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.

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

NASA Technical Reports Server (NTRS)

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

1991-01-01

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

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.

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 growth of HVPE-GaN doped with germanium

NASA Astrophysics Data System (ADS)

Iwinska, M.; Takekawa, N.; Ivanov, V. Yu.; Amilusik, M.; Kruszewski, P.; Piotrzkowski, R.; Litwin-Staszewska, E.; Lucznik, B.; Fijalkowski, M.; Sochacki, T.; Teisseyre, H.; Murakami, H.; Bockowski, M.

2017-12-01

Crystallization by hydride vapor phase epitaxy method of gallium nitride single crystals doped with germanium and properties of the obtained material are described in this paper. Growth was performed in hydrogen and nitrogen carrier gas. The results were studied and compared. Influence of different flows of germanium tetrachloride, precursor of germanium, on the grown crystals was investigated. Ammonothermal GaN substrates were used as seeds for crystallization. Structural, electrical, and optical properties of HVPE-GaN doped with germanium are presented and discussed in detail. They were compared to properties of HVPE-GaN doped with silicon and also grown on native seeds of high quality.

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.

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.

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.

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.

Synthesis, pharmacology, crystal properties, and quantitative solvation studies from a drug transport perspective for three new 1,2,4-thiadiazoles.

PubMed

Perlovich, German L; Volkova, Tatyana V; Proshin, Alexey N; Sergeev, Dmitriy Yu; Bui, Cong Trinh; Petrova, Ludmila N; Bachurin, Sergey O

2010-09-01

A novel 1,2,4-thiadiazoles were synthesized. Crystal structures of these compounds were solved by X-ray diffraction experiments and comparative analysis of molecular conformational states, packing architecture, and hydrogen bonds networks were carried out. Thermodynamic aspects of sublimation processes of studied compounds were determined using temperature dependencies of vapor pressure. Thermophysical characteristics of the molecular crystals were obtained and compared with the sublimation and structural parameters. Solubility and solvation processes of 1,2,4-thiadiazoles in buffer, n-hexane and n-octanol were studied within the wide range of temperature intervals and thermodynamic functions were calculated. Specific and nonspecific interactions of molecules resolved in crystals and solvents were estimated and compared. Distribution processes of compounds in buffer/n-octanol and buffer/n-hexane systems (describing different types of membranes) were investigated. Analysis of transfer processes of studied molecules from the buffer to n-octanol/n-hexane phases was carried out by the diagram method with evaluation of the enthalpic and entropic terms. This approach allows us to design drug molecules with optimal passive transport properties. Calcium-blocking properties of the substances were evaluated.

Effects of hydrogen bond on the melting point of azole explosives

NASA Astrophysics Data System (ADS)

Wang, Jian-Hua; Shen, Chen; Liu, Yu-Cun; Luo, Jin; Duan, Yingjie

2018-07-01

Melting point is an important index to determine whether an explosive can be a melt cast carrier. In this study, the relationship among the molecular structure, crystal structure, and melting point of explosives was investigated by using nitroazole compounds. Hydrogen bonds influence crystal packing modes in chemically understandable ways. Hydrogen bonds also affect the changes in entropy and enthalpy in balancing melting process. Hence, different types of hydrogen bonds in explosive crystal structures were compared when the relationship between the molecular structure and the melting point of nitroazole explosives were analyzed. The effects of methyl and amino groups on intermolecular hydrogen bonds were also compared. Results revealed that the methyl and amino groups connected on the N(1) of the heterocyclic compound can reduce the melting point of azole explosive. This finding is possible because methyl and amino groups destroy the intermolecular hydrogen bond of the heterocyclic compound.

Impact of Lu/Gd ratio and activator concentration on structure and scintillation properties of LGSO:Ce crystals

NASA Astrophysics Data System (ADS)

Sidletskiy, O.; Bondar, V.; Grinyov, B.; Kurtsev, D.; Baumer, V.; Belikov, K.; Katrunov, K.; Starzhinsky, N.; Tarasenko, O.; Tarasov, V.; Zelenskaya, O.

2010-02-01

We have studied the dependence of structural and scintillation characteristics of Lu 2 xGd 2-2 xSiO 5:Ce (LGSO:Ce) crystals on cation composition. LGSO:Ce crystals at x=0-1 have been obtained by the Czochralski method. We report here a strong correlation between ionic radii of trivalent cations and their distribution between non-equivalent sites in lattice. By choosing the optimal Lu/Gd ratio and Ce concentration we were able to obtain the light output by˜70%, as compared to LSO:Ce crystals, and energy resolution ˜7 at% 662 KeV ( 137Cs); the afterglow level was decreased by 1-3 orders of magnitude as compared to LSO:Ce. We also discuss the possible mechanisms of control on scintillation characteristics of mixed orthosilicates.

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.

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.

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

Gaia: automated quality assessment of protein structure models.

PubMed

Kota, Pradeep; Ding, Feng; Ramachandran, Srinivas; Dokholyan, Nikolay V

2011-08-15

Increasing use of structural modeling for understanding structure-function relationships in proteins has led to the need to ensure that the protein models being used are of acceptable quality. Quality of a given protein structure can be assessed by comparing various intrinsic structural properties of the protein to those observed in high-resolution protein structures. In this study, we present tools to compare a given structure to high-resolution crystal structures. We assess packing by calculating the total void volume, the percentage of unsatisfied hydrogen bonds, the number of steric clashes and the scaling of the accessible surface area. We assess covalent geometry by determining bond lengths, angles, dihedrals and rotamers. The statistical parameters for the above measures, obtained from high-resolution crystal structures enable us to provide a quality-score that points to specific areas where a given protein structural model needs improvement. We provide these tools that appraise protein structures in the form of a web server Gaia (http://chiron.dokhlab.org). Gaia evaluates the packing and covalent geometry of a given protein structure and provides quantitative comparison of the given structure to high-resolution crystal structures. dokh@unc.edu Supplementary data are available at Bioinformatics online.

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.

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.

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.

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

Crystal structure of new AsS{sub 2} compound

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

Bolotina, N. B., E-mail: bolotina@ns.crys.ras.ru; Brazhkin, V. V.; Dyuzheva, T. I.

2013-01-15

AsS{sub 2} single crystals have been obtained for the first time from an As{sub 2}S{sub 3} melt at pressures above 6 GPa and temperatures above 800 K in the As{sub 2}S{sub 3} {yields} AsS + AsS{sub 2} reaction. The monoclinic structure of the new high-pressure phase is solved by X-ray diffraction analysis and compared to the structure of high-pressure AsS phase, which was studied previously.

Microgravity

NASA Image and Video Library

2000-05-05

This computer graphic depicts the relative complexity of crystallizing large proteins in order to study their structures through x-ray crystallography. Insulin is a vital protein whose structure has several subtle points that scientists are still trying to determine. Large molecules such as insuline are complex with structures that are comparatively difficult to understand. For comparison, a sugar molecule (which many people have grown as hard crystals in science glass) and a water molecule are shown. These images were produced with the Macmolecule program. Photo credit: NASA/Marshall Space Flight Center (MSFC)

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.

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).

Hydrogen-bond coordination in organic crystal structures: statistics, predictions and applications.

PubMed

Galek, Peter T A; Chisholm, James A; Pidcock, Elna; Wood, Peter A

2014-02-01

Statistical models to predict the number of hydrogen bonds that might be formed by any donor or acceptor atom in a crystal structure have been derived using organic structures in the Cambridge Structural Database. This hydrogen-bond coordination behaviour has been uniquely defined for more than 70 unique atom types, and has led to the development of a methodology to construct hypothetical hydrogen-bond arrangements. Comparing the constructed hydrogen-bond arrangements with known crystal structures shows promise in the assessment of structural stability, and some initial examples of industrially relevant polymorphs, co-crystals and hydrates are described.

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.

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

Physical aspects of dexibuprofen and racemic ibuprofen.

PubMed

Leising, G; Resel, R; Stelzer, F; Tasch, S; Lanziner, A; Hantich, G

1996-12-01

This article presents a comparative study of ibuprofen materials in their solid state. Ibuprofen crystallizes into two different structures for the S(+) enantiomer (dexibuprofen) and racemic ibuprofen. The crystal structure of ibuprofen, its optical absorption and photoluminescence, and the thermodynamic results (melting point and heat of fusion) are discussed. From these physicochemical properties, the authors conclude that dexibuprofen, which is the most active species pharmaceutically, and racemic ibuprofen are inherently different solid-state materials.

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.

Changes in the IR Spectra of Aqueous Solutions of Alkali Metal Chlorides during Crystallization

NASA Astrophysics Data System (ADS)

Koroleva, A. V.; Matveev, V. K.; Koroleva, L. A.; Pentin, Yu. A.

2018-02-01

The IR spectra of aqueous solutions of sodium chloride and rubidium chloride with the same concentration of 0.1 M upon freezing are studied in the middle IR region. The changes that occur in the absorption bands of the bending ν2, compound ν2 + νL, and stretching (ν1, 2ν2, and ν3) vibrations of water molecules with gradual crystallization of the solutions are studied. The obtained spectra of crystallized solutions are compared to the IR spectrum of ice Ih. Analysis allows conclusions about the structure of the investigated frozen crystallized solutions.

Survey of predictors of propensity for protein production and crystallization with application to predict resolution of crystal structures

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

Gao, Jianzhao; Wu, Zhonghua; Hu, Gang

Selection of proper targets for the X-ray crystallography will benefit biological research community immensely. Several computational models were proposed to predict propensity of successful protein production and diffraction quality crystallization from protein sequences. We reviewed a comprehensive collection of 22 such predictors that were developed in the last decade. We found that almost all of these models are easily accessible as webservers and/or standalone software and we demonstrated that some of them are widely used by the research community. We empirically evaluated and compared the predictive performance of seven representative methods. The analysis suggests that these methods produce quite accuratemore » propensities for the diffraction-quality crystallization. We also summarized results of the first study of the relation between these predictive propensities and the resolution of the crystallizable proteins. We found that the propensities predicted by several methods are significantly higher for proteins that have high resolution structures compared to those with the low resolution structures. Moreover, we tested a new meta-predictor, MetaXXC, which averages the propensities generated by the three most accurate predictors of the diffraction-quality crystallization. MetaXXC generates putative values of resolution that have modest levels of correlation with the experimental resolutions and it offers the lowest mean absolute error when compared to the seven considered methods. We conclude that protein sequences can be used to fairly accurately predict whether their corresponding protein structures can be solved using X-ray crystallography. Moreover, we also ascertain that sequences can be used to reasonably well predict the resolution of the resulting protein crystals.« less

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

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.

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

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

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

2013-09-01

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

Crystal Structure of Garnet-Related Li-Ion Conductor Li7–3xGaxLa3Zr2O12: Fast Li-Ion Conduction Caused by a Different Cubic Modification?

PubMed Central

2016-01-01

Li-oxide garnets such as Li7La3Zr2O12 (LLZO) are among the most promising candidates for solid-state electrolytes to be used in next-generation Li-ion batteries. The garnet-structured cubic modification of LLZO, showing space group Ia-3d, has to be stabilized with supervalent cations. LLZO stabilized with Ga3+ shows superior properties compared to LLZO stabilized with similar cations; however, the reason for this behavior is still unknown. In this study, a comprehensive structural characterization of Ga-stabilized LLZO is performed by means of single-crystal X-ray diffraction. Coarse-grained samples with crystal sizes of several hundred micrometers are obtained by solid-state reaction. Single-crystal X-ray diffraction results show that Li7–3xGaxLa3Zr2O12 with x > 0.07 crystallizes in the acentric cubic space group I-43d. This is the first definite record of this cubic modification for LLZO materials and might explain the superior electrochemical performance of Ga-stabilized LLZO compared to its Al-stabilized counterpart. The phase transition seems to be caused by the site preference of Ga3+. 7Li NMR spectroscopy indicates an additional Li-ion diffusion process for LLZO with space group I-43d compared to space group Ia-3d. Despite all efforts undertaken to reveal structure–property relationships for this class of materials, this study highlights the potential for new discoveries. PMID:27019548

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.

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.

Relative Sizes of Organic Molecules

NASA Technical Reports Server (NTRS)

2000-01-01

This computer graphic depicts the relative complexity of crystallizing large proteins in order to study their structures through x-ray crystallography. Insulin is a vital protein whose structure has several subtle points that scientists are still trying to determine. Large molecules such as insuline are complex with structures that are comparatively difficult to understand. For comparison, a sugar molecule (which many people have grown as hard crystals in science glass) and a water molecule are shown. These images were produced with the Macmolecule program. Photo credit: NASA/Marshall Space Flight Center (MSFC)

Correlating Single Crystal Structure, Nanomechanical, and Bulk Compaction Behavior of Febuxostat Polymorphs.

PubMed

Yadav, Jayprakash A; Khomane, Kailas S; Modi, Sameer R; Ugale, Bharat; Yadav, Ram Naresh; Nagaraja, C M; Kumar, Navin; Bansal, Arvind K

2017-03-06

Febuxostat exhibits unprecedented solid forms with a total of 40 polymorphs and pseudopolymorphs reported. Polymorphs differ in molecular arrangement and conformation, intermolecular interactions, and various physicochemical properties, including mechanical properties. Febuxostat Form Q (FXT Q) and Form H1 (FXT H1) were investigated for crystal structure, nanomechanical parameters, and bulk deformation behavior. FXT Q showed greater compressibility, densification, and plastic deformation as compared to FXT H1 at a given compaction pressure. Lower mechanical hardness of FXT Q (0.214 GPa) as compared to FXT H1 (0.310 GPa) was found to be consistent with greater compressibility and lower mean yield pressure (38 MPa) of FXT Q. Superior compaction behavior of FXT Q was attributed to the presence of active slip systems in crystals which offered greater plastic deformation. By virtue of greater compressibility and densification, FXT Q showed higher tabletability over FXT H1. Significant correlation was found with anticipation that the preferred orientation of molecular planes into a crystal lattice translated nanomechanical parameters to a bulk compaction process. Moreover, prediction of compactibility of materials based on true density or molecular packing should be carefully evaluated, as slip-planes may cause deviation in the structure-property relationship. This study supported how molecular level crystal structure confers a bridge between particle level nanomechanical parameters and bulk level deformation behavior.

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

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

a Study of the Synchrotron Laue Method for Quantitative Crystal Structure Analysis.

NASA Astrophysics Data System (ADS)

Gomez de Anderez, Dora M.

1990-01-01

Available from UMI in association with The British Library. Quantitative crystal structure analyses have been carried out on small molecule crystals using synchrotron radiation and the Laue method. A variety of single crystal structure determinations and associated refinements are used and compared with the monochromatic analyses. The new molecular structure of 7-amino-5-bromo -4-methyl-2-oxo-1,2,3,4-tetrahidro-1, 6 -naphthyridine-8-carbonitrile (C_{10 }H_9ON_4 Br.H_2O) has been determined, first using monochromatic Mo Kalpha radiation and a four-circle diffractometer, then using synchrotron Laue diffraction photography. The structure refinements showed a R-factor of 4.97 and 14.0% for the Mo Kalpha and Laue data respectively. The molecular structure of (S)-2-chloro-2-fluoro-N-((S)-1-phenylethyl) ethanamide, (C_{10}H _{11}ClFNO), has been determined using the same crystal throughout for X-ray monochromatic analyses (Mo Kalpha and Cu K alpha) followed by synchrotron Laue data collection. The Laue and monochromatic data compare favourably. The R -factors (on F) were 6.23, 6.45 and 8.19% for the Mo K alpha, Cu Kalpha and Laue data sets respectively. The molecular structure of 3-(5-hydroxy-3-methyl-1-phenylpyrazol-4-yl)-1,3-diphenyl -prop- 2-en-1-one, (C_{25 }H_{20}N _2O_2) has been determined using the synchrotron Laue method. The results compare very well with Mo Kalpha monochromatic data. The R-factors (on F) were 4.60 and 5.29% for Mo Kalpha and Laue analysis respectively. The Laue method is assessed in locating the 20 hydrogen atoms in this structure. The structure analysis of the benzil compound ((C_6H_5 O.CO_2)) is carried out using the synchrotron Laue method firstly at room temperature and secondly at low temperature -114 ^circC. The structure shows an R-factor (on F) of 13.06% and 6.85% for each data set respectively. The synchrotron Laue method was used to collect data for ergocalciferol (Vitamin D_2). The same crystal was also used to record oscillation data with the synchrotron radiation monochromatic beam. A new molecular structure of (Dinitrato-(N,N ^'-dimethylethylene-diamine)copper(II)) has been determined using Mo Kalpha radiation on a four circle diffractometer. The refinement resulted in an R-factor (on F) of 4.06%.

A Study of the Synchrotron Laue Method for Quantitative Crystal Structure Analysis

NASA Astrophysics Data System (ADS)

Gomez de Anderez, Dora M.

1990-01-01

Quantitative crystal structure analyses have been carried out on small molecule crystals using synchrotron radiation and the Laue method. A variety of single crystal structure determinations and associated refinements are used and compared with the monochromatic analyses. The new molecular structure of 7-amino-5-bromo -4-methyl-2-oxo-1,2,3,4 -tetrahidro-1,6 -naphthyridine-8-carbonitrile (C_{10 }H_9ON_4 BrcdotH_2O) has been determined, first using monochromatic Mo K alpha radiation and a four-circle diffractometer, then using synchrotron Laue diffraction photography. The structure refinements showed an R-factor of 4.97 and 14.0% for the Mo Kalpha and Laue data respectively. The molecular structure of (S)-2-chloro-2-fluoro-N-((S)-1-phenylethyl) ethanamide, (C_{10}H _{11}ClFNO), has been determined using the same crystal throughout for X-ray monochromatic analyses (Mo Kalpha and Cu K alpha) followed by synchrotron Laue data collection. The Laue and monochromatic data compare favourably. The R -factors (on F) were 6.23, 6.45 and 8.19% for the Mo K alpha, Cu Kalpha and Laue data sets respectively. The molecular structure of 3-(5-hydroxy-3-methyl-1-phenylpyrazol-4-yl)-1,3-diphenyl -prop-2-en-1-one, (C_{25}H _{20}N_2 O_2) has been determined using the synchrotron Laue method. The results compare very well with Mo Kalpha monochromatic data. The R-factors (on F) were 4.60 and 5.29% for Mo Kalpha and Laue analyses respectively. The Laue method is assessed in locating the 20 hydrogen atoms in this structure. The structure analyses of the benzil compound ((C_6H_5 OcdotCO_2)) is carried out using the synchrotron Laue method firstly at room temperature and secondly at low temperature. The structure shows an R-factor (on F) of 13.06% and 6.85% for each data set respectively. The synchrotron Laue method was used to collect data for ergocalciferol (Vitamin D_2). The same crystal was also used to record oscillation data with the synchrotron radiation monochromatic beam. A new molecular structure of (Dinitrato-(N,N ^'-dimethylethylene-diamine)copper(II)) has been determined using Mo Kalpha radiation on a four circle diffractometer. The refinement resulted in an R-factor (on F) of 4.06%.

Thermodynamic and structural aspects of novel 1,2,4-thiadiazoles in solid and biological mediums.

PubMed

Perlovich, German L; Proshin, Alexey N; Volkova, Tatyana V; Bui, Cong Trinh; Bachurin, Sergey O

2011-10-03

Novel 1,2,4-thiadiazoles were synthesized. Crystal structures of these compounds were solved by X-ray diffraction experiments, and comparative analysis of packing architecture and hydrogen bond networks was carried out. Thermodynamic aspects of sublimation processes of the compounds under study were analyzed using temperature dependencies of vapor pressure. Thermophysical characteristics of the molecular crystals were obtained and compared with the sublimation and structural parameters. The melting points correlate with sublimation Gibbs energies. Moreover, an increase of donor-acceptor interactions in crystal structures leads to growth of Gibbs energy values. Relationships between the melting points and the fragmental contributions to the packing energies were established: R(1)-R(4) fragmental interactions are responsible for the fusion processes of this class of compounds. Solubility and solvation processes of 1,2,4-thiadiazoles in buffer, n-hexane and n-octanol were studied within a wide range of temperature intervals, and their thermodynamic functions were calculated. Specific and nonspecific interactions of molecules resolved in crystals and solvents were estimated and compared. It was found that the melting points correlate with sublimation Gibbs energies. Distribution processes of compounds in buffer/n-octanol and buffer/n-hexane systems (describing different types of membranes) were investigated. Transfer processes of the studied molecules from the buffer to n-octanol/n-hexane phases were analyzed by the diagram method with evaluation of the enthalpic and entropic terms. This approach allowed us to design drug molecules with optimal passive transport properties. Calcium-blocking properties of the substances were evaluated. The trend between the ability to inhibit Glu-Ca uptake and the distribution coefficients in buffer/hexane system was observed.

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

PubMed Central

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

2017-01-01

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

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

PubMed

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

2017-01-01

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

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.

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.

Self-propagating high-temperature synthesis and luminescent properties of ytterbium doped rare earth (Y, Sc, Lu) oxides nanopowders

NASA Astrophysics Data System (ADS)

Permin, D. A.; Novikova, A. V.; Balabanov, S. S.; Gavrishchuk, E. M.; Kurashkin, S. V.; Savikin, A. P.

2018-04-01

This paper describes a comparative study of structural and luminescent properties of 5%Yb-doped yttrium, scandium, and lutetium oxides (Yb:RE2O3) powders and ceramics fabricated by self-propagating high-temperature synthesis. According to X-ray diffractometry and electron microscopy the chosen method ensures preparation of low-agglomerated cubic Ctype crystal structured powders at one step. No crucial differences in luminescence spectra were found the Yb:RE2O3 powders and ceramics. It was shown that the emission lifetimes of the Yb:RE2O3 powders are lowered by crystal structure defects, while its values for ceramics samples are compared to that of monocrystals and more influenced by rare earth impurities.

Computational research on lithium ion battery materials

NASA Astrophysics Data System (ADS)

Tang, Ping

Crystals of LiFePO4 and related materials have recently received a lot of attention due to their very promising use as cathodes in rechargeable lithium ion batteries. This thesis studied the electronic structures of FePO 4 and LiMPO4, where M=Mn, Fe, Co and Ni within the framework of density-functional theory. The first study compared the electronic structures of the LiMPO 4 and FePO4 materials in their electrochemically active olivine form, using the LAPW (linear augmented plane wave) method [1]. A comparison of results for various spin configurations suggested that the ferromagnetic configuration can serve as a useful approximation for studying general features of these systems. The partial densities of states for the LiMPO4 materials are remarkably similar to each other, showing the transition metal 3d states forming narrow bands above the O 2p band. By contrast, in absence of Li, the majority spin transition metal 3d states are well-hybridized with the O 2p band in FePO4. The second study compared the electronic structures of FePO4 in several crystal structures including an olivine, monoclinic, quartz-like, and CrVO4-like form [2,3]. For this work, in addition to the LAPW method, PAW (Projector Augmented Wave) [4], and PWscf (plane-wave pseudopotential) [5] methods were used. By carefully adjusting the computational parameters, very similar results were achieved for the three independent computational methods. Results for the relative stability of the four crystal structures are reported. In addition, partial densities of state analyses show qualitative information about the crystal field splittings and bond hybridizations and help rationalize the understanding of the electrochemical and stability properties of these materials.

Fermi surfaces of the pyrite-type cubic AuSb2 compared with split Fermi surfaces of the ullmannite-type cubic chiral NiSbS and PdBiSe

NASA Astrophysics Data System (ADS)

Nishimura, K.; Kakihana, M.; Nakamura, A.; Aoki, D.; Harima, H.; Hedo, M.; Nakama, T.; Ōnuki, Y.

2018-05-01

We grew high-quality single crystals of AuSb2 with the pyrite (FeS2)-type cubic structure by the Bridgman method and studied the Fermi surface properties by the de Haas-van Alphen (dHvA) experiment and the full potential LAPW band calculation. The Fermi surfaces of AuSb2 are found to be similar to those of NiSbS and PdBiSe with the ullmannite (NiSbS)-type cubic chiral structure because the crystal structures are similar each other and the number of valence electrons is the same between two different compounds. Note that each Fermi surface splits into two Fermi surfaces in NiSbS and PdBiSe, reflecting the non-centrosymmetric crystal structure.

A study of tantalum pentoxide Ta 2O 5 structures up to 28 GPa

DOE PAGES

Stavrou, Elissaios; Zaug, Joseph M.; Bastea, Sorin; ...

2017-05-02

In this study, tantalum pentoxide Ta 2O 5 with the orthorhombic L-Ta 2O 5 structure has been experimentally studied up to 28.3 GPa (at ambient temperature) using synchrotron angle-dispersive powder X-ray diffraction (XRD). The ambient pressure phase remains stable up to 25 GPa where with increased pressure a crystalline to amorphous phase transition occurs. A detailed equation of state (EOS), including pressure dependent lattice parameters, is reported. The results of this study were compared with a previous high-pressure XRD study by Li et al. A clear discrepancy between the ambient-pressure crystal structures and, consequently, the reported EOSs between the twomore » studies was revealed. Finally, he origin of this discrepancy is attributed to two different crystal structures used to index the XRD patterns.« less

Study of the bending vibration characteristic of phononic crystals beam-foundation structures by Timoshenko beam theory

NASA Astrophysics Data System (ADS)

Zhang, Yan; Ni, Zhi-Qiang; Jiang, Lin-Hua; Han, Lin; Kang, Xue-Wei

2015-07-01

Vibration problems wildly exist in beam-foundation structures. In this paper, finite periodic composites inspired by the concept of ideal phononic crystals (PCs), as well as Timoshenko beam theory (TBT), are proposed to the beam anchored on Winkler foundation. The bending vibration band structure of the PCs Timoshenko beam-foundation structure is derived from the modified transfer matrix method (MTMM) and Bloch's theorem. Then, the frequency response of the finite periodic composite Timoshenko beam-foundation structure by the finite element method (FEM) is performed to verify the above theoretical deduction. Study shows that the Timoshenko beam-foundation structure with periodic composites has wider attenuation zones compared with homogeneous ones. It is concluded that TBT is more available than Euler beam theory (EBT) in the study of the bending vibration characteristic of PCs beam-foundation structures with different length-to-height ratios.

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.

Numerical analysis of light extraction enhancement of GaN-based thin-film flip-chip light-emitting diodes with high-refractive-index buckling nanostructures

NASA Astrophysics Data System (ADS)

Yue, Qing-Yang; Yang, Yang; Cheng, Zhen-Jia; Guo, Cheng-Shan

2018-06-01

In this work, the light extraction efficiency enhancement of GaN-based thin-film flip-chip (TFFC) light-emitting diodes (LEDs) with high-refractive-index (TiO2) buckling nanostructures was studied using the three-dimensional finite difference time domain method. Compared with 2-D photonic crystals, the buckling structures have the advantages of a random directionality and a broad distribution in periodicity, which can effectively extract the guided light propagating in all azimuthal directions over a wide spectrum. Numerical studies revealed that the light extraction efficiency of buckling-structured LEDs reaches 1.1 times that of triangular lattice photonic crystals. The effects of the buckling structure feature sizes and the thickness of the N-GaN layer on the light extraction efficiency for TFFC LEDs were also investigated systematically. With optimized structural parameters, a significant light extraction enhancement of about 2.6 times was achieved for TiO2 buckling-structured TFFC LEDs compared with planar LEDs.

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.

