grown from the melt. Four new metastable forms were identified and their crystal structures were solved using a combination of computational crystal structure prediction algorithms and X-ray powder diffraction. With five crystal structures, coumarin has become one of the few rigid molecules showing extensive polymorphism at ambient conditions. We demonstrate the crucial role of advanced electronic structure calculations including many-body dispersion effects for accurate ranking of the stability of coumarin polymorphs and themore » need to account for anharmonic vibrational contributions to their free energy. As such, coumarin is a model system for studying weak intermolecular interactions, crystallization mechanisms, and kinetic effects.« less

Powder diffraction and crystal structure prediction identify four new coumarin polymorphs

DOE PAGES

Shtukenberg, Alexander G.; Zhu, Qiang; Carter, Damien J.; ...

2017-05-15

Coumarin, a simple, commodity chemical isolated from beans in 1820, has, to date, only yielded one solid state structure. Here, we report a rich polymorphism of coumarin grown from the melt. Four new metastable forms were identified and their crystal structures were solved using a combination of computational crystal structure prediction algorithms and X-ray powder diffraction. With five crystal structures, coumarin has become one of the few rigid molecules showing extensive polymorphism at ambient conditions. We demonstrate the crucial role of advanced electronic structure calculations including many-body dispersion effects for accurate ranking of the stability of coumarin polymorphs and themore » need to account for anharmonic vibrational contributions to their free energy. As such, coumarin is a model system for studying weak intermolecular interactions, crystallization mechanisms, and kinetic effects.« less

A Two-Tailed Phosphopeptide Crystallizes to Form a Lamellar Structure.

PubMed

Pellach, Michal; Mondal, Sudipta; Harlos, Karl; Mance, Deni; Baldus, Marc; Gazit, Ehud; Shimon, Linda J W

2017-03-13

The crystal structure of a designed phospholipid-inspired amphiphilic phosphopeptide at 0.8 Å resolution is presented. The phosphorylated β-hairpin peptide crystallizes to form a lamellar structure that is stabilized by intra- and intermolecular hydrogen bonding, including an extended β-sheet structure, as well as aromatic interactions. This first reported crystal structure of a two-tailed peptidic bilayer reveals similarities in thickness to a typical phospholipid bilayer. However, water molecules interact with the phosphopeptide in the hydrophilic region of the lattice. Additionally, solid-state NMR was used to demonstrate correlation between the crystal structure and supramolecular nanostructures. The phosphopeptide was shown to self-assemble into semi-elliptical nanosheets, and solid-state NMR provides insight into the self-assembly mechanisms. This work brings a new dimension to the structural study of biomimetic amphiphilic peptides with determination of molecular organization at the atomic level. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Synthesis, crystal structure, thermal and nonlinear optical properties of new metal-organic single crystal: Tetrabromo (piperazinium) zincate (II) (TBPZ)

NASA Astrophysics Data System (ADS)

Boopathi, K.; Babu, S. Moorthy; Ramasamy, P.

2018-04-01

Tetrabromo (piperazinium) zincate, a new metal-organic crystal has been synthesized and its single crystal grown by slow evaporation method. The grown crystal has characterized by structural, spectral, thermal, linear and nonlinear optical properties. Single crystal X-ray diffractions study reveals that grown crystal belongs to orthorhombic crystal system with space group P212121. The presence of functional groups is identified by FT-IR spectral analysis. Thermal stability of the crystal was ascertained by TG-DTA measurement. The second order harmonic generation efficiency was measured using Kurtz and Perry technique and it was found to be 1.5 times that of KDP.

TaRh2B2 and NbRh2B2: Superconductors with a chiral noncentrosymmetric crystal structure.

PubMed

Carnicom, Elizabeth M; Xie, Weiwei; Klimczuk, Tomasz; Lin, Jingjing; Górnicka, Karolina; Sobczak, Zuzanna; Ong, Nai Phuan; Cava, Robert J

2018-05-01

It is a fundamental truth in solid compounds that the physical properties follow the symmetry of the crystal structure. Nowhere is the effect of symmetry more pronounced than in the electronic and magnetic properties of materials-even the projection of the bulk crystal symmetry onto different crystal faces is known to have a substantial impact on the surface electronic states. The effect of bulk crystal symmetry on the properties of superconductors is widely appreciated, although its study presents substantial challenges. The effect of a lack of a center of symmetry in a crystal structure, for example, has long been understood to necessitate that the wave function of the collective electron state that gives rise to superconductivity has to be more complex than usual. However, few nonhypothetical materials, if any, have actually been proven to display exotic superconducting properties as a result. We introduce two new superconductors that in addition to having noncentrosymmetric crystal structures also have chiral crystal structures. Because the wave function of electrons in solids is particularly sensitive to the host material's symmetry, crystal structure chirality is expected to have a substantial effect on their superconducting wave functions. Our two experimentally obtained chiral noncentrosymmetric superconducting materials have transition temperatures to superconductivity that are easily experimentally accessible, and our basic property characterization suggests that their superconducting properties may be unusual. We propose that their study may allow for a more in-depth understanding of how chirality influences the properties of superconductors and devices that incorporate them.

Discovering H-bonding rules in crystals with inductive logic programming.

PubMed

Ando, Howard Y; Dehaspe, Luc; Luyten, Walter; Van Craenenbroeck, Elke; Vandecasteele, Henk; Van Meervelt, Luc

2006-01-01

In the domain of crystal engineering, various schemes have been proposed for the classification of hydrogen bonding (H-bonding) patterns observed in 3D crystal structures. In this study, the aim is to complement these schemes with rules that predict H-bonding in crystals from 2D structural information only. Modern computational power and the advances in inductive logic programming (ILP) can now provide computational chemistry with the opportunity for extracting structure-specific rules from large databases that can be incorporated into expert systems. ILP technology is here applied to H-bonding in crystals to develop a self-extracting expert system utilizing data in the Cambridge Structural Database of small molecule crystal structures. A clear increase in performance was observed when the ILP system DMax was allowed to refer to the local structural environment of the possible H-bond donor/acceptor pairs. This ability distinguishes ILP from more traditional approaches that build rules on the basis of global molecular properties.

Study on sensing property of one-dimensional ring mirror-defect photonic crystal

NASA Astrophysics Data System (ADS)

Chen, Ying; Luo, Pei; Cao, Huiying; Zhao, Zhiyong; Zhu, Qiguang

2018-02-01

Based on the photon localization and the photonic bandgap characteristics of photonic crystals (PCs), one-dimensional (1D) ring mirror-defect photonic crystal structure is proposed. Due to the introduction of mirror structure, a defect cavity is formed in the center of the photonic crystal, and then the resonant transmission peak can be obtained in the bandgap of transmission spectrum. The transfer matrix method is used to establish the relationship model between the resonant transmission peak and the structure parameters of the photonic crystals. Using the rectangular air gate photonic crystal structure, the dynamic monitoring of the detected gas sample parameters can be achieved from the shift of the resonant transmission peak. The simulation results show that the Q-value can attain to 1739.48 and the sensitivity can attain to 1642 nm ṡ RIU-1, which demonstrates the effectiveness of the sensing structure. The structure can provide certain theoretical reference for air pollution monitoring and gas component analysis.

Development and photoelectric properties of In/p-Ag{sub 3}AsS{sub 3} surface-barrier structures

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

Rud', V. Yu., E-mail: rudvas@spbstu.ru; Rud', Yu. V.; Terukov, E. I.

2010-08-15

Homogeneous p-Ag{sub 3}AsS{sub 3} bulk single crystals with rhombic structure have been grown by planar crystallization from melts with atomic composition corresponding to this ternary compound. Photosensitive surface-barrier structures based on the interface between the surface of these crystals and thin films of pure indium are fabricated for the first time. The photosensitivity of fabricated structures is studied in natural and linearly polarized light. Photosensitivity spectra of In/p-Ag{sub 3}AsS{sub 3} structures are measured for the first time and used to determine the nature and energy of interband transitions in p-Ag{sub 3}AsS{sub 3} crystals. The phenomenon of natural photopleochroism is studiedmore » for surface-barrier structures grown on oriented p-Ag{sub 3}AsS{sub 3} single crystals. It is concluded that Ag{sub 3}AsS{sub 3} single crystals can be used in photoconverters of natural and linearly polarized light.« less

Crystal growth, structural, low temperature thermoluminescence and mechanical properties of cubic fluoroperovskite single crystal (LiBaF3)

NASA Astrophysics Data System (ADS)

Daniel, D. Joseph; Ramasamy, P.; Ramaseshan, R.; Kim, H. J.; Kim, Sunghwan; Bhagavannarayana, G.; Cheon, Jong-Kyu

2017-10-01

Polycrystalline compounds of LiBaF3 were synthesized using conventional solid state reaction route and the phase purity was confirmed using powder X-ray diffraction technique. Using vertical Bridgman technique single crystal was grown from melt. Rocking curve measurements have been carried out to study the structural perfection of the grown crystal. The single peak of diffraction curve clearly reveals that the grown crystal was free from the structural grain boundaries. The low temperature thermoluminescence of the X-ray irradiated sample has been analyzed and found four distinguishable peaks having maximum temperatures at 18, 115, 133 and 216 K. Activation energy (E) and frequency factor (s) for the individual peaks have been studied using Peak shape method and the computerized curve fitting method combining with the Tmax- TStop procedure. Nanoindentation technique was employed to study the mechanical behaviour of the crystal. The indentation modulus and Vickers hardness of the grown crystal have values of 135.15 GPa and 680.81 respectively, under the maximum indentation load of 10 mN.

Overview of electron crystallography of membrane proteins: crystallization and screening strategies using negative stain electron microscopy.

PubMed

Nannenga, Brent L; Iadanza, Matthew G; Vollmar, Breanna S; Gonen, Tamir

2013-01-01

Electron cryomicroscopy, or cryoEM, is an emerging technique for studying the three-dimensional structures of proteins and large macromolecular machines. Electron crystallography is a branch of cryoEM in which structures of proteins can be studied at resolutions that rival those achieved by X-ray crystallography. Electron crystallography employs two-dimensional crystals of a membrane protein embedded within a lipid bilayer. The key to a successful electron crystallographic experiment is the crystallization, or reconstitution, of the protein of interest. This unit describes ways in which protein can be expressed, purified, and reconstituted into well-ordered two-dimensional crystals. A protocol is also provided for negative stain electron microscopy as a tool for screening crystallization trials. When large and well-ordered crystals are obtained, the structures of both protein and its surrounding membrane can be determined to atomic resolution.

Studies on synthesis, growth, structural, thermal, linear and nonlinear optical properties of organic picolinium maleate single crystals.

PubMed

Pandi, P; Peramaiyan, G; Sudhahar, S; Chakkaravarthi, G; Mohan Kumar, R; Bhagavannarayana, G; Jayavel, R

2012-12-01

Picolinium maleate (PM), an organic material has been synthesised and single crystals were grown by slow evaporation technique. The structure of the grown crystal was elucidated by using single crystal X-ray diffraction analysis. PM crystal belongs to the monoclinic crystallographic system with space group P2(1)/c. The crystalline perfection of the grown crystals was analyzed by high-resolution X-ray diffraction rocking curve measurements. The presence of functional groups in PM was identified by FTIR and FT-NMR spectral analyses. Thermal behaviour and stability of picolinium maleate were studied by TGA/DTA analyses. UV-Vis spectral studies reveal that PM crystals are transparent in the wavelength region 327-1100 nm. The laser damage threshold value of PM crystal was found to be 4.3 GW/cm(2) using Nd:YAG laser. The Kurtz and Perry powder second harmonic generation technique confirms the nonlinear optical property of the grown crystal. Copyright © 2012 Elsevier B.V. All rights reserved.

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.

Kinetic products in coordination networks: ab initio X-ray powder diffraction analysis.

PubMed

Martí-Rujas, Javier; Kawano, Masaki

2013-02-19

Porous coordination networks are materials that maintain their crystal structure as molecular "guests" enter and exit their pores. They are of great research interest with applications in areas such as catalysis, gas adsorption, proton conductivity, and drug release. As with zeolite preparation, the kinetic states in coordination network preparation play a crucial role in determining the final products. Controlling the kinetic state during self-assembly of coordination networks is a fundamental aspect of developing further functionalization of this class of materials. However, unlike for zeolites, there are few structural studies reporting the kinetic products made during self-assembly of coordination networks. Synthetic routes that produce the necessary selectivity are complex. The structural knowledge obtained from X-ray crystallography has been crucial for developing rational strategies for design of organic-inorganic hybrid networks. However, despite the explosive progress in the solid-state study of coordination networks during the last 15 years, researchers still do not understand many chemical reaction processes because of the difficulties in growing single crystals suitable for X-ray diffraction: Fast precipitation can lead to kinetic (metastable) products, but in microcrystalline form, unsuitable for single crystal X-ray analysis. X-ray powder diffraction (XRPD) routinely is used to check phase purity, crystallinity, and to monitor the stability of frameworks upon guest removal/inclusion under various conditions, but rarely is used for structure elucidation. Recent advances in structure determination of microcrystalline solids from ab initio XRPD have allowed three-dimensional structure determination when single crystals are not available. Thus, ab initio XRPD structure determination is becoming a powerful method for structure determination of microcrystalline solids, including porous coordination networks. Because of the great interest across scientific disciplines in coordination networks, especially porous coordination networks, the ability to determine crystal structures when the crystals are not suitable for single crystal X-ray analysis is of paramount importance. In this Account, we report the potential of kinetic control to synthesize new coordination networks and we describe ab initio XRPD structure determination to characterize these networks' crystal structures. We describe our recent work on selective instant synthesis to yield kinetically controlled porous coordination networks. We demonstrate that instant synthesis can selectively produce metastable networks that are not possible to synthesize by conventional solution chemistry. Using kinetic products, we provide mechanistic insights into thermally induced (573-723 K) (i.e., annealing method) structural transformations in porous coordination networks as well as examples of guest exchange/inclusion reactions. Finally, we describe a memory effect that allows the transfer of structural information from kinetic precursor structures to thermally stable structures through amorphous intermediate phases. We believe that ab initio XRPD structure determination will soon be used to investigate chemical processes that lead intrinsically to microcrystalline solids, which up to now have not been fully understood due to the unavailability of single crystals. For example, only recently have researchers used single-crystal X-ray diffraction to elucidate crystal-to-crystal chemical reactions taking place in the crystalline scaffold of coordination networks. The potential of ab initio X-ray powder diffraction analysis goes beyond single-crystal-to-single-crystal processes, potentially allowing members of this field to study intriguing in situ reactions, such as reactions within pores.

Effect of L-aspartic acid on the growth, structure and spectral studies of Zinc (tris) Thiourea Sulphate (ZTS) single crystals

NASA Astrophysics Data System (ADS)

Samuel, Bincy Susan; Krishnamurthy, R.; Rajasekaran, R.

2014-11-01

Single crystals of pure and L-aspartic acid doped Zinc (Tris) Thiourea Sulphate (ZTS) were grown from aqueous solution by solution growth method. The cell parameters and structure of the grown crystals were determined by X-ray diffraction studies. The presence of functional group in the compound has been confirmed by FTIR and FT-Raman analysis. The optical transparency range has been studied through UV-Vis spectroscopy. TGA/DTA studies show thermal stability of the grown crystals. Microhardness study reveals that the hardness number (Hv) increases with load for pure and doped ZTS crystals. Dielectric studies have been carried out and the results are discussed. The second harmonic generation was confirmed for L-aspartic acid doped ZTS which is greater than pure ZTS.

Synthesis, growth, structural, optical, luminescence, surface and HOMO LUMO analysis of 2-[2-(4-cholro-phenyl)-vinyl]-1-methylquinolinium naphthalene-2-sulfonate organic single crystals grown by a slow evaporation technique

NASA Astrophysics Data System (ADS)

Karthigha, S.; Kalainathan, S.; Maheswara Rao, Kunda Uma; Hamada, Fumio; Yamada, Manabu; Kondo, Yoshihiko

2016-02-01

Single crystals of 2-[2-(4-cholro-phenyl)-vinyl]-1-methylquinolinium naphthalene-2-sulfonate (4CLNS) were grown by a slow evaporation technique. The formation of molecule was confirmed from 1H NMR and FTIR analysis. The confirmation of crystal structure was done by single crystal XRD and atomic packing of grown crystal was identified. The grown single crystal crystallized in triclinic structure with centrosymmetric space group P-1. The crystalline nature of the synthesised material was recorded by powder XRD. The optical absorption properties of the grown crystals were analyzed by UV-vis spectral studies. The thermal behaviour of the title material has been studied by TG/DTA analysis which revealed the stability of the compound till its melting point 276.7 °C. The third order nonlinear optical property of 4CLNS was investigated in detail by Z scan technique and it confirms that the title crystal is suitable for photonic devices and NLO optical applications. Emissions at 519 nm in green region of the EM spectrum were found by photoluminescence studies. The charge transfer occurring within the molecule is explained by the calculated HOMO and LUMO energies.

Combinatorial and High Throughput Discovery of High Temperature Piezoelectric Ceramics

DTIC Science & Technology

2011-10-10

the known candidate piezoelectric ferroelectric perovskites. Unlike most computational studies on crystal chemistry, where the starting point is some...studies on crystal chemistry, where the starting point is some form of electronic structure calculation, we use a data driven approach to initiate our...experimental measurements reported in the literature. Given that our models are based solely on crystal and electronic structure data and did not

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

First-principles study on structure stabilities of α-S and Na-S battery systems

NASA Astrophysics Data System (ADS)

Momida, Hiroyoshi; Oguchi, Tamio

2014-03-01

To understand microscopic mechanisms of charge and discharge reactions in Na-S batteries, there has been increasing needs to study fundamental atomic and electronic structures of elemental S as well as that of Na-S phases. The most stable form of S is known to be an orthorhombic α-S crystal at ambient temperature and pressure, and α-S consists of puckered S8 rings which crystallize in space group Fddd . In this study, the crystal structure of α-S is examined by using first-principles calculations with and without the van der Waals interaction corrections of Grimme's method, and results clearly show that the van der Waals interactions between the S8 rings have crucial roles on cohesion of α-S. We also study structure stabilities of Na2S, NaS, NaS2, and Na2S5 phases with reported crystal structures. Using calculated total energies of the crystal structure models, we estimate discharge voltages assuming discharge reactions from 2Na+ xS -->Na2Sx, and discharge reactions in Na/S battery systems are discussed by comparing with experimental results. This work was partially supported by Elements Strategy Initiative for Catalysts and Batteries (ESICB) of Ministry of Education, Culture, Sports, Science, and Technology (MEXT), Japan.

Structural study of quasi-one-dimensional vanadium pyroxene LiVSi{sub 2}O{sub 6} single crystals

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

Ishii, Yuto; Matsushita, Yoshitaka; Oda, Migaku

Single crystals of quasi-one-dimensional vanadium pyroxene LiVSi{sub 2}O{sub 6} were synthesized and the crystal structures at 293 K and 113 K were studied using X-ray diffraction experiments. We found a structural phase transition from the room-temperature crystal structure with space group C2/c to a low-temperature structure with space group P2{sub 1}/c, resulting from a rotational displacement of SiO{sub 4} tetrahedra. The temperature dependence of magnetic susceptibility shows a broad maximum around 116 K, suggesting an opening of the Haldane gap expected for one-dimensional antiferromagnets with S=1. However, an antiferromagnetic long-range order was developed below 24 K, probably caused by amore » weak inter-chain magnetic coupling in the compound. - Graphical abstract: Low temperature crystal structure of LiVSi{sub 2}O{sub 6} and an orbital arrangement within the V-O zig-zag chain along the c-axis. - Highlights: • A low temperature structure of LiVSi{sub 2}O{sub 6} was determined by single crystal X-ray diffraction measurements. • The origin of the structural transition is a rotational displacement of SiO{sub 4} tetrahedra. • The uniform orbital overlap in the V-O zigzag chain makes the system a quasi one-dimensional antiferromagnet.« less

Crystallized N-terminal domain of influenza virus matrix protein M1 and method of determining and using same

NASA Technical Reports Server (NTRS)

Luo, Ming (Inventor); Sha, Bingdong (Inventor)

2000-01-01

The matrix protein, M1, of influenza virus strain A/PR/8/34 has been purified from virions and crystallized. The crystals consist of a stable fragment (18 Kd) of the M1 protein. X-ray diffraction studies indicated that the crystals have a space group of P3.sub.t 21 or P3.sub.2 21. Vm calculations showed that there are two monomers in an asymmetric unit. A crystallized N-terminal domain of M1, wherein the N-terminal domain of M1 is crystallized such that the three dimensional structure of the crystallized N-terminal domain of M1 can be determined to a resolution of about 2.1 .ANG. or better, and wherein the three dimensional structure of the uncrystallized N-terminal domain of M1 cannot be determined to a resolution of about 2.1 .ANG. or better. A method of purifying M1 and a method of crystallizing M1. A method of using the three-dimensional crystal structure of M1 to screen for antiviral, influenza virus treating or preventing compounds. A method of using the three-dimensional crystal structure of M1 to screen for improved binding to or inhibition of influenza virus M1. The use of the three-dimensional crystal structure of the M1 protein of influenza virus in the manufacture of an inhibitor of influenza virus M1. The use of the three-dimensional crystal structure of the M1 protein of influenza virus in the screening of candidates for inhibition of influenza virus M1.

A framework for multi-scale simulation of crystal growth in the presence of polymers.

PubMed

Mandal, Taraknath; Huang, Wenjun; Mecca, Jodi M; Getchell, Ashley; Porter, William W; Larson, Ronald G

2017-03-01

We present a multi-scale simulation method for modeling crystal growth in the presence of polymer excipients. The method includes a coarse-grained (CG) model for small molecules of known crystal structure whose force field is obtained using structural properties from atomistic simulations. This CG model is capable of stabilizing the molecular crystal structure and capturing the crystal growth from the melt for a wide range of small organic molecules, as demonstrated by application of our method to the molecules isoniazid, urea, sulfamethoxazole, prilocaine, oxcarbazepine, and phenytoin. This CG model can also be used to study the effect of additives, such as polymers, on the inhibition of crystal growth by polymers, as exemplified by our simulation of suppression of the rate of crystal growth of phenytoin, an active pharmaceutical ingredient (API), by a cellulose excipient, functionalized with acetate (Ac), hydroxy-propyl (Hp) and succinate (Su) groups. We show that the efficacy of the cellulosic polymers in slowing crystal growth of small molecules strongly depends on the functional group substitution on the cellulose backbone, with the acetate substituent group slowing crystal growth more than does the deprotonated succinate group, which we confirm by experimental drug supersaturation studies.

Fundamental Studies of Crystal Growth of Microporous Materials

NASA Technical Reports Server (NTRS)

Singh, Ramsharan; Doolittle, John, Jr.; Payra, Pramatha; Dutta, Prabir K.; George, Michael A.; Ramachandran, Narayanan; Schoeman, Brian J.

2003-01-01

Microporous materials are framework structures with well-defined porosity, often of molecular dimensions. Zeolites contain aluminum and silicon atoms in their framework and are the most extensively studied amongst all microporous materials. Framework structures with P, Ga, Fe, Co, Zn, B, Ti and a host of other elements have also been made. Typical synthesis of microporous materials involve mixing the framework elements (or compounds, thereof) in a basic solution, followed by aging in some cases and then heating at elevated temperatures. This process is termed hydrothermal synthesis, and involves complex chemical and physical changes. Because of a limited understanding of this process, most synthesis advancements happen by a trial and error approach. There is considerable interest in understanding the synthesis process at a molecular level with the expectation that eventually new framework structures will be built by design. The basic issues in the microporous materials crystallization process include: (a) Nature of the molecular units responsible for the crystal nuclei formation; (b) Nature of the nuclei and nucleation process; (c) Growth process of the nuclei into crystal; (d) Morphological control and size of the resulting crystal; (e) Surface structure of the resulting crystals; and (f) Transformation of frameworks into other frameworks or condensed structures.

Growth, structure, Hirshfeld surface and spectroscopic properties of 2-amino-4-hydroxy-6-methylpyrimidinium-2,3-pyrazinedicorboxylate single crystal

NASA Astrophysics Data System (ADS)

Faizan, Mohd; Alam, Mohammad Jane; Afroz, Ziya; Rodrigues, Vítor Hugo Nunes; Ahmad, Shabbir

2018-03-01

The present work is focused on the crystal structure, vibrational spectroscopy and DFT calculations of hydrogen bonded 2,3-pyrazinedicorboxylic acid and 2-amino-4-hydroxy-6-methylpyrimidine (PDCA-.AHMP+) crystal. The crystal structure has been determined using single crystal X-ray diffraction analysis which shows that the crystal belongs to monoclinic space group P21/n. The PDCA-.AHMP+ crystal has been characterized by FTIR, FT-Raman and FT-NMR spectroscopic techniques. The FTIR and FT-Raman spectra of the complex have unique spectroscopic feature as compared with those of the starting material to confirm salt formation. The theoretical vibrational studies have been performed to understand the modes of the vibrations of asymmetric unit of the complex by DFT methods. Hirschfeld surface and 2D fingerprint plots analyses were carried out to investigate the intermolecular interactions and its contribution in the building of PDCA-.AHMP+ crystal. The experimental and simulated 13C and 1H NMR studies have assisted in structural analysis of PDCA-.AHMP+ crystal. The electronic spectroscopic properties of the complex were explored by the experimental as well as theoretical electronic spectra simulated using TD-DFT/IEF-PCM method at B3LYP/6-311++G (d,p) level of theory. In addition, frontier molecular orbitals, molecular electrostatic potential map (MEP) and nonlinear optical (NLO) properties using DFT method have been also presented.

Morphological, spectroscopic and thermal studies of samarium chloride coordinated single crystal grown by slow evaporation method

NASA Astrophysics Data System (ADS)

Slathia, Goldy; Raina, Bindu; Gupta, Rashmi; Bamzai, K. K.

2018-05-01

The synthesis of samarium chloride coordinated single crystal was carried out at room temperature by slow evaporation method. The crystal possesses a well defined hexagonal morphology with six symmetrically equivalent growth sectors separated by growth boundaries. The theoretical morphology has been established by structural approach using Bravaise-Friedele-Donnaye-Harker (BFDH) law. Fourier transform infra red spectroscopy was carried in order to study the geometry and structure of the crystal. The detailed thermogravimetric analysis elucidates the thermal stability of the complex.

Specific Features of the Domain Structure of BaTiO3 Crystals during Thermal Heating and Cooling

NASA Astrophysics Data System (ADS)

Kiselev, D. A.; Ilina, T. S.; Malinkovich, M. D.; Sergeeva, O. N.; Bolshakova, N. N.; Semenova, E. M.; Kuznetsova, Yu. V.

2018-04-01

This paper presents the results of the study of the domain structure of barium titanate crystals in a wide temperature range including the Curie point ( T C) using the polarization-optical method in the reflected light and the force microscopy of the piezoelectric response. It is shown that a new a-c domain structure forms during cyclic heating of the crystal above T C and subsequent cooling to the ferroelectric phase. The role of uncompensated charges appeared on the crystal surface during the phase transition and their influence on the formation of the domain structure during cooling are discussed.

Tailoring the Crystal Structure Toward Optimal Super Conductors

DTIC Science & Technology

2016-06-23

AFRL-AFOSR-VA-TR-2016-0210 TAILORING THE CRYSTAL STRUCTURE TOWARD OPTIMAL SUPERCONDUCTORS Emilia Morosan WILLIAM MARSH RICE UNIV HOUSTON TX Final...TAILORING THE CRYSTAL STRUCTURE TOWARD OPTIMAL SUPERCONDUCTORS 5a. CONTRACT NUMBER FA9550-11-1-0023 5b. GRANT NUMBER 5c. PROGRAM ELEMENT NUMBER 6...studied the properties of layered transition metal compounds in search of unconventional superconductors . The aim is to identify ground states competing

Synthesis, crystal structure, vibrational spectroscopy and photoluminescence of new hybrid compound containing chlorate anions of stanate (II)

NASA Astrophysics Data System (ADS)

Lassoued, Mohamed Saber; Abdelbaky, Mohammed S. M.; Lassoued, Abdelmajid; Meroño, Rafael Mendoza; Gadri, Abdellatif; Ammar, Salah; Ben Salah, Abdelhamid; García-Granda, Santiago

2017-08-01

The present work aimed at studying a new organic-inorganic bis (4-amino quinolinium) hexachloro stanate (II) dihydrate compound. It was prepared and characterized by single crystal X-ray diffraction, X-ray powder, Hirshfeld surface, Spectroscopy measurement, thermal study and photoluminescence properties. It was found to crystallize in the monoclinic system (P21/c space group) with the following lattice parameters: a = 7.2558(6) Å, b = 13.4876(5) Å, c = 17.2107(13) Å, β = 102.028 (12)°. Its crystal structure was determined and refined down to an R value of 0.06 and a wR value of 0.087. The structure consisted of two different alternating organic-inorganic layers. The crystal packing was stabilized by Nsbnd H⋯Cl and Osbnd H⋯Cl hydrogen bonds and π-π interactions. Hirshfeld surface analysis was used to investigate intermolecular interactions, as well 2D finger plots were conducted to reveal the contribution of these interactions in the crystal structure quantitatively. The X-ray powder is in agreement with the X-ray structure. Scanning electronic microscopy (SEM) was carried out. Furthermore, the room temperature Infra Red (IR) spectrum of the title compound was analyzed on the basis of data found in the literature. Solid state 13C NMR spectrum shows ten signals, confirming the solid state structure determined by X-ray diffraction. Thermal analysis shows two anomalies at 380 and 610 °C. The optical properties of the crystal were studied using optical absorption UV-visible and photoluminescence (PL) spectroscopy, which were investigated at room temperature.

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

Protein Crystal Quality Studies

NASA Technical Reports Server (NTRS)

1998-01-01

Eddie Snell, Post-Doctoral Fellow the National Research Council (NRC) uses a reciprocal space mapping diffractometer for macromolecular crystal quality studies. The diffractometer is used in mapping the structure of macromolecules such as proteins to determine their structure and thus understand how they function with other proteins in the body. This is one of several analytical tools used on proteins crystallized on Earth and in space experiments. Photo credit: NASA/Marshall Space Flight Center (MSFC)

Preliminary crystallographic studies of four crystal forms of serum albumin

NASA Technical Reports Server (NTRS)

Carter, D. C.; Chang, B.; Ho, J. X.; Keeling, K.; Krishnasami, Z.

1994-01-01

Several crystal forms of serum albumin suitable for three-dimensional structure determination have been grown. These forms include crystals of recombinant and wild-type human serum albumin, baboon serum albumin, and canine serum albumin. The intrinsic limits of X-ray diffraction for these crystals are in the range 0.28-0.22 nm. Two of the crystal forms produced from human and canine albumin include incorporated long-chain fatty acids. Molecular replacement experiments have been successfully conducted on each crystal form using the previously determined atomic coordinates of human serum albumin illustrating the conserved tertiary structure.

Synthesis and structural study of 4-(2-chlorophenyl)-2-ethoxy-5,6,7,8,9,10-hexahydrocycloocta[B] pyridine-3-carbonitrile

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

Fathima, K. Saiadali; Vasumathi, M.; Anitha, K., E-mail: singlecrystalxrd@gmail.com

2016-05-23

The novel organic material C{sub 20}H{sub 21}ClN{sub 2}O was synthesized by One-Pot synthesis method and the single crystals were grown by slow evaporation solution growth technique. The crystal structure was elucidated by subjecting the grown crystals to the single crystal x-ray diffraction analysis and was refined by full matrix least-squares method to R=0.039 for 2746 reflections. Crystal system of the grown crystal was found to be monoclinic with the space group P2{sub 1}/a and a=9.196(4) Å, b=13.449(4) Å, c=14.818(4) Å, β= 101.542(3)°, V=1795.6(11) Å{sup 3} and Z=4. In this crystal structure, cyclooctanone prefers to reside in a chair-boat conformation. Themore » structure is stabilized by attractive molecular force such as CH/π interaction called hydrophobic interaction.« less

Analysis of synthetic diamond single crystals by X-ray topography and double-crystal diffractometry

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

Prokhorov, I. A., E-mail: igor.prokhorov@mail.ru; Ralchenko, V. G.; Bolshakov, A. P.

2013-12-15

Structural features of diamond single crystals synthesized under high pressure and homoepitaxial films grown by chemical vapor deposition (CVD) have been analyzed by double-crystal X-ray diffractometry and topography. The conditions of a diffraction analysis of diamond crystals using Ge monochromators have been optimized. The main structural defects (dislocations, stacking faults, growth striations, second-phase inclusions, etc.) formed during crystal growth have been revealed. The nitrogen concentration in high-pressure/high-temperature (HPHT) diamond substrates is estimated based on X-ray diffraction data. The formation of dislocation bundles at the film-substrate interface in the epitaxial structures has been revealed by plane-wave topography; these dislocations are likelymore » due to the relaxation of elastic macroscopic stresses caused by the lattice mismatch between the substrate and film. The critical thicknesses of plastic relaxation onset in CVD diamond films are calculated. The experimental techniques for studying the real diamond structure in optimizing crystal-growth technology are proven to be highly efficient.« less

Conjugation in multi-tetrazole derivatives: a new design direction for energetic materials.

PubMed

Sun, Shuyang; Lu, Ming

2018-06-23

Multi-tetrazole derivatives with conjugated structures were designed and investigated in this study. Using quantum chemistry methods, the crystal structures, electrostatic potentials (ESPs), multicenter bond orders, HOMO-LUMO energy gaps, and detonation properties of the derivatives were calculated. As expected, these molecules with conjugated structures showed low energies of their crystal structures, molecular layering in their crystals, high average ESPs, high multicenter bond order values, and enhanced detonation properties. The derivative 1,2-di(1H-tetrazol-5-yl)diazene (N2) was predicted to have the best density (1.87 g/cm 3 ), detonation velocity (9006 m/s), and detonation pressure (36.8 GPa) of the designed molecules, while its total crystal energy was low, suggesting that it is relatively stable. Its sensitivity was also low, as the molecular stacking that occurs in its crystal allows external forces to be dissipated into movements of crystal layers. Finally, its multicenter bond order was high, indicating a highly conjugated structure.

Structure of Cs{sub 4}(HSO{sub 4}){sub 3}(H{sub 2}PO{sub 4}) single crystals

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

Makarova, I. P., E-mail: makarova@crys.ras.ru; Grebenev, V. V.; Vasil’ev, I. I.

2016-01-15

Single crystals of Cs{sub 4}(HSO{sub 4}){sub 3}(H{sub 2}PO{sub 4}) are synthesized and studied for the first time. The new compound is found in the course of studies of the phase diagram of the CsHSO{sub 4}–CsH{sub 2}PO{sub 4}–H{sub 2}O triple system. Data on the atomic crystal structure of single-crystalline and powder specimens, as well as on structural phase transitions, are obtained.

Crystallization of toxic glycol solvates of rifampin from glycerin and propylene glycol contaminated with ethylene glycol or diethylene glycol.

PubMed

de Villiers, Melgardt M; Caira, Mino R; Li, Jinjing; Strydom, Schalk J; Bourne, Susan A; Liebenberg, Wilna

2011-06-06

This study was initiated when it was suspected that syringe blockage experienced upon administration of a compounded rifampin suspension was caused by the recrystallization of toxic glycol solvates of the drug. Single crystal X-ray structure analysis, powder X-ray diffraction, thermal analysis and gas chromatography were used to identify the ethylene glycol in the solvate crystals recovered from the suspension. Controlled crystallization and solubility studies were used to determine the ease with which toxic glycol solvates crystallized from glycerin and propylene glycol contaminated with either ethylene or diethylene glycol. The single crystal structures of two distinct ethylene glycol solvates of rifampin were solved while thermal analysis, GC analysis and solubility studies confirmed that diethylene glycol solvates of the drug also crystallized. Controlled crystallization studies showed that crystallization of the rifampin solvates from glycerin and propylene glycol depended on the level of contamination and changes in the solubility of the drug in the contaminated solvents. Although the exact source of the ethylene glycol found in the compounded rifampin suspension is not known, the results of this study show how important it is to ensure that the drug and excipients comply with pharmacopeial or FDA standards.

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.

An ultraviolet crosslink in the hammerhead ribozyme dependent on 2-thiocytidine or 4-thiouridine substitution.

PubMed Central

Wang, L; Ruffner, D E

1997-01-01

The hammerhead domain is one of the smallest known ribozymes. Like other ribozymes it catalyzes site-specific cleavage of a phosphodiester bond. The hammerhead ribozyme has been the subject of a vast number of biochemical and structural studies aimed at determining the structure and mechanism of cleavage. Recently crystallographic analysis has produced a structure for the hammerhead. As the hammerhead is capable of undergoing cleavage within the crystal, it would appear that the crystal structure is representative of the catalytically active solution structure. However, the crystal structure conflicts with much of the biochemical data and reveals a catalytic metal ion binding site expected to be of very low affinity. Clearly, additional studies are needed to reconcile the discrepancies and provide a clear understanding of the structure and mechanism of the hammerhead ribozyme. Here we demonstrate that a unique crosslink can be induced in the hammerhead with 2-thiocytidine or 4-thiouridine substitution at different locations within the conserved core. Generation of the same crosslink with different modifications at different positions suggests that the structure trapped by the crosslink may be relevant to the catalytically active solution structure of the hammerhead ribozyme. As this crosslink appears to be incompatible with the crystal structure, this provides yet another indication that the active solution and crystal structures may differ significantly. PMID:9336468

Growth, structural, optical, thermal and laser damage threshold studies of an organic single crystal: 1,3,5 – triphenylbenzene (TPB)

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

Raja, R. Subramaniyan; Babu, G. Anandha; Ramasamy, P., E-mail: E-mail-ramasamyp@ssn.edu.in

2016-05-23

Good quality single crystals of pure hydrocarbon 1,3,5-Triphenylbenzene (TPB) have been successfully grown using toluene as a solvent using controlled slow cooling solution growth technique. TPB crystallizes in orthorhombic structure with the space group Pna2{sub 1}. The structural perfection of the grown crystal has been analysed by high resolution X-ray diffraction measurements. The range and percentage of the optical transmission are ascertained by recording the UV-vis spectrum. Thermo gravimetric analysis (TGA) and differential thermal analysis (DTA) were used to study its thermal properties. Powder second harmonic generation studies were carried out to explore its NLO properties. Laser damage threshold valuemore » has been determined using Nd:YAG laser operating at 1064 nm.« less

Fundamental Studies of Crystal Growth of Microporous Materials

NASA Technical Reports Server (NTRS)

Dutta, P.; George, M.; Ramachandran, N.; Schoeman, B.; Curreri, Peter A. (Technical Monitor)

2002-01-01

Microporous materials are framework structures with well-defined porosity, often of molecular dimensions. Zeolites contain aluminum and silicon atoms in their framework and are the most extensively studied amongst all microporous materials. Framework structures with P, Ga, Fe, Co, Zn, B, Ti and a host of other elements have also been made. Typical synthesis of microporous materials involve mixing the framework elements (or compounds, thereof) in a basic solution, followed by aging in some cases and then heating at elevated temperatures. This process is termed hydrothermal synthesis, and involves complex chemical and physical changes. Because of a limited understanding of this process, most synthesis advancements happen by a trial and error approach. There is considerable interest in understanding the synthesis process at a molecular level with the expectation that eventually new framework structures will be built by design. The basic issues in the microporous materials crystallization process include: (1) Nature of the molecular units responsible for the crystal nuclei formation; (2) Nature of the nuclei and nucleation process; (3) Growth process of the nuclei into crystal; (4) Morphological control and size of the resulting crystal; (5) Surface structure of the resulting crystals; (6) Transformation of frameworks into other frameworks or condensed structures. The NASA-funded research described in this report focuses to varying degrees on all of the above issues and has been described in several publications. Following is the presentation of the highlights of our current research program. The report is divided into five sections: (1) Fundamental aspects of the crystal growth process; (2) Morphological and Surface properties of crystals; (3) Crystal dissolution and transformations; (4) Modeling of Crystal Growth; (5) Relevant Microgravity Experiments.

Crystal growth, physical properties and computational insights of semi-organic non-linear optical crystal diphenylguanidinium perchlorate grown by conventional solvent evaporation method

NASA Astrophysics Data System (ADS)

Kajamuhideen, M. S.; Sethuraman, K.; Ramamurthi, K.; Ramasamy, P.

2018-02-01

A splendid nonlinear optical single crystals diphenylguanidinium perchlorate (DPGP) was lucratively grown by low cost solvent evaporation method with the dimensions of 8 × 4 × 2 mm3. Structural and morphological studies of grown crystal were confirmed using X-ray diffraction studies. The presence of diverse functional groups was identified using FTIR and RAMAN studies. The molecular structure of a grown crystal was inveterate by NMR studies. The optical transmittance of DPGP crystal was analyzed using UV-vis-NIR studies. Photoluminescence spectrum shows sharp, well defined emission peak at 388 nm. Thermal studies assign that adduct is stable with the melting point of 164 °C. Microhardness studies declare that DPGP crystal belongs to the soft material class and their yield strength and elastic stiffness constant values were evaluated. Photoconductivity studies revealed the negative photoconductive nature of DPGP crystal. Second harmonic generation (SHG) efficiency of the DPGP crystal was 1.4 times that of potassium dihydrogen phosphate. Etching studies were carried out for different etching time. The dielectric studies were performed at different frequency. Laser damage threshold properties of DPGP crystal were examined using Nd:YAG laser system. The HOMO-LUMO energy gap evident the charge transfer interaction of the molecule. The calculated first order hyperpolarizability value is 5 times greater than that of urea. Thus, the grown DPGP single crystals are well suited for NLO device fabrications.

Zero-n gap in one dimensional photonic crystal

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

Chobey, Mahesh K., E-mail: mahesh01chobey@gmail.com; Suthar, B.

2016-05-06

We study a one-dimensional (1-D) photonic crystal composed of Double Positive (DPS) and Double Negative (DNG) material. This structure shows omnidirectional photonic bandgap, which is insensitive with angle of incidence and polarization. To study the effect of structural parameters on the photonic band structure, we have calculated photonic band gap at various thicknesses of DPS and DNG.

Topological Classification of Crystalline Insulators through Band Structure Combinatorics

NASA Astrophysics Data System (ADS)

Kruthoff, Jorrit; de Boer, Jan; van Wezel, Jasper; Kane, Charles L.; Slager, Robert-Jan

2017-10-01

We present a method for efficiently enumerating all allowed, topologically distinct, electronic band structures within a given crystal structure in all physically relevant dimensions. The algorithm applies to crystals without time-reversal, particle-hole, chiral, or any other anticommuting or anti-unitary symmetries. The results presented match the mathematical structure underlying the topological classification of these crystals in terms of K -theory and therefore elucidate this abstract mathematical framework from a simple combinatorial perspective. Using a straightforward counting procedure, we classify all allowed topological phases of spinless particles in crystals in class A . Employing this classification, we study transitions between topological phases within class A that are driven by band inversions at high-symmetry points in the first Brillouin zone. This enables us to list all possible types of phase transitions within a given crystal structure and to identify whether or not they give rise to intermediate Weyl semimetallic phases.

Structural and spectroscopic investigations on deuteron glasses belonging to the potassium dihydrogen phosphate family

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

Choudhury, Rajul Ranjan, E-mail: rajul@barc.gov.in; Chitra, R.; Abraham, Geogy J.

2015-06-24

X-ray powder diffraction and Raman measurements were performed on the mixed crystals of deuterated potassium dihydrogen phosphate (DKDP) and deuterated ammonium dihydrogen phosphate (DADP) grown at our lab. These crystals are known to behave like deuteron glasses due to frustration between ferroelectric and antiferroelectric ordering. Both spectral as well as structural studies indicate that crystals belonging to the glassy regions of the crystal composition have stronger O-D-O hydrogen bonds as compared to those belong to the ferroelectric or antiferroelectric regions of the crystal composition.

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.

The crystal structure of the new ternary antimonide Dy 3Cu 20+xSb 11-x ( x≈2)

NASA Astrophysics Data System (ADS)

Fedyna, L. O.; Bodak, O. I.; Fedorchuk, A. O.; Tokaychuk, Ya. O.

2005-06-01

New ternary antimonide Dy 3Cu 20+xSb 11-x ( x≈2) was synthesized and its crystal structure was determined by direct methods from X-ray powder diffraction data (diffractometer DRON-3M, Cu Kα-radiation, R=6.99%,R=12.27%,R=11.55%). The compound crystallizes with the own cubic structure type: space group F 4¯ 3m, Pearson code cF272, a=16.6150(2) Å,Z=8. The structure of the Dy 3Cu 20Sb 11-x ( x≈2) can be obtained from the structure type BaHg 11 by doubling of the lattice parameter and subtraction of 16 atoms. The studied structure was compared with the structures of known compounds, which crystallize in the same space group with similar cell parameters.

Crystalline structures of particles interacting through the harmonic-repulsive pair potential

NASA Astrophysics Data System (ADS)

Levashov, V. A.

2017-09-01

The behavior of identical particles interacting through the harmonic-repulsive pair potential has been studied in 3D using molecular dynamics simulations at a number of different densities. We found that at many densities, as the temperature of the systems decreases, the particles crystallize into complex structures whose formation has not been anticipated in previous studies on the harmonic-repulsive pair potential. In particular, at certain densities, crystallization into the structure I a 3 ¯ d (space group #230) with 16 particles in the unit cell occupying Wyckoff special positions (16b) was observed. This crystal structure has not been observed previously in experiments or in computer simulations of single component atomic or soft matter systems. At another density, we observed a liquid which is rather stable against crystallization. Yet, we observed crystallization of this liquid into the monoclinic C2/c (space group #15) structure with 32 particles in the unit cell occupying four different non-special Wyckoff (8f) sites. In this structure particles located at different Wyckoff sites have different energies. From the perspective of the local atomic environment, the organization of particles in this structure resembles the structure of some columnar quasicrystals. At a different value of the density, we did not observe crystallization at all despite rather long molecular dynamics runs. At two other densities, we observed the formation of the β S n distorted diamond structures instead of the expected diamond structure. Possibly, we also observed the formation of the R 3 ¯ c hexagonal lattice with 24 particles per unit cell occupying non-equivalent positions.

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

Do All X-ray Structures of Protein-Ligand Complexes Represent Functional States? EPOR, a Case Study.

PubMed

Corbett, Michael S P; Mark, Alan E; Poger, David

2017-02-28

Based on differences between the x-ray crystal structures of ligand-bound and unbound forms, the activation of the erythropoietin receptor (EPOR) was initially proposed to involve a cross-action scissorlike motion. However, the validity of the motions involved in the scissorlike model has been recently challenged. Here, atomistic molecular dynamics simulations are used to examine the structure of the extracellular domain of the EPOR dimer in the presence and absence of erythropoietin and a series of agonistic or antagonistic mimetic peptides free in solution. The simulations suggest that in the absence of crystal packing effects, the EPOR chains in the different dimers adopt very similar conformations with no clear distinction between the agonist and antagonist-bound complexes. This questions whether the available x-ray crystal structures of EPOR truly represent active or inactive conformations. The study demonstrates the difficulty in using such structures to infer a mechanism of action, especially in the case of membrane receptors where just part of the structure has been considered in addition to potential confounding effects that arise from the comparison of structures in a crystal as opposed to a membrane environment. The work highlights the danger of assigning functional significance to small differences between structures of proteins bound to different ligands in a crystal environment without consideration of the effects of the crystal lattice and thermal motion. Copyright © 2017 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Synthesis and crystal structure analysis of uranyl triple acetates

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

Klepov, Vladislav V., E-mail: vladislavklepov@gmail.com; Department of Chemistry, Samara National Research University, 443086 Samara; Serezhkina, Larisa B.

2016-12-15

Single crystals of triple acetates NaR[UO{sub 2}(CH{sub 3}COO){sub 3}]{sub 3}·6H{sub 2}O (R=Mg, Co, Ni, Zn), well-known for their use as reagents for sodium determination, were grown from aqueous solutions and their structural and spectroscopic properties were studied. Crystal structures of the mentioned phases are based upon (Na[UO{sub 2}(CH{sub 3}COO){sub 3}]{sub 3}){sup 2–} clusters and [R(H{sub 2}O){sub 6}]{sup 2+} aqua-complexes. The cooling of a single crystal of NaMg[UO{sub 2}(CH{sub 3}COO){sub 3}]{sub 3}·6H{sub 2}O from 300 to 100 K leads to a phase transition from trigonal to monoclinic crystal system. Intermolecular interactions between the structural units and their mutual packing were studiedmore » and compared from the point of view of the stereoatomic model of crystal structures based on Voronoi-Dirichlet tessellation. Using this method we compared the crystal structures of the triple acetates with Na[UO{sub 2}(CH{sub 3}COO){sub 3}] and [R(H{sub 2}O){sub 6}][UO{sub 2}(CH{sub 3}COO){sub 3}]{sub 2} and proposed reasons of triple acetates stability. Infrared and Raman spectra were collected and their bands were assigned. - Graphical abstract: Single crystals of uranium based triple acetates, analytical reagents for sodium determination, were synthesized and structurally, spectroscopically and topologically characterized. The structures were compared with the structures of compounds from preceding families [M(H{sub 2}O){sub 6})][UO{sub 2}(CH{sub 3}COO){sub 3}]{sub 2} (M = Mg, Co, Ni, Zn) and Na[UO{sub 2}(CH{sub 3}COO){sub 3}]. Analysis was performed with the method of molecular Voronoi-Dirichlet polyhedra to reveal a large contribution of the hydrogen bonds into intermolecular interactions which can be a reason of low solubility of studied complexes.« less

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.

Synthesis, structure and characterization of a hybrid centrosymmetric material (4-dimethylaminopyridinium nitrate gallic acid monohydrate) well-designed for non-linear optics

NASA Astrophysics Data System (ADS)

Ennaceur, Nasreddine; Jalel, Boutheina; Henchiri, Rokaya; Cordier, Marie; Ledoux-Rak, Isabelle

2018-01-01

Hybrid material: 4-Dimethylaminopyridinium nitrate gallic acid monohydrate abbreviated DNGA monohydrate has been successfully synthesized by slow evaporation method at room temperature. X-ray diffraction (XRD) on a single crystal showed that the latter was crystallized in P-1 space group. Likewise, thermal analyses demonstrated the stability of our crystal up to 80 °C. Besides, the analysis of the infrared spectrum (FTIR), allowed us to confirm the presence of the different groups present in the structure. Furthermore, by studying the UV-Visible spectrum, the transparency of our crystal was proven. Despite the fact that of having a centrosymmetric structure, the nonlinear optical properties of our single crystal, which was tested by Kurtz-Perry technique, proved that its second harmonic generation efficiency was 1.22 times more than that of KDP (potassium dihydrogen phosphate) single crystal. This nonlinear optical behavior of the studied compound was also determined through the calculations of polarizability and first hyperpolarizability values.

Free-falling Crystals: Biological Macromolecular Crystal Growth Studies in Low Earth Orbit

NASA Technical Reports Server (NTRS)

Judge, Russell A.; Snell, E. H.; Pusey, M. L.; Whitaker, Ann F. (Technical Monitor)

2001-01-01

Spacecraft orbiting the earth experience a reduced acceleration environment due to being in a state of continuous free-fall. This state colloquially termed microgravity, has produced improved X-ray diffraction quality crystals of biological macromolecules. Improvements in X-ray diffraction resolution (detail) or signal to noise, provide greater detail in the three-dimensional molecular structure providing information about the molecule, how it works, how to improve its function or how to impede it. Greater molecular detail obtained by crystallization in microgravity, has important implications for structural biology. In this article we examine the theories behind macromolecule crystal quality improvement in microgravity using results obtained from studies with the model protein, chicken egg white lysozyme.