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

PubMed

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

2017-07-27

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

The Structure of Cognitive Abilities in Youths with Manic Symptoms: A Factorial Invariance Study

ERIC Educational Resources Information Center

Beaujean, A. Alexander; Freeman, Megan Joseph; Youngstrom, Eric; Carlson, Gabrielle

2012-01-01

This study compared the structure of cognitive ability (specifically, verbal/crystallized ["Gc"] and visual-spatial ability ["Gv"]), as measured in the Wechsler Intelligence Scale for Children, in youth with manic symptoms with a nationally representative group of similarly aged youth. Multigroup confirmatory factor analysis…

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

DOE PAGES

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

2017-07-13

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

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

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

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

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

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

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

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

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

Stochastic generation of complex crystal structures combining group and graph theory with application to carbon

NASA Astrophysics Data System (ADS)

Shi, Xizhi; He, Chaoyu; Pickard, Chris J.; Tang, Chao; Zhong, Jianxin

2018-01-01

A method is introduced to stochastically generate crystal structures with defined structural characteristics. Reasonable quotient graphs for symmetric crystals are constructed using a random strategy combined with space group and graph theory. Our algorithm enables the search for large-size and complex crystal structures with a specified connectivity, such as threefold sp2 carbons, fourfold sp3 carbons, as well as mixed sp2-sp3 carbons. To demonstrate the method, we randomly construct initial structures adhering to space groups from 75 to 230 and a range of lattice constants, and we identify 281 new sp3 carbon crystals. First-principles optimization of these structures show that most of them are dynamically and mechanically stable and are energetically comparable to those previously proposed. Some of the new structures can be considered as candidates to explain the experimental cold compression of graphite.

Two rhodamine 6G derivative compounds: a structural and fluorescence single-crystal study.

PubMed

Di Paolo, Matias; Bossi, Mariano L; Baggio, Ricardo; Suarez, Sebastián A

2016-10-01

The synthesis, characterization, structural analysis and fluorescence properties of two rhodamine 6G derivatives are described, namely a propargylamine derivative, 3',6'-bis(ethylamino)-2',7'-dimethyl-2-(methylcyanide)spiro[isoindole-1,9'-xanthen]-3(2H)-one (I), and a γ-aminobutyric acid (GABA) derivative, 3',6'-bis(ethylamino)-2',7'-dimethyl-3-oxospiro[isoindole-1,9'-xanthen]-2(3H)-yl)butyricacid (II). Both structures are compared with four similar ones from the Cambridge Structural Database (CSD), and the interactions involved in the stabilization are analyzed using the atoms in molecules (AIM) theory. Finally, a single-crystal in-situ reaction study is presented, carried out by fluorescence methods, which enabled the `opening' of the spirolactam ring in the solid phase.

Theoretical and experimental studies on vibrational and nonlinear optic properties of guanidinium 3-nitrobenzoate. Differences and similarity between guanidinium 3-nitrobenzoate and guanidinium 4-nitrobenzoate complexes

NASA Astrophysics Data System (ADS)

Drozd, Marek

2018-03-01

According to literature data two structures of guanidine with nitrobenzoic acids are known. For guanidinium 4-nitrobenzoate the detailed studies of X-ray structure, vibrational and theoretical properties were performed. This compound was classified as second harmonic generator with efficiency of 3.3 times that KDP, standard crystal. On the contrary to mentioned above results for the guanidinium 3-nitrobenzoate the basic X-ray diffraction study was performed, only. On the basis of established crystallographic results, the detailed investigation of geometry and vibrational properties were made on the basis of theoretical calculation. According to this data the equilibrium geometry of investigated molecule was established. On the basis of this calculation the detailed computational studies of vibrational properties were performed. The theoretical IR and Raman frequencies, intensities and PED analysis are presented. Additionally, the NBO charges, HOMO and LUMO shapes and NLO properties of titled crystal were calculated. On the basis of these results the crystal was classified as second order generator in NLO but with bigger efficiency that guanidinium 4-nitorobenzoate compound. The obtained data are compared with experimental crystallographic and vibrational results for real crystal of guanidinium 3-nitrobenzoate. Additionally, the theoretical vibrational spectra are compared with literature calculations of guanidinium 4-nitrobenzoate compound.

Band structures in fractal grading porous phononic crystals

NASA Astrophysics Data System (ADS)

Wang, Kai; Liu, Ying; Liang, Tianshu; Wang, Bin

2018-05-01

In this paper, a new grading porous structure is introduced based on a Sierpinski triangle routine, and wave propagation in this fractal grading porous phononic crystal is investigated. The influences of fractal hierarchy and porosity on the band structures in fractal graidng porous phononic crystals are clarified. Vibration modes of unit cell at absolute band gap edges are given to manifest formation mechanism of absolute band gaps. The results show that absolute band gaps are easy to form in fractal structures comparatively to the normal ones with the same porosity. Structures with higher fractal hierarchies benefit multiple wider absolute band gaps. This work provides useful guidance in design of fractal porous phononic crystals.

High-quality photonic crystals with a nearly complete band gap obtained by direct inversion of woodpile templates with titanium dioxide.

PubMed

Marichy, Catherine; Muller, Nicolas; Froufe-Pérez, Luis S; Scheffold, Frank

2016-02-25

Photonic crystal materials are based on a periodic modulation of the dielectric constant on length scales comparable to the wavelength of light. These materials can exhibit photonic band gaps; frequency regions for which the propagation of electromagnetic radiation is forbidden due to the depletion of the density of states. In order to exhibit a full band gap, 3D PCs must present a threshold refractive index contrast that depends on the crystal structure. In the case of the so-called woodpile photonic crystals this threshold is comparably low, approximately 1.9 for the direct structure. Therefore direct or inverted woodpiles made of high refractive index materials like silicon, germanium or titanium dioxide are sought after. Here we show that, by combining multiphoton lithography and atomic layer deposition, we can achieve a direct inversion of polymer templates into TiO2 based photonic crystals. The obtained structures show remarkable optical properties in the near-infrared region with almost perfect specular reflectance, a transmission dip close to the detection limit and a Bragg length comparable to the lattice constant.

Synthesis, spectral, structural prediction and computational studies of octylcarbazole ornamented 3-phenothiazinal

NASA Astrophysics Data System (ADS)

Karuppasamy, Ayyanar; Udhaya kumar, Chandran; Karthikeyan, Subramanian; Velayutham Pillai, Muthiah Pillai; Ramalingan, Chennan

2017-11-01

A novel conjugated octylcarbazole ornamented 3-phenothiazinal, 10-(9-octyl-9H-carbazol-3-yl)-10H-phenothiazine-3-carbaldehyde (OCPTC) was synthesized and fully characterized by 1H-NMR, 13C-NMR, elemental and single crystal XRD analyses. The optimized geometrical structure, vibrational frequencies and NMR have been computed with M06-2X method using 6-31+G(d,p) basis set. Total electronic energies and HOMO-LUMO energy gaps in gas phase are discussed. The geometrical parameters of the title compound obtained from single crystal XRD studies have been found in accord with the calculated (DFT) values. The experimental and theoretical FT-IR and NMR results of the title molecule have been investigated. The experimentally observed vibrational frequencies have been compared with the calculated ones, which are in good agreement with each other. Single crystal X-ray structural analysis of OCPTC, evidences the ''butterfly conformation'' of phenothiazine ring with nearly perpendicular orientation of the carbazole structural motif to the phenothiazine moiety.

The 2.1Å Crystal Structure of an Acyl-CoA Synthetase from Methanosarcina acetivorans reveals an alternate acyl binding pocket for small branched acyl substrates†,‡

PubMed Central

Shah, Manish B.; Ingram-Smith, Cheryl; Cooper, Leroy L.; Qu, Jun; Meng, Yu; Smith, Kerry S.; Gulick, Andrew M.

2009-01-01

The acyl-AMP forming family of adenylating enzymes catalyze two-step reactions to activate a carboxylate with the chemical energy derived from ATP hydrolysis. X-ray crystal structures have been determined for multiple members of this family and, together with biochemical studies, provide insights into the active site and catalytic mechanisms used by these enzymes. These studies have shown that the enzymes use a domain rotation of 140° to reconfigure a single active site to catalyze the two partial reactions. We present here the crystal structure of a new medium chain acyl-CoA synthetase from Methanosarcina acetivorans. The binding pocket for the three substrates is analyzed, with many conserved residues present in the AMP binding pocket. The CoA binding pocket is compared to the pockets of both acetyl-CoA synthetase and 4-chlorobenzoate:CoA ligase. Most interestingly, the acyl binding pocket of the new structure is compared with other acyl- and aryl-CoA synthetases. A comparison of the acyl-binding pocket of the acyl-CoA synthetase from M. acetivorans with other structures identifies a shallow pocket that is used to bind the medium chain carboxylates. These insights emphasize the high sequence and structural diversity among this family in the area of the acyl binding pocket. PMID:19544569

Real-space study of the optical absorption in alternative phases of silicon

NASA Astrophysics Data System (ADS)

Ong, Chin Shen; Coh, Sinisa; Cohen, Marvin L.; Louie, Steven G.

2017-12-01

We introduce a real-space approach to understand the relationship between optical absorption and crystal structure. We apply this approach to alternative phases of silicon, with a focus on the Si20 crystal phase as a case study. We find that about 83% of the changes in the calculated low-energy absorption in Si20 as compared to Si in the diamond structure can be attributed to reducing the differences between the on-site energies of the bonding and antibonding orbitals as well as increasing the hopping integrals for specific Si-Si bonds.

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

PubMed

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

2010-05-20

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

Habit modification of potassium acid phthalate (KAP) single crystals by impurities

NASA Astrophysics Data System (ADS)

Murugakoothan, P.; Mohan Kumar, R.; Ushasree, P. M.; Jayavel, R.; Dhanasekaran, R.; Ramasamy, P.

1999-12-01

Nonlinear optical materials potassium dihydrogen phosphate (KDP), urea and L-arginine phosphate (LAP)-doped KAP crystals were grown by the slow cooling method. The LAP-doped crystals show pronounced habit modification compared to KDP and urea doping. The effect of these impurities on growth kinetics, surface morphology, habit modification, structure, optical and mechanical properties have been studied. Among the three impurities, urea doping yields high mechanical stability and optical transmission and for KDP and LAP doping there is a decrease in optical transmission.

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

NASA Astrophysics Data System (ADS)

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

2018-02-01

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

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 structures of N-(3-fluoro-benzo-yl)benzene-sulfonamide and N-(3-fluoro-benzo-yl)-4-methyl-benzene-sulfonamide.

PubMed

Suchetan, P A; Naveen, S; Lokanath, N K; Lakshmikantha, H N; Srivishnu, K S; Supriya, G M

2016-04-01

The crystal structures of two N-(aryl-sulfon-yl)aryl-amides, namely N-(3-fluoro-benzo-yl)benzene-sulfonamide, C13H10FNO3S, (I), and N-(3-fluoro-benzo-yl)-4-methyl-benzene-sulfonamide, C14H12FNO3S, (II), are described and compared with related structures. The dihedral angle between the benzene rings is 82.73 (10)° in (I) compared to 72.60 (12)° in (II). In the crystal of (I), the mol-ecules are linked by C-H⋯O and C-H⋯π inter-actions, resulting in a three-dimensional grid-like architecture, while C-H⋯O inter-actions lead to one-dimensional ribbons in (II). The crystals of both (I) and (II) feature strong but non-structure-directing N-H⋯O hydrogen bonds with R 2 (2)(8) ring motifs. The structure of (I) also features π-π stacking inter-actions.

Structural Analysis of Chemokine Receptor–Ligand Interactions

PubMed Central

2017-01-01

This review focuses on the construction and application of structural chemokine receptor models for the elucidation of molecular determinants of chemokine receptor modulation and the structure-based discovery and design of chemokine receptor ligands. A comparative analysis of ligand binding pockets in chemokine receptors is presented, including a detailed description of the CXCR4, CCR2, CCR5, CCR9, and US28 X-ray structures, and their implication for modeling molecular interactions of chemokine receptors with small-molecule ligands, peptide ligands, and large antibodies and chemokines. These studies demonstrate how the integration of new structural information on chemokine receptors with extensive structure–activity relationship and site-directed mutagenesis data facilitates the prediction of the structure of chemokine receptor–ligand complexes that have not been crystallized. Finally, a review of structure-based ligand discovery and design studies based on chemokine receptor crystal structures and homology models illustrates the possibilities and challenges to find novel ligands for chemokine receptors. PMID:28165741

Radiation-damage-assisted ferroelectric domain structuring in magnesium-doped lithium niobate

NASA Astrophysics Data System (ADS)

Jentjens, L.; Peithmann, K.; Maier, K.; Steigerwald, H.; Jungk, T.

2009-06-01

Irradiation of 5% magnesium-doped lithium niobate crystals (LiNbO3:Mg) with high-energy, low-mass 3He ions, which are transmitted through the crystal, changes the domain reversal properties of the material. This enables easier domain engineering compared to non-irradiated material and assists the formation of small-sized periodically poled domains in LiNbO3:Mg. Periodic domain structures exhibiting a width of ≈520 nm are obtained in radiation-damaged sections of the crystals. The ferroelectric poling behavior between irradiated and non-treated material is compared.

Production, purification, crystallization and preliminary X-ray structural studies of adeno-associated virus serotype 5

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

DiMattia, Michael; Govindasamy, Lakshmanan; Levy, Hazel C.

2005-10-01

The production, purification, crystallization and preliminary crystallographic analysis of empty adeno-associated virus serotype 5 capsids are reported. Adeno-associated virus serotype 5 (AAV5) is under development for gene-therapy applications for the treatment of cystic fibrosis. To elucidate the structural features of AAV5 that control its enhanced transduction of the apical surface of airway epithelia compared with other AAV serotypes, X-ray crystallographic studies of the viral capsid have been initiated. The production, purification, crystallization and preliminary crystallographic analysis of empty AAV5 viral capsids are reported. The crystals diffract X-rays to beyond 3.2 Å resolution using synchrotron radiation and belong to the orthorhombicmore » space group P2{sub 1}2{sub 1}2{sub 1}, with unit-cell parameters a = 264.7, b = 447.9, c = 629.7 Å. There is one complete T = 1 viral capsid per asymmetric unit. The orientation and position of the viral capsid in the asymmetric unit have been determined by rotation and translation functions, respectively, and the AAV5 structure determination is in progress.« less

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.

The effect of tailor-made additives on crystal growth of methyl paraben: Experiments and modelling

NASA Astrophysics Data System (ADS)

Cai, Zhihui; Liu, Yong; Song, Yang; Guan, Guoqiang; Jiang, Yanbin

2017-03-01

In this study, methyl paraben (MP) was selected as the model component, and acetaminophen (APAP), p-methyl acetanilide (PMAA) and acetanilide (ACET), which share the similar molecular structure as MP, were selected as the three tailor-made additives to study the effect of tailor-made additives on the crystal growth of MP. HPLC results indicated that the MP crystals induced by the three additives contained MP only. Photographs of the single crystals prepared indicated that the morphology of the MP crystals was greatly changed by the additives, but PXRD and single crystal diffraction results illustrated that the MP crystals were the same polymorph only with different crystal habits, and no new crystal form was found compared with other references. To investigate the effect of the additives on the crystal growth, the interaction between additives and facets was discussed in detail using the DFT methods and MD simulations. The results showed that APAP, PMAA and ACET would be selectively adsorbed on the growth surfaces of the crystal facets, which induced the change in MP crystal habits.

The room temperature crystal structure of a bacterial phytochrome determined by serial femtosecond crystallography

DOE PAGES

Edlund, Petra; Takala, Heikki; Claesson, Elin; ...

2016-10-19

Phytochromes are a family of photoreceptors that control light responses of plants, fungi and bacteria. A sequence of structural changes, which is not yet fully understood, leads to activation of an output domain. Time-resolved serial femtosecond crystallography (SFX) can potentially shine light on these conformational changes. Here we report the room temperature crystal structure of the chromophore-binding domains of the Deinococcus radiodurans phytochrome at 2.1 Å resolution. The structure was obtained by serial femtosecond X-ray crystallography from microcrystals at an X-ray free electron laser. We find overall good agreement compared to a crystal structure at 1.35 Å resolution derived frommore » conventional crystallography at cryogenic temperatures, which we also report here. The thioether linkage between chromophore and protein is subject to positional ambiguity at the synchrotron, but is fully resolved with SFX. As a result, the study paves the way for time-resolved structural investigations of the phytochrome photocycle with time-resolved SFX.« less

The room temperature crystal structure of a bacterial phytochrome determined by serial femtosecond crystallography

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

Edlund, Petra; Takala, Heikki; Claesson, Elin

Phytochromes are a family of photoreceptors that control light responses of plants, fungi and bacteria. A sequence of structural changes, which is not yet fully understood, leads to activation of an output domain. Time-resolved serial femtosecond crystallography (SFX) can potentially shine light on these conformational changes. Here we report the room temperature crystal structure of the chromophore-binding domains of the Deinococcus radiodurans phytochrome at 2.1 Å resolution. The structure was obtained by serial femtosecond X-ray crystallography from microcrystals at an X-ray free electron laser. We find overall good agreement compared to a crystal structure at 1.35 Å resolution derived frommore » conventional crystallography at cryogenic temperatures, which we also report here. The thioether linkage between chromophore and protein is subject to positional ambiguity at the synchrotron, but is fully resolved with SFX. As a result, the study paves the way for time-resolved structural investigations of the phytochrome photocycle with time-resolved SFX.« less

Comparative spectroscopic analysis of urinary calculi inhibition by Larrea Tridentata infusion and NDGA chemical extract

NASA Astrophysics Data System (ADS)

Manciu, Felicia

2012-10-01

In the present comparative spectroscopic study we try to understand calcium oxalate kidney stone formation as well as its inhibition by using a traditional medicine approach with Larrea Tridentata (LT) herbal extracts and nordihydroguaiaretic acid (NDGA), which is a chemical extract of the LT bush. The samples were synthesized without and with LT or NDGA using a simplified single diffusion gel growth technique. While the use of infusion from LT decreases the sizes of calcium oxalate crystals and also changes their structure from monohydrate for pure crystals to dihydrate for crystals grown with different amounts of inhibitor, both Raman and infrared absorption spectroscopic techniques, which are the methods of analysis employed in this work, reveal that NDGA is not responsible for the change in the morphology of calcium oxalate crystals and does not contribute significantly to the inhibition process. The presence of NDGA slightly affects the structure of the crystals by modifying the strength of the C-C bonds as seen in the Raman data. Also, the current infrared absorption results demonstrate the presence of NDGA in the samples through a vibrational line that corresponds to the double bond between carbon atoms of the ester group of NDGA.

Crystal Structure and Crystal Chemistry of Some Common REE Minerals and Nanpingite

NASA Astrophysics Data System (ADS)

Ni, Yunxiang

1995-01-01

Part I. Crystal structure and crystal chemistry of fluorocarbonate minerals. The crystal structure of bastnasite-(Ce) have been solved in P-62c and refined to R = 0.018. The structure is composed of (001) (CeF) layers interspersed with (CO_3) layers in a 1:1 ratio. The Ce atom is coordinated in rm CeO_6F_3 polyhedra. The atomic arrangement of synchysite-(Ce) has been solved and refined to R = 0.036 with a monoclinic space group C2/c. It possesses a (001) layer structure, with layers of (Ca) and (CeF) separated by layers of carbonate groups. The layers stack in a manner analogous to C2/c muscovite. Polytypism similar to the micas may exist in synchysite. The crystal structures of cordylite-(Ce) have been solved in P6 _3/mmc and refined to R = 0.023. The structure and chemical formula are different from those deduced by Oftedal. The formula is rm MBaCe_2(CO _3)_4F, where M is rm Na^+, Ca^{2+}_{1/2 }+ O_{1/2}, or any solution. The presence of (NaF) layer in the structure is the key difference from the Oftedal's structure. This redefinition of the chemical formula and crystal structure of cordylite will be proposed to IMA-CNMMN. Part II. Crystal structure and crystal chemistry of monazite-xenotime series. Monazite is monoclinic, P2 _1/n, and xenotime is isostructural with zircon (I4_1/amd). Both atomic arrangements are based on (001) chains of intervening phosphate tetrahedra and RE polyhedra, with a REO_8 polyhedron in xenotime that accommodates HRE (Tb - Lu) and a REO_9 polyhedron in monazite that preferentially incorporates LRE (La - Gd). As the structure "transforms" from xenotime to monazite, the crystallographic properties are comparable along the (001) chains, with structural adjustments of 2.2 A along (010) to accommodate the different size RE atoms. Part III. Crystal structure of nanpingite-2M _2, the Cs end-member of muscovite. The crystal structure of nanpingite has been refined to R = 0.058. Compared to K^+ in muscovite, the largest interlayer Cs^+ in nanpingite increases (001) separation between adjacent 2:1 layers, but has little effect on the dimensions in (001). The existence of rare 2M_2 polytype in nanpingite is attributed to this large layer separation, which minimizes the repulsion of the superimposed (along (001)) basal oxygens in neighboring tetrahedral layers.

Synthesis, stereochemistry, crystal structure, docking study and biological evaluation of some new N-benzylpiperidin-4-ones

NASA Astrophysics Data System (ADS)

Ponnuswamy, S.; Kayalvizhi, R.; Sethuvasan, S.; Sugumar, P.; Ponnuswamy, M. N.

2018-03-01

Two new N-benzylpiperidin-4-ones 3 and 4 have been synthesized and characterized using IR, 1D and 2D NMR spectral studies. The NMR data of N-benzylpiperidin-4-ones 3 and 4 reveal that the compounds prefer to exist in chair conformation with equatorial orientation of the bulky substituents and the single crystal X-ray structure of compound 4 also reveals a similar conformation in solid state. Furthermore, the antimicrobial studies carried out for the compounds 1-4 indicate moderate activities with the selected strains. The antioxidant potency of 3 is superior whereas 4 exhibits moderate activity when compared to that of standard drug. The results of molecular docking studies with the AmpC β-lactamase enzyme indicate that compound 3 shows better docking score and binding energy than the co-crystal ligand.

Structural and optical properties of WTe2 single crystals synthesized by DVT technique

NASA Astrophysics Data System (ADS)

Dixit, Vijay; Vyas, Chirag; Pathak, V. M.; Soalanki, G. K.; Patel, K. D.

2018-05-01

Layered transition metal di-chalcogenide (LTMDCs) crystals have attracted much attention due to their potential in optoelectronic device applications recently due to realization of their monolayer based structures. In the present investigation we report growth of WTe2 single crystals by direct vapor transport (DVT) technique. These crystals are then characterized by energy dispersive analysis of x-rays (EDAX) to study stoichiometric composition after growth. The structural properties are studied by x-ray diffraction (XRD) and selected area electron diffraction (SAED) is used to confirm orthorhombic structure of grown WTe2 crystal. Surface morphological properties of the crystals are also studied by scanning electron microscope (SEM). The optical properties of the grown crystals are studied by UV-Visible spectroscopy which gives direct band gap of 1.44 eV for grown WTe2 single crystals.

Synthesis, crystal structure refinement, and nonlinear-optical properties of CaB{sub 3}O{sub 5}(OH): Comparative crystal chemistry of calcium triborates

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

Yamnova, N. A., E-mail: aks.crys@gmail.com; Aksenov, S. M.; Stefanovich, S. Yu.

Calcium triborate CaB{sub 3}O5(OH) obtained by hydrothermal synthesis in the Ca(OH){sub 2}–H{sub 3}BO{sub 3}–Na{sub 2}CO{sub 3}–KCl system is studied by single-crystal X-ray diffraction. The parameters of the orthorhombic unit cell are as follows: a = 13.490(1), b = 6.9576(3), and c = 4.3930(2) Å; V = 412.32(3) Å{sup 3} and space group Pna2{sub 1}. The structure is refined in the anisotropic approximation of the atomic displacement parameters to R = 4.28% using 972 vertical bar F vertical bar > 4σ(F). It is confirmed that the crystal structure of Ca triborate CaB{sub 3}O{sub 5}(OH) is identical to that described earlier. Themore » hydrogen atom is localized. An SHG signal stronger than that of the quartz standard is registered. The phase transition of calcium triborate into calciborite is found on heating. The comparative crystal-chemical analysis of a series of borates with the general chemical formula 2CaO · 3B{sub 2}O{sub 3} · nH{sub 2}O (n = 0–13) with the constant CaO: B{sub 2}O{sub 3}= 2: 3 ratio and variable content of water is performed.« less

Glycine glycinium picrate—Reinvestigation of the structure and vibrational spectra

NASA Astrophysics Data System (ADS)

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

2011-01-01

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

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

DOE PAGES

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

2014-08-21

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

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

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

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

2014-10-01

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

The influence of growth environment on the crystallization of nortriptyline hydrochloride, a tricyclic antidepressant

NASA Astrophysics Data System (ADS)

MacCalman, M. L.; Roberts, K. J.; Hendriksen, B. A.

1993-03-01

The preparation of the nortriptyline hydrochloride, an important pharmaceutical product, by crystallization from both alcohol and aqueous solutions is presented. At low temperatures this material shows a higher solubility in absolute alcohol compared to aqueous solutions in a trend which reverses at higher temperatures. Examination of crystals prepared from alcohol solutions reveal essentially a needle-like crystal habit which is in excellent agreement with morphological predictions based on the bulk crystallographic structure. In contrast crystals prepared from aqueous solution at high temperatures reveal a particulate structure dominated by heavily agglomerated crystallites with plate-like morphology. When this material is crystallized at the lower temperatures, where the solubility curve is steep, X-ray and thermal analysis appear to show that crystallization results in a new polymorphic structure associated with a less agglomerated product.

A comparative study on the luminescence properties of Ce3+/Tb3+ doped Gd-based host nanomaterials

NASA Astrophysics Data System (ADS)

Jadhao, Charushila Vasant; Rani, Barkha; Sahu, Niroj Kumar

2018-04-01

A comparative study on the crystal phases and their respective luminescence behaviour of Gd3+ based host materials such as GdPO4, GdF3, GdVO4 and Gd2O3 sensitized with 7at.% Ce3+ and activated with 5 at.% Tb3+ have been reported. The nanomaterials were prepared by polyol method using ethylene glycol as solvent and found to have different crystal structures such as monoclinic, orthorhombic, tetragonal and cubic phase. Clear characteristics emission from Tb3+ has been observed in all the samples when excited in the absorption wavelength of Ce3+ and Gd3+ (˜280 nm). Among all the above materials, intense emission of Tb3+ is found in GdPO4 followed by GdF3, Gd2O3 and GdVO4 respectively. The Tb3+ emission is strongly influenced by the energy transfer process and crystal structure of the host materials and hence this study will be important for choosing suitable materials for display devices and biomedical applications.

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

NASA Astrophysics Data System (ADS)

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

2018-05-01

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

Vibrational spectroscopic studies of an organic non-linear optical crystal 8-hydroxyquinolinium picrate

NASA Astrophysics Data System (ADS)

Krishna Kumar, V.; Nagalakshmi, R.

2007-04-01

8-Hydroxyquinolinium picrate (8-HQP) was synthesized by the addition of equimolar quantities of 8-hydroxyquinoline (8-HQ) and picric acid (PA). Single crystals were grown from N, N dimethyl formamide (DMF) by restricted evaporation method at room temperature. The solubility of 8-HQP was determined in different solvents at various temperatures. The structural characterization of the grown crystals was carried out by X-ray diffraction. Vibrational modes were classified on the basis of group theoretical analysis and the spectral bands were compared with those of parent compounds in order to propose a tentative assignment by recording FT-IR, FT-Raman and polarized Raman spectra in different crystal orientations. The crystal possess lower cut-off at 230 nm and good transparency as confirmed by optical transmittance studies.

Growth, structural, thermal, linear and nonlinear optical and laser damage threshold studies of picolinium tartrate monohydrate single crystals.

PubMed

Peramaiyan, G; Pandi, P; Sornamurthy, B M; Bhagavannarayana, G; Mohan Kumar, R

2012-09-01

Picolinium tartrate monohydrate (PTM), a novel organic nonlinear optical material was synthesized and bulk crystals were grown from aqueous solution by slow cooling technique. The cell parameters of the grown crystal were found by single and powder X-ray diffraction analyses. The crystalline perfection of the grown crystals has been analyzed by high-resolution X-ray diffraction (HRXRD) rocking curve measurements. The presence of functional groups in the grown crystal was identified by FTIR and FT-Raman spectral analyses. UV-Vis spectral studies reveal PTM crystals are transparent in the wavelength region of 295-1100 nm. The thermal characteristics of PTM were analyzed by TGA/DTA studies. The dielectric and mechanical behaviours of PTM crystals were investigated. Dislocation density was estimated to be 2.89 × 10(3) cm(-2) on the flat-surface of PTM crystals from the etching studies. The laser induced surface damage threshold for the grown crystal was measured using Nd:YAG laser. Its second harmonic generation relative efficiency was measured by Kurtz and Perry powder technique and was observed to be comparable with KDP crystal. Copyright © 2012 Elsevier B.V. All rights reserved.

Synthesis, spectral characterization, crystal structure and molecular docking study of 2,7-diaryl-1,4-diazepan-5-ones

NASA Astrophysics Data System (ADS)

Sethuvasan, S.; Sugumar, P.; Maheshwaran, V.; Ponnuswamy, M. N.; Ponnuswamy, S.

2016-07-01

In this study, a series of variously substituted r-2,c-7-diaryl-1,4-diazepan-5-ones 9-16 have been synthesized using Schmidt rearrangement and are characterized by IR, mass and 1D & 2D NMR spectral data. The proton NMR coupling constant and estimated dihedral angles reveal that the compounds 9-16 prefer a chair conformation with equatorial orientation of alkyl and aryl groups. Single crystal X-ray structure has been solved for compounds 9 and 11 which also indicates the preference for distorted chair conformation with equatorial orientation of substituents. The compounds 9-16 have been docked with the structure of Methicillin-resistant Staphylococcus aureus (MRSA) and the results demonstrate that compound 10 is having better docking score and glide energy than others and it is comparable to co-crystal ligand. Furthermore, all the compounds have been evaluated for their antibacterial and antioxidant activities. All the compounds show moderate antibacterial activity and only 11 exhibits better activity against S. aures and Escherichia coli. The compounds 11, 13 and 14 exhibit half of the antioxidant power when compared to the BHT and the remaining compounds show moderate activity.

Four highly pseudosymmetric and/or twinned structures of d(CGCGCG) 2 extend the repertoire of crystal structures of Z-DNA

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

Luo, Zhipu; Dauter, Zbigniew; Gilski, Miroslaw

DNA oligomer duplexes containing alternating cytosines and guanines in their sequences tend to form left-handed helices of the Z-DNA type, with the sugar and phosphate backbone in a zigzag conformation and a helical repeat of two successive nucleotides. Z-DNA duplexes usually crystallize as hexagonally arranged parallel helical tubes, with various relative orientations and translation of neighboring duplexes. Four novel high-resolution crystal structures of d(CGCGCG) 2duplexes are described here. They are characterized by a high degree of pseudosymmetry and/or twinning, with three or four independent duplexes differently oriented in a monoclinicP2 1lattice of hexagonal metric. The various twinning criteria give somewhatmore » conflicting indications in these complicated cases of crystal pathology. The details of molecular packing in these crystal structures are compared with other known crystal forms of Z-DNA.« less

Applications of the Cambridge Structural Database in organic chemistry and crystal chemistry.

PubMed

Allen, Frank H; Motherwell, W D Samuel

2002-06-01

The Cambridge Structural Database (CSD) and its associated software systems have formed the basis for more than 800 research applications in structural chemistry, crystallography and the life sciences. Relevant references, dating from the mid-1970s, and brief synopses of these papers are collected in a database, DBUse, which is freely available via the CCDC website. This database has been used to review research applications of the CSD in organic chemistry, including supramolecular applications, and in organic crystal chemistry. The review concentrates on applications that have been published since 1990 and covers a wide range of topics, including structure correlation, conformational analysis, hydrogen bonding and other intermolecular interactions, studies of crystal packing, extended structural motifs, crystal engineering and polymorphism, and crystal structure prediction. Applications of CSD information in studies of crystal structure precision, the determination of crystal structures from powder diffraction data, together with applications in chemical informatics, are also discussed.

Elastic and viscoelastic effects in rubber/air acoustic band gap structures: A theoretical and experimental study

NASA Astrophysics Data System (ADS)

Merheb, B.; Deymier, P. A.; Jain, M.; Aloshyna-Lesuffleur, M.; Mohanty, S.; Berker, A.; Greger, R. W.

2008-09-01

The transmission of acoustic waves through centimeter-scale elastic and viscoelastic two-dimensional silicone rubber/air phononic crystal structures is investigated theoretically and experimentally. We introduce a finite difference time domain method for two-dimensional elastic and viscoelastic composite structures. Elastic fluid-solid phononic crystals composed of a two-dimensional array of cylindrical air inclusions in a solid rubber matrix, as well as an array of rubber cylinders in an air matrix, are shown to behave similarly to fluid-fluid composite structures. These systems exhibit very wide band gaps in their transmission spectra that extend to frequencies in the audible range of the spectrum. This effect is associated with the very low value of the transverse speed of sound in rubber compared to that of the longitudinal polarization. The difference in transmission between elastic and viscoelastic rubber/air crystals results from attenuation of transmission over a very wide frequency range, leaving only narrow passing bands at very low frequencies. These phononic crystals demonstrate the practical design of elastic or viscoelastic solid rubber/air acoustic band gap sound barriers with small dimensions.

Effect of cationic substitution on the double-well hydrogen-bond potential in [K1-x(NH4)x]3H(SO4)2 proton conductors: a single-crystal neutron diffraction study.

PubMed

Choudhury, R R; Chitra, R; Selezneva, E V; Makarova, I P

2017-10-01

The structure of the mixed crystal [K 1-x (NH 4 ) x ] 3 H(SO 4 ) 2 as obtained from single-crystal neutron diffraction is compared with the previously reported room-temperature neutron structure of crystalline K 3 H(SO 4 ) 2 . The two structures are very similar, as indicated by the high value of their isostructurality index (94.8%). It was found that the replacement of even a small amount (3%) of K + with NH 4 + has a significant influence on the short strong hydrogen bond connecting the two SO 4 2- ions. Earlier optical measurements had revealed that the kinetics of the superionic transition in the solid solution [K 1-x (NH 4 ) x ] 3 H(SO 4 ) 2 are much faster than in K 3 H(SO 4 ) 2 ; this reported difference in the kinetics of the superionic phase transition in this class of crystal is explained on the basis of the difference in strength of the hydrogen-bond interactions in the two structures.

The growth and perfection of β-cyclotetramethylene-tetranitramine (HMX) studied by laboratory and synchrotron X-ray topography

NASA Astrophysics Data System (ADS)

Gallagher, H. G.; Sherwood, J. N.; Vrcelj, R. M.

2017-10-01

An examination has been made of the defect structure of crystals of the energetic material β-cyclotetramethylene-tetranitramine (HMX) using both Laboratory (Lang method) and Synchrotron (Bragg Reflection and Laue method) techniques. The results of the three methods are compared with particular attention to the influence of potential radiation damage caused to the samples by the latter, more energetic, technique. The comparison shows that both techniques can be confidently used to evaluate the defect structures yielding closely similar results. The results show that, even under the relatively casual preparative methods used (slow evaporation of unstirred solutions at constant temperature), HMX crystals of high perfection can be produced. The crystals show well defined bulk defect structures characteristic of organic materials in general: growth dislocations, twins, growth sector boundaries, growth banding and solvent inclusions. The distribution of the defects in specific samples is correlated with the morphological variation of the grown crystals. The results show promise for the further evaluation and characterisation of the structure and properties of dislocations and other defects and their involvement in mechanical and energetic processes in this material.

Tunable alumina 2D photonic-crystal structures via biomineralization of peacock tail feathers

NASA Astrophysics Data System (ADS)

Jiang, Yonggang; Wang, Rui; Feng, Lin; Li, Jian; An, Zhonglie; Zhang, Deyuan

2018-04-01

Peacock tail feathers with subtle periodic nanostructures exhibit diverse striking brilliancy, which can be applied as natural templates to fabricate artificial photonic crystals (PhCs) via a biomineralization method. Alumina photonic-crystal structures are successfully synthesized via an immersion and two-step calcination process. The lattice constants of the artificial PhCs are greatly reduced compared to their natural matrices. The lattice constants are tunable by modifying the final annealing conditions in the biomineralization process. The reflection spectra of the alumina photonic-crystal structures are measured, which is related to their material and structural parameters. This work suggests a facile fabrication process to construct alumina PhCs with a high-temperature resistance.

Study of linear optical parameters of sodium sulphide nano-particles added ADP crystals

NASA Astrophysics Data System (ADS)

Kochuparampil, A. P.; Joshi, J. H.; Dixit, K. P.; Jethva, H. O.; Joshi, M. J.

2017-05-01

Ammonium Dihydrogen Phosphate (ADP) is one of the nonlinear optical crystals. It is having various applications like optical mixing, electro-optical modulator, harmonic generators, etc. Chalcogenide compounds are poorly soluble in water and difficult to add in the water soluble ADP crystals. The solubility of Chalcogenide compounds can be increased by synthesizing the nano-structured samples with suitable capping agent. In the present study sodium sulphide was added in to ADP to modify its linear optical parameters. Sodium sulphide nano particles were synthesized by co-precipitation technique using Ethylene diamine as capping agent followed by microwave irradiation. The powder XRD confirmed the nano-structured nature of sodium sulphide nano particles. The solubility of nanoparticles of sodium sulphide increased significantly in water compared to the bulk. Pure and Na2S added ADP crystals were grown by slow solvent evaporation method at room temperature. The presence of sodium in ADP was confirmed by AAS. The UV-Vis spectra were recorded for all crystals. Various optical parameters like, transmittance, energy band gap, extinction coefficient, refractive index, optical conductivity, etc. were evaluated. The electronic polarizibility of pure and doped crystals calculated from energy band gap. The effect of doping concentration was found on various parameters.

Nanoliter-Scale Protein Crystallization and Screening with a Microfluidic Droplet Robot

PubMed Central

Zhu, Ying; Zhu, Li-Na; Guo, Rui; Cui, Heng-Jun; Ye, Sheng; Fang, Qun

2014-01-01

Large-scale screening of hundreds or even thousands of crystallization conditions while with low sample consumption is in urgent need, in current structural biology research. Here we describe a fully-automated droplet robot for nanoliter-scale crystallization screening that combines the advantages of both automated robotics technique for protein crystallization screening and the droplet-based microfluidic technique. A semi-contact dispensing method was developed to achieve flexible, programmable and reliable liquid-handling operations for nanoliter-scale protein crystallization experiments. We applied the droplet robot in large-scale screening of crystallization conditions of five soluble proteins and one membrane protein with 35–96 different crystallization conditions, study of volume effects on protein crystallization, and determination of phase diagrams of two proteins. The volume for each droplet reactor is only ca. 4–8 nL. The protein consumption significantly reduces 50–500 fold compared with current crystallization stations. PMID:24854085

Nanoliter-scale protein crystallization and screening with a microfluidic droplet robot.

PubMed

Zhu, Ying; Zhu, Li-Na; Guo, Rui; Cui, Heng-Jun; Ye, Sheng; Fang, Qun

2014-05-23

Large-scale screening of hundreds or even thousands of crystallization conditions while with low sample consumption is in urgent need, in current structural biology research. Here we describe a fully-automated droplet robot for nanoliter-scale crystallization screening that combines the advantages of both automated robotics technique for protein crystallization screening and the droplet-based microfluidic technique. A semi-contact dispensing method was developed to achieve flexible, programmable and reliable liquid-handling operations for nanoliter-scale protein crystallization experiments. We applied the droplet robot in large-scale screening of crystallization conditions of five soluble proteins and one membrane protein with 35-96 different crystallization conditions, study of volume effects on protein crystallization, and determination of phase diagrams of two proteins. The volume for each droplet reactor is only ca. 4-8 nL. The protein consumption significantly reduces 50-500 fold compared with current crystallization stations.

Effect of solvents on the bulk growth of 4-aminobenzophenone single crystals: A potential material for blue and green lasers

NASA Astrophysics Data System (ADS)

Natarajan, V.; Usharani, S.; Arivanandhan, M.; Anandan, P.; Hayakawa, Y.

2015-06-01

Although 4-aminobenzophenone (4-ABP) is the best derivative of benzophenone with 260 times higher second harmonic generation (SHG) efficiency than potassium dihydrogen phosphate (KDP), growth of high quality bulk crystal still remains a difficult task. In the present work, the effect of solvents on solubility and growth aspects of 4-ABP was investigated to grow inclusion free 4-ABP crystals. The growth processes were discussed based on solute-solvent interaction in two different growth media of ethyl acetate and ethanol. The growth rate and thereby solvent inclusions are relatively higher in ethyl acetate grown crystal than the crystal grown from ethanol. The structural, thermal and optical properties of 4-ABP crystals were studied. The enthalpy of 4-ABP melting process was estimated from differential thermal analysis. The optical transmission study shows that 4-ABP crystals grown from ethanol has high transparency compared to ethyl acetate grown sample due to solvent inclusion in the later crystal.

Atomic density functional and diagram of structures in the phase field crystal model

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

Ankudinov, V. E., E-mail: vladimir@ankudinov.org; Galenko, P. K.; Kropotin, N. V.

2016-02-15

The phase field crystal model provides a continual description of the atomic density over the diffusion time of reactions. We consider a homogeneous structure (liquid) and a perfect periodic crystal, which are constructed from the one-mode approximation of the phase field crystal model. A diagram of 2D structures is constructed from the analytic solutions of the model using atomic density functionals. The diagram predicts equilibrium atomic configurations for transitions from the metastable state and includes the domains of existence of homogeneous, triangular, and striped structures corresponding to a liquid, a body-centered cubic crystal, and a longitudinal cross section of cylindricalmore » tubes. The method developed here is employed for constructing the diagram for the homogeneous liquid phase and the body-centered iron lattice. The expression for the free energy is derived analytically from density functional theory. The specific features of approximating the phase field crystal model are compared with the approximations and conclusions of the weak crystallization and 2D melting theories.« less

A new pseudopolymorph of diphenic acid and 4,4‧-bipyridine co-crystal: Structural and theoretical study

NASA Astrophysics Data System (ADS)

Soleimannejad, Janet; Nazarnia, Esfandiar; Stoeckli-Evans, Helen

2014-11-01

A new pseudopolymorph (B; tetragonal, I41/acd) of the cocrystal biphenyl-2,2‧-dicarboxylic acid (diphenic acid) and 4,4‧-bipyridine was synthesized. Its solid-state structure and supramolecular synthons responsible for extending the supramolecular network have been compared with those of the previously reported polymorph (A; triclinic, P1bar). DFT calculations at the B3LYP/6-311G++ (2d,2p) level have been performed. Energies of the intermolecular hydrogen bonds in the crystal structure were calculated and their electronic aspects were investigated by NBO and AIM analysis.

Structure and Stability of Molecular Crystals with Many-Body Dispersion-Inclusive Density Functional Tight Binding.

PubMed

Mortazavi, Majid; Brandenburg, Jan Gerit; Maurer, Reinhard J; Tkatchenko, Alexandre

2018-01-18

Accurate prediction of structure and stability of molecular crystals is crucial in materials science and requires reliable modeling of long-range dispersion interactions. Semiempirical electronic structure methods are computationally more efficient than their ab initio counterparts, allowing structure sampling with significant speedups. We combine the Tkatchenko-Scheffler van der Waals method (TS) and the many-body dispersion method (MBD) with third-order density functional tight-binding (DFTB3) via a charge population-based method. We find an overall good performance for the X23 benchmark database of molecular crystals, despite an underestimation of crystal volume that can be traced to the DFTB parametrization. We achieve accurate lattice energy predictions with DFT+MBD energetics on top of vdW-inclusive DFTB3 structures, resulting in a speedup of up to 3000 times compared with a full DFT treatment. This suggests that vdW-inclusive DFTB3 can serve as a viable structural prescreening tool in crystal structure prediction.

A novel structure of gel grown strontium cyanurate crystal and its structural, optical, electrical characterization

NASA Astrophysics Data System (ADS)

Divya, R.; Nair, Lekshmi P.; Bijini, B. R.; Nair, C. M. K.; Gopakumar, N.; Babu, K. Rajendra

2017-12-01

Strontium cyanurate crystals with novel structure and unique optical property like mechanoluminescence have been grown by conventional gel method. Transparent crystals were obtained. The single crystal X-ray diffraction analysis reveals the exquisite structure of the grown crystal. The crystal is centrosymmetric and has a three dimensional polymeric structure. The powder X ray diffraction analysis confirms its crystalline nature. The functional groups present in the crystal were identified by Fourier transform infrared spectroscopy. Elemental analysis confirmed the composition of the complex. A study of thermal properties was done by thermo gravimetric analysis and differential thermal analysis. The optical properties like band gap, refractive index and extinction coefficient were evaluated from the UV visible spectral analysis. The etching study was done to reveal the dislocations in the crystal which in turn explains mechanoluminescence emission. The mechanoluminescence property exhibited by the crystal makes it suitable for stress sensing applications. Besides being a centrosymmetric crystal, it also exhibits NLO behavior. Dielectric properties were studied and theoretical calculations of Fermi energy, valence electron plasma energy, penn gap and polarisability have been done.

Crystal Structure Variations of Sn Nanoparticles upon Heating

NASA Astrophysics Data System (ADS)

Mittal, Jagjiwan; Lin, Kwang-Lung

2018-04-01

Structural changes in Sn nanoparticles during heating below the melting point have been investigated using differential scanning calorimetry (DSC), x-ray diffraction (XRD) analysis, electron diffraction (ED), and high-resolution transmission electron microscopy (HRTEM). DSC revealed that the heat required to melt the nanoparticles (28.43 J/g) was about half compared with Sn metal (52.80 J/g), which was attributed to the large surface energy contribution for the nanoparticles. ED and XRD analyses of the Sn nanoparticles revealed increased intensity for crystal planes having large interplaner distances compared with regular crystal planes with increasing heat treatment temperature (HTT). HRTEM revealed an increase in interlayer spacing at the surface and near joints between nanoparticles with the HTT, leading to an amorphous structure of nanoparticles at the surface at 220°C. These results highlight the changes that occur in the morphology and crystal structure of Sn nanoparticles at the surface and in the interior with increase of the heat treatment temperature.

Clay pigment structure characterisation as a guide for provenance determination--a comparison between laboratory powder micro-XRD and synchrotron radiation XRD.

PubMed

Švarcová, Silvie; Bezdička, Petr; Hradil, David; Hradilová, Janka; Žižak, Ivo

2011-01-01

Application of X-ray diffraction (XRD)-based techniques in the analysis of painted artworks is not only beneficial for indisputable identification of crystal constituents in colour layers, but it can also bring insight in material crystal structure, which can be affected by their geological formation, manufacturing procedure or secondary changes. This knowledge might be helpful for art historic evaluation of an artwork as well as for its conservation. By way of example of kaolinite, we show that classification of its crystal structure order based on XRD data is useful for estimation of its provenance. We found kaolinite in the preparation layer of a Gothic wall painting in a Czech church situated near Karlovy Vary, where there are important kaolin deposits. Comparing reference kaolin materials from eight various Czech deposits, we found that these can be differentiated just according to the kaolinite crystallinity. Within this study, we compared laboratory powder X-ray micro-diffraction (micro-XRD) with synchrotron radiation X-ray diffraction analysing the same real sample. We found that both techniques led to the same results.

Effects of dry etching processes on exciton and polariton characteristics in ZnTe

NASA Astrophysics Data System (ADS)

Sun, J. H.; Xie, W. B.; Shen, W. Z.; Ogawa, H.; Guo, Q. X.

2003-12-01

We have employed temperature-dependent reflection spectra to study the effects of reactive ion etching (RIE) on the exciton and polariton characteristics in ZnTe crystals exposed to CH4/H2 gases under different rf plasma powers. Classic exciton-polariton theory has been used to calculate the reflection spectra. By comparing with an as-grown ZnTe crystal and the temperature-dependent behavior, we are able to identify the excitons and RIE-induced polariton structures in these dry etched ZnTe crystals. An increase of the rf plasma power will lead to an increase of defect density in the surface damage layers, resulting in a decrease of the photon energies of the observed exciton and polariton structures.

Analysis of nucleoside-binding proteins by ligand-specific elution from dye resin: application to Mycobacterium tuberculosis aldehyde dehydrogenases.

PubMed

Kim, Chang-Yub; Webster, Cecelia; Roberts, Justin K M; Moon, Jin Ho; Alipio Lyon, Emily Z; Kim, Heungbok; Yu, Minmin; Hung, Li-Wei; Terwilliger, Thomas C

2009-12-01

We show that Cibacron Blue F3GA dye resin chromatography can be used to identify ligands that specifically interact with proteins from Mycobacterium tuberculosis, and that the identification of these ligands can facilitate structure determination by enhancing the quality of crystals. Four native Mtb proteins of the aldehyde dehydrogenase (ALDH) family were previously shown to be specifically eluted from a Cibacron Blue F3GA dye resin with nucleosides. In this study we characterized the nucleoside-binding specificity of one of these ALDH isozymes (recombinant Mtb Rv0223c) and compared these biochemical results with co-crystallization experiments with different Rv0223c-nucleoside pairings. We found that the strongly interacting ligands (NAD and NADH) aided formation of high-quality crystals, permitting solution of the first Mtb ALDH (Rv0223c) structure. Other nucleoside ligands (AMP, FAD, adenosine, GTP and NADP) exhibited weaker binding to Rv0223c, and produced co-crystals diffracting to lower resolution. Difference electron density maps based on crystals of Rv0223c with various nucleoside ligands show most share the binding site where the natural ligand NAD binds. From the high degree of similarity of sequence and structure compared to human mitochondrial ALDH-2 (BLAST Z-score = 53.5 and RMSD = 1.5 A), Rv0223c appears to belong to the ALDH-2 class. An altered oligomerization domain in the Rv0223c structure seems to keep this protein as monomer whereas native human ALDH-2 is a multimer.

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

Ozkendir, Osman Murat, E-mail: ozkendir@gmail.com

Highlights: • Crystal and electronic structure properties of Nd{sub x}Ti{sub 1−x}BO{sub 2+d} structure were investigated. • New crystal structures for Nd–Ti complexes are determined. • Distortions in the crystal structure were observed as a result of Boron shortage. • Prominent change in electronic properties of the samples with the increasing Nd amount. - Abstract: Neodymium substituted TiBO{sub 3} samples were investigated according to their crystal, electric and electronic properties. Studies were conducted by X-ray absorption fine structure spectroscopy (XAFS) technique for the samples with different substitutions in the preparation processes. To achieve better crystal structure results during the study, XRDmore » pattern results were supported by extended-XAFS (EXAFS) analysis. The electronic structure analysis were studied by X-ray absorption near-edge structure spectroscopy (XANES) measurements at the room temperatures. Due to the substituted Nd atoms, prominent changes in crystal structure, new crystal geometries for Nd-Ti complexes, phase transitions in the crystals structure were detected according to the increasing Nd substitutions in the samples. In the entire stages of the substitutions, Nd atoms were observed as governing the whole phenomena due to their dominant characteristics in Ti geometries. Besides, electrical resistivity decay was determined in the materials with the increasing amount of Nd substitution.« less

Structural, crystal structure, Hirshfeld surface analysis and physicochemical studies of a new chlorocadmate template by 1-(2-hydroxyethyl)piperazine

NASA Astrophysics Data System (ADS)

Soudani, S.; Jeanneau, E.; Jelsch, C.; Lefebvre, F.; Ben Nasr, C.

2016-11-01

The synthesis, crystal structure and spectroscopic characterization of a new chlorocadmate template by the 1-(2-hydroxyethyl)piperazine ligand are reported. In the atomic arrangement, the CdCl5O entities are deployed in corrugated rows along the a-axis at y = 1/4 and y = 3/4 to form layers parallel to the (a,b) plane. In these crystals, piperazinediium cations are in a chair conformation and are inserted between these layers through Nsbnd H⋯Cl, Csbnd H⋯Cl, Osbnd H⋯Cl and Nsbnd H⋯O hydrogen bonds to form infinite three-dimensional network. Investigation of intermolecular interactions and crystal packing via Hirshfeld surface analysis reveals that H⋯Cl and Csbnd H⋯Hsbnd C intermolecular interactions are the most abundant contacts of the organic cation in the crystal packing. The crystal contacts enrichments reveals that, the Cd++ … Cl- salt bridges, the Cd⋯O complexation and Osbnd H⋯Cl- and Nsbnd H⋯Cl-strong H-bonds are the driving forces in the packing formation. The presence of twelve independent chloride anions and four organic cation in the asymmetric unit allowed comparing their contact propensities. The 13C and 15N CP-MAS NMR spectra are in agreement with the X-ray structure. Additional characterization of this compound has also been performed by IR spectroscopy.

Melting of anisotropic colloidal crystals in two dimensions

NASA Astrophysics Data System (ADS)

Eisenmann, C.; Keim, P.; Gasser, U.; Maret, G.

2004-09-01

The crystal structure and melting transition of two-dimensional colloids interacting via an anisotropic magnetic dipole-dipole potential are studied. Anisotropy is achieved by tilting the external magnetic field inducing the dipole moments of the colloidal particles away from the direction perpendicular to the particle plane. We find a centred rectangular lattice and a two-step melting similar to the phase transitions of the corresponding isotropic crystals via a quasi-hexatic phase. The latter is broadened compared to the hexatic phase for isotropic interaction potential due to strengthening of orientational order.

Anisotropic surface physicochemical properties of spodumene and albite crystals: Implications for flotation separation

NASA Astrophysics Data System (ADS)

Xu, Longhua; Peng, Tiefeng; Tian, Jia; Lu, Zhongyuan; Hu, Yuehua; Sun, Wei

2017-12-01

Aluminosilicate minerals (e.g., spodumene, albite) have complex crystal structures and similar surface chemistries, but they have poor selectivity compared to traditional fatty acid collectors, making flotation separation difficult. Previous research has mainly considered the mineral crystal structure as a whole. In contrast, the surface characteristics at the atomic level and the effects of different crystal interfaces on the flotation behavior have rarely been investigated. This study focuses on investigating the surface anisotropy quantitatively, including the chemical bond characteristics, surface energies, and broken bond densities, using density functional theory and classical theoretical calculations. In addition, the anisotropy of the surface wettability and adsorption characteristics were examined using contact angle, zeta potential, and Fourier-transform infrared measurements. Finally, these surface anisotropies with different flotation behaviors were investigated and interpreted using molecular dynamics simulations, scanning electron microscopy, and X-ray photoelectron spectroscopy. This systematic research offers new ideas concerning the selective grinding and stage flotation of aluminosilicate minerals based on the crystal characteristics.

Pt(II) and Pd(II) complexes with ibuprofen hydrazide: Characterization, theoretical calculations, antibacterial and antitumor assays and studies of interaction with CT-DNA

NASA Astrophysics Data System (ADS)

Manzano, Carlos M.; Bergamini, Fernando R. G.; Lustri, Wilton R.; Ruiz, Ana Lúcia T. G.; de Oliveira, Ellen C. S.; Ribeiro, Marcos A.; Formiga, André L. B.; Corbi, Pedro P.

2018-02-01

Palladium(II) and platinum(II) complexes with a hydrazide derivative of ibuprofen (named HIB) were synthesized and characterized by chemical and spectroscopic methods. Elemental and thermogravimetric analyses, as well as ESI-QTOF-MS studies for both complexes, confirmed a 1:2:2 metal/HIB/Cl- molar ratio. The crystal structure of the palladium(II) complex was solved by single crystal X-ray diffractometric analysis, which permitted identifying the coordination formula [PdCl2(HIB)2]. Crystallographic studies also indicate coordination of HIB to the metal by the NH2 group. Nuclear magnetic resonance and infrared spectroscopies reinforced the coordination observed in the crystal structure and suggested that the platinum(II) complex presents similar coordination modes and structure when compared with the Pd(II) complex. The complexes had their structures optimized with the aid of DFT methods. In vitro antiproliferative assays showed that the [PdCl2(HIB)2] complex is active over ovarian cancer cell line OVCAR-03, while biophysical studies indicated its capacity to interact with CT-DNA. The complexes were inactive over Staphylococcus aureus, Escherichia coli and Pseudomonas aeruginosa bacterial strains.