Life in the fast lane for protein crystallization and X-ray crystallography

NASA Technical Reports Server (NTRS)

Pusey, Marc L.; Liu, Zhi-Jie; Tempel, Wolfram; Praissman, Jeremy; Lin, Dawei; Wang, Bi-Cheng; Gavira, Jose A.; Ng, Joseph D.

2005-01-01

The common goal for structural genomic centers and consortiums is to decipher as quickly as possible the three-dimensional structures for a multitude of recombinant proteins derived from known genomic sequences. Since X-ray crystallography is the foremost method to acquire atomic resolution for macromolecules, the limiting step is obtaining protein crystals that can be useful of structure determination. High-throughput methods have been developed in recent years to clone, express, purify, crystallize and determine the three-dimensional structure of a protein gene product rapidly using automated devices, commercialized kits and consolidated protocols. However, the average number of protein structures obtained for most structural genomic groups has been very low compared to the total number of proteins purified. As more entire genomic sequences are obtained for different organisms from the three kingdoms of life, only the proteins that can be crystallized and whose structures can be obtained easily are studied. Consequently, an astonishing number of genomic proteins remain unexamined. In the era of high-throughput processes, traditional methods in molecular biology, protein chemistry and crystallization are eclipsed by automation and pipeline practices. The necessity for high-rate production of protein crystals and structures has prevented the usage of more intellectual strategies and creative approaches in experimental executions. Fundamental principles and personal experiences in protein chemistry and crystallization are minimally exploited only to obtain "low-hanging fruit" protein structures. We review the practical aspects of today's high-throughput manipulations and discuss the challenges in fast pace protein crystallization and tools for crystallography. Structural genomic pipelines can be improved with information gained from low-throughput tactics that may help us reach the higher-bearing fruits. Examples of recent developments in this area are reported from the efforts of the Southeast Collaboratory for Structural Genomics (SECSG).

Life in the Fast Lane for Protein Crystallization and X-Ray Crystallography

NASA Technical Reports Server (NTRS)

Pusey, Marc L.; Liu, Zhi-Jie; Tempel, Wolfram; Praissman, Jeremy; Lin, Dawei; Wang, Bi-Cheng; Gavira, Jose A.; Ng, Joseph D.

2004-01-01

The common goal for structural genomic centers and consortiums is to decipher as quickly as possible the three-dimensional structures for a multitude of recombinant proteins derived from known genomic sequences. Since X-ray crystallography is the foremost method to acquire atomic resolution for macromolecules, the limiting step is obtaining protein crystals that can be useful of structure determination. High-throughput methods have been developed in recent years to clone, express, purify, crystallize and determine the three-dimensional structure of a protein gene product rapidly using automated devices, commercialized kits and consolidated protocols. However, the average number of protein structures obtained for most structural genomic groups has been very low compared to the total number of proteins purified. As more entire genomic sequences are obtained for different organisms from the three kingdoms of life, only the proteins that can be crystallized and whose structures can be obtained easily are studied. Consequently, an astonishing number of genomic proteins remain unexamined. In the era of high-throughput processes, traditional methods in molecular biology, protein chemistry and crystallization are eclipsed by automation and pipeline practices. The necessity for high rate production of protein crystals and structures has prevented the usage of more intellectual strategies and creative approaches in experimental executions. Fundamental principles and personal experiences in protein chemistry and crystallization are minimally exploited only to obtain "low-hanging fruit" protein structures. We review the practical aspects of today s high-throughput manipulations and discuss the challenges in fast pace protein crystallization and tools for crystallography. Structural genomic pipelines can be improved with information gained from low-throughput tactics that may help us reach the higher-bearing fruits. Examples of recent developments in this area are reported from the efforts of the Southeast Collaboratory for Structural Genomics (SECSG).

Study of the In2O3 molecule in the free state and in the crystal

NASA Astrophysics Data System (ADS)

Kaplan, Ilya G.; Miranda, Ulises; Trakhtenberg, Leonid I.

2018-03-01

The nanomaterials based on the In2O3 molecule are widely used as catalysts and sensors among other applications. In the present study, we discuss the possibility of using nanoclusters of In2O3 as molecular photomotors. A comparative analysis of the electronic structure of the In2O3 molecule in the free state and in the crystal is performed. For the free In2O3 molecule the geometry of its lowest structures, V-shape and linear, was optimised at the CCSD(T) level, which is the most precise computational method applied up to date to study In2O3. Using experimental crystallographic data, we determined the geometry of In2O3 in the crystal. It has a zigzag, not symmetric structure and possesses a dipole moment with magnitude slightly smaller than that of the V-structure of the free molecule (the linear structure due to its symmetry has no dipole moment). According to the Natural Atomic population analysis, the chemical structure of the linear In2O3 can be represented as O = In-O-In = O; the V-shaped molecule has the similar double- and single-bond structure. The construction of nanoclusters from ´bricksʼ of In2O3 with geometry extracted from crystal (or nanoclusters extracted directly from crystal) and their use as photo-driven molecular motors are discussed.

Structuring β-Ga2O3 photonic crystal photocatalyst for efficient degradation of organic pollutants.

PubMed

Li, Xiaofang; Zhen, Xiuzheng; Meng, Sugang; Xian, Jiangjun; Shao, Yu; Fu, Xianzhi; Li, Danzhen

2013-09-03

Coupling photocatalysts with photonic crystals structure is based on the unique property of photonic crystals in confining, controlling, and manipulating the incident photons. This combination enhances the light absorption in photocatalysts and thus greatly improves their photocatalytic performance. In this study, Ga2O3 photonic crystals with well-arranged skeleton structures were prepared via a dip-coating infiltration method. The positions of the electronic band absorption for Ga2O3 photonic crystals could be made to locate on the red edge, on the blue edge, and away from the edge of their photonic band gaps by changing the pore sizes of the samples, respectively. Particularly, the electronic band absorption of the Ga2O3 photonic crystal with a pore size of 135 nm was enhanced more than other samples by making it locate on the red edge of its photonic band gap, which was confirmed by the higher instantaneous photocurrent and photocatalytic activity for the degradation of various organic pollutants under ultraviolet light irradiation. Furthermore, the degradation mechanism over Ga2O3 photonic crystals was discussed. The design of Ga2O3 photonic crystals presents a prospective application of photonic crystals in photocatalysis to address light harvesting and quantum efficiency problems through manipulating photons or constructing photonic crystal structure as groundwork.

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.

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.

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

Crystallization of Proteins from Crude Bovine Rod Outer Segments☆

PubMed Central

Baker, Bo Y.; Gulati, Sahil; Shi, Wuxian; Wang, Benlian; Stewart, Phoebe L.; Palczewski, Krzysztof

2015-01-01

Obtaining protein crystals suitable for X-ray diffraction studies comprises the greatest challenge in the determination of protein crystal structures, especially for membrane proteins and protein complexes. Although high purity has been broadly accepted as one of the most significant requirements for protein crystallization, a recent study of the Escherichia coli proteome showed that many proteins have an inherent propensity to crystallize and do not require a highly homogeneous sample (Totir et al., 2012). As exemplified by RPE65 (Kiser, Golczak, Lodowski, Chance, & Palczewski, 2009), there also are cases of mammalian proteins crystallized from less purified samples. To test whether this phenomenon can be applied more broadly to the study of proteins from higher organisms, we investigated the protein crystallization profile of bovine rod outer segment (ROS) crude extracts. Interestingly, multiple protein crystals readily formed from such extracts, some of them diffracting to high resolution that allowed structural determination. A total of seven proteins were crystallized, one of which was a membrane protein. Successful crystallization of proteins from heterogeneous ROS extracts demonstrates that many mammalian proteins also have an intrinsic propensity to crystallize from complex biological mixtures. By providing an alternative approach to heterologous expression to achieve crystallization, this strategy could be useful for proteins and complexes that are difficult to purify or obtain by recombinant techniques. PMID:25950977

Tackling both the player and the ball: lessons from crystallographic studies on the N-utilization substance B (NusB) from Mycobacterium tuberculosis

NASA Astrophysics Data System (ADS)

Haire, L. F.; Gopal, B.

2001-11-01

The N-utilization substance B (NusB) from Mycobacterium tuberculosis is an important element in a complex assembly of other proteins and ribonucleic acid effecting transcription antitermination in this organism. The cloning and overexpression of the protein in E. coli, followed by the purification, crystallization, and use of selenomethionine samples to obtain phase information by anomalous dispersion techniques, allows us to investigate the fine interplay of sample engineering and modification of crystallization parameters leading to successful structure determination. Knowledge of the crystal structure and the surface properties of the protein allows an analysis of the packing of the NusB dimers in the crystal lattice. This exercise, albeit post facto, helps to demonstrate how biophysical and functional information could help 'rationalize' the course of obtaining protein crystals suitable for structural studies.

Structure and Growth Control of Organic-Inorganic Halide Perovskites for Optoelectronics: From Polycrystalline Films to Single Crystals.

PubMed

Chen, Yani; He, Minhong; Peng, Jiajun; Sun, Yong; Liang, Ziqi

2016-04-01

Recently, organic-inorganic halide perovskites have sparked tremendous research interest because of their ground-breaking photovoltaic performance. The crystallization process and crystal shape of perovskites have striking impacts on their optoelectronic properties. Polycrystalline films and single crystals are two main forms of perovskites. Currently, perovskite thin films have been under intensive investigation while studies of perovskite single crystals are just in their infancy. This review article is concentrated upon the control of perovskite structures and growth, which are intimately correlated for improvements of not only solar cells but also light-emitting diodes, lasers, and photodetectors. We begin with the survey of the film formation process of perovskites including deposition methods and morphological optimization avenues. Strategies such as the use of additives, thermal annealing, solvent annealing, atmospheric control, and solvent engineering have been successfully employed to yield high-quality perovskite films. Next, we turn to summarize the shape evolution of perovskites single crystals from three-dimensional large sized single crystals, two-dimensional nanoplates, one-dimensional nanowires, to zero-dimensional quantum dots. Siginificant functions of perovskites single crystals are highlighted, which benefit fundamental studies of intrinsic photophysics. Then, the growth mechanisms of the previously mentioned perovskite crystals are unveiled. Lastly, perspectives for structure and growth control of perovskites are outlined towards high-performance (opto)electronic devices.

A comparative study of two polymorphs of L-aspartic acid hydrochloride.

PubMed

Benali-Cherif, Rim; Takouachet, Radhwane; Bendeif, El-Eulmi; Benali-Cherif, Nourredine

2014-07-01

Two polymorphs of L-aspartic acid hydrochloride, C4H8NO4(+)·Cl(-), were obtained from the same aqueous solution. Their crystal structures have been determined from single-crystal data collected at 100 K. The crystal structures revealed three- and two-dimensional hydrogen-bonding networks for the triclinic and orthorhombic polymorphs, respectively. The cations and anions are connected to one another via N-H···Cl and O-H···Cl interactions and form alternating cation-anion layer-like structures. The two polymorphs share common structural features; however, the conformations of the L-aspartate cations and the crystal packings are different. Furthermore, the molecular packing of the orthorhombic polymorph contains more interesting interactions which seems to be a favourable factor for more efficient charge transfer within the crystal.

Observing the overall rocking motion of a protein in a crystal

NASA Astrophysics Data System (ADS)

Ma, Peixiang; Xue, Yi; Coquelle, Nicolas; Haller, Jens D.; Yuwen, Tairan; Ayala, Isabel; Mikhailovskii, Oleg; Willbold, Dieter; Colletier, Jacques-Philippe; Skrynnikov, Nikolai R.; Schanda, Paul

2015-10-01

The large majority of three-dimensional structures of biological macromolecules have been determined by X-ray diffraction of crystalline samples. High-resolution structure determination crucially depends on the homogeneity of the protein crystal. Overall `rocking' motion of molecules in the crystal is expected to influence diffraction quality, and such motion may therefore affect the process of solving crystal structures. Yet, so far overall molecular motion has not directly been observed in protein crystals, and the timescale of such dynamics remains unclear. Here we use solid-state NMR, X-ray diffraction methods and μs-long molecular dynamics simulations to directly characterize the rigid-body motion of a protein in different crystal forms. For ubiquitin crystals investigated in this study we determine the range of possible correlation times of rocking motion, 0.1-100 μs. The amplitude of rocking varies from one crystal form to another and is correlated with the resolution obtainable in X-ray diffraction experiments.

Structural, chemical and physical properties of pure and La3+ doped L-Threonine acetate crystals

NASA Astrophysics Data System (ADS)

Senthamizhan, A.; Sambathkumar, K.; Nithiyanantham, S.; Venkatachalapathy, M.; Rajkamal, N.

2017-12-01

The pure and La3+ doped L- Threonine crystals can be grown by slow evaporation techniques. The crystal structure were examined through X-Ray diffraction (XRD) analysis, confirmed the P212121 system. The quantitative nature of dopant can be analyzed with Inductively Coupled Plasma (ICP) study. The Fourier Transform Infra-Red (FTIR) and Fourier Transform (FT- Raman) investigations yields the possible stretching/bonding with their functional groups and the qualitative/quantitative nature of both crystals is analyzed. The optical behavior of crystals can be studied through Ultra Violet (UV) - Visible spectrometer. The mechanical, thermal and decomposition studies can be carried out through Vickers hardness test, Thermo Gravometric Analysis (TGA) and Differential Thermal Analysis (DTA). The Non Linear Optical (NLO) properties are found more than Potassium Phosphate (KDP) through Kurtz powders technique. The dielectric and optical absorption studies for both pure and L-doped crystals were studied and interpreted all the properties. The La3+ dopant increases the properties are investigated.

Synthesis, crystal growth, structural and physicochemical studies of novel binary organic complex: 4-chloroaniline-3-hydroxy-4-methoxybenzaldehyde

NASA Astrophysics Data System (ADS)

Sharma, K. P.; Reddi, R. S. B.; Bhattacharya, S.; Rai, R. N.

2012-06-01

The solid-state reaction, which is solvent free and green synthesis, has been adopted to explore the novel compound. The phase diagram of 4-chloroaniline (CA) and 3-hydroxy-4-methoxybenzaldehyde (HMB) system shows the formation of a novel 1:1 molecular complex, and two eutectics on either sides of complex. Thermochemical studies of complex and eutectics have been carried out for various properties such as heat of fusion, entropy of fusion, Jackson's parameters, interfacial energy and excess thermodynamic functions. The formation of molecular complex was also studied by IR, NMR, elemental analysis and UV-Vis absorption spectra. The single crystal of molecular complex was grown and its XRD study confirms the formation of complex and identifies the crystal structure and atomic packing of crystal of complex. Transmission spectra of grown crystal of the complex show 70% transmittance efficiency with cut off wavelength 412 nm. The band gap and refractive index of the crystal of complex have also been studied.

Hydrostatic Compression of 2,4,6,8,10,12 hexanitrohexaaza isowurtzitane (CL20) Co Crystals

DTIC Science & Technology

2016-12-01

crystal with analyses of the unit cell volume, band structure , elastic coefficients, and optical absorption Approved for public release...studied and for each system the high pressure (to 50 GPa) unit cell parameters, bulk modulus, and estimates of the shock, particle, and sound ...List of Figures Fig. 1 Experimental unit cell structures of ε-CL20 and co-crystals. For each structure , the CL20 molecules are red and the guest

Reduced-temperature crystallization of thin amorphous Fe80B20 films studied via empirical modeling of extended x-ray absorption fine structure

NASA Astrophysics Data System (ADS)

Harris, V. G.; Oliver, S. A.; Ayers, J. D.; Das, B. N.; Koon, N. C.

1996-04-01

The evolution of the local atomic environment around Fe atoms in very thin (15 nm), amorphous, partially crystallized and fully crystallized films of Fe80B20 was studied using extended x-ray absorption fine structure (EXAFS) measurements. The relative atomic fraction of each crystalline phase present in the annealed samples was extracted from the Fe EXAFS data by a least-squares fitting procedure, using data collected from t-Fe3B, t-Fe2B, and α-Fe standards. The type and relative fraction of the crystallization products follows the trends previously measured in Fe80B20 melt-spun ribbons, except for the fact that crystallization temperatures are ≊200 K lower than those measured in bulk equivalents. This greatly reduced crystallization temperature may arise from the dominant role of surface nucleation sites in the crystallization of very thin amorphous films.

Synthesis and structural characterization of bulk Sb2Te3 single crystal

NASA Astrophysics Data System (ADS)

Sultana, Rabia; Gahtori, Bhasker; Meena, R. S.; Awana, V. P. S.

2018-05-01

We report the growth and characterization of bulk Sb2Te3 single crystal synthesized by the self flux method via solid state reaction route from high temperature melt (850˚C) and slow cooling (2˚C/hour) of constituent elements. The single crystal X-ray diffraction pattern showed the 00l alignment and the high crystalline nature of the resultant sample. The rietveld fitted room temperature powder XRD revealed the phase purity and rhombohedral structure of the synthesized crystal. The formation and analysis of unit cell structure further verified the rhombohedral structure composed of three quintuple layers stacked one over the other. The SEM image showed the layered directional growth of the synthesized crystal carried out using the ZEISS-EVOMA-10 scanning electron microscope The electrical resistivity measurement was carried out using the conventional four-probe method on a quantum design Physical Property Measurement System (PPMS). The temperature dependent electrical resistivity plot for studied Sb2Te3 single crystal depicts metallic behaviour in the absence of any applied magnetic field. The synthesis as well as the structural characterization of as grown Sb2Te3 single crystal is reported and discussed in the present letter.

Exchange-Hole Dipole Dispersion Model for Accurate Energy Ranking in Molecular Crystal Structure Prediction.

PubMed

Whittleton, Sarah R; Otero-de-la-Roza, A; Johnson, Erin R

2017-02-14

Accurate energy ranking is a key facet to the problem of first-principles crystal-structure prediction (CSP) of molecular crystals. This work presents a systematic assessment of B86bPBE-XDM, a semilocal density functional combined with the exchange-hole dipole moment (XDM) dispersion model, for energy ranking using 14 compounds from the first five CSP blind tests. Specifically, the set of crystals studied comprises 11 rigid, planar compounds and 3 co-crystals. The experimental structure was correctly identified as the lowest in lattice energy for 12 of the 14 total crystals. One of the exceptions is 4-hydroxythiophene-2-carbonitrile, for which the experimental structure was correctly identified once a quasi-harmonic estimate of the vibrational free-energy contribution was included, evidencing the occasional importance of thermal corrections for accurate energy ranking. The other exception is an organic salt, where charge-transfer error (also called delocalization error) is expected to cause the base density functional to be unreliable. Provided the choice of base density functional is appropriate and an estimate of temperature effects is used, XDM-corrected density-functional theory is highly reliable for the energetic ranking of competing crystal structures.

Seeding for sirtuins: microseed matrix seeding to obtain crystals of human Sirt3 and Sirt2 suitable for soaking

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

Rumpf, Tobias; Gerhardt, Stefan; Einsle, Oliver, E-mail: einsle@biochemie.uni-freiburg.de

2015-11-18

In the present study, microseed matrix seeding was successfully applied to obtain a large number of crystals of the human sirtuin isotypes Sirt2 and Sirt3. These crystals appeared predictably in diverse crystallization conditions, diffracted to a higher resolution than reported in the literature and were subsequently used to study the protein–ligand interactions of two indole inhibitors. Sirtuins constitute a family of NAD{sup +}-dependent enzymes that catalyse the cleavage of various acyl groups from the ∊-amino group of lysines. They regulate a series of cellular processes and their misregulation has been implicated in various diseases, making sirtuins attractive drug targets. Tomore » date, only a few sirtuin modulators have been reported that are suitable for cellular research and their development has been hampered by a lack of structural information. In this work, microseed matrix seeding (MMS) was used to obtain crystals of human Sirt3 in its apo form and of human Sirt2 in complex with ADP ribose (ADPR). Crystal formation using MMS was predictable, less error-prone and yielded a higher number of crystals per drop than using conventional crystallization screening methods. The crystals were used to solve the crystal structures of apo Sirt3 and of Sirt2 in complex with ADPR at an improved resolution, as well as the crystal structures of Sirt2 in complex with ADPR and the indoles EX527 and CHIC35. These Sirt2–ADPR–indole complexes unexpectedly contain two indole molecules and provide novel insights into selective Sirt2 inhibition. The MMS approach for Sirt2 and Sirt3 may be used as the basis for structure-based optimization of Sirt2/3 inhibitors in the future.« less

Rare-earth metal gallium silicides via the gallium self-flux method. Synthesis, crystal structures, and magnetic properties of RE(Ga 1–xSi x)₂ (RE=Y, La–Nd, Sm, Gd–Yb, Lu)

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

Darone, Gregory M.; Hmiel, Benjamin; Zhang, Jiliang

Fifteen ternary rare-earth metal gallium silicides have been synthesized using molten Ga as a molten flux. They have been structurally characterized by single-crystal and powder X-ray diffraction to form with three different structures—the early to mid-late rare-earth metals RE=La–Nd, Sm, Gd–Ho, Yb and Y form compounds with empirical formulae RE(Ga xSi 1–x)₂ (0.38≤x≤0.63), which crystallize with the tetragonal α-ThSi₂ structure type (space group I4₁/amd, No. 141; Pearson symbol tI12). The compounds of the late rare-earth crystallize with the orthorhombic α-GdSi₂ structure type (space group Imma, No. 74; Pearson symbol oI12), with refined empirical formula REGa xSi 2–x–y (RE=Ho, Er, Tm;more » 0.33≤x≤0.40, 0.10≤y≤0.18). LuGa₀.₃₂₍₁₎Si₁.₄₃₍₁₎ crystallizes with the orthorhombic YbMn₀.₁₇Si₁.₈₃ structure type (space group Cmcm, No. 63; Pearson symbol oC24). Structural trends are reviewed and analyzed; the magnetic susceptibilities of the grown single-crystals are presented. - Graphical abstract: This article details the exploration of the RE–Ga–Si ternary system with the aim to systematically investigate the structural “boundaries” between the α-ThSi₂ and α-GdSi₂-type structures, and studies of the magnetic properties of the newly synthesized single-crystalline materials. Highlights: • Light rare-earth gallium silicides crystallize in α-ThSi₂ structure type. • Heavy rare-earth gallium silicides crystallize in α-GdSi₂ structure type. • LuGaSi crystallizes in a defect variant of the YbMn₀.₁₇Si₁.₈₃ structure type.« less

Growth and microtopographic study of CuInSe{sub 2} single crystals

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

Chauhan, Sanjaysinh M.; Chaki, Sunil, E-mail: sunilchaki@yahoo.co.in; Deshpande, M. P.

2016-05-23

The CuInSe{sub 2} single crystals were grown by chemical vapour transport (CVT) technique using iodine as transporting agent. The elemental composition of the as-grown CuInSe{sub 2} single crystals was determined by energy dispersive analysis of X-ray (EDAX). The unit cell crystal structure and lattice parameters were determined by X-ray diffraction (XRD) technique. The surface microtopographic study of the as-grown CuInSe{sub 2} single crystals surfaces were done to study the defects, growth mechanism, etc. of the CVT grown crystals.

Crystallization and preliminary X-ray diffraction study of the protealysin precursor belonging to the peptidase family M4

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

Gromova, T. Yu., E-mail: duk@img.ras.ru; Demidyuk, I. V.; Kostrov, S. V.

2008-09-15

A protealysin precursor (the enzyme of the peptidase family M4) was crystallized for the first time. The crystal-growth conditions were found, and single crystals of the protein with dimensions of 0.3-0.5 mm were grown. The preliminary X-ray diffraction study of the enzyme was performed. The protealysin precursor was shown to crystallize in two crystal modifications suitable for the X-ray diffraction study of the three-dimensional structure of the protein molecule at atomic resolution.

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.

In situ X-ray data collection and structure phasing of protein crystals at Structural Biology Center 19-ID

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

Michalska, Karolina; Tan, Kemin; Chang, Changsoo

A prototype of a 96-well plate scanner forin situdata collection has been developed at the Structural Biology Center (SBC) beamline 19-ID, located at the Advanced Photon Source, USA. The applicability of this instrument for protein crystal diffraction screening and data collection at ambient temperature has been demonstrated. Several different protein crystals, including selenium-labeled, were used for data collection and successful SAD phasing. Without the common procedure of crystal handling and subsequent cryo-cooling for data collection atT= 100 K, crystals in a crystallization buffer show remarkably low mosaicity (<0.1°) until deterioration by radiation damage occurs. Data presented here show that cryo-coolingmore » can cause some unexpected structural changes. Based on the results of this study, the integration of the plate scanner into the 19-ID end-station with automated controls is being prepared. With improvement of hardware and software,in situdata collection will become available for the SBC user program including remote access.« less

Amorphous photonic crystals with only short-range order.

PubMed

Shi, Lei; Zhang, Yafeng; Dong, Biqin; Zhan, Tianrong; Liu, Xiaohan; Zi, Jian

2013-10-04

Distinct from conventional photonic crystals with both short- and long-range order, amorphous photonic crystals that possess only short-range order show interesting optical responses owing to their unique structural features. Amorphous photonic crystals exhibit unique light scattering and transport, which lead to a variety of interesting phenomena such as isotropic photonic bandgaps or pseudogaps, noniridescent structural colors, and light localization. Recent experimental and theoretical advances in the study of amorphous photonic crystals are summarized, focusing on their unique optical properties, artificial fabrication, bionspiration, and potential applications. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

A photonic crystal ring resonator formed by SOI nano-rods.

PubMed

Chiu, Wei-Yu; Huang, Tai-Wei; Wu, Yen-Hsiang; Chan, Yi-Jen; Hou, Chia-Hunag; Chien, Huang Ta; Chen, Chii-Chang

2007-11-12

The design, fabrication and measurement of a silicon-on-insulator (SOI) two-dimensional photonic crystal ring resonator are demonstrated in this study. The structure of the photonic crystal is comprised of silicon nano-rods arranged in a hexagonal lattice on an SOI wafer. The photonic crystal ring resonator allows for the simultaneous separation of light at wavelengths of 1.31 and 1.55mum. The device is fabricated by e-beam lithography. The measurement results confirm that a 1.31mum/1.55mum wavelength ring resonator filter with a nano-rod photonic crystal structure can be realized.

Neutron protein crystallography: A complementary tool for locating hydrogens in proteins.

PubMed

O'Dell, William B; Bodenheimer, Annette M; Meilleur, Flora

2016-07-15

Neutron protein crystallography is a powerful tool for investigating protein chemistry because it directly locates hydrogen atom positions in a protein structure. The visibility of hydrogen and deuterium atoms arises from the strong interaction of neutrons with the nuclei of these isotopes. Positions can be unambiguously assigned from diffraction at resolutions typical of protein crystals. Neutrons have the additional benefit to structural biology of not inducing radiation damage in protein crystals. The same crystal could be measured multiple times for parametric studies. Here, we review the basic principles of neutron protein crystallography. The information that can be gained from a neutron structure is presented in balance with practical considerations. Methods to produce isotopically-substituted proteins and to grow large crystals are provided in the context of neutron structures reported in the literature. Available instruments for data collection and software for data processing and structure refinement are described along with technique-specific strategies including joint X-ray/neutron structure refinement. Examples are given to illustrate, ultimately, the unique scientific value of neutron protein crystal structures. Copyright © 2015 Elsevier Inc. All rights reserved.

The "Sticky Patch" Model of Crystallization and Modification of Proteins for Enhanced Crystallizability.

PubMed

Derewenda, Zygmunt S; Godzik, Adam

2017-01-01

Crystallization of macromolecules has long been perceived as a stochastic process, which cannot be predicted or controlled. This is consistent with another popular notion that the interactions of molecules within the crystal, i.e., crystal contacts, are essentially random and devoid of specific physicochemical features. In contrast, functionally relevant surfaces, such as oligomerization interfaces and specific protein-protein interaction sites, are under evolutionary pressures so their amino acid composition, structure, and topology are distinct. However, current theoretical and experimental studies are significantly changing our understanding of the nature of crystallization. The increasingly popular "sticky patch" model, derived from soft matter physics, describes crystallization as a process driven by interactions between select, specific surface patches, with properties thermodynamically favorable for cohesive interactions. Independent support for this model comes from various sources including structural studies and bioinformatics. Proteins that are recalcitrant to crystallization can be modified for enhanced crystallizability through chemical or mutational modification of their surface to effectively engineer "sticky patches" which would drive crystallization. Here, we discuss the current state of knowledge of the relationship between the microscopic properties of the target macromolecule and its crystallizability, focusing on the "sticky patch" model. We discuss state-of-the-art in silico methods that evaluate the propensity of a given target protein to form crystals based on these relationships, with the objective to design variants with modified molecular surface properties and enhanced crystallization propensity. We illustrate this discussion with specific cases where these approaches allowed to generate crystals suitable for structural analysis.

Second harmonic generation and crystal growth of new chalcone derivatives

NASA Astrophysics Data System (ADS)

Patil, P. S.; Dharmaprakash, S. M.; Ramakrishna, K.; Fun, Hoong-Kun; Sai Santosh Kumar, R.; Narayana Rao, D.

2007-05-01

We report on the synthesis, crystal structure and optical characterization of chalcone derivatives developed for second-order nonlinear optics. The investigation of a series of five chalcone derivatives with the second harmonic generation powder test according to Kurtz and Perry revealed that these chalcones show efficient second-order nonlinear activity. Among them, high-quality single crystals of 3-Br-4'-methoxychalcone (3BMC) were grown by solvent evaporation solution growth technique. Grown crystals were characterized by X-ray powder diffraction (XRD), laser damage threshold, UV-vis-NIR and refractive index measurement studies. Infrared spectroscopy, thermogravimetric analysis and differential thermal analysis measurements were performed to study the molecular vibration and thermal behavior of 3BMC crystal. Thermal analysis does not show any structural phase transition.

Growth of a New Ternary BON Crystal on Si(100) by Plasma-Assisted MOCVD and Study on the Effects of Fed Gas and Growth Temperature

NASA Astrophysics Data System (ADS)

Chen, G. C.; Lee, S.-B.; Boo, J.-H.

A new ternary BOxNy crystal was grown on Si(100) substrate at 500°C by low-frequency (100 kHz) radio-frequency (rf) derived plasma-assisted MOCVD with an organoborate precursor. The as-grown deposits were characterized by SEM, TED, XPS, XRD, AFM and FT-IR. The experimental results showed that BOxNy crystal was apt to be formed at N-rich atmosphere and high temperature. The decrease of hydrogen flux in fed gases was of benefit to form BON crystal structure. The crystal structure of BOxNy was as similar to that of H3BO3 in this study.

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.

Specific features of the structural and magnetic states of a Zn1 - x Ni x Se crystal ( x = 0.0025) at low temperatures

NASA Astrophysics Data System (ADS)

Dubinin, S. F.; Sokolov, V. I.; Parkhomenko, V. D.; Teploukhov, S. G.; Gruzdev, N. B.

2008-12-01

The magnetic state and the structure of a Zn1 - x Ni x Se ( x = 0.0025) bulk crystal were studied at low temperatures. It is revealed that the magnetic and crystal structures below T ≅ 15 K are dependent on the cooling rate of this dilute semiconductor. For example, on fast cooling to 4.2 K, about 10% hexagonal ferromagnetic phase is formed in the crystal. During heating, the phase disappears at T ≅ 15 K. The results obtained are discussed with allowance for the specific features of the Jahn-Teller distortions in this compound.

Dipicolinate salt of imidazole: Discovering its structure and properties using different experimental methodologies and quantum chemical investigations

NASA Astrophysics Data System (ADS)

Thirumurugan, R.; Anitha, K.

2018-03-01

A novel organic proton transfer complex of imidazolium dipicolinate (ID) has been synthesized and it was grown as single crystals using slow evaporation method. The molecular structure of synthesized compound and vibrational modes of its functional groups were confirmed by (1H and 13C) NMR, FTIR and FT-Raman spectroscopic studies, respectively. Single crystal X-ray diffraction (SCXRD) analysis confirmed the orthorhombic system with noncentrosymmetric (NCS), P212121, space group of grown ID crystal. UV-Vis-NIR spectral study confirmed its high optical transparency within the region of 285-1500 nm. Powder second harmonic generation (SHG) efficiency of ID crystal was confirmed and it was 6.8 times that of KDP crystal. TG-DTA and DSC analysis revealed the higher thermal stability of grown crystal as 249 °C. The dielectric response and mechanical behaviour of grown crystal were studied effectively. Density functional theory calculations were performed to probe the relationship between the structure and its properties including molecular optimization, Mulliken atomic charge distribution, frontier molecular orbital (FMOs) and molecular electrostatic potential map (MEP) analysis and first hyperpolarizability. All these experimental and computational results were discussed in this communication and it endorsed the ID compound as a potential NLO candidate could be employed in optoelectronics device applications in near future.

Shaping Crystal-Crystal Phase Transitions

NASA Astrophysics Data System (ADS)

Du, Xiyu; van Anders, Greg; Dshemuchadse, Julia; Glotzer, Sharon

Previous computational and experimental studies have shown self-assembled structure depends strongly on building block shape. New synthesis techniques have led to building blocks with reconfigurable shape and it has been demonstrated that building block reconfiguration can induce bulk structural reconfiguration. However, we do not understand systematically how this transition happens as a function of building block shape. Using a recently developed ``digital alchemy'' framework, we study the thermodynamics of shape-driven crystal-crystal transitions. We find examples of shape-driven bulk reconfiguration that are accompanied by first-order phase transitions, and bulk reconfiguration that occurs without any thermodynamic phase transition. Our results suggest that for well-chosen shapes and structures, there exist facile means of bulk reconfiguration, and that shape-driven bulk reconfiguration provides a viable mechanism for developing functional materials.

Crystal and magnetic structure of the La1-xCaxMnO3 compound (0.11⩽x⩽0.175)

NASA Astrophysics Data System (ADS)

Pissas, M.; Margiolaki, I.; Papavassiliou, G.; Stamopoulos, D.; Argyriou, D.

2005-08-01

We studied the crystal and magnetic structure of the La1-xCaxMnO3 compound for (0.11⩽x⩽0.175) using stoichiometric samples. For x<0.13 the system’s ground state is insulating canted antiferromagnetic. For 0.13⩽x⩽0.175 below the Jahn-Teller transition temperature (TJT) the crystal structure undergoes a monoclinic distortion. The crystal structure can be described with P21/c space group which permits two Mn sites. The unit-cell strain parameter s=2(a-c)/(a+c) increases for Ta>b/2) structure.

Epitaxial Growth of an Organic p-n Heterojunction: C60 on Single-Crystal Pentacene.

PubMed

Nakayama, Yasuo; Mizuno, Yuta; Hosokai, Takuya; Koganezawa, Tomoyuki; Tsuruta, Ryohei; Hinderhofer, Alexander; Gerlach, Alexander; Broch, Katharina; Belova, Valentina; Frank, Heiko; Yamamoto, Masayuki; Niederhausen, Jens; Glowatzki, Hendrik; Rabe, Jürgen P; Koch, Norbert; Ishii, Hisao; Schreiber, Frank; Ueno, Nobuo

2016-06-01

Designing molecular p-n heterojunction structures, i.e., electron donor-acceptor contacts, is one of the central challenges for further development of organic electronic devices. In the present study, a well-defined p-n heterojunction of two representative molecular semiconductors, pentacene and C60, formed on the single-crystal surface of pentacene is precisely investigated in terms of its growth behavior and crystallographic structure. C60 assembles into a (111)-oriented face-centered-cubic crystal structure with a specific epitaxial orientation on the (001) surface of the pentacene single crystal. The present experimental findings provide molecular scale insights into the formation mechanisms of the organic p-n heterojunction through an accurate structural analysis of the single-crystalline molecular contact.

Correlation of lattice defects and thermal processing in the crystallization of titania nanotube arrays

NASA Astrophysics Data System (ADS)

Hosseinpour, Pegah M.; Yung, Daniel; Panaitescu, Eugen; Heiman, Don; Menon, Latika; Budil, David; Lewis, Laura H.

2014-12-01

Titania nanotubes have the potential to be employed in a wide range of energy-related applications such as solar energy-harvesting devices and hydrogen production. As the functionality of titania nanostructures is critically affected by their morphology and crystallinity, it is necessary to understand and control these factors in order to engineer useful materials for green applications. In this study, electrochemically-synthesized titania nanotube arrays were thermally processed in inert and reducing environments to isolate the role of post-synthesis processing conditions on the crystallization behavior, electronic structure and morphology development in titania nanotubes, correlated with the nanotube functionality. Structural and calorimetric studies revealed that as-synthesized amorphous nanotubes crystallize to form the anatase structure in a three-stage process that is facilitated by the creation of structural defects. It is concluded that processing in a reducing gas atmosphere versus in an inert environment provides a larger unit cell volume and a higher concentration of Ti3+ associated with oxygen vacancies, thereby reducing the activation energy of crystallization. Further, post-synthesis annealing in either reducing or inert atmospheres produces pronounced morphological changes, confirming that the nanotube arrays thermally transform into a porous morphology consisting of a fragmented tubular architecture surrounded by a network of connected nanoparticles. This study links explicit data concerning morphology, crystallization and defects, and shows that the annealing gas environment determines the details of the crystal structure, the electronic structure and the morphology of titania nanotubes. These factors, in turn, impact the charge transport and consequently the functionality of these nanotubes as photocatalysts.

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.

Exploring Molecular Speciation and Crystallization Mechanism of Amorphous 2-Phenylamino Nicotinic Acid.

PubMed

Kalra, Arjun; Lubach, Joseph W; Munson, Eric J; Li, Tonglei

2018-02-07

Molecular understanding of phase stability and transition of the amorphous state helps in formulation and manufacturing of poorly-soluble drugs. Crystallization of a model compound, 2-phenylamino nicotinic acid (2PNA), from the amorphous state was studied using solid-state analytical methods. Our previous report suggests that 2PNA molecules mainly develop intermolecular -COOH∙∙∙pyridine N (acid-pyridine) interactions in the amorphous state. In the current study, the molecular speciation is explored with regard to the phase transition from the amorphous to the crystalline state. Using spectroscopic techniques, the molecular interactions and structural evolvement during the recrystallization from the glassy state were investigated. The results unveiled that the structurally heterogeneous amorphous state contains acid-pyridine aggregates - either as hydrogen-bonded neutral molecules or as zwitterions - as well as a population of carboxylic acid dimers. Phase transition from the amorphous state results in crystal structures composed of carboxylic acid dimer (acid-acid) synthon or acid-pyridine chains depending on the crystallization conditions employed. The study underlines the structural evolvement, as well as its impact on the metastability, of amorphous samples from local, supramolecular assemblies to long-range intermolecular ordering through crystallization.

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.

Protein Crystal Quality Studies

NASA Technical Reports Server (NTRS)

1998-01-01

Eddie Snell (standing), Post-Doctoral Fellow the National Research Council (NRC),and Marc Pusey of Marshall Space Flight Center (MSFC) use a reciprocal space mapping diffractometer for marcromolecular crystal quality studies. The diffractometer is used in mapping the structure of marcromolecules such as proteins to determine their structure and thus understand how they function with other proteins in the body. This is one of several analytical tools used on proteins crystalized on Earth and in space experiments. Photo credit: NASA/Marshall Space Flight Center (MSFC)

A hetero-micro-seeding strategy for readily crystallizing closely related protein variants.

PubMed

Islam, Mohammad M; Kuroda, Yutaka

2017-11-04

Protein crystallization remains difficult to rationalize and screening for optimal crystallization conditions is a tedious and time consuming procedure. Here, we report a hetero-micro-seeding strategy for producing high resolution crystals of closely related protein variants, where micro crystals from a readily crystallized variant are used as seeds to develop crystals of other variants less amenable to crystallization. We applied this strategy to Bovine Pancreatic Trypsin Inhibitor (BPTI) variants, which would not crystallize using standard crystallization practice. Out of six variants in our analysis, only one called BPTI-[5,55]A14G formed well behaving crystals; and the remaining five (A14GA38G, A14GA38V, A14GA38L, A14GA38I, and A14GA38K) could be crystallized only using micro-seeds from the BPTI-[5,55]A14G crystal. All hetero-seeded crystals diffracted at high resolution with minimum mosaicity, retaining the same space group and cell dimension. Moreover, hetero-micro-seeding did not introduce any biases into the mutant's structure toward the seed structure, as demonstrated by A14GA38I structures solved using micro-seeds from A14GA38G, A14GA38L and A14GA38I. Though hetero-micro-seeding is a simple and almost naïve strategy, this is the first direct demonstration of its workability. We believe that hetero-micro-seeding, which is contrasting with the popular idea that crystallization requires highly purified proteins, could contribute a new tool for rapidly solving protein structures in mutational analysis studies. Copyright © 2017 Elsevier Inc. All rights reserved.

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

Preparation, structural characterization, and decomposition studies of two new γ-octamolybdates of 4-methylpyridine.

PubMed

Szymańska, Anna; Nitek, Wojciech; Rutkowska-Zbik, Dorota; Łasocha, Wiesław

We synthesized two new γ-octamolybdates, and determined their crystal structures from single-crystal X-ray diffraction data. Orange-yellow tetrakis(4-methylpyridinium) bis(4-methylpyridine)-γ-octamolybdate 1 crystallizes in space group P2 1 /c with a  = 11.586(2) Å, b  = 15.526(2) Å, c  = 16.247(2) Å, β  = 118.753(1)º, Z  = 2. White tetrakis(4-methylpyridinium) bis(4-methylpyridine)-γ-octamolybdate hydrate 2 crystallizes in space group C2/c with a  = 27.086(4) Å, b  = 11.917(2) Å, c  = 19.332(2) Å, β  = 124.427(1)º, Z  = 4. Results of crystal structure determinations are presented and discussed in this paper. Thermal stability and decomposition studies of the obtained two new γ-octamolybdates were performed using TG/DSC and XRPD methods. Both compounds decomposed with the formation of 4-methylpyridinium β-octamolybdate. The two compounds are pseudo-polymorphs, exhibiting both striking similarities as well as significant differences in their structures and properties.

Crystal structure, vibrational and DFT simulation studies of melaminium dihydrogen phosphite monohydrate

NASA Astrophysics Data System (ADS)

Arjunan, V.; Kalaivani, M.; Marchewka, M. K.; Mohan, S.

2013-08-01

The crystal structure investigations of melamine with phosphorous acid, namely melaminium dihydrogenphosphite monohydrate (C3N6H7·H2PO3·H2O) have been investigated by means of single crystal X-ray diffraction method. The title compound crystallizes in monoclinic crystal system, and the space group is P21/c with a = 10.069 Å, b = 21.592 Å, c = 12.409 Å and Z = 12. The vibrational assignments and analysis of melaminium dihydrogen phosphite monohydrate have also been performed by FTIR, FT-Raman and far-infrared spectral studies. The quantum chemical simulations were performed with DFT (B3LYP) method using 6-31G**, cc-pVTZ, and 6-311++G** basis sets to determine the energy, structural, thermodynamic parameters and vibrational frequencies of melaminium dihydrogen phosphite monohydrate. The hydrogen atom from phosphorous acid was transferred to the melamine molecule giving the singly protonated melaminium cation. The ability of ions to form spontaneous three-dimensional structure through weak Osbnd H···O and Nsbnd H···O hydrogen bonds shows notable vibrational effects.

Purification, isolation, crystallization, and preliminary X-ray diffraction study of the BTB domain of the centrosomal protein 190 from Drosophila melanogaster

NASA Astrophysics Data System (ADS)

Boyko, K. M.; Nikolaeva, A. Yu.; Kachalova, G. S.; Bonchuk, A. N.; Popov, V. O.

2017-11-01

The spatial organization of the genome is controlled by a special class of architectural proteins, including proteins containing BTB domains that are able to dimerize or multimerize. The centrosomal protein 190 is one of such architectural proteins. The purification, crystallization, and preliminary X-ray diffraction study of the BTB domain of the centrosomal protein 190 are reported. The crystallization conditions were found by the vapor-diffusion technique. The crystals diffracted to 1.5 Å resolution and belonged to sp. gr. P3221. The structure was solved by the molecular replacement method. The structure refinement is currently underway.

First X-ray crystal structure and internal reference diffusion-ordered NMR spectroscopy study of the prototypical Posner reagent, MeCu(SPh)Li(THF)3.

PubMed

Bertz, Steven H; Hardin, Richard A; Heavey, Thomas J; Jones, Daniel S; Monroe, T Blake; Murphy, Michael D; Ogle, Craig A; Whaley, Tara N

2013-07-29

Grow slow: The usual direct treatment of MeLi and CuSPh did not yield X-ray quality crystals of MeCu(SPh)Li. An indirect method starting from Me2CuLi⋅LiSPh and chalcone afforded the desired crystals by the slow reaction of the intermediate π-complex (see scheme). This strategy produced the first X-ray crystal structure of a Posner cuprate. A complementary NMR study showed that the contact ion pair was also the main species in solution. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Single crystal, liquid crystal, and hybrid organic semiconductors

NASA Astrophysics Data System (ADS)

Twieg, Robert J.; Getmanenko, Y.; Lu, Z.; Semyonov, A. N.; Huang, S.; He, P.; Seed, A.; Kiryanov, A.; Ellman, B.; Nene, S.

2003-07-01

The synthesis and characterization of organic semiconductors is being pursued in three primary structure formats: single crystal, liquid crystal and organic-inorganic hybrid. The strategy here is to share common structures, synthesis methods and fabrication techniques across these formats and to utilize common characterization tools such as the time of flight technique. The single crystal efforts concentrate on aromatic and heteroaromatic compounds including simple benzene derivatives and derivatives of the acenes. The structure-property relationships due to incorporation of small substituents and heteroatoms are being examined. Crystals are grown by solution, melt or vapor transport techniques. The liquid crystal studies exploit their self-organizing properties and relative ease of sample preparation. Though calamitic systems tha deliver the largest mobilities are higher order smectics, even some unusual twist grain boundary phases are being studied. We are attempting to synthesize discotic acene derivatives with appropriate substitution patterns to render them mesogenic. The last format being examined is the hybrid organic-inorganic class. Here, layered materials of alternating organic and inorganic composition are designed and synthesized. Typical materials are conjugated aromatic compounds, usually functinalized with an amine or a pyridine and reacted with appropriate reactive metal derivatives to incorporate them into metal oxide or sulfide layers.

Deducing 2D Crystal Structure at the Solid/Liquid Interface with Atomic Resolution by Combined STM and SFG Study

NASA Astrophysics Data System (ADS)

McClelland, Arthur; Ahn, Seokhoon; Matzger, Adam J.; Chen, Zhan

2009-03-01

Supplemented by computed models, Scanning Tunneling Microscopy (STM) can provide detailed structure of 2D crystals formed at the liquid/solid interface with atomic resolution. However, some structural information such as functional group orientations in such 2D crystals needs to be tested experimentally to ensure the accuracy of the deduced structures. Due to the limited sensitivity, many other experimental techniques such as Raman and infrared spectroscopy have not been allowed to provide such structural information of 2D crystals. Here we showed that Sum Frequency Generation Vibrational Spectroscopy (SFG) can measure average orientation of functional groups in such 2D crystals, or physisorbed monolayers, providing key experimental data to aid in the modeling and interpretation of the STM images. The usefulness of combining these two techniques is demonstrated with a phthalate diesters monolayer formed at the 1-phenyloctane/ highly oriented pyrolytic graphite (HOPG) interface. The spatial orientation of the ester C=O of the monolayer was successfully determined using SFG.

Synthesis and Crystal Structure Study of 2’-Se-Adenosine-Derivatized DNA

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

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

2010-01-01

The selenium derivatization of nucleic acids is a novel and promising strategy for 3D structure determination of nucleic acids. Selenium can serve as an excellent anomalous scattering center to solve the phase problem, which is one of the two major bottlenecks in macromolecule X-ray crystallography. The other major bottleneck is crystallization. It has been demonstrated that the incorporated selenium functionality at the 2'-positions of the nucleosides and nucleotides is stable and does not cause significant structure perturbation. Furthermore, it was observed that the 2'-Se-derivatization could facilitate crystallization of oligonucleotides with fast crystal growth and high diffraction quality. Herein, we describemore » a convenient synthesis of the 2'-Se-adenosine phosphoramidite, and report the first synthesis and X-ray crystal structure determination of the DNA containing the 2'-Se-A derivatization. The 3D structure of 2'-Se-A-DNA decamer [5'-GTACGCGT(2'-Se-A)C-3']{sub 2} was determined at 1.75 {angstrom} resolution, the 2'-Se-functionality points to the minor groove, and the Se-modified and native structures are virtually identical. Moreover, we have observed that the 2'-Se-A modification can greatly facilitate the crystal growth with high diffraction quality. In conjunction with the crystallization facilitation by the 2'-Se-U and 2'-Se-T, this novel observation on the 2'-Se-A functionality suggests that the 2'-Se moiety is sole responsible for the crystallization facilitation and the identity of nucleobases does not influence the crystal growth significantly.« less

Co-crystallization phase transformations in all π-conjugated block copolymers with different main-chain moieties.

PubMed

Lee, Yi-Huan; Chen, Wei-Chih; Yang, Yi-Lung; Chiang, Chi-Ju; Yokozawa, Tsutomu; Dai, Chi-An

2014-05-21

Driven by molecular affinity and balance in the crystallization kinetics, the ability to co-crystallize dissimilar yet self-crystallizable blocks of a block copolymer (BCP) into a uniform domain may strongly affect its phase diagram. In this study, we synthesize a new series of crystalline and monodisperse all-π-conjugated poly(2,5-dihexyloxy-p-phenylene)-b-poly(3-(2-ethylhexyl)thiophene) (PPP-P3EHT) BCPs and investigate this multi-crystallization effect. Despite vastly different side-chain and main-chain structures, PPP and P3EHT blocks are able to co-crystallize into a single uniform domain comprising PPP and P3EHT main-chains with mutually interdigitated side-chains spaced in-between. With increasing P3EHT fraction, PPP-P3EHTs undergo sequential phase transitions and form hierarchical superstructures including predominately PPP nanofibrils, co-crystalline nanofibrils, a bilayer co-crystalline/pure P3EHT lamellar structure, a microphase-separated bilayer PPP-P3EHT lamellar structure, and finally P3EHT nanofibrils. In particular, the presence of the new co-crystalline lamellar structure is the manifestation of the interaction balance between self-crystallization and co-crystallization of the dissimilar polymers on the resulting nanostructure of the BCP. The current study demonstrates the co-crystallization nature of all-conjugated BCPs with different main-chain moieties and may provide new guidelines for the organization of π-conjugated BCPs for future optoelectronic applications.

Ab initio NMR Confirmed Evolutionary Structure Prediction for Organic Molecular Crystals

NASA Astrophysics Data System (ADS)

Pham, Cong-Huy; Kucukbenli, Emine; de Gironcoli, Stefano

2015-03-01

Ab initio crystal structure prediction of even small organic compounds is extremely challenging due to polymorphism, molecular flexibility and difficulties in addressing the dispersion interaction from first principles. We recently implemented vdW-aware density functionals and demonstrated their success in energy ordering of aminoacid crystals. In this work we combine this development with the evolutionary structure prediction method to study cholesterol polymorphs. Cholesterol crystals have paramount importance in various diseases, from cancer to atherosclerosis. The structure of some polymorphs (e.g. ChM, ChAl, ChAh) have already been resolved while some others, which display distinct NMR spectra and are involved in disease formation, are yet to be determined. Here we thoroughly assess the applicability of evolutionary structure prediction to address such real world problems. We validate the newly predicted structures with ab initio NMR chemical shift data using secondary referencing for an improved comparison with experiments.