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

PubMed Central

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

1995-01-01

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

Bulk growth of <001> organic nonlinear optical (NLO) L-arginine 4-nitrophenolate 4-nitrophenol dihydrate (LAPP) single crystals by SR method

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

Pandian, Muthu Senthil, E-mail: senthilpandianm@ssn.edu.in; Sivasubramani, V.; Ramasamy, P.

2015-06-24

A transparent uniaxial L-arginine 4-nitrophenolate 4-nitrophenol dehydrate (LAPP) single crystal having dimension of 20 mm diameter and 45 mm length was grown by Sankaranarayanan-Ramasamy (SR) method with a growth rate of 1 mm per day. Using an identical solution the conventional crystal grown to a dimension of 8×5×5 mm{sup 3} was obtained over a period of 30 days. The crystal structure has been confirmed by single crystal X-ray diffraction measurement. The crystalline perfection of LAPP crystals grown by slow evaporation solution technique (SEST) and SR method were characterized using Vickers microhardness, UV-Vis NIR, chemical etching, dark and photo current measurements. The above study indicatesmore » that the crystal quality of the Sankaranarayanan-Ramasamy (SR) method grown LAPP is good compared to the conventional method grown crystal.« less

Structured laser gain-medium by new bonding for power micro-laser

NASA Astrophysics Data System (ADS)

Kausas, Arvydas; Zheng, Lihe; Taira, Takunori

2017-02-01

In this work, we have compared the Q-switched performance of single rod crystal to a newly developed distributed face cooling structure. This structure was made by surface activated bonding technology and allowed to combine transparent heatsink to a gain crystal at room temperature. The Sapphire and Nd3+:YAG crystal plates were combined in this fashion to produce eight crystal chip which was further used to obtain Q-switch pulses with Cr4+:YAG crystal as saturable absorber. Energy of 9 mJ and pulse duration of 815 ps were achieved. Although the energy obtained with single rod system was 10 mJ, the degradation of the beam prevents such crystal to be used in further applications. This is the first demonstration of distributed face cooling system outperformed conventionally single rod system.

Production, Purification, Crystallization and Preliminary X-ray Structural Studies of Adeno-Associated Virus Serotype 5

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

DiMattia,M.; Govindasamy, L.; Levy, H.

2005-01-01

Adeno-associated virus serotype 5 (AAV5) is under development for gene-therapy applications for the treatment of cystic fibrosis. To elucidate the structural features of AAV5 that control its enhanced transduction of the apical surface of airway epithelia compared with other AAV serotypes, X-ray crystallographic studies of the viral capsid have been initiated. The production, purification, crystallization and preliminary crystallographic analysis of empty AAV5 viral capsids are reported. The crystals diffract X-rays to beyond 3.2 Angstroms resolution using synchrotron radiation and belong to the orthorhombic space group P2{sub 1}2{sub 1}2{sub 1}, with unit-cell parameters a = 264.7, b = 447.9, c =more » 629.7 Angstroms. There is one complete T = 1 viral capsid per asymmetric unit. The orientation and position of the viral capsid in the asymmetric unit have been determined by rotation and translation functions, respectively, and the AAV5 structure determination is in progress.« less

Characterization of LaF 3 coatings prepared at different temperatures and rates

NASA Astrophysics Data System (ADS)

Yu, Hua; Shen, Yanming; Cui, Yun; Qi, Hongji; Shao, JianDa; Fan, ZhengXiu

2008-01-01

LaF 3 thin films were prepared by thermal boat evaporation at different substrate temperatures and various deposition rates. X-ray diffraction (XRD), Lambda 900 spectrophotometer and X-ray photoelectron spectroscopy (XPS) were employed to study crystal structure, transmittance and chemical composition of the coatings, respectively. Laser-induce damage threshold (LIDT) was determined by a tripled Nd:YAG laser system with a pulse width of 8 ns. It is found that the crystal structure became more perfect and the refractive index increased gradually with the temperature rising. The LIDT was comparatively high at high temperature. In the other hand, the crystallization status also became better and the refractive index increased when the deposition rate enhanced at a low level. If the rate was super rapid, the crystallization worsened instead and the refractive index would lessen greatly. On the whole, the LIDT decreased with increasing rate.

Transmission properties of 2D metamaterial photonic crystals

NASA Astrophysics Data System (ADS)

Mejía-Salazar, Jorge; Porras-Montenegro, Nelson

2014-03-01

By using the finite difference time domain technique, we have performed a theoretical study of the transmission properties in 2D photonic crystals composed by circular cilyndrical metamaterial rods. Numerical transmission spectra was compared with its corresponding photonic band structure in the case of an infinite periodic 2D array obtaining a very good agreement. On the other hand, we have characterized the corresponding symmetries for this system and the results were compared with its corresponding conventional plasmonic metamaterial counterpart. J.R. M-S is funded by the Colombian Agency COLCIENCIAS.

Electron tomography and computer visualisation of a three-dimensional 'photonic' crystal in a butterfly wing-scale.

PubMed

Argyros, A; Manos, S; Large, M C J; McKenzie, D R; Cox, G C; Dwarte, D M

2002-01-01

A combination of transmission electron tomography and computer modelling has been used to determine the three-dimensional structure of the photonic crystals found in the wing-scales of the Kaiser-I-Hind butterfly (Teinopalpus imperialis). These scales presented challenges for electron microscopy because the periodicity of the structure was comparable to the thickness of a section and because of the complex connectivity of the object. The structure obtained has been confirmed by taking slices of the three-dimensional computer model constructed from the tomography and comparing these with transmission electron microscope (TEM) images of microtomed sections of the actual scale. The crystal was found to have chiral tetrahedral repeating units packed in a triclinic lattice.

Molecular modeling studies of novel retro-binding tripeptide active-site inhibitors of thrombin.

PubMed

Lau, W F; Tabernero, L; Sack, J S; Iwanowicz, E J

1995-08-01

A novel series of retro-binding tripeptide thrombin active-site inhibitors was recently developed (Iwanowicz, E. I. et al. J. Med. Chem. 1994, 37, 2111(1)). It was hypothesized that the binding mode for these inhibitors is similar to that of the first three N-terminal residues of hirudin. This binding hypothesis was subsequently verified when the crystal structure of a member of this series, BMS-183,507 (N-[N-[N-[4-(Aminoiminomethyl)amino[-1-oxobutyl]-L- phenylalanyl]-L-allo-threonyl]-L-phenylalanine, methyl ester), was determined (Taberno, L.J. Mol. Biol. 1995, 246, 14). The methodology for developing the binding models of these inhibitors, the structure-activity relationships (SAR) and modeling studies that led to the elucidation of the proposed binding mode is described. The crystal structure of BMS-183,507/human alpha-thrombin is compared with the crystal structure of hirudin/human alpha-thrombin (Rydel, T.J. et al. Science 1990, 249,227; Rydel, T.J. et al. J. Mol Biol. 1991, 221, 583; Grutter, M.G. et al. EMBO J. 1990, 9, 2361) and with the computational binding model of BMS-183,507.

A novel numerical framework for self-similarity in plasticity: Wedge indentation in single crystals

NASA Astrophysics Data System (ADS)

Juul, K. J.; Niordson, C. F.; Nielsen, K. L.; Kysar, J. W.

2018-03-01

A novel numerical framework for analyzing self-similar problems in plasticity is developed and demonstrated. Self-similar problems of this kind include processes such as stationary cracks, void growth, indentation etc. The proposed technique offers a simple and efficient method for handling this class of complex problems by avoiding issues related to traditional Lagrangian procedures. Moreover, the proposed technique allows for focusing the mesh in the region of interest. In the present paper, the technique is exploited to analyze the well-known wedge indentation problem of an elastic-viscoplastic single crystal. However, the framework may be readily adapted to any constitutive law of interest. The main focus herein is the development of the self-similar framework, while the indentation study serves primarily as verification of the technique by comparing to existing numerical and analytical studies. In this study, the three most common metal crystal structures will be investigated, namely the face-centered cubic (FCC), body-centered cubic (BCC), and hexagonal close packed (HCP) crystal structures, where the stress and slip rate fields around the moving contact point singularity are presented.

Nanocrystal grain growth and device architectures for high-efficiency CdTe ink-based photovoltaics.

PubMed

Crisp, Ryan W; Panthani, Matthew G; Rance, William L; Duenow, Joel N; Parilla, Philip A; Callahan, Rebecca; Dabney, Matthew S; Berry, Joseph J; Talapin, Dmitri V; Luther, Joseph M

2014-09-23

We study the use of cadmium telluride (CdTe) nanocrystal colloids as a solution-processable "ink" for large-grain CdTe absorber layers in solar cells. The resulting grain structure and solar cell performance depend on the initial nanocrystal size, shape, and crystal structure. We find that inks of predominantly wurtzite tetrapod-shaped nanocrystals with arms ∼5.6 nm in diameter exhibit better device performance compared to inks composed of smaller tetrapods, irregular faceted nanocrystals, or spherical zincblende nanocrystals despite the fact that the final sintered film has a zincblende crystal structure. Five different working device architectures were investigated. The indium tin oxide (ITO)/CdTe/zinc oxide structure leads to our best performing device architecture (with efficiency >11%) compared to others including two structures with a cadmium sulfide (CdS) n-type layer typically used in high efficiency sublimation-grown CdTe solar cells. Moreover, devices without CdS have improved response at short wavelengths.

Crystal structure, vibrational, spectral investigation, quantum chemical DFT calculations and thermal behavior of Diethyl [hydroxy (phenyl) methyl] phosphonate

NASA Astrophysics Data System (ADS)

Ouksel, Louiza; Chafaa, Salah; Bourzami, Riadh; Hamdouni, Noudjoud; Sebais, Miloud; Chafai, Nadjib

2017-09-01

Single Diethyl [hydroxy (phenyl) methyl] phosphonate (DHPMP) crystal with chemical formula C11H17O4P, was synthesized via the base-catalyzed Pudovik reaction and Lewis acid as catalyst. The results of SXRD analyzes indicate that this compound crystallizes into a mono-clinic system with space group P21/n symmetry and Z = 4. The crystal structure parameters are a = 9.293 Å, b = 8.103 Å, c = 17.542 Å, β = 95.329° and V = 1315.2 Å3, the structure displays one inter-molecular O-H⋯O hydrogen bonding. The UV-Visible absorption spectrum shows that the crystal exhibits a good optical transmission in the visible domain, and strong absorption in middle ultraviolet one. The vibrational frequencies of various functional groups present in DHPMP crystal have been deduced from FT-IR and FT-Raman spectra and then compared with theoretical values performed with DFT (B3LYP) method using 6-31G (p, d) basis sets. Chemical and thermodynamic parameters such as: ionization potential (I), electron affinity (A), hardness (σ), softness (η), electronegativity (χ) and electrophilicity index (ω), are also calculated using the same theoretical method. The thermal decomposition behavior of DHPMP, studied by using thermogravimetric analysis (TDG), shows a thermal stability until to 125 °C.

Hydrogen bonding intermolecular effect on electro-optical response of doped 6PCH nematic liquid crystal with some azo dyes

NASA Astrophysics Data System (ADS)

Kiani, S.; Zakerhamidi, M. S.; Tajalli, H.

2016-05-01

Previous studies on the electro-optical responses of dye-doped liquid crystal have shown that dopant material have a considerable effect on their electro-optical responses. Despite the studies carried out on electro-optical properties of dye-doped liquid crystal, no attention has been paid to study of the interaction and structural effects in this procedure. In this paper, linear dyes and with similar structure were selected as dopants. The only difference in used dyes is the functional groups in their tails. So, doping of these dyes into liquid crystals determines the influence of interaction type on electro-optical behaviours of the doped systems. Therefore, in this work, two aminoazobenzene (;A-dye;: hydrogen bond donor) and dimethyl-aminoazobenzene (;B-dye;) dyes with different compositional percentages in liquid crystal host were used. Electro-optical Kerr behaviour, the pre-transition temperature and third order nonlinear susceptibility were investigated. The obtained results effectively revealed that type of interactions between the dye and liquid crystal is determinative of behavioral difference of doped system, compared to pure liquid crystal. Also, pre-transitional behaviour and thereupon Kerr electro-optical responses were affected by formed interactions into doped systems. In other words, it will be shown that addition of any dopants in liquid crystal, regardless of the nature of interactions, cannot cause appropriate electro-optical responses. In fact, type of dye, nature of interactions between dopant and liquid crystalline host as well as concentration of dye are the key factors in selecting the appropriate liquid crystal and dopant dye.

Atomic Scale Medium Range Order and Relaxation Dynamics in Metallic Glass

NASA Astrophysics Data System (ADS)

Zhang, Pei

We studied the atomic scale structure of bulk metallic glass (BMG) with the combination of fluctuation electron microscopy (FEM) and hybrid reverse Monte Carlo (HRMC) simulation. Medium range order (MRO), which occupies the length scale between short range order (SRO) and long-range order, plays an important role on the properties of metallic glass, but the characterization of MRO in experiment is difficult because conventional techniques are not sensitive to the structure at MRO scale. Compared with the X-ray and neutron which can measure SRO by two-body correlation functions, FEM is an effective way to detect MRO structure through three and four-body correlation functions, providing information about the size, distribution, and internal structure of MRO combing HRMC modeling. Thickness estimation is necessary in FEM experiment and HRMC calculation, so in Chapter 3, we measured the elastic and inelastic mean free paths of metallic glass alloys based on focused ion beam prepared thin samples with measured thickness gradients. We developed a model based on the Wentzel atomic model to predict the elastic mean free path for other amorphous materials. In Chapter 4, we studied the correlation of MRO and glass forming ability ZrCuAl alloy. Results from Variable resolution fluctuation microscopy show that in Zr50Cu35Al15 the crystal-like clusters shrink but become more ordered, while icosahedral-like clusters grow. Compared with Zr50Cu45Al5, Zr50Cu35Al15 with poorer glass forming ability exhibits more stable crystal-like structure under annealing, indicating that destabilizing crystal-like structures is important to achieve better glass forming ability in this alloy. In Chapter 5, we studied the crystallization and MRO structural in deformed and quenched Ni60Nb40 metallic glass. The deformed Ni60Nb40 contains fewer icosahedral-like Voronoi clusters and more crystal-like and bcc-like Voronoi clusters. The crystal-like and bcc-like medium range order clusters may be the structural origin for its lower crystallization temperature compared with quenched alloy. Dynamics heterogeneity is proposed to be the microscopic origin of the dynamic nature of glass transition. Some experimental evidence and simulation have indicated that different regions of materials indeed relax at fast or slow rate. However, the spatial distribution of relaxation time visualized from the experiment as the direct evidence of heterogeneous dynamics is still challenging. We proposed to measure the structural dynamics of supercooled metallic glasses with electron correlation microscopy (ECM) technique at the nanometer scale. ECM was developed as a way to measure structural relaxation times of liquids with nanometer-scale spatial resolution using the coherent electron scattering equivalent of photon correlation spectroscopy. In chapter 6, we studied the experimental requirements of ECM to obtain reliable results. For example, the trajectory length must be at least 40 times the relaxation time to obtain a well-converged g2( t), and the time per frame must be less than 0.1 time the relaxation time to obtain sufficient sampling. ECM experiment was firstly realized in scanning transmission electron microscopy (STEM) mode and applied to measure the structural relaxation time of Pd based metallic glass. In order to overcome the drift problem and capture the spatial information, we developed ECM experiment in dark field (DF) mode. In Chapter 7, through DF-ECM, we visualized the spatially heterogeneous dynamics by in-situ heating Pt57.5Cu14.7Ni 5.3P22.5 nanowire into supercooled liquid state, and quantify the size of the heterogeneity by four-point correlation function. The thickness effect and temporal evolution of the heterogeneous domain were also discussed. Additionally, a fast near-surface dynamics was discovered, providing an effective mechanism for surface crystallization of liquids by homogeneous nucleation.

The effect of crystal structure of TiO2 nanotubes on the formation of calcium phosphate coatings during biomimetic deposition

NASA Astrophysics Data System (ADS)

Liu, Yi; Kim, Sun; McLeod, John A.; Li, Jun; Guo, Xiaoxuan; Sham, Tsun-Kong; Liu, Lijia

2017-02-01

The crystallization process of bioactive calcium phosphate (CaP) species via biomimetic deposition onto anodic TiO2 nanotubes is investigated. The porous surface of nanostructured TiO2 provides an ideal substrate for CaP crystallization. The compositions of CaP coatings are studied using X-ray absorption near-edge structures (XANES) at the Ca K-edge. Using detection modes with different probing depths, both the surface of the CaP coating and the CaP-TiO2 interface are simultaneously analyzed. Calcium phosphate (CaP) species, such as hydroxyapatite (HAp), octacalcium phosphate (Ca8(HPO4)2(PO4)4·5H2O, OCP), brushite (CaHPO4·2H2O, DCPD), and amorphous calcium phosphate (ACP), are found in the CaP coatings. TiO2 nanotubes of amorphous and anatase phases are comparatively studied to determine their effect on the efficiency of CaP formation and the phase transformation among CaP species in prolonged deposition time. It is found the composition of CaP coating has a strong dependency on the crystal structure of TiO2 substrate and the kinetics (deposition time).

Growth of NBT-BT single crystals by flux method and their structural, morphological and electrical characterizations

NASA Astrophysics Data System (ADS)

Kanuru, Sreenadha Rao; Baskar, K.; Dhanasekaran, R.; Kumar, Binay

2016-05-01

In this paper, one of the important, eco-friendly polycrystalline material, (1-x)(Na0.5Bi0.5)TiO3 (NBT) - xBaTiO3 (BT) of different compositions (x=0.07, 0.06 and 0.05 wt%) around the morphotropic phase boundary (MPB) were synthesized by solid state reaction technique. And the single crystals with 13×7×7 mm3, 12×12×7 mm3 and 10×7×4 mm3 dimensions were grown by self flux method. The morphology, crystal structure and unit-cell parameters have been studied and the monoclinic phase has been identified for 0.07 wt% of BT. Higher BT concentration changes the crystal habit and the mechanism has been studied clearly. Raman spectroscopy at room-temperature confirms the presence of functional groups. The quality of the as grown single crystals was examined by high resolution x-ray diffraction analysis. The dielectric properties of the as grown crystals were investigated in the frequency range of 20 Hz-2 MHz from room temperature to 450 °C. The broad dielectric peak and frequency dispersion demonstrates the relaxor behavior of grown crystals. The dielectric constant (εr), transition temperature (Tm), and depolarization temperature (Td) of the grown crystals are found to be comparatively good. The diffusive factor (γ) from Curie-Weiss law confirms the as grown NBT-BT single crystals are relaxor in nature.

Comparative analysis of thermal behavior, isothermal crystallization kinetics and polymorphism of palm oil fractions.

PubMed

Zhang, Xia; Li, Lin; Xie, He; Liang, Zhili; Su, Jianyu; Liu, Guoqin; Li, Bing

2013-01-15

Thermal behavior of palm stearin (PS) and palm olein (PO) was explored by monitoring peak temperature transitions by differential scanning calorimetry (DSC). The fatty acid composition (FAC), isothermal crystallization kinetics studied by pulsed Nuclear Magnetic Resonance (pNMR) and isothermal microstructure were also compared. The results indicated that the fatty acid composition had an important influence on the crystallization process. PS and PO both exhibited more multiple endotherms than exotherms which showed irregular peak shapes. An increasing in cooling rate, generally, was associated with an increase in peak size. Application of the Avaimi equation to isothermal crystallization of PS and PO revealed different nucleation and growth mechanisms based on the Avrami exponents. PS quickly reached the end of crystallization because of more saturated triacylglycerol (TAG). The Avrami index of PS were the same as PO under the same isothermal condition at lower temperatrue, indicating that the crystallization mechanism of the two samples based on super-cooling state were the same. According to the polarized light microscope (PLM) images, crystal morphology of PS and PO was different. With the temperature increased, the structure of crystal network of both PS and PO gradually loosened.

Temperature Dependence of Density, Viscosity and Electrical Conductivity for Hg-Based II-VI Semiconductor Melts

NASA Technical Reports Server (NTRS)

Li, C.; Ban, H.; Lin, B.; Scripa, R. N.; Su, C.-H.; Lehoczky, S. L.

2004-01-01

The relaxation phenomenon of semiconductor melts, or the change of melt structure with time, impacts the crystal growth process and the eventual quality of the crystal. The thermophysical properties of the melt are good indicators of such changes in melt structure. Also, thermophysical properties are essential to the accurate predication of the crystal growth process by computational modeling. Currently, the temperature dependent thermophysical property data for the Hg-based II-VI semiconductor melts are scarce. This paper reports the results on the temperature dependence of melt density, viscosity and electrical conductivity of Hg-based II-VI compounds. The melt density was measured using a pycnometric method, and the viscosity and electrical conductivity were measured by a transient torque method. Results were compared with available published data and showed good agreement. The implication of the structural changes at different temperature ranges was also studied and discussed.

Impact of Protein-Metal Ion Interactions on the Crystallization of Silk Fibroin Protein

NASA Astrophysics Data System (ADS)

Hu, Xiao; Lu, Qiang; Kaplan, David; Cebe, Peggy

2009-03-01

Proteins can easily form bonds with a variety of metal ions, which provides many unique biological functions for the protein structures, and therefore controls the overall structural transformation of proteins. We use advanced thermal analysis methods such as temperature modulated differential scanning calorimetry and quasi-isothermal TMDSC, combined with Fourier transform infrared spectroscopy, and scanning electron microscopy, to investigate the protein-metallic ion interactions in Bombyx mori silk fibroin proteins. Silk samples were mixed with different metal ions (Ca^2+, K^+, Ma^2+, Na^+, Cu^2+, Mn^2+) with different mass ratios, and compared with the physical conditions in the silkworm gland. Results show that all metallic ions can directly affect the crystallization behavior and glass transition of silk fibroin. However, different ions tend to have different structural impact, including their role as plasticizer or anti-plasticizer. Detailed studies reveal important information allowing us better to understand the natural silk spinning and crystallization process.

Effect of Li and NH4 doping on the crystal perfection, second harmonic generation efficiency and laser damage threshold of potassium pentaborate crystals

NASA Astrophysics Data System (ADS)

Vigneshwaran, A. N.; Kalainathan, S.; Raja, C. Ramachandra

2018-03-01

Potassium pentaborate (KB5) is an excellent nonlinear optical material especially in the UV region. In this work, Li and NH4 doped KB5 crystals were grown using slow evaporation solution growth method. The incorporation of dopant has been confirmed and analysed by Energy dispersive X-ray analysis (EDAX), Inductively coupled plasma (ICP) analysis and Raman spectroscopy. The crystalline perfection of pure and doped KB5 crystals was studied by High resolution X-ray diffraction (HRXRD) analysis. Structural grain boundaries were observed in doped crystals. Second harmonic generation was confirmed for pure and doped crystals and output values revealed the enhancement of SHG efficiency in doped crystals. Resistance against laser damage was carried out using 1064 nm Nd-YAG laser of pulse width 10 ns. The laser damage threshold value is increased in Li doped crystal and decreased in NH4 doped crystal when compared to pure KB5 crystal.

Optical and dielectric studies of KH2PO4 crystal influenced by organic ligand of citric acid and L-valine: A single crystal growth and comparative study

NASA Astrophysics Data System (ADS)

Anis, Mohd; Hakeem, D. A.; Muley, G. G.

In the present study pure, citric acid (CA) and L-valine (LV) doped potassium dihydrogen phosphate (KDP) crystals have been grown with the aim to investigate the nonlinear optical applications facilitated by UV-visible, third order nonlinear optical (TONLO) and dielectric properties. The structural parameters of grown crystals have been confirmed by single crystal X-ray diffraction analysis. The enhancement in optical transparency of KDP crystal due to addition of CA and LV has been examined within 200-900 nm by means of UV-visible spectral analysis. In addition, the transmittance data have been used to evaluate the effect of dopants on reflectance, refractive index and extinction coefficient of grown crystals in the visible region. The Z-scan analysis has been performed at 632.8 nm to identify the nature of photoinduced nonlinear refraction and nonlinear absorption in doped KDP crystals. The influence of π-bonded ligand of dopant CA and LV on TONLO susceptibility (χ3), refractive index (n2) and absorption coefficient (β) of KDP crystals has been evaluated to discuss laser assisted device applications. The decrease in dielectric constant and dielectric loss of KDP crystal due to addition of CA and LV has been explored using the temperature dependent dielectric studies.

Co-crystallization of cholesterol and calcium phosphate as related to atherosclerosis

NASA Astrophysics Data System (ADS)

Hirsch, Danielle; Azoury, Reuven; Sarig, Sara

1990-09-01

Calcification of atherosclerotic plaques occurs very frequently and aggravates the disease. In biological systems, epitaxial relationships between crystal structures may be important in nucleating the deposit of a solid phase. The biologically preferred calcium phosphate species, apatite, and cholesterol crystal have structurally compatible crystallographic faces which allow epitaxial growth of one crystal upon another. The present study describes a new approach to explore, in vitro, the crystallization processes of calcium phosphate (CaP) with cholesterol (CS) and cholestanol (CN) which are related to atherosclerosis. Aqueous solutions containing calcium and phosphate ions or CaP crystals as hydroxyapatite were added into saturated ethanolic solutions of CS or CS and 10% CN. After precipitation, crystals were collected and analyzed by nuclear magnetic resonance (NMR), infra-red (IR), X-ray, scanning electron microscope (SEM-LINK), differential scanning calorimeter (DSC) and atomic absorption. The principal result is the well-formed crystals precipitation when an aqueous solution and CaP seed crystals were added to saturated solutions of CS and 10% CN. Cholesterol-cholestanol dihydrate (CC2W) crystals precipitated in the presence of CaP seeds were compared to the CC2W crystals obtained without the mineral compound. The results of this comparison indicate a special link between crystals of CaP and CC2W, and support the epitaxial relationship between the two kinds of crystals. The potential of CC2W crystals to be precipitated by CaP seed crystals prove likewise the possible significant role of the cholestanol metabolite in the process of cholesterol crystallization and calcification in the arteries.

Crystallization and textural porosity of synthetic clay minerals.

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

Carrado, K. A.; Csencsits, R.; Thiyagarajan, P.