The Cytoplasmic Permeation Pathway of Neurotransmitter Transporters†

PubMed Central

Rudnick, Gary

2011-01-01

Ion-coupled solute transporters are responsible for transporting nutrients, ions and signaling molecules across a variety of biological membranes. Recent high-resolution crystal structures of several transporters from protein families that were previously thought to be unrelated show common structural features indicating a large structural family representing transporters from all kingdoms of life. This review describes studies that led to an understanding of the conformational changes required for solute transport in this family. The first structure in this family showed the bacterial amino acid transporter LeuT, which is homologous to neurotransmitter transporters, in an extracellularly-oriented conformation with a molecule of leucine occluded at the substrate site. Studies with the mammalian serotonin transporter identified positions, buried in the LeuT structure, that defined a potential pathway leading from the cytoplasm to the substrate binding site. Modeling studies utilized an inverted structural repeat within the LeuT crystal structure to predict the conformation of LeuT in which the cytoplasmic permeation pathway, consisting of positions identified in SERT, was open for substrate diffusion to the cytoplasm. From the difference between the model and the crystal structures, a simple “rocking bundle” mechanism was proposed, in which a 4-helix bundle changed its orientation with respect to the rest of the protein to close the extracellular pathway and open the cytoplasmic one. Subsequent crystal structures from structurally related proteins provide evidence supporting this model for transport. PMID:21774491

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.

Amplified emission and modified spectral features in an opal hetero-structure mediated by passive defect mode localization

NASA Astrophysics Data System (ADS)

Rout, Dipak; Kumar, Govind; Vijaya, R.

2018-01-01

A photonic crystal hetero-structure consisting of a passive planar defect of SiO2 thin film sandwiched between two identical opals grown by inward growing self-assembly method using Rhodamine-B dye-doped polystyrene microspheres is studied for the characteristics of dye emission. The optical properties and the defect mode characteristics of the hetero-structure are studied from the reflection and transmission measurements. Laser-induced fluorescence from the hetero-structure showed amplified and spectrally narrowed emission compared to the photonic crystal emphasizing the role of the defect mode and distributed feedback. The enhanced emission is also complemented by the reduction in fluorescence decay time in the case of the hetero-structure in comparison to the 3D photonic crystals.

Effects of Convective Transport of Solute and Impurities on Defect-Causing Kinetics Instabilities in Protein Crystallization

NASA Technical Reports Server (NTRS)

Vekilov, Peter G.

2003-01-01

Insight into the crystallization processes of biological macromolecules into crystals or aggregates can provide valuable guidelines in many fundamental and applied fields. Such insight will prompt new means to regulate protein phase transitions in-vivo, e.g., polymerization of hemoglobin S in the red cells, crystallization of crystallins in the eye lens, etc. Understanding of protein crystal nucleation will help achieve narrow crystallite size distributions, needed for sustained release of pharmaceutical protein preparations such as insulin or interferon. Traditionally, protein crystallization studies have been related to the pursuit of crystal perfection needed to improve the structure details provided by x-ray, electron or neutron diffraction methods. Crystallization trials for the purposes of structural biology carried out in space have posed an intriguing question related to the inconsistency of the effects of the microgravity growth on the quality of the crystals.

Structure and Growth Control of Organic–Inorganic Halide Perovskites for Optoelectronics: From Polycrystalline Films to Single Crystals

PubMed Central

Chen, Yani; He, Minhong; Peng, Jiajun; Sun, Yong

2016-01-01

Recently, organic–inorganic halide perovskites have sparked tremendous research interest because of their ground‐breaking photovoltaic performance. The crystallization process and crystal shape of perovskites have striking impacts on their optoelectronic properties. Polycrystalline films and single crystals are two main forms of perovskites. Currently, perovskite thin films have been under intensive investigation while studies of perovskite single crystals are just in their infancy. This review article is concentrated upon the control of perovskite structures and growth, which are intimately correlated for improvements of not only solar cells but also light‐emitting diodes, lasers, and photodetectors. We begin with the survey of the film formation process of perovskites including deposition methods and morphological optimization avenues. Strategies such as the use of additives, thermal annealing, solvent annealing, atmospheric control, and solvent engineering have been successfully employed to yield high‐quality perovskite films. Next, we turn to summarize the shape evolution of perovskites single crystals from three‐dimensional large sized single crystals, two‐dimensional nanoplates, one‐dimensional nanowires, to zero‐dimensional quantum dots. Siginificant functions of perovskites single crystals are highlighted, which benefit fundamental studies of intrinsic photophysics. Then, the growth mechanisms of the previously mentioned perovskite crystals are unveiled. Lastly, perspectives for structure and growth control of perovskites are outlined towards high‐performance (opto)electronic devices. PMID:27812463

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.

Crystal structure of enolase from Drosophila melanogaster.

PubMed

Sun, Congcong; Xu, Baokui; Liu, Xueyan; Zhang, Zhen; Su, Zhongliang

2017-04-01

Enolase is an important enzyme in glycolysis and various biological processes. Its dysfunction is closely associated with diseases. Here, the enolase from Drosophila melanogaster (DmENO) was purified and crystallized. A crystal of DmENO diffracted to 2.0 Å resolution and belonged to space group R32. The structure was solved by molecular replacement. Like most enolases, DmENO forms a homodimer with conserved residues in the dimer interface. DmENO possesses an open conformation in this structure and contains conserved elements for catalytic activity. This work provides a structural basis for further functional and evolutionary studies of enolase.

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

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.

Crystal structure, electronic structure, temperature-dependent optical and scintillation properties of CsCe 2Br 7

DOE PAGES

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

2015-10-05

CsCe 2Br 7 is a self-activated inorganic scintillator that shows promising performance, but the understanding of the important structure-property relationships is lacking. In this work, we conduct a comprehensive study on CCsCe 2Br 7. The crystal structure of CsCe 2Br 7 is refined using single crystal X-ray study for the first time. It crystallizes into the orthorhombic crystal system with Pmnb space group. Its electronic structure is revealed by Density Functional Theory (DFT) calculations. Two cerium emission centers are identified and the energy barriers related to the thermal quenching to 4f ground states of Ce 3+ for these two Cemore » centers are evaluated. CsCe 2Br 7 single crystal has better light yield and energy resolution than CsCe 2Cl 7, but with an additional slow decay component of 1.7 s. The existence of a deep trap with a depth of 0.9 eV in CsCe 2Cl 7 contributes to its higher afterglow level in comparison to that of CsCe 2Br 7. The most possible point defects in CsCe 2Cl 7 and CsCe 2Br 7 are proposed by considering the vapour pressure in the growth atmosphere upon melting point.« less

Atomic Scale Structure-Chemistry Relationships at Oxide Catalyst Surfaces and Interfaces

NASA Astrophysics Data System (ADS)

McBriarty, Martin E.

Oxide catalysts are integral to chemical production, fuel refining, and the removal of environmental pollutants. However, the atomic-scale phenomena which lead to the useful reactive properties of catalyst materials are not sufficiently understood. In this work, the tools of surface and interface science and electronic structure theory are applied to investigate the structure and chemical properties of catalytically active particles and ultrathin films supported on oxide single crystals. These studies focus on structure-property relationships in vanadium oxide, tungsten oxide, and mixed V-W oxides on the surfaces of alpha-Al2O3 and alpha-Fe2O 3 (0001)-oriented single crystal substrates, two materials with nearly identical crystal structures but drastically different chemical properties. In situ synchrotron X-ray standing wave (XSW) measurements are sensitive to changes in the atomic-scale geometry of single crystal model catalyst surfaces through chemical reaction cycles, while X-ray photoelectron spectroscopy (XPS) reveals corresponding chemical changes. Experimental results agree with theoretical calculations of surface structures, allowing for detailed electronic structure investigations and predictions of surface chemical phenomena. The surface configurations and oxidation states of V and W are found to depend on the coverage of each, and reversible structural shifts accompany chemical state changes through reduction-oxidation cycles. Substrate-dependent effects suggest how the choice of oxide support material may affect catalytic behavior. Additionally, the structure and chemistry of W deposited on alpha-Fe 2O3 nanopowders is studied using X-ray absorption fine structure (XAFS) measurements in an attempt to bridge single crystal surface studies with real catalysts. These investigations of catalytically active material surfaces can inform the rational design of new catalysts for more efficient and sustainable chemistry.

Study of the specific features of single-crystal boron microstructure

NASA Astrophysics Data System (ADS)

Blagov, A. E.; Vasil'ev, A. L.; Dmitriev, V. P.; Ivanova, A. G.; Kulikov, A. G.; Marchenkov, N. V.; Popov, P. A.; Presnyakov, M. Yu.; Prosekov, P. A.; Pisarevskii, Yu. V.; Targonskii, A. V.; Chernaya, T. S.; Chernyshov, D. Yu.

2017-09-01

A complex study of the structure of β-boron single crystal grown by the floating-zone method, with sizes significantly exceeding the analogs known in the literature, has been performed. The study includes X-ray diffraction analysis and X-ray diffractometry (measurement of pole figures and rocking curves), performed on both laboratory and synchrotron sources; atomic-resolution scanning transmission electron microscopy with spherical aberration correction; and energy-dispersive microanalysis. X-ray diffraction analysis using synchrotron radiation has been used to refine the β-boron structure and find impurity Si atoms. The relative variations in the unit-cell parameters a and c for the crystal bulk are found to be δ a/ a ≈ 0.4 and δ c/ c ≈ 0.1%. X-ray diffractometry has revealed that the single-crystal growth axis coincides with the [2\\bar 2013] crystallographic axis and makes an angle of 21.12° with the [0001] threefold axis. Electron microscopy data have confirmed that the sample under study is a β-boron crystal, which may contain 0.3-0.4 at % Si as an impurity. Planar defects (stacking faults and dislocations) are found. The results of additional measurements of the temperature dependence of the thermal conductivity of the crystal in the range of 50-300 K are indicative of its high structural quality.

Experimental correlation of melt structures, nucleation rates, and thermal histories of silicate melts

NASA Technical Reports Server (NTRS)

Boynton, W. V.; DRAKE; HILDEBRAND; JONES; LEWIS; TREIMAN; WARK

1987-01-01

The theory and measurement of the structure of liquids is an important aspect of modern metallurgy and igneous petrology. Liquid structure exerts strong controls on both the types of crystals that may precipitate from melts and on the chemical composition of those crystals. An interesting aspect of melt structure studies is the problem of melt memories; that is, a melt can retain a memory of previous thermal history. This memory can influence both nucleation behavior and crystal composition. This melt memory may be characterized quantitatively with techniques such as Raman, infrared and NMR spectroscopy to provide information on short-range structure. Melt structure studies at high temperature will take advantage of the microgravity conditions of the Space Station to perform containerless experiments. Melt structure determinations at high temperature (experiments that are greatly facilitated by containerless technology) will provide invaluable information for materials science, glass technology, and geochemistry. In conjunction with studies of nucleation behavior and nucleation rates, information relevant to nucleation in magma chambers in terrestrial planets will be acquired.

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.

Space-Time Crystal and Space-Time Group

NASA Astrophysics Data System (ADS)

Xu, Shenglong; Wu, Congjun

2018-03-01

Crystal structures and the Bloch theorem play a fundamental role in condensed matter physics. We extend the static crystal to the dynamic "space-time" crystal characterized by the general intertwined space-time periodicities in D +1 dimensions, which include both the static crystal and the Floquet crystal as special cases. A new group structure dubbed a "space-time" group is constructed to describe the discrete symmetries of a space-time crystal. Compared to space and magnetic groups, the space-time group is augmented by "time-screw" rotations and "time-glide" reflections involving fractional translations along the time direction. A complete classification of the 13 space-time groups in one-plus-one dimensions (1 +1 D ) is performed. The Kramers-type degeneracy can arise from the glide time-reversal symmetry without the half-integer spinor structure, which constrains the winding number patterns of spectral dispersions. In 2 +1 D , nonsymmorphic space-time symmetries enforce spectral degeneracies, leading to protected Floquet semimetal states. We provide a general framework for further studying topological properties of the (D +1 )-dimensional space-time crystal.

Space-Time Crystal and Space-Time Group.

PubMed

Xu, Shenglong; Wu, Congjun

2018-03-02

Crystal structures and the Bloch theorem play a fundamental role in condensed matter physics. We extend the static crystal to the dynamic "space-time" crystal characterized by the general intertwined space-time periodicities in D+1 dimensions, which include both the static crystal and the Floquet crystal as special cases. A new group structure dubbed a "space-time" group is constructed to describe the discrete symmetries of a space-time crystal. Compared to space and magnetic groups, the space-time group is augmented by "time-screw" rotations and "time-glide" reflections involving fractional translations along the time direction. A complete classification of the 13 space-time groups in one-plus-one dimensions (1+1D) is performed. The Kramers-type degeneracy can arise from the glide time-reversal symmetry without the half-integer spinor structure, which constrains the winding number patterns of spectral dispersions. In 2+1D, nonsymmorphic space-time symmetries enforce spectral degeneracies, leading to protected Floquet semimetal states. We provide a general framework for further studying topological properties of the (D+1)-dimensional space-time crystal.

Synthesis, structural, thermal and Hirshfeld surface analysis of novel [1,2,4]triazolo[3,4-b][1,3,4] thiadiazine carrying 1,4-benzothiazine-3-one moiety

NASA Astrophysics Data System (ADS)

Shruthi, C.; Ravindrachary, V.; Guruswamy, B.; Lokanath, N. K.; Kumara, Karthik; Goveas, Janet

2018-05-01

Needle shaped single crystal of the title compound was grown by slow evaporation solution growth technique using ethanol as solvent. The grown single crystal was characterized using FT-IR, Single crystal XRD and Thermal analysis. The FT-IR spectrum confirms the molecular structure and identifies the different functional groups present in the compound. Single crystal XRD study reveals that the crystallized compound belongs to the monoclinic crystal system with P21/c space group and the corresponding cell parameters were identified. The thermal stability of the material was determined using both TGA and DTA analysis. The intermolecular interaction of each individual atom in the crystal lattice was estimated using Hirshfeld surface and finger print analysis.

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.

Crystal growth, thermal and optical studies of semiorganic nonlinear optical material: L-lysine hydrochloride dihydrate

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

Kalaiselvi, D.; Mohan Kumar, R.; Jayavel, R.

2008-07-01

Single crystals of L-lysine hydrochloride dihydrate (LLHCD), a nonlinear optical material, have been grown by slow cooling technique from its aqueous solution. LLHCD was found to be highly soluble in water. The grown crystals have been subjected to single crystal X-ray diffraction to confirm the structure and to estimate the lattice parameters. The vibrational structure of the molecule is elucidated from FTIR spectra. Thermal analysis revealed the thermal stability of the grown crystals. The optical transmittance spectrum shows that the material possesses good optical transparency in the entire visible region with a UV cut-off wavelength at 228 nm. The mechanicalmore » properties of the grown crystal have been studied using Vicker's microhardness test. The laser damage threshold of 52.25 MW/cm{sup 2} has been measured by irradiating Q-switched Nd:YAG laser (1064 nm)« less

Thermal crystallization mechanism of silk fibroin protein

NASA Astrophysics Data System (ADS)

Hu, Xiao

In this thesis, the thermal crystallization mechanism of silk fibroin protein from Bombyx mori silkworm, was treated as a model for the general study of protein based materials, combining theories from both biophysics and polymer physics fields. A systematic and scientific path way to model the dynamic beta-sheet crystallization process of silk fibroin protein was presented in the following sequence: (1) The crystallinity, fractions of secondary structures, and phase compositions in silk fibroin proteins at any transition stage were determined. Two experimental methods, Fourier transform infrared spectroscopy (FTIR) with Fourier self-deconvolution, and specific reversing heat capacity, were used together for the first time for modeling the static structures and phases in the silk fibroin proteins. The protein secondary structure fractions during the crystallization were quantitatively determined. The possibility of existence of a "rigid amorphous phase" in silk protein was also discussed. (2) The function of bound water during the crystallization process of silk fibroin was studied using heat capacity, and used to build a silk-water dynamic crystallization model. The fundamental concepts and thermal properties of silk fibroin with/without bound water were discussed. Results show that intermolecular bound water molecules, acting as a plasticizer, will cause silk to display a water-induced glass transition around 80°C. During heating, water is lost, and the change of the microenvironment in the silk fibroin chains induces a mesophase prior to thermal crystallization. Real time FTIR during heating and isothermal holding above Tg show the tyrosine side chain changes only during the former process, while beta sheet crystallization occurs only during the latter process. Analogy is made between the crystallization of synthetic polymers according to the four-state scheme of Strobl, and the crystallization process of silk fibroin, which includes an intermediate precursor stage before crystallization. (3) The beta-sheet crystallization kinetics in silk fibroin protein were measured using X-ray, FTIR and heat flow, and the structure reveals the formation mechanism of the silk crystal network. Avrami kinetics theories, which were established for studies of synthetic polymer crystal growth, were for the first time extended to investigate protein self-assembly in multiblock silk fibroin samples. The Avrami exponent, n, was close to two for all methods, indicating formation of beta sheet crystals in silk proteins is different from the 3-D spherulitic crystal growth found in most synthetic homopolymers. A microphase separation pattern after chymotrypsin enzyme biodegradation was shown in the protein structures using scanning electron microscopy. A model was then used to explain the crystallization of silk fibroin protein by analogy to block copolymers. (4) The effects of metal ions during the crystallization of silk fibroin was investigated using thermal analysis. Advanced thermal analysis methods were used to analyze the thermal protein-metallic ion interactions in silk fibroin proteins. Results show that K+ and Ca2+ metallic salts play different roles in silk fibroin proteins, which either reduce (K+) or increase (Ca2+ ) the glass transition (Tg) of pure silk protein and affect the thermal stability of this structure.

Molecular Modeling and Experimental Investigations of Nonlinear Optical Compounds Monosubstituted Derivatives of Dicyanovinylbenzene

NASA Technical Reports Server (NTRS)

Timofeeva, Tatiana V.; Nesterov, Vladimir N.; Antipin, Mikhail Yu.; Clark, Ronald D.; Sanghadasa, Mohan; Cardelino, Beatriz H.; Moore, Craig E.; Frazier, Donald O.

1999-01-01

A search for potential nonlinear optical compounds was performed using the Cambridge Structure Database and molecular modeling. We investigated a series of monosubstituted derivatives of dicyanovinylbenzene, since the nonlinear optical (NLO) properties of such derivatives (o-methoxy-dicyanovinylbenzene, DIVA) were studied earlier. The molecular geometry of these compounds was investigated with x-ray analysis and discussed along with the results of molecular mechanics and ab initio quantum chemical calculations. The influence of crystal packing on the planarity of the molecules of this series has been revealed. Two new compounds from the series studied, ortho-F and para-Cl-dicyanovinylbenzene, according to powder measurements, were found to be NLO compounds in the crystal state about 10 times more active than urea. The peculiarities of crystal structure formation in the framework of balance between van der Waals and electrostatic interactions have been discussed. The crystal shape of DIVA and two new NLO compounds have been calculated on the basis of the known crystal structure.

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.

Purification, crystallization and preliminary crystallographic studies of the TLDc domain of oxidation resistance protein 2 from zebrafish

PubMed Central

Alsarraf, Husam M. A. B.; Laroche, Fabrice; Spaink, Herman; Thirup, Søren; Blaise, Mickael

2011-01-01

Cell metabolic processes are constantly producing reactive oxygen species (ROS), which have deleterious effects by triggering, for example, DNA damage. Numerous enzymes such as catalase, and small compounds such as vitamin C, provide protection against ROS. The TLDc domain of the human oxidation resistance protein has been shown to be able to protect DNA from oxidative stress; however, its mechanism of action is still not understood and no structural information is available on this domain. Structural information on the TLDc domain may therefore help in understanding exactly how it works. Here, the purification, crystallization and preliminary crystallographic studies of the TLDc domain from zebrafish are reported. Crystals belonging to the orthorhombic space group P21212 were obtained and diffracted to 0.97 Å resolution. Selenomethionine-substituted protein could also be crystallized; these crystals diffracted to 1.1 Å resolution and the structure could be solved by SAD/MAD methods. PMID:22102041

Synthesis, crystal structure analysis, molecular docking studies and density functional theory predictions of the local reactive properties and degradation properties of a novel halochalcone

NASA Astrophysics Data System (ADS)

Arshad, Suhana; Pillai, Renjith Raveendran; Zainuri, Dian Alwani; Khalib, Nuridayanti Che; Razak, Ibrahim Abdul; Armaković, Stevan; Armaković, Sanja J.

2017-09-01

In the present study, single crystals of E)-3-(3,5-dichlorophenyl)-1-(4-fluorophenyl)prop-2-en-1-one, were prepared and structurally characterized by single crystal X-ray diffraction analysis. The molecular structure crystallized in monoclinic crystal system with P21/c space group. Sensitivity of the title molecule towards electrophilic attacks has been examined by calculations of average localized ionization energies (ALIE) and their mapping to electron density surface. Further determination of atoms that could be important reactive centres has been performed by calculations of Fukui functions. Sensitivity of title molecule towards autoxidation and hydrolysis mechanisms has been assessed by calculations of bond dissociation energies and radial distribution functions (RDF), respectively. Also, in order to explore possible binding mode of the title compound towards Dihydrofolate reductase enzyme, we have utilized in silico molecular docking to explore possible binding modes of the title compound with the DHFR enzyme.

Low-temperature crystal and magnetic structure of α – RuCl 3

DOE PAGES

Cao, Huibo B.; Yan, Jiaqiang; Bridges, Craig A.; ...

2016-04-19

Here, single crystals of the Kitaev spin-liquid candidate α – RuCl 3 have been studied to determine the low-temperature bulk properties, the structure, and the magnetic ground state. Refinements of x-ray diffraction data show that the low-temperature crystal structure is described by space group C2/m with a nearly perfect honeycomb lattice exhibiting less than 0.2% in-plane distortion. The as-grown single crystals exhibit only one sharp magnetic transition at T N = 7 K. The magnetic order below this temperature exhibits a propagation vector of k=(0,1,1/3), which coincides with a three-layer stacking of the C2/m unit cells. Magnetic transitions at highermore » temperatures up to 14 K can be introduced by deformations of the crystal that result in regions in the crystal with a two-layer stacking sequence. The best-fit symmetry-allowed magnetic structure of the as-grown crystals shows that the spins lie in the ac plane, with a zigzag configuration in each honeycomb layer. The three-layer repeat out-of-plane structure can be refined as a 120° spiral order or a collinear structure with a spin direction of 35° away from the a axis. The collinear spin configuration yields a slightly better fit and also is physically preferred. The average ordered moment in either structure is less than 0.45(5) μB per Ru 3+ ion.« less

Formation of the Structure of a Eutectic Alloy of the Nb - Si System During Directed Crystallization with Liquid-Metal Coolant

NASA Astrophysics Data System (ADS)

Bondarenko, Yu. A.; Echin, A. B.; Kolodyazhnyi, M. Yu.; Surova, V. A.

2017-11-01

Peculiarities of the structure of a refractory eutectic alloy of the Nb - Si system, formed by the method of directed crystallization with liquid-metal coolant, have been studied. Characteristic zones of microstructure of the ingot obtained upon directed crystallization are considered, the alloy composition is analyzed, and volume fractions of phases in the Nb - Si composite are determined.

Anagostic interactions in chiral separation. Polymorphism in a [Co(II)(L)] complex: Crystallographic and theoretical studies

NASA Astrophysics Data System (ADS)

Awwadi, Firas F.; Hodali, Hamdallah A.

2018-02-01

Syntheses and crystal structures of two polymorphs of the complex [Co(II)(L)], where H2L = 2,2'-[cis-1,2-diaminocyclohexanediylbis (nitrilo-methylidyne)]bis (5-dimethyl-amino]phenol, have been studied. The two polymorphs concomitantly crystallized by vapour diffusion of solvent. The first polymorph (I) crystallized as a racemate in the centrosymmetric tetragonal I41/a space group. The second polymorph (II) crystallized in the chiral orthorhombic space group P212121. The chiral conformers of symmetrical cis-1,2-disubstituted cyclohexane molecules cannot be resolved in the liquid or gas phases, due to the rapid ring inversion. In the present study, the two chiral conformers are present in crystals of polymorph I, whereas, only one chiral conformer is present in crystals of polymorph II. Crystal structure analysis indicated that the formation of two different polymorphs of [Co(II)(L)] complex can be rationalized based on Csbnd H⋯Co anagostic interactions. Density Functional Theory (DFT) calculations indicated that Csbnd H⋯Co interactions are due to HOMO-LUMO interactions.

Serial crystallography captures enzyme catalysis in copper nitrite reductase at atomic resolution from one crystal.

PubMed

Horrell, Sam; Antonyuk, Svetlana V; Eady, Robert R; Hasnain, S Samar; Hough, Michael A; Strange, Richard W

2016-07-01

Relating individual protein crystal structures to an enzyme mechanism remains a major and challenging goal for structural biology. Serial crystallography using multiple crystals has recently been reported in both synchrotron-radiation and X-ray free-electron laser experiments. In this work, serial crystallography was used to obtain multiple structures serially from one crystal (MSOX) to study in crystallo enzyme catalysis. Rapid, shutterless X-ray detector technology on a synchrotron MX beamline was exploited to perform low-dose serial crystallography on a single copper nitrite reductase crystal, which survived long enough for 45 consecutive 100 K X-ray structures to be collected at 1.07-1.62 Å resolution, all sampled from the same crystal volume. This serial crystallography approach revealed the gradual conversion of the substrate bound at the catalytic type 2 Cu centre from nitrite to nitric oxide, following reduction of the type 1 Cu electron-transfer centre by X-ray-generated solvated electrons. Significant, well defined structural rearrangements in the active site are evident in the series as the enzyme moves through its catalytic cycle, namely nitrite reduction, which is a vital step in the global denitrification process. It is proposed that such a serial crystallography approach is widely applicable for studying any redox or electron-driven enzyme reactions from a single protein crystal. It can provide a 'catalytic reaction movie' highlighting the structural changes that occur during enzyme catalysis. The anticipated developments in the automation of data analysis and modelling are likely to allow seamless and near-real-time analysis of such data on-site at some of the powerful synchrotron crystallographic beamlines.

The ‘Sticky Patch’ Model of Crystallization and Modification of Proteins for Enhanced Crystallizability

PubMed Central

Derewenda, Zygmunt S.; Godzik, Adam

2017-01-01

Crystallization of macromolecules has long been perceived as a stochastic process, which cannot be predicted or controlled. This is consistent with another popular notion that the interactions of molecules within the crystal, i.e. crystal contacts, are essentially random and devoid of specific physicochemical features. In contrast, functionally relevant surfaces, such as oligomerization interfaces and specific protein-protein interaction sites, are under evolutionary pressures so their amino acid composition, structure and topology are distinct. However, current theoretical and experimental studies are significantly changing our understanding of the nature of crystallization. The increasingly popular ‘sticky patch’ model, derived from soft matter physics, describes crystallization as a process driven by interactions between select, specific surface patches, with properties thermodynamically favorable for cohesive interactions. Independent support for this model comes from various sources including structural studies and bioinformatics. Proteins that are recalcitrant to crystallization can be modified for enhanced crystallizability through chemical or mutational modification of their surface to effectively engineer ‘sticky patches’ which would drive crystallization. Here, we discuss the current state of knowledge of the relationship between the microscopic properties of the target macromolecule and its crystallizability, focusing on the ‘sticky patch’ model. We discuss state-of-art in silico methods that evaluate the propensity of a given target protein to form crystals based on these relationships, with the objective to design of variants with modified molecular surface properties and enhanced crystallization propensity. We illustrate this discussion with specific cases where these approaches allowed to generate crystals suitable for structural analysis. PMID:28573570

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

Nucleation and Crystallization of Globular Proteins: What we Know and What is Missing

NASA Technical Reports Server (NTRS)

Rosenberger, F.; Vekilov, P. G.; Muschol, M.; Thomas, B. R.

1996-01-01

Recently. much progress has been made in understanding the nucleation and crystallization of globular proteins, including the formation of compositional and structural crystal defects, Insight into the interactions of (screened) protein macro-ions in solution, obtained from light scattering, small angle X-ray scattering and osmotic pressure studies. can guide the search for crystallization conditions. These studies show that the nucleation of globular proteins is governed by the same principles as that of small molecules. However, failure to account for direct and indirect (hydrodynamic) protein interactions in the solutions results in unrealistic aggregation scenarios. Microscopic studies of numerous proteins reveal that crystals grow by the attachment of growth units through the same layer-spreading mechanisms as inorganic crystals. Investigations of the growth kinetics of hen-egg-white lysozyme (HEWL) reveal non-steady behavior under steady external conditions. Long-term variations in growth rates are due to changes in step-originating dislocation groups. Fluctuations on a shorter timescale reflect the non-linear dynamics of layer growth that results from the interplay between interfacial kinetics and bulk transport. Systematic gel electrophoretic analyses suggest that most HEWL crystallization studies have been performed with material containing other proteins at percent levels. Yet, sub-percent levels of protein impurities impede growth step propagation and play a role in the formation of structural/compositional inhomogeneities. In crystal growth from highly purified HEWL solutions, however, such inhomogeneities are much weaker and form only in response to unusually large changes in growth conditions. Equally important for connecting growth conditions to crystal perfection and diffraction resolution are recent advances in structural characterization through high-resolution Bragg reflection profiling and X-ray topography.

An Example of Body-Centered Cubic Crystal Structure: The Atomium in Brussels as an Educative Tool for Introductory Materials Chemistry

ERIC Educational Resources Information Center

Pinto, Gabriel

2012-01-01

When students are introduced to the ways in which atoms are arranged in crystal structures, transposing the textbook illustrations into three-dimensional structures is difficult for some of them. To facilitate this transition, this article describes an approach to the study of the structure of solids through a well-known monument, the Atomium in…

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

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.

Structure of initial crystals formed during human amelogenesis

NASA Astrophysics Data System (ADS)

Cuisinier, F. J. G.; Voegel, J. C.; Yacaman, J.; Frank, R. M.

1992-02-01

X-ray diffraction analysis revealed only the existence of carbonated hydroxyapatite (c.HA) during amelogenesis, whereas conventional transmission electron microscopy investigations showed that developing enamel crystals have a ribbon-like habit. The described compositional changes could be an indication for the presence of minerals different from c.HA. However, the absence of identification of such a mineral shows the need of studies by high resolution electron microscopy (HREM) of initial formed human enamel crystals. We demonstrate the existence of two crystal families involved in the early stages of biomineralization: (a) nanometer-size particles which appeared as a precursor phase; (b) ribbon-like crystals, with a structure closely related to c.HA, which by a progressive thickening process tend to attain the mature enamel crystal habit.

Growth, structural, physical and computational perspectives of trans-4-hydroxy-l-proline: a promising organic nonlinear optical material with large laser-induced damage threshold

NASA Astrophysics Data System (ADS)

Thirumurugan, Ramaiah; Anitha, Kandasamy

2017-05-01

In this work, a systematic study of an organic nonlinear optical (NLO) material, trans-4-hydroxy-l-proline (THP), C5H9NO3 is reported. An optical quality single crystals of THP have been successfully grown by using slow evaporation solution growth technique (SEST). The single crystal x-ray diffraction (SXRD) analysis reveals that grown crystal belongs to the orthorhombic system with non-centrosymmetric space group (NCS), P212121. Powder x-ray diffraction (PXRD) analysis shows relatively a good crystalline nature. The molecular structure of THP was recognized by NMR (1H and 13C) studies and its vibrational modes were confirmed by FTIR and FT-Raman vibrational studies. UV-Vis-NIR spectrum of grown crystal shows high optical transparency in the visible and near-IR region with low near-UV cut-off wavelength at 218 nm. Photoluminescence study confirms ultraviolet wavelength emission of THP crystal. The second harmonic generation (SHG) efficiency of grown crystal is 1.6 times greater with respect to standard potassium dihydrogen phosphate (KDP). Nonlinear refractive index (n 2) and nonlinear absorption coefficient (β) were determined using the Z-scan technique. The title compound owns high thermal stability of 294 °C and specific heat capacity (C P) of 1.21 J g-1 K-1 at 300 K and 11.33 J g-1 K-1 at 539 K (melting point). The laser-induced damage threshold (LDT) value of grown crystal was measured as 7.25 GW cm-2. The crystal growth mechanism and defects of grown crystal were studied by chemical etching technique. Mechanical strength was extensively studied by Vickers microhardness test and crystal void percentage analysis. Moreover, density functional theory (DFT) studies were carried out to probe the Mulliken charge distribution, frontier molecular orbitals (FMOs) and first order hyperpolarizability (β) of the optimized molecular structure to get a better insight of the molecular properties. These characterization results endorse that grown THP crystal as a suitable candidate for NLO applications with large LDT.

Structural characterization, AC conductivity, optical properties and biochemical study of a new hybrid phosphate: Scavenger of free radicals

NASA Astrophysics Data System (ADS)

Fezai, Ramzi; Hemissi, Hanene; Mezni, Ali; Rzaigui, Mohamed

2017-12-01

Single crystal of the hybrid compound [p-(F)C6H4NH3]6P6O18·2H2O has been grown with sizes up to 0.65 × 0.45 × 0.3 mm3 by the slow evaporation method. The crystal structure of this material was determined by single crystal X-ray diffraction. It crystallizes in the triclinic space group P 1 bar with the lattice parameters a = 10.16(3) Å, b = 15.87(3) Å, c = 16.36(4) Å, α = 80.93(2)°, β = 85.92(18)°, γ = 85.31(2)°, V = 2591.1(12) Å3 and Z = 2. Its crystal structure is a packing of alternated inorganic and organic layers parallel to (a, c) planes. The cohesion of the structure is essentially ensured by a hydrogen bonding network as well as electrostatic and Van Der Waals interactions and also F…F interactions so as to increase the stability of the 3D-network. The effect of the nature of the substituent in para-position with respect to amine group on obtained structures and on other studied properties was discussed. Crystal symmetry is confirmed by 31P MAS-NMR. Furthermore, IR characteristics and thermal analysis are given. The luminescent properties of this material have been carried out at room temperature based on UV absorption spectroscopy data. AC conductivity of this compound has been investigated by means of impedance spectroscopy measurements in the 303-383 K temperature range. The antioxidant study was determined, in vitro, using 1,1-diphenyl-2-picrylhydrazyl (DPPH), hydroxyl radical and reducing power and with ascorbic acid as a control. X-rays structural results are correlated with electrical and antioxidant findings.

Anharmonic vibrational spectroscopy, NBO charges and global chemical reactivity studies on the charge transfer PDCA-.AHMP+ single crystal using DFT calculations

NASA Astrophysics Data System (ADS)

Faizan, Mohd; Afroz, Ziya; Bhat, Sheeraz Ahmad; Alam, Mohamad Jane; Ahmad, Shabbir; Ahmad, Afaq

2018-04-01

The charge transfer (CT) complex of the 2-amino-4-hydroxy-6-methylpyrimidine and 2,3 pyrazinedicarboxylic acid (PDCA-.AHMP+) was synthesized and its single crystal was grown by solution method. The structure of the crystalline complex has been investigated by single crystal X-ray diffraction (SCXRD). The vibrational features of the complex have been studied with the help of FTIR spectra and DFT computation. The anharmonic corrections in vibrational frequencies are made using the GVPT2 method at B3LYP/6-311++G(d,p) level of theory. The frontier molecular orbitals and global chemical reactivity have been calculated to understand the pharmacological aspect of the synthesized crystal. Furthermore, Hirshfeld electrostatic potential (ESP) surface, void space in the crystal structure and natural as well as Mulliken atomic charges are studied.

Crystallization of isoelectrically homogeneous cholera toxin

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

Spangler, B.D.; Westbrook, E.M.

1989-02-07

Past difficulty in growing good crystals of cholera toxin has prevented the study of the crystal structure of this important protein. The authors have determined that failure of cholera toxin to crystallize well has been due to its heterogeneity. They have now succeeded in overcoming the problem by isolating a single isoelectric variant of this oligomeric protein (one A subunit and five B subunits). Cholera toxin purified by their procedure readily forms large single crystals. The crystal form has been described previously. They have recorded data from native crystals of cholera toxin to 3.0-{angstrom} resolution with our electronic area detectors.more » With these data, they have found the orientation of a 5-fold symmetry axis within these crystals, perpendicular to the screw dyad of the crystal. They are now determining the crystal structure of cholera toxin by a combination of multiple heavy-atom isomorphous replacement and density modification techniques, making use of rotational 5-fold averaging of the B subunits.« less

The importance of proper crystal-chemical and geometrical reasoning demonstrated using layered single and double hydroxides

PubMed Central

Richardson, Ian G.

2013-01-01

Atomistic modelling techniques and Rietveld refinement of X-ray powder diffraction data are widely used but often result in crystal structures that are not realistic, presumably because the authors neglect to check the crystal-chemical plausibility of their structure. The purpose of this paper is to reinforce the importance and utility of proper crystal-chemical and geometrical reasoning in structural studies. It is achieved by using such reasoning to generate new yet fundamental information about layered double hydroxides (LDH), a large, much-studied family of compounds. LDH phases are derived from layered single hydroxides by the substitution of a fraction (x) of the divalent cations by trivalent. Equations are derived that enable calculation of x from the a parameter of the unit cell and vice versa, which can be expected to be of widespread utility as a sanity test for extant and future structure determinations and computer simulation studies. The phase at x = 0 is shown to be an α form of divalent metal hydroxide rather than the β polymorph. Crystal-chemically sensible model structures are provided for β-Zn(OH)2 and Ni- and Mg-based carbonate LDH phases that have any trivalent cation and any value of x, including x = 0 [i.e. for α-M(OH)2·mH2O phases]. PMID:23719702

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

Studies on the growth aspects, structural, thermal, dielectric and third order nonlinear optical properties of solution grown 4-methylpyridinium p-nitrophenolate single crystal

NASA Astrophysics Data System (ADS)

Devi, S. Reena; Kalaiyarasi, S.; Zahid, I. MD.; Kumar, R. Mohan

2016-11-01

An ionic organic optical crystal of 4-methylpyridinium p-nitrophenolate was grown from methanol by slow evaporation method at ambient temperature. Powder and single crystal X-ray diffraction studies revealed the crystal system and its crystalline perfection. The rocking curve recorded from HRXRD study confirmed the crystal quality. FTIR spectral analysis confirmed the functional groups present in the title compound. UV-visible spectral study revealed the optical window and band gap of grown crystal. The thermal, electrical and surface laser damage threshold properties of harvested crystal were examined by using TGA/DTA, LCR/Impedance Analyzer and Nd:YAG laser system respectively. The third order nonlinear optical property of grown crystal was elucidated by Z-scan technique.

Revisiting the blind tests in crystal structure prediction: accurate energy ranking of molecular crystals.

PubMed

Asmadi, Aldi; Neumann, Marcus A; Kendrick, John; Girard, Pascale; Perrin, Marc-Antoine; Leusen, Frank J J

2009-12-24

In the 2007 blind test of crystal structure prediction hosted by the Cambridge Crystallographic Data Centre (CCDC), a hybrid DFT/MM method correctly ranked each of the four experimental structures as having the lowest lattice energy of all the crystal structures predicted for each molecule. The work presented here further validates this hybrid method by optimizing the crystal structures (experimental and submitted) of the first three CCDC blind tests held in 1999, 2001, and 2004. Except for the crystal structures of compound IX, all structures were reminimized and ranked according to their lattice energies. The hybrid method computes the lattice energy of a crystal structure as the sum of the DFT total energy and a van der Waals (dispersion) energy correction. Considering all four blind tests, the crystal structure with the lowest lattice energy corresponds to the experimentally observed structure for 12 out of 14 molecules. Moreover, good geometrical agreement is observed between the structures determined by the hybrid method and those measured experimentally. In comparison with the correct submissions made by the blind test participants, all hybrid optimized crystal structures (apart from compound II) have the smallest calculated root mean squared deviations from the experimentally observed structures. It is predicted that a new polymorph of compound V exists under pressure.

Crystal structures of tiotropium bromide and its monohydrate in view of combined solid-state nuclear magnetic resonance and gauge-including projector-augmented wave studies.

PubMed

Pindelska, Edyta; Szeleszczuk, Lukasz; Pisklak, Dariusz Maciej; Majka, Zbigniew; Kolodziejski, Waclaw

2015-07-01

Tiotropium bromide is an anticholinergic bronchodilator used in the management of chronic obstructive pulmonary disease. The crystal structures of this compound and its monohydrate have been previously solved and published. However, in this paper, we showed that those structures contain some major errors. Our methodology based on combination of the solid-state nuclear magnetic resonance (NMR) spectroscopy and quantum mechanical gauge-including projector-augmented wave (GIPAW) calculations of NMR shielding constants enabled us to correct those errors and obtain reliable structures of the studied compounds. It has been proved that such approach can be used not only to perform the structural analysis of a drug substance and to identify its polymorphs, but also to verify and optimize already existing crystal structures. © 2015 Wiley Periodicals, Inc. and the American Pharmacists Association.

Beyond the Flipped Classroom: A Highly Interactive Cloud-Classroom (HIC) Embedded into Basic Materials Science Courses

ERIC Educational Resources Information Center

Liou, Wei-Kai; Bhagat, Kaushal Kumar; Chang, Chun-Yen

2016-01-01

The present study compares the highly interactive cloud-classroom (HIC) system with traditional methods of teaching materials science that utilize crystal structure picture or real crystal structure model, in order to examine its learning effectiveness across three dimensions: knowledge, comprehension and application. The aim of this study was to…

Effect of filling factor on photonic bandgap of chalcogenide photonic crystal

NASA Astrophysics Data System (ADS)

Singh, Rajpal; Suthar, B.; Bhargava, A.

2018-05-01

In the present work, the photonic band structure of 1-D chalcogenide photonic crystal of As2S3/air multilayered structure is calculated using the plane wave expansion method. The study is extended to investigate the effect of filling factor on the photonic bandgap. The increase of bandgap is explained in the study.

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

Highly sensitive quartz crystal microbalance based biosensor using Au dendrite structure

NASA Astrophysics Data System (ADS)

Asai, Naoto; Terasawa, Hideaki; Shimizu, Tomohiro; Shingubara, Shoso; Ito, Takeshi

2018-02-01

A Au dendrite structure was obtained by only electroplating under a suitable potential. A blanch like nanostructure was formed along the crystal orientation. In this study, we attempted to fabricate a Au dendrite structure on the electrode of a quartz crystal by electroplating to increase the specific surface area. We estimated the effective surface area by cyclic voltammetry (CV) and monitored the frequency shift induced by antigen-antibody interaction by the quartz crystal microbalance (QCM) method. The dendrite structure with the largest surface area was formed under -0.95 V for 5 min. In the measurement of the antigen-antibody interaction, the frequency shifts of 40, 80, and 110 Hz were obtained with the dendrite structured QCM chips formed at the above potential for 1, 1.5, and 2.0 min, respectively. The sensitivity was improved compared with that QCM chip having a flat surface electrode.

Distinct molecular structures and hydrogen bond patterns of α,α-diethyl-substituted cyclic imide, lactam, and acetamide derivatives in the crystalline phase

NASA Astrophysics Data System (ADS)

Krivoshein, Arcadius V.; Ordonez, Carlos; Khrustalev, Victor N.; Timofeeva, Tatiana V.

2016-10-01

α,α-Dialkyl- and α-alkyl-α-aryl-substituted cyclic imides, lactams, and acetamides show promising anticonvulsant, anxiolytic, and anesthetic activities. While a number of crystal structures of various α-substituted cyclic imides, lactams, and acetamides were reported, no in-depth comparison of crystal structures and solid-state properties of structurally matched compounds have been carried out so far. In this paper, we report molecular structure and intermolecular interactions of three α,α-diethyl-substituted compounds - 3,3-diethylpyrrolidine-2,5-dione, 3,3-diethylpyrrolidin-2-one, and 2,2-diethylacetamide - in the crystalline phase, as studied using single-crystal X-ray diffraction and IR spectroscopy. We found considerable differences in the patterns of H-bonding and packing of the molecules in crystals. These differences correlate with the compounds' melting points and are of significance to physical pharmacy and formulation development of neuroactive drugs.

Investigation of angular dependence on photonic bandgap for 1-D photonic crystal

NASA Astrophysics Data System (ADS)

Nigam, Anjali; Suthar, B.; Bhargava, A.; Vijay, Y. K.

2018-05-01

In the present communication, we study the one-dimensional photonic crystal structure. The photonic band structure has been obtained using Plane Wave Expansion Method (PWEM). The studied has been extended to investigate the angular dependence on photonic bandgap for 1-D photonic crystal. The photonic bandgap is same both for TE and TM mode for normal incidence, while both mode move separate with an incidence angle. The photonic bandgap is almost unaffected with angle for TE mode while the bandgap decreases with an incidence angle for TM mode.

Synthesis, growth, structural, spectral, thermal, chemical etching, linear and nonlinear optical and mechanical studies of an organic single crystal 4-chloro 4-nitrostilbene (CONS): a potential NLO material.

PubMed

Dinakaran, Paul M; Kalainathan, S

2013-07-01

4-Chloro 4-nitrostilbene (CONS) a new organic nonlinear optical material has been synthesized. Employing slow evaporation method, good optical quality single crystals (dimensions up to 6×2×3 mm(3)) have been grown using ethyl methyl ketone (EMK) as a solvent. The grown crystals have been subjected to various characterizations such as single crystal X-ray diffraction, powder XRD, Fourier Transform Infrared spectroscopy (FTIR), proton NMR, solid UV absorption, SHG studies. Single crystal X-ray diffraction reveals that the crystal system belongs to monoclinic with noncentrosymmetric space group P21. The UV-Vis absorption spectrum has been recorded and found that the cut off wavelength is 380 nm. Functional groups and the structure of the title compound have been confirmed by FTIR and (1)H NMR spectroscopic analyses respectively. Molecular mass of the CONS confirmed by the high resolution mass spectral analysis .The thermal behavior of the grown crystal has been studied by TG/DTA analysis and it shows the melting point is at 188.66 °C. Dislocations and growth pattern present in the grown crystal revealed by the etching study. The mechanical strength of the CONS crystal has been studied by Vicker's hardness measurement. The SHG efficiency of the grown crystal has been determined by Kurtz and Perry powder test which revealed that the CONS crystal (327 mV) has 15 times greater efficiency than that of KDP (21.7 mV). Copyright © 2013 Elsevier B.V. All rights reserved.

Protein crystal structure obtained at 2.9 Å resolution from injecting bacterial cells into an X-ray free-electron laser beam

PubMed Central

Sawaya, Michael R.; Cascio, Duilio; Gingery, Mari; Rodriguez, Jose; Goldschmidt, Lukasz; Colletier, Jacques-Philippe; Messerschmidt, Marc M.; Boutet, Sébastien; Koglin, Jason E.; Williams, Garth J.; Brewster, Aaron S.; Nass, Karol; Hattne, Johan; Botha, Sabine; Doak, R. Bruce; Shoeman, Robert L.; DePonte, Daniel P.; Park, Hyun-Woo; Federici, Brian A.; Sauter, Nicholas K.; Schlichting, Ilme; Eisenberg, David S.

2014-01-01

It has long been known that toxins produced by Bacillus thuringiensis (Bt) are stored in the bacterial cells in crystalline form. Here we describe the structure determination of the Cry3A toxin found naturally crystallized within Bt cells. When whole Bt cells were streamed into an X-ray free-electron laser beam we found that scattering from other cell components did not obscure diffraction from the crystals. The resolution limits of the best diffraction images collected from cells were the same as from isolated crystals. The integrity of the cells at the moment of diffraction is unclear; however, given the short time (∼5 µs) between exiting the injector to intersecting with the X-ray beam, our result is a 2.9-Å-resolution structure of a crystalline protein as it exists in a living cell. The study suggests that authentic in vivo diffraction studies can produce atomic-level structural information. PMID:25136092

Identification of surface domain structure on enamel crystals using polyamidoamine dendrimer

NASA Astrophysics Data System (ADS)

Chen, Haifeng; Clarkson, Brian H.; Orr, Bradford; Majoros, Istvan; Banaszak Holl, Mark M.

2002-03-01

The control of hydroxyapatite crystal nucleation and crystal growth is central to the mineralization and remineralization of enamel and dentin of teeth. However, the precise biomolecular mechanisms involved remain obscure. The intimate association between the crystal's surface and extracellular protein components implies a modulating role for organic crystal interactions probably mediated via specific crystal surface domains. These include lattice defects and specific stereochemical arrays on associated organic molecules. The nature of protein-crystal interaction depends upon the physical forces of attraction / repulsion between specific biomolecular groups and crystal surface domains. The proposed study is to utilize specific polyamidoamine (PAMAM) dendrimers, also known as “artificial proteins”, acting as nanoprobe. These will be used to probe specific surface domain on the surface of the naturally derived crystals of hydroxyapatite and to determine how control of growth and dissolution may be affected at the biomolecular level. The hydroxyapatite crystals are extracted from the maturation stage enamel of rats. Three types of PAMAM dendrimers, respectively with amine-, carboxylic acid and methyl-capped surface, will be applied in the study. The dendrimer binding on the surface of the hydoxyapatite crystals will be characterized using atomic force microscopy (AFM). The different dendrimer binding on the crystals will disclose the specific surface domain structure on the crystals, which is assumed to be important in binding the extracellular protein.

The first mammalian aldehyde oxidase crystal structure: insights into substrate specificity.

PubMed

Coelho, Catarina; Mahro, Martin; Trincão, José; Carvalho, Alexandra T P; Ramos, Maria João; Terao, Mineko; Garattini, Enrico; Leimkühler, Silke; Romão, Maria João

2012-11-23

Aldehyde oxidases have pharmacological relevance, and AOX3 is the major drug-metabolizing enzyme in rodents. The crystal structure of mouse AOX3 with kinetics and molecular docking studies provides insights into its enzymatic characteristics. Differences in substrate and inhibitor specificities can be rationalized by comparing the AOX3 and xanthine oxidase structures. The first aldehyde oxidase structure represents a major advance for drug design and mechanistic studies. Aldehyde oxidases (AOXs) are homodimeric proteins belonging to the xanthine oxidase family of molybdenum-containing enzymes. Each 150-kDa monomer contains a FAD redox cofactor, two spectroscopically distinct [2Fe-2S] clusters, and a molybdenum cofactor located within the protein active site. AOXs are characterized by broad range substrate specificity, oxidizing different aldehydes and aromatic N-heterocycles. Despite increasing recognition of its role in the metabolism of drugs and xenobiotics, the physiological function of the protein is still largely unknown. We have crystallized and solved the crystal structure of mouse liver aldehyde oxidase 3 to 2.9 Å. This is the first mammalian AOX whose structure has been solved. The structure provides important insights into the protein active center and further evidence on the catalytic differences characterizing AOX and xanthine oxidoreductase. The mouse liver aldehyde oxidase 3 three-dimensional structure combined with kinetic, mutagenesis data, molecular docking, and molecular dynamics studies make a decisive contribution to understand the molecular basis of its rather broad substrate specificity.

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.

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.

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.