2002-12-01

The crystallization of synthetic layered magnesium silicate hectorite clays from both silica sol and organosilane sources is compared. For the silica sol-derived clays, a templating method is employed wherein organic or polymeric molecules are included during clay crystallization that are then removed from the composites via calcination. The mechanism of silane-derived hectorite formation is followed by XRD, TGA, 29Si MAS NMR, and small angle X-ray scattering (SAXS), and results are compared to those obtained for the sol-derived hectorite. The mechanism appears to be similar but the rate is approximately doubled when the silane is used rather than silica sol. Analyticalmore » transmission electron microscopy (TEM) is exploited to glean structural morphology information towards resolving the nature of the resulting pore network structures. Results are compared with nitrogen adsorption-desorption isotherm behavior; dominant hysteresis loops are present in the type IV isotherms. Pore size distributions based on both the adsorption and desorption isotherms are compared. Small angle neutron scattering (SANS) experiments reveal that the average particle size increases as synthetic laponite < sol-derived hectorite < silane-derived hectorite < natural hectorite. Contrast matching SANS studies in aqueous and organic solvents are carried out to extract information about pore accessibility.« less

A phase width for CaGaSn. Crystal structure of mixed intermetallic Ca{sub 4}Ga{sub 4+x}Sn{sub 4−x} and SmGa{sub x}Sn{sub 3−x}, stability, geometry and electronic structure

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

Tillard, Monique, E-mail: mtillard@univ-montp2.fr

X-ray single-crystal structure has been established for new compositions in intermetallic systems of tin and gallium. Crystals were successfully obtained in alloys prepared from elements. The structure of SmGaSn{sub 2} (cubic Pm3̄m, a=4.5778(8) Å, Z=1, R1=0.012) is described with atomic disorder at all Sn/Ga positions and the structure of Ca{sub 4}Ga{sub 4.9}Sn{sub 3.1} (hexagonal, P6{sub 3}/mmc, a=4.2233(9), c=17.601(7) Å, Z=1, R1=0.062) raises an interesting question about existence of a composition domain for CaGaSn. Finally, Ca{sub 4}Ga{sub 4.9}Sn{sub 3.1} should be considered as a particular composition of Ca{sub 4}Ga{sub 4+x}Sn{sub 4−x}, a compound assumed to exist in the range x ~more » 0−1. Partial atomic ordering characterizes the Sn/Ga puckered layers of hexagons whose geometries are analyzed and discussed comparatively with analogous arrangements in AlB{sub 2} related hexagonal compounds. The study is supported by rigid band model and DFT calculations performed for different experimental and hypothetic arrangements. - Graphical abstract: A phase width for Ca{sub 4}Ga{sub 4+x}Sn{sub 4−x} belonging to the hexagonal YPtAs structure-type. - Highlights: • Single crystals of mixed tin gallium ternary intermetallics were obtained. • Partial ordering at metal sites and phase width are evidenced for Ca{sub 4}Ga{sub 4+x}Sn{sub 4−x}. • Layer deviation to flatness is studied comparatively with related structures. • Geometry and stability analyses based on DFT calculations are provided.« less

Comparative study of crystallization process in metallic melts using ab initio molecular dynamics simulations

NASA Astrophysics Data System (ADS)

Debela, Tekalign T.; Wang, X. D.; Cao, Q. P.; Zhang, D. X.; Jiang, J. Z.

2017-05-01

The crystallization process of liquid metals is studied using ab initio molecular dynamics simulations. The evolution of short-range order during quenching in Pb and Zn liquids is compared with body-centered cubic (bcc) Nb and V, and hexagonal closed-packed (hcp) Mg. We found that the fraction and type of the short-range order depends on the system under consideration, in which the icosahedral symmetry seems to dominate in the body-centered cubic metals. Although the local atomic structures in stable liquids are similar, liquid hcp-like Zn, bcc-like Nb and V can be deeply supercooled far below its melting point before crystallization while the supercooled temperature range in liquid Pb is limited. Further investigations into the nucleation process reveal the process of polymorph selection. In the body-centered cubic systems, the polymorph selection occurs in the supercooled state before the nucleation is initiated, while in the closed-packed systems it starts at the time of onset of crystallization. Atoms with bcc-like lattices in all studied supercooled liquids are always detected before the polymorph selection. It is also found that the bond orientational ordering is strongly correlated with the crystallization process in supercooled Zn and Pb liquids.

Biomineral nanoparticles are space-filling

NASA Astrophysics Data System (ADS)

Yang, Li; Killian, Christopher E.; Kunz, Martin; Tamura, Nobumichi; Gilbert, P. U. P. A.

2011-02-01

Sea urchin biominerals have been shown to form from aggregating nanoparticles of amorphous calcium carbonate (ACC), which then crystallize into macroscopic single crystals of calcite. Here we measure the surface areas of these biominerals and find them to be comparable to those of space-filling macroscopic geologic calcite crystals. These biominerals differ from synthetic mesocrystals, which are invariably porous. We propose that space-filling ACC is the structural precursor for echinoderm biominerals.Sea urchin biominerals have been shown to form from aggregating nanoparticles of amorphous calcium carbonate (ACC), which then crystallize into macroscopic single crystals of calcite. Here we measure the surface areas of these biominerals and find them to be comparable to those of space-filling macroscopic geologic calcite crystals. These biominerals differ from synthetic mesocrystals, which are invariably porous. We propose that space-filling ACC is the structural precursor for echinoderm biominerals. This article was submitted as part of a Themed Issue on Crystallization and Formation Mechanisms of Nanostructures. Other papers on this topic can be found in issue 11 of vol. 2 (2010). This issue can be found from the Nanoscale homepage [http://www.rsc.org/nanoscale

Crystal structure analysis of Great Cormorant (Phalacrocorax carbo) Hemoglobin.

PubMed

Ganapathy, Jagadeesan; Palayam, Malathy; Pennathur, Gautam; Sanmargam, Aravindhan; Krishnasamy, Gunasekaran

2018-06-20

Hemoglobin (Hb) molecule consists of α2β2 dimers arranged in fashion having pseudo-222 symmetry. The subunits are composed of the specific functional prosthetic group "heme'' and a protein moiety "globin". Bird Hbs are functionally similar to mammalian Hbs and regulated by inositol pentaphosphate (IPP) but they are structurally dissimilar with mammalian Hbs in adaptation to vital environment such as high altitudes, high speed flights and oxygen affinity. The insufficient structural studies on avian Hbs limit us to understand their degree of adaptation to such critical environments. So far, detailed structural studies of bar-headed goose (BHG) and graylag goose (GLG) Hb structures were reported to expose their remarkable difference in molecular level adaptation. The striking contrasts to its close relative the bar headed goose, which lives at high altitude and capable of tolerating severe hypoxic environment is mainly due its structural features. The Great Cormorant (GCT) can fly and swim, the dual characteristic of GCT leads to study the details of adaptation of high oxygen affinity in avian species and to know about the role of amino acid substitutions at α1β1 interface, the crystal structure of Great cormorant is studied. The structure of GCT Hb has been solved at 3.5Å resolution and it is compared with the other high oxygen affinity Hb (graylag goose (GLG), bar headed goose (BHG) and human (HMN) hemoglobin) structures. To determine the crystal structure of Great Cormorant (GCT) Hemoglobin and to compare its three dimensional structure with other high and low oxygen affinity hemoglobin species to understand its characteristic features of high oxygen affinity. The GCT hemoglobin has been purified, crystallized and data sets were processed using iMosflm. The integrated data has been solved using Molecular replacement method using Graylag hemoglobin (1FAW) as the template. The structure refinement has been carried out using Refmac which reduced the Rwork and Rfree to 23% and 27% respectively. The structure has been deposited in Protein Data Bank with PDB code: 3WR1. The Great cormorant hemoglobin consists of 287 amino acids, two heme and one water molecule located in alpha heme site. The structure has been crystallized in a tetragonal system having half a molecule in the assymetric unit. In order to characterize the tertiary and quaternary structural differences, the structure of cormorant hemoglobin is compared with GLG, BHG and human Hb. The larger variation observed between GCT and human Hb indicates that GCT Hb differs remarkably from human. The α1β1 interface of Great cormorant Hb is similar to bar-headed goose Hb with few amino acid substitutions. It has been found that the interaction which is common among avian hemoglobins (α119 Pro- β55Leu) is altered by Ala 119 in GCT. This intra-dimer contact (α119 Pro - β 55 Leu) disruption leads to high oxygen affinity in BGH Hb. In cormorant, GLG and human the proline is unchanged but interestingly, in cormorant Hb, the β55 position was found to be Thr instead of Leu. Similar kind of substitutions (β 55 Leu - Ser) observed in Andean goose Hb structure leads to elevated oxygen affinity between Hb-O2. To our surprise, such type of substitution at β 55 (Thr) in cormorant Hb confirms that it is comparable with Andean goose Hb structure. Thus the sequence, structural differences at alpha, beta heme pocket and interface contacts confirms that GCT adopts high oxygen affinity conformation. The three dimensional structure of Great cormorant hemoglobin has been investigated to understand its unique structural features to adopt during hypoxia condition. The comparative studies of GCT's α, β heme pockets and the subunit interface with other Hbs reveal its similarities with goose Hbs. Also the loss of α119 - β55 contact in GCT and its unique mutation (Leu β55 Thr ) as in goose Hbs may play an important role in oxygen affinity. Thus by comparing the sequence and overall structural similarities with high and low oxygen affinity species, it appears that GCT has more possibilities to subsist with low oxygen demand. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

Preparation, crystal structure, vibrational spectral and density functional studies of bis (4-nitrophenol)-2,4,6-triamino-1,3,5-triazine monohydrate

NASA Astrophysics Data System (ADS)

Kanagathara, N.; Marchewka, M. K.; Drozd, M.; Renganathan, N. G.; Gunasekaran, S.; Anbalagan, G.

2013-10-01

An organic-organic salt, bis (4-nitrophenol) 2,4,6-triamino 1,3,5-triazine monohydrate (BNPM) has been prepared by slow evaporation technique at room temperature. Single crystal X-ray diffraction analysis reveals that the compound crystallizes in triclinic system with centrosymmetric space group P-1. IR and Raman spectra of BNPM have been recorded and analyzed. The study has been extended to confocal Raman spectral analysis. Band assignments have been made for the melamine and p-nitrophenol molecules. Vibrational spectra have also been discussed on the basis of quantum chemical density functional theory calculations using Firefly (PC GAMESS) Version 7.1 G. Vibrational frequencies are calculated and scaled values are compared with the experimental one. The Mulliken charges, HOMO-LUMO orbital energies are calculated and analyzed. The chemical structure of the compound was established by 1H NMR and 13C NMR spectra.

Tailoring single-cycle electromagnetic pulses in the 2-9 THz frequency range using DAST/SiO₂ multilayer structures pumped at Ti:sapphire wavelength.

PubMed

Stepanov, Andrei G; Rogov, Andrii; Bonacina, Luigi; Wolf, Jean-Pierre; Hauri, Christoph P

2014-09-08

We present a numerical parametric study of single-cycle electromagnetic pulse generation in a DAST/SiO₂multilayer structure via collinear optical rectification of 800 nm femtosecond laser pulses. It is shown that modifications of the thicknesses of the DAST and SiO₂layers allow tuning of the average frequency of the generated THz pulses in the frequency range from 3 to 6 THz. The laser-to-THz energy conversion efficiency in the proposed structures is compared with that in a bulk DAST crystal and a quasi-phase-matching periodically poled DAST crystal and shows significant enhancement.

Crystal structure of bile salt hydrolase from Lactobacillus salivarius.

PubMed

Xu, Fuzhou; Guo, Fangfang; Hu, Xiao Jian; Lin, Jun

2016-05-01

Bile salt hydrolase (BSH) is a gut-bacterial enzyme that negatively influences host fat digestion and energy harvesting. The BSH enzyme activity functions as a gateway reaction in the small intestine by the deconjugation of glycine-conjugated or taurine-conjugated bile acids. Extensive gut-microbiota studies have suggested that BSH is a key mechanistic microbiome target for the development of novel non-antibiotic food additives to improve animal feed production and for the design of new measures to control obesity in humans. However, research on BSH is still in its infancy, particularly in terms of the structural basis of BSH function, which has hampered the development of BSH-based strategies for improving human and animal health. As an initial step towards the structure-function analysis of BSH, C-terminally His-tagged BSH from Lactobacillus salivarius NRRL B-30514 was crystallized in this study. The 1.90 Å resolution crystal structure of L. salivarius BSH was determined by molecular replacement using the structure of Clostridium perfringens BSH as a starting model. It revealed this BSH to be a member of the N-terminal nucleophile hydrolase superfamily. Crystals of apo BSH belonged to space group P21212, with unit-cell parameters a = 90.79, b = 87.35, c = 86.76 Å (PDB entry 5hke). Two BSH molecules packed perfectly as a dimer in one asymmetric unit. Comparative structural analysis of L. salivarius BSH also identified potential residues that contribute to catalysis and substrate specificity.

Growth, crystalline perfection, spectral, thermal and theoretical studies on imidazolium L-tartrate crystals.

PubMed

Meena, K; Muthu, K; Meenatchi, V; Rajasekar, M; Bhagavannarayana, G; Meenakshisundaram, S P

2014-04-24

Transparent optical quality single crystals of imidazolium L-tartrate (IMLT) were grown by conventional slow evaporation solution growth technique. Crystal structure of the as-grown IMLT was determined by single crystal X-ray diffraction analysis. Thermal analysis reveals the purity of the crystal and the sample is stable up to the melting point. Good transmittance in the visible region is observed and the band gap energy is estimated using diffuse reflectance data by the application of Kubelka-Munk algorithm. The powder X-ray diffraction study reveals the crystallinity of the as-grown crystal and it is compared with that of the experimental one. An additional peak in high resolution X-ray diffraction (HRXRD) indicates the presence of an internal structural low angle boundary. Second harmonic generation (SHG) activity of IMLT is significant as estimated by Kurtz and Perry powder technique. HOMO-LUMO energies and first-order molecular hyperpolarizability of IMLT have been evaluated using density functional theory (DFT) employing B3LYP functional and 6-31G(d,p) basis set. The optimized geometry closely resembles the ORTEP. The vibrational patterns present in the molecule are confirmed by FT-IR coinciding with theoretical patterns. Copyright © 2014 Elsevier B.V. All rights reserved.

Production, Purification and Preliminary X-ray Crystallographic Studies of Adeno-Associated Virus Serotype 9

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

Mitchell, M.; Nam, H; Carter, A

2009-01-01

Adeno-associated virus (AAV) serotype 9, which is under development for gene-delivery applications, shows significantly enhanced capsid-associated transduction efficiency in muscle compared with other AAV serotypes. With the aim of characterizing the structural determinants of this property, the purification, crystallization and preliminary X-ray crystallographic analyses of the AAV9 viral capsid are reported. The crystals diffracted X-rays to 2.8 A resolution using synchrotron radiation and belonged to the trigonal space group P32, with unit-cell parameters a = b = 251.0, c = 640.0 A. There are three complete viral capsids in the crystal unit cell. The orientation and position of the asymmetricmore » unit capsid have been determined by molecular-replacement methods and structure determination is in progress.« less

Crystal structure, spectral property, antimicrobial activity and DFT calculation of N-(coumarin-3-yl)-N‧-(2-amino-5-phenyl-1,3,4-thiadiazol-2-yl) urea

NASA Astrophysics Data System (ADS)

Zhang, Hong-Song; Zhang, Kong-Yan; Chen, Li-Chuan; Li, Yao-Xin; Chai, Lan-Qin

2017-10-01

N-(coumarin-3-yl)-N‧-(2-amino-5-phenyl-1,3,4-thiadiazol-2-yl) urea was synthesized and characterized by elemental analysis, IR, 1H NMR, 13C NMR, UV-Vis and emission spectroscopy, as well as by single-crystal X-ray diffraction. X-ray crystallographic analyses have indicated that the crystal structure consists of two dimethyl sulfoxide (DMSO) solvent molecules and the structural geometry of DMSO is a trigonal pyramid in shape. In the crystal structure, a self-assembling two-dimensional (2-D) layer supramolecular architecture is formed through intermolecular hydrogen bonds, Cdbnd O···π (thiadiazole ring) and π···π stacking interactions. The geometry of the compound has been optimized by the DFT method and the results are compared with the X-ray diffraction data. The electronic transitions and spectral features of the compound were carried out by using DFT/B3LYP method. In addition, the antimicrobial activity was also studied, and the highest occupied molecular orbital (HOMO), lowest unoccupied molecular orbital (LUMO), and HOMO-LUMO gap were also calculated.

High-pressure crystal structures of an insensitive energetic crystal: 1,1-diamino-2,2-dinitroethene

DOE PAGES

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

2015-12-03

Understanding the insensitivity/stability of insensitive high explosive crystals requires detailed structural information at high pressures and high temperatures of interest. Synchrotron single crystal x-ray diffraction experiments were used to determine the high-pressure structures of 1,1-diamino-2,2-dinitroethene (FOX-7), a prototypical insensitive high explosive. The phase transition around 4.5 GPa was investigated and the structures were determined at 4.27 GPa (α’-phase) and 5.9 GPa (ε-phase). The α’-phase (monoclinic, P2 1/ n), structurally indistinguishable from the ambient α-phase, transforms to the new ε-phase (triclinic, P1). The most notable features of the ε-phase, compared to the α’-phase, are: formation of planar layers and flattening ofmore » molecules. Density functional theory (DFT-D2) calculations complemented the experimental results. Furthermore, the results presented here are important for understanding the molecular and crystalline attributes governing the high-pressure insensitivity/stability of insensitive high explosive crystals.« less

High-pressure crystal structures of an insensitive energetic crystal: 1,1-diamino-2,2-dinitroethene

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

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

Understanding the insensitivity/stability of insensitive high explosive crystals requires detailed structural information at high pressures and high temperatures of interest. Synchrotron single crystal x-ray diffraction experiments were used to determine the high-pressure structures of 1,1-diamino-2,2-dinitroethene (FOX-7), a prototypical insensitive high explosive. The phase transition around 4.5 GPa was investigated and the structures were determined at 4.27 GPa (α’-phase) and 5.9 GPa (ε-phase). The α’-phase (monoclinic, P2 1/ n), structurally indistinguishable from the ambient α-phase, transforms to the new ε-phase (triclinic, P1). The most notable features of the ε-phase, compared to the α’-phase, are: formation of planar layers and flattening ofmore » molecules. Density functional theory (DFT-D2) calculations complemented the experimental results. Furthermore, the results presented here are important for understanding the molecular and crystalline attributes governing the high-pressure insensitivity/stability of insensitive high explosive crystals.« less

Superheating Suppresses Structural Disorder in Layered BiI3 Semiconductors Grown by the Bridgman Method

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

Johns, Paul M.; Sulekar, Soumitra; Yeo, Shinyoung

2016-01-01

The susceptibility of layered structures to stacking faults is a problem in some of the more attractive semiconductor materials for ambient-temperature radiation detectors. In the work presented here, Bridgman-grown BiI3 layered single crystals are investigated to understand and eliminate this structural disorder, which reduces radiation detector performance. The use of superheating gradients has been shown to improve crystal quality in non-layered semiconductor crystals; thus the technique was here explored to improve the growth of BiI3. When investigating the homogeneity of non-superheated crystals, highly geometric void defects were found to populate the bulk of the crystals. Applying a superheating gradient tomore » the melt prior to crystal growth improved structural quality and decreased defect density from the order of 4600 voids per cm3 to 300 voids per cm3. Corresponding moderate improvements to electronic properties also resulted from the superheat gradient method of crystal growth. Comparative measurements through infrared microscopy, etch-pit density, x-ray rocking curves, and sheet resistivity readings show that superheat gradients in BiI3 growth led to higher quality crystals.« less

Selenium Derivatization of Nucleic Acids for Crystallography

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

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

2007-01-01

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

Growth of LiNbO{sub 3}:Er Crystals and concentration dependences of their properties

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

Palatnikov, M. N., E-mail: palat-mn@chemy.kolasc.net.ru; Biryukova, I. V.; Shcherbina, O. B.

2016-11-15

A series of lithium niobate (LiNbO{sub 3}) crystals of congruent and stoichiometric compositions, doped with erbium, have been grown under non-steady-state thermal conditions. A series of LiNbO{sub 3}:Zn crystals, nominally pure LiNbO{sub 3} crystals of congruent and stoichiometric compositions, and a LiNbO{sub 3}:B crystal have also been grown. Both growth conditions and concentration dependences of physicochemical, ferroelectric, and structural characteristics of LiNbO{sub 3}:Er crystals are investigated. The growth regular domain microstructures and periodic nanostructures in LiNbO{sub 3}:Er crystals are analyzed by optical microscopy and atomic force microscopy (AFM). A comparative study of the optical homogeneity and photorefractive properties of LiNbO{submore » 3}:Er crystals of congruent and stoichiometric compositions and the Raman spectra of LiNbO{sub 3} crystals of different compositions is performed.« less

A hybrid phononic crystal for roof application.

PubMed

Wan, Qingmian; Shao, Rong

2017-11-01

Phononic crystal is a type of acoustic material, and the study of phononic crystals has attracted great attention from national research institutions. Meanwhile, noise reduction in the low-frequency range has always encountered difficulties and troubles in the engineering field. In order to obtain a unique and effective low-frequency noise reduction method, in this paper a low frequency noise attenuation system based on phononic crystal structure is proposed and demonstrated. The finite element simulation of the band gap is consistent with the final test results. The effects of structure parameters on the band gaps were studied by changing the structure parameters and the band gaps can be controlled by suitably tuning structure parameters. The structure and results provide a good support for phononic crystal structures engineering application.

Influence of mixing and ultrasound frequency on antisolvent crystallisation of sodium chloride.

PubMed

Lee, Judy; Ashokkumar, Muthupandian; Kentish, Sandra E

2014-01-01

Ultrasound is known to promote nucleation of crystals and produce a narrower size distribution in a controlled and reproducible manner for the crystallisation process. Although there are various theories that suggest cavitation bubbles are responsible for sonocrystallisation, most studies use power ultrasonic horns that generate both intense shear and cavitation and this can mask the role that cavitation bubbles play. High frequency ultrasound from a plate transducer can be used to examine the effect of cavitation bubbles without the intense shear effect. This study reports the crystal size and morphology with various mixing speeds and ultrasound frequencies. The results show high frequency ultrasound produced sodium chloride crystals of similar size distribution as an ultrasonic horn. In addition, ultrasound generated sodium chloride crystals having a more symmetrical cubic structure compared to crystals produced by a high shear mixer. Copyright © 2013 Elsevier B.V. All rights reserved.

Predicting patchy particle crystals: variable box shape simulations and evolutionary algorithms.

PubMed

Bianchi, Emanuela; Doppelbauer, Günther; Filion, Laura; Dijkstra, Marjolein; Kahl, Gerhard

2012-06-07

We consider several patchy particle models that have been proposed in literature and we investigate their candidate crystal structures in a systematic way. We compare two different algorithms for predicting crystal structures: (i) an approach based on Monte Carlo simulations in the isobaric-isothermal ensemble and (ii) an optimization technique based on ideas of evolutionary algorithms. We show that the two methods are equally successful and provide consistent results on crystalline phases of patchy particle systems.

Crystal structure of hemoglobin from the maned wolf (Chrysocyon brachyurus) using synchrotron radiation.

PubMed

Fadel, Valmir; Canduri, Fernanda; Olivieri, Johnny R; Smarra, André L S; Colombo, Marcio F; Bonilla-Rodriguez, Gustavo O; de Azevedo, Walter F

2003-12-01

Crystal structure of hemoglobin isolated from the Brazilian maned wolf (Chrysocyon brachyurus) was determined using standard molecular replacement technique and refined using maximum-likelihood and simulated annealing protocols to 1.87A resolution. Structural and functional comparisons between hemoglobins from the Chrysocyon brachyurus and Homo sapiens are discussed, in order to provide further insights in the comparative biochemistry of vertebrate hemoglobins.

Protein crystal growth in microgravity: Temperature induced large scale crystallization of insulin

NASA Technical Reports Server (NTRS)

Long, Marianna M.; Delucas, Larry J.; Smith, C.; Carson, M.; Moore, K.; Harrington, Michael D.; Pillion, D. J.; Bishop, S. P.; Rosenblum, W. M.; Naumann, R. J.

1994-01-01

One of the major stumbling blocks that prevents rapid structure determination using x-ray crystallography is macro-molecular crystal growth. There are many examples where crystallization takes longer than structure determination. In some cases, it is impossible to grow useful crystals on earth. Recent experiments conducted in conjuction with NASA on various Space Shuttle missions have demonstrated that protein crystals often grow larger and display better internal molecular order than their earth-grown counterparts. This paper reports results from three Shuttle flights using the Protein Crystallization Facility (PCF). The PCF hardware produced large, high-quality insulin crystals by using a temperature change as the sole means to affect protein solubility and thus, crystallization. The facility consists of cylinders/containers with volumes of 500, 200, 100, and 50 ml. Data from the three Shuttle flights demonstrated that larger, higher resolution crystals (as evidenced by x-ray diffraction data) were obtained from the microgravity experiments when compared to earth-grown crystals.

Crystal structure of a new variety of lead dodecaborate Pb{sub 6}(Li{sub 0.65}Na{sub 0.19})[B{sub 12}O{sub 24}]I{sub 0.84} {center_dot} 0.168H{sub 2}O and its comparison with beryl and cordierite

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

Belokoneva, E. L., E-mail: elbel@geol.msu.ru; Derkach, I. K.; Dimitrova, O. V.

2013-05-15

Crystals of a new representative of ring-radical dodecaborates Pb{sub 6}(Li{sub 0.65}Na{sub 0.19})[B{sub 12}O{sub 24}]I{sub 0.84} {center_dot} 0.168H{sub 2}O, space group R3bar m , are obtained under hydrothermal conditions. The structure is determined with-out preliminary knowledge of the chemical formula. It is close to that of the Pb{sub 6}[B{sub 12}O{sub 24}] {center_dot} H{sub 2}O dodecaborate studied earlier, but unlike the latter structure it contains admixtures of iodide anion, lithium cation, and water molecule, which incompletely populate positions in channels. The formation of the second variety, which brings to light ion-exchange properties of the crystals, is due to mineralizing ions available inmore » the concen-trated solution in the course of crystallization. The new compound is compared with beryl and cordierite, which have close structures with channels capable of capturing various groups. Structures of synthetic Na and Ag dodecaborates with analogous but distorted ring dodecaborate radicals are discussed.« less

Hemispherical Laue camera

DOEpatents

Li, James C. M.; Chu, Sungnee G.

1980-01-01

A hemispherical Laue camera comprises a crystal sample mount for positioning a sample to be analyzed at the center of sphere of a hemispherical, X-radiation sensitive film cassette, a collimator, a stationary or rotating sample mount and a set of standard spherical projection spheres. X-radiation generated from an external source is directed through the collimator to impinge onto the single crystal sample on the stationary mount. The diffracted beam is recorded on the hemispherical X-radiation sensitive film mounted inside the hemispherical film cassette in either transmission or back-reflection geometry. The distances travelled by X-radiation diffracted from the crystal to the hemispherical film are the same for all crystal planes which satisfy Bragg's Law. The recorded diffraction spots or Laue spots on the film thereby preserve both the symmetry information of the crystal structure and the relative intensities which are directly related to the relative structure factors of the crystal orientations. The diffraction pattern on the exposed film is compared with the known diffraction pattern on one of the standard spherical projection spheres for a specific crystal structure to determine the orientation of the crystal sample. By replacing the stationary sample support with a rotating sample mount, the hemispherical Laue camera can be used for crystal structure determination in a manner previously provided in conventional Debye-Scherrer cameras.

Phononic crystal diffraction gratings

NASA Astrophysics Data System (ADS)

Moiseyenko, Rayisa P.; Herbison, Sarah; Declercq, Nico F.; Laude, Vincent

2012-02-01

When a phononic crystal is interrogated by an external source of acoustic waves, there is necessarily a phenomenon of diffraction occurring on the external enclosing surfaces. Indeed, these external surfaces are periodic and the resulting acoustic diffraction grating has a periodicity that depends on the orientation of the phononic crystal. This work presents a combined experimental and theoretical study on the diffraction of bulk ultrasonic waves on the external surfaces of a 2D phononic crystal that consists of a triangular lattice of steel rods in a water matrix. The results of transmission experiments are compared with theoretical band structures obtained with the finite-element method. Angular spectrograms (showing frequency as a function of angle) determined from diffraction experiments are then compared with finite-element simulations of diffraction occurring on the surfaces of the crystal. The experimental results show that the diffraction that occurs on its external surfaces is highly frequency-dependent and has a definite relation with the Bloch modes of the phononic crystal. In particular, a strong influence of the presence of bandgaps and deaf bands on the diffraction efficiency is found. This observation opens perspectives for the design of efficient phononic crystal diffraction gratings.

The structural basis for enhanced silver reflectance in Koi fish scale and skin.