Structure and morphology of magnetite anaerobically-produced by a marine magnetotactic bacterium and a dissimilatory iron-reducing bacterium

USGS Publications Warehouse

Sparks, N.H.C.; Mann, S.; Bazylinski, D.A.; Lovley, D.R.; Jannasch, H.W.; Frankel, R.B.

1990-01-01

Intracellular crystals of magnetite synthesized by cells of the magnetotactic vibroid organism, MV-1, and extracellular crystals of magnetite produced by the non-magnetotactic dissimilatory iron-reducing bacterium strain GS-15, were examined using high-resolution transmission electron microscopy, electron diffraction and 57Fe Mo??ssbauer spectroscopy. The magnetotactic bacterium contained a single chain of approximately 10 crystals aligned along the long axis of the cell. The crystals were essentially pure stoichiometric magnetite. When viewed along the crystal long axis the particles had a hexagonal cross-section whereas side-on they appeared as rectangules or truncated rectangles of average dimension, 53 ?? 35 nm. These findings are explained in terms of a three-dimensional morphology comprising a hexagonal prism of {110} faces which are capped and truncated by {111} end faces. Electron diffraction and lattice imaging studies indicated that the particles were structurally well-defined single crystals. In contrast, magnetite particles produced by the strain, GS-15 were irregular in shape and had smaller mean dimensions (14 nm). Single crystals were imaged but these were not of high structural perfection. These results highlight the influence of intracellular control on the crystallochemical specificity of bacterial magnetites. The characterization of these crystals is important in aiding the identification of biogenic magnetic materials in paleomagnetism and in studies of sediment magnetization. ?? 1990.

A perspective on the structural studies of inner membrane electrochemical potential-driven transporters.

PubMed

Lemieux, M Joanne

2008-09-01

Electrochemical potential-driven transporters represent a vast array of proteins with varied substrate specificities. While diverse in size and substrate specificity, they are all driven by electrochemical potentials. Over the past five years there have been increasing numbers of X-ray structures reported for this family of transporters. Structural information is available for five subfamilies of electrochemical potential-driven transporters. No structural information exists for the remaining 91 subfamilies. In this review, the various subfamilies of electrochemical potential-driven transporters are discussed. The seven reported structures for the electrochemical potential-driven transporters and the methods for their crystallization are also presented. With a few exceptions, overall crystallization trends have been very similar for the transporters despite their differences in substrate specificity and topology. Also discussed is why the structural studies on these transporters were successful while others are not as fruitful. With the plethora of transporters with unknown structures, this review provides incentive for crystallization of transporters in the remaining subfamilies for which no structural information exists.

Chemical composition, crystal size and lattice structural changes after incorporation of strontium into biomimetic apatite.

PubMed

Li, Z Y; Lam, W M; Yang, C; Xu, B; Ni, G X; Abbah, S A; Cheung, K M C; Luk, K D K; Lu, W W

2007-03-01

Recently, strontium (Sr) as ranelate compound has become increasingly popular in the treatment of osteoporosis. However, the lattice structure of bone crystal after Sr incorporation is yet to be extensively reported. In this study, we synthesized strontium-substituted hydroxyapatite (Sr-HA) with different Sr content (0.3%, 1.5% and 15% Sr-HA in mole ratio) to simulate bone crystals incorporated with Sr. The changes in chemical composition and lattice structure of apetite after synthetic incorporation of Sr were evaluated to gain insight into bone crystal changes after incorporation of Sr. X-ray diffraction (XRD) patterns revealed that 0.3% and 1.5% Sr-HA exhibited single phase spectrum, which was similar to that of HA. However, 15% Sr-HA induced the incorporation of HPO4(2-) and more CO3(2-), the crystallinity reduced dramatically. Transmission electron microscopy (TEM) images showed that the crystal length and width of 0.3% and 1.5% Sr-HA increased slightly. Meanwhile, the length and width distribution were broadened and the aspect ratio decreased from 10.68+/-4.00 to 7.28+/-2.80. The crystal size and crystallinity of 15% Sr-HA dropped rapidly, which may suggest that the fundamental crystal structure is changed. The findings from this work indicate that current clinical dosage which usually results in Sr incorporation of below 1.5% may not change chemical composition and lattice structure of bone, while it will broaden the bone crystal size distribution and strengthen the bone.

A comparative study on the crystal structure of bicycle analogues to the natural phytotoxin helminthosporins

NASA Astrophysics Data System (ADS)

Barbosa, Luiz Cláudio de Almeida; Teixeira, Robson Ricardo; Nogueira, Leonardo Brandão; Maltha, Celia Regina Alvares; Doriguetto, Antônio Carlos; Martins, Felipe Terra

2016-02-01

Herein we described structural insights of a series of analogues to helminthosporin phytotoxins. The key reaction used to prepare the compounds corresponded to the [3 + 4] cycloaddition between the oxyallyl cation generated from 2,4-dibromopentan-3-one and different furans. Their structures were confirmed upon IR, NMR and X-ray diffraction analyses. While bicycles 7, 8 and 9 crystallize in the centrosymmetric monoclinic space group P21/c, compound 10 was solved in the noncentrosymmetric orthorhombic space group P212121. The solid materials obtained were shown to be racemic crystals (7, 8, 9) or racemic conglomerate (10). In all compounds, there is formation of a bicycle featured by fused tetrahydropyranone and 2,5-dihydrofuran rings. They adopt chair and envelope conformations, respectively. Crystal packing of all compounds is stabilized through C-H•••O contacts. Conformational aspects as well as similarities and differences among the crystal structures of the synthesized analogues are discussed.

Combinatorial selection of molecular conformations and supramolecular synthons in quercetin cocrystal landscapes: a route to ternary solids

PubMed Central

Dubey, Ritesh; Desiraju, Gautam R.

2015-01-01

The crystallization of 28 binary and ternary cocrystals of quercetin with dibasic coformers is analyzed in terms of a combinatorial selection from a solution of preferred molecular conformations and supramolecular synthons. The crystal structures are characterized by distinctive O—H⋯N and O—H⋯O based synthons and are classified as nonporous, porous and helical. Variability in molecular conformation and synthon structure led to an increase in the energetic and structural space around the crystallization event. This space is the crystal structure landscape of the compound and is explored by fine-tuning the experimental conditions of crystallization. In the landscape context, we develop a strategy for the isolation of ternary cocrystals with the use of auxiliary template molecules to reduce the molecular and supramolecular ‘confusion’ that is inherent in a molecule like quercetin. The absence of concomitant polymorphism in this study highlights the selectivity in conformation and synthon choice from the virtual combinatorial library in solution. PMID:26175900

Structure of Profiled Crystals Based on Solid Solutions of Bi2Te3 and Their X-Ray Diagnostics

NASA Astrophysics Data System (ADS)

Voronin, A. I.; Bublik, V. T.; Tabachkova, N. Yu.; Belov, Yu. M.

2011-05-01

In this work, we used x-ray structural diagnostic data to reveal the formation of structural regularities in profiled polycrystalline ingots based on Bi and Sb chalcogenide solid solutions. In Bi2Te3 lattice crystals, the solid phase grows such that the cleavage surfaces are perpendicular to the crystallization front. The crystallization singularity determines the nature of the growth texture. Because texture is an important factor determining the anisotropy of properties, which in turn determines the suitability of an ingot for production of modules and the possibility of figure of merit improvement, its diagnostics is an important issue for technology testing. Examples of texture analysis using the method of straight pole figure (SPF) construction for profiled crystals are provided. The structure of the surface layers in the profiled ingots was studied after electroerosion cutting. In addition, the method of estimation of the disturbed layer depth based on the nature of texture changes was used.

Fluorination of Metal Phthalocyanines: Single-Crystal Growth, Efficient N-Channel Organic Field-Effect Transistors, and Structure-Property Relationships

PubMed Central

Jiang, Hui; Ye, Jun; Hu, Peng; Wei, Fengxia; Du, Kezhao; Wang, Ning; Ba, Te; Feng, Shuanglong; Kloc, Christian

2014-01-01

The fluorination of p-type metal phthalocyanines produces n-type semiconductors, allowing the design of organic electronic circuits that contain inexpensive heterojunctions made from chemically and thermally stable p- and n-type organic semiconductors. For the evaluation of close to intrinsic transport properties, high-quality centimeter-sized single crystals of F16CuPc, F16CoPc and F16ZnPc have been grown. New crystal structures of F16CuPc, F16CoPc and F16ZnPc have been determined. Organic single-crystal field-effect transistors have been fabricated to study the effects of the central metal atom on their charge transport properties. The F16ZnPc has the highest electron mobility (~1.1 cm2 V−1 s−1). Theoretical calculations indicate that the crystal structure and electronic structure of the central metal atom determine the transport properties of fluorinated metal phthalocyanines. PMID:25524460

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

Study of Inverse Ni-based Photonic Crystal using the Microradian X-ray Diffraction

NASA Astrophysics Data System (ADS)

Vasilieva, A. V.; Grigoryeva, N. A.; Mistonov, A. A.; Sapoletova, N. A.; Napolskii, K. S.; Eliseev, A. A.; Lukashin, A. V.; Tretyakov, Yu D.; Petukhov, A. V.; Byelov, D.; Chernyshov, D.; Okorokov, A. I.; Bouwman, W. G.; Grigoriev, S. V.

2010-10-01

Inverse photonic nickel-based crystal films formed by electrocrystallization of metal inside the voids of polymer artificial opal have been studied using the microradian X-ray diffraction. Analysis of the diffraction images agrees with an face-centred cubic (FCC) structure with the lattice constant a0 = 650 ± 10 nm and indicates two types of stacking sequences coexisting in the crystal (twins of ABCABC... and ACBACB... ordering motifs), the ratio between them being 4:5 The transverse structural correlation length Ltran is 2.4 ± 0.1 μm, which corresponds to a sample thickness of 6 layers. The in-plane structural correlation length Llong is 3.4 ± 0.2 μm, and the structure mosaic is of order of 10°.

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

Single crystal structure and SHG of defect pyrochlores CsB{sup V}MoO{sub 6} (B{sup V}=Nb,Ta)

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

Fukina, D.G., E-mail: dianafuk@yandex.ru; Suleimanov, E.V.; Yavetskiy, R.P.

2016-09-15

The crystal structure and non-linear optical properties of CsNbMoO{sub 6} and CsTaMoO{sub 6} defect pyrochlores have been studied. The single crystals of these compounds grown by the flux method possess an octahedral faceting and reach up to 50 µm in size. The crystal structures of CsB{sup V}MoO{sub 6} (B{sup V}=Nb, Ta) were investigated by X-ray diffraction method. Both compounds crystallize in the cubic symmetry with noncentrosymmetric space group F-43m. The second harmonic generation of CsNbMoO{sub 6} and CsTaMoO{sub 6}was found to be 1.6×10{sup −2} and 8.5×10{sup −4} of lithium niobate, correspondingly. It has been determined that distortions of [MO{sub 6}]more » polyhedra (M=Nb, Ta, Mo) as well as polarizability and covalency of Nb–O and Ta–O bonds have a great effect on the second harmonic generation. - Highlights: • CsNbMoO{sub 6} and CsTaMoO{sub 6} homogeneous single crystals have been grown. • The crystal structure of CsTaMoO{sub 6} has been studied. • Nonlinear optical properties of CsNbMoO{sub 6} and CsTaMoO{sub 6} have been found. • The microscopic origin of the second harmonic generation (SHG) response have been identified.« less

Relationship Between Equilibrium Forms of Lysozyme Crystals and Precipitant Anions

NASA Technical Reports Server (NTRS)

Nadarajah, Arunan

1996-01-01

Molecular forces, such as electrostatic, hydrophobic, van der Waals and steric forces, are known to be important in determining protein interactions. These forces are affected by the solution conditions and changing the pH, temperature or the ionic strength of the solution can sharply affect protein interactions. Several investigations of protein crystallization have shown that this process is also strongly dependent on solution conditions. As the ionic strength of the solution is increased, the initially soluble protein may either crystallize or form an amorphous precipitate at high ionic strengths. Studies done on the model protein hen egg white lysozyme have shown that different crystal forms can be easily and reproducibly obtained, depending primarily on the anion used to desolubilize the protein. In this study we employ pyranine to probe the effect of various anions on the water structure. Additionally, lysozyme crystallization was carried out at these conditions and the crystal form was determined by X-ray crystallography. The goal of the study was to understand the physico-chemical basis for the effect of changing the anion concentration on the equilibrium form of lysozyme crystals. It will also verify the hypothesis that the anions, by altering the bulk water structure in the crystallizing solutions, alter the surface energy of the between the crystal faces and the solution and, consequently, the equilibrium form of the crystals.

Plasticity of the Binding Site of Renin: Optimized Selection of Protein Structures for Ensemble Docking.

PubMed

Strecker, Claas; Meyer, Bernd

2018-05-29

Protein flexibility poses a major challenge to docking of potential ligands in that the binding site can adopt different shapes. Docking algorithms usually keep the protein rigid and only allow the ligand to be treated as flexible. However, a wrong assessment of the shape of the binding pocket can prevent a ligand from adapting a correct pose. Ensemble docking is a simple yet promising method to solve this problem: Ligands are docked into multiple structures, and the results are subsequently merged. Selection of protein structures is a significant factor for this approach. In this work we perform a comprehensive and comparative study evaluating the impact of structure selection on ensemble docking. We perform ensemble docking with several crystal structures and with structures derived from molecular dynamics simulations of renin, an attractive target for antihypertensive drugs. Here, 500 ns of MD simulations revealed binding site shapes not found in any available crystal structure. We evaluate the importance of structure selection for ensemble docking by comparing binding pose prediction, ability to rank actives above nonactives (screening utility), and scoring accuracy. As a result, for ensemble definition k-means clustering appears to be better suited than hierarchical clustering with average linkage. The best performing ensemble consists of four crystal structures and is able to reproduce the native ligand poses better than any individual crystal structure. Moreover this ensemble outperforms 88% of all individual crystal structures in terms of screening utility as well as scoring accuracy. Similarly, ensembles of MD-derived structures perform on average better than 75% of any individual crystal structure in terms of scoring accuracy at all inspected ensembles sizes.

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

The Use of Atomic-Force Microscopy for Studying the Crystallization Process of Amorphous Alloys

NASA Astrophysics Data System (ADS)

Elmanov, G. N.; Ivanitskaya, E. A.; Dzhumaev, P. S.; Skrytniy, V. I.

The crystallization process of amorphous alloys is accompanied by the volume changes as a result of structural phase transitions. This leads to changes in the surface topography, which was studied by atomic force microscopy (AFM). The changes of the surface topography, structure and phase composition during multistage crystallization process of the metallic glasses with composition Ni71,5Cr6,8Fe2,7B11,9Si7,1 and Ni63,4Cr7,4Fe4,3Mn0,8B15,6Si8,5 (AWS BNi2) has been investigated. The obtained results on changing of the surface topography in crystallization process are in good agreement with the data of X-ray diffraction analysis (XRD). The nature of redistribution of some alloy components in the crystallization process has been suggested.

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.

Bulk growth of undoped and Nd3+ doped zinc thiourea chloride (ZTC) monocrystal: Exploring the remarkably enhanced structural, optical, electrical and mechanical performance of Nd3+ doped ZTC crystal for NLO device applications

NASA Astrophysics Data System (ADS)

Anis, Mohd; Muley, Gajanan. G.

2017-05-01

In current scenario good quality crystals are demanded for NLO device application hence present communication is aimed to grow bulk crystal and investigate the doping effect of rare earth element Nd3+ on structural, linear-nonlinear optical, luminescence, mechanical and dielectric properties of zinc thiourea chloride (ZTC) crystal. The ZTC crystal of dimension 21×10×8 mm3 and the Nd3+ doped ZTC crystal of dimension 27×17×5 mm3 have been grown from aqueous solution by slow evaporation technique. The elemental analysis of Nd3+ doped ZTC single crystal has been performed by means of energy dispersive spectroscopic technique. The powder X-ray diffraction technique has been employed to confirm the crystalline phase and identify the effect of Nd3+ doping on structural dimensions of ZTC crystal. The grown crystals have been characterized by UV-Vis-NIR study in the range of 190-1100 nm to ascertain the enhancement in optical transparency of ZTC crystal facilitated by dopant Nd3+. The recorded transmittance data has been utilized to investigate the vital optical constants of grown crystals. The second order nonlinear optical behavior of grown crystals has been evaluated by means of Kurtz-Perry test and the second harmonic generation efficiency of Nd3+ doped ZTC crystal is found to be 1.24 times higher than ZTC crystal. The luminescence analysis has been performed to examine the electronic purity and the color centered photoluminescence emission nature of pure and Nd3+ doped ZTC crystals. The influence of Nd3+ ion on mechanical behavior of ZTC crystal has been investigated by means of microhardness studies. The nature of dielectric constant and dielectric loss of pure and Nd3+ doped ZTC crystal has been examined in the range of 40-100 °C under dielectric study. The Z-scan technique has been employed using the He-Ne laser to investigate the third order nonlinear optical (TONLO) nature of Nd3+ doped ZTC single crystal. The magnitude of TONLO susceptibility, absorption coefficient and refraction has been determined using the Z-scan transmittance data.

Towards solution and refinement of organic crystal structures by fitting to the atomic pair distribution function

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

Prill, Dragica; Juhas, Pavol; Billinge, Simon J. L.

2016-01-01

In this study, a method towards the solution and refinement of organic crystal structures by fitting to the atomic pair distribution function (PDF) is developed. Approximate lattice parameters and molecular geometry must be given as input. The molecule is generally treated as a rigid body. The positions and orientations of the molecules inside the unit cell are optimized starting from random values. The PDF is obtained from carefully measured X-ray powder diffraction data. The method resembles `real-space' methods for structure solution from powder data, but works with PDF data instead of the diffraction pattern itself. As such it may bemore » used in situations where the organic compounds are not long-range-ordered, are poorly crystalline, or nanocrystalline. The procedure was applied to solve and refine the crystal structures of quinacridone (β phase), naphthalene and allopurinol. In the case of allopurinol it was even possible to successfully solve and refine the structure in P1 with four independent molecules. As an example of a flexible molecule, the crystal structure of paracetamol was refined using restraints for bond lengths, bond angles and selected torsion angles. In all cases, the resulting structures are in excellent agreement with structures from single-crystal data.« less

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

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

Structural and computational study of 1,2,4-triazolin-5-thione derivative and its DMSO solvate

NASA Astrophysics Data System (ADS)

Dybała, Izabela; Wawrzycka-Gorczyca, Irena; Struga, Marta

2017-11-01

The solid state structure of 3-(4-phenyl-5-oxo-1,2,4-triazolin-1-ylmethyl)-4-cyclohexyl-1,2,4-triazolin-5-thione (1) was characterized by FT-IR and X-ray diffraction experiment. Additionally, molecular and crystal structure of its DMSO solvate (1DMSO) has been determined by X-ray diffraction method. The influence of DMSO molecules incorporation to the crystal lattice on geometry of triazolin-5-thione derivative molecule and crystal packing was analyzed. Non-covalent bonds within the crystals are additionally visualized by determination of Hirshfeld surfaces. According to results of conformational analysis in gas, molecule of triazolin-5-thione derivative adopts the lowest energy conformation in 1DMSO crystal. The crystal structure of 1 and 1DMSO were compared with previously described structurally similar compounds, in which the cyclohexyl substituent was replaced by aromatic one (phenyl/methoxyphenyl). Very interesting differences in molecules association were found by comparing the crystal structures of 1 and 1DMSO with their, mentioned above, aromatic derivatives. Interesting properties of triazolin-5-thione derivatives are connected with their π-electron delocalization effects, thus aromaticity of heterocyclic fragments has been investigated by means of the HOMA index. Comparison of aromaticity calculations results with association tendency of molecules shows that triazolin-5-one fragments reach higher aromaticity when nitrogen atom from this moiety acts as a donor in strong Nsbnd H⋯N hydrogen bonds.

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 Nucleation and Growth of Protein Crystals

NASA Technical Reports Server (NTRS)

Pusey, Marc

2004-01-01

Obtaining crystals of suitable size and high quality continues to be a major bottleneck in macromolecular crystallography. Currently, structural genomics efforts are achieving on average about a 10% success rate in going from purified protein to a deposited crystal structure. Growth of crystals in microgravity was proposed as a means of overcoming size and quality problems, which subsequently led to a major NASA effort in microgravity crystal growth, with the agency also funding research into understanding the process. Studies of the macromolecule crystal nucleation and growth process were carried out in a number of labs in an effort to understand what affected the resultant crystal quality on Earth, and how microgravity improved the process. Based upon experimental evidence, as well as simple starting assumptions, we have proposed that crystal nucleation occurs by a series of discrete self assembly steps, which 'set' the underlying crystal symmetry. This talk will review the model developed, and its origins, in our laboratory for how crystals nucleate and grow, and will then present, along with preliminary data, how we propose to use this model to improve the success rate for obtaining crystals from a given protein.

Solid-state reaction kinetics and optical studies of cadmium doped magnesium hydrogen phosphate crystals

NASA Astrophysics Data System (ADS)

Verma, Madhu; Gupta, Rashmi; Singh, Harjinder; Bamzai, K. K.

2018-04-01

The growth of cadmium doped magnesium hydrogen phosphate was successfully carried out by using room temperature solution technique i.e., gel encapsulation technique. Grown crystals were confirmed by single crystal X-ray diffraction (XRD). The structure of the grown crystal belongs to orthorhombic crystal system and crystallizes in centrosymmetric space group. Kinetics of the decomposition of the grown crystals were studied by non-isothermal analysis. Thermo gravimetric / differential thermo analytical (TG/DTA) studies revealed that the grown crystal is stable upto 119 °C. The various steps involved in the thermal decomposition of the material have been analysed using Horowitz-Metzger, Coats-Redfern and Piloyan-Novikova equations for evaluating various kinetic parameters. The optical studies shows that the grown crystals possess wide transmittance in the visible region and significant optical band gap of 5.5ev with cut off wavelength of 260 nm.

Structural, spectroscopic and DFT study of 4-methoxybenzohydrazide Schiff bases. A new series of polyfunctional ligands.

PubMed

Ferraresi-Curotto, Verónica; Echeverría, Gustavo A; Piro, Oscar E; Pis-Diez, Reinaldo; González-Baró, Ana C

2015-02-25

Five Schiff bases obtained from condensation of 4-methoxybenzohydrazide with related aldehydes, namely o-vanillin, vanillin, 5-bromovanillin, 5-chlorosalicylaldehyde and 5-bromosalicylaldehyde were prepared. A detailed structural and spectroscopic study is reported. The crystal structures of four members of the family were determined and compared with one another. The hydrazones obtained from 5-chlorosalicylaldehyde and 5-bromosalicylaldehyde resulted to be isomorphic to each other. The solid-state structures are stabilized by intra-molecular O-H⋯N interactions in salicylaldehyde derivatives between the O-H moiety from the aldehyde and the hydrazone nitrogen atom. All crystals are further stabilized by inter-molecular H-bonds mediated by the crystallization water molecule. A comparative analysis between experimental and theoretical results is presented. The conformational space was searched and geometries were optimized both in gas phase and including solvent effects. The structure is predicted for the compound for which the crystal structure was not determined. Infrared and electronic spectra were measured and assigned with the help of data obtained from computational methods based on the Density Functional Theory. Copyright © 2014 Elsevier B.V. All rights reserved.

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.

Synthesis and characterization of a prominent NLO active MOF of lead with 1,5-naphthalenedisulfonic acid

NASA Astrophysics Data System (ADS)

Prasad, S. Shibu; Sudarsanakumar, M. R.; Dhanya, V. S.; Suma, S.; Kurup, M. R. Prathapachandra

2018-09-01

A new metal-organic framework of lead, [Pb(1,5-nds)(H2O)3]n (1,5-nds = 1,5-naphthalenedisulfonate) having prominent nonlinear optical property has been prepared by single gel diffusion technique at ambient condition using sodium metasilicate. The second harmonic generation efficiency was analyzed using Kurtz and Perry powder method and was found to be 30 times as large as potassium dihydrogen phosphate (KDP). Single crystal X-ray diffraction studies reveal the crystal structure. The grown crystals were further characterized by elemental analysis, powder XRD study, thermogravimetry, FT-IR and UV-visible spectral studies. The Pb2S2O4 rings in the crystal structure form a 1D channel. Hydrogen bonding and π-π interactions provide additional stability to the compound. Photoluminescence studies were also carried out.

NMR and NQR parameters of ethanol crystal

NASA Astrophysics Data System (ADS)

Milinković, M.; Bilalbegović, G.

2012-04-01

Electric field gradients and chemical shielding tensors of the stable monoclinic crystal phase of ethanol are computed. The projector-augmented wave (PAW) and gauge-including projector-augmented wave (GIPAW) models in the periodic plane-wave density functional theory are used. The crystal data from X-ray measurements, as well as the structures where either all atomic, or only hydrogen atom positions are optimized in the density functional theory are analyzed. These structural models are also studied by including the semi-empirical van der Waals correction to the density functional theory. Infrared spectra of these five crystal models are calculated.

Tautomerism and isomerism in some antitrichinellosis active benzimidazoles: Morphological study in polarized light, quantum chemical computations

NASA Astrophysics Data System (ADS)

Anichina, Kameliya; Mavrova, Anelia; Yancheva, Denitsa; Tsenov, Jordan; Dimitrov, Rasho

2017-12-01

The morphology of the crystal structure of some antitrichinellosis active benzimidazole derivatives including (1H-benzimidazol-2-ylthio)acetic acids, [1,3]thiazolo[3,2-a]benzimidazol-3(2H)-ones, 1H-benzimidazol-2-ylthioacetylpiperazines and starting 2-mercapto benzimidazoles, was studied by the use of Polarized Light Microscopy (PLM). Characterization of the crystal phase was complimented by Differential scanning calorimetry analysis (DSC) and spectroscopic data. DFT computations were performed in order to investigate the prototropic tautomerism and the geometry of the molecule of the synthesized compounds. One distinct type of crystal structure for each one of 5 or 6-methyl-(1H-benzimidazol-2-ylthio)acetic acid 6 was observed by PLM - dendritic and needle-shaped formations. Compound 14, containing a methyl substituent in the benzimidazole ring crystallized also into two phases; while for the unsubstituted compound 13 a separation of phases does not take place. The influence of the both solvents - chloroform and ethanol on the phase separation and the formation of the crystalline structure of compound 14 was investigated. The morphological study showed that the cyclization of 6 in the presence of acetic anhydride in pyridine medium led to a mixture of 6-methyl-[1,3]tiazolo[3,2-a]benzimidazol-3(2H)-one (10a) and 7-methyl-[1,3]thiazolo[3,2-a]-benzimidazole-3(2H)-one (10b), which crystallized in the form of fibrils and spherulites respectively. It was found that a difference in the crystal structures of substituted and unsubstituted benzimidazol-2-thiones, respectively benzimidazol-2-thiol derivatives exists, which may be due not only to the thiol-thione tautomerism but to the prototropic properties of the hydrogen atom in first position of the ring. The calculation results indicated that the thione form is more stable than the thiol tautomer by 51-55 kJ mol-1. But at the same time ΔG for the two thiol tautomers is below 0.5 kJ mol-1. In solid phase the 5(6)-substituted-1H-benzimidazol-2-thiols crystallized in two different crystal structures while the unsubstituted 1H-benzimidazol-2-thiol possess one type of crystal structure.

Crystal structure, optical and thermal studies of a new organic nonlinear optical material: L-Histidinium maleate 1.5-hydrate

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

Gonsago, C. Alosious; Albert, Helen Merina; Karthikeyan, J.

2012-07-15

Highlights: ► L-Histidinium maleate 1.5-hydrate, a new organic crystal has been grown for the first time. ► The crystal structure is reported for the first time (CCDC 845975). ► The crystal belongs to monoclinic system with space group P2{sub 1}, Z = 4, a = 11.4656(7) Å, b = 8.0530(5) Å, c = 14.9705(9) Å and β = 101.657(2)°. ► The optical absorption study substantiates the complete transparency of the crystal. ► Kurtz powder SHG test confirms the nonlinear property of the crystal. -- Abstract: A new organic nonlinear optical material L-histidinium maleate 1.5-hydrate (LHM) with the molecular formula C{submore » 10}H{sub 16}N{sub 3}O{sub 7.5} has been successfully synthesized from aqueous solution by slow solvent evaporation method. The structural characterization of the grown crystal was carried out by single crystal X-ray diffraction at 293(2) K. In the crystal, molecules are linked through inter and intramolecular N-H⋯O and O-H⋯O hydrogen bonds, generate edge fused ring motif. The hydrogen bonded motifs are linked to each other to form a three dimensional network. The FT-IR spectroscopy was used to identify the functional groups of the synthesized compound. The optical behavior of the grown crystal was examined by UV–visible spectral analysis, which shows that the optical absorption is almost negligible in the wavelength range 280–1300 nm. The nonlinear optical property was confirmed by the powder technique of Kurtz and Perry. The thermal behavior of the grown crystal was analyzed by thermogravimetric analysis.« 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

Validation of experimental molecular crystal structures with dispersion-corrected density functional theory calculations.

PubMed

van de Streek, Jacco; Neumann, Marcus A

2010-10-01

This paper describes the validation of a dispersion-corrected density functional theory (d-DFT) method for the purpose of assessing the correctness of experimental organic crystal structures and enhancing the information content of purely experimental data. 241 experimental organic crystal structures from the August 2008 issue of Acta Cryst. Section E were energy-minimized in full, including unit-cell parameters. The differences between the experimental and the minimized crystal structures were subjected to statistical analysis. The r.m.s. Cartesian displacement excluding H atoms upon energy minimization with flexible unit-cell parameters is selected as a pertinent indicator of the correctness of a crystal structure. All 241 experimental crystal structures are reproduced very well: the average r.m.s. Cartesian displacement for the 241 crystal structures, including 16 disordered structures, is only 0.095 Å (0.084 Å for the 225 ordered structures). R.m.s. Cartesian displacements above 0.25 A either indicate incorrect experimental crystal structures or reveal interesting structural features such as exceptionally large temperature effects, incorrectly modelled disorder or symmetry breaking H atoms. After validation, the method is applied to nine examples that are known to be ambiguous or subtly incorrect.

Surface Modification and Nanojunction Fabrication with Molecular Metal Wires

DTIC Science & Technology

2012-12-21

single - crystal X-ray diffraction studies of 2 and 3. Both the single - crystal structural data of 2 and 3 and the spectroscopic/voltammetric data...structure, magnetic properties, and single -molecule conductance of two new trinuclear metal string complexes, [Ni3(dzp)4(NCS)2] (2) and [ Co3 (dzp)4(NCS...modifying the crystallization conditions. The [s- Co3 (dpa)4(Cl)2] contains a symmetrical tricobalt framework with identical Co–Co bond lengths (2.34 Å

Synthesis, crystal structure and growth of a new inorganic- organic hybrid compound for nonlinear optical applications: Aquadiiodo (3-aminopropanoic acid) cadmium (II)

NASA Astrophysics Data System (ADS)

Boopathi, K.; Babu, S. Moorthy; Jagan, R.; Ramasamy, P.

2017-12-01

The new inorganic-organic hybrid material aquadiiodo (3-aminopropanoic acid) cadmium (II) [ADI (3-AP) Cd] has been successfully synthesized and good quality crystals have been grown by slow evaporation solution technique. The structure was determined by single crystal X-ray diffraction at room temperature. The compound crystallizes in monoclinic crystal system with centro symmetric space group P21/c and four molecules in the unit cell. The structure of the title compound was further confirmed by 1H and 13C nuclear magnetic resonance spectral analysis. FT-IR spectroscopy was used to confirm the presence of various functional groups in the compound. The transmittance and optical parameters of the crystal were studied by UV- Visible-NIR spectroscopy. The thermal stability of the grown crystal was evaluated using thermogravimetric and differential thermal analyses. Mechanical hardness has been identified by Vickers micro hardness study and work hardening coefficient was calculated. Dielectric measurement was carried out as a function of frequency and results are discussed. The growth mechanism of the crystal was assessed by chemical etching studies. The third-order nonlinear optical susceptibility of [ADI (3-AP) Cd] was derived using the Z-scan technique, and it was 3.24955 × 10-8 esu. The positive nonlinear refractive index 2.48505 × 10-11 m2/W, is an indication of self-defocusing optical nonlinearity of the sample. It is believed that the [ADI (3-AP) Cd] is a promising new candidate for developing efficient nonlinear optical and optical power limiting devices.

In-situ and real-time growth observation of high-quality protein crystals under quasi-microgravity on earth.

PubMed

Nakamura, Akira; Ohtsuka, Jun; Kashiwagi, Tatsuki; Numoto, Nobutaka; Hirota, Noriyuki; Ode, Takahiro; Okada, Hidehiko; Nagata, Koji; Kiyohara, Motosuke; Suzuki, Ei-Ichiro; Kita, Akiko; Wada, Hitoshi; Tanokura, Masaru

2016-02-26

Precise protein structure determination provides significant information on life science research, although high-quality crystals are not easily obtained. We developed a system for producing high-quality protein crystals with high throughput. Using this system, gravity-controlled crystallization are made possible by a magnetic microgravity environment. In addition, in-situ and real-time observation and time-lapse imaging of crystal growth are feasible for over 200 solution samples independently. In this paper, we also report results of crystallization experiments for two protein samples. Crystals grown in the system exhibited magnetic orientation and showed higher and more homogeneous quality compared with the control crystals. The structural analysis reveals that making use of the magnetic microgravity during the crystallization process helps us to build a well-refined protein structure model, which has no significant structural differences with a control structure. Therefore, the system contributes to improvement in efficiency of structural analysis for "difficult" proteins, such as membrane proteins and supermolecular complexes.

Exploring contribution of intermolecular interactions in supramolecular layered assembly of naphthyridine co-crystals: Insights from Hirshfeld surface analysis of their crystalline states

NASA Astrophysics Data System (ADS)

Seth, Saikat Kumar; Das, Nirmal Kumar; Aich, Krishnendu; Sen, Debabrata; Fun, Hoong-Kun; Goswami, Shyamaprasad

2013-09-01

Co-crystals of 1a and 1b have been prepared by slow evaporation of the solutions of mixtures of 2,7-dimethyl-1,8-naphthyridine (1), urea (a) and thiourea (b). The structures of the complexes are determined by the single crystal X-ray diffraction and a detailed investigation of the crystal packing and classification of intermolecular interactions is presented by means of Hirshfeld surface analysis which is of considerable current interest in crystal engineering. The X-ray study reveals that the co-crystal formers are envisioned to produce N-H⋯N hydrogen bond as well as N-H⋯O/N-H⋯S pair-wise hydrogen bonds and also the weaker aromatic π⋯π interactions which cooperatively take part in the crystal packing. The recurring feature of the self-assembly in the compounds is the appearance of the molecular ribbon through multiple hydrogen bonding which are further stacked into molecular layers by π⋯π stacking interactions. Hirshfeld surface analysis for visually analyzing intermolecular interactions in crystal structures employing molecular surface contours and 2D Fingerprint plots have been used to examine molecular shapes. Crystal structure analysis supported with the Hirshfeld surface and fingerprint plots enabled the identification of the significant intermolecular interactions.

Synthesis and structural study of N-isopropenylbenzimidazolone

NASA Astrophysics Data System (ADS)

Mondieig, D.; Negrier, Ph.; Leger, J. M.; Lakhrissi, L.; El Assyry, A.; Lakhrissi, B.; Essassi, E. M.; Benali, B.; Boucetta, A.

2015-05-01

The synthesis and the crystal structure of the N-isopropenylbenzimidazolone (C10H10N2O) are presented. The synthesis was performed by Meth-Cohen method by reaction of o-phenylenediamine with ethyl acetoacetate in refluxed xylene. The single crystal structure was determined at room temperature by means of X-rays diffraction. The crystal system is monoclinic, with space group C2/c and eight molecules per unit cell. The unit cell dimensions are: a = 15.978(1) Å, b = 6.100(2) Å, c = 18.222(2) Å, β = 90.16(1)° and V = 1776.0(6) Å3.

Magnetic and structural instabilities in CePd 2Al 2 and LaPd 2Al 2

NASA Astrophysics Data System (ADS)

Chapon, L. C.; Goremychkin, E. A.; Osborn, R.; Rainford, B. D.; Short, S.

2006-05-01

We have investigated the crystal and magnetic structure of the RPd 2Al 2 compounds (R=La, Ce) by neutron powder diffraction (ND) and inelastic neutron scattering (INS). The ND study shows that both compounds undergo a structural phase transition from tetragonal to orthorhombic symmetry at 91.5 K (La) and 13.5 K (Ce). In the case of CePd 2Al 2 the crystal field excitation spectrum, which has an extra peak that cannot be explained by a standard crystal field model, indicates the presence of strong magneto-elastic coupling.

Crystallization of Membrane Proteins by Vapor Diffusion

PubMed Central

Delmar, Jared A.; Bolla, Jani Reddy; Su, Chih-Chia; Yu, Edward W.

2016-01-01

X-ray crystallography remains the most robust method to determine protein structure at the atomic level. However, the bottlenecks of protein expression and purification often discourage further study. In this chapter, we address the most common problems encountered at these stages. Based on our experiences in expressing and purifying antimicrobial efflux proteins, we explain how a pure and homogenous protein sample can be successfully crystallized by the vapor diffusion method. We present our current protocols and methodologies for this technique. Case studies show step-by-step how we have overcome problems related to expression and diffraction, eventually producing high quality membrane protein crystals for structural determinations. It is our hope that a rational approach can be made of the often anecdotal process of membrane protein crystallization. PMID:25950974

Liquid Structures and Physical Properties -- Ground Based Studies for ISS Experiments

NASA Technical Reports Server (NTRS)

Kelton, K. F.; Bendert, J. C.; Mauro, N. A.

2012-01-01

Studies of electrostatically-levitated supercooled liquids have demonstrated strong short- and medium-range ordering in transition metal and alloy liquids, which can influence phase transitions like crystal nucleation and the glass transition. The structure is also related to the liquid properties. Planned ISS experiments will allow a deeper investigation of these results as well as the first investigations of a new type of coupling in crystal nucleation in primary crystallizing liquids, resulting from a linking of the stochastic processes of diffusion with interfacial-attachment. A brief description of the techniques used for ground-based studies and some results relevant to planned ISS investigations are discussed.

Multi-temperature study of potassium uridine-5'-monophosphate: electron density distribution and anharmonic motion modelling.

PubMed

Jarzembska, Katarzyna N; Řlepokura, Katarzyna; Kamiński, Radosław; Gutmann, Matthias J; Dominiak, Paulina M; Woźniak, Krzysztof

2017-08-01

Uridine, a nucleoside formed of a uracil fragment attached to a ribose ring via a β-N1-glycosidic bond, is one of the four basic components of ribonucleic acid. Here a new anhydrous structure and experimental charge density distribution analysis of a uridine-5'-monophosphate potassium salt, K(UMPH), is reported. The studied case constitutes the very first structure of a 5'-nucleotide potassium salt according to the Cambridge Structural Database. The excellent crystal quality allowed the collection of charge density data at various temperatures, i.e. 10, 100, 200 and 300 K on one single crystal. Crystal structure and charge density data were analysed thoroughly in the context of related literature-reported examples. Detailed analysis of the charge density distribution revealed elevated anharmonic motion of part of the uracil ring moiety relatively weakly interacting with the neighbouring species. The effect was manifested by alternate positive and negative residual density patterns observed for these atoms, which `disappear' at low temperature. It also occurred that the potassium cation, quite uniformly coordinated by seven O atoms from all molecular fragments of the UMPH - anion, including the O atom from the ribofuranose ring, can be treated as spherical in the charge density model which was supported by theoretical calculations. Apart from the predominant electrostatic interactions, four relatively strong hydrogen bond types further support the stability of the crystal structure. This results in a compact and quite uniform structure (in all directions) of the studied crystal, as opposed to similar cases with layered architecture reported in the literature.

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.

Purification, crystallization, preliminary X-ray diffraction and molecular-replacement studies of great cormorant (Phalacrocorax carbo) haemoglobin

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

Jagadeesan, G.; Malathy, P.; Gunasekaran, K.

2014-10-25

The great cormorant hemoglobin has been isolated, purified and crystallized and the three dimensional structure is solved using molecular replacement technique. Haemoglobin is the iron-containing oxygen-transport metalloprotein that is present in the red blood cells of all vertebrates. In recent decades, there has been substantial interest in attempting to understand the structural basis and functional diversity of avian haemoglobins. Towards this end, purification, crystallization, preliminary X-ray diffraction and molecular-replacement studies have been carried out on cormorant (Phalacrocorax carbo) haemoglobin. Crystals were grown by the hanging-drop vapour-diffusion method using PEG 3350, NaCl and glycerol as precipitants. The crystals belonged to themore » trigonal system P3{sub 1}21, with unit-cell parameters a = b = 55.64, c = 153.38 Å, β = 120.00°; a complete data set was collected to a resolution of 3.5 Å. Matthews coefficient analysis indicated that the crystals contained a half-tetramer in the asymmetric unit.« less

Combined crystal structure prediction and high-pressure crystallization in rational pharmaceutical polymorph screening

PubMed Central

Neumann, M. A.; van de Streek, J.; Fabbiani, F. P. A.; Hidber, P.; Grassmann, O.

2015-01-01

Organic molecules, such as pharmaceuticals, agro-chemicals and pigments, frequently form several crystal polymorphs with different physicochemical properties. Finding polymorphs has long been a purely experimental game of trial-and-error. Here we utilize in silico polymorph screening in combination with rationally planned crystallization experiments to study the polymorphism of the pharmaceutical compound Dalcetrapib, with 10 torsional degrees of freedom one of the most flexible molecules ever studied computationally. The experimental crystal polymorphs are found at the bottom of the calculated lattice energy landscape, and two predicted structures are identified as candidates for a missing, thermodynamically more stable polymorph. Pressure-dependent stability calculations suggested high pressure as a means to bring these polymorphs into existence. Subsequently, one of them could indeed be crystallized in the 0.02 to 0.50 GPa pressure range and was found to be metastable at ambient pressure, effectively derisking the appearance of a more stable polymorph during late-stage development of Dalcetrapib. PMID:26198974

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.

An intermolecular binding mechanism involving multiple LysM domains mediates carbohydrate recognition by an endopeptidase

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

Wong, Jaslyn E. M. M.; Midtgaard, Søren Roi; Gysel, Kira

The crystal and solution structures of the T. thermophilus NlpC/P60 d, l-endopeptidase as well as the co-crystal structure of its N-terminal LysM domains bound to chitohexaose allow a proposal to be made regarding how the enzyme recognizes peptidoglycan. LysM domains, which are frequently present as repetitive entities in both bacterial and plant proteins, are known to interact with carbohydrates containing N-acetylglucosamine (GlcNAc) moieties, such as chitin and peptidoglycan. In bacteria, the functional significance of the involvement of multiple LysM domains in substrate binding has so far lacked support from high-resolution structures of ligand-bound complexes. Here, a structural study of themore » Thermus thermophilus NlpC/P60 endopeptidase containing two LysM domains is presented. The crystal structure and small-angle X-ray scattering solution studies of this endopeptidase revealed the presence of a homodimer. The structure of the two LysM domains co-crystallized with N-acetyl-chitohexaose revealed a new intermolecular binding mode that may explain the differential interaction between LysM domains and short or long chitin oligomers. By combining the structural information with the three-dimensional model of peptidoglycan, a model suggesting how protein dimerization enhances the recognition of peptidoglycan is proposed.« less

High-speed prediction of crystal structures for organic molecules

NASA Astrophysics Data System (ADS)

Obata, Shigeaki; Goto, Hitoshi

2015-02-01

We developed a master-worker type parallel algorithm for allocating tasks of crystal structure optimizations to distributed compute nodes, in order to improve a performance of simulations for crystal structure predictions. The performance experiments were demonstrated on TUT-ADSIM supercomputer system (HITACHI HA8000-tc/HT210). The experimental results show that our parallel algorithm could achieve speed-ups of 214 and 179 times using 256 processor cores on crystal structure optimizations in predictions of crystal structures for 3-aza-bicyclo(3.3.1)nonane-2,4-dione and 2-diazo-3,5-cyclohexadiene-1-one, respectively. We expect that this parallel algorithm is always possible to reduce computational costs of any crystal structure predictions.

Studies on Aspirin Crystals Generated by a Modified Vapor Diffusion Method.

PubMed

Mittal, Amit; Malhotra, Deepak; Jain, Preeti; Kalia, Anupama; Shunmugaperumal, Tamilvanan

2016-08-01

The objectives of the current investigation were (1) to study the influence of selected two different non-solvents (diethylether and dichloromethane) on the drug crystal formation of a model drug, aspirin (ASP-I) by the modified vapor diffusion method and (2) to characterize and compare the generated crystals (ASP-II and ASP-III) using different analytical techniques with that of unprocessed ASP-I. When compared to the classical vapor diffusion method which consumes about 15 days to generate drug crystals, the modified method needs only 12 h to get the same. Fourier transform-infrared spectroscopy (FT-IR) reveals that the internal structures of ASP-II and ASP-III crystals were identical when compared with ASP-I. Although the drug crystals showed a close similarity in X-ray diffraction patterns, the difference in the relative intensities of some of the diffraction peaks (especially at 2θ values of around 7.7 and 15.5) could be attributed to the crystal habit or crystal size modification. Similarly, the differential scanning calorimetry (DSC) study speculates that only the crystal habit modifications might occur but without involving any change in internal structure of the generated drug polymorphic form I. This is further substantiated from the scanning electron microscopy (SEM) pictures that indicated the formation of platy shape for the ASP-II crystals and needle shape for the ASP-III crystals. In addition, the observed slow dissolution of ASP crystals should indicate polymorph form I formation. Thus, the modified vapor diffusion method could routinely be used to screen and legally secure all possible forms of other drug entities too.

Bidomain structures formed in lithium niobate and lithium tantalate single crystals by light annealing

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

Kubasov, I. V., E-mail: kubasov.ilya@gmail.com; Kislyuk, A. M.; Bykov, A. S.

The bidomain structures produced by light external heating in z-cut lithium niobate and lithium tantalate single crystals are formed and studied. Interdomain regions about 200 and 40 μm wide in, respectively, LiNbO{sub 3} and LiTaO{sub 3} bidomain crystals are visualized and studied by optical microscopy and piezoresponse force microscopy. Extended chains and lines of domains in the form of thin layers with a width less than 10 μm in volume, which penetrate the interdomain region and spread over distances of up to 1 mm, are found.

Photonic crystals, amorphous materials, and quasicrystals

PubMed Central

Edagawa, Keiichi

2014-01-01

Photonic crystals consist of artificial periodic structures of dielectrics, which have attracted much attention because of their wide range of potential applications in the field of optics. We may also fabricate artificial amorphous or quasicrystalline structures of dielectrics, i.e. photonic amorphous materials or photonic quasicrystals. So far, both theoretical and experimental studies have been conducted to reveal the characteristic features of their optical properties, as compared with those of conventional photonic crystals. In this article, we review these studies and discuss various aspects of photonic amorphous materials and photonic quasicrystals, including photonic band gap formation, light propagation properties, and characteristic photonic states. PMID:27877676

Photonic crystals, amorphous materials, and quasicrystals.

PubMed

Edagawa, Keiichi

2014-06-01

Photonic crystals consist of artificial periodic structures of dielectrics, which have attracted much attention because of their wide range of potential applications in the field of optics. We may also fabricate artificial amorphous or quasicrystalline structures of dielectrics, i.e. photonic amorphous materials or photonic quasicrystals. So far, both theoretical and experimental studies have been conducted to reveal the characteristic features of their optical properties, as compared with those of conventional photonic crystals. In this article, we review these studies and discuss various aspects of photonic amorphous materials and photonic quasicrystals, including photonic band gap formation, light propagation properties, and characteristic photonic states.

Zeolite Crystal Growth (ZCG) Flight on USML-2

NASA Technical Reports Server (NTRS)

Sacco, Albert, Jr.; Bac, Nurcan; Warzywoda, Juliusz; Guray, Ipek; Marceau, Michelle; Sacco, Teran L.; Whalen, Leah M.

1997-01-01

The extensive use of zeolites and their impact on the world's economy has resulted in many efforts to characterize their structure, and improve the knowledge base for nucleation and growth of these crystals. The zeolite crystal growth (ZCG) experiment on USML-2 aimed to enhance the understanding of nucleation and growth of zeolite crystals, while attempting to provide a means of controlling the defect concentration in microgravity. Zeolites A, X, Beta, and Silicalite were grown during the 16 day - USML-2 mission. The solutions where the nucleation event was controlled yielded larger and more uniform crystals of better morphology and purity than their terrestrial/control counterparts. The external surfaces of zeolite A, X, and Silicalite crystals grown in microgravity were smoother (lower surface roughness) than their terrestrial controls. Catalytic studies with zeolite Beta indicate that crystals grown in space exhibit a lower number of Lewis acid sites located in micropores. This suggests fewer structural defects for crystals grown in microgravity. Transmission electron micrographs (TEM) of zeolite Beta crystals also show that crystals grown in microgravity were free of line defects while terrestrial/controls had substantial defects.

Fabrication of ceramic layer-by-layer infrared wavelength photonic band gap crystals

NASA Astrophysics Data System (ADS)

Kang, Henry Hao-Chuan

Photonic band gap (PBG) crystals, also known as photonic crystals, are periodic dielectric structures which form a photonic band gap that prohibit the propagation of electromagnetic (EM) waves of certain frequencies at any incident angles. Photonic crystals have several potential applications including zero-threshold semiconductor lasers, the inhibiting spontaneous emission, dielectric mirrors, and wavelength filters. If defect states are introduced in the crystals, light can be guided from one location to another or even a sharp bending of light in submicron scale can be achieved. This generates the potential for optical waveguide and optical circuits, which will contribute to the improvement in the fiber-optic communications and the development of high-speed computers. The goal of this dissertation research is to explore techniques for fabricating 3D ceramic layer-by-layer (LBL) photonic crystals operating in the infrared frequency range, and to characterize the infilling materials properties that affect the fabrication process as well as the structural and optical properties of the crystals. While various approaches have been reported in literature for the fabrication of LBL structure, the uniqueness of this work ties with its cost-efficiency and relatively short process span. Besides, very few works have been reported on fabricating ceramic LBL crystals at mid-IR frequency range so far. The fabrication techniques reported here are mainly based on the concepts of microtransfer molding with the use of polydimethyl siloxane (PDMS) as molds/stamps. The infilling materials studied include titanium alkoxide precursors and aqueous suspensions of nanosize titania particles (slurries). Various infilling materials were synthesized to determine viscosities, effects on drying and firing shrinkages, effects on film surface roughness, and their moldability. Crystallization and phase transformation of the materials were also monitored using DTA, TGA and XRD. Mutilayer crystal structures of 2.5 and 1.0 mum periodicity have been successfully built. The structures of the fabricated crystals are inspected with scanning electron microscopy (SEM) and the optical characteristics are examined with optical microscopy and FtIR spectroscopy.

Local Atomic Arrangements and Band Structure of Boron Carbide.