PubMed

Gur, Dvir; Leshem, Ben; Oron, Dan; Weiner, Steve; Addadi, Lia

2014-12-10

Fish have evolved biogenic multilayer reflectors composed of stacks of intracellular anhydrous guanine crystals separated by cytoplasm, to produce the silvery luster of their skin and scales. Here we compare two different variants of the Japanese Koi fish; one of them with enhanced reflectivity. Our aim is to determine how biology modulates reflectivity, and from this to obtain a mechanistic understanding of the structure and properties governing the intensity of silver reflectance. We measured the reflectance of individual scales with a custom-made microscope, and then for each individual scale we characterized the structure of the guanine crystal/cytoplasm layers using high-resolution cryo-SEM. The measured reflectance and the structural-geometrical parameters were used to calculate the reflectance of each scale, and the results were compared to the experimental measurements. We show that enhanced reflectivity is obtained with the same basic guanine crystal/cytoplasm stacks, but the structural arrangement between the stack, inside the stacks, and relative to the scale surface is varied when reflectivity is enhanced. Finally, we propose a model that incorporates the basic building block parameters, the crystal orientation inside the tissue, and the resulting reflectance and explains the mechanistic basis for reflectance enhancement.

Millimeter-Wave Spectroscopy, X-ray Crystal Structure, and Quantum Chemical Studies of Diketene: Resolving Ambiguities Concerning the Structure of the Ketene Dimer.

PubMed

Orr, Vanessa L; Esselman, Brian J; Dorman, P Matisha; Amberger, Brent K; Guzei, Ilia A; Woods, R Claude; McMahon, Robert J

2016-10-06

The pure rotational spectrum of diketene has been studied in the millimeter-wave region from ∼240 to 360 GHz. For the ground vibrational state and five vibrationally excited satellites (ν 24 , 2ν 24 , 3ν 24 , 4ν 24 , and ν 16 ), the observed spectrum allowed for the measurement, assignment, and least-squares fitting a total of more than 10 000 distinct rotational transitions. In each case, the transitions were fit to single-state, complete or near-complete sextic centrifugally distorted rotor models to near experimental error limits using Kisiel's ASFIT. Additionally, we obtained less satisfactory least-squares fits to single-state centrifugally distorted rotor models for three additional vibrational states: ν 24 + ν 16 , ν 23 , and 5ν 24 . The structure of diketene was optimized at the CCSD(T)/ANO1 level, and the vibration-rotation interaction (α i ) values for each normal mode were determined with a CCSD(T)/ANO1 VPT2 anharmonic frequency calculation. These α i values were helpful in identifying the previously unreported ν 16 and ν 23 fundamental states. We obtained a single-crystal X-ray structure of diketene at -173 °C. The bond distances are increased in precision by more than an order of magnitude compared to those in the 1958 X-ray crystal structure. The improved accuracy of the crystal structure geometry resolves the discrepancy between previous computational and experimental structures. The rotational transition frequencies provided herein should be useful for a millimeter-wave or terahertz search for diketene in the interstellar medium.

Salts of diisopropylammonium - A non-toxic alternate to perovskite ferroelectrics

NASA Astrophysics Data System (ADS)

Kabir, Ekramul; Khatun, M.; Ghosh, T.; Raihan, Mustafa J.; Rahman, M.

2018-04-01

Organic ferroelectric crystals - diisopropylammonium bromide (DIPAB) and diisopropylammonium iodide (DIPAI) have been synthesized using different chemical methods. However the polarization values of these crystals are found comparable to that of inorganic ferroelectric materials. Monoclinic polar structure have been found for the crystals but the polarization and other electrical properties of DIPAB are much stable than those of DIPAI crystals. Hydroscopic nature of DIPAI crystals seems to be responsible for unstable electrical properties.

The crystal structure of human soluble CD14 reveals a bent solenoid with a hydrophobic amino-terminal pocket1

PubMed Central

Kelley, Stacy L.; Lukk, Tiit; Nair, Satish K.; Tapping, Richard I.

2012-01-01

Human monocyte differentiation antigen CD14 is a pattern recognition receptor that enhances innate immune responses to infection by sensitizing host cells to bacterial lipopolysaccharide (LPS; endotoxin), lipoproteins, lipoteichoic acid and other acylated microbial products. CD14 physically delivers these lipidated microbial products to various Toll-like receptor signaling complexes that subsequently induce intracellular proinflammatory signaling cascades upon ligand binding. The ensuing cellular responses are usually protective to the host, but can also result in host fatality through sepsis. In this work, we have determined the X-ray crystal structure of human CD14. The structure reveals a bent solenoid typical of leucine rich repeat proteins with an amino terminal pocket that presumably binds acylated ligands including LPS. Comparison of human and mouse CD14 structures show great similarity in overall protein fold. However, compared to mouse CD14, human CD14 contains an expanded pocket and alternative rim residues that are likely to be important for LPS binding and cell activation. The X-ray crystal structure of human CD14 presented herein may foster additional ligand bound structural studies, virtual docking studies, and drug design efforts to mitigate LPS induced sepsis and other inflammatory diseases. PMID:23264655

Radio- and photoluminescence properties of Ce/Tb co-doped glasses with huntite-like composition

NASA Astrophysics Data System (ADS)

Lorenzi, Roberto; Golubev, Nikita V.; Ziaytdinova, Mariyam Z.; Jarý, Vítězslav; Babin, Vladimir; Malashkevich, Georgii E.; Paleari, Alberto; Sigaev, Vladimir N.; Fasoli, Mauro; Nikl, Martin

2018-04-01

Optical properties of yttria-aluminoborate (YAB) glasses with general composition 10(CexTbyY(1-x-y))-30Al2O3-60B2O3 are investigated and compared with data available on YAB crystals with huntite-like structure. Ce doped samples show optical features ascribable to preferential location of rare earth ions in sites with specific geometry similar to that observed in crystalline structures. Samples prepared with Tb ions as emission activator and Ce ions as sensitizer have been studied within the framework of non-radiative energy transfer. The resulting Förster radius is of 4.6 ± 0.5 Å comparable with that observed in Ce/Tb co-doped YAl3(BO3)4 crystals. The investigated materials possess radio- and photoluminescence emission efficiencies and performances comparable to that of crystalline counterparts with the advantage of having easiness of preparation and workability typical of glassy systems.

A STUDY OF DISLOCATION STRUCTURE OF SUBBOUNDARIES IN MOLYBDENUM SINGLE CRYSTALS,

DTIC Science & Technology

MOLYBDENUM, *DISLOCATIONS), GRAIN STRUCTURES(METALLURGY), SINGLE CRYSTALS, ZONE MELTING, ELECTRON BEAM MELTING, GRAIN BOUNDARIES, MATHEMATICAL ANALYSIS, ETCHED CRYSTALS, ETCHING, ELECTROEROSIVE MACHINING, CHINA

Effect of acetate and nitrate anions on the molecular structure of 3-(hydroxyimino)-2-butanone-2-(1H-benzimidazol-2-yl)hydrazone

NASA Astrophysics Data System (ADS)

Kamat, Vinayak; Naik, Krishna; Revankar, Vidyanand K.

2017-04-01

A novel Schiff base ligand 3-(hydroxyimino)-2-butanone-2-(1H-benzimidazol-2-yl)hydrazone has been synthesized by the condensation reaction of 2-Hydrazinobenzimidazole with diacetyl monoxime in presence of acetic acid catalyst. The ligand has crystallized as its acetate salt, due to the charge-assisted hydrogen bonding between protonated benzimidazole ring and acetate anion. Efforts to synthesize the zinc(II) complex of the title compound, has resulted in the formation of a nitrate salt of the ligand, instead of coordination complex of zinc(II). Acetate salt has crystallized in monoclinic P 21/n, while the nitrate salt has crystallized in a triclinic crystal system with P -1 space group. Hirshfeld surface analysis is presented for both of the crystal structures. Structures of synthesized molecules are even computationally optimized using DFT. A comparative structural approach between the synthesized molecules and DFT optimized structure of bare ligand without any counterions is analyzed in terms of bond parameters. Hydrogen bonding is explained keeping the anions as the central dogma. Mass fragmentation pattern of the organic molecule and comparative account of IR, 1H and 13C NMR chemical shifts are also presented. Compounds are screened for their antibacterial and antifungal potencies against few pathogenic microorganisms. The organic motif is found be an excellent antifungal agent.

Sixty years from discovery to solution: crystal structure of bovine liver catalase form III

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

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

2012-03-27

The crystallization and structural characterization of bovine liver catalase (BLC) has been intensively studied for decades. Forms I and II of BLC have previously been fully characterized using single-crystal X-ray diffraction. Form III has previously been analyzed by electron microscopy, but owing to the thinness of this crystal form an X-ray crystal structure had not been determined. Here, the crystal structure of form III of BLC is presented in space group P212121, with unit-cell parameters a = 68.7, b = 173.7, c = 186.3 {angstrom}. The asymmetric unit is composed of the biological tetramer, which is packed in a tetrahedronmore » motif with three other BLC tetramers. This higher resolution structure has allowed an assessment of the previously published electron-microscopy studies.« less

Crystal structure of spinach plastocyanin at 1.7 A resolution.

PubMed Central

Xue, Y.; Okvist, M.; Hansson, O.; Young, S.

1998-01-01

The crystal structure of plastocyanin from spinach has been determined using molecular replacement, with the structure of plastocyanin from poplar as a search model. Successful crystallization was facilitated by site-directed mutagenesis in which residue Gly8 was substituted with Asp. The region around residue 8 was believed to be too mobile for the wild-type protein to form crystals despite extensive screening. The current structure represents the oxidized plastocyanin, copper (II), at low pH (approximately 4.4). In contrast to the similarity in the core region as compared to its poplar counterpart, the structure shows some significant differences in loop regions. The most notable is the large shift of the 59-61 loop where the largest shift is 3.0 A for the C(alpha) atom of Glu59. This results in different patterns of electrostatic potential around the acidic patches for the two proteins. PMID:9792096

Use of Crystal Structure Informatics for Defining the Conformational Space Needed for Predicting Crystal Structures of Pharmaceutical Molecules.

PubMed

Iuzzolino, Luca; Reilly, Anthony M; McCabe, Patrick; Price, Sarah L

2017-10-10

Determining the range of conformations that a flexible pharmaceutical-like molecule could plausibly adopt in a crystal structure is a key to successful crystal structure prediction (CSP) studies. We aim to use conformational information from the crystal structures in the Cambridge Structural Database (CSD) to facilitate this task. The conformations produced by the CSD Conformer Generator are reduced in number by considering the underlying rotamer distributions, an analysis of changes in molecular shape, and a minimal number of molecular ab initio calculations. This method is tested for five pharmaceutical-like molecules where an extensive CSP study has already been performed. The CSD informatics-derived set of crystal structure searches generates almost all the low-energy crystal structures previously found, including all experimental structures. The workflow effectively combines information on individual torsion angles and then eliminates the combinations that are too high in energy to be found in the solid state, reducing the resources needed to cover the solid-state conformational space of a molecule. This provides insights into how the low-energy solid-state and isolated-molecule conformations are related to the properties of the individual flexible torsion angles.

SoMIR framework for designing high-NDBP photonic crystal waveguides.

PubMed

Mirjalili, Seyed Mohammad

2014-06-20

This work proposes a modularized framework for designing the structure of photonic crystal waveguides (PCWs) and reducing human involvement during the design process. The proposed framework consists of three main modules: parameters module, constraints module, and optimizer module. The first module is responsible for defining the structural parameters of a given PCW. The second module defines various limitations in order to achieve desirable optimum designs. The third module is the optimizer, in which a numerical optimization method is employed to perform optimization. As case studies, two new structures called Ellipse PCW (EPCW) and Hypoellipse PCW (HPCW) with different shape of holes in each row are proposed and optimized by the framework. The calculation results show that the proposed framework is able to successfully optimize the structures of the new EPCW and HPCW. In addition, the results demonstrate the applicability of the proposed framework for optimizing different PCWs. The results of the comparative study show that the optimized EPCW and HPCW provide 18% and 9% significant improvements in normalized delay-bandwidth product (NDBP), respectively, compared to the ring-shape-hole PCW, which has the highest NDBP in the literature. Finally, the simulations of pulse propagation confirm the manufacturing feasibility of both optimized structures.

Monoclinic Tungsten Oxide with {100} Facet Orientation and Tuned Electronic Band Structure for Enhanced Photocatalytic Oxidations.

PubMed

Zhang, Ning; Chen, Chen; Mei, Zongwei; Liu, Xiaohe; Qu, Xiaolei; Li, Yunxiang; Li, Siqi; Qi, Weihong; Zhang, Yuanjian; Ye, Jinhua; Roy, Vellaisamy A L; Ma, Renzhi

2016-04-27

Exploring surface-exposed highly active crystal facets for photocatalytic oxidations is promising in utilizing monoclinic WO3 semiconductor. However, the previously reported highly active facets for monoclinic WO3 were mainly toward enhancing photocatalytic reductions. Here we report that the WO3 with {100} facet orientation and tuned surface electronic band structure can effectively enhance photocatalytic oxidation properties. The {100} faceted WO3 single crystals are synthesized via a facile hydrothermal method. The UV-visible diffuse reflectance, X-ray photoelectron spectroscopy valence band spectra, and photoelectrochemical measurements suggest that the {100} faceted WO3 has a much higher energy level of valence band maximum compared with the normal WO3 crystals without preferred orientation of the crystal face. The density functional theory calculations reveal that the shift of O 2p and W 5d states in {100} face induce a unique band structure. In comparison with the normal WO3, the {100} faceted WO3 exhibits an O2 evolution rate about 5.1 times in water splitting, and also shows an acetone evolution rate of 4.2 times as well as CO2 evolution rate of 3.8 times in gaseous degradation of 2-propanol. This study demonstrates an efficient crystal face engineering route to tune the surface electronic band structure for enhanced photocatalytic oxidations.

In situ study of the growth and degradation processes in tetragonal lysozyme crystals on a silicon substrate by high-resolution X-ray diffractometry

NASA Astrophysics Data System (ADS)

Kovalchuk, M. V.; Prosekov, P. A.; Marchenkova, M. A.; Blagov, A. E.; D'yakova, Yu. A.; Tereshchenko, E. Yu.; Pisarevskii, Yu. V.; Kondratev, O. A.

2014-09-01

The results of an in situ study of the growth of tetragonal lysozyme crystals by high-resolution X-ray diffractometry are considered. The crystals are grown by the sitting-drop method on crystalline silicon substrates of different types: both on smooth substrates and substrates with artificial surface-relief structures using graphoepitaxy. The crystals are grown in a special hermetically closed crystallization cell, which enables one to obtain images with an optical microscope and perform in situ X-ray diffraction studies in the course of crystal growth. Measurements for lysozyme crystals were carried out in different stages of the crystallization process, including crystal nucleation and growth, developed crystals, the degradation of the crystal structure, and complete destruction.

On the growth of CH3NH3PbI3-xClx single crystal and characterization

NASA Astrophysics Data System (ADS)

Su, J.; Wang, W. F.; Lei, Y.; Zhang, L.; Xu, L. H.; Wang, D.; Lu, D.; Bai, Y.

2018-05-01

In this paper, CH3NH3PbI3-xClx crystal was grown by solution cooling method with CH3NH3I and PbCl2 as raw materials. Lead compounds and CH3NH3PbI3-xClx crystal with size about 6 mm × 4 mm × 2 mm were obtained. The chemical reactions with different CH3NH3I/PbCl2 ratios were analyzed. XPS shows the content of chlorine in CH3NH3PbI3-xClx is about 0.91%. PXRD, FT-IR, Raman and absorbance spectra were used to study the structure and optical properties of CH3NH3PbI3-xClx by comparing with CH3NH3PbI3 crystal. The CH3NH3PbI3-xClx crystal grown is of tetragonal structure with the lattice constants a = b = 8.8165 Å, c = 12.7920 Å and the bandgap value of 1.57 eV.

New Directions in Biotechnology

NASA Technical Reports Server (NTRS)

2003-01-01

The macromolecule crystallization program within NASA is undergoing considerable pressure, particularly budgetary pressure. While it has shown some successes, they have not lived up to the expectations of others, and technological advances may rapidly overtake the natural advantages offered by crystallization in microgravity. Concomitant with the microgravity effort has been a research program to study the macromolecule crystallization process. It was believed that a better understanding of the process would lead to growth of improved crystals for X-ray diffraction studies. The results of the various research efforts have been impressive in improving our understanding of macromolecule crystallization, but have not led to any improved structures. Macromolecule crystallization for structure determination is "one of", the job being unique for every protein and finished once a structure is obtained. However, the knowledge gained is not lost, but instead lays the foundation for developments in new areas of biotechnology and nanotechnology. In this it is highly analogous to studies into small molecule crystallization, the results of which have led to our present day microelectronics-based society. We are conducting preliminary experiments into areas such as designed macromolecule crystals, macromolecule-inorganic hybrid structures, and macromolecule-based nanotechnology. In addition, our protein crystallization studies are now being directed more towards industrial and new approaches to membrane protein crystallization.

Crystal Structure of the Catalytic Domain of Drosophila [beta]1,4-Galactosyltransferase-7

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

Ramakrishnan, Boopathy; Qasba, Pradman K.

2010-11-03

The {beta}1,4-galactosyltransferase-7 ({beta}4Gal-T7) enzyme, one of seven members of the {beta}4Gal-T family, transfers in the presence of manganese Gal from UDP-Gal to an acceptor sugar (xylose) that is attached to a side chain hydroxyl group of Ser/Thr residues of proteoglycan proteins. It exhibits the least protein sequence similarity with the other family members, including the well studied family member {beta}4Gal-T1, which, in the presence of manganese, transfers Gal from UDP-Gal to GlcNAc. We report here the crystal structure of the catalytic domain of {beta}4Gal-T7 from Drosophila in the presence of manganese and UDP at 1.81 {angstrom} resolution. In the crystalmore » structure, a new manganese ion-binding motif (HXH) has been observed. Superposition of the crystal structures of {beta}4Gal-T7 and {beta}4Gal-T1 shows that the catalytic pocket and the substrate-binding sites in these proteins are similar. Compared with GlcNAc, xylose has a hydroxyl group (instead of an N-acetyl group) at C2 and lacks the CH{sub 2}OH group at C5; thus, these protein structures show significant differences in their acceptor-binding site. Modeling of xylose in the acceptor-binding site of the {beta}4Gal-T7 crystal structure shows that the aromatic side chain of Tyr{sup 177} interacts strongly with the C5 atom of xylose, causing steric hindrance to any additional group at C5. Because Drosophila Cd7 has a 73% protein sequence similarity to human Cd7, the present crystal structure offers a structure-based explanation for the mutations in human Cd7 that have been linked to Ehlers-Danlos syndrome.« less

In-situ study on growth units of Ba2Mg(B3O6)2 crystal

NASA Astrophysics Data System (ADS)

Lv, X. S.; Sun, Y. L.; Tang, X. L.; Wan, S. M.; Zhang, Q. L.; You, J. L.; Yin, S. T.

2013-05-01

BMBO (Ba2Mg(B3O6)2 crystal) is an excellent birefringent crystal and a potential stimulated Raman scattering (SRS) crystal. In this paper, high temperature Raman spectroscopy was used to in-situ study the melt structure near a BMBO crystal-melt interface. [B3O6]3- groups were found in this region. The result reveals that both of BaO bonds and MgO bonds are the weak bonds in the BMBO crystal structure. During the melting process, the crystal structure broke into Ba2+ ions, Mg2+ ions and [B3O6]3- groups. Our experimental results confirmed that the well-developed faces of BMBO crystals are the (001), (101) and (012) faces. Based on attachment energy theory, the crystal growth habit was discussed. The (001) (101) and (012) crystal faces linked by the weak BaO bonds and MgO bonds have smaller attachment energies and slower growth rates, and thus present in the final morphology. The (012) crystal face has a multi-terrace structure, which suggests that BMBO crystal grows with a layer-by-layer mode.

Structural Studies on Intact Clostridium botulinum Neurotoxins Complexed with Inhibitors Leading to Drug Design

DTIC Science & Technology

2009-02-01

compounds via virtual screening. These compounds include small molecules – transition state analogues and benzimidazoles . Since there is a commonality in...Crystal structure of BoNT/E has been determined helping us to understand the faster action of BoNT/E compared to BoNT/A. • A subset of benzimidazole

Influence of the liquid crystal behaviour on the Langmuir and Langmuir-Blodgett film supramolecular architecture of an ionic liquid crystal.

PubMed

Pérez-Gregorio, Víctor; Giner, Ignacio; López, M Carmen; Gascón, Ignacio; Cavero, Emma; Giménez, Raquel

2012-06-01

A new luminescent ionic liquid crystal, called Ipz-2, has been synthesised and its mesophase behaviour and also at the air-liquid interface has been studied and compared with Ipz, another ionic pyrazole derivative, with a similar molecular structure, previously studied. The X-ray diffraction pattern shows that Ipz-2 exhibits hexagonal columnar mesomorphism, while Ipz adopts lamellar mesophases. Langmuir films of both compounds are flat and homogeneous at large areas per molecule, but create different supramolecular structures under further compression. Ipz-2 Langmuir films have been transferred onto solid substrates, and Atomic Force Microscopy (AFM) images of the Langmuir-Blodgett films have shown that large columnar structures hundreds of nm in diameter are formed on top of the initial monolayer, in contrast with well-defined trilayer LB films obtained for Ipz. Our results show that Ipz-2 has a tendency to stack in columnar arrangements both in liquid crystalline bulk and in Langmuir and Langmuir-Blodgett films. Copyright © 2012 Elsevier Inc. All rights reserved.

Crystal structure, spectral, thermal and dielectric studies of a new zinc benzoate single crystal

NASA Astrophysics Data System (ADS)

Bijini, B. R.; Prasanna, S.; Deepa, M.; Nair, C. M. K.; Rajendra Babu, K.

2012-11-01

Single crystals of zinc benzoate with a novel structure were grown in gel media. Sodium metasilicate of gel density 1.04 g/cc at pH 6 was employed to yield transparent single crystals. The crystal structure of the compound was ascertained by single crystal X-ray diffractometry. It was noted that the crystal belongs to monoclinic system with space group P21/c with unit cell parameters a = 10.669(1) Å, b = 12.995(5) Å, c = 19.119(3) Å, and β = 94.926(3)°. The crystal was seen to possess a linear polymeric structure along b-axis; with no presence of coordinated or lattice water. CHN analysis established the stoichiometric composition of the crystal. The existence of functional groups present in the single crystal system was confirmed by FT-IR studies. The thermal characteristic of the sample was analysed by TGA-DTA techniques, and the sample was found to be thermally stable up to 280 °C. The kinetic and thermodynamic parameters were also determined. UV-Vis spectroscopy corroborated the transparency of the crystal and revealed the optical band gap to be 4 eV. Dielectric studies showed decrease in the dielectric constant of the sample with increase in frequency.

Optical characteristics of novel bulk and nanoengineered laser host materials

NASA Astrophysics Data System (ADS)

Prasad, Narasimha S.; Sova, Stacey; Kelly, Lisa; Bevan, Talon; Arnold, Bradley; Cooper, Christopher; Choa, Fow-Sen; Singh, N. B.

2018-02-01

The hexagonal apatite single crystals have been investigated for their applications as laser host materials. Czochralksi and flux growth methods have been utilized to obtain single crystals. For low temperature processing (<100 0C), several techniques for crystal growth have been developed. The hexagonal apatite structure (space group P63/m) is characteristic of several compounds, some of which have extremely interesting and useful properties as laser hosts and bone materials. Calcium lanthanum silicate (Nd-doped) and lanthanum aluminate material systems were studied in detail. Nanoengineered calcium and lanthanum based silicates were synthesized by a solution method and their optical and morphological characteristics were compared with Czochralski grown bulk hydroxyapatite single crystals. Materials were evaluated by absorbance, fluorescence and Raman characteristics. Neodymium, iron and chromium doped crystals grown by a solution method showed weak but similar optical properties to that of Czochralski grown single crystals.

X-ray scattering study of pyrochlore iridates: Crystal structure, electronic, and magnetic excitations

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

Clancy, J. P.; Gretarsson, H.; Lee, E. K. H.

2016-07-06

We have investigated the structural, electronic, and magnetic properties of the pyrochlore iridates Eu 2Ir 2O 7 and Pr 2Ir 2O 7 using a combination of resonant elastic x-ray scattering, x-ray powder diffraction, and resonant inelastic x-ray scattering (RIXS). The structural parameters of Eu 2Ir 2O 7 have been examined as a function of temperature and applied pressure, with a particular emphasis on regions of the phase diagram where electronic and magnetic phase transitions have been reported. We find no evidence of crystal symmetry change over the range of temperatures (~6 to 300 K) and pressures (~0.1 to 17 GPa)more » studied. We have also investigated the electronic and magnetic excitations in single-crystal samples of Eu 2Ir 2O 7 and Pr 2Ir 2O 7 using high-resolution Ir L- 3-edge RIXS. In spite of very different ground state properties, we find that these materials exhibit qualitatively similar excitation spectra, with crystal field excitations at ~3-5 eV, spin-orbit excitations at ~ 0.5-1 eV, and broad low-lying excitations below ~0.15 eV. In single-crystal samples of "Eu-rich" Eu 2Ir 2O 7 (found to possess an actual stoichiometry of Eu 2.18Ir 1.82O 7.06) we observe highly damped magnetic excitations at ~45 meV, which display significant momentum dependence. Here, we compare these results with recent dynamical structure factor calculations« less

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

Cebe, Peggy; Partlow, Benjamin P.; Kaplan, David L.

Using fast scanning calorimetry (FSC), we investigated the glass transition and crystal melting of samples of B. mori silk fibroin containing Silk I and/or Silk II crystals. Due to the very short residence times at high temperatures during such measurements, thermal decomposition of silk protein can be significantly suppressed. FSC was performed at 2000 K/s using the Mettler Flash DSC1 on fibroin films with masses around 130–270 ng. Films were prepared with different crystalline fractions (ranging from 0.26 to 0.50) and with different crystal structures (Silk I, Silk II, or mixed) by varying the processing conditions. These included water annealingmore » at different temperatures, exposure to 50% MeOH in water, or autoclaving. The resulting crystal structure was examined using wide angle X-ray scattering. Degree of crystallinity was evaluated from Fourier transform infrared (FTIR) spectroscopy and from analysis of the heat capacity increment at the glass transition temperature. Silk fibroin films prepared by water annealing at 25 °C were the least crystalline and had Silk I structure. FTIR and FSC studies showed that films prepared by autoclaving or 50% MeOH exposure were the most crystalline and had Silk II structure. Intermediate crystalline fraction and mixed Silk I/Silk II structures were found in films prepared by water annealing at 37 °C. FSC results indicate that Silk II crystals exhibit endotherms of narrower width and have higher mean melting temperature Tm(II) = 351 ± 2.6 °C, compared to Silk I crystals which melt at Tm(I) = 292 ± 3.8 °C. Films containing mixed Silk I/Silk II structure showed two clearly separated endothermic peaks. Evidence suggests that the two types of crystals melt separately and do not thermally interconvert on the extremely short time scale (0.065 s between onset and end of melting) of the FSC experiment.« less

Synthesis, growth, structural and optical studies of a novel organic Piperazine (bis) p-toluenesulfonate single crystal.

PubMed

Rekha, P; Peramaiyan, G; NizamMohideen, M; Kumar, R Mohan; Kanagadurai, R

2015-03-15

A novel organic single crystal of Piperazinium (bis) p-toluenesulfonate (PPTS) was grown by a slow evaporation solution growth technique. The structure of the grown crystal was determined using single crystal X-ray diffraction analysis. The PPTS crystal belongs to the triclinic crystal system with space group of P1¯. The presence of functional groups was confirmed by FTIR spectral analysis. The optical transmittance range and cut-off wavelength were identified by UV-vis-NIR spectral studies. The luminescent properties of PPTS crystal were investigated. The thermal behavior of PPTS crystal was studied by TG-DT analyses. Copyright © 2014 Elsevier B.V. All rights reserved.

Study, selection, and preparation of solid cationic conductors. [characteristics of solid electrolytes for rechargeable high energy and high power density batteries

NASA Technical Reports Server (NTRS)

Roth, W. L.; Muller, O.

1974-01-01

Crystal chemical principles and transport theory have been used to predict structures and specific compounds which might find application as solid electrolytes in rechargeable high energy and high power density batteries operating at temperatures less than 200 C. Structures with 1-, 2-, and 3-dimensional channels were synthesized and screened by nuclear magnetic resonance, dielectric loss, and conductivity. There is significant conductivity at room temperature in some of the materials but none attain a level that is comparable to beta-alumina. Microwave and fast pulse methods were developed to measure conductivity in powders and in small crystals.

Grand canonical ensemble Monte Carlo simulation of the dCpG/proflavine crystal hydrate.

PubMed

Resat, H; Mezei, M

1996-09-01

The grand canonical ensemble Monte Carlo molecular simulation method is used to investigate hydration patterns in the crystal hydrate structure of the dCpG/proflavine intercalated complex. The objective of this study is to show by example that the recently advocated grand canonical ensemble simulation is a computationally efficient method for determining the positions of the hydrating water molecules in protein and nucleic acid structures. A detailed molecular simulation convergence analysis and an analogous comparison of the theoretical results with experiments clearly show that the grand ensemble simulations can be far more advantageous than the comparable canonical ensemble simulations.

The preparation and characterization of a lithium borate glass prepared by the gel technique

NASA Technical Reports Server (NTRS)

Weinberg, M. C.; Neilson, G. F.; Smith, G. L.; Dunn, B.; Moore, G. S.; Mackenzie, J. D.

1985-01-01

The preparation of an amorphous lithium borate gel by the metal organic procedure is described. In addition, a preliminary evaluation of the behavior of the gel upon heating is given. In particular the crystallization tendency of the gel is studied with the aid of DTA and X-ray diffraction, and the structural changes in the gel are monitored with the aid of IR spectroscopy. The glass produced from the lithium borate gel is compared to both the gel precursor material and a glass of similar composition prepared by conventional techniques. Specifically, the relevant water contents, crystallization behavior, and structural features are contrasted.

The crystal structure of dihydrodipicolinate synthase from Escherichia coli with bound pyruvate and succinic acid semialdehyde: unambiguous resolution of the stereochemistry of the condensation product.

PubMed

Boughton, Berin A; Dobson, Renwick C J; Hutton, Craig A

2012-08-01

The crystal structure of Escherichia coli dihydrodipicolinate synthase with pyruvate and substrate analogue succinic acid semialdehyde condensed with the active site lysine-161 was solved to a resolution of 2.3 Å. Comparative analysis to a previously reported structure both resolves the configuration at the aldol addition center, where the final addition product clearly displays the (S)-configuration, and the final conformation of the adduct within the active site. Direct comparison to two other crystal structures found in the Protein Data Bank, 1YXC, and 3DU0, demonstrates significant similarity between the active site residues of these structures. Copyright © 2012 Wiley Periodicals, Inc.

The effect of thermal history on crystalline structure and mechanical properties of β-nucleated isotactic polypropylene

NASA Astrophysics Data System (ADS)

Tian, Yefei; Zhou, Jian; Feng, Jiachun

2018-04-01

The effect of thermal history on β-nucleated iPP was systematically investigated by comparing the variance of crystalline microstructures and mechanical property of stepwise crystallized sample and annealed sample, which experienced different thermal history. The mechanical property tests exhibit that that the toughness of stepwise crystallized sample and annealed sample were both decreased compared to control sample, while the tensile strength of the stepwise crystallized sample increased slightly. Structure investigation showed that the α-relaxation peak, which is related to the assignment of chains in rigid amorphous phase, moved to the high temperature region for stepwise crystallized sample, while it moved to the low temperature region for annealed sample. The results indicated the weakening in rigid amorphous fraction (RAF) and the increase in lamellar thickness of β-iPP after stepwise crystallization treatment. For annealed sample, the RAF strengthened and lamellar thickness decreased slightly after thermal treatment. A mechanism of crystalline microstructures evolution of restricted area between the main lamellar under different treatments was proposed.

Microgravity

NASA Image and Video Library

1992-06-25

Zeolites are crystalline aluminosilicates that have complex framework structures. However, there are several features of zeolite crystals that make unequivocal structure determinations difficult. The acquisition of reliable structural information on zeolites is greatly facilitated by the availability of high-quality specimens. For structure determinations by conventional diffraction techniques, large single-crystal specimens are essential. Alternatively, structural determinations by powder profile refinement methods relax the constraints on crystal size, but still require materials with a high degree of crystalline perfection. Studies conducted at CAMMP (Center for Advanced Microgravity Materials Processing) have demonstrated that microgravity processing can produce larger crystal sizes and fewer structural defects relative to terrestrial crystal growth. Principal Investigator: Dr. Albert Sacco

Zeolites

NASA Technical Reports Server (NTRS)

1992-01-01

Zeolites are crystalline aluminosilicates that have complex framework structures. However, there are several features of zeolite crystals that make unequivocal structure determinations difficult. The acquisition of reliable structural information on zeolites is greatly facilitated by the availability of high-quality specimens. For structure determinations by conventional diffraction techniques, large single-crystal specimens are essential. Alternatively, structural determinations by powder profile refinement methods relax the constraints on crystal size, but still require materials with a high degree of crystalline perfection. Studies conducted at CAMMP (Center for Advanced Microgravity Materials Processing) have demonstrated that microgravity processing can produce larger crystal sizes and fewer structural defects relative to terrestrial crystal growth. Principal Investigator: Dr. Albert Sacco

Structure-activity relationship of the ionic cocrystal: 5-amino-2-naphthalene sulfonate·ammonium ions for pharmaceutical applications

NASA Astrophysics Data System (ADS)

Sangeetha, M.; Mathammal, R.

2018-02-01

The ionic cocrystals of 5-amino-2-naphthalene sulfonate · ammonium ions (ANSA-ṡNH4+) were grown under slow evaporation method and examined in detail for pharmaceutical applications. The crystal structure and intermolecular interactions were studied from the single X-ray diffraction analysis and the Hirshfeld surfaces. The 2D fingerprint plots displayed the inter-contacts possible in the ionic crystal. Computational DFT method was established to determine the structural, physical and chemical properties. The molecular geometries obtained from the X-ray studies were compared with the optimized geometrical parameters calculated using DFT/6-31 + G(d,p) method. The band gap energy calculated from the UV-Visible spectral analysis and the HOMO-LUMO energy gap are compared. The theoretical UV-Visible calculations helped in determining the type of electronic transition taking place in the title molecule. The maximum absorption bands and transitions involved in the molecule represented the drug reaction possible. Non-linear optical properties were characterized from SHG efficiency measurements experimentally and the NLO parameters are also calculated from the optimized structure. The reactive sites within the molecule are detailed from the MEP surface maps. The molecular docking studies evident the structure-activity of the ionic cocrystal for anti-cancer drug property.

Feasibility Studies of Parametric X-rays Use in a Medical Environment

NASA Astrophysics Data System (ADS)

Sones, Bryndol; Danon, Yaron; Blain, Ezekiel

2009-03-01

Parametric X-rays (PXR) are produced from the interaction of relativistic electrons with the periodic structure of crystal materials. Smooth X-ray energy tunability is achieved by rotating the crystal with respects to the electron beam direction. Experiments at the Rensselaer Polytechnic Institute 60-MeV LINAC produce quasi-monochromatic X-rays (6-35 keV) from various target crystals to include highly oriented pyrolytic graphite (HOPG), LiF, Si, Ge, Cu, and W using electron beam currents up to 6 uA. These experiments demonstrate the first PXR images and some of the merits of thin metallic crystals. Recent experiments with a 100-μm thick Cu crystal improve the Cu PXR (with energy ˜12 keV) to Cu fluorescence ratio by a factor of 20 compared to a 1 mm-thick Cu crystal. This study uses Monte Carlo techniques to investigate (1) PXR dose compared to emissions from simulated Mo, Rh, and W anodes for mammography applications and (2) electron scattering effects when considering LiF111, Si111, and Cu111 PXR production using electron beams with energies of 20-30 MeV. Advantages in using monochromatic PXR compared to X-rays from Mo and Rh anodes in mammography applications result in a dose per incident photon reduction by a factor of 2. Using 20 MeV electrons, the thinner Cu111 crystal for 15 keV PXR production results in an electron scattering angle of 30.7+/-0.2 mrad offering the best potential for PXR from lower energy electrons.

Oral bioavailability enhancement of β-lapachone, a poorly soluble fast crystallizer, by cocrystal, amorphous solid dispersion, and crystalline solid dispersion.

PubMed

Liu, Chengyu; Liu, Zhengsheng; Chen, Yuejie; Chen, Zhen; Chen, Huijun; Pui, Yipshu; Qian, Feng

2018-03-01

The aim of this paper was to compare the in vitro dissolution and in vivo bioavailability of three solubility enhancement technologies for β-lapachone (LPC), a poorly water soluble compound with extremely high crystallization propensity. LPC cocrystal was prepared by co-grinding LPC with resorcinol. LPC crystalline and amorphous solid dispersions (CSD and ASD) were obtained by spray drying with Poloxamer 188 and HPMC-AS, respectively. The cocrystal structure was solved by single crystal x-ray diffraction. All formulations were characterized by WAXRD, DSC, POM and SEM. USP II and intrinsic dissolution studies were used to compare the in vitro dissolution of these formulations, and a crossover dog pharmacokinetic study was used to compare their in vivo bioavailability. An 1:1 LPC-resorcinol cocrystal with higher solubility and faster dissolution rate was obtained, yet it converted to LPC crystal rapidly in solution. LPC/HPMC-AS ASD was confirmed to be amorphous and uniform, while the crystal and crystallite sizes of LPC in CSD were found to be ∼1-3 μm and around 40 nm, respectively. These formulations performed similarly during USP II dissolution, while demonstrated dramatically different oral bioavailability of ∼32%, ∼5%, and ∼1% in dogs, for CSD, co-crystal, and ASD, respectively. CSD showed the fastest intrinsic dissolution rate among the three. The three formulations showed poor IVIVC which could be due to rapid and unpredictable crystallization kinetics. Considering all the reasons, we conclude that for molecules with extremely high crystallization tendency that cannot be inhibited by any pharmaceutical excipients, size-reduction technologies such as CSD could be advantageous for oral bioavailability enhancement in vivo than technologies only generating transient but not sustained supersaturation. Copyright © 2018 Elsevier B.V. All rights reserved.

Structural changes of anodic layer on titanium in sulfate solution as a function of anodization duration in constant current mode

NASA Astrophysics Data System (ADS)

Komiya, Shinji; Sakamoto, Kouta; Ohtsu, Naofumi

2014-03-01

The present study investigated the effect of anodization time, in constant current mode, on the anodic oxide layer formed on titanium (Ti). Anodization of the Ti substrate was　carried out in a 0.1 M (NH4)2SO4 aqueous solution with reaction times of various durations, after which the characteristics and photocatalytic activity were investigated in detail. The TiO2 layer fabricated in a short duration exhibited comparatively flat surface morphology and an anatase-type crystal structure. This layer acted as a photocatalyst only under ultraviolet light (UV) illumination. Upon prolonging the anodization, the layer structure changed drastically. The surface morphology became rough, and the crystal structure changed to rutile-type TiO2. Furthermore, the layer showed photocatalytic activity both under UV and visible light illumination. Further anodization increased the amount of methylene blue (MB) adsorbed on the surface, but did not cause additional change to the structure of the anodic layer. The surface morphology and crystal structure of the anodic layer were predominantly controlled by the anodization time; thus, the anodization time is an important parameter for controlling the characteristics of the anodic layer.

Ab initio study of structural and mechanical property of solid molecular hydrogens

NASA Astrophysics Data System (ADS)

Ye, Yingting; Yang, Li; Yang, Tianle; Nie, Jinlan; Peng, Shuming; Long, Xinggui; Zu, Xiaotao; Du, Jincheng

2015-06-01

Ab initio calculations based on density functional theory (DFT) were performed to investigate the structural and the elastic properties of solid molecular hydrogens (H2). The influence of molecular axes of H2 on structural relative stabilities of hexagonal close-packed (hcp) and face-centered cubic (fcc) structured hydrogen molecular crystals were systematically investigated. Our results indicate that for hcp structures, disordered hydrogen molecule structure is more stable, while for fcc structures, Pa3 hydrogen molecular crystal is most stable. The cohesive energy of fcc H2 crystal was found to be lower than hcp. The mechanical properties of fcc and hcp hydrogen molecular crystals were obtained, with results consistent with previous theoretical calculations. In addition, the effects of zero point energy (ZPE) and van der Waals (vdW) correction on the cohesive energy and the stability of hydrogen molecular crystals were systematically studied and discussed.

Hierarchically structured photonic crystals for integrated chemical separation and colorimetric detection.

PubMed

Fu, Qianqian; Zhu, Biting; Ge, Jianping

2017-02-16

A SiO 2 colloidal photonic crystal film with a hierarchical porous structure is fabricated to demonstrate an integrated separation and colorimetric detection of chemical species for the first time. This new photonic crystal based thin layer chromatography process requires no dyeing, developing and UV irradiation compared to the traditional TLC. The assembling of mesoporous SiO 2 particles via a supersaturation-induced-precipitation process forms uniform and hierarchical photonic crystals with micron-scale cracks and mesopores, which accelerate the diffusion of developers and intensify the adsorption/desorption between the analytes and silica for efficient separation. Meanwhile, the chemical substances infiltrated to the voids of photonic crystals cause an increase of the refractive index and a large contrast of structural colors towards the unloaded part, so that the sample spots can be directly recognized with the naked eye before and after separation.

The potential for the indirect crystal structure verification of methyl glycosides based on acetates' parent structures: GIPAW and solid-state NMR approaches

NASA Astrophysics Data System (ADS)

Szeleszczuk, Łukasz; Gubica, Tomasz; Zimniak, Andrzej; Pisklak, Dariusz M.; Dąbrowska, Kinga; Cyrański, Michał K.; Kańska, Marianna

2017-10-01

A convenient method for the indirect crystal structure verification of methyl glycosides was demonstrated. Single-crystal X-ray diffraction structures for methyl glycoside acetates were deacetylated and subsequently subjected to DFT calculations under periodic boundary conditions. Solid-state NMR spectroscopy served as a guide for calculations. A high level of accuracy of the modelled crystal structures of methyl glycosides was confirmed by comparison with published results of neutron diffraction study using RMSD method.

Praseodymium Cuprate Thin Film Cathodes for Intermediate Temperature Solid Oxide Fuel Cells: Roles of Doping, Orientation, and Crystal Structure.

PubMed

Mukherjee, Kunal; Hayamizu, Yoshiaki; Kim, Chang Sub; Kolchina, Liudmila M; Mazo, Galina N; Istomin, Sergey Ya; Bishop, Sean R; Tuller, Harry L

2016-12-21

Highly textured thin films of undoped, Ce-doped, and Sr-doped Pr 2 CuO 4 were synthesized on single crystal YSZ substrates using pulsed laser deposition to investigate their area-specific resistance (ASR) as cathodes in solid-oxide fuel cells (SOFCs). The effects of T' and T* crystal structures, donor and acceptor doping, and a-axis and c-axis orientation on ASR were systematically studied using electrochemical impedance spectroscopy on half cells. The addition of both Ce and Sr dopants resulted in improvements in ASR in c-axis oriented films, as did the T* crystal structure with the a-axis orientation. Pr 1.6 Sr 0.4 CuO 4 is identified as a potential cathode material with nearly an order of magnitude faster oxygen reduction reaction kinetics at 600 °C compared to thin films of the commonly studied cathode material La 0.6 Sr 0.4 Co 0.8 Fe 0.2 O 3-δ . Orientation control of the cuprate films on YSZ was achieved using seed layers, and the anisotropy in the ASR was found to be less than an order of magnitude. The rare-earth doped cuprate was found to be a versatile system for study of relationships between bulk properties and the oxygen reduction reaction, critical for improving SOFC performance.

Structural properties of ultrafine Ba-hexaferrite nanoparticles

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

Makovec, Darko, E-mail: Darko.Makovec@ijs.si; Primc, Darinka; Sturm, Saso

2012-12-15

Crystal structure of ultrafine Ba-hexaferrite (BaFe{sub 12}O{sub 19}) nanoparticles was studied using X-ray diffractometry (XRD), high-resolution transmission electron microscopy (HRTEM), energy-dispersive X-ray spectroscopy (EDXS), X-ray absorption fine structure (XAFS), and Moessbauer spectroscopy (MS), to be compared to the structure of larger nanoparticles and the bulk. The nanoparticles were synthesized with hydrothermal treatment of an appropriate suspension of Ba and Fe hydroxides in the presence of a large excess of OH{sup -}. The ultrafine nanoparticles were formed in a discoid shape, {approx}10 nm wide and only {approx}3 nm thick, comparable to the size of the hexagonal unit cell in the c-direction.more » The HRTEM image analysis confirmed the hexaferrite structure, whereas EDXS showed the composition matching the BaFe{sub 12}O{sub 19} formula. XAFS and MS analyses showed considerable disorder of the structure, most probably responsible for the low magnetization. - Graphical abstract: Left: HREM image of an ultrafine Ba-hexaferrite nanoparticle (inset: TEM image of the nanoparticles); Right: the experimental HRTEM image is compared with calculated image and corresponding atomic model. Highlights: Black-Right-Pointing-Pointer Crystal structure of ultrafine Ba-hexaferrite (BaFe{sub 12}O{sub 19}) nanoparticles was compared to the structure of the bulk. Black-Right-Pointing-Pointer Thickness the discoid nanoparticles was comparable to the size of the hexagonal unit cell in the c-direction. Black-Right-Pointing-Pointer Considerable disorder of the nanoparticles' structure is most probably responsible for their low magnetization.« less

Crystal structure and theoretical studies of derivative of imidazo-1,2,4-triazine

NASA Astrophysics Data System (ADS)

Dybała, Izabela; Sztanke, Krzysztof

2016-09-01

In this study, we present the result of X-ray structure analysis of methyl [8-(3-chlorophenyl)-4-oxo-2,3,4,6,7,8-heksahydroimidazo[2,1-c][1,2,4]triazin-3-yl]acetate (1). The molecule conformation is flat, with a chlorophenyl substituent and the ester moiety lying in the plain of the heterobicyclic scaffold. Its conformation is stabilized by an intramolecular Nsbnd H…O hydrogen bond. Within the crystalline structure of 1, molecules associate with one another by weak Csbnd H…O, Csbnd H…Cl and Csbnd H…π bonds. The molecular and crystal structure of 1 was compared with the previously described structurally similar compound possessing the same bicyclic rigid core and similar chemical nature of the functional ester moiety. Very interesting differences in molecules geometry and association were observed. Non-covalent bonds within the crystals are additionally visualized by determination of Hirshfeld surfaces. Moreover, the quantum chemical calculation for 1 in the gas phase were carried out. The DFT calculation methods was used to optimize of molecule geometry and obtain molecular energy profiles with respect to selected torsion angles. The quantum chemical conformational analysis that was carried out for compound 1 in the gas phase suggests that in the solid state the molecules adopt the minimum energy conformation.

Critical detonation thickness in vapor-deposited hexanitroazobenzene (HNAB) films with different preparation conditions

NASA Astrophysics Data System (ADS)

Tappan, Alexander; Knepper, Robert; Marquez, Michael; Ball, J.; Miller, Jill

2013-06-01

At Sandia National Laboratories, we have coined the term ``microenergetics'' to describe sub-millimeter energetic material studies aimed at gaining knowledge of combustion and detonation behavior at the mesoscale. Films of the high explosive hexanitroazobenzene (HNAB) have been deposited through physical vapor deposition. HNAB deposits in an amorphous state that crystallizes over time and modest heating accelerates this crystallization. HNAB films were prepared under different crystallization temperatures, and characterized with surface profilometry and scanning electron microscopy. The critical detonation thickness for HNAB at different crystallization conditions was determined in a configuration where charge width was large compared to film thickness, and thus side losses did not play a role in detonation propagation. The results of these experiments will be discussed in the context of small sample geometry, deposited film morphology, crystal structure, and density.

Evolution of Nano-structured Quasicrystals from Amorphous alloys

NASA Astrophysics Data System (ADS)

Xing, L. Q.; Kelton, K. F.

2002-03-01

Ta shows a significant effect on the precipitation of quasicrystals in (Zr_1-xTa_x)_64Cu_18Ni_8Al_10 amorphous alloys. The amorphous alloy made without Ta forms precipitates of tetragonal Zr_2Cu primary phases upon annealing. The addition of a small amount of Ta ( ~ 3 at%) to the alloy initiates the precipitation of primary icosahedral quasicrystal phases. Moreover, as the Ta concentration increases, the size of the precipitates decreases dramatically. To study the effect of Ta in this alloy system and to understand the mechanism for the precipitation of nano-structured quasicrystals, we have investigated the crystallization characteristics of the alloys made with different Ta concentration using DSC, checked the structures of the annealed samples with TEM and X-ray diffraction, and analyzed the kinetics of the crystallization processes. The kinetic parameter and the measured crystal size distribution will be compared with theoretical predictions from conventional nucleation and growth model and from a new model for nucleation that couples the long-range diffusion flux with the interfacial attachment processes.

Structural study of piracetam polymorphs and cocrystals: crystallography redetermination and quantum mechanics calculations.

PubMed

Tilborg, Anaëlle; Jacquemin, Denis; Norberg, Bernadette; Perpète, Eric; Michaux, Catherine; Wouters, Johan

2011-12-01

Pharmaceutical compounds are mostly developed as solid dosage forms containing a single-crystal form. It means that the selection of a particular crystal state for a given molecule is an important step for further clinical outlooks. In this context, piracetam, a pharmaceutical molecule known since the sixties for its nootropic properties, is considered in the present work. This molecule is analyzed using several experimental and theoretical approaches. First, the conformational space of the molecule has been systematically explored by performing a quantum mechanics scan of the two most relevant dihedral angles of the lateral chain. The predicted stable conformations have been compared to all the reported experimental geometries retrieved from the Cambridge Structural Database (CSD) covering polymorphs and cocrystals structures. In parallel, different batches of powders have been recrystallized. Under specific conditions, single crystals of polymorph (III) of piracetam have been obtained, an outcome confirmed by crystallographic analysis. © 2011 International Union of Crystallography. Printed in Singapore – all rights reserved.

Structural analysis of as-deposited and annealed low-temperature gallium arsenide

NASA Astrophysics Data System (ADS)

Matyi, R. J.; Melloch, M. R.; Woodall, J. M.

1993-04-01

The structure of GaAs grown at low substrate temperatures (LT-GaAs) by molecular beam epitaxy has been studied using high resolution X-ray diffraction methods. Double crystal rocking curves from the as-deposited LT-GaAs show well defined interference fringes, indicating a high level of structural perfection. Triple crystal diffraction analysis of the as-deposited sample showed significantly less diffuse scattering near the LT-GaAs 004 reciprocal lattice point compared with the substrate 004 reciprocal lattice point, suggesting that despite the incorporation of approximately 1% excess arsenic, the epitaxial layer had superior crystalline perfection than did the GaAs substrate. Triple crystal scans of annealed LT-GaAs showed an increase in the integrated diffuse intensity by approximately a factor of three as the anneal temperature was increased from 700 to 900°C. Analogous to the effects of SiO2 precipitates in annealed Czochralski silicon, the diffuse intensity is attributed to distortions in the epitaxial LT-GaAs lattice by arsenic precipitates.

Why don't we find more polymorphs?

PubMed

Price, Sarah L

2013-08-01

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

Discovery of highly potent, selective, covalent inhibitors of JAK3

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

Kempson, James; Ovalle, Damaso; Guo, Junqing

A useful and novel set of tool molecules have been identified which bind irreversibly to the JAK3 active site cysteine residue. The design was based on crystal structure information and a comparative study of several electrophilic warheads.

Molecular and crystal structure and the Hirshfeld surface analysis of 1-amino-1-deoxy-α-D-sorbopyranose and 1-amino-1-deoxy-α-D-psicopyranose ("D-sorbosamine" and "D-psicosamine") derivatives

NASA Astrophysics Data System (ADS)

Mossine, Valeri V.; Barnes, Charles L.; Mawhinney, Thomas P.

2018-05-01

Sorbosamine and psicosamine are the last two 1-amino-1-deoxy-hexuloses for which no structural data were available. We report on a13C NMR and a single crystal X-ray diffraction study of 1-deoxy-1-(N-methylphenylamino)-D-sorbose (1) and 1-deoxy-1-(N-methylphenylamino)-D-psicose (2). In solutions, both aminosugars are conformationally unstable and establish equilibria, with 90.7% α-pyranose, 3.8% α-furanose, 1.0% β-pyranose, 0.5% β-furanose, and 4.0% acyclic keto form for 1 and 32.4% α-furanose, 27.2% α-pyranose, 21.0% β-pyranose, 9.1% β-furanose, and 11.0% acyclic keto form for 2. X-ray diffraction data provided detailed structural information on 1 and 2 in the α-pyranose form. Both molecules adopt the 5C2 ring conformations, the bond distances and valence angles compare well with respective pyranose structures. All hydroxyl groups in crystal structures of both 1 and 2 participate in two-dimensional hydrogen bonding networks, the H-bonding pattern in 1 is dominated by co-crystallized water molecules. The Hirshfeld surface analysis revealed a significant contribution of non- or weakly polar interactions to the packing forces for both molecules, with crystal structure of 2 featuring short H⋯H contacts. Other structural features found in 2 are a significant planarity of the tertiary amino group (the pyramid heights are 0.127 Å in 2 vs 0.231 Å in 1), a concomitant non-involvement of the amine nitrogen in heteroatom contacts, and a unique anti-periplanar conformation around the C1sbnd C2 bond.

Crystal structure of a Schistosoma mansoni septin reveals the phenomenon of strand slippage in septins dependent on the nature of the bound nucleotide.

PubMed

Zeraik, Ana E; Pereira, Humberto M; Santos, Yuri V; Brandão-Neto, José; Spoerner, Michael; Santos, Maiara S; Colnago, Luiz A; Garratt, Richard C; Araújo, Ana P U; DeMarco, Ricardo

2014-03-14

Septins are filament-forming GTP-binding proteins involved in important cellular events, such as cytokinesis, barrier formation, and membrane remodeling. Here, we present two crystal structures of the GTPase domain of a Schistosoma mansoni septin (SmSEPT10), one bound to GDP and the other to GTP. The structures have been solved at an unprecedented resolution for septins (1.93 and 2.1 Å, respectively), which has allowed for unambiguous structural assignment of regions previously poorly defined. Consequently, we provide a reliable model for functional interpretation and a solid foundation for future structural studies. Upon comparing the two complexes, we observe for the first time the phenomenon of a strand slippage in septins. Such slippage generates a front-back communication mechanism between the G and NC interfaces. These data provide a novel mechanistic framework for the influence of nucleotide binding to the GTPase domain, opening new possibilities for the study of the dynamics of septin filaments.

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

PubMed

Du, Wen-Ge Han; Noodleman, Louis

2013-12-16

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

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

NASA Astrophysics Data System (ADS)

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

2018-05-01

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

[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.

Crystallographic studies of the Anthrax lethal toxin. Annual report

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

Frederick, C.A.

1996-07-01

The lethal form of Anthrax results from the inhalation of anthrax spores. Death is primarily due to the effects of the lethal toxin (Protective Antigen (PA) + Lethal Factor) from the causative agent, Bacillus anthracis. All the Anthrax vaccines currently in use or under development contain or produce PA, the major antigenic component of anthrax toxin, and there is a clear need for an improved vaccine for human use. In the previous report we described the first atomic resolution structure of PA, revealing that the molecule is composed largely of beta-sheets organized into four domains. This information can be usedmore » in the design. of recombinant PA vaccines. In this report we describe additional features of the full-length PA molecule derived from further crystallographic refinement and careful examination of the structure. We compare two crystal forms of PA grown at different pH values and discuss the functional implications. A complete definition of the function of each domain must await the crystal structure of the PA63 heptamer. We have grown crystals of the heptamer under both detergent and detergent-free conditions, and made substantial progress towards the crystal structure. The mechanism of anthrax intoxication in the light of our results is reviewed.« less

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.