PubMed

Rasim, Karsten; Ramlau, Reiner; Leithe-Jasper, Andreas; Mori, Takao; Burkhardt, Ulrich; Borrmann, Horst; Schnelle, Walter; Carbogno, Christian; Scheffler, Matthias; Grin, Yuri

2018-05-22

Boron carbide, the simple chemical combination of boron and carbon, is one of the best-known binary ceramic materials. Despite that, a coherent description of its crystal structure and physical properties resembles one of the most challenging problems in materials science. By combining ab initio computational studies, precise crystal structure determination from diffraction experiments, and state-of-the-art high-resolution transmission electron microscopy imaging, this concerted investigation reveals hitherto unknown local structure modifications together with the known structural alterations. The mixture of different local atomic arrangements within the real crystal structure reduces the electron deficiency of the pristine structure CBC+B 12 , answering the question about electron precise character of boron carbide and introducing new electronic states within the band gap, which allow a better understanding of physical properties. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

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.

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

Wang, Bingnan

Photonic crystals and metamaterials, both composed of artificial structures, are two interesting areas in electromagnetism and optics. New phenomena in photonic crystals and metamaterials are being discovered, including some not found in natural materials. This thesis presents my research work in the two areas. Photonic crystals are periodically arranged artificial structures, mostly made from dielectric materials, with period on the same order of the wavelength of the working electromagnetic wave. The wave propagation in photonic crystals is determined by the Bragg scattering of the periodic structure. Photonic band-gaps can be present for a properly designed photonic crystal. Electromagnetic waves withmore » frequency within the range of the band-gap are suppressed from propagating in the photonic crystal. With surface defects, a photonic crystal could support surface modes that are localized on the surface of the crystal, with mode frequencies within the band-gap. With line defects, a photonic crystal could allow the propagation of electromagnetic waves along the channels. The study of surface modes and waveguiding properties of a 2D photonic crystal will be presented in Chapter 1. Metamaterials are generally composed of artificial structures with sizes one order smaller than the wavelength and can be approximated as effective media. Effective macroscopic parameters such as electric permittivity ϵ, magnetic permeability μ are used to characterize the wave propagation in metamaterials. The fundamental structures of the metamaterials affect strongly their macroscopic properties. By designing the fundamental structures of the metamaterials, the effective parameters can be tuned and different electromagnetic properties can be achieved. One important aspect of metamaterial research is to get artificial magnetism. Metallic split-ring resonators (SRRs) and variants are widely used to build magnetic metamaterials with effective μ < 1 or even μ < 0. Varactor based nonlinear SRRs are built and modeled to study the nonlinearity in magnetic metamaterials and the results will be presented in Chapter 3. Negative refractive index n is one of the major target in the research of metamaterials. Negative n can be obtained with a metamaterial with both ϵ and μ negative. As an alternative, negative index for one of the circularly polarized waves could be achieved with metamaterials having a strong chirality ?. In this case neither ϵ} nor μ negative is required. My work on chiral metamaterials will be presented in Chapter 4.« less

(NZ)CH...O contacts assist crystallization of a ParB-like nuclease.

PubMed

Shaw, Neil; Cheng, Chongyun; Tempel, Wolfram; Chang, Jessie; Ng, Joseph; Wang, Xin-Yu; Perrett, Sarah; Rose, John; Rao, Zihe; Wang, Bi-Cheng; Liu, Zhi-Jie

2007-07-07

The major bottleneck for determination of 3 D structures of proteins using X-rays is the production of diffraction quality crystals. Often proteins are subjected to chemical modification to improve the chances of crystallization Here, we report the successful crystallization of a nuclease employing a reductive methylation protocol. The key to crystallization was the successful introduction of 44 new cohesive (NZ) CH...O contacts (3.2-3.7 A) by the addition of 2 methyl groups to the side chain amine nitrogen (NZ) of 9 lysine residues of the nuclease. The new contacts dramatically altered the crystallization properties of the protein, resulting in crystals that diffracted to 1.2 A resolution. Analytical ultracentrifugation analysis and thermodynamics results revealed a more compact protein structure with better solvent exclusion of buried Trp residues in the folded state of the methylated protein, assisting crystallization. In this study, introduction of novel cohesive (NZ)CH...O contacts by reductive methylation resulted in the crystallization of a protein that had previously resisted crystallization in spite of extensive purification and crystallization space screening. Introduction of (NZ)CH...O contacts could provide a solution to crystallization problems for a broad range of protein targets.

Highly reproducible alkali metal doping system for organic crystals through enhanced diffusion of alkali metal by secondary thermal activation.

PubMed

Lee, Jinho; Park, Chibeom; Song, Intek; Koo, Jin Young; Yoon, Taekyung; Kim, Jun Sung; Choi, Hee Cheul

2018-05-16

In this paper, we report an efficient alkali metal doping system for organic single crystals. Our system employs an enhanced diffusion method for the introduction of alkali metal into organic single crystals by controlling the sample temperature to induce secondary thermal activation. Using this system, we achieved intercalation of potassium into picene single crystals with closed packed crystal structures. Using optical microscopy and Raman spectroscopy, we confirmed that the resulting samples were uniformly doped and became K 2 picene single crystal, while only parts of the crystal are doped and transformed into K 2 picene without secondary thermal activation. Moreover, using a customized electrical measurement system, the insulator-to-semiconductor transition of picene single crystals upon doping was confirmed by in situ electrical conductivity and ex situ temperature-dependent resistivity measurements. X-ray diffraction studies showed that potassium atoms were intercalated between molecular layers of picene, and doped samples did not show any KH- nor KOH-related peaks, indicating that picene molecules are retained without structural decomposition. During recent decades, tremendous efforts have been exerted to develop high-performance organic semiconductors and superconductors, whereas as little attention has been devoted to doped organic crystals. Our method will enable efficient alkali metal doping of organic crystals and will be a resource for future systematic studies on the electrical property changes of these organic crystals upon doping.

Synthesis, spectroscopic, crystal structure, biological activities and theoretical studies of 2-[(2E)-2-(2-chloro-6-fluorobenzylidene)hydrazinyl]pyridine

NASA Astrophysics Data System (ADS)

Dilek Özçelik, Nefise; Tunç, Tuncay; Çatak Çelik, Raziye; Erzengin, Mahmut; Özışık, Hacı

2017-05-01

We report in this paper the synthesis, spectroscopic, crystal structure, biological activities and theoretical results of the title compound. The crystal structure was defined by the X-ray diffraction (XRD) method. In addition, this newly synthesized hydrazone derivative was also subjected to its possible antioxidant activity with free radical scavenging ability of 2,2-diphenyl-1-picrylhydrazyl (DPPH) radicals using butylated hydroxytoluene (BHT) as standard antioxidant. The structural calculations were performed by the density functional theory using the B3LYP method with 6-311++G(2d,2p) basis set. The calculated values were compared with experimental results.

Synthesis, crystal structure and luminescent properties of a new pyrochlore type tungstate CsGa0.333W1.667O6

NASA Astrophysics Data System (ADS)

Zhao, Dan; Zhao, Ji; Fan, Yun-Chang; Ma, Zhao; Zhang, Rui-Juan; Liu, Bao-Zhong

2018-06-01

High temperature solution reaction leads to a new tungstate compound CsGa0.333W1.667O6, whose structure was determined by single-crystal X-ray diffraction analysis. The results show that it crystallizes in pyrochlore structure with cubic space group Fd-3m and a = 10.2529 (13) Å. In this structure, Ga and W atoms are in a statistical disorder manner. The self-activated luminescent properties CsGa0.333W1.667O6 were studied. Under the excitation of 323 nm, the emission spectrum exhibits a blue emission centered at 466 nm with the chromaticity coordinates (0.1838, 0.1814).

Experimental and density functional theory (DFT): A dual approach to probe the key properties of creatininium L-tartrate monohydrate single crystal for nonlinear optical applications

NASA Astrophysics Data System (ADS)

Thirumurugan, R.; Babu, B.; Anitha, K.; Chandrasekaran, J.

2017-12-01

A novel organic nonlinear optical (NLO) material, creatininium L-tartrate monohydrate (CTM) was synthesized and it was grown as single crystals with optical quality. 1H and 13C NMR spectral studies were performed and molecular structure of synthesized CTM compound was confirmed. Single crystal X-ray diffraction (SXRD) analysis confirmed that CTM was crystallized in orthorhombic system with non-centrosymmetric (NCS), P212121, space group. The grown crystal exhibited admirable properties such as second harmonic generation efficiency (SHG) (1.9 times KDP), and high laser damage threshold (LDT) value of 3.7 GW cm-2. CTM crystal displayed high transparency (∼60%) in the visible and near-IR region with low cut-off wavelength at 249 nm. Photoluminescence study confirmed blue wavelength emission (∼463 nm) of grown crystal. Thermal and mechanical behaviours have been successfully analysed for grown crystals. The dielectric studies were carried out for grown crystal as a function of frequencies at different temperatures. Hirshfeld surface and fingerprint plots provided the percentage of individual interactions contributed by each atom. Moreover, density functional theory (DFT) calculations have been employed to probe the frontier molecular orbitals (FMOs) and first hyperpolarizability (β) analysis of the optimized CTM structure. These results validated CTM as a suitable NLO candidate and were discussed in this work.

SAD phasing with in-house cu Ka radiation using barium as anomalous scatterer.

PubMed

Dhanasekaran, V; Velmurugan, D

2011-12-01

Phasing of lysozyme crystals using co-crystallized barium ions was performed using single-wavelength anomalous diffraction (SAD) method using Cu Ka radiation with in-house source of data collection. As the ion binding sites vary with respect to the pH of the buffer during crystallization, the highly isomorphic forms of lysozyme crystals grown at acidic and alkaline pH were used for the study. Intrinsic sulphur anomalous signal was also utilized with anomalous signal from lower occupancy ions for phasing. The study showed that to solve the structure by SAD technique, 2.8-fold data redundancy was sufficient when barium was used as an anomalous marker in the in-house copper X-ray radiation source for data collection. Therefore, co-crystallization of proteins with barium containing salt can be a powerful tool for structure determination using lab source.

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

Kuz'mina, L. G., E-mail: kuzmina@igic.ras.ru; Kucherepa, N. S.; Syrbu, S. A.

The crystal and molecular structure of p-(decaoxybenzylidene)-p'-toluidine C{sub 10}H{sub 21}O-C{sub 6}H{sub 4}-CH=N-C{sub 6}H{sub 4}-CH{sub 3} is studied. The molecule is nearly planar. In the crystal packing, loose regions formed by aliphatic fragments of molecules alternate with pseudostacks of aromatic fragments of molecules that are related by the centers of symmetry. The stacks are built of dimers, in which molecules are linked by {pi}-stacking interactions between benzene rings. There are no weak directional interactions between dimers in a stack. The presence of a single structure-forming element in the crystal, namely, the {pi}-stacking interactions in the dimers, along with the similarity ofmore » the crystal packing to that of the C{sub 8}H{sub 17}O-homologue, which forms a nematic mesophase on melting, indicate that the crystals under study should exhibit nematic properties.« less

Crystal structure of a putative exo-β-1,3-galactanase from Bifidobacterium bifidum S17

PubMed Central

Godoy, Andre S.; de Lima, Mariana Z. T.; Camilo, Cesar M.; Polikarpov, Igor

2016-01-01

Given the current interest in second-generation biofuels, carbohydrate-active enzymes have become the most important tool to overcome the structural recalcitrance of the plant cell wall. While some glycoside hydrolase families have been exhaustively described, others remain poorly characterized, especially with regard to structural information. The family 43 glycoside hydrolases are a diverse group of inverting enzymes; the available structure information on these enzymes is mainly from xylosidases and arabinofuranosidase. Currently, only one structure of an exo-β-1,3-galactanase is available. Here, the production, crystallization and structure determination of a putative exo-β-1,3-galactanase from Bifidobacterium bifidum S17 (BbGal43A) are described. BbGal43A was successfully produced and showed activity towards synthetic galactosides. BbGal43A was subsequently crystallized and data were collected to 1.4 Å resolution. The structure shows a single-domain molecule, differing from known homologues, and crystal contact analysis predicts the formation of a dimer in solution. Further biochemical studies are necessary to elucidate the differences between BbGal43A and its characterized homologues. PMID:27050262

Experimental study of modification mechanism at a wear-resistant surfacing

NASA Astrophysics Data System (ADS)

Dema, R. R.; Amirov, R. N.; Kalugina, O. B.

2018-01-01

In the study, a simulation of the crystallization process was carried out for the deposition of the near-eutectic structure alloys with inoculants presence in order to reveal the regularities of the inoculant effect and parameters of the process mode simulating surfacing on the structure of the crystallization front and on the nucleation rate and kinetics of growth of equiaxed crystallites of primary phases occurring in the volume of the melt. The simulation technique of primary crystallization of alloys similar to eutectic alloys in the presence of modifiers is offered. The possibility of fully eutectic structure during surfacing of nominal hypereutectic alloys of type white cast irons in wide range of deviations from the nominal composition is revealed.

Path-integral and Ornstein-Zernike study of quantum fluid structures on the crystallization line

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

Sesé, Luis M., E-mail: msese@ccia.uned.es

2016-03-07

Liquid neon, liquid para-hydrogen, and the quantum hard-sphere fluid are studied with path integral Monte Carlo simulations and the Ornstein-Zernike pair equation on their respective crystallization lines. The results cover the whole sets of structures in the r-space and the k-space and, for completeness, the internal energies, pressures and isothermal compressibilities. Comparison with experiment is made wherever possible, and the possibilities of establishing k-space criteria for quantum crystallization based on the path-integral centroids are discussed. In this regard, the results show that the centroid structure factor contains two significant parameters related to its main peak features (amplitude and shape) thatmore » can be useful to characterize freezing.« less

A review on the synthesis, crystal growth, structure and physical properties of rare earth based quaternary intermetallic compounds

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

Mumbaraddi, Dundappa; Sarkar, Sumanta; Peter, Sebastian C., E-mail: sebastiancp@jncasr.ac.in

2016-04-15

This review highlights the synthesis and crystal growth of quaternary intermetallic compounds based on rare earth metals. In the first part of this review, we highlight briefly about intermetallics and their versatile properties in comparison to the constituent elements. In the next part, we have discussed about various synthesis techniques with more focus on the metal flux technique towards the well shaped crystal growth of novel compounds. In the subsequent parts, several disordered quaternary compounds have been reviewed and then outlined most known ordered quaternary compounds with their complex structure. A special attention has been given to the ordered compoundsmore » with structural description and relation to the parent binary and ternary compounds. The importance of electronic and structural feature is highlighted as the key roles in designing these materials for emerging applications. - Graphical abstract: Rare earth based quaternary intermetallic compounds crystallize in complex novel crystal structures. The diversity in the crystal structure may induce unique properties and can be considered them as future materials. - Highlights: • Crystal growth and crystal structure of quaternary rare earth based intermetallics. • Structural complexity of quaternary compounds in comparison to the parent compounds. • Novel quaternary compounds display unique crystal structure.« less

Growth and characterization of hexamethylenetetramine crystals grown from solution

NASA Astrophysics Data System (ADS)

Babu, B.; Chandrasekaran, J.; Balaprabhakaran, S.

2014-06-01

Organic nonlinear optical single crystals of hexamethylenetetramine (HMT; 10 × 10 × 5 mm3) were prepared by crystallization from methanol solution. The grown crystals were subjected to various characterization techniques such as single crystal XRD, powder XRD, UV-Vis and electrical studies. Single crystal XRD analysis confirmed the crystalline structure of the grown crystals. Their crystalline nature was also confirmed by powder XRD technique. The optical transmittance property was identified from UV-Vis spectrum. Dielectric measurements were performed as a function of frequency at different temperatures. DC conductivity and photoconductivity studies were also carried out for the crystal. The powder second harmonic generation efficiency (SHG) of the crystal was measured using Nd:YAG laser and the efficiency was found to be two times greater than that of potassium dihydrogen phosphate (KDP).

Crystallization of Stretched Polyimides: A Structure-Property Study

NASA Technical Reports Server (NTRS)

Hinkley, Jeffrey A.; Dezern, James F.

2002-01-01

A simple rotational isomeric state model was used to detect the degree to which polyimide repeat units might align to give an extended crystal. It was found experimentally that the hallmarks of stretch-crystallization were more likely to occur in materials whose molecules could readily give extended, aligned conformations. A proposed screening criterion was 84% accurate in selecting crystallizing molecules.

Self-organization processes and topological defects in nanolayers in a nematic liquid crystal

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

Chuvyrov, A. N.; Girfanova, F. M.; Mal'tsev, I. S.

Atomic force microscopy is used to study the self-organization processes that occur during the formation of topological defects in nanomolecular layers in a nematic liquid crystal with the homeotropic orientation of its molecules with respect to the substrate. In this case, a smectic monolayer with a thickness of one molecule length (about 2.2 nm) forms on the substrate, and a nanomolecular layer of a nematic liquid crystal forms above this monolayer. In such virtually two-dimensional layers, numerous different nanoclusters, namely, hut structures, pyramids, raft structures with symmetry C{sub nm} (where n = 2, 4, 5, 6, 7, ?, {infinity}), cones,more » and nanopools, form [1]. They have a regular shape close to the geometry of solid crystals. Modulated linear structures and topological point defects appear spontaneously in the nanopools and raft structures.« less

Generation of Protein Crystals Using a Solution-Stirring Technique

NASA Astrophysics Data System (ADS)

Adachi, Hiroaki; Niino, Ai; Matsumura, Hiroyoshi; Takano, Kazufumi; Kinoshita, Takayoshi; Warizaya, Masaichi; Inoue, Tsuyoshi; Mori, Yusuke; Sasaki, Takatomo

2004-06-01

Crystals of bovine adenosine deaminase (ADA) were grown over a two week period in the presence of an inhibitor, whereas ADA crystals did not form using conventional crystallization methods when the inhibitor was excluded. To obtain ADA crystals in the absence of the inhibitor, a solution-stirring technique was used. The crystals obtained using this technique were found to be of high quality and were shown to have high structural resolution for X-ray diffraction analysis. The results of this study indicate that the stirring technique is a useful method for obtaining crystals of proteins that do not crystallize using conventional techniques.

Solid-state reaction kinetics of neodymium doped magnesium hydrogen phosphate system

NASA Astrophysics Data System (ADS)

Gupta, Rashmi; Slathia, Goldy; Bamzai, K. K.

2018-05-01

Neodymium doped magnesium hydrogen phosphate (NdMHP) crystals were grown by using gel encapsulation technique. Structural characterization of the grown crystals has been carried out by single crystal X-ray diffraction (XRD) and it revealed that NdMHP crystals crystallize in orthorhombic crystal system with space group Pbca. Kinetics of the decomposition of the grown crystals has been studied by non-isothermal analysis. The estimation of decomposition temperatures and weight loss has been made from the thermogravimetric/differential thermo analytical (TG/DTA) in conjuncture with DSC studies. The various steps involved in the thermal decomposition of the material have been analysed using Horowitz-Metzger, Coats-Redfern and Piloyan-Novikova equations for evaluating various kinetic parameters.

Molecular Modeling and Experimental Study of Nonlinear Optical Compounds: Mono-Substituted Derivatives of Dicyanovinylbenzene

NASA Technical Reports Server (NTRS)

Timofeeva, Tatyana V.; Nesterov, Vladimir N.; Antipin, Mikhael Y.; Clark, R. D.; Sanghadasa, M.; Cardelino, B. H.; Moore, C. E.; Frazier, Donald O.

2000-01-01

A search for potential nonlinear optical (NLO) compounds has been performed using the Cambridge Structural Database and molecular modeling. We have studied a series of mono-substituted derivatives of dicyanovinylbenzene as the NLO properties of one of its derivatives (o-methoxy-dicyanovinylbenzene, DIVA) were described earlier. The molecular geometry in the series of the compounds studied was investigated with an X- ray analysis and discussed along with results of molecular mechanics and ab initio quantum chemical calculations. The influence of crystal packing on the molecular planarity has been revealed. Two new compounds from the series studied were found to be active for second harmonic generation (SHG) in the powder. The measurements of SHG efficiency have shown that the o-F- and p-Cl-derivatives of dicyanovinylbenzene are about 10 and 20- times more active than urea, respectively. The peculiarities of crystal structure formation in the framework of balance between the van der Waals and electrostatic interactions have been discussed. The crystal morphology of DIVA and two new SHG-active compounds have been calculated on the basis of their known crystal structures.

Study on structural, morphological, optical and thermal properties of guanidine carbonate doped nickel sulfate hexahydrate crystal.

PubMed

Silambarasan, A; Rajesh, P; Ramasamy, P

2015-01-05

The single crystal of guanidine carbonate doped nickel sulfate hexahydrate was grown from solution for ultraviolet filters. The single crystal XRD confirms that the grown single crystal belongs to the tetragonal system with the space group of P4₁2₁2. The crystallinity of the grown crystal was estimated by powder X-ray diffraction studies. The optical transmission and thermal stability of as-grown guanidine carbonate doped nickel sulfate single crystals have been studied. The optical transmission spectrum demonstrates the characteristics of ultraviolet filters. The TG/DTA studies confirm the thermal properties of grown crystals. Thermo-gravimetric analysis showed that the dehydration temperature of the guanidine carbonate doped nickel sulfate crystal is about 100 °C, which is much higher than that of pure nickel sulfate hexahydrate (NSH) crystals which is 72 °C. The growth behaviors and dislocation density were detected under the high resolution XRD and etching studies respectively. Copyright © 2014 Elsevier B.V. All rights reserved.

Studies on the growth, structural, spectral and third-order nonlinear optical properties of ammonium 3-carboxy-4-hydroxy benzenesulfonate monohydrate single crystal.

PubMed

Silambarasan, A; Krishna Kumar, M; Thirunavukkarasu, A; Mohan Kumar, R; Umarani, P R

2015-01-25

An organic nonlinear optical bulk single crystal, Ammonium 3-carboxy-4-hydroxy benzenesulfonate monohydrate (ACHBS) was successfully grown by solution growth technique. Single crystal X-ray diffraction study confirms that, the grown crystal belongs to P21/c space group. Powder X-ray diffraction and high resolution X-ray diffraction analyses revealed the crystallinity of the grown crystal. Infrared spectral analysis showed the vibrational behavior of chemical bonds and its functional groups. The thermal stability and decomposition stages of the grown crystal were studied by TG-DTA analysis. UV-Visible transmittance studies showed the transparency region and cut-off wavelength of the grown crystal. The third-order nonlinear optical susceptibility of the grown crystal was estimated by Z-scan technique using He-Ne laser source. The mechanical property of the grown crystal was studied by using Vicker's microhardness test. Copyright © 2014 Elsevier B.V. All rights reserved.

Growth and dielectric, mechanical, thermal and etching studies of an organic nonlinear optical L-arginine trifluoroacetate (LATF) single crystal

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

Arjunan, S.; Department of Physics, Presidency College, Chennai 600005; Mohan Kumar, R.

2008-08-04

L-arginine trifluoroacetate, an organic nonlinear optical material, has been synthesized from aqueous solution. Bulk single crystal of dimension 57 mm x 5 mm x 3 mm has been grown by temperature lowering technique. Powder X-ray diffraction studies confirmed the monoclinic structure of the grown L-arginine trifluoroacetate crystal. Linear optical property of the grown crystal has been studied by UV-vis spectrum. Dielectric response of the L-arginine trifluoroacetate crystal was analysed for different frequencies and temperatures in detail. Microhardness study on the sample reveals that the crystal possesses relatively higher hardness compared to many organic crystals. Thermal analyses confirmed that the L-argininemore » trifluoroacetate material is thermally stable upto 212 deg. C. The etching studies have been performed to assess the perfection of the L-arginine trifluoroacetate crystal. Kurtz powder second harmonic generation test confirms the nonlinear optical properties of the as-grown L-arginine trifluoroacetate crystal.« less

Growing Larger Crystals for Neutron Diffraction

NASA Technical Reports Server (NTRS)

Pusey, Marc

2003-01-01

Obtaining crystals of suitable size and high quality has been a major bottleneck in macromolecular crystallography. With the advent of advanced X-ray sources and methods the question of size has rapidly dwindled, almost to the point where if one can see the crystal then it was big enough. Quality is another issue, and major national and commercial efforts were established to take advantage of the microgravity environment in an effort to obtain higher quality crystals. Studies of the macromolecule crystallization process were carried out in many labs in an effort to understand what affected the resultant crystal quality on Earth, and how microgravity improved the process. While technological improvements are resulting in a diminishing of the minimum crystal size required, neutron diffraction structural studies still require considerably larger crystals, by several orders of magnitude, than X-ray studies. From a crystal growth physics perspective there is no reason why these 'large' crystals cannot be obtained: the question is generally more one of supply than limitations mechanism. This talk will discuss our laboratory s current model for macromolecule crystal growth, with highlights pertaining to the growth of crystals suitable for neutron diffraction studies.

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.

Likelihood-based modification of experimental crystal structure electron density maps

DOEpatents

Terwilliger, Thomas C [Sante Fe, NM

2005-04-16

A maximum-likelihood method for improves an electron density map of an experimental crystal structure. A likelihood of a set of structure factors {F.sub.h } is formed for the experimental crystal structure as (1) the likelihood of having obtained an observed set of structure factors {F.sub.h.sup.OBS } if structure factor set {F.sub.h } was correct, and (2) the likelihood that an electron density map resulting from {F.sub.h } is consistent with selected prior knowledge about the experimental crystal structure. The set of structure factors {F.sub.h } is then adjusted to maximize the likelihood of {F.sub.h } for the experimental crystal structure. An improved electron density map is constructed with the maximized structure factors.

Crystallogenesis of bacteriophage P22 tail accessory factor gp26 at acidic and neutral pH

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

Cingolani, Gino, E-mail: cingolag@upstate.edu; Andrews, Dewan; Casjens, Sherwood

2006-05-01

The crystallogenesis of bacteriophage P22 tail-fiber gp26 is described. To study possible pH-induced conformational changes in gp26 structure, native trimeric gp26 has been crystallized at acidic pH (4.6) and a chimera of gp26 fused to maltose-binding protein (MBP-gp26) has been crystallized at neutral and alkaline pH (7-10). Gp26 is one of three phage P22-encoded tail accessory factors essential for stabilization of viral DNA within the mature capsid. In solution, gp26 exists as an extended triple-stranded coiled-coil protein which shares profound structural similarities with class I viral membrane-fusion protein. In the cryo-EM reconstruction of P22 tail extracted from mature virions, gp26more » forms an ∼220 Å extended needle structure emanating from the neck of the tail, which is likely to be brought into contact with the cell’s outer membrane when the viral DNA-injection process is initiated. To shed light on the potential role of gp26 in cell-wall penetration and DNA injection, gp26 has been crystallized at acidic, neutral and alkaline pH. Crystals of native gp26 grown at pH 4.6 diffract X-rays to 2.0 Å resolution and belong to space group P2{sub 1}, with a dimer of trimeric gp26 molecules in the asymmetric unit. To study potential pH-induced conformational changes in the gp26 structure, a chimera of gp26 fused to maltose-binding protein (MBP-gp26) was generated. Hexagonal crystals of MBP-gp26 were obtained at neutral and alkaline pH using the high-throughput crystallization robot at the Hauptman–Woodward Medical Research Institute, Buffalo, NY, USA. These crystals diffract X-rays to beyond 2.0 Å resolution. Structural analysis of gp26 crystallized at acidic, neutral and alkaline pH is in progress.« less

Single-crystal growth, structure refinement and the properties of Bis(glycine) Strontium Chloride

NASA Astrophysics Data System (ADS)

Balaji, S. R.; Balu, T.; Rajasekaran, T. R.

2018-02-01

Single crystals of Bis (glycine) Strontium Chloride (BGSC) were grown by means of slow evaporation process by using analar grade Glycine and Strontium Chloride Hexahydrate as a parent compound from its aqueous solution at room temperature. The final chemical composition, [{{Sr}}{({{{C}}}2{{{H}}}5{{{NO}}}2)}2{{{Cl}}}2].{{{H}}}4{{{O}}}3+{{{H}}}8{{{O}}}3, formed were metallic light colorless block, about the size of 28 mm × 9 mm × 8 mm. A single-crystal x-ray diffraction study revealed an ordered superstructure with orthorhombic symmetry that could be assigned to the space group Pbcn. The structure in BGSC, revealed in the electron density distribution was analyzed by the direct methods (SHELXS-2014) and refined by least squares full matrix method (SHELXL-2014). The crystal structure, including anisotropic atomic displacement parameters for each atom and isotropic atomic displacement parameters for hydrogen atom, was refined to R1 = 0.0395, wR2 = 0.0776 using 1097 independent reflections. The FTIR spectrum of BGSC confirms the protonation of amino groups and the different molecular groups present in BGSC vibrate in different modes. Reverse Indentation Size Effect (RISE) was revealed in BGSC in the micro-hardness analysis using Vicker’s micro-hardness analysis. DTA and DSC results ruled out the possibility of structural change independent of mass change. The AFM studies shows fine nano size fiber like structure of the grown crystals.

Research on bandgaps in two-dimensional phononic crystal with two resonators.

PubMed

Gao, Nansha; Wu, Jiu Hui; Yu, Lie

2015-02-01

In this paper, the bandgap properties of a two-dimensional phononic crystal with the two resonators is studied and embedded in a homogenous matrix. The resonators are not connected with the matrix but linked with connectors directly. The dispersion relationship, transmission spectra, and displacement fields of the eigenmodes of this phononic crystal are studied with finite-element method. In contrast to the phononic crystals with one resonators and hollow structure, the proposed structures with two resonators can open bandgaps at lower frequencies. This is a very interesting and useful phenomenon. Results show that, the opening of the bandgaps is because of the local resonance and the scattering interaction between two resonators and matrix. An equivalent spring-pendulum model can be developed in order to evaluate the frequencies of the bandgap edge. The study in this paper is beneficial to the design of opening and tuning bandgaps in phononic crystals and isolators in low-frequency range. Copyright © 2014 Elsevier B.V. All rights reserved.

Optical, Fluorescence with quantum analysis of hydrazine (1, 3- Dinitro Phenyl) by DFT and Ab initio approach

NASA Astrophysics Data System (ADS)

Cecily Mary Glory, D.; Sambathkumar, K.; Madivanane, R.; Velmurugan, G.; Gayathri, R.; Nithiyanantham, S.; Venkatachalapathy, M.; Rajkamal, N.

2018-07-01

Experimental and computational study of molecular structure, vibrational and UV-spectral analysis of Hydrazine (1, 3- Dinitrophenyl) (HDP) derivatives. The crystal was grown by slow cooling method and the crystalline perfection of single crystals was evaluated by high resolution X-ray diffractometry (HRXRD) using a multicrystal X-ray diffractometer. Fluorescence, FT-IR and FT-Raman spectra of HDP crystal were recorded. The assignments of the vibrational spectra have been carried out with the help of normal co-ordinate analysis (NCA) followed by scaled quantum force field methodology (SQMFF). NMR studies have confirmed respectively the crystal structure and functional groups of the grown crystal. The energy and oscillator strength calculated by Time-Dependent Density Functional Theory (TD-DFT) result complements the experimental findings. The calculated MESP, UV, HOMO-LUMO energies show that charge transfer done within the molecule. And various thermodynamic parameters are studied. Fukui determines the local reactive site of electrophilic, nucleophilic, descriptor.

Synthesis, structural, optical, thermal and dielectric studies on new organic nonlinear optical crystal by solution growth technique.

PubMed

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

2013-04-15

Single crystals of L-phenylalanine-benzoic acid (LPBA) were successfully grown from aqueous solution by solvent evaporation technique. Purity of the crystals was increased by the method of recrystallization. The XRD analysis confirms that the crystal belongs to the monoclinic system with noncentrosymmetric space group P21. The chemical structure of compound was established by FT-NMR technique. The presence of functional groups was estimated qualitatively by Fourier transform infrared analysis (FT-IR). Ultraviolet-visible spectral analyses showed that the crystal has low UV cut-off at 254 nm combined with very good transparency of 90% in a wide range. The optical band gap was estimated to be 6.91 eV. Thermal behavior has been studied with TGA/DTA analyses. The existence of second harmonic generation (SHG) efficiency was found to be 0.56 times the value of KDP. The dielectric behavior of the sample was also studied for the first time. Copyright © 2013 Elsevier B.V. All rights reserved.

Effect of doping with nickel ions on the structural state of a zinc oxide crystal

NASA Astrophysics Data System (ADS)

Dubinin, S. F.; Sokolov, V. I.; Parkhomenko, V. D.; Maksimov, V. I.; Gruzdev, N. B.

2009-10-01

The fine structure of a hexagonal zinc oxide crystal doped with nickel ions of the composition Zn1 - x Ni x O has been studied using neutron diffraction and magnetic measurements. It is established that even at very low doping levels ( x = 0.0004), the crystal undergoes local distortions in basal planes of the initial hexagonal lattice. The local distortions are assumed to be sources of the formation of ferromagnetism in compounds of this class.

Modelling of Surfaces. Part 1: Monatomic Metallic Surfaces Using Equivalent Crystal Theory

NASA Technical Reports Server (NTRS)

Bozzolo, Guillermo; Ferrante, John; Rodriguez, Agustin M.

1994-01-01

We present a detailed description of equivalent crystal theory focusing on its application to the study of surface structure. While the emphasis is in the structure of the algorithm and its computational aspects, we also present a comprehensive discussion on the calculation of surface energies of metallic systems with equivalent crystal theory and other approaches. Our results are compared to experiment and other semiempirical as well as first-principles calculations for a variety of fcc and bcc metals.

Crystal structure of a cytochrome P450 2B6 genetic variant in complex with the inhibitor 4-(4-chlorophenyl)imidazole at 2.0-A resolution.

PubMed

Gay, Sean C; Shah, Manish B; Talakad, Jyothi C; Maekawa, Keiko; Roberts, Arthur G; Wilderman, P Ross; Sun, Ling; Yang, Jane Y; Huelga, Stephanie C; Hong, Wen-Xu; Zhang, Qinghai; Stout, C David; Halpert, James R

2010-04-01

The structure of the K262R genetic variant of human cytochrome P450 2B6 in complex with the inhibitor 4-(4-chlorophenyl)imidazole (4-CPI) has been determined using X-ray crystallography to 2.0-A resolution. Production of diffraction quality crystals was enabled through a combination of protein engineering, chaperone coexpression, modifications to the purification protocol, and the use of unique facial amphiphiles during crystallization. The 2B6-4-CPI complex is virtually identical to the rabbit 2B4 structure bound to the same inhibitor with respect to the arrangement of secondary structural elements and the placement of active site residues. The structure supports prior P450 2B6 homology models based on other mammalian cytochromes P450 and is consistent with the limited site-directed mutagenesis studies on 2B6 and extensive studies on P450 2B4 and 2B1. Although the K262R genetic variant shows unaltered binding of 4-CPI, altered binding affinity, kinetics, and/or product profiles have been previously shown with several other ligands. On the basis of new P450 2B6 crystal structure and previous 2B4 structures, substitutions at residue 262 affect a hydrogen-bonding network connecting the G and H helices, where subtle differences could be transduced to the active site. Docking experiments indicate that the closed protein conformation allows smaller ligands such as ticlopidine to bind to the 2B6 active site in the expected orientation. However, it is unknown whether 2B6 undergoes structural reorganization to accommodate bulkier molecules, as previously inferred from multiple P450 2B4 crystal structures.

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.

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.

Overexpression, crystallization and preliminary X-ray crystallographic analysis of the phosphotriesterase from Mycobacterium tuberculosis.

PubMed

Zhang, Liang; Chen, Ruyi; Dong, Zhe; Li, Xin

2013-01-01

Organophosphates (OPs) are extremely toxic compounds that are used as insecticides or even as chemical warfare agents. Phosphotriesterases (PHPs) are responsible for the detoxification of OPs by catalysing their degradation. Almost 100 PHP structures have been solved to date, yet the crystal structure of the phosphotriesterase from Mycobacterium tuberculosis (mPHP) remains unavailable. This study reports the first crystallization of mPHP. The crystal belonged to space group C222(1), with unit-cell parameters a = 68.03, b = 149.60, c = 74.23 Å, α = β = γ = 90°. An analytical ultracentrifugation experiment suggested that mPHP exists as a dimer in solution, even though one molecule is calculated to be present in the asymmetric unit according to the structural data.

Overexpression, crystallization and preliminary X-ray crystallographic analysis of the phosphotriesterase from Mycobacterium tuberculosis

PubMed Central

Zhang, Liang; Chen, Ruyi; Dong, Zhe; Li, Xin

2013-01-01

Organophosphates (OPs) are extremely toxic compounds that are used as insecticides or even as chemical warfare agents. Phosphotriesterases (PHPs) are responsible for the detoxification of OPs by catalysing their degradation. Almost 100 PHP structures have been solved to date, yet the crystal structure of the phosphotriesterase from Mycobacterium tuberculosis (mPHP) remains unavailable. This study reports the first crystallization of mPHP. The crystal belonged to space group C2221, with unit-cell parameters a = 68.03, b = 149.60, c = 74.23 Å, α = β = γ = 90°. An analytical ultracentrifugation experiment suggested that mPHP exists as a dimer in solution, even though one molecule is calculated to be present in the asymmetric unit according to the structural data. PMID:23295488

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.

Hemoglobin redux: combining neutron and X-ray diffraction with mass spectrometry to analyse the quaternary state of oxidized hemoglobins

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

Mueser, Timothy C., E-mail: timothy.mueser@utoledo.edu; Griffith, Wendell P.; Kovalevsky, Andrey Y.

2010-11-01

X-ray and neutron diffraction studies of cyanomethemoglobin are being used to evaluate the structural waters within the dimer–dimer interface involved in quaternary-state transitions. Improvements in neutron diffraction instrumentation are affording the opportunity to re-examine the structures of vertebrate hemoglobins and to interrogate proton and solvent position changes between the different quaternary states of the protein. For hemoglobins of unknown primary sequence, structural studies of cyanomethemoglobin (CNmetHb) are being used to help to resolve sequence ambiguity in the mass spectra. These studies have also provided additional structural evidence for the involvement of oxidized hemoglobin in the process of erythrocyte senescence. X-raymore » crystal studies of Tibetan snow leopard CNmetHb have shown that this protein crystallizes in the B state, a structure with a more open dyad, which possibly has relevance to RBC band 3 protein binding and erythrocyte senescence. R-state equine CNmetHb crystal studies elaborate the solvent differences in the switch and hinge region compared with a human deoxyhemoglobin T-state neutron structure. Lastly, comparison of histidine protonation between the T and R state should enumerate the Bohr-effect protons.« less

Bismuth doping effect on crystal structure and photodegradation activity of Bi-TiO2 nanoparticles

NASA Astrophysics Data System (ADS)

Wu, Ming-Chung; Chang, Yin-Hsuan; Lin, Ting-Han

2017-04-01

The bismuth precursor is adopted as dopant to synthesize bismuth doped titanium dioxide nanoparticles (Bi-TiO2 NPs) with sol-gel method following by the thermal annealing treatment. We systematically developed a series of Bi-TiO2 NPs at several calcination temperatures and discovered the corresponding crystal structure by varying the bismuth doping concentration. At a certain 650 °C calcination temperature, the crystal structure of bismuth titanate (Bi2Ti2O7) is formed when the bismuth doping concentration is as high as 10.0 mol %. The photocatalytic activity of Bi-TiO2 NPs is increased by varying the doping concentration at the particular calcination temperature. By the definition X-ray diffraction (XRD) structural identification, a phase diagram of Bi-TiO2 NPs in doping concentration versus calcination temperature is provided. It can be useful for further study in the crystal structure engineering and the development of photocatalyst.

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

Insight into Evolution, Processing and Performance of Multi-length-scale Structures in Planar Heterojunction Perovskite Solar Cells.

PubMed

Huang, Yu-Ching; Tsao, Cheng-Si; Cho, Yi-Ju; Chen, Kuan-Chen; Chiang, Kai-Ming; Hsiao, Sheng-Yi; Chen, Chang-Wen; Su, Chun-Jen; Jeng, U-Ser; Lin, Hao-Wu

2015-09-04

The structural characterization correlated to the processing control of hierarchical structure of planar heterojunction perovskite layer is still incomplete due to the limitations of conventional microscopy and X-ray diffraction. This present study performed the simultaneously grazing-incidence small-angle scattering and wide-angle scattering (GISAXS/GIWAXS) techniques to quantitatively probe the hierarchical structure of the planar heterojunction perovskite solar cells. The result is complementary to the currently microscopic study. Correlation between the crystallization behavior, crystal orientation, nano- and meso-scale internal structure and surface morphology of perovskite film as functions of various processing control parameters is reported for the first time. The structural transition from the fractal pore network to the surface fractal can be tuned by the chloride percentage. The GISAXS/GIWAXS measurement provides the comprehensive understanding of concurrent evolution of the film morphology and crystallization correlated to the high performance. The result can provide the insight into formation mechanism and rational synthesis design.

Insight into Evolution, Processing and Performance of Multi-length-scale Structures in Planar Heterojunction Perovskite Solar Cells

NASA Astrophysics Data System (ADS)

Huang, Yu-Ching; Tsao, Cheng-Si; Cho, Yi-Ju; Chen, Kuan-Chen; Chiang, Kai-Ming; Hsiao, Sheng-Yi; Chen, Chang-Wen; Su, Chun-Jen; Jeng, U.-Ser; Lin, Hao-Wu

2015-09-01

The structural characterization correlated to the processing control of hierarchical structure of planar heterojunction perovskite layer is still incomplete due to the limitations of conventional microscopy and X-ray diffraction. This present study performed the simultaneously grazing-incidence small-angle scattering and wide-angle scattering (GISAXS/GIWAXS) techniques to quantitatively probe the hierarchical structure of the planar heterojunction perovskite solar cells. The result is complementary to the currently microscopic study. Correlation between the crystallization behavior, crystal orientation, nano- and meso-scale internal structure and surface morphology of perovskite film as functions of various processing control parameters is reported for the first time. The structural transition from the fractal pore network to the surface fractal can be tuned by the chloride percentage. The GISAXS/GIWAXS measurement provides the comprehensive understanding of concurrent evolution of the film morphology and crystallization correlated to the high performance. The result can provide the insight into formation mechanism and rational synthesis design.

Polymer-Induced Heteronucleation for Protein Single Crystal Growth: Structural Elucidation of Bovine Liver Catalase and Concanavalin A Forms

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

Foroughi, Leila M.; Kang, You-Na; Matzger, Adam J.

Obtaining single crystals for X-ray diffraction remains a major bottleneck in structural biology; when existing crystal growth methods fail to yield suitable crystals, often the target rather than the crystallization approach is reconsidered. Here we demonstrate that polymer-induced heteronucleation, a powerful technique that has been used for small molecule crystallization form discovery, can be applied to protein crystallization by optimizing the heteronucleant composition and crystallization formats for crystallizing a wide range of protein targets. Applying these advances to two benchmark proteins resulted in dramatically increased crystal size, enabling structure determination, for a half century old form of bovine liver catalasemore » (BLC) that had previously only been characterized by electron microscopy, and the discovery of two new forms of concanavalin A (conA) from the Jack bean and accompanying structural elucidation of one of these forms.« less

N-2-Hydroxy-4-methoxyacetophenone- N'-4-nitrobenzoyl hydrazine: Synthesis and structural characterization

NASA Astrophysics Data System (ADS)

Bessy Raj, B. N.; Kurup, M. R. Prathapachandra

2007-04-01

A new aroyl hydrazone, N-2-hydroxy-4-methoxyacetophenone- N'-4-nitrobenzoyl hydrazine was prepared by the condensation reaction of 2-hydroxy-4-methoxyacetophenone and 4-nitrobenzoyl hydrazine. Characterization of the compound was done by elemental analysis and electronic, infrared and NMR spectral analyses. The complete structural assignment of the compound was done by NMR studies by using COSY homonuclear and HSQC heteronuclear techniques. The crystal and molecular structure was determined by single crystal X-ray diffraction studies: crystallized in the monoclinic system, space group P2 1/ n, Z = 4, a = 7.3343(9) Å, b = 20.3517(9) Å, c = 10.1375(5) Å, α = 90.00°, β = 95.735(7)° and γ = 90.00°. From the crystal structure, it is concluded that the compound exists as the keto isomer in the solid state. There is a completely extended conformation in the central part of the molecule C5 sbnd C8 dbnd N1 sbnd N2 sbnd C10 dbnd O2 with an E configuration at the double bond of the hydrazinic bridge.

Crystal structure determination of new antimitotic agent bis(p-fluorobenzyl)trisulfide.

PubMed

An, Haoyun; Hu, Xiurong; Gu, Jianming; Chen, Linshen; Xu, Weiming; Mo, Xiaopeng; Xu, Wanhong; Wang, Xiaobo; Xu, Xiao

2008-01-01

The purpose of this research was to investigate the physical characteristics and crystalline structure of bis(p-fluorobenzyl)trisulfide, a new anti-tumor agent. Methods used included X-ray single crystal diffraction, X-ray powder diffraction (XRPD), Fourier-transform infrared (FT-IR) spectroscopy, differential scanning calorimetric (DSC) and thermogravimetric (TG) analyses. The findings obtained with X-ray single crystal diffraction showed that a monoclinic unit cell was a = 12.266(1) A, b = 4.7757(4) A, c = 25.510(1) A, beta = 104.25(1) degrees ; cell volume = 1,448.4(2) A(3), Z = 4, and space group C2/c. The XRPD studies of the four crystalline samples, obtained by recrystallization from four different solvents, indicated that they had the same diffraction patterns. The diffraction pattern stimulated from the crystal structure data is in excellent agreement with the experimental results. In addition, the identical FT-IR spectra of the four crystalline samples revealed absorption bands corresponding to S-S and C-S stretching as well as the characteristic aromatic substitution. Five percent weight loss at 163.3 degrees C was observed when TG was used to study the decomposition process in the temperature range of 20-200 degrees C. DSC also allowed for the determination of onset temperatures at 60.4(1)-60.7(3) degrees C and peak temperatures at 62.1(3)-62.4(3) degrees C for the four crystalline samples studied. The results verified that the single crystal structure shared the same crystal form with the four crystalline samples investigated.

Synthesis, characterization, crystal structure and theoretical study of a compound with benzodiazole ring: antimicrobial activity and DNA binding.

PubMed

Latha, P; Kodisundaram, P; Sundararajan, M L; Jeyakumar, T

2014-08-14

2-(Thiophen-2-yl)-1-((thiophen-2-yl)methyl)-1H-1,3-benzodiazole (HL) is synthesized and characterized by elemental analysis, UV-Vis, FT-IR, (1)H, (13)C NMR, mass spectra, scanning electron microscope (SEM) and single crystal X-ray diffraction. The crystal structure is stabilized by intermolecular CH⋯N and CH⋯π interactions. The molecular structure is also optimized at the B3LYP/6-31G level using density functional theory (DFT). The structural parameters from the theory are nearer to those of crystal, the calculated total energy of coordination is -1522.814a.u. The energy of HOMO-LUMO and the energy gap are -0.20718, -0.04314, 0.16404a.u, respectively. All data obtained from the spectral studies support the structural properties of the compound HL. The benzimidazole ring is essentially planar. The in vitro biological screening effects of the synthesized compound is tested against four bacterial and four fungal strains by well diffusion method. Antioxidant property and DNA binding behaviour of the compound has been investigated using spectrophotometric method. Copyright © 2014 Elsevier B.V. All rights reserved.

Growth and studies of cyclohexylammonium 4-methoxy benzoate single crystal for nonlinear optical applications

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

Sathya, P.; Gopalakrishnan, R., E-mail: krgkrishnan@annauniv.edu

2015-06-24

Cyclohexylammonium 4-Methoxy Benzoate (C4MB) was synthesised and the functional groups were confirmed by FTIR analysis. The purified C4MB (by repeated recrystallisation) was used for single crystal growth. Single crystal of cyclohexylammonium 4-methoxy benzoate was successfully grown by slow evaporation solution growth method at ambient temperature. Structural orientations were determined from single crystal X-ray diffractometer. Optical absorption and cut off wavelength were identified by UV-Visible spectroscopy. Thermal stability of the crystal was studied from thermogravimetric and differential thermal analyses curves. Mechanical stability of the grown crystal was analysed by Vicker’s microhardness tester. The Second Harmonic Generation (SHG) study revealed that themore » C4MB compound exhibits the SHG efficiency 3.3 times greater than KDP crystal.« less

Artificial crystals with 3d metal and palladium particles subjected to high-temperature heat treatment

NASA Astrophysics Data System (ADS)

Rinkevich, A. B.; Nemytova, O. V.; Perov, D. V.; Samoylovich, M. I.; Kuznetsov, E. A.

2018-04-01

High-temperature heat treatment has valuable impact on the structure and physical properties of artificial crystals with 3d metal and palladium particles. Artificial crystals are obtained by means of introduction of particles into the interspherical voids of opal matrices. The magnetic properties are studied at the temperatures ranging from 2 to 300 K and in fields up to 350 kOe. Microwave properties are investigated in the millimeter frequency range. The complex dielectric permittivity of several nanocomposites is measured. The influence of heat treatment up to 960 °C on the structure of artificial crystals is clarified.

Broadband continuous-variable entanglement source using a chirped poling nonlinear crystal

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

Zhao, J. S.; Sun, L.; Yu, X. Q.

2010-01-15

Aperiodically poled nonlinear crystal can be used as a broadband continuous-variable entanglement source and has strong stability under perturbations. We study the conversion dynamics of the sum-frequency generation and the quantum correlation of the two pump fields in a chirped-structure nonlinear crystal using the quantum stochastic method. The results show that there exists a frequency window for the pumps where two optical fields can perform efficient upconversion. The two pump fields are demonstrated to be entangled in the window and the chirped-structure crystal can be used as a continuous-variable entanglement source with a broad response bandwidth.

In situ data collection and structure refinement from microcapillary protein crystallization

PubMed Central

Yadav, Maneesh K.; Gerdts, Cory J.; Sanishvili, Ruslan; Smith, Ward W.; Roach, L. Spencer; Ismagilov, Rustem F.; Kuhn, Peter; Stevens, Raymond C.

2007-01-01

In situ X-ray data collection has the potential to eliminate the challenging task of mounting and cryocooling often fragile protein crystals, reducing a major bottleneck in the structure determination process. An apparatus used to grow protein crystals in capillaries and to compare the background X-ray scattering of the components, including thin-walled glass capillaries against Teflon, and various fluorocarbon oils against each other, is described. Using thaumatin as a test case at 1.8 Å resolution, this study demonstrates that high-resolution electron density maps and refined models can be obtained from in situ diffraction of crystals grown in microcapillaries. PMID:17468785

Growth and structure of a new photonic crystal: Chlorine substituted chalcone

NASA Astrophysics Data System (ADS)

Sarveshwara, H. P.; Raghavendra, S.; A, Jayarama; Menezes, Anthoni Praveen; Dharmaprakash, S. M.

2015-06-01

A new organic photonic material 3-(2, 4-dichlorophenyl)-1-(2,5-dimethylthiophen-3-yl)propan-1-one(DMTP) has been synthesized and crystallised in acetone solution. The functional groups present in the new material were identified by FTIR spectroscopy. The material is optically transparent in the wavelength range of 400-1100 nm. The crystal structure of DMTP was determined by single crystal X-ray diffraction. The title compound crystallizes in monoclinic system with a centrosymmetric space group P21/c. The Z-scan study revealed that the optical limiting property exhibited by the DMTP molecule is based on the reverse saturable absorption phenomena.

Femtosecond X-ray protein nanocrystallography.

PubMed

Chapman, Henry N; Fromme, Petra; Barty, Anton; White, Thomas A; Kirian, Richard A; Aquila, Andrew; Hunter, Mark S; Schulz, Joachim; DePonte, Daniel P; Weierstall, Uwe; Doak, R Bruce; Maia, Filipe R N C; Martin, Andrew V; Schlichting, Ilme; Lomb, Lukas; Coppola, Nicola; Shoeman, Robert L; Epp, Sascha W; Hartmann, Robert; Rolles, Daniel; Rudenko, Artem; Foucar, Lutz; Kimmel, Nils; Weidenspointner, Georg; Holl, Peter; Liang, Mengning; Barthelmess, Miriam; Caleman, Carl; Boutet, Sébastien; Bogan, Michael J; Krzywinski, Jacek; Bostedt, Christoph; Bajt, Saša; Gumprecht, Lars; Rudek, Benedikt; Erk, Benjamin; Schmidt, Carlo; Hömke, André; Reich, Christian; Pietschner, Daniel; Strüder, Lothar; Hauser, Günter; Gorke, Hubert; Ullrich, Joachim; Herrmann, Sven; Schaller, Gerhard; Schopper, Florian; Soltau, Heike; Kühnel, Kai-Uwe; Messerschmidt, Marc; Bozek, John D; Hau-Riege, Stefan P; Frank, Matthias; Hampton, Christina Y; Sierra, Raymond G; Starodub, Dmitri; Williams, Garth J; Hajdu, Janos; Timneanu, Nicusor; Seibert, M Marvin; Andreasson, Jakob; Rocker, Andrea; Jönsson, Olof; Svenda, Martin; Stern, Stephan; Nass, Karol; Andritschke, Robert; Schröter, Claus-Dieter; Krasniqi, Faton; Bott, Mario; Schmidt, Kevin E; Wang, Xiaoyu; Grotjohann, Ingo; Holton, James M; Barends, Thomas R M; Neutze, Richard; Marchesini, Stefano; Fromme, Raimund; Schorb, Sebastian; Rupp, Daniela; Adolph, Marcus; Gorkhover, Tais; Andersson, Inger; Hirsemann, Helmut; Potdevin, Guillaume; Graafsma, Heinz; Nilsson, Björn; Spence, John C H

2011-02-03

X-ray crystallography provides the vast majority of macromolecular structures, but the success of the method relies on growing crystals of sufficient size. In conventional measurements, the necessary increase in X-ray dose to record data from crystals that are too small leads to extensive damage before a diffraction signal can be recorded. It is particularly challenging to obtain large, well-diffracting crystals of membrane proteins, for which fewer than 300 unique structures have been determined despite their importance in all living cells. Here we present a method for structure determination where single-crystal X-ray diffraction 'snapshots' are collected from a fully hydrated stream of nanocrystals using femtosecond pulses from a hard-X-ray free-electron laser, the Linac Coherent Light Source. We prove this concept with nanocrystals of photosystem I, one of the largest membrane protein complexes. More than 3,000,000 diffraction patterns were collected in this study, and a three-dimensional data set was assembled from individual photosystem I nanocrystals (∼200 nm to 2 μm in size). We mitigate the problem of radiation damage in crystallography by using pulses briefer than the timescale of most damage processes. This offers a new approach to structure determination of macromolecules that do not yield crystals of sufficient size for studies using conventional radiation sources or are particularly sensitive to radiation damage.

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.

Towards protein-crystal centering using second-harmonic generation (SHG) microscopy

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

Kissick, David J.; Dettmar, Christopher M.; Becker, Michael

2013-05-01

The potential of second-harmonic generation (SHG) microscopy for automated crystal centering to guide synchrotron X-ray diffraction of protein crystals has been explored. The potential of second-harmonic generation (SHG) microscopy for automated crystal centering to guide synchrotron X-ray diffraction of protein crystals was explored. These studies included (i) comparison of microcrystal positions in cryoloops as determined by SHG imaging and by X-ray diffraction rastering and (ii) X-ray structure determinations of selected proteins to investigate the potential for laser-induced damage from SHG imaging. In studies using β{sub 2} adrenergic receptor membrane-protein crystals prepared in lipidic mesophase, the crystal locations identified by SHGmore » images obtained in transmission mode were found to correlate well with the crystal locations identified by raster scanning using an X-ray minibeam. SHG imaging was found to provide about 2 µm spatial resolution and shorter image-acquisition times. The general insensitivity of SHG images to optical scatter enabled the reliable identification of microcrystals within opaque cryocooled lipidic mesophases that were not identified by conventional bright-field imaging. The potential impact of extended exposure of protein crystals to five times a typical imaging dose from an ultrafast laser source was also assessed. Measurements of myoglobin and thaumatin crystals resulted in no statistically significant differences between structures obtained from diffraction data acquired from exposed and unexposed regions of single crystals. Practical constraints for integrating SHG imaging into an active beamline for routine automated crystal centering are discussed.« less

VO{sub 2} (A): Reinvestigation of crystal structure, phase transition and crystal growth mechanisms

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

Rao Popuri, Srinivasa; University of Bordeaux, ICMCB, UPR 9048, F-33608 Pessac; National Institute for Research and Development in Electrochemistry and Condensed Matter, Timisoara, Plautius Andronescu Str. No. 1, 300224 Timisoara

2014-05-01

Well crystallized VO{sub 2} (A) microrods were grown via a single step hydrothermal reaction in the presence of V{sub 2}O{sub 5} and oxalic acid. With the advantage of high crystalline samples, we propose P4/ncc as an appropriate space group at room temperature. From morphological studies, we found that the oriented attachment and layer by layer growth mechanisms are responsible for the formation of VO{sub 2} (A) micro rods. The structural and electronic transitions in VO{sub 2} (A) are strongly first order in nature, and a marked difference between the structural transition temperatures and electronic transitions temperature was evidenced. The reversiblemore » intra- (LTP-A to HTP-A) and irreversible inter- (HTP-A to VO{sub 2} (M1)) structural phase transformations were studied by in-situ powder X-ray diffraction. Attempts to increase the size of the VO{sub 2} (A) microrods are presented and the possible formation steps for the flower-like morphologies of VO{sub 2} (M1) are described. - Graphical abstract: Using a single step and template free hydrothermal synthesis, well crystallized VO{sub 2} (A) microrods were prepared and the P4/ncc space group was assigned to the room temperature crystal structure. Reversible and irreversible phase transitions among different VO{sub 2} polymorphs were identified and their progressive nature was highlighted. Attempts to increase the microrods size, involving layer by layer formation mechanisms, are presented. - Highlights: • Highly crystallized VO{sub 2} (A) microrods were grown via a single step hydrothermal process. • The P4/ncc space group was determined for VO{sub 2} (A) at room temperature. • The electronic structure and progressive nature of the structural phase transition were investigated. • A weak coupling between structural and electronic phase transitions was identified. • Different crystallite morphologies were discussed in relation with growth mechanisms.« less

Laser stimulated third harmonic generation studies in ZnO-Ta2O5-B2O3 glass ceramics entrenched with Zn3Ta2O8 crystal phases

NASA Astrophysics Data System (ADS)

Siva Sesha Reddy, A.; Jedryka, J.; Ozga, K.; Ravi Kumar, V.; Purnachand, N.; Kityk, I. V.; Veeraiah, N.

2018-02-01

In this study zinc borate glasses doped with different concentrations Ta2O5 were synthesized and were crystallized by heat treatment for prolonged times. The samples were characterized by XRD, SEM, IR and Raman spectroscopy techniques. The SEM images of the crystallized samples have indicated that the samples contain randomly distributed crystal grains with size ∼1 μm entrenched in the residual amorphous phase. XRD studies have exhibited diffraction peaks identified as being due to the reflections from (1 1 1) planes of monoclinic Zn3Ta2O8 crystal phase that contains intertwined tetrahedral zinc and octahedral tantalate structural units. The concentration of such crystal phases in the bulk samples is observed to increase with increase of Ta2O5 up to 3.0 mol%. The IR and Raman spectroscopy studies have confirmed the presence of ZnO4 and TaO6 structural units in the glass network in addition to the conventional borate structural units. For measuring third harmonic generation (THG) in the samples, the samples were irradiated with 532 nm laser beam and the intensity of THG of probing beam (Nd:YAG λ = 1064 nm 20 ns pulsed laser (ω)) is measured as a function of fundamental beam power varying up to 200 J/m2. The intensity of THG is found to be increasing with increase of fundamental beam power and found to be the maximal for the glass crystallized with 3.0 mol% of Ta2O5. The intensity of THG of the ceramicized samples is found to be nearly 5 times higher with respect to that of pre-crystallized samples. The generation of 3ω is attributed to the perturbation/interaction between Zn3Ta2O8 anisotropic crystal grains and the incident probing beam.

Fragment-Based Electronic Structure Approach for Computing Nuclear Magnetic Resonance Chemical Shifts in Molecular Crystals.

PubMed

Hartman, Joshua D; Beran, Gregory J O

2014-11-11

First-principles chemical shielding tensor predictions play a critical role in studying molecular crystal structures using nuclear magnetic resonance. Fragment-based electronic structure methods have dramatically improved the ability to model molecular crystal structures and energetics using high-level electronic structure methods. Here, a many-body expansion fragment approach is applied to the calculation of chemical shielding tensors in molecular crystals. First, the impact of truncating the many-body expansion at different orders and the role of electrostatic embedding are examined on a series of molecular clusters extracted from molecular crystals. Second, the ability of these techniques to assign three polymorphic forms of the drug sulfanilamide to the corresponding experimental (13)C spectra is assessed. This challenging example requires discriminating among spectra whose (13)C chemical shifts differ by only a few parts per million (ppm) across the different polymorphs. Fragment-based PBE0/6-311+G(2d,p) level chemical shielding predictions correctly assign these three polymorphs and reproduce the sulfanilamide experimental (13)C chemical shifts with 1 ppm accuracy. The results demonstrate that fragment approaches are competitive with the widely used gauge-invariant projector augmented wave (GIPAW) periodic density functional theory calculations.

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.

Photonic crystal slab waveguides in moderate index contrast media: Generalized transverse Bragg waveguides

NASA Astrophysics Data System (ADS)

Burckel, David Bruce

One of the anticipated advantages of photonic crystal waveguides is the ability to tune waveguide dispersion and propagation characteristics to achieve desired properties. The majority of research into photonic crystal waveguides centers around high index contrast photonic crystal waveguides with complete in-plane bandgaps in the photonic crystal cladding. This work focuses on linear photonic crystal waveguides in moderate index materials, with insufficient index contrast to guarantee a complete in-plane bandgap. Using a technique called Interferometric Lithography (IL) as well as standard semiconductor processing steps, a process flow for creating large area (˜cm 2), linear photonic crystal waveguides in a spin-deposited photocurable polymer is outlined. The study of such low index contrast photonic crystal waveguides offers a unique opportunity to explore the mechanisms governing waveguide confinement and photonic crystal behavior in general. Results from two optical characterization experiments are provided. In the first set of experiments, rhodamine 590 organic laser dye was incorporated into the polymer prior to fabrication of the photonic crystal slab. Emission spectra from waveguide core modes exhibit no obvious spectral selectivity owing to variation in the periodicity or geometry of the photonic crystal. In addition, grating coupled waveguides were fabricated, and a single frequency diode laser was coupled into the waveguide in order to study the transverse mode structure. To this author's knowledge, the optical mode profile images are the first taken of photonic crystal slab waveguides, exhibiting both simple low order mode structure as well as complex high order mode structure inconsistent with effective index theory. However, no obvious correlation between the mode structure and photonic crystal period or geometry was evident. Furthermore, in both the laser dye-doped and grating coupled waveguides, low loss waveguiding was observed regardless of wavelength to period ratio. These optical results indicated a need for a deeper understanding of the confinement/guiding mechanisms in such waveguide structures. A simplification of the full 2-D problem to a more tractable "tilted 1-D" geometry led to the proposal of a new waveguide geometry, Generalized Transverse Bragg Waveguides (GTBW), as well as a new propagation mode characterized by spatial variation in both the transverse direction as well as the direction of propagation. GTBW demonstrate many of the same dispersion tunability traits exhibited in complete bandgap photonic crystal waveguides, under more modest fabrication demands, and moreover provide much insight into photonic crystal waveguide modes of all types. Generalized Transverse Bragg Waveguides are presented in terms of the standard physical properties associated with waveguides, including the dispersion relation, expressions for the spatial field profile, and the concepts of phase and group velocity. In addition, the proposal of at least one obvious application, semiconductor optical amplifiers, is offered.

Crystal structure of minoxidil at low temperature and polymorph prediction.

PubMed

Martín-Islán, Africa P; Martín-Ramos, Daniel; Sainz-Díaz, C Ignacio

2008-02-01

An experimental and theoretical investigation on crystal forms of the popular and ubiquitous pharmaceutical Minoxidil is presented here. A new crystallization method is presented for Minoxidil (6-(1-piperidinyl)-2,4-pyrimidinediamide 3-oxide) in ethanol-poly(ethylene glycol), yielding crystals with good quality. The crystal structure is determined at low temperature, with a final R value of 0.035, corresponding to space group P2(1) (monoclinic) with cell dimensions a = 9.357(1) A, b = 8.231(1) A, c = 12.931(2) A, and beta = 90.353(4) degrees . Theoretical calculations of the molecular structure of Minoxidil are set forward using empirical force fields and quantum-mechanical methods. A theoretical prediction for Minoxidil crystal structure shows many possible polymorphs. The predicted crystal structures are compared with X-ray experimental data obtained in our laboratory, and the experimental crystal form is found to be one of the lowest energy polymorphs.

Complex assembly, crystallization and preliminary X-ray crystallographic studies of rhesus macaque MHC Mamu-A*01 complexed with an immunodominant SIV-Gag nonapeptide

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

Chu, Fuliang; Graduate School, Chinese Academy of Sciences, Beijing; Lou, Zhiyong

2005-06-01

Crystallization of the first rhesus macaque MHC class I complex. Simian immunodeficiency virus (SIV) infection in rhesus macaques has been used as the best model for the study of human immunodeficiency virus (HIV) infection in humans, especially in the cytotoxic T-lymphocyte (CTL) response. However, the structure of rhesus macaque (or any other monkey model) major histocompatibility complex class I (MHC I) presenting a specific peptide (the ligand for CTL) has not yet been elucidated. Here, using in vitro refolding, the preparation of the complex of the rhesus macaque MHC I allele (Mamu-A*01) with human β{sub 2}m and an immunodominant peptide,more » CTPYDINQM (Gag-CM9), derived from SIV Gag protein is reported. The complex (45 kDa) was crystallized; the crystal belongs to space group I422, with unit-cell parameters a = b = 183.8, c = 155.2 Å. The crystal contains two molecules in the asymmetric unit and diffracts X-rays to 2.8 Å resolution. The structure is being solved by molecular replacement and this is the first attempt to determined the crystal structure of a peptide–nonhuman primate MHC complex.« less

Comparison study of morphology and crystallization behavior of polyethylene and poly(ethylene oxide) on single-walled carbon nanotubes.

PubMed

Zheng, Xiaoli; Xu, Qun

2010-07-29

In this work, we provided a comparison study of morphology and crystallization behavior of polyethylene (PE) and poly(ethylene oxide) (PEO) on single-walled carbon nanotubes (SWNTs) with assistance of supercritical CO(2). The resulting polymer/SWNT nanohybrids were characterized by transmission electron microscopy, scanning electron microscopy, Fourier transform infrared spectroscopy, Raman spectra, wide-angle X-ray diffraction, and differential scanning calorimetry. SWNT small bundles were decorated by PE lamellar crystals, forming nanohybrid "shish-kebab" (NHSK) structure, whereas SWNTs were only wrapped by a thin amorphous polymer coating in the case of PEO. The varying morphologies of the nanohybrids were found to depend on the molecular conformation and the interactions between polymer chains and SWNTs. Nonisothermal experiments showed that SWNTs provided heterogeneous nucleation sites for PE crystallization, while the NHSK structure hindered polymer chain diffusion and crystal growth. Also, SWNTs played antinucleation effect on PEO. In addition, the formation mechanism analysis indicated that PE chains preferred to form a homogeneous coating along the tube axis before proceeding to kebab crystal growth. The purpose of this work is to enlarge the area of theoretical understanding of introducing precisely hierarchical structures on carbon nanotubes, which are important for functional design in nanodevice applications.

Isothermal crystallization of poly(3-hydroxybutyrate) studied by terahertz two-dimensional correlation spectroscopy

NASA Astrophysics Data System (ADS)

Hoshina, Hiromichi; Ishii, Shinya; Morisawa, Yusuke; Sato, Harumi; Noda, Isao; Ozaki, Yukihiro; Otani, Chiko

2012-01-01

The isothermal crystallization of poly(3-hydroxybutylate) (PHB) was studied by monitoring the temporal evolution of terahertz absorption spectra in conjunction with spectral analysis using two-dimensional correlation spectroscopy. Correlation between the absorption peaks and the sequential order of the changes in spectral intensity extracted from synchronous and asynchronous plots indicated that crystallization of PHB at 90 °C is a two step process, in which C-H...O=C hydrogen bonds are initially formed before well-defined crystal structures are established.

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.

Studies of Nucleation, Growth, Specific Heat, and Viscosity of Undercooled Melts of Quasicrystals and Polytetrahedral-Phase-Forming Alloys

NASA Technical Reports Server (NTRS)

Kelton, K. F.; Croat, T. K.; Gangopadhyay, A.; Holland-Moritz, D.; Hyers, Robert W.; Rathz, Thomas J.; Robinson, Michael B.; Rogers, Jan R.

2001-01-01

Undercooling experiments and thermal physical property measurements of metallic alloys on the International Space Station (ISS) are planned. This recently-funded research focuses on fundamental issues of the formation and structure of highly-ordered non-crystallographic phases (quasicrystals) and related crystal phases (crystal approximants), and the connections between the atomic structures of these phases and those of liquids and glasses. It extends studies made previously by us of the composition dependence of crystal nucleation processes in silicate and metallic glasses, to the case of nucleation from the liquid phase. Motivating results from rf-levitation and drop-tube measurements of the undercooling of Ti/Zr-based liquids that form quasicrystals and crystal approximants are discussed. Preliminary measurements by electrostatic levitation (ESL) are presented.

Purification, crystallization and initial crystallographic characterization of the Ginkgo biloba 11S seed globulin ginnacin

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

Jin, Tengchuan; Chen, Yu-Wei; Howard, Andrew

2008-07-01

The crystallization of ginnacin, the 11S seed storage protein from G. biloba, is reported. Ginkgo biloba, a well known ‘living fossil’ native to China, is grown worldwide as an ornamental shade plant. Medicinal and nutritional uses of G. biloba in Asia have a long history. However, ginkgo seed proteins have not been well studied at the biochemical and molecular level. In this study, the G. biloba 11S seed storage protein ginnacin was purified by sequential anion-exchange and gel-filtration chromatography. A crystallization screen was performed and well diffracting single crystals were obtained by the vapor-diffusion method. A molecular-replacement structural solution hasmore » been obtained. There are six protomers in an asymmetric unit. Structure refinement is currently in progress.« less

Fluorescence XAS using Ge PAD: Application to High-Temperature Superconducting Thin Film Single Crystals

NASA Astrophysics Data System (ADS)

Oyanagi, H.; Tsukada, A.; Naito, M.; Saini, N. L.; Zhang, C.

2007-02-01

A Ge pixel array detector (PAD) with 100 segments was used in fluorescence x-ray absorption spectroscopy (XAS) study, probing local structure of high temperature superconducting thin film single crystals. Independent monitoring of individual pixel outputs allows real-time inspection of interference of substrates which has long been a major source of systematic error. By optimizing grazing-incidence angle and azimuthal orientation, smooth extended x-ray absorption fine structure (EXAFS) oscillations were obtained, demonstrating that strain effects can be studied using high-quality data for thin film single crystals grown by molecular beam epitaxy (MBE). The results of (La,Sr)2CuO4 thin film single crystals under strain are related to the strain dependence of the critical temperature of superconductivity.

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.

High-throughput crystallization screening.

PubMed

Skarina, Tatiana; Xu, Xiaohui; Evdokimova, Elena; Savchenko, Alexei

2014-01-01

Protein structure determination by X-ray crystallography is dependent on obtaining a single protein crystal suitable for diffraction data collection. Due to this requirement, protein crystallization represents a key step in protein structure determination. The conditions for protein crystallization have to be determined empirically for each protein, making this step also a bottleneck in the structure determination process. Typical protein crystallization practice involves parallel setup and monitoring of a considerable number of individual protein crystallization experiments (also called crystallization trials). In these trials the aliquots of purified protein are mixed with a range of solutions composed of a precipitating agent, buffer, and sometimes an additive that have been previously successful in prompting protein crystallization. The individual chemical conditions in which a particular protein shows signs of crystallization are used as a starting point for further crystallization experiments. The goal is optimizing the formation of individual protein crystals of sufficient size and quality to make them suitable for diffraction data collection. Thus the composition of the primary crystallization screen is critical for successful crystallization.Systematic analysis of crystallization experiments carried out on several hundred proteins as part of large-scale structural genomics efforts allowed the optimization of the protein crystallization protocol and identification of a minimal set of 96 crystallization solutions (the "TRAP" screen) that, in our experience, led to crystallization of the maximum number of proteins.

Transfiguring structural, optical and dielectric properties of cadmium thiourea acetate crystal by the addition of L-threonine for laser assisted device applications

NASA Astrophysics Data System (ADS)

Kulkarni, Rupali B.; Anis, Mohd; Hussaini, S. S.; Shirsat, Mahendra D.

2018-03-01

Present investigation reports the growth of pure and L-threonine (LT) doped cadmium thiourea acetate (CTA) crystals by slow solution evaporation technique followed by structural, optical and dielectric characterization studies. A bulk single crystal of LT-CTA has been grown at temperature 38 °C. The single crystal x-ray diffraction technique has been employed to confirm the structural parameters of pure and LT doped CTA crystals. The increase in optical transparency of LT-CTA crystal was ascertained in the range of 200 to 900 nm using UV-visible spectral analysis. The widened optical band gap of the LT-CTA crystal is found to be 4.7 eV. Pure and doped crystals are subjected to FT-IR analysis to indicate the presence of functional groups quantitatively. Appreciable enhancement in second harmonic generation (SHG) efficiency of LT-CTA crystal with reference to parent CTA was confirmed from Kurtz-Perry SHG test (1.31 times of CTA crystal). The assertive influence of LT on electrical properties of grown crystals has been investigated in the temperature range 35 °C-120 °C. Electronic purity and the color centered photoluminescence emission nature of pure and IA-CTA crystals were justified by luminescence analysis. With the aid of single beam Z-scan analysis, the Kerr lensing nonlinearity was identified and the magnitude of TONLO parameters has been determined. The cubic susceptibility (χ3) and figure of merit (FOM) was found to be 4.81 × 10-4esu and 978.35. Results vitalize LT-CTA for laser stabilization systems.

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.

High-throughput crystal-optimization strategies in the South Paris Yeast Structural Genomics Project: one size fits all?

PubMed

Leulliot, Nicolas; Trésaugues, Lionel; Bremang, Michael; Sorel, Isabelle; Ulryck, Nathalie; Graille, Marc; Aboulfath, Ilham; Poupon, Anne; Liger, Dominique; Quevillon-Cheruel, Sophie; Janin, Joël; van Tilbeurgh, Herman

2005-06-01

Crystallization has long been regarded as one of the major bottlenecks in high-throughput structural determination by X-ray crystallography. Structural genomics projects have addressed this issue by using robots to set up automated crystal screens using nanodrop technology. This has moved the bottleneck from obtaining the first crystal hit to obtaining diffraction-quality crystals, as crystal optimization is a notoriously slow process that is difficult to automatize. This article describes the high-throughput optimization strategies used in the Yeast Structural Genomics project, with selected successful examples.

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

Protein nanocrystallography: growth mechanism and atomic structure of crystals induced by nanotemplates.

PubMed

Pechkova, E; Vasile, F; Spera, R; Fiordoro, S; Nicolini, C

2005-11-01

Protein nanocrystallography, a new technology for crystal growth based on protein nanotemplates, has recently been shown to produce diffracting, stable and radiation-resistant lysozyme crystals. This article, by computing these lysozyme crystals' atomic structures, obtained by the diffraction patterns of microfocused synchrotron radiation, provides a possible mechanism for this increased stability, namely a significant decrease in water content accompanied by a minor but significant alpha-helix increase. These data are shown to be compatible with the circular dichroism and two-dimensional Fourier transform spectra of high-resolution H NMR of proteins dissolved from the same nanotemplate-based crystal versus those from a classical crystal. Finally, evidence for protein direct transfer from the nanotemplate to the drop and the participation of the template proteins in crystal nucleation and growth is provided by high-resolution NMR spectrometry and mass spectrometry. Furthermore, the lysozyme nanotemplate appears stable up to 523 K, as confirmed by a thermal denaturation study using spectropolarimetry. The overall data suggest that heat-proof lysozyme presence in the crystal provides a possible explanation of the crystal's resistance to synchrotron radiation.

Structure of Greyhound hemoglobin: origin of high oxygen affinity.

PubMed

Bhatt, Veer S; Zaldívar-López, Sara; Harris, David R; Couto, C Guillermo; Wang, Peng G; Palmer, Andre F

2011-05-01

This study presents the crystal structure of Greyhound hemoglobin (GrHb) determined to 1.9 Å resolution. GrHb was found to crystallize with an α₁β₁ dimer in the asymmetric unit and belongs to the R2 state. Oxygen-affinity measurements combined with the fact that GrHb crystallizes in the R2 state despite the high-salt conditions used for crystallization strongly indicate that GrHb can serve as a model high-oxygen-affinity hemoglobin (Hb) for higher mammals, especially humans. Structural analysis of GrHb and its comparison with the R2-state of human Hb revealed several regions that can potentially contribute to the high oxygen affinity of GrHb and serve to rationalize the additional stability of the R2-state of GrHb. A previously well studied hydrophobic cluster of bar-headed goose Hb near α119 was also incorporated in the comparison between GrHb and human Hb. Finally, a structural comparison with generic dog Hb and maned wolf Hb was conducted, revealing that in contrast to GrHb these structures belong to the R state of Hb and raising the intriguing possibility of an additional allosteric factor co-purifying with GrHb that can modulate its quaternary structure.

In situ determination of crystal structure and chemistry of minerals at Earth's deep lower mantle conditions

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

Yuan, Hongsheng; Zhang, Li

Recent advances in experimental techniques and data processing allow in situ determination of mineral crystal structure and chemistry up to Mbar pressures in a laser-heated diamond anvil cell (DAC), providing the fundamental information of the mineralogical constitution of our Earth's interior. This work highlights several recent breakthroughs in the field of high-pressure mineral crystallography, including the stability of bridgmanite, the single-crystal structure studies of post-perovskite and H-phase as well as the identification of hydrous minerals and iron oxides in the deep lower mantle. The future development of high-pressure crystallography is also discussed.

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.

Supramolecular architectures constructed through self-assembly of a chalcone and substituted diazo-β-diketones

NASA Astrophysics Data System (ADS)

Prajapati, R.; Mishra, L.; Grabowski, S. J.; Govil, G.; Dubey, S. K.

2008-05-01

Organic compounds namely pyridyl chalcone viz. 3-[4-(3-oxo-3-pyridin-2-yl-propenyl)-phenyl]-1-pyridin-2-yl-propenone (L 1), p-cholorophenyldiazopentane-2,4-dione (L 2) and p-methyl phenyldiazopentane-2,4-dione (L 3) have been characterized by their single-crystal X-ray crystallographic studies. Several structural motifs resulting upon their self-association through probable non-covalent interactions have been discussed. The studies of related motifs found in Cambridge Structural Database are performed and the results are related to the structural data obtained for crystal structures reported here in.

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

Inorganic Crystal Structure Database (ICSD)

National Institute of Standards and Technology Data Gateway

SRD 84 FIZ/NIST Inorganic Crystal Structure Database (ICSD) (PC database for purchase)   The Inorganic Crystal Structure Database (ICSD) is produced cooperatively by the Fachinformationszentrum Karlsruhe(FIZ) and the National Institute of Standards and Technology (NIST). The ICSD is a comprehensive collection of crystal structure data of inorganic compounds containing more than 140,000 entries and covering the literature from 1915 to the present.

Growth, piezoelectric study and particle size dependent SHG of an 80 mm long SR grown imidazolium l-tartrate single crystals

NASA Astrophysics Data System (ADS)

Jauhar, RO MU; Era, Paavai; Murugakoothan, P.

2018-05-01

Single crystal of imidazolium l-tartrate (IMLT), an organic nonlinear optical material, was successfully grown by slow evaporation solution growth technique (SEST) and Sankaranarayanan - Ramasamy (SR) method. The crystal structure and its lattice parameters were confirmed by single crystal X-ray diffraction study. The IMLT crystal belongs to monoclinic crystal system having a = 7.579(6) Å, b = 6.911(4) Å, c = 8.9281(5) Å, β = 101.45(8)°, volume, V = 458.33 Å3. The d33 coefficient found from the the piezoelectric study is 23 pC/N. The relative second harmonic generation efficiency of IMLT was found to be 3.16 times that of reference KDP material.

Crystallographic analysis of ground and space thermostable T1 lipase crystal obtained via counter diffusion method approach.

PubMed

Mohamad Aris, Sayangku Nor Ariati; Thean Chor, Adam Leow; Mohamad Ali, Mohd Shukuri; Basri, Mahiran; Salleh, Abu Bakar; Raja Abd Rahman, Raja Noor Zaliha

2014-01-01

Three-dimensional structure of thermostable lipase is much sought after nowadays as it is important for industrial application mainly found in the food, detergent, and pharmaceutical sectors. Crystallization utilizing the counter diffusion method in space was performed with the aim to obtain high resolution diffracting crystals with better internal order to improve the accuracy of the structure. Thermostable T1 lipase enzyme has been crystallized in laboratory on earth and also under microgravity condition aboard Progress spacecraft to the ISS in collaboration with JAXA (Japanese Aerospace Exploration Agency). This study is conducted with the aims of improving crystal packing and structure resolution. The diffraction data set for ground grown crystal was collected to 1.3 Å resolution and belonged to monoclinic C2 space group with unit cell parameters a = 117.40 Å, b = 80.95 Å, and c = 99.81 Å, whereas the diffraction data set for space grown crystal was collected to 1.1 Å resolution and belonged to monoclinic C2 space group with unit cell parameters a = 117.31 Å, b = 80.85 Å, and c = 99.81 Å. The major difference between the two crystal growth systems is the lack of convection and sedimentation in microgravity environment resulted in the growth of much higher quality crystals of T1 lipase.

Fine tuning of optical signals in nanoporous anodic alumina photonic crystals by apodized sinusoidal pulse anodisation.

PubMed

Santos, Abel; Law, Cheryl Suwen; Chin Lei, Dominique Wong; Pereira, Taj; Losic, Dusan

2016-11-03

In this study, we present an advanced nanofabrication approach to produce gradient-index photonic crystal structures based on nanoporous anodic alumina. An apodization strategy is for the first time applied to a sinusoidal pulse anodisation process in order to engineer the photonic stop band of nanoporous anodic alumina (NAA) in depth. Four apodization functions are explored, including linear positive, linear negative, logarithmic positive and logarithmic negative, with the aim of finely tuning the characteristic photonic stop band of these photonic crystal structures. We systematically analyse the effect of the amplitude difference (from 0.105 to 0.840 mA cm -2 ), the pore widening time (from 0 to 6 min), the anodisation period (from 650 to 950 s) and the anodisation time (from 15 to 30 h) on the quality and the position of the characteristic photonic stop band and the interferometric colour of these photonic crystal structures using the aforementioned apodization functions. Our results reveal that a logarithmic negative apodisation function is the most optimal approach to obtain unprecedented well-resolved and narrow photonic stop bands across the UV-visible-NIR spectrum of NAA-based gradient-index photonic crystals. Our study establishes a fully comprehensive rationale towards the development of unique NAA-based photonic crystal structures with finely engineered optical properties for advanced photonic devices such as ultra-sensitive optical sensors, selective optical filters and all-optical platforms for quantum computing.

Experimental and quantum chemical studies of a new organic proton transfer compound, 1H-imidazole-3-ium-3-hydroxy-2,4,6-trinitrophenolate

NASA Astrophysics Data System (ADS)

Dhamodharan, P.; Sathya, K.; Dhandapani, M.

2018-02-01

A new proton transfer compound, 1H-imidazole-3-ium-3-hydroxy-2,4,6-trinitrophenolate (IMHTP), was crystallized by slow evaporation-solution growth technique. 1H and 13C NMR spectral studies confirm the molecular structure of the grown crystal. Single crystal X-ray diffraction study confirms that IMHTP crystallizes in monoclinic system with space group P21/c. Thermal curves (TG/DTA) show that the material is thermally stable up to 198 °C. The crystal emits fluorescence at 510 nm, proving its utility in making green light emitting materials in optical applications. The stable molecular structure was optimized by Gaussian 09 program with B3LYP/6-311++G(d,p) level of basis set. The frontier molecular orbital study shows that the charge transfer interaction occurs within the complex. The calculated first-order hyperpolarizability value of IMHTP is 44 times higher than that the reference material, urea. The electrostatic potential map was used to probe into electrophilic and nucleophilic reactive sites present in the molecule.

From molecule to solid: The prediction of organic crystal structures

NASA Astrophysics Data System (ADS)

Dzyabchenko, A. V.

2008-10-01

A method for predicting the structure of a molecular crystal based on the systematic search for a global potential energy minimum is considered. The method takes into account unequal occurrences of the structural classes of organic crystals and symmetry of the multidimensional configuration space. The programs of global minimization PMC, comparison of crystal structures CRYCOM, and approximation to the distributions of the electrostatic potentials of molecules FitMEP are presented as tools for numerically solving the problem. Examples of predicted structures substantiated experimentally and the experience of author’s participation in international tests of crystal structure prediction organized by the Cambridge Crystallographic Data Center (Cambridge, UK) are considered.

Crystallization and preliminary X-ray diffraction analysis of central structure domains from mumps virus F protein

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

Liu, Yueyong; Xu, Yanhui; Zhu, Jieqing

2005-09-01

Single crystals of the central structure domains from mumps virus F protein have been obtained by the hanging-drop vapour-diffusion method. A diffraction data set has been collected to 2.2 Å resolution. Fusion of members of the Paramyxoviridae family involves two glycoproteins: the attachment protein and the fusion protein. Changes in the fusion-protein conformation were caused by binding of the attachment protein to the cellular receptor. In the membrane-fusion process, two highly conserved heptad-repeat (HR) regions, HR1 and HR2, are believed to form a stable six-helix coiled-coil bundle. However, no crystal structure has yet been determined for this state in themore » mumps virus (MuV, a member of the Paramyxoviridae family). In this study, a single-chain protein consisting of two HR regions connected by a flexible amino-acid linker (named 2-Helix) was expressed, purified and crystallized by the hanging-drop vapour-diffusion method. A complete X-ray data set was obtained in-house to 2.2 Å resolution from a single crystal. The crystal belongs to space group C2, with unit-cell parameters a = 161.2, b = 60.8, c = 40.1 Å, β = 98.4°. The crystal structure will help in understanding the molecular mechanism of Paramyxoviridae family membrane fusion.« less

Habit modification of bis-thiourea zinc chloride (ZTC) semi organic crystals by impurities

NASA Astrophysics Data System (ADS)

Ruby Nirmala, L.; Thomas Joseph Prakash, J.

2013-06-01

Single crystals of bis-thiourea zinc chloride (ZTC) doped with metal ion (Li+) possess excellent nonlinear optical properties. These crystals were grown by slow evaporation solution growth technique. The effect of Li+ dopant on the growth and properties of ZTC single crystal were investigated and reported. The grown crystals were crystallized in orthorhombic structure with non-centro symmetric space group Pn21a through the parent compound. The amount of dopant incorporated in the parent crystal was revealed by the inductively coupled plasma (ICP-OES) studies. The FT-IR spectroscopy study was done for finding and confirming the functional groups present in the compound. The UV-Visible spectral study was carried out to find the optical behavior and transparency nature of the grown crystal. TG/DTA measurements and Vickers microhardness measurements were traced to find out the thermal and mechanical stability of the grown crystals respectively. Using Nd:YAG laser, the Second harmonic generation (SHG) for the grown crystals were confirmed.

Habit modification of bis-thiourea zinc chloride (ZTC) semi organic crystals by impurities.

PubMed

Ruby Nirmala, L; Thomas Joseph Prakash, J

2013-06-01

Single crystals of bis-thiourea zinc chloride (ZTC) doped with metal ion (Li(+)) possess excellent nonlinear optical properties. These crystals were grown by slow evaporation solution growth technique. The effect of Li(+) dopant on the growth and properties of ZTC single crystal were investigated and reported. The grown crystals were crystallized in orthorhombic structure with non-centro symmetric space group Pn21a through the parent compound. The amount of dopant incorporated in the parent crystal was revealed by the inductively coupled plasma (ICP-OES) studies. The FT-IR spectroscopy study was done for finding and confirming the functional groups present in the compound. The UV-Visible spectral study was carried out to find the optical behavior and transparency nature of the grown crystal. TG/DTA measurements and Vickers microhardness measurements were traced to find out the thermal and mechanical stability of the grown crystals respectively. Using Nd:YAG laser, the Second harmonic generation (SHG) for the grown crystals were confirmed. Copyright © 2013 Elsevier B.V. All rights reserved.

Structural analysis of benzothienobenzothiophene-based soluble organic semiconducting crystals grown by liquid crystal solvent

NASA Astrophysics Data System (ADS)

Shibata, Yosei; Matsuzaki, Tomoya; Ishinabe, Takahiro; Fujikake, Hideo

2018-06-01

In this study, we analyzed organic semiconducting single crystals composed of benzothienobenzothiophene derivatives (2,7-dioctyl[1]benzothieno[3,2-b][1]benzothiophene, C8-BTBT) grown by nematic-phase liquid crystal (LC) solvent. As a result, we clarified that the crystal b-axis direction of the C8-BTBT single crystals was consistent with the LC alignment direction. By optical evaluation and simulation based on density functional theory, we found that the C8-BTBT single crystals in LC solvent exhibited a novel molecular conformation having alkyl chains oriented toward the b-axis.

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.

Exploring Solid-State Structure and Physical Properties: A Molecular and Crystal Model Exercise

ERIC Educational Resources Information Center

Bindel, Thomas H.

2008-01-01

A crystal model laboratory exercise is presented that allows students to examine relations among the microscopic-macroscopic-symbolic levels, using crystalline mineral samples and corresponding crystal models. Students explore the relationship between solid-state structure and crystal form. Other structure-property relationships are explored. The…

Myelin structures formed by thermotropic smectic liquid crystals

NASA Astrophysics Data System (ADS)

Peddireddy, Karthik Reddy; Kumar, Pramoda; Thutupalli, Shashi; Herminghaus, Stephan; Bahr, Christian

2014-03-01

We report on transient structures, formed by thermotropic smectic-A liquid crystals, resembling the myelin figures of lyotropic lamellar liquid crystals. The thermotropic myelin structures form during the solubilization of a smectic-A droplet in an aqueous phase containing a cationic surfactant at concentrations above the critical micelle concentration. Similar to the lyotropic myelin figures, the thermotropic myelins appear in an optical microscope as flexible tube-like structures growing at the smectic/aqueous interface. Polarizing microscopy and confocal fluorescence microscopy show that the smectic layers are parallel to the tube surface and form a cylindrically bent arrangement around a central line defect in the tube. We study the growth behavior of this new type of myelins and discuss similarities and differences to the classical lyotropic myelin figures.

Blue phase liquid crystal phase transition for cyano compound chiral nematic liquid crystal mixtures with three two-ring core structures and chiral dopant concentrations

NASA Astrophysics Data System (ADS)

Shin, Jaesun; Kim, Beomjong; Jung, Wansu; Fahad, Mateen; Park, SangJin; Hong, Sung-Kyu

2017-05-01

Blue phase (BP) temperature range of a chiral nematic liquid crystal (LC) mixture is dependent upon the host nematic LC chemical structure and chiral dopant concentration. In this study, we investigated BP phase transition behaviour and helical twisting power (HTP) using three chiral dopant concentrations of cyano compound chiral nematic LC mixtures incorporating three two-ring core structures in the host nematic LCs. The effect of the host nematic LC core structure, HTP and chiral dopant concentrations were considered on BP temperature ranges, for two types of complete BPI and BPII without isotropic phase (Iso) and two types of coexistence state of BPI+Iso and BPII+Iso.

Calcium Oxalate Accumulation in Malpighian Tubules of Silkworm (Bombyx mori)

NASA Astrophysics Data System (ADS)

Wyman, Aaron J.; Webb, Mary Alice

2007-04-01

Silkworm provides an ideal model system for study of calcium oxalate crystallization in kidney-like organs, called Malpighian tubules. During their growth and development, silkworm larvae accumulate massive amounts of calcium oxalate crystals in their Malpighian tubules with no apparent harm to the organism. This manuscript reports studies of crystal structure in the tubules along with analyses identifying molecular constituents of tubule exudate.

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.

Infrared Fibers for Use in Space-Based Smart Structures

NASA Technical Reports Server (NTRS)

Tucker, Dennis S.; Nettles, Alan T.; Brantley, Lott W. (Technical Monitor)

2001-01-01

Infrared optical fibers are finding a number of applications including laser surgery, remote sensing, and nuclear radiation resistant links. Utilizing these fibers in space-based structures is another application, which can be exploited. Acoustic and thermal sensing are two areas in which these fibers could be utilized. In particular, fibers could be embedded in IM7/8552 toughened epoxy and incorporated into space structures both external and internal. ZBLAN optical fibers are a candidate, which have been studied extensively over the past 20 years for terrestrial applications. For the past seven years the effects of gravity on the crystallization behavior of ZBLAN optical fiber has been studied. It has been found that ZBLAN crystallization is suppressed in microgravity. This lack of crystallization leads to a fiber with better transmission characteristics than its terrestrial counterpart.

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.

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.

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.

Finite element method analysis of band gap and transmission of two-dimensional metallic photonic crystals at terahertz frequencies.

PubMed

Degirmenci, Elif; Landais, Pascal

2013-10-20

Photonic band gap and transmission characteristics of 2D metallic photonic crystals at THz frequencies have been investigated using finite element method (FEM). Photonic crystals composed of metallic rods in air, in square and triangular lattice arrangements, are considered for transverse electric and transverse magnetic polarizations. The modes and band gap characteristics of metallic photonic crystal structure are investigated by solving the eigenvalue problem over a unit cell of the lattice using periodic boundary conditions. A photonic band gap diagram of dielectric photonic crystal in square lattice array is also considered and compared with well-known plane wave expansion results verifying our FEM approach. The photonic band gap designs for both dielectric and metallic photonic crystals are consistent with previous studies obtained by different methods. Perfect match is obtained between photonic band gap diagrams and transmission spectra of corresponding lattice structure.

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.

Double layer zinc-UDP coordination polymers: structure and properties.

PubMed

Qiu, Qi-Ming; Gu, Leilei; Ma, Hongwei; Yan, Li; Liu, Minghua; Li, Hui

2018-05-17

A homochiral Zn-UDP coordination polymer with an alternating parallel ABAB sequence was constructed and studied by X-ray single crystal diffraction analysis. Its crystal structure shows that there are potentially open sites in the 2D layers. The activation of the sites makes the coordination polymer a fluorescent sensor for novel heterogeneous detection of amino acids.

Synthesis, crystal structure, characterizations and magnetic study of a novel two-dimensional iron fluoride

NASA Astrophysics Data System (ADS)

Bouketaya, Sabrine; Smida, Mouna; Abdelbaky, Mohammed S. M.; Dammak, Mohamed; García-Granda, Santiago

2018-06-01

A new hybrid compound formulated as [Fe3F8(H2O)2](Am2TAZ)2 (Am2TAZ= 3,5-diamino-1,2,4-triazole) was prepared under hydrothermal conditions. The crystal structure was solved by single-crystal X-ray diffraction and the bulk was characterized by thermal analyses (TG-MS), vibrational spectroscopy (FTIR, Raman), Ultraviolet-visible spectroscopy (UV-Vis), and scanning electron microscopy (SEM-EDX). It crystallizes in the triclinic system space group P 1 ̅ with unit cell parameters a= 7.100(2) Å, b= 7.658(2) Å, c= 8.321(2) Å, α = 107.330(20)°, β = 111.842(18)°, γ = 93.049(17)°, Z = 1 and V= 394.01(17) Å3. The studied X-ray crystal structure shows the two oxidation states for iron atoms (Fe2+, Fe3+) and generates a 2D inorganic network, built up of inorganic layers constructed from infinite inorganic chains running along a axis. In fact, these chains are connected via (Fe3+(3)F6) octahedral. OW-H…F and N-H…F hydrogen bonds, making up the whole 3D network, are strongly linked in the layers. Magnetization measurements were performed, exhibiting the paramagnetic feature of the studied compound above 150 K.

Mechanical Characterization of Partially Crystallized Sphere Packings

NASA Astrophysics Data System (ADS)

Hanifpour, M.; Francois, N.; Vaez Allaei, S. M.; Senden, T.; Saadatfar, M.

2014-10-01

We study grain-scale mechanical and geometrical features of partially crystallized packings of frictional spheres, produced experimentally by a vibrational protocol. By combining x-ray computed tomography, 3D image analysis, and discrete element method simulations, we have access to the 3D structure of internal forces. We investigate how the network of mechanical contacts and intergranular forces change when the packing structure evolves from amorphous to near perfect crystalline arrangements. We compare the behavior of the geometrical neighbors (quasicontracts) of a grain to the evolution of the mechanical contacts. The mechanical coordination number Zm is a key parameter characterizing the crystallization onset. The high fluctuation level of Zm and of the force distribution in highly crystallized packings reveals that a geometrically ordered structure still possesses a highly random mechanical backbone similar to that of amorphous packings.

Hemispherical Brillouin zone imaging of a diamond-type biological photonic crystal

PubMed Central

Wilts, Bodo D.; Michielsen, Kristel; De Raedt, Hans; Stavenga, Doekele G.

2012-01-01

The brilliant structural body colours of many animals are created by three-dimensional biological photonic crystals that act as wavelength-specific reflectors. Here, we report a study on the vividly coloured scales of the diamond weevil, Entimus imperialis. Electron microscopy identified the chitin and air assemblies inside the scales as domains of a single-network diamond (Fd3m) photonic crystal. We visualized the topology of the first Brillouin zone (FBZ) by imaging scatterometry, and we reconstructed the complete photonic band structure diagram (PBSD) of the chitinous photonic crystal from reflectance spectra. Comparison with calculated PBSDs indeed showed a perfect overlap. The unique method of non-invasive hemispherical imaging of the FBZ provides key insights for the investigation of photonic crystals in the visible wavelength range. The characterized extremely large biophotonic nanostructures of E. imperialis are structurally optimized for high reflectance and may thus be well suited for use as a template for producing novel photonic devices, e.g. through biomimicry or direct infiltration from dielectric material. PMID:22188768

Effect of water on self-assembled tubules in β-sitosterol + γ-oryzanol-based organogels

NASA Astrophysics Data System (ADS)

den Adel, Ruud; Heussen, Patricia C. M.; Bot, Arjen

2010-10-01

Mixtures of β-sitosterol and γ-oryzanol form a network in triglyceride oil that may serve as an alternative to the network of small crystallites of triglycerides occurring in regular oil structuring. The present x-ray diffraction study investigates the relation between the crystal forms of the individual compounds and the mixture in oil, water and emulsion. β-Sitosterol and γ-oryzanol form normal crystals in oil, in water, or in emulsions. The crystals are sensitive to the presence of water. The mixture of β-sitosterol + γ-oryzanol forms crystals in water and emulsions that can be traced back to the crystals of the pure compounds. Only in oil, a completely different structure emerges in the mixture of β-sitosterol + γ-oryzanol, which bears no relation to the structures that are formed by both individual compounds, and which can be identified as a self-assembled tubule (diameter 7.2±0.1 nm, wall thickness 0.8±0.2 nm).

Synthesis, growth, structural and optical studies of organic nonlinear optical material--piperazine-1,4-diium bis 2,4,6-trinitrophenolate.

PubMed

Suguna, S; Anbuselvi, D; Jayaraman, D; Nagaraja, K S; Jeyaraj, B

2014-11-11

Piperazine-1,4-diium bis 2,4,6-trinitrophenolate is one of the useful organic materials with nonlinear optical (NLO) and pharmaceutical applications. The material was grown by slow evaporation solution growth method at room temperature. The crystal system and lattice parameters were identified by single crystal XRD analysis. The grown material crystallizes in monoclinic system with P21/n space group. The main functional groups NH2, NO2, CN, CC, and phenolic 'O' atom were identified using FTIR analysis. The protons and carbons of grown crystal with various chemical environments were studied by 1H and 13C NMR spectroscopy to confirm the molecular structure. The optical properties of the crystal were studied by UV-vis-NIR spectroscopy and the transmission 100% range starts from 532 nm onwards. The optical band gap was measured as 2.63 eV from the plot of (αhν)2 versus hν. The thermal stability was detected at 304.1°C using TG-DTA analysis. The dielectric studies of the sample were carried out at different temperatures in the frequency range from 50 Hz to 5 MHz to establish the dielectric nature of the crystal. Photoconductivity measurements were carried out on the grown crystal. The Second Harmonic Generation (SHG) of the crystal was tested to confirm the nonlinear optical property. Copyright © 2014 Elsevier B.V. All rights reserved.

Salvage of failed protein targets by reductive alkylation.

PubMed

Tan, Kemin; Kim, Youngchang; Hatzos-Skintges, Catherine; Chang, Changsoo; Cuff, Marianne; Chhor, Gekleng; Osipiuk, Jerzy; Michalska, Karolina; Nocek, Boguslaw; An, Hao; Babnigg, Gyorgy; Bigelow, Lance; Joachimiak, Grazyna; Li, Hui; Mack, Jamey; Makowska-Grzyska, Magdalena; Maltseva, Natalia; Mulligan, Rory; Tesar, Christine; Zhou, Min; Joachimiak, Andrzej

2014-01-01

The growth of diffraction-quality single crystals is of primary importance in protein X-ray crystallography. Chemical modification of proteins can alter their surface properties and crystallization behavior. The Midwest Center for Structural Genomics (MCSG) has previously reported how reductive methylation of lysine residues in proteins can improve crystallization of unique proteins that initially failed to produce diffraction-quality crystals. Recently, this approach has been expanded to include ethylation and isopropylation in the MCSG protein crystallization pipeline. Applying standard methods, 180 unique proteins were alkylated and screened using standard crystallization procedures. Crystal structures of 12 new proteins were determined, including the first ethylated and the first isopropylated protein structures. In a few cases, the structures of native and methylated or ethylated states were obtained and the impact of reductive alkylation of lysine residues was assessed. Reductive methylation tends to be more efficient and produces the most alkylated protein structures. Structures of methylated proteins typically have higher resolution limits. A number of well-ordered alkylated lysine residues have been identified, which make both intermolecular and intramolecular contacts. The previous report is updated and complemented with the following new data; a description of a detailed alkylation protocol with results, structural features, and roles of alkylated lysine residues in protein crystals. These contribute to improved crystallization properties of some proteins.

Salvage of Failed Protein Targets by Reductive Alkylation

PubMed Central

Tan, Kemin; Kim, Youngchang; Hatzos-Skintges, Catherine; Chang, Changsoo; Cuff, Marianne; Chhor, Gekleng; Osipiuk, Jerzy; Michalska, Karolina; Nocek, Boguslaw; An, Hao; Babnigg, Gyorgy; Bigelow, Lance; Joachimiak, Grazyna; Li, Hui; Mack, Jamey; Makowska-Grzyska, Magdalena; Maltseva, Natalia; Mulligan, Rory; Tesar, Christine; Zhou, Min; Joachimiak, Andrzej

2014-01-01

The growth of diffraction-quality single crystals is of primary importance in protein X-ray crystallography. Chemical modification of proteins can alter their surface properties and crystallization behavior. The Midwest Center for Structural Genomics (MCSG) has previously reported how reductive methylation of lysine residues in proteins can improve crystallization of unique proteins that initially failed to produce diffraction-quality crystals. Recently, this approach has been expanded to include ethylation and isopropylation in the MCSG protein crystallization pipeline. Applying standard methods, 180 unique proteins were alkylated and screened using standard crystallization procedures. Crystal structures of 12 new proteins were determined, including the first ethylated and the first isopropylated protein structures. In a few cases, the structures of native and methylated or ethylated states were obtained and the impact of reductive alkylation of lysine residues was assessed. Reductive methylation tends to be more efficient and produces the most alkylated protein structures. Structures of methylated proteins typically have higher resolution limits. A number of well-ordered alkylated lysine residues have been identified, which make both intermolecular and intramolecular contacts. The previous report is updated and complemented with the following new data; a description of a detailed alkylation protocol with results, structural features, and roles of alkylated lysine residues in protein crystals. These contribute to improved crystallization properties of some proteins. PMID:24590719

Crystal growth, structural, optical, spectral and thermal studies of tris(L-phenylalanine)L-phenylalaninium nitrate: a new organic nonlinear optical material.

PubMed

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

2011-10-15

Tris(L-phenylalanine)L-phenylalaninium nitrate, C(9)H(12)NO(2)(+)·NO(3)(-)·3C(9)H(11)NO(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. Copyright © 2011 Elsevier B.V. All rights reserved.

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.

The effect of micro-structure on upconversion luminescence of Nd3+/Yb3+ co-doped La2O3-TiO2-ZrO2 glass-ceramics

NASA Astrophysics Data System (ADS)

Zhang, Minghui; Wen, Haiqin; Pan, Xiuhong; Yu, Jianding; Jiang, Meng; Yu, Huimei; Tang, Meibo; Gai, Lijun; Ai, Fei

2018-03-01

Nd3+/Yb3+ co-doped La2O3-TiO2-ZrO2 glasses have been prepared by aerodynamic levitation method. The glasses show high refractive index of 2.28 and Abbe number of 18.3. Glass-ceramics heated at 880 °C for 50 min perform the strongest upconversion luminescence. X-ray diffraction patterns of glass-ceramics with different depths indicate that rare earth ions restrain crystallization. Body crystallization mechanism mixed with surface crystallization is confirmed in the heat treatment. Surface crystals achieve priority to grow, resulting in important effects on upconversion luminescence. The results of atomic force microscope and scanning electron microscope indicate that crystal particles with uniform size distribute densely and homogenously on the surface and large amount of glass matrix exists in the glass ceramics heated at 880 °C for 50 min. Crystals in the glass-ceramics present dense structure and strong boundaries, which can reduce the mutual nonradiative relaxation rate among rare earth ions and then improve upconversion luminescence effectively. Based on micro-structural study, the mechanism that upconversion luminescence can be improved by heat treatment has been revealed. The results of micro-structural analysis agree well with the spectra.

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).

Superconductivity at 5 K in quasi-one-dimensional Cr-based KCr3As3 single crystals

NASA Astrophysics Data System (ADS)

Mu, Qing-Ge; Ruan, Bin-Bin; Pan, Bo-Jin; Liu, Tong; Yu, Jia; Zhao, Kang; Chen, Gen-Fu; Ren, Zhi-An

2017-10-01

Recently a new family of Cr-based A2Cr3As3 (A =K , Rb, Cs) superconductors was reported, which own a rare quasi-one-dimensional (Q1D) crystal structure with infinite (Cr3As3) 2 - chains and exhibit intriguing superconducting characteristics possibly derived from spin-triplet electron pairing. The crystal structure of A2Cr3As3 is actually a slight variation of the hexagonal TlFe3Te3 prototype, although they have different lattice symmetry. Here we report superconductivity in a 133-type KCr3As3 compound that belongs to the latter structure. The single crystals of KCr3As3 were prepared by the deintercalation of K ions from K2Cr3As3 crystals which were grown from a high-temperature solution growth method, and it owns a centrosymmetric lattice in contrast to the noncentrosymmetric K2Cr3As3 . After annealing at a moderate temperature, the KCr3As3 crystals show superconductivity at 5 K revealed by electrical resistivity, magnetic susceptibility, and heat capacity measurements. The discovery of this KCr3As3 superconductor provides a different structural instance to study the exotic superconductivity in these Q1D Cr-based superconductors.

Extending the applicability of the Goldschmidt tolerance factor to arbitrary ionic compounds

PubMed Central

Sato, Toyoto; Takagi, Shigeyuki; Deledda, Stefano; Hauback, Bjørn C.; Orimo, Shin-ichi

2016-01-01

Crystal structure determination is essential for characterizing materials and their properties, and can be facilitated by various tools and indicators. For instance, the Goldschmidt tolerance factor (T) for perovskite compounds is acknowledged for evaluating crystal structures in terms of the ionic packing. However, its applicability is limited to perovskite compounds. Here, we report on extending the applicability of T to ionic compounds with arbitrary ionic arrangements and compositions. By focussing on the occupancy of constituent spherical ions in the crystal structure, we define the ionic filling fraction (IFF), which is obtained from the volumes of crystal structure and constituent ions. Ionic compounds, including perovskites, are arranged linearly by the IFF, providing consistent results with T. The linearity guides towards finding suitable unit cell and composition, thus tackling the main obstacle for determining new crystal structures. We demonstrate the utility of the IFF by solving the structure of three hydrides with new crystal structures. PMID:27032978

Extending the applicability of the Goldschmidt tolerance factor to arbitrary ionic compounds.

PubMed

Sato, Toyoto; Takagi, Shigeyuki; Deledda, Stefano; Hauback, Bjørn C; Orimo, Shin-ichi

2016-04-01

Crystal structure determination is essential for characterizing materials and their properties, and can be facilitated by various tools and indicators. For instance, the Goldschmidt tolerance factor (T) for perovskite compounds is acknowledged for evaluating crystal structures in terms of the ionic packing. However, its applicability is limited to perovskite compounds. Here, we report on extending the applicability of T to ionic compounds with arbitrary ionic arrangements and compositions. By focussing on the occupancy of constituent spherical ions in the crystal structure, we define the ionic filling fraction (IFF), which is obtained from the volumes of crystal structure and constituent ions. Ionic compounds, including perovskites, are arranged linearly by the IFF, providing consistent results with T. The linearity guides towards finding suitable unit cell and composition, thus tackling the main obstacle for determining new crystal structures. We demonstrate the utility of the IFF by solving the structure of three hydrides with new crystal structures.

Optical Anisotropy of Photonic Crystals of Cubic Symmetry Induced by Multiple Diffraction of Light

NASA Astrophysics Data System (ADS)

Ukleev, T. A.; Shevchenko, N. N.; Iurasova, D. I.; Sel'kin, A. V.

2018-05-01

The optical spectra of Bragg reflection from opal-like photonic crystals under conditions of the resonant enhancement of the multiple diffraction of light have been studied experimentally and theoretically using the photonic crystal structures prepared of monodisperse polystyrene globules. It is shown that the reflection signal registered in mutually orthogonal configurations of the polarizer and analyzer is related to the intrinsic optical anisotropy of the crystals and is a specific manifestation of the multiple Bragg diffraction in three-dimensional photonic crystals.

Special Features of the Structure of Single-Crystal Refractory Nickel Alloy Under Directed Crystallization

NASA Astrophysics Data System (ADS)

Bondarenko, Yu. A.; Echin, A. B.; Surova, V. A.; Kolodyazhnyi, M. Yu.

2017-05-01

The effect of the conditions of directed crystallization (the temperature gradient and the crystallization rate) on the dendrite spacing, on the size of the particles of the hardening γ'-phase in the arms and arm spaces of the dendrites, on the volume fraction and size of the pores, on the size of the particles of the eutectic γ/γ'-phase, and on the features of dendritic segregation in a single-crystal castable refractory alloy is studied.

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

Correlation between the conformational states of F1-ATPase as determined from its crystal structure and single-molecule rotation

PubMed Central

Okuno, Daichi; Fujisawa, Ryo; Iino, Ryota; Hirono-Hara, Yoko; Imamura, Hiromi; Noji, Hiroyuki

2008-01-01

F1-ATPase is a rotary molecular motor driven by ATP hydrolysis that rotates the γ-subunit against the α3β3 ring. The crystal structures of F1, which provide the structural basis for the catalysis mechanism, have shown essentially 1 stable conformational state. In contrast, single-molecule studies have revealed that F1 has 2 stable conformational states: ATP-binding dwell state and catalytic dwell state. Although structural and single-molecule studies are crucial for the understanding of the molecular mechanism of F1, it remains unclear as to which catalytic state the crystal structure represents. To address this issue, we introduced cysteine residues at βE391 and γR84 of F1 from thermophilic Bacillus PS3. In the crystal structures of the mitochondrial F1, the corresponding residues in the ADP-bound β (βDP) and γ were in direct contact. The βE190D mutation was additionally introduced into the β to slow ATP hydrolysis. By incorporating a single copy of the mutant β-subunit, the chimera F1, α3β2β(E190D/E391C)γ(R84C), was prepared. In single-molecule rotation assay, chimera F1 showed a catalytic dwell pause in every turn because of the slowed ATP hydrolysis of β(E190D/E391C). When the mutant β and γ were cross-linked through a disulfide bond between βE391C and γR84C, F1 paused the rotation at the catalytic dwell angle of β(E190D/E391C), indicating that the crystal structure represents the catalytic dwell state and that βDP is the catalytically active form. The former point was again confirmed in experiments where F1 rotation was inhibited by adenosine-5′-(β,γ-imino)-triphosphate and/or azide, the most commonly used inhibitors for the crystallization of F1. PMID:19075235

From screen to structure with a harvestable microfluidic device.

PubMed

Stojanoff, Vivian; Jakoncic, Jean; Oren, Deena A; Nagarajan, V; Poulsen, Jens-Christian Navarro; Adams-Cioaba, Melanie A; Bergfors, Terese; Sommer, Morten O A

2011-08-01

Advances in automation have facilitated the widespread adoption of high-throughput vapour-diffusion methods for initial crystallization screening. However, for many proteins, screening thousands of crystallization conditions fails to yield crystals of sufficient quality for structural characterization. Here, the rates of crystal identification for thaumatin, catalase and myoglobin using microfluidic Crystal Former devices and sitting-drop vapour-diffusion plates are compared. It is shown that the Crystal Former results in a greater number of identified initial crystallization conditions compared with vapour diffusion. Furthermore, crystals of thaumatin and lysozyme obtained in the Crystal Former were used directly for structure determination both in situ and upon harvesting and cryocooling. On the basis of these results, a crystallization strategy is proposed that uses multiple methods with distinct kinetic trajectories through the protein phase diagram to increase the output of crystallization pipelines.

Experimental and theoretical study of pure and doped crystals: Gd2O2S, Gd2O2S:Eu3+ and Gd2O2S:Tb3+

NASA Astrophysics Data System (ADS)

Wang, Fei; Chen, Xiumin; Liu, Dachun; Yang, Bin; Dai, Yongnian

2012-08-01

Quantum chemistry and experimental method were used to study on pure and doped Gd2O2S crystals in this paper. The band structure and DOS diagrams of pure and doped Gd2O2S crystals which calculated by using DFT (Density Functional Theory) method were illustrated to explain the luminescent properties of impurities in crystals. The calculations of the crystal structure were finished by using the program of CASTEP (Cambridge Sequential Total Energy Package). The samples showed the characteristic emissions of Tb3+ ions with 5D4-7FJ transitions and Eu3+ ions with 5D0-7FJ transitions which emit pure green luminescence and red luminescence respectively. The experimental excitation spectra of Tb3+ and Eu3+ doped Gd2O2S are in agreement of the DOS diagrams over the explored energy range, which has allowed a better understanding of different luminescence mechanisms of Tb3+ and Eu3+ in Gd2O2S crystals.

Single crystals of (FeIn{sub 2}S{sub 4}){sub x} · (CuIn{sub 5}S{sub 8}){sub 1–x} alloys: Crystal structure, nuclear gamma resonance spectra, and thermal expansion

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

Bodnar, I. V., E-mail: chemzav@bsuir.by; Zhafar, M. A.; Kasyuk, Yu. V.

FeIn{sub 2}S{sub 4} and CuIn{sub 5}S{sub 8} compounds and (FeIn{sub 2}S{sub 4}){sub x} · (CuIn{sub 5}S{sub 8}){sub 1–x} alloy single crystals are grown by planar crystallization. It is shown that both of the initial FeIn{sub 2}S{sub 4} and CuIn{sub 5}S{sub 8} compounds and alloys on their basis crystallize with the formation of the cubic spinel structure. It is established that the unit-cell parameter a linearly varies with the composition parameter x. By means of nuclear gamma resonance spectroscopy in the transmission mode of measurements, the local states of iron ions in the alloys are studied. For the single crystals grownmore » in the study, thermal expansion is explored using the dilatometry technique, the thermal-expansion coefficients are determined, and the Debye temperature and rms (root-mean-square) dynamic displacements are calculated.« less

Microstructure and conductivity of in-situ polymerized poly(3,4-ethylenedioxythiophene) (PEDOT) crystals

NASA Astrophysics Data System (ADS)

Liu, Jinglin; Ouyang, Liangqi; Wu, Jinghang; Kuo, Chin-Chen; Wei, Bin; Martin, David

2013-03-01

Conjugated polymers are widely used in organic solar cells, biomedical devices, and chemical sensors. Both chemical and electrochemical methods have been developed for preparing conducting polymers, but the extent of crystalline order is usually modest. Here we synthesized highly-ordered brominated (3,4-ethylenedioxythiophene) (EDOT-Br) monomer crystals via electrochemical methods. The kinetics of the synthesis was studied with a Quartz Crystal Microbalance (QCM) and Cyclic Voltammetry (CV). The chemical structure of the EDOT-Br monomer has been confirmed by Nuclear Magnetic Resonance (NMR), Ultraviolet-Visible Spectroscopy (UV-Vis), Fourier Transform Infrared Spectroscopy (FTIR), and Mass Spectrometry (MS). The EDOT-Br monomer crystals can be in-situ polymerized into highly ordered PEDOT conjugated polymer crystals by annealing at temperatures below the EDOT-Br melting point. The crystalline structure was studied by optical microscopy, electron microscopy and X-Ray analysis. The conductivity and electrochemical properties of both the EDOT-Br monomer and corresponding PEDOT polymer crystals were examined with electrochemical impedance spectroscopy (EIS) and CV. This work was supported by NSF, DMR- 1103027.

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.

The microdopant effects of surfactant elements on structure-phase transitions during the rapid quenched crystallization of Fe-C-based melts

NASA Astrophysics Data System (ADS)

Polukhin, V. A.; Belyakova, R. M.; Rigmant, L. K.

2008-02-01

The nature of microdopant effects of surfactant Te and H2 reagents on structure-phase transitions in rapidly quenched and crystallized eutectic Fe-C-based melts were studied by experimental and computer methods. On the base of results of statistic-geometrical analysis the new information about the structure changes in multi-scaling systems -from meso- to nano-ones were obtained.

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.

Crystal structure of a putative exo-β-1,3-galactanase from Bifidobacterium bifidum S17

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

Godoy, Andre S.; de Lima, Mariana Z. T.; Camilo, Cesar M.

2016-03-16

Given the current interest in second-generation biofuels, carbohydrate-active enzymes have become the most important tool to overcome the structural recalcitrance of the plant cell wall. While some glycoside hydrolase families have been exhaustively described, others remain poorly characterized, especially with regard to structural information. The family 43 glycoside hydrolases are a diverse group of inverting enzymes; the available structure information on these enzymes is mainly from xylosidases and arabinofuranosidase. Currently, only one structure of an exo-β-1,3-galactanase is available. Here, the production, crystallization and structure determination of a putative exo-β-1,3-galactanase fromBifidobacterium bifidumS17 (BbGal43A) are described.BbGal43A was successfully produced and showed activitymore » towards synthetic galactosides.BbGal43A was subsequently crystallized and data were collected to 1.4 Å resolution. The structure shows a single-domain molecule, differing from known homologues, and crystal contact analysis predicts the formation of a dimer in solution. Further biochemical studies are necessary to elucidate the differences betweenBbGal43A and its characterized homologues.« less

Structure of fructose bisphosphate aldolase from Bartonella henselae bound to fructose 1,6-bisphosphate.

PubMed

Gardberg, Anna; Abendroth, Jan; Bhandari, Janhavi; Sankaran, Banumathi; Staker, Bart

2011-09-01

Fructose bisphosphate aldolase (FBPA) enzymes have been found in a broad range of eukaryotic and prokaryotic organisms. FBPA catalyses the cleavage of fructose 1,6-bisphosphate into glyceraldehyde 3-phosphate and dihydroxyacetone phosphate. The SSGCID has reported several FBPA structures from pathogenic sources, including the bacterium Brucella melitensis and the protozoan Babesia bovis. Bioinformatic analysis of the Bartonella henselae genome revealed an FBPA homolog. The B. henselae FBPA enzyme was recombinantly expressed and purified for X-ray crystallographic studies. The purified enzyme crystallized in the apo form but failed to diffract; however, well diffracting crystals could be obtained by cocrystallization in the presence of the native substrate fructose 1,6-bisphosphate. A data set to 2.35 Å resolution was collected from a single crystal at 100 K. The crystal belonged to the orthorhombic space group P2(1)2(1)2(1), with unit-cell parameters a=72.39, b=127.71, c=157.63 Å. The structure was refined to a final free R factor of 22.2%. The structure shares the typical barrel tertiary structure and tetrameric quaternary structure reported for previous FBPA structures and exhibits the same Schiff base in the active site.

Active crystals on a sphere

NASA Astrophysics Data System (ADS)

Praetorius, Simon; Voigt, Axel; Wittkowski, Raphael; Löwen, Hartmut

2018-05-01

Two-dimensional crystals on curved manifolds exhibit nontrivial defect structures. Here we consider "active crystals" on a sphere, which are composed of self-propelled colloidal particles. Our work is based on a phase-field-crystal-type model that involves a density and a polarization field on the sphere. Depending on the strength of the self-propulsion, three different types of crystals are found: a static crystal, a self-spinning "vortex-vortex" crystal containing two vortical poles of the local velocity, and a self-translating "source-sink" crystal with a source pole where crystallization occurs and a sink pole where the active crystal melts. These different crystalline states as well as their defects are studied theoretically here and can in principle be confirmed in experiments.

Protein Crystal Malic Enzyme

NASA Technical Reports Server (NTRS)

1992-01-01

Malic Enzyme is a target protein for drug design because it is a key protein in the life cycle of intestinal parasites. After 2 years of effort on Earth, investigators were unable to produce any crystals that were of high enough quality and for this reason the structure of this important protein could not be determined. Crystals obtained from one STS-50 were of superior quality allowing the structure to be determined. This is just one example why access to space is so vital for these studies. Principal Investigator is Larry DeLucas.

Defect dynamics in active nematics

PubMed Central

Giomi, Luca; Bowick, Mark J; Mishra, Prashant; Sknepnek, Rastko; Cristina Marchetti, M

2014-01-01

Topological defects are distinctive signatures of liquid crystals. They profoundly affect the viscoelastic behaviour of the fluid by constraining the orientational structure in a way that inevitably requires global changes not achievable with any set of local deformations. In active nematic liquid crystals, topological defects not only dictate the global structure of the director, but also act as local sources of motion, behaving as self-propelled particles. In this article, we present a detailed analytical and numerical study of the mechanics of topological defects in active nematic liquid crystals. PMID:25332389

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.

Synthesis, structural, thermal and optical studies of 1-ethyl-2,6-dimethyl-4-hydroxy pyridinium halides.

PubMed

Dhanuskodi, S; Manivannan, S; Kirschbaum, K

2006-05-15

1-Ethyl-2,6-dimethyl-4-hydroxy pyridinium chloride dihydrate and bromide dihydrate salts have been synthesized and their single crystals were grown by the slow evaporation of aqueous solution at 30 degrees C. The grown crystals were characterized by elemental analysis, FT-NMR and FT-IR techniques to confirm the formation of the expected compound. Optical transmittance window in aqueous solution was found to be 275-1100 nm by UV-vis-NIR technique. Thermogravimetric and differential thermal analyses reveal thermal stability and the presence of two water molecules in the crystal lattices. The crystal structure of chloride salt was also determined by X-ray diffraction method.

Crystallization dynamics on curved surfaces

NASA Astrophysics Data System (ADS)

García, Nicolás A.; Register, Richard A.; Vega, Daniel A.; Gómez, Leopoldo R.

2013-07-01

We study the evolution from a liquid to a crystal phase in two-dimensional curved space. At early times, while crystal seeds grow preferentially in regions of low curvature, the lattice frustration produced in regions with high curvature is rapidly relaxed through isolated defects. Further relaxation involves a mechanism of crystal growth and defect annihilation where regions with high curvature act as sinks for the diffusion of domain walls. The pinning of grain boundaries at regions of low curvature leads to the formation of a metastable structure of defects, characterized by asymptotically slow dynamics of ordering and activation energies dictated by the largest curvatures of the system. These glassylike ordering dynamics may completely inhibit the appearance of the ground-state structures.

Crystal structure of an orthomyxovirus matrix protein reveals mechanisms for self-polymerization and membrane association.

PubMed

Zhang, Wenting; Zheng, Wenjie; Toh, Yukimatsu; Betancourt-Solis, Miguel A; Tu, Jiagang; Fan, Yanlin; Vakharia, Vikram N; Liu, Jun; McNew, James A; Jin, Meilin; Tao, Yizhi J

2017-08-08

Many enveloped viruses encode a matrix protein. In the influenza A virus, the matrix protein M1 polymerizes into a rigid protein layer underneath the viral envelope to help enforce the shape and structural integrity of intact viruses. The influenza virus M1 is also known to mediate virus budding as well as the nuclear export of the viral nucleocapsids and their subsequent packaging into nascent viral particles. Despite extensive studies on the influenza A virus M1 (FLUA-M1), only crystal structures of its N-terminal domain are available. Here we report the crystal structure of the full-length M1 from another orthomyxovirus that infects fish, the infectious salmon anemia virus (ISAV). The structure of ISAV-M1 assumes the shape of an elbow, with its N domain closely resembling that of the FLUA-M1. The C domain, which is connected to the N domain through a flexible linker, is made of four α-helices packed as a tight bundle. In the crystal, ISAV-M1 monomers form infinite 2D arrays with a network of interactions involving both the N and C domains. Results from liposome flotation assays indicated that ISAV-M1 binds membrane via electrostatic interactions that are primarily mediated by a positively charged surface loop from the N domain. Cryoelectron tomography reconstruction of intact ISA virions identified a matrix protein layer adjacent to the inner leaflet of the viral membrane. The physical dimensions of the virion-associated matrix layer are consistent with the 2D ISAV-M1 crystal lattice, suggesting that the crystal lattice is a valid model for studying M1-M1, M1-membrane, and M1-RNP interactions in the virion.

AFM Studies of Salt Concentration Effects on the (110) Surface Structure of Tetragonal Lysozyme Crystals

NASA Technical Reports Server (NTRS)

Pusey, Marc Lee; Gorti, Sridhar; Forsythe, Elizabeth; Konnert, John

2002-01-01

Previous high resolution AFM studies of the (110) surface of tetragonal chicken egg white lysozyme crystals had shown that only one of two possible molecular surfaces is present, those constituting the completed 43 helices. These suggested that the crystal growth process was by the solution-phase assembly of the growth units, which then attach to the surface. However, the best fit for the imaged surfaces, vs. those predicted based upon the bulk crystallographic coordinates, were obtained when the packing about the 43 helices was "tightened up", while maintaining the underlying crystallographic unit cell spacing. This results in a widening of the gap between adjacent helices, and the top- most layer(s) may no longer be in contact. We postulated that the tightened packing about the helices is a result of the high salt concentrations in the bulk solution, used to crystallize the protein, driving hydrophobic interactions. Once the crystal surface is sufficiently buried by subsequent growth layers the ratio of salt to protein molecules decreases and the helices relax to their bulk crystallographic coordinates. The crystal surface helix structure is thus a reflection of the solution structure, and the tightness of the packing about the 43 helices would be a function of the bulk salt concentration. AFM images of the (110) surface of tetragonal lysozyme crystals grown under low (2%) and high (5%) NaCl concentrations reveal differences in the packing about the 43 helices consistent with the above proposal.

Hydrolytic degradation of N,N‧-ethylenedimaleimide: Crystal structures of key intermediates and proposed mechanisms

NASA Astrophysics Data System (ADS)

Tan, Xue-Jie; Cheng, Shuang-Shuang; Shi, Yan; Xing, Dian-Xiang; Liu, Yun; Li, Hui; Feng, Wen-Quan; Yang, Jian-Bo

2016-12-01

Maleimide groups are used extensively in bioconjugation reactions, but limited mechanistic studies are available regarding their hydrolysis reactions. In this paper, five single-crystal structures related with the reaction of four-step hydrolytic degradation of N,N‧-ethylenedimaleimide have been investigated. On the basis of experimental results, the reaction mechanisms without or with water catalysis are proposed, which could provide some enlightenment into the study of similar hydrolytic degradations.

Optical spectra and band structure of Ag(x)Ga(x)Ge(1-x)Se2 (x = 0.333, 0.250, 0.200, 0.167) single crystals: experiment and theory.

PubMed

Reshak, A H; Parasyuk, O V; Fedorchuk, A O; Kamarudin, H; Auluck, S; Chyský, J

2013-12-05

Theoretical and experimental studies of the Ag(x)Ga(x)Ge(1-x)Se2 (x = 0.333, 0.250, 0.200, 0.167) single crystals are performed. These crystals possess a lot of intrinsic defects which are responsible for their optoelectronic features. The theoretical investigations were performed by means of DFT calculations using different exchange-correlation potentials. The experimental studies were carried out using the modulated VUV ellipsometry for dielectric constants and birefringence studies. The comparison of the structure obtained from X-ray with the theoretically optimized structure is presented. The crucial role of the intrinsic defect states is manifested in the choice of the exchange correlation potential used. The data may be applicable for a large number of the ternary chalcogenides which are sensitive to the presence of the local disordered states near the band edges.

Lecithin based lamellar liquid crystals as a physiologically acceptable dermal delivery system for ascorbyl palmitate.

PubMed

Gosenca, Mirjam; Bešter-Rogač, Marija; Gašperlin, Mirjana

2013-09-27

Liquid crystalline systems with a lamellar structure have been extensively studied as dermal delivery systems. Ascorbyl palmitate (AP) is one of the most studied and used ascorbic acid derivatives and is employed as an antioxidant to prevent skin aging. The aim of this study was to develop and characterize skin-compliant dermal delivery systems with a liquid crystalline structure for AP. First, a pseudoternary phase diagram was constructed using Tween 80/lecithin/isopropyl myristate/water at a Tween 80/lecithin mass ratio of 1/1, and the region of lamellar liquid crystals was identified. Second, selected unloaded and AP-loaded lamellar liquid crystal systems were physicochemically characterized with polarizing optical microscopy, small-angle X-ray scattering, differential scanning calorimetry, and rheology techniques. The interlayer spacing and rheological parameters differ regarding quantitative composition, whereas the microstructure of the lamellar phase was affected by the AP incorporation, resulting either in additional micellar structures (at 25 and 32 °C) or being completely destroyed at higher temperature (37°C). After this, the study was oriented towards in vitro cytotoxicity evaluation of lamellar liquid crystal systems on a keratinocyte cell line. The results suggest that the lamellar liquid crystals that were developed could be used as a physiologically acceptable dermal delivery system. Copyright © 2013 Elsevier B.V. All rights reserved.

Crystal structures of inhibitor complexes of human T-cell leukemia virus (HTLV-1) protease

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

Satoh, Tadashi; Li, Mi; Nguyen, Jeffrey-Tri

2010-09-28

Human T-cell leukemia virus type 1 (HTLV-1) is a retrovirus associated with several serious diseases, such as adult T-cell leukemia and tropical spastic paraparesis/myelopathy. For a number of years, the protease (PR) encoded by HTLV-1 has been a target for designing antiviral drugs, but that effort was hampered by limited available structural information. We report a high-resolution crystal structure of HTLV-1 PR complexed with a statine-containing inhibitor, a significant improvement over the previously available moderate-resolution structure. We also report crystal structures of the complexes of HTLV-1 PR with five different inhibitors that are more compact and more potent. A detailedmore » study of structure-activity relationships was performed to interpret in detail the influence of the polar and hydrophobic interactions between the inhibitors and the protease.« less

Crystal Structures of Inhibitir Complexes of Human T-Cell Leukemia Virus (HTLV-1) Protease

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

Satoh, Tadashi; Li, Mi; Nguyen, Jeffrey-Tri

2010-09-17

Human T-cell leukemia virus type 1 (HTLV-1) is a retrovirus associated with several serious diseases, such as adult T-cell leukemia and tropical spastic paraparesis/myelopathy. For a number of years, the protease (PR) encoded by HTLV-1 has been a target for designing antiviral drugs, but that effort was hampered by limited available structural information. We report a high-resolution crystal structure of HTLV-1 PR complexed with a statine-containing inhibitor, a significant improvement over the previously available moderate-resolution structure. We also report crystal structures of the complexes of HTLV-1 PR with five different inhibitors that are more compact and more potent. A detailedmore » study of structure-activity relationships was performed to interpret in detail the influence of the polar and hydrophobic interactions between the inhibitors and the protease.« less

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

Experimental (FTIR, Raman, UV-visible and PL) and theoretical (DFT and TDDFT) studies on bis(8-hydroxyquinolinium) tetrachlorocobaltate(II) compound

NASA Astrophysics Data System (ADS)

Chaouachi, Soumaya; Elleuch, Slim; Hamdi, Besma; Zouari, Ridha

2016-12-01

The purpose of this paper is to present the chemical preparation, crystal structure, vibrational study and optical features for new organic-inorganic compound [C9H8NO]2CoCl4 abbreviated [8-HQ]2CoCl4. The structural study by X-ray diffraction prove that this compound crystallize in a monoclinic unit-cell with space group C2/c (point group 2/m = C2h). It is built of tetrahedra [CoCl4]2- anions and (C9H8NO)+ cations in the 1/2 ratio. The crystal structure is stabilized by network three-dimensional of Nsbnd H⋯Cl, Nsbnd H⋯O, Osbnd H⋯Cl, Csbnd H⋯Cl hydrogen bonds, and offset π-π stacking interactions. Also, the Hirshfeld Surface projections and Fingerprint plots were elucidated the relative contribution of the type, nature and explore the H⋯Cl, C⋯H, C⋯C, C⋯N, H⋯O intermolecular contacts in the crystal in a visual manner. Furthermore, vibrational analysis of the structural groups in the compound was carried out by both Fourier transforms infrared (FT-IR) and Raman spectra. The spectral data are complemented by good information at the region characteristic of metal-ligand, which evidences coordination through the compound. The optical properties of the crystal were studied by using optical absorption UV-visible and photoluminescence (PL) spectroscopy studies. Theoretical calculations were performed using density functional theory (DFT) at (DFT/B3LYP/LanL2DZ) level in the aim of aiding in studying structural, vibrational and optical properties of the investigated compound. Good relationship consistency is found between the experimental and theoretical studies. Inspection of the optical properties has lead to confirm the exhibition of a green photoluminescence and the occurrence of charge transfer phenomenon in this material.

Spectroscopic and DFT-based computational studies on the molecular electronic structural characteristics and the third-order nonlinear property of an organic NLO crystal: (E)-N‧-(4-chlorobenzylidene)-4-methylbenzenesulfonohydrazide

NASA Astrophysics Data System (ADS)

Sasikala, V.; Sajan, D.; Joseph, Lynnette; Balaji, J.; Prabu, S.; Srinivasan, P.

2017-04-01

Single crystals of (E)-N‧-(4-chlorobenzylidene)-4-methylbenzenesulfonohydrazide (CBMBSH) have been grown by slow evaporation crystal growth method. The structure stabilizing intramolecular donor-acceptor interactions and the presence of the Nsbnd H⋯O, Csbnd H⋯O and Csbnd H⋯C(π) hydrogen bonds in the crystal were confirmed by vibrational spectroscopic and DFT methods. The linear optical absorption characteristics of the solvent phase of CBMBSH were investigated using UV-Vis-NIR spectroscopic and TD-DFT approaches. The 2PA assisted RSA nonlinear absorption and the optical limiting properties of CBMBSH were studied using the open-aperture Z-scan method. The topological characteristics of the electron density have been determined using the quantum theory of atoms in molecules method.

Protein crystal growth and the International Space Station

NASA Technical Reports Server (NTRS)

DeLucas, L. J.; Moore, K. M.; Long, M. M.

1999-01-01

Protein structural information plays a key role in understanding biological structure-function relationships and in the development of new pharmaceuticals for both chronic and infectious diseases. The Center for Macromolecular Crystallography (CMC) has devoted considerable effort studying the fundamental processes involved in macromolecular crystal growth both in a 1-g and microgravity environment. Results from experiments performed on more than 35 U.S. space shuttle flights have clearly indicated that microgravity can provide a beneficial environment for macromolecular crystal growth. This research has led to the development of a new generation of pharmaceuticals that are currently in preclinical or clinical trials for diseases such as cutaneous T-cell lymphoma, psoriasis, rheumatoid arthritis, AIDS, influenza, stroke and other cardiovascular complications. The International Space Station (ISS) provides an opportunity to have complete crystallographic capability on orbit, which was previously not possible with the space shuttle orbiter. As envisioned, the x-ray Crystallography Facility (XCF) will be a complete facility for growing protein crystals; selecting, harvesting, and mounting sample crystals for x-ray diffraction; cryo-freezing mounted crystals if necessary; performing x-ray diffraction studies; and downlinking the data for use by crystallographers on the ground. Other advantages of such a facility include crystal characterization so that iterations in the crystal growth conditions can be made, thereby optimizing the final crystals produced in a three month interval on the ISS.

Satellite Tobacco Mosaic Virus Structure

NASA Technical Reports Server (NTRS)

2000-01-01

The structure of the Satellite Tobacco Mosaic Viurus (STMV)--one of the smallest viruses known--has been successfully reduced using STMV crystals grown aboard the Space Shuttle in 1992 and 1994. The STMV crystals were up to 30 times the volume of any seen in the laboratory. At the time they gave the best resolution data ever obtained on any virus crystal. STMV is a small icosahedral plant virus, consisting of a protein shell made up of 60 identical protein subunits of molecular weight 17,500. Particularly noteworthy is the fact that, in contrast to the crystals grown on Earth, the crystals grown under microgravity conditions were visually perfect, with no striations or clumping of crystals. Furthermore, the x-ray diffraction data obtained from the space-grown crystals was of a much higher quality than the best data available at that time from ground-based crystals. This stylized ribbon model shows the protein coat in white and the nucleic acid in yellow. STMV is used because it is a simple protein to work with; studies are unrelated to tobacco. Credit: Dr. Alex McPherson, University of California at Irvin.

Increasing dissolution of trospium chloride by co-crystallization with urea

NASA Astrophysics Data System (ADS)

Skořepová, Eliška; Hušák, Michal; Čejka, Jan; Zámostný, Petr; Kratochvíl, Bohumil

2014-08-01

The search for various solid forms of an active pharmaceutical ingredient (API) is an important step in drug development. Our aim was to prepare co-crystals of trospium chloride, an anticholinergic drug used for the treatment of incontinence, and to investigate if they have advantageous properties for drug formulation. Phase identification was done by powder X-ray diffraction and single-crystal X-ray diffraction. The chemical composition was verified by solution NMR and the dissolution rate of the prepared phases was studied by IDR (intrinsic dissolution rate). For further analysis of phase stability and transitions, combined thermal analysis and temperature-resolved X-ray powder diffraction were used. Urea was selected as a co-crystallization partner. Trospium chloride urea (1:1) co-crystal was prepared by a solvent evaporation. From single-crystal data, the co-crystal structure was solved in a space group P21/c and compared to previously published structures of trospium chloride. Intrinsic dissolution rate revealed that the co-crystal dissolves 32% faster than pure API. However, its low thermal and pressure stability makes it a challenging choice for the final drug formulation.

Plastically bendable crystals of probenecid and its cocrystal with 4,4‧-Bipyridine

NASA Astrophysics Data System (ADS)

Nath, Naba K.; Hazarika, Mousumi; Gupta, Poonam; Ray, Nisha R.; Paul, Amit K.; Nauha, Elisa

2018-05-01

Recent findings of plastically bendable molecular crystals led to the realization that design based strategies are required for these materials to be useful in real life application. We have coincidentally discovered plastically bendable crystals of a drug molecule probenecid. Based on the structural features of its crystals at room temperature, we hypothesized that introduction of a molecular spacer between two hydrogen bonded molecules of probenecid, by replacing the carboxylic acid homodimer with similar dimeric hydrogen bonding synthon, would not disturb the layered molecular packing of probenecid. As a consequence, the new multi-component crystal would retain flexibility similar to the original probenecid crystals. Herein we have attempted to prove this hypothesis and we were successful in the case of probenecid: 4,4‧-bipyridine cocrystal. As designed, in the crystal structure 4,4‧-bypyridine molecule acted as spacer and connected two probenecid molecules resulting in the retention of the slip planes which are necessary for a molecular crystal to be plastically bendable. DFT computational calculations were carried out to account for the hydrogen bonding synthons between probenecid and the coformers under study.

Crystal Structures of Apo and Liganded 4-Oxalocrotonate Decarboxylase Uncover a Structural Basis for the Metal-Assisted Decarboxylation of a Vinylogous β-Keto Acid.

PubMed

Guimarães, Samuel L; Coitinho, Juliana B; Costa, Débora M A; Araújo, Simara S; Whitman, Christian P; Nagem, Ronaldo A P

2016-05-10

The enzymes in the catechol meta-fission pathway have been studied for more than 50 years in several species of bacteria capable of degrading a number of aromatic compounds. In a related pathway, naphthalene, a toxic polycyclic aromatic hydrocarbon, is fully degraded to intermediates of the tricarboxylic acid cycle by the soil bacteria Pseudomonas putida G7. In this organism, the 83 kb NAH7 plasmid carries several genes involved in this biotransformation process. One enzyme in this route, NahK, a 4-oxalocrotonate decarboxylase (4-OD), converts 2-oxo-3-hexenedioate to 2-hydroxy-2,4-pentadienoate using Mg(2+) as a cofactor. Efforts to study how 4-OD catalyzes this decarboxylation have been hampered because 4-OD is present in a complex with vinylpyruvate hydratase (VPH), which is the next enzyme in the same pathway. For the first time, a monomeric, stable, and active 4-OD has been expressed and purified in the absence of VPH. Crystal structures for NahK in the apo form and bonded with five substrate analogues were obtained using two distinct crystallization conditions. Analysis of the crystal structures implicates a lid domain in substrate binding and suggests roles for specific residues in a proposed reaction mechanism. In addition, we assign a possible function for the NahK N-terminal domain, which differs from most of the other members of the fumarylacetoacetate hydrolase superfamily. Although the structural basis for metal-dependent β-keto acid decarboxylases has been reported, this is the first structural report for that of a vinylogous β-keto acid decarboxylase and the first crystal structure of a 4-OD.

Synthesis, Structural and Antioxidant Studies of Some Novel N-Ethyl Phthalimide Esters

PubMed Central

Chandraju, Siddegowda; Win, Yip-Foo; Tan, Weng Kang; Quah, Ching Kheng; Fun, Hoong-Kun

2015-01-01

A series of N-ethyl phthalimide esters 4(a-n) were synthesized and characterized by spectroscopic studies. Further, the molecular structure of majority of compounds were analysed by single crystal X-ray diffraction studies. The X-ray analysis revealed the importance of substituents on the crystal stability and molecular packing. All the synthesized compounds were tested for in vitro antioxidant activity by DPPH radical scavenging, FRAP and CUPRAC methods. Few of them have shown good antioxidant activity. PMID:25742494

Synthesis, structural and antioxidant studies of some novel N-ethyl phthalimide esters.

PubMed

Chidan Kumar, C S; Loh, Wan-Sin; Chandraju, Siddegowda; Win, Yip-Foo; Tan, Weng Kang; Quah, Ching Kheng; Fun, Hoong-Kun

2015-01-01

A series of N-ethyl phthalimide esters 4(a-n) were synthesized and characterized by spectroscopic studies. Further, the molecular structure of majority of compounds were analysed by single crystal X-ray diffraction studies. The X-ray analysis revealed the importance of substituents on the crystal stability and molecular packing. All the synthesized compounds were tested for in vitro antioxidant activity by DPPH radical scavenging, FRAP and CUPRAC methods. Few of them have shown good antioxidant activity.

Synthesis, structural, optical and thermal properties of N-methyl-N-aryl benzamide organic single crystals grown by a slow evaporation technique

NASA Astrophysics Data System (ADS)

Prabukanthan, P.; Lakshmi, R.; Harichandran, G.; Kumar, C. Sudarsana

2018-03-01

The organic materials, N-methyl-N-aryl benzamides were synthesized from benzoylation of N-methyl-4-nitrobenzenamine (MNBA) using suitably substituted benzoyl chlorides. The products were purified by recrystallization and their single crystal were grown by a slow evaporation technique. The crystals were characterized by FTIR, UV-Vis-NIR, 1H &13C NMR, and single & powder X-ray diffraction. Thermal stability of the crystals was studied by thermogravimetric analysis (TGA) and differential scanning calorimetry (DSC). Dielectric and NLO properties of MNPB, FMNPB and MMNPB crystals were studied. The second harmonic generation (SHG) has been confirmed by the Kurtz powder test for all these crystals and the SHG efficiency of MMNPB crystal was found to be 2.25 times higher than that of KDP crystal.

Study of crystallization mechanisms of Fe nanoparticle

NASA Astrophysics Data System (ADS)

Kien, P. H.; Trang, G. T. T.; Hung, P. K.

2017-06-01

In this paper, the nanoparticle (NP) Fe was investigated by means of molecular dynamics simulation. The crystallization mechanism was studied through the time evolution of crystal cluster and potential energies of different atom types. The simulation shows that the NP was crystallized into bcc crystal structure when it was annealed at 900 K for long times. At early stage of the annealing, small nuclei form in different places of NP and dissolve for short times. After long times some nuclei form and gather nearby which create the stable clusters in the core of NP. After that the crystal clusters grow in the direction to cover the core and then to spread into the surface of NP. Analyzing the energies of different type atoms, we found that the crystal growth is originated from specific atomic arrangement in the boundary region of crystal clusters.

Serial snapshot crystallography for materials science with SwissFEL

DOE PAGES

Dejoie, Catherine; Smeets, Stef; Baerlocher, Christian; ...

2015-04-21

New opportunities for studying (sub)microcrystalline materials with small unit cells, both organic and inorganic, will open up when the X-ray free electron laser (XFEL) presently being constructed in Switzerland (SwissFEL) comes online in 2017. Our synchrotron-based experiments mimicking the 4%-energy-bandpass mode of the SwissFEL beam show that it will be possible to record a diffraction pattern of up to 10 randomly oriented crystals in a single snapshot, to index the resulting reflections, and to extract their intensities reliably. The crystals are destroyed with each XFEL pulse, but by combining snapshots from several sets of crystals, a complete set of datamore » can be assembled, and crystal structures of materials that are difficult to analyze otherwise will become accessible. Even with a single shot, at least a partial analysis of the crystal structure will be possible, and with 10–50 femtosecond pulses, this offers tantalizing possibilities for time-resolved studies.« less

Synthesis, growth, structure and nonlinear optical properties of a semiorganic 2-carboxy pyridinium dihydrogen phosphate single crystal

NASA Astrophysics Data System (ADS)

Nagapandiselvi, P.; Baby, C.; Gopalakrishnan, R.

2015-09-01

A new semiorganic compound namely, 2-carboxy pyridinium dihydrogen phosphate (2CPDP) was synthesised and grown as single crystals by slow evaporation solution growth technique. Single crystal XRD showed that 2CPDP belongs to monoclinic crystal system with space group P21/n. The molecular structure was further confirmed by modern spectroscopic techniques like FT-NMR (1H, 13C &31P), FT-IR, UV-Vis-NIR and Fluorescence. The UV-Vis-NIR analysis revealed suitability of the crystal for nonlinear optical applications. The photo active nature of the material is established from fluorescence studies. TG-DSC analysis showed that 2CPDP was thermally stable up to 170 °C. The dependence of dielectric properties on frequency and temperature were also studied. Nonlinear optical absorption determined from open aperture Z-Scan analysis by employing picosecond Nd-YAG laser, revealed that 2CPDP can serve as a promising candidate for optical limiting applications.

Synthesis, characterization and biological activities of semicarbazones and their copper complexes.

PubMed

Venkatachalam, Taracad K; Bernhardt, Paul V; Noble, Chris J; Fletcher, Nicholas; Pierens, Gregory K; Thurecht, Kris J; Reutens, David C

2016-09-01

Substituted semicarbazones/thiosemicarbazones and their copper complexes have been prepared and several single crystal structures examined. The copper complexes of these semicarbazone/thiosemicarbazones were prepared and several crystal structures examined. The single crystal X-ray structure of the pyridyl-substituted semicarbazone showed two types of copper complexes, a monomer and a dimer. We also found that the p-nitrophenyl semicarbazone formed a conventional 'magic lantern' acetate-bridged dimer. Electron Paramagnetic Resonance (EPR) of several of the copper complexes was consistent with the results of single crystal X-ray crystallography. The EPR spectra of the p-nitrophenyl semicarbazone copper complex in dimethylsulfoxide (DMSO) showed the presence of two species, confirming the structural information. Since thiosemicarbazones and semicarbazones have been reported to exhibit anticancer activity, we examined the anticancer activity of several of the derivatives reported in the present study and interestingly only the thiosemicarbazone showed activity while the semicarbazones were not active indicating that introduction of sulphur atom alters the biological profile of these thiosemicarbazones. Copyright © 2016 Elsevier Inc. All rights reserved.

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.

Cytotoxicity of copper(II)-complexes with some S-alkyl derivatives of thiosalicylic acid. Crystal structure of the binuclear copper(II)-complex with S-ethyl derivative of thiosalicylic acid

NASA Astrophysics Data System (ADS)

Nikolić, Miloš V.; Mijajlović, Marina Ž.; Jevtić, Verica V.; Ratković, Zoran R.; Novaković, Slađana B.; Bogdanović, Goran A.; Milovanović, Jelena; Arsenijević, Aleksandar; Stojanović, Bojana; Trifunović, Srećko R.; Radić, Gordana P.

2016-07-01

The spectroscopically predicted structure of the obtained copper(II)-complex with S-ethyl derivative of thiosalicylic acid was confirmed by X-ray structural study and compared to previously reported crystal structure of the Cu complex with S-methyl derivative. Single crystals suitable for X-ray measurements were obtained by slow crystallization from a water solution. Cytotoxic effects of S-alkyl (R = benzyl (L1), methyl (L2), ethyl (L3), propyl (L4) and butyl (L5)) derivatives of thiosalicylic acid and the corresponding binuclear copper(II)-complexes on murine colon carcinoma cell lines, CT26 and CT26.CL25 and human colon carcinoma cell line HCT-116 were reported here. The analysis of cancer cell viability showed that all the tested complexes had low cytotoxic effect on murine colon carcinoma cell lines, but several times higher cytotoxicity on normal human colon carcinoma cells.

Structural studies of the nudix hydrolase DR1025 from deinococcus radiodurans and its ligand complexes

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

Ranatunga, Wasantha; Hill, Emma E.; Mooster, Jana L.

We have determined the crystal structure, at 1.4, of the Nudix hydrolase DR1025 from the extremely radiation resistant bacterium Deinococcus radiodurans. The protein forms an intertwined homodimer by exchanging N-terminal segments between chains. We have identified additional conserved elements of the Nudix fold, including the metal-binding motif, a kinked b-strand characterized by a proline two positions upstream of the Nudix consensus sequence, and participation of the N-terminal extension in the formation of the substrate-binding pocket. Crystal structures were also solved of DR1025 crystallized in the presence of magnesium and either a GTP analog or Ap4A (both at 1.6 resolution). Inmore » the Ap4Aco-crystal, the electron density indicated that the product of asymmetric hydrolysis, ATP, was bound to the enzyme. The GTP analog bound structure showed that GTP was bound almost identically as ATP. Neither nucleoside triphosphate was further cleaved.« less

Crystal structures and theoretical studies of polyphosphate LiZnP3O9 for nonlinear optical applications

NASA Astrophysics Data System (ADS)

Xie, Zhiqing; Su, Xin; Ding, Hanqin; Li, Hongyi

2018-06-01

Nonlinear optical materials have attracted worldwide attention owing to their wide range of applications, specially in the laser field. Phosphates with noncentrosymmetric structures are potential candidates for novel ultraviolet (UV)-NLO materials, because they usually display short UV cut-off edges. In this work, a polyphosphate, the LiZnP3O9 polyphosphate crystals were grown through spontaneous crystallization from high-temperature melts. It crystallizes in the orthorhombic space group P212121 with unit cell parameters a = 8.330(3) Å, b = 8.520(3) Å, c = 8.635(3) Å, and Z = 4. In the structure, all the P atoms are coordinated by four oxygen atoms forming the [PO4] tetrahedra and further connected to generate a zig-zag [PO3]∞ anionic framework. Thermal analysis, IR spectroscopy, UV-vis-NIR diffuse reflectance spectrum and powder second harmonic generation measurements are performed. In addition, the first-principles calculation was employed for better understanding the structure-property relationships of LiZnP3O9.

Influence of encapsulated functional lipids on crystal structure and chemical stability in solid lipid nanoparticles: Towards bioactive-based design of delivery systems.

PubMed

Salminen, Hanna; Gömmel, Christina; Leuenberger, Bruno H; Weiss, Jochen

2016-01-01

We investigated the influence of physicochemical properties of encapsulated functional lipids--vitamin A, β-carotene and ω-3 fish oil--on the structural arrangement of solid lipid nanoparticles (SLN). The relationship between the crystal structure and chemical stability of the incorporated bioactive lipids was evaluated with different emulsifier compositions of a saponin-rich, food-grade Quillaja extract alone or combined with high-melting or low-melting lecithins. The major factors influencing the structural arrangement and chemical stability of functional lipids in solid lipid dispersions were their solubility in the aqueous phase and their crystallization temperature in relation to that of the carrier lipid. The results showed that the stabilization of the α-subcell crystals in the lattice of the carrier lipid is a key parameter for forming stable solid lipid dispersions. This study contributes to a better understanding of SLN as a function of the bioactive lipid. Copyright © 2015 Elsevier Ltd. All rights reserved.

Electron microscopy and positron annihilation study of CdSe nanoclusters embedded in MgO

NASA Astrophysics Data System (ADS)

van Huis, M. A.; van Veen, A.; Schut, H.; Eijt, S. W. H.; Kooi, B. J.; De Hosson, J. Th. M.

2004-06-01

CdSe nanoclusters are created in MgO by means of co-implantation of 280 keV, 1 × 10 16 Cd ions cm -2 and 210 keV, 1 × 10 16 Se ions cm -2 in single crystals of MgO(0 0 1) and subsequent thermal annealing at a temperature of 1300 K. The structural properties and the orientation relationship between the CdSe and the MgO are investigated using cross-sectional transmission electron microscopy (XTEM). The crystal structure of the nanoclusters depends on their size. The smallest nanoclusters with a size below 5 nm have the cubic rocksalt crystal structure. The larger nanoclusters have a different (most likely the cubic sphalerite) crystal structure. The defect evolution in the sample after ion implantation and during thermal annealing is investigated using Doppler broadening positron beam analysis (PBA). The defect evolution in samples co-implanted with Cd and Se is compared to the defect evolution in samples implanted with only Cd or only Se ions.

Swinging Symmetry, Multiple Structural Phase Transitions, and Versatile Physical Properties in RECuGa3 (RE = La-Nd, Sm-Gd).

PubMed

Subbarao, Udumula; Rayaprol, Sudhindra; Dally, Rebecca; Graf, Michael J; Peter, Sebastian C

2016-01-19

The compounds RECuGa3 (RE = La-Nd, Sm-Gd) were synthesized by various techniques. Preliminary X-ray diffraction (XRD) analyses at room temperature suggested that the compounds crystallize in the tetragonal system with either the centrosymmetric space group I4/mmm (BaAl4 type) or the non-centrosymmetric space group I4mm (BaNiSn3 type). Detailed single-crystal XRD, neutron diffraction, and synchrotron XRD studies of selected compounds confirmed the non-centrosymmetric BaNiSn3 structure type at room temperature with space group I4mm. Temperature-dependent single-crystal XRD, powder XRD, and synchrotron beamline measurements showed a structural transition between centro- and non-centrosymmetry followed by a phase transition to the Rb5Hg19 type (space group I4/m) above 400 K and another transition to the Cu3Au structure type (space group Pm3̅m) above 700 K. Combined single-crystal and synchrotron powder XRD studies of PrCuGa3 at high temperatures revealed structural transitions at higher temperatures, highlighting the closeness of the BaNiSn3 structure to other structure types not known to the RECuGa3 family. The crystal structure of RECuGa3 is composed of eight capped hexagonal prism cages [RE4Cu4Ga12] occupying one rare-earth atom in each ring, which are shared through the edge of Cu and Ga atoms along the ab plane, resulting in a three-dimensional network. Resistivity and magnetization measurements demonstrated that all of these compounds undergo magnetic ordering at temperatures between 1.8 and 80 K, apart from the Pr and La compounds: the former remains paramagnetic down to 0.3 K, while superconductivity was observed in the La compound at T = 1 K. It is not clear whether this is intrinsic or due to filamentary Ga present in the sample. The divalent nature of Eu in EuCuGa3 was confirmed by magnetization measurements and X-ray absorption near edge spectroscopy and is further supported by the crystal structure analysis.

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

Sparse and incomplete factorial matrices to screen membrane protein 2D crystallization

PubMed Central

Lasala, R.; Coudray, N.; Abdine, A.; Zhang, Z.; Lopez-Redondo, M.; Kirshenbaum, R.; Alexopoulos, J.; Zolnai, Z.; Stokes, D.L.; Ubarretxena-Belandia, I.

2014-01-01

Electron crystallography is well suited for studying the structure of membrane proteins in their native lipid bilayer environment. This technique relies on electron cryomicroscopy of two-dimensional (2D) crystals, grown generally by reconstitution of purified membrane proteins into proteoliposomes under conditions favoring the formation of well-ordered lattices. Growing these crystals presents one of the major hurdles in the application of this technique. To identify conditions favoring crystallization a wide range of factors that can lead to a vast matrix of possible reagent combinations must be screened. However, in 2D crystallization these factors have traditionally been surveyed in a relatively limited fashion. To address this problem we carried out a detailed analysis of published 2D crystallization conditions for 12 β-barrel and 138 α-helical membrane proteins. From this analysis we identified the most successful conditions and applied them in the design of new sparse and incomplete factorial matrices to screen membrane protein 2D crystallization. Using these matrices we have run 19 crystallization screens for 16 different membrane proteins totaling over 1,300 individual crystallization conditions. Six membrane proteins have yielded diffracting 2D crystals suitable for structure determination, indicating that these new matrices show promise to accelerate the success rate of membrane protein 2D crystallization. PMID:25478971

Crystal structures, in-silico study and anti-microbial potential of synthetic monocarbonyl curcuminoids

NASA Astrophysics Data System (ADS)

Ud Din, Zia; Serrano, N. F. G.; Ademi, Kastriot; Sousa, C. P.; Deflon, Victor Marcelo; Maia, Pedro Ivo da Silva; Rodrigues-Filho, Edson

2017-09-01

In this work the screening of 20 unsymmetrical chalcone and curcuminoids analogues in regard of their antimicrobial properties was conducted. Electron donating groups in the aromatic rings in the chalcone and curcuminoid derivatives produced higher antimicrobial effect. Compounds 1, 9 and 15 exhibited good activity against Escherichia coli and Staphylococcus aureus. These compounds were further evaluated against nine micro-organisms of pathological interest. Pharmmaper was used for target fishing of compounds against important bacterial targets. Molecular Docking helped to verify the results of these compounds against the selected bacterial target D-alanyl-D-alanine carboxypeptidase (PDB ID: 1PW1). The crystal structure of ligand and docked conformers in the active site of 1PW1 were analyzed. As a result structure-activity relationships are proposed. Structures of compounds 14 and 16 were obtained through single crystals X-ray diffraction studies. Compound 14 crystallizes in monoclinic space group P21/c with unit cell dimensions a = 13.1293(3) Å, b = 17.5364(4) Å, c = 15.1433(3) Å, β = 95.6440(10), V = 3469.70(13) Å3 and Z = 8. Compound 16 crystallizes in triclinic space group Pī with unit cell dimensions a = 6.8226(4) Å, b = 7.2256(4) Å, c = 18.1235(12) Å, β = 87.322(4), V = 850.57(9) Å3 and Z = 2.

Femtosecond X-ray protein nanocrystallography

PubMed Central

Chapman, Henry N.; Fromme, Petra; Barty, Anton; White, Thomas A.; Kirian, Richard A.; Aquila, Andrew; Hunter, Mark S.; Schulz, Joachim; DePonte, Daniel P.; Weierstall, Uwe; Doak, R. Bruce; Maia, Filipe R. N. C.; Martin, Andrew V.; Schlichting, Ilme; Lomb, Lukas; Coppola, Nicola; Shoeman, Robert L.; Epp, Sascha W.; Hartmann, Robert; Rolles, Daniel; Rudenko, Artem; Foucar, Lutz; Kimmel, Nils; Weidenspointner, Georg; Holl, Peter; Liang, Mengning; Barthelmess, Miriam; Caleman, Carl; Boutet, Sébastien; Bogan, Michael J.; Krzywinski, Jacek; Bostedt, Christoph; Bajt, Saša; Gumprecht, Lars; Rudek, Benedikt; Erk, Benjamin; Schmidt, Carlo; Hömke, André; Reich, Christian; Pietschner, Daniel; Strüder, Lothar; Hauser, Günter; Gorke, Hubert; Ullrich, Joachim; Herrmann, Sven; Schaller, Gerhard; Schopper, Florian; Soltau, Heike; Kühnel, Kai-Uwe; Messerschmidt, Marc; Bozek, John D.; Hau-Riege, Stefan P.; Frank, Matthias; Hampton, Christina Y.; Sierra, Raymond G.; Starodub, Dmitri; Williams, Garth J.; Hajdu, Janos; Timneanu, Nicusor; Seibert, M. Marvin; Andreasson, Jakob; Rocker, Andrea; Jönsson, Olof; Svenda, Martin; Stern, Stephan; Nass, Karol; Andritschke, Robert; Schröter, Claus-Dieter; Krasniqi, Faton; Bott, Mario; Schmidt, Kevin E.; Wang, Xiaoyu; Grotjohann, Ingo; Holton, James M.; Barends, Thomas R. M.; Neutze, Richard; Marchesini, Stefano; Fromme, Raimund; Schorb, Sebastian; Rupp, Daniela; Adolph, Marcus; Gorkhover, Tais; Andersson, Inger; Hirsemann, Helmut; Potdevin, Guillaume; Graafsma, Heinz; Nilsson, Björn; Spence, John C. H.

2012-01-01

X-ray crystallography provides the vast majority of macromolecular structures, but the success of the method relies on growing crystals of sufficient size. In conventional measurements, the necessary increase in X-ray dose to record data from crystals that are too small leads to extensive damage before a diffraction signal can be recorded1-3. It is particularly challenging to obtain large, well-diffracting crystals of membrane proteins, for which fewer than 300 unique structures have been determined despite their importance in all living cells. Here we present a method for structure determination where single-crystal X-ray diffraction ‘snapshots’ are collected from a fully hydrated stream of nanocrystals using femtosecond pulses from a hard-X-ray free-electron laser, the Linac Coherent Light Source4. We prove this concept with nanocrystals of photosystem I, one of the largest membrane protein complexes5. More than 3,000,000 diffraction patterns were collected in this study, and a three-dimensional data set was assembled from individual photosystem I nanocrystals (~200 nm to 2 μm in size). We mitigate the problem of radiation damage in crystallography by using pulses briefer than the timescale of most damage processes6. This offers a new approach to structure determination of macromolecules that do not yield crystals of sufficient size for studies using conventional radiation sources or are particularly sensitive to radiation damage. PMID:21293373

Structure of organic solids at low temperature and high pressure.

PubMed

Lee, Rachael; Howard, Judith A K; Probert, Michael R; Steed, Jonathan W

2014-07-07

This tutorial review looks at structural and supramolecular chemistry of molecular solids under extreme conditions, and introduces the instrumentation and facilities that enable single crystal diffraction studies on molecular crystals at both high pressure and low temperature. The equipment used for crystallography under extreme conditions is explored, particularly pressure cells such as the diamond anvil cell, and their mechanism of action, as well as the cryogenic apparatus which allows materials to be cooled to significantly low temperatures. The review also covers recent advances in the structural chemistry of molecular solids under extreme conditions with an emphasis on the use of single crystal crystallography in high pressure and low temperature environments to probe polymorphism and supramolecular interactions.

Microscopic Optical Characterization of Free Standing III-Nitride Substrates, ZnO Bulk Crystals, and III-V Structures for Non-Linear Optics. Part 2

DTIC Science & Technology

2010-05-18

strong radiation hardness of ZnO. Positron annihilation studies have revealed the presence of Zn vacancies under high energy electron irradiation, as...SUPPLEMENTARY NOTES 14. ABSTRACT CL study of ammonothermal GaN crystals. Preliminary results on ammonothermal AlGaN crystals show a clear...prevalence of deep level luminescence Study of the luminescence spectral characteristics. Optimization of the excitonic emission vs deep level emission

Crystal structure of the kinase domain of human protein tyrosine kinase 6 (PTK6) at 2.33 Å resolution.

PubMed

Thakur, Manish Kumar; Kumar, Amit; Birudukota, Swarnakumari; Swaminathan, Srinivasan; Tyagi, Rajiv; Gosu, Ramachandraiah

2016-09-16

Human Protein tyrosine kinase 6 (PTK6) (EC:2.7.10.2), also known as the breast tumor kinase (BRK), is an intracellular non-receptor Src-related tyrosine kinase expressed in a majority of human breast tumors and breast cancer cell lines, but its expression is low or completely absent in normal mammary glands. In the recent past, several studies have suggested that PTK6 is a potential therapeutic target in cancer. To understand its structural and functional properties, the PTK6 kinase domain (PTK6-KD) gene was cloned, overexpressed in a baculo-insect cell system, purified and crystallized at room temperature. X-ray diffraction data to 2.33 Å resolution was collected on a single PTK6-KD crystal, which belonged to the triclinic space group P1. The Matthews coefficient calculation suggested the presence of four protein molecules per asymmetric unit, with a solvent content of ∼50%.The structure has been solved by molecular replacement and crystal structure data submitted to the protein data bank under the accession number 5D7V. This is the first report of apo PTK6-KD structure crystallized in DFG-in and αC-helix-out conformation. Copyright © 2016 Elsevier Inc. All rights reserved.

The effect of sulfated polysaccharides on the crystallization of calcite superstructures

NASA Astrophysics Data System (ADS)

Fried, Ruth; Mastai, Yitzhak

2012-01-01

Calcite with unique morphology and uniform size has been successfully synthesized in the presence of classes of polysaccharides based on carrageenans. In the crystallization of calcite, the choice of different carrageenans, (iota, lambda and kappa), as additives concedes systematic study of the influence of different chemical structures and particularly molecular charge on the formation of CaCO 3 crystals. The uniform calcite superstructures are formed by assemblies and aggregation of calcite crystals. The mechanism for the formation of calcite superstructures was studied by a variety of techniques, SEM, TEM, XRD, time-resolved conductivity and light scattering measurements, focusing on the early stages of crystals' nucleation and aggregation.

Periodic order and defects in Ni-based inverse opal-like crystals on the mesoscopic and atomic scale

NASA Astrophysics Data System (ADS)

Chumakova, A. V.; Valkovskiy, G. A.; Mistonov, A. A.; Dyadkin, V. A.; Grigoryeva, N. A.; Sapoletova, N. A.; Napolskii, K. S.; Eliseev, A. A.; Petukhov, A. V.; Grigoriev, S. V.

2014-10-01

The structure of inverse opal crystals based on nickel was probed on the mesoscopic and atomic levels by a set of complementary techniques such as scanning electron microscopy and synchrotron microradian and wide-angle diffraction. The microradian diffraction revealed the mesoscopic-scale face-centered-cubic (fcc) ordering of spherical voids in the inverse opal-like structure with unit cell dimension of 750±10nm. The diffuse scattering data were used to map defects in the fcc structure as a function of the number of layers in the Ni inverse opal-like structure. The average lateral size of mesoscopic domains is found to be independent of the number of layers. 3D reconstruction of the reciprocal space for the inverse opal crystals with different thickness provided an indirect study of original opal templates in a depth-resolved way. The microstructure and thermal response of the framework of the porous inverse opal crystal was examined using wide-angle powder x-ray diffraction. This artificial porous structure is built from nickel crystallites possessing stacking faults and dislocations peculiar for the nickel thin films.

Spirocyclic character of ixazomib citrate revealed by comprehensive XRD, NMR and DFT study

NASA Astrophysics Data System (ADS)

Skorepova, Eliska; Čerňa, Igor; Vlasáková, Růžena; Zvoníček, Vít; Tkadlecová, Marcela; Dušek, Michal

2017-11-01

Ixazomib citrate is a very recently approved anti-cancer drug. Until now, to the best of our knowledge, no one has been able to solve any crystal structures of this compound. In this work, we present the crystal structures of two isostructural solvates of ixazomib citrate. In all currently available literature, the molecule is characterized as containing a single optically active carbon atom and a borate cycle formed when ixazomib is reacted with citric acid to form a stabilized ixazomib citrate that can be administered orally. However, the crystal structures revealed that none of the up-to-date presented structural formulas of ixazomib citrate are fully accurate. In addition to the citrate ring, another 5-membered ring is formed. These two rings are connected by the boron atom, making this compound a spirocyclic borate. By spirocyclization, the boron atom becomes tetrahedral and therefore optically active. In the crystal structures, ixazomib citrate was found to be in forms of two RR and RS stereoisomers. The results are supported by solid-state and solution NMR and DFT quantum mechanical calculations.

Study of rare earth local moment magnetism and strongly correlated phenomena in various crystal structures

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

Kong, Tai

Benefiting from unique properties of 4f electrons, rare earth based compounds are known for offering a versatile playground for condensed matter physics research as well as industrial applications. This thesis focuses on three specific examples that further explore the rare earth local moment magnetism and strongly correlated phenomena in various crystal structures.

Synthesis, structural, optical and thermal studies of an organic nonlinear optical 4-aminopyridinium maleate single crystal.

PubMed

Pandi, P; Peramaiyan, G; Kumar, M Krishna; Kumar, R Mohan; Jayavel, R

2012-03-01

Synthesis and growth of a novel organic nonlinear optical (NLO) crystal of 4-aminopyridinium maleate (4APM) in larger size by the slow evaporation solution growth technique are reported. Single crystal and powder X-ray diffraction analyses reveal that 4APM crystallizes in monoclinic system with space group P2(1) with cell parameters a=8.140(4)Å, b=5.457(5)Å, c=10.926(10)Å and volume=481.4(7)Å(3). The grown crystal has been characterized by Fourier transform infrared and UV-visible spectral analyses. Thermogravimetric analysis (TGA) and differential thermal analysis (DTA) have been carried out to study its thermal properties. Dielectric measurements have been carried out to study the distribution of charges within the crystal. The mechanical strength of the crystal has been studied by using Vickers' microhardness test. The etching studies have been carried out on the grown crystal. The Kurtz and Perry powder SHG technique confirms the NLO property of the grown crystal and the SHG efficiency of 4APM was found to be 4.8 times greater than that of KDP crystal. Copyright © 2011 Elsevier B.V. All rights reserved.

Optical, structural, thermal and dielectric spectroscopy characterizations of seeded melt grown 2-hydroxy biphenyl single crystal.

PubMed

Sadhasivam, S; Rajesh, Narayana Perumal

2014-09-15

Organic single crystal of 2-hydroxy biphenyl (2-HB) was grown by top seeded melt growth method. Scanning electron microscopy studies has been carried out on the surface of the grown crystals to investigate the nature of growth and defects. The crystalline perfection and lattice parameters of 2-HB has been determined by single crystal XRD analysis and it belongs to orthorhombic crystal system with space group Fdd2. The functional groups and molecular associations were confirmed by FT-IR. The optical characteristics such as cut-off and transmittance were carried out using UV-Vis-NIR spectra. Absence of absorption in the region between 320 and 1100 nm makes the grown crystal desirable to optical applications. Thermal stability of grown crystals was characterized by thermogravimetric (TGA), differential thermal analysis (DTA) and differential scanning calorimetric (DSC) analyses. Broadband dielectric studies reveals that dielectric constant of grown crystal is low. The resistivity of grown crystal was studied by impedance analysis. The second harmonic generation intensity of 3.8 mJ was studied. The grown crystal belongs to soft material studied by hardness test. Copyright © 2014 Elsevier B.V. All rights reserved.

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

Doping effect in layer structured SrBi2Nb2O9 ferroelectrics

NASA Astrophysics Data System (ADS)

Wu, Yun; Forbess, Mike J.; Seraji, Seana; Limmer, Steven J.; Chou, Tammy P.; Nguyen, Carolyn; Cao, Guozhong

2001-11-01

This article reports a systematic study of doping effects on the crystal structure, microstructure, dielectric, and electrical properties of layer-structured strontium bismuth niobate, SrBi2Nb2O9 (SBN), ferroelectrics. Substitution in both the A site (Sr2+ by Ca2+ and Ba2+) and B site (Nb5+ by V5+) up to 30 at % were studied. It was found that crystal lattice constant, dielectric, and electrical properties of SBN ferroelectrics varied appreciably with the type and amount of dopants. The relationships among the ionic radii, structural constraint imposed by [Bi2O2]2+ interlayers, and properties were discussed.

Simulation and Experimental Studies on Grain Selection and Structure Design of the Spiral Selector for Casting Single Crystal Ni-Based Superalloy.

PubMed

Zhang, Hang; Xu, Qingyan

2017-10-27

Grain selection is an important process in single crystal turbine blades manufacturing. Selector structure is a control factor of grain selection, as well as directional solidification (DS). In this study, the grain selection and structure design of the spiral selector were investigated through experimentation and simulation. A heat transfer model and a 3D microstructure growth model were established based on the Cellular automaton-Finite difference (CA-FD) method for the grain selector. Consequently, the temperature field, the microstructure and the grain orientation distribution were simulated and further verified. The average error of the temperature result was less than 1.5%. The grain selection mechanisms were further analyzed and validated through simulations. The structural design specifications of the selector were suggested based on the two grain selection effects. The structural parameters of the spiral selector, namely, the spiral tunnel diameter ( d w ), the spiral pitch ( h b ) and the spiral diameter ( h s ), were studied and the design criteria of these parameters were proposed. The experimental and simulation results demonstrated that the improved selector could accurately and efficiently produce a single crystal structure.

Simulation and Experimental Studies on Grain Selection and Structure Design of the Spiral Selector for Casting Single Crystal Ni-Based Superalloy

PubMed Central

Zhang, Hang; Xu, Qingyan

2017-01-01

Grain selection is an important process in single crystal turbine blades manufacturing. Selector structure is a control factor of grain selection, as well as directional solidification (DS). In this study, the grain selection and structure design of the spiral selector were investigated through experimentation and simulation. A heat transfer model and a 3D microstructure growth model were established based on the Cellular automaton-Finite difference (CA-FD) method for the grain selector. Consequently, the temperature field, the microstructure and the grain orientation distribution were simulated and further verified. The average error of the temperature result was less than 1.5%. The grain selection mechanisms were further analyzed and validated through simulations. The structural design specifications of the selector were suggested based on the two grain selection effects. The structural parameters of the spiral selector, namely, the spiral tunnel diameter (dw), the spiral pitch (hb) and the spiral diameter (hs), were studied and the design criteria of these parameters were proposed. The experimental and simulation results demonstrated that the improved selector could accurately and efficiently produce a single crystal structure. PMID:29077067

Structural analysis of β-glucosidase mutants derived from a hyperthermophilic tetrameric structure

PubMed Central

Nakabayashi, Makoto; Kataoka, Misumi; Mishima, Yumiko; Maeno, Yuka; Ishikawa, Kazuhiko

2014-01-01

β-Glucosidase from Pyrococcus furiosus (BGLPf) is a hyperthermophilic tetrameric enzyme which can degrade cellooligosaccharides to glucose under hyperthermophilic conditions and thus holds promise for the saccharification of lignocellulosic biomass at high temperature. Prior to the production of large amounts of this enzyme, detailed information regarding the oligomeric structure of the enzyme is required. Several crystals of BGLPf have been prepared over the past ten years, but its crystal structure had not been solved until recently. In 2011, the first crystal structure of BGLPf was solved and a model was constructed at somewhat low resolution (2.35 Å). In order to obtain more detailed structural data on BGLPf, the relationship between its tetrameric structure and the quality of the crystal was re-examined. A dimeric form of BGLPf was constructed and its crystal structure was solved at a resolution of 1.70 Å using protein-engineering methods. Furthermore, using the high-resolution crystal structural data for the dimeric form, a monomeric form of BGLPf was constructed which retained the intrinsic activity of the tetrameric form. The thermostability of BGLPf is affected by its oligomeric structure. Here, the biophysical and biochemical properties of engineered dimeric and monomeric BGLPfs are reported, which are promising prototype models to apply to the saccharification reaction. Furthermore, details regarding the oligomeric structures of BGLPf and the reasons why the mutations yielded improved crystal structures are discussed. PMID:24598756

Powder XRD and dielectric studies of gel grown calcium pyrophosphate crystals

NASA Astrophysics Data System (ADS)

Parekh, Bharat; Parikh, Ketan; Joshi, Mihir

2013-06-01

Formation of calcium pyrophosphate dihydrate (CPPD) crystals in soft tissues such as cartilage, meniscus and synovial tissue leads to CPPD deposition diseases. The appearance of these crystals in the synovial fluid can give rise to an acute arthritic attack with pain and inflammation of the joints, a condition called pseudo-gout. The growth of CPP crystals has been carried out, in the present study, using the single diffusion gel growth technique, which can broadly mimic in vitro the condition in soft tissues. The crystals were characterized by different techniques. The FTIR study revealed the presence of various functional groups. Powder XRD study was also carried out to verify the crystal structure. The dielectric study was carried out at room temperature by applying field of different frequency from 500 Hz to 1 MHz. The dielectric constant, dielectric loss and a.c. resistivity decreased as frequency increased, whereas the a.c. conductivity increased as frequency increased.

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

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

Crystallization and preliminary X-ray diffraction study of phosphopantetheine adenylyltransferase from M. tuberculosis crystallizing in space group P3{sub 2}

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

Timofeev, V. I., E-mail: tostars@mail.ru; Chupova, L. A.; Esipov, R. S.

Crystals of M. tuberculosis phosphopantetheine adenylyltransferase were grown in microgravity by the capillary counter-diffusion method through a gel layer. The X-ray diffraction data set suitable for the determination of the three-dimensional structure at atomic resolution was collected from one crystal at the Spring-8 synchrotron facility to 2.00-Å resolution. The crystals belong to sp. gr. P3{sub 2} and have the following unit-cell parameters: a = b = 106.47 Å, c = 71.32 Å, α = γ = 90°, β = 120°. The structure was solved by the molecular-replacement method. There are six subunits of the enzyme comprising a hexamer per asymmetricmore » unit. The hexamer is a biologically active form of phosphopantetheine adenylyltransferase from M. tuberculosis.« less

Comment on the paper "Synthesis, growth, structural, spectral, thermal, chemical etching, linear and nonlinear optical and mechanical studies of an organic single crystal 4-chloro 4-nitrostilbene (CONS): a potential NLO material" by P.M. Dinakaran, S. Kalainathan [Spectrochim. Acta A 111 (2013) 123-130].

PubMed

Srinivasan, Bikshandarkoil R; Dhuri, Sunder N; Nadkarni, V S

2014-01-03

We argue that (trans)-4-chloro-4'-nitrostilbene is not a new organic nonlinear optical material as claimed by Dinakaran and Kalainathan [P.M. Dinakaran, S. Kalainathan, Synthesis, growth, structural, spectral, thermal, chemical etching, linear and nonlinear optical and mechanical studies of an organic single crystal 4-Chloro 4-Nitrostilbene (CONS): a potential NLO material, Spectrochim. Acta A 111 (2013) 123-130], but instead a well-known compound whose synthesis, spectral data, single crystal structure and second harmonic generation (SHG) efficiency are well documented in the literature. The title paper is completely erroneous. Copyright © 2013 Elsevier B.V. All rights reserved.

Structure of new Hg0.75V0.25Ba2CuO4+δ superconducting single crystals.Effect of overdoping on the magnetization second peak

NASA Astrophysics Data System (ADS)

Villard, G.; Pelloquin, D.; Maignan, A.

1998-10-01

Superconducting crystals (Tc=88 K) of the `1201' mercury cuprate have been grown by using vanadium as stabilizer of the (HgOδ) mercury layer. Its shortened c-axis parameter, c=9.345 Å, is linked to the substitution of small VO4 tetrahedra for HgO2 stick deduced from the structural study. The regular layer stacking is confirmed by high resolution microscopy, and cationic analysis coupled to an electron microscope leads to the average formula Hg0.75V0.25Ba2CuO4+δ for these overdoped crystals in good agreement with the structural refinements. One of the major result of the structural part is the mobility of oxygens located at the [BaO]∞ layer level. The superconducting properties of crystals with typical 800×500×10 μm3 dimensions have been investigated by magnetic measurements. Well-marked fishtail features are exhibited on their M(H) curves. The corresponding second peak line differs from that of optimized 1201 crystals demonstrating the important consequences on the superconducting properties of the vanadium for mercury substitution.

Control of Partial Coalescence of Self-Assembled Metal Nano-Particles across Lyotropic Liquid Crystals Templates towards Long Range Meso-Porous Metal Frameworks Design

PubMed Central

Dumée, Ludovic F.; Lemoine, Jean-Baptiste; Ancel, Alice; Hameed, Nishar; He, Li; Kong, Lingxue

2015-01-01

The formation of purely metallic meso-porous metal thin films by partial interface coalescence of self-assembled metal nano-particles across aqueous solutions of Pluronics triblock lyotropic liquid crystals is demonstrated for the first time. Small angle X-ray scattering was used to study the influence of the thin film composition and processing conditions on the ordered structures. The structural characteristics of the meso-structures formed demonstrated to primarily rely on the lyotropic liquid crystal properties while the nature of the metal nano-particles used as well as the their diameters were found to affect the ordered structure formation. The impact of the annealing temperature on the nano-particle coalescence and efficiency at removing the templating lyotropic liquid crystals was also analysed. It is demonstrated that the lyotropic liquid crystal is rendered slightly less thermally stable, upon mixing with metal nano-particles and that low annealing temperatures are sufficient to form purely metallic frameworks with average pore size distributions smaller than 500 nm and porosity around 45% with potential application in sensing, catalysis, nanoscale heat exchange, and molecular separation. PMID:28347094

Synthesis, crystal structure, Hirshfeld surfaces analysis and anti-ischemic activity of cinnamide derivatives

NASA Astrophysics Data System (ADS)

Zhong, Jian-gang; Han, Jia-pei; Li, Xiao-feng; Xu, Yi; Zhong, Yan; Wu, Bin

2018-02-01

Two cinnamide derivatives, namely, (E)-1-(4-(bis(4-methylphenyl)- methyl)piperazin-1-yl)-3-(3,4-diethoxyphenyl)prop-2-en-1-one (5) and (E)-1-(4-(bis- (4-fluorophenyl)methyl)piperazin-1-yl)-3-(4-methoxyphenyl)prop-2-en-1-one (6), have been synthesized and characterized by IR spectra, High resolution mass spectra, 1H NMR spectra, 13C NMR spectra. The compound 5 is a novel compound and has never been reported in the literature. Their crystal structures were studied by single-crystal X-ray diffraction. They all crystallize in the monoclinic system. The single-crystal X-ray revealed that compound 5 has infinite X-shaped 1-D polymeric chains structure and compound 6 has a layered 3-D structure by intermolecular interactions. Hirshfeld surface analysis demonstrated the presence of H⋯H, O⋯H, C⋯H, F⋯H, Csbnd H⋯π and π⋯π intermolecular interactions. In addition, the MTT assay results indicated that the compounds 5 and 6 display effective activities against neurotoxicity which is induced by glutamine in PC12 cells. The in vivo experiment indicated that the compound 6 has a good protective effect on cerebral infarction.

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.

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

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.

Theoretical and experimental studies of hyperreflective polymer-network cholesteric liquid crystal structures with helicity inversion

NASA Astrophysics Data System (ADS)

Tasolamprou, A. C.; Mitov, M.; Zografopoulos, D. C.; Kriezis, E. E.

2009-03-01

Single-layer cholesteric liquid crystals exhibit a reflection coefficient which is at most 50% for unpolarized incident light. We give theoretical and experimental evidence of single-layer polymer-stabilized cholesteric liquid-crystalline structures that demonstrate hyper-reflective properties. Such original features are derived by the concurrent and randomly interlaced presence of both helicities. The fundamental properties of such structures are revealed by detailed numerical simulations based on a stochastic approach.

A Comparison of Cocrystal Structure Solutions from Powder and Single Crystal Techniques

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

S Lapidus; P Stephens; K Arora

We demonstrate the effectiveness and accuracy of high resolution powder diffraction for determination of cocrystal structures through a double-blind study. Structures of 10 cocrystals of varying complexity were determined independently using single crystal and powder techniques. The two methodologies give identical molecular packing and hydrogen bond topology, and an rms difference in covalent bond lengths of 0.035 {angstrom}. Powder techniques are clearly sufficient to establish a complete characterization of cocrystal geometry.

What does the Sr-substituted 2.1 Å resolution crystal structure of photosystem II reveal about the water oxidation mechanism?

PubMed

Terrett, Richard; Petrie, Simon; Pace, Ron J; Stranger, Robert

2014-03-25

A density functional study of the Sr-substituted photosystem II water oxidising complex demonstrates that its recent X-ray crystal structure is consistent with a (Mn(III))4 oxidation state pattern, and with a Sr-bound hydroxide ion. The Sr-water-hydroxide interactions rationalize differences in the exchange rates of substrate water and kinetics of dioxygen bond formation relative to the Ca-containing structure.

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

Bowley, S.; Okumura, N; Lord, S

'A:a' knob-hole interactions and D:D interfacial interactions are important for fibrin polymerization. Previous studies with recombinant ?N308K fibrinogen, a substitution at the D:D interface, showed impaired polymerization. We examined the molecular basis for this loss of function by solving the crystal structure of ?N308K fragment D. In contrast to previous fragment D crystals, the ?N308K crystals belonged to a tetragonal space group with an unusually long unit cell (a = b = 95 Angstroms, c = 448.3 Angstroms). Alignment of the normal and ?N308K structures showed the global structure of the variant was not changed and the knob 'A' peptidemore » GPRP was bound as usual to hole 'a'. The substitution introduced an elongated positively charged patch in the D:D region. The structure showed novel, symmetric D:D crystal contacts between ?N308K molecules, indicating the normal asymmetric D:D interface in fibrin would be unstable in this variant. We examined GPRP binding to ?N308K in solution by plasmin protection assay. The results showed weaker peptide binding, suggesting that 'A:a' interactions were altered. We examined fibrin network structures by scanning electron microscopy and found the variant fibers were thicker and more heterogeneous than normal fibers. Considered together, our structural and biochemical studies indicate both 'A:a' and D:D interactions are weaker. We conclude that stable protofibrils cannot assemble from ?N308K monomers, leading to impaired polymerization.« less

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

Purification, crystallization and preliminary X-ray diffraction studies of parakeet (Psittacula krameri) haemoglobin

PubMed Central

Jaimohan, S. M.; Naresh, M. D.; Arumugam, V.; Mandal, A. B.

2009-01-01

Birds often show efficient oxygen management in order to meet the special demands of their metabolism. However, the structural studies of avian haemo­globins (Hbs) are inadequate for complete understanding of the mechanism involved. Towards this end, purification, crystallization and preliminary X-ray diffraction studies have been carried out for parakeet Hb. Parakeet Hb was crystallized as the met form in low-salt buffered conditions after extracting haemoglobin from crude blood by microcentrifugation and purifying the sample by column chromatography. Good-quality crystals were grown from 10% PEG 3350 and a crystal diffracted to about 2.8 Å resolution. Preliminary diffraction data showed that the Hb crystal belonged to the monoclinic system (space group C2), with unit-cell parameters a = 110.68, b = 64.27, c = 56.40 Å, β = 109.35°. Matthews volume analysis indicated that the crystals contained a half-tetramer in the asymmetric unit. PMID:19851014

Purification, crystallization and preliminary X-ray diffraction studies of parakeet (Psittacula krameri) haemoglobin.

PubMed

Jaimohan, S M; Naresh, M D; Arumugam, V; Mandal, A B

2009-10-01

Birds often show efficient oxygen management in order to meet the special demands of their metabolism. However, the structural studies of avian haemoglobins (Hbs) are inadequate for complete understanding of the mechanism involved. Towards this end, purification, crystallization and preliminary X-ray diffraction studies have been carried out for parakeet Hb. Parakeet Hb was crystallized as the met form in low-salt buffered conditions after extracting haemoglobin from crude blood by microcentrifugation and purifying the sample by column chromatography. Good-quality crystals were grown from 10% PEG 3350 and a crystal diffracted to about 2.8 A resolution. Preliminary diffraction data showed that the Hb crystal belonged to the monoclinic system (space group C2), with unit-cell parameters a = 110.68, b = 64.27, c = 56.40 A, beta = 109.35 degrees . Matthews volume analysis indicated that the crystals contained a half-tetramer in the asymmetric unit.

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.

X-ray diffraction studies of enkephalins. Crystal structure of [(4'-bromo) Phe4,Leu5]enkephalin.

PubMed Central

Ishida, T; Kenmotsu, M; Mino, Y; Inoue, M; Fujiwara, T; Tomita, K; Kimura, T; Sakakibara, S

1984-01-01

In order to investigate the structure-activity relationship of [Leu5]- and [Met5]enkephalins, [(4'-bromo)Phe4, Leu5]-, [(4'-bromo)Phe4, Met5]- and [Met5] enkephalins were synthesized and crystallized. The crystal structure of [(4'-bromo) Phe4, Leu5]- enkephalin was determined by X-ray diffraction method using the heavy atom method and refined to R = 0.092 by the least-squares method. The molecule in this crystal took essentially the same type I' beta-turn conformation found in [Leu5]enkephalin [Smith & Griffin (1978) Science 199, 1214-1216). On the other hand, the preliminary three-dimensional Patterson analyses showed that the most probable conformations of [(4'-bromo)Phe4,Met5]- and [Met5]enkephalins are both the dimeric extended forms. Based on these insights, the biologically active conformation of enkephalin was discussed in relation to the mu- and delta-receptors. PMID:6721829

Unique Chiral Interpenetrating d-f Heterometallic MOFs as Luminescent Sensors.

PubMed

Wu, Zhi-Lei; Dong, Jie; Ni, Wei-Yan; Zhang, Bo-Wen; Cui, Jian-Zhong; Zhao, Bin

2015-06-01

One novel three-dimensional (3D) 3d-4f metal-organic framework (MOF), [TbZn(L)(CO3)2(H2O)]n (1) [HL = 4'-(4-carboxyphenyl)-2,2':6',2″-terpyridine], has been successfully synthesized and structurally characterized. Structural analysis shows that compound 1 features a unique chiral interpenetrating 3D framework for the first time. The resulting crystals of 1 are composed of enantiomers 1a (P41) and 1b (P43), as was clearly confirmed by the crystal structure and the corresponding circular dichroism (CD) analyses of eight randomly selected crystals. The investigations on CD spectra based on every single crystal clearly assigned the Cotton effect signals. The powder X-ray diffraction measurement of 1 after being immersed in common solvents reveals that 1 possess excellent solvent stability. Furthermore, luminescent studies imply that 1 displays highly selective luminescent sensing of aldehydes, such as formol, acetaldehyde, and propanal.

Synthesis, crystal structures, spectral, thermal and antimicrobial properties of new Zn(II) 5-iodo- and 5-bromosalicylates

NASA Astrophysics Data System (ADS)

Košická, Petra; Győryová, Katarína; Smolko, Lukáš; Gyepes, Róbert; Hudecová, Daniela

2018-03-01

Two new analogous zinc(II) complexes containing 5-iodo- and 5-bromosalicylate ligands, respectively, were prepared in single-crystal form and characterized by IR spectroscopy, thermal analysis and elemental analysis. The solid-state structures of prepared complexes were determined by single crystal X-ray crystallography. Both complexes are isostructural and their crystal structures composed of neutral molecules [Zn(5-Xsal)2(H2O)2] (where X = Br, I, sal = salicylato). Central Zn(II) atom is in both complexes coordinated by six oxygen atoms, four of which are from two chelate bonded 5-halosalicylates and remaining two from coordinated water molecules. The found chelate binding mode is in line with the Δ values calculated from IR spectral data. Antimicrobial activity of prepared complexes was studied against selected bacteria, yeast and filamentous fungi. Obtained results indicate that 5-iodosalicylate complex is more antimicrobially active than its 5-bromo substituted analogue.

Crystal growth, perfection, linear and nonlinear optical, photoconductivity, dielectric, thermal and laser damage threshold properties of 4-methylimidazolium picrate: an interesting organic crystal for photonic and optoelectronic devices

NASA Astrophysics Data System (ADS)

Rajesh, K.; Arun, A.; Mani, A.; Praveen Kumar, P.

2016-10-01

The 4-methylimidazolium picrate has been synthesized and characterized successfully. Single and powder x-ray diffraction studies were conducted which confirmed the crystal structure, and the value of the strain was calculated. The crystal perfection was determined by a HRXR diffractometer. The transmission spectrum exhibited a better transmittance of the crystal in the entire visible region with a lower cut-off wavelength of 209 nm. The linear absorption value was calculated by the optical limiting method. A birefringence study was also carried out. Second and third order nonlinear optical properties of the crystal were found by second harmonic generation and the z-scan technique. The crystals were also characterized by dielectric measurement and a photoconductivity analyzer to determine the dielectric property and the optical conductivity of the crystal. The laser damage threshold activity of the grown crystal was studied by a Q-switched Nd:YAG laser beam. Thermal studies established that the compound did not undergo a phase transition and was stable up to 240 °C.

X-ray laser diffraction for structure determination of the rhodopsin-arrestin complex

NASA Astrophysics Data System (ADS)

Zhou, X. Edward; Gao, Xiang; Barty, Anton; Kang, Yanyong; He, Yuanzheng; Liu, Wei; Ishchenko, Andrii; White, Thomas A.; Yefanov, Oleksandr; Han, Gye Won; Xu, Qingping; de Waal, Parker W.; Suino-Powell, Kelly M.; Boutet, Sébastien; Williams, Garth J.; Wang, Meitian; Li, Dianfan; Caffrey, Martin; Chapman, Henry N.; Spence, John C. H.; Fromme, Petra; Weierstall, Uwe; Stevens, Raymond C.; Cherezov, Vadim; Melcher, Karsten; Xu, H. Eric

2016-04-01

Serial femtosecond X-ray crystallography (SFX) using an X-ray free electron laser (XFEL) is a recent advancement in structural biology for solving crystal structures of challenging membrane proteins, including G-protein coupled receptors (GPCRs), which often only produce microcrystals. An XFEL delivers highly intense X-ray pulses of femtosecond duration short enough to enable the collection of single diffraction images before significant radiation damage to crystals sets in. Here we report the deposition of the XFEL data and provide further details on crystallization, XFEL data collection and analysis, structure determination, and the validation of the structural model. The rhodopsin-arrestin crystal structure solved with SFX represents the first near-atomic resolution structure of a GPCR-arrestin complex, provides structural insights into understanding of arrestin-mediated GPCR signaling, and demonstrates the great potential of this SFX-XFEL technology for accelerating crystal structure determination of challenging proteins and protein complexes.

X-ray laser diffraction for structure determination of the rhodopsin-arrestin complex.

PubMed

Zhou, X Edward; Gao, Xiang; Barty, Anton; Kang, Yanyong; He, Yuanzheng; Liu, Wei; Ishchenko, Andrii; White, Thomas A; Yefanov, Oleksandr; Han, Gye Won; Xu, Qingping; de Waal, Parker W; Suino-Powell, Kelly M; Boutet, Sébastien; Williams, Garth J; Wang, Meitian; Li, Dianfan; Caffrey, Martin; Chapman, Henry N; Spence, John C H; Fromme, Petra; Weierstall, Uwe; Stevens, Raymond C; Cherezov, Vadim; Melcher, Karsten; Xu, H Eric

2016-04-12

Serial femtosecond X-ray crystallography (SFX) using an X-ray free electron laser (XFEL) is a recent advancement in structural biology for solving crystal structures of challenging membrane proteins, including G-protein coupled receptors (GPCRs), which often only produce microcrystals. An XFEL delivers highly intense X-ray pulses of femtosecond duration short enough to enable the collection of single diffraction images before significant radiation damage to crystals sets in. Here we report the deposition of the XFEL data and provide further details on crystallization, XFEL data collection and analysis, structure determination, and the validation of the structural model. The rhodopsin-arrestin crystal structure solved with SFX represents the first near-atomic resolution structure of a GPCR-arrestin complex, provides structural insights into understanding of arrestin-mediated GPCR signaling, and demonstrates the great potential of this SFX-XFEL technology for accelerating crystal structure determination of challenging proteins and protein complexes.

X-ray laser diffraction for structure determination of the rhodopsin-arrestin complex

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

Zhou, X. Edward; Gao, Xiang; Barty, Anton

Here, serial femtosecond X-ray crystallography (SFX) using an X-ray free electron laser (XFEL) is a recent advancement in structural biology for solving crystal structures of challenging membrane proteins, including G-protein coupled receptors (GPCRs), which often only produce microcrystals. An XFEL delivers highly intense X-ray pulses of femtosecond duration short enough to enable the collection of single diffraction images before significant radiation damage to crystals sets in. Here we report the deposition of the XFEL data and provide further details on crystallization, XFEL data collection and analysis, structure determination, and the validation of the structural model. The rhodopsin-arrestin crystal structure solvedmore » with SFX represents the first near-atomic resolution structure of a GPCR-arrestin complex, provides structural insights into understanding of arrestin-mediated GPCR signaling, and demonstrates the great potential of this SFX-XFEL technology for accelerating crystal structure determination of challenging proteins and protein complexes.« less

X-ray laser diffraction for structure determination of the rhodopsin-arrestin complex

PubMed Central

Zhou, X. Edward; Gao, Xiang; Barty, Anton; Kang, Yanyong; He, Yuanzheng; Liu, Wei; Ishchenko, Andrii; White, Thomas A.; Yefanov, Oleksandr; Han, Gye Won; Xu, Qingping; de Waal, Parker W.; Suino-Powell, Kelly M.; Boutet, Sébastien; Williams, Garth J.; Wang, Meitian; Li, Dianfan; Caffrey, Martin; Chapman, Henry N.; Spence, John C.H.; Fromme, Petra; Weierstall, Uwe; Stevens, Raymond C.; Cherezov, Vadim; Melcher, Karsten; Xu, H. Eric

2016-01-01

Serial femtosecond X-ray crystallography (SFX) using an X-ray free electron laser (XFEL) is a recent advancement in structural biology for solving crystal structures of challenging membrane proteins, including G-protein coupled receptors (GPCRs), which often only produce microcrystals. An XFEL delivers highly intense X-ray pulses of femtosecond duration short enough to enable the collection of single diffraction images before significant radiation damage to crystals sets in. Here we report the deposition of the XFEL data and provide further details on crystallization, XFEL data collection and analysis, structure determination, and the validation of the structural model. The rhodopsin-arrestin crystal structure solved with SFX represents the first near-atomic resolution structure of a GPCR-arrestin complex, provides structural insights into understanding of arrestin-mediated GPCR signaling, and demonstrates the great potential of this SFX-XFEL technology for accelerating crystal structure determination of challenging proteins and protein complexes. PMID:27070998

X-ray laser diffraction for structure determination of the rhodopsin-arrestin complex

DOE PAGES

Zhou, X. Edward; Gao, Xiang; Barty, Anton; ...

2016-04-12

Here, serial femtosecond X-ray crystallography (SFX) using an X-ray free electron laser (XFEL) is a recent advancement in structural biology for solving crystal structures of challenging membrane proteins, including G-protein coupled receptors (GPCRs), which often only produce microcrystals. An XFEL delivers highly intense X-ray pulses of femtosecond duration short enough to enable the collection of single diffraction images before significant radiation damage to crystals sets in. Here we report the deposition of the XFEL data and provide further details on crystallization, XFEL data collection and analysis, structure determination, and the validation of the structural model. The rhodopsin-arrestin crystal structure solvedmore » with SFX represents the first near-atomic resolution structure of a GPCR-arrestin complex, provides structural insights into understanding of arrestin-mediated GPCR signaling, and demonstrates the great potential of this SFX-XFEL technology for accelerating crystal structure determination of challenging proteins and protein complexes.« less

Statistical Analysis of Crystallization Database Links Protein Physico-Chemical Features with Crystallization Mechanisms

PubMed Central

Fusco, Diana; Barnum, Timothy J.; Bruno, Andrew E.; Luft, Joseph R.; Snell, Edward H.; Mukherjee, Sayan; Charbonneau, Patrick

2014-01-01

X-ray crystallography is the predominant method for obtaining atomic-scale information about biological macromolecules. Despite the success of the technique, obtaining well diffracting crystals still critically limits going from protein to structure. In practice, the crystallization process proceeds through knowledge-informed empiricism. Better physico-chemical understanding remains elusive because of the large number of variables involved, hence little guidance is available to systematically identify solution conditions that promote crystallization. To help determine relationships between macromolecular properties and their crystallization propensity, we have trained statistical models on samples for 182 proteins supplied by the Northeast Structural Genomics consortium. Gaussian processes, which capture trends beyond the reach of linear statistical models, distinguish between two main physico-chemical mechanisms driving crystallization. One is characterized by low levels of side chain entropy and has been extensively reported in the literature. The other identifies specific electrostatic interactions not previously described in the crystallization context. Because evidence for two distinct mechanisms can be gleaned both from crystal contacts and from solution conditions leading to successful crystallization, the model offers future avenues for optimizing crystallization screens based on partial structural information. The availability of crystallization data coupled with structural outcomes analyzed through state-of-the-art statistical models may thus guide macromolecular crystallization toward a more rational basis. PMID:24988076

Statistical analysis of crystallization database links protein physico-chemical features with crystallization mechanisms.

PubMed

Fusco, Diana; Barnum, Timothy J; Bruno, Andrew E; Luft, Joseph R; Snell, Edward H; Mukherjee, Sayan; Charbonneau, Patrick

2014-01-01

X-ray crystallography is the predominant method for obtaining atomic-scale information about biological macromolecules. Despite the success of the technique, obtaining well diffracting crystals still critically limits going from protein to structure. In practice, the crystallization process proceeds through knowledge-informed empiricism. Better physico-chemical understanding remains elusive because of the large number of variables involved, hence little guidance is available to systematically identify solution conditions that promote crystallization. To help determine relationships between macromolecular properties and their crystallization propensity, we have trained statistical models on samples for 182 proteins supplied by the Northeast Structural Genomics consortium. Gaussian processes, which capture trends beyond the reach of linear statistical models, distinguish between two main physico-chemical mechanisms driving crystallization. One is characterized by low levels of side chain entropy and has been extensively reported in the literature. The other identifies specific electrostatic interactions not previously described in the crystallization context. Because evidence for two distinct mechanisms can be gleaned both from crystal contacts and from solution conditions leading to successful crystallization, the model offers future avenues for optimizing crystallization screens based on partial structural information. The availability of crystallization data coupled with structural outcomes analyzed through state-of-the-art statistical models may thus guide macromolecular crystallization toward a more rational basis.

Eukaryotic major facilitator superfamily transporter modeling based on the prokaryotic GlpT crystal structure.

PubMed

Lemieux, M Joanne

2007-01-01

The major facilitator superfamily (MFS) of transporters represents the largest family of secondary active transporters and has a diverse range of substrates. With structural information for four MFS transporters, we can see a strong structural commonality suggesting, as predicted, a common architecture for MFS transporters. The rate for crystal structure determination of MFS transporters is slow, making modeling of both prokaryotic and eukaryotic transporters more enticing. In this review, models of eukaryotic transporters Glut1, G6PT, OCT1, OCT2 and Pho84, based on the crystal structures of the prokaryotic GlpT, based on the crystal structure of LacY are discussed. The techniques used to generate the different models are compared. In addition, the validity of these models and the strategy of using prokaryotic crystal structures to model eukaryotic proteins are discussed. For comparison, E. coli GlpT was modeled based on the E. coli LacY structure and compared to the crystal structure of GlpT demonstrating that experimental evidence is essential for accurate modeling of membrane proteins.

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.

Crystal Engineering; How molecules build solids

NASA Astrophysics Data System (ADS)

Williams, Jeffrey H.

2017-09-01

There are more than 20 million chemicals in the literature, with new materials being synthesized each week. Most of these molecules are stable, and the 3-dimensional arrangement of the atoms in the molecules, in the various solids may be determined by routine x-ray crystallography. When this is done, it is found that this vast range of molecules, with varying sizes and shapes can be accommodated by only a handful of solid structures. This limited number of architectures for the packing of molecules of all shapes and sizes, to maximize attractive intermolecular forces and minimizing repulsive intermolecular forces, allows us to develop simple models of what holds the molecules together in the solid. In this volume we look at the origin of the molecular architecture of crystals; a topic that is becoming increasingly important and is often termed, crystal engineering. Such studies are a means of predicting crystal structures, and of designing crystals with particular properties by manipulating the structure and interaction of large molecules. That is, creating new crystal architectures with desired physical characteristics in which the molecules pack together in particular architectures; a subject of particular interest to the pharmaceutical industry.