Improved performance of HgCdTe infrared detector focal plane arrays by modulating light field based on photonic crystal structure

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

Liang, Jian; Hu, Weida, E-mail: wdhu@mail.sitp.ac.cn; Ye, Zhenhua

2014-05-14

An HgCdTe long-wavelength infrared focal plane array photodetector is proposed by modulating light distributions based on the photonic crystal. It is shown that a promising prospect of improving performance is better light harvest and dark current limitation. To optimize the photon field distributions of the HgCdTe-based photonic crystal structure, a numerical method is built by combining the finite-element modeling and the finite-difference time-domain simulation. The optical and electrical characteristics of designed HgCdTe mid-wavelength and long-wavelength photon-trapping infrared detector focal plane arrays are obtained numerically. The results indicate that the photon crystal structure, which is entirely compatible with the large infraredmore » focal plane arrays, can significantly reduce the dark current without degrading the quantum efficiency compared to the regular mesa or planar structure.« less

Calculated photonic structures for infrared emittance control

NASA Astrophysics Data System (ADS)

Rung, Andreas; Ribbing, Carl G.

2002-06-01

Using an available program package based on the transfer-matrix method, we calculated the photonic band structure for two different structures: a quasi-three-dimensional crystal of square air rods in a high-index matrix and an opal structure of high-index spheres in a matrix of low index, epsilon = 1.5. The high index used is representative of gallium arsenide in the thermal infrared range. The geometric parameters of the rod dimension, sphere radius, and lattice constants were chosen to give total reflectance for normal incidence, i.e., minimum thermal emittance, in either one of the two infrared atmospheric windows. For these four photonic crystals, the bulk reflectance spectra and the wavelength-averaged thermal emittance as a function of crystal thickness were calculated. The results reveal that potentially useful thermal signature suppression is obtained for crystals as thin as 20-50 mum, i.e., comparable with that of a paint layer.

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.

Room-Temperature Deformation and Martensitic Transformation of Two Co-Cr-Based Alloys

NASA Astrophysics Data System (ADS)

Cai, S.; Schaffer, J. E.; Huang, D.; Gao, J.; Ren, Y.

2018-05-01

Deformation of two Co-Cr alloys was studied by in situ synchrotron X-ray diffraction. Both alloys show stress-induced martensite transformation, which is affected by phase stabilities and transformation strains. Crystal structure of WC in Co-20Cr-15W-10Ni is identified. Compared with other phases present, it is elastically isotropic, exhibits high strength, and can elastically withstand strains exceeding 1 pct. Texture change during phase transformation is explained based on the crystal orientation relationship between γ- and ɛ-phases.

Room-Temperature Deformation and Martensitic Transformation of Two Co-Cr-Based Alloys

NASA Astrophysics Data System (ADS)

Cai, S.; Schaffer, J. E.; Huang, D.; Gao, J.; Ren, Y.

2018-07-01

Deformation of two Co-Cr alloys was studied by in situ synchrotron X-ray diffraction. Both alloys show stress-induced martensite transformation, which is affected by phase stabilities and transformation strains. Crystal structure of WC in Co-20Cr-15W-10Ni is identified. Compared with other phases present, it is elastically isotropic, exhibits high strength, and can elastically withstand strains exceeding 1 pct. Texture change during phase transformation is explained based on the crystal orientation relationship between γ- and ɛ-phases.

Ground Based Program for the Physical Analysis of Macromolecular Crystal Growth

NASA Technical Reports Server (NTRS)

Malkin, Alexander J.

1998-01-01

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

Influence of two different template removal methods on the micromorphology, crystal structure, and photocatalytic activity of hollow CdS nanospheres

NASA Astrophysics Data System (ADS)

Wang, Han; Jin, Tingting; Zheng, Xing; Jiang, Bo; Zhu, Chaosheng; Yuan, Xiangdong; Zheng, Jingtang; Wu, Mingbo

2016-11-01

Hollow cadmium sulfide (CdS) nanospheres of about 260 nm average diameters and about 30 nm shell thickness can be easily synthesized via a sonochemical process, in which polystyrene (PS) nanoparticles were employed as templates. In order to remove the PS templates, both etching and calcination were applied in this paper. The influence of the two different template removal methods on the surface micromorphology, crystal structure, and photocatalytic activity of hollow CdS nanospheres was carefully performed a comparative study. Results of X-ray diffraction, scanning electron microscopy, transmission electron microscopy, energy dispersive X-ray, FT-IR, thermogravimetric analysis, Brunauer-Emmett-Teller, diffused reflectance spectra, and decolorization experiments showed that the different template removal methods exhibited a significant influence on the surface micromorphology, crystal structure, and photocatalytic activity of hollow CdS nanospheres. The CdS hollow nanospheres as-prepared by etching had pure cubic sphalerite structure, higher -OH content, less defects and exhibited good photocatalytic activity for rhodamine-B, Methylene Blue and methyl orange under UV-vis light irradiation. However, CdS hollow nanospheres obtained by calcination with a hexagonal crystal structure, less -OH content, more defects have shown worse photocatalytic activity. This indicated that surface micromorphology and crystalline phase were mainly factors influencing photocatalytic activity of hollow CdS nanospheres.

Binary photonic crystal for refractometric applications (TE case)

NASA Astrophysics Data System (ADS)

Taya, Sofyan A.; Shaheen, Somaia A.

2018-04-01

In this work, a binary photonic crystal is proposed as a refractometric sensor. The dispersion relation and the sensitivity are derived for transverse electric (TE) mode. In our analysis, the first layer is considered to be the analyte layer and the second layer is assumed to be left-handed material (LHM), dielectric or metal. It is found that the sensitivity of the LHM structure is the highest among other structures. It is possible for LHM photonic crystal to achieve a sensitivity improvement of 412% compared to conventional slab waveguide sensor.

Crystal structures of C4 form maize and quaternary complex of E. coli phosphoenolpyruvate carboxylases.

PubMed

Matsumura, Hiroyoshi; Xie, Yong; Shirakata, Shunsuke; Inoue, Tsuyoshi; Yoshinaga, Takeo; Ueno, Yoshihisa; Izui, Katsura; Kai, Yasushi

2002-12-01

Phosphoenolpyruvate carboxylase (PEPC) catalyzes the first step in the fixation of atmospheric CO(2) during C(4) photosynthesis. The crystal structure of C(4) form maize PEPC (ZmPEPC), the first structure of the plant PEPCs, has been determined at 3.0 A resolution. The structure includes a sulfate ion at the plausible binding site of an allosteric activator, glucose 6-phosphate. The crystal structure of E. coli PEPC (EcPEPC) complexed with Mn(2+), phosphoenolpyruvate analog (3,3-dichloro-2-dihydroxyphosphinoylmethyl-2-propenoate), and an allosteric inhibitor, aspartate, has also been determined at 2.35 A resolution. Dynamic movements were found in the ZmPEPC structure, compared with the EcPEPC structure, around two loops near the active site. On the basis of these molecular structures, the mechanisms for the carboxylation reaction and for the allosteric regulation of PEPC are proposed.

Solution Structures of Mycobacterium tuberculosis Thioredoxin C and Models of the Intact Thioredoxin System Suggest New Approaches to Inhibitor and Drug Design

PubMed Central

Olson, Andrew L.; Neumann, Terrence S.; Cai, Sheng; Sem, Daniel S.

2012-01-01

Here we report the NMR solution structures of Mycobacterium tuberculosis (M. tuberculosis) thioredoxin C in both oxidized and reduced states, with discussion of structural changes that occur in going between redox states. The NMR solution structure of the oxidized TrxC corresponds closely to that of the crystal structure, except in the C-terminal region. It appears that crystal packing effects have caused an artifactual shift in the α4 helix in the previously reported crystal structure, compared to the solution structure. Based on these TrxC structures, chemical shift mapping, a previously reported crystal structure of the M. tuberculosis thioredoxin reductase (not bound to a Trx) and structures for intermediates in the E. coli thioredoxin catalytic cycle, we have modeled the complete M. tuberculosis thioredoxin system for the various steps in the catalytic cycle. These structures and models reveal pockets at the TrxR/TrxC interface in various steps in the catalytic cycle, which can be targeted in the design of uncompetitive inhibitors as potential anti-mycobacterial agents, or as chemical genetic probes of function. PMID:23229911

Bismuth zinc vanadate, BiZn{sub 2}VO{sub 6}: New crystal structure type and electronic structure

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

Eliziario Nunes, Sayonara; Department of Materials Engineering, Federal University of São Carlos, 13565-905 São Carlos, SP; Wang, Chun-Hai

2015-02-15

We report a combined experimental and computational study of the crystal structure and electronic properties of bismuth zinc vanadate, BiZn{sub 2}VO{sub 6}, known for its visible light photocatalytic activity. The crystal structure has been solved from laboratory powder X-ray diffraction data using the repeated minimisations from random starting values method. BiZn{sub 2}VO{sub 6} adopts a new structure type, based on the following building blocks: corner- and edge-sharing ZnO{sub 4} tetrahedra, ZnO{sub 6} octahedra and VO{sub 4} tetrahedra, and Bi{sub 2}O{sub 12} dimers. It is the only known member of the BiM{sub 2}AO{sub 6} (M=Pb, Ca, Cd, Mn, Zn, Mg, Cu;more » A=V, P, As) family which does not appear to be structurally closely related to others. The electronic structure of BiZn{sub 2}VO{sub 6}, calculated by DFT methods, shows that it is an indirect gap semiconductor with a calculated band gap of 1.6 eV, which compares favourably to the experimentally measured value of 2.4 eV. - Graphical abstract: The crystal structure of BiZn{sub 2}VO{sub 6}, a new structure type in the BiM{sub 2}AO{sub 6} (M=Mg, Ca, Cd, Cu, Pb, Mn, Zn; A=V, P, As) family. - Highlights: • Structure solution from PXRD data by repeated minimisations from random starting values. • New structure type in the BiM{sub 2}AO{sub 6} (M=Pb, Ca, Cd, Mn, Zn, Mg, Cu; A=V, P, As) family. • Electronic structure calculation.« less

Ab initio random structure searching of organic molecular solids: assessment and validation against experimental data.

PubMed

Zilka, Miri; Dudenko, Dmytro V; Hughes, Colan E; Williams, P Andrew; Sturniolo, Simone; Franks, W Trent; Pickard, Chris J; Yates, Jonathan R; Harris, Kenneth D M; Brown, Steven P

2017-10-04

This paper explores the capability of using the DFT-D ab initio random structure searching (AIRSS) method to generate crystal structures of organic molecular materials, focusing on a system (m-aminobenzoic acid; m-ABA) that is known from experimental studies to exhibit abundant polymorphism. Within the structural constraints selected for the AIRSS calculations (specifically, centrosymmetric structures with Z = 4 for zwitterionic m-ABA molecules), the method is shown to successfully generate the two known polymorphs of m-ABA (form III and form IV) that have these structural features. We highlight various issues that are encountered in comparing crystal structures generated by AIRSS to experimental powder X-ray diffraction (XRD) data and solid-state magic-angle spinning (MAS) NMR data, demonstrating successful fitting for some of the lowest energy structures from the AIRSS calculations against experimental low-temperature powder XRD data for known polymorphs of m-ABA, and showing that comparison of computed and experimental solid-state NMR parameters allows different hydrogen-bonding motifs to be discriminated.

Four-port coupled channel-guide device based on 2D photonic crystal structure

NASA Astrophysics Data System (ADS)

Camargo, Edilson A.; Chong, Harold M. H.; De La Rue, Richard M.

2004-12-01

We have fabricated and measured a four-port coupled channel-waveguide device using W1 channel waveguides oriented along ΓK directions in a two-dimensional (2D) hole-based planar photonic crystal (PhC) based on silicon-on-insulator (SOI) waveguide material, at operation wavelengths around 1550 nm. 2D FDTD simulations and experimental results are shown and compared. The structure has been designed using a mode conversion approach, combined with coupled-mode concepts. The overall length of the photonic crystal structure is typically about 39 μm and the structure has been fabricated using a combination of direct-write electron-beam lithography (EBL) and dry-etch processing. Devices were measured using a tunable laser with end-fire coupling into the planar structure.

Crystal structure of TBC1D15 GTPase‐activating protein (GAP) domain and its activity on Rab GTPases

PubMed Central

Chen, Yan‐Na; Gu, Xin; Zhou, X. Edward; Wang, Weidong; Cheng, Dandan; Ge, Yinghua; Ye, Fei

2017-01-01

Abstract TBC1D15 belongs to the TBC (Tre‐2/Bub2/Cdc16) domain family and functions as a GTPase‐activating protein (GAP) for Rab GTPases. So far, the structure of TBC1D15 or the TBC1D15·Rab complex has not been determined, thus, its catalytic mechanism on Rab GTPases is still unclear. In this study, we solved the crystal structures of the Shark and Sus TBC1D15 GAP domains, to 2.8 Å and 2.5 Å resolution, respectively. Shark‐TBC1D15 and Sus‐TBC1D15 belong to the same subfamily of TBC domain‐containing proteins, and their GAP‐domain structures are highly similar. This demonstrates the evolutionary conservation of the TBC1D15 protein family. Meanwhile, the newly determined crystal structures display new variations compared to the structures of yeast Gyp1p Rab GAP domain and TBC1D1. GAP assays show that Shark and Sus GAPs both have higher catalytic activity on Rab11a·GTP than Rab7a·GTP, which differs from the previous study. We also demonstrated the importance of arginine and glutamine on the catalytic sites of Shark GAP and Sus GAP. When arginine and glutamine are changed to alanine or lysine, the activities of Shark GAP and Sus GAP are lost. PMID:28168758

Relationship between mechanical properties and crystal structure in cocrystals and salt of paracetamol.

PubMed

Ahmed, Hamzah; Shimpi, Manishkumar R; Velaga, Sitaram P

2017-01-01

Objectives were to study mechanical properties of various solid forms of paracetamol and relate to their crystal structures. Paracetamol form I (PRA), its cocrystals with oxalic acid (PRA-OXA) and 4,4-bipyridine (PRA-BPY) and hydrochloride salt (PRA-HCL) were selected. Cocrystals and salt were scaled-up using rational crystallization methods. The resulting materials were subjected to different solid-state characterizations. The powders were sieved and 90-360 µm sieve fraction was considered. These powders were examined by scanning electron microscopy (SEM) and densities were determined. Tablets were made at applied pressures of 35-180 MPa under controlled conditions and the tablet height, diameter and hardness were measured. Tensile strength and porosity of the tablets were estimated using well known models. Crystal structures of these systems were visualized and slip planes were identified. Cocrystal and salt of PRA were physically pure. Sieved powders had comparable morphologies and particle size. The apparent and theoretical densities of powders were similar, but no clear trends were observed. The tensile strengths of these compacts were increased with increasing pressure whereas tabletability decreased in the order oxalic acid > PRA-HCL ≈ PRA-OXA > BPY > PRA-BPY. Tablet tensile strength decreases exponentially with increasing porosity with the exception of PRY-BPY and BPY. Slip plane prediction based on attachment energies may not be independently considered. However, it was possible to explain the improved mechanical properties of powders based on the crystal structure. Cocrystallization and salt formation have introduced structural features that are responsible for improved tableting properties of PRA.

Design of ultra compact polarization splitter based on complete photonic band gap

NASA Astrophysics Data System (ADS)

Sinha, R. K.; Nagpal, Yogita

2005-11-01

Certain select structures in photonic crystals (PhCs) exhibit complete photonic band gap i.e. a frequency region where the photonic band gaps for both polarizations (i.e. transverse electric and transverse magnetic modes) exist and overlap. One of the most fundamental applications of the photonic band gap structures is the design of photonic crystal waveguides, which can be made by inserting linear defects in the photonic crystal structures. By setting closely two parallel 2D PhC waveguides, a directional waveguide coupler can be designed, which can be used to design a polarization splitter. In this paper we design a polarization splitter in a photonic crystal structure composed of two dimensional honeycomb pattern of dielectric rods in air. This photonic crystal structure exhibits a complete photonic band gap that extends from λ = 1.49 μm to λ = 1.61 μm, where lambda is the wavelength in free space, providing a large bandwidth of 120 nm. A polarization splitter can be made by designing a polarization selective coupler. The coupling lengths at various wavelengths for both polarizations have been calculated using the Finite Difference Time Domain method. It has been shown that the coupling length, for TE polarization is much smaller as compared to that for the TM polarization. This principle is used to design a polarization splitter of length 32 μm at λ = 1.55 μm. Further, the spectral response of the extinction ratios for both polarizations in the two waveguides at propagation distance of 32 μm has been studied.

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

X-ray Studies of Regenerated Cellulose Fibers Wet Spun from Cotton Linter Pulp in NaOH/Thiourea Aqueous Solutions

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

Chen,X.; Burger, C.; Fang, D.

Regenerated cellulose fibers were fabricated by dissolution of cotton linter pulp in NaOH (9.5 wt%) and thiourea (4.5 wt%) aqueous solution followed by wet-spinning and multi-roller drawing. The multi-roller drawing process involved three stages: coagulation (I), coagulation (II) and post-treatment (III). The crystalline structure and morphology of regenerated cellulose fiber was investigated by synchrotron wide-angle X-ray diffraction (WAXD) and small-angle X-ray scattering (SAXS) techniques. Results indicated that only the cellulose II crystal structure was found in regenerated cellulose fibers, proving that the cellulose crystals were completely transformed from cellulose I to II structure during spinning from NaOH/thiourea aqueous solution. Themore » crystallinity, orientation and crystal size at each stage were determined from the WAXD analysis. Drawing of cellulose fibers in the coagulation (II) bath (H{sub 2}SO{sub 4}/H{sub 2}O) was found to generate higher orientation and crystallinity than drawing in the post-treatment (III). Although the post-treatment process also increased crystal orientation, it led to a decrease in crystallinity with notable reduction in the anisotropic fraction. Compared with commercial rayon fibers fabricated by the viscose process, the regenerated cellulose fibers exhibited higher crystallinity but lower crystal orientation. SAXS results revealed a clear scattering maximum along the meridian direction in all regenerated cellulose fibers, indicating the formation of lamellar structure during spinning.« less

Synthesis, spectral characterization and X-ray crystal structure studies of 3-(benzo[d][1,3]dioxol-5-yl)-5-(3-methylthiophen-2-yl)-4,5-dihydro-1H-pyrazole-1-carboxamide: Hirshfeld surface, DFT and thermal analysis

NASA Astrophysics Data System (ADS)

Kumara, Karthik; Dileep Kumar, A.; Naveen, S.; Ajay Kumar, K.; Lokanath, N. K.

2018-06-01

A novel pyrazole derivative, 3-(benzo[d][1,3]dioxol-5-yl)-5-(3-methylthiophen-2-yl)-4,5-dihydro-1H-pyrazole-1-carboxamide was synthesized and characterized by elemental analysis, FT-IR, NMR (1H and 13C), MS, UV-visible spectra and finally the structure was confirmed by the single crystal X-ray diffraction studies. The title compound (C16H15N3O3S) crystallized in the triclinic crystal system, with the space group Pī. A dihedral angle of 65.84(1)° between the pyrazole and the thiophene rings confirms the twisted conformation between them. The X-ray structure revealed that the pyrazole ring adopts an E-form and an envelope conformation on C7 atom. The crystal and molecular structure of the title compound is stabilized by inter molecular hydrogen bonds. The compound possesses three dimensional supramolecular self-assembly, in which Csbnd H⋯O and Nsbnd H⋯O chains build up two dimensional arrays, which are extended to 3D network through Csbnd H···Cg and Csbnd O···Cg interactions. The structure also exhibits intramolecular hydrogen bonds of the type Nsbnd H⋯N and π···π stacking interactions, which contributes to the crystal packing. Further, Hirshfeld surface analysis was carried out for the graphical visualization of several short intermolecular interactions on the molecular surface while the 2D finger-print plot provides percentage contribution of each individual atom-to-atom interactions. The thermal decomposition of the compound has been studied by thermogravimetric analysis. The molecular geometries and electronic structures of the compounds were fully optimized, calculated with ab-initio methods by HF, DFT/B3LYP functional in combination of different basis set with different solvent environment and the structural parameters were compared with the experimental data. The Mulliken atomic charges and molecular electrostatic potential on molecular van der Waals (vdW) surface were calculated to know the electrophilic and nucleophilic regions of the molecular surface. Nonlinear optical properties of the title compound were also discussed based on the polarizability and hyperpolarizability values.

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.

Influence of non-covalent modification of multiwalled carbon nanotubes on the crystallization behaviour of binary blends of polypropylene and polyamide 6.

PubMed

Mukhopadhyay, Nabaneeta; Panwar, Ajay S; Kumar, Gulshan; Samajdar, I; Bhattacharyya, Arup R

2015-02-14

Blends of polypropylene (PP) and polyamide 6 (PA6) with multiwalled carbon nanotubes (MWNTs) were prepared using different processing strategies in a twin-screw micro-compounder. The effect of MWNTs on the crystallization behaviour of the PP phase and the PA6 phase of the blend has been investigated through non-isothermal crystallization studies by differential scanning calorimetric analysis. Furthermore, the effect of the addition of the compatibilizer (PP-g-MA) and the modification of MWNTs (m-MWNTs) with a non-covalent organic modifier (Li-salt of 6 amino hexanoic acid, Li-AHA) has also been studied in context to the crystallization behaviour of the PP and PA6 phase in the blend. The crystallization studies have indicated a significant increase in bulk crystallization temperature of the PP phase in the blend in the presence of MWNTs. Moreover, the formation of 'trans-lamellar crystalline' structure consisting of PA6 'trans-crystalline lamellae' on MWNTs surface was facilitated in the case of blends prepared via 'protocol 2' as compared to the corresponding blends prepared via 'protocol 1'. Wide angle X-ray diffraction analysis has showed the existence of a β-polymorph of the PP phase due to incorporation of the PA6 phase in the blend. Addition of MWNTs in the blends has facilitated further β-crystalline structure formation of the PP phase. In the presence of m-MWNTs, a higher β-fraction was observed in the PP phase as compared to the blend with pristine MWNTs. Addition of PP-g-MA has suppressed the β-phase formation in the PP phase in the blend. X-ray bulk texture analysis revealed that incorporation of PA6 as well as pristine/modified MWNTs has influenced the extent of orientation of the PP chains towards specific crystalline planes in various blend compositions of PP and PA6.

Synthesis, crystal structures and spectroscopic properties of triazine-based hydrazone derivatives; a comparative experimental-theoretical study.

PubMed

Arshad, Muhammad Nadeem; Bibi, Aisha; Mahmood, Tariq; Asiri, Abdullah M; Ayub, Khurshid

2015-04-03

We report here a comparative theoretical and experimental study of four triazine-based hydrazone derivatives. The hydrazones are synthesized by a three step process from commercially available benzil and thiosemicarbazide. The structures of all compounds were determined by using the UV-Vis., FT-IR, NMR (1H and 13C) spectroscopic techniques and finally confirmed unequivocally by single crystal X-ray diffraction analysis. Experimental geometric parameters and spectroscopic properties of the triazine based hydrazones are compared with those obtained from density functional theory (DFT) studies. The model developed here comprises of geometry optimization at B3LYP/6-31G (d, p) level of DFT. Optimized geometric parameters of all four compounds showed excellent correlations with the results obtained from X-ray diffraction studies. The vibrational spectra show nice correlations with the experimental IR spectra. Moreover, the simulated absorption spectra also agree well with experimental results (within 10-20 nm). The molecular electrostatic potential (MEP) mapped over the entire stabilized geometries of the compounds indicated their chemical reactivates. Furthermore, frontier molecular orbital (electronic properties) and first hyperpolarizability (nonlinear optical response) were also computed at the B3LYP/6-31G (d, p) level of theory.

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.

Planning deficits in polysubstance dependent users: Differential associations with severity of drug use and intelligence.

PubMed

Valls-Serrano, C; Verdejo-García, A; Caracuel, A

2016-05-01

Polysubstance use is associated with alterations in different components of executive functioning such as working memory and response inhibition. Nevertheless, less attention has been given to executive planning skills, which are required to benefit of low structured interventions. This study examines the association between severity of use of cocaine, heroin, alcohol, fluid and crystallized intelligence and planning tasks varying on degree of structure. Data were collected from 60 polysubstance users and 30 healthy controls. Cognitive assessment consisted of three planning tasks with different structure levels: Stockings of Cambridge, Zoo Map test, and Multiple Errands Test. Polysubstance users had significant planning deficits across the three tasks compared to healthy controls. Hierarchical regression models showed that severity of drug use and fluid and crystallized intelligence significantly explained performance in all the planning tasks. However, these associations were higher for low-structured real world tasks. These low-structured tasks also showed a unique association with crystallized but not fluid intelligence. Drug abuse is negatively associated with planning abilities, and intelligence is positively associated with planning performance in real-world tasks. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

Biocatalysis with thermostable enzymes: structure and properties of a thermophilic 'ene'-reductase related to old yellow enzyme.

PubMed

Adalbjörnsson, Björn V; Toogood, Helen S; Fryszkowska, Anna; Pudney, Christopher R; Jowitt, Thomas A; Leys, David; Scrutton, Nigel S

2010-01-25

We report the crystal structure of a thermophilic "ene" reductase (TOYE) isolated from Thermoanaerobacter pseudethanolicus E39. The crystal structure reveals a tetrameric enzyme and an active site that is relatively large compared to most other structurally determined and related Old Yellow Enzymes. The enzyme adopts higher order oligomeric states (octamers and dodecamers) in solution, as revealed by sedimentation velocity and multiangle laser light scattering. Bead modelling indicates that the solution structure is consistent with the basic tetrameric structure observed in crystallographic studies and electron microscopy. TOYE is stable at high temperatures (T(m)>70 degrees C) and shows increased resistance to denaturation in water-miscible organic solvents compared to the mesophilic Old Yellow Enzyme family member, pentaerythritol tetranitrate reductase. TOYE has typical ene-reductase properties of the Old Yellow Enzyme family. There is currently major interest in using Old Yellow Enzyme family members in the preparative biocatalysis of a number of activated alkenes. The increased stability of TOYE in organic solvents is advantageous for biotransformations in which water-miscible organic solvents and biphasic reaction conditions are required to both deliver novel substrates and minimize product racemisation.

Investigation of Structural Re-ordering of Hydrogen Bonds in LiNbO3:Mg Crystals Around the Threshold Concentration of Magnesium

NASA Astrophysics Data System (ADS)

Sidorov, N. V.; Teplyakova, N. A.; Palatnikov, M. N.; Bobreva, L. A.

2017-09-01

Crystals of LiNbO3congr and LiNbO3:Mg (0.19-5.91 mole %) were studied by IR and Raman spectroscopy. It was found that the intensities of the bands corresponding to the stretching vibrations of the OH groups in the IR spectra of LiNbO3:Mg crystals change and components of the bands disappear with increase of the Mg content. This was explained by disappearance of the OH groups close to {Nb}_{Li}^{4+}-{V}_{Li}- defects as a result of displacement of NbLi defects by Mg cations. In the Raman spectra of the LiNbO3:Mg (5.1 mole %) compared with the congruent crystal the lines corresponding to the vibrations of oxygen atoms in the oxygen octahedra and the stretching bridge vibrations of the oxygen atoms along the polar axis become broader, and new low-intensity lines that may correspond to pseudoscalar vibrations of A2-type symmetry also appear. The broadening of the lines is due to deformation of the oxygen octahedra caused both by increase of the Mg content in the crystal structure and by change in the localization of the protons. Suppression of the photorefraction effect in the LiNbO3:Mg crystals with Mg contents above the threshold level can be explained by change in the localization of the protons in the structure and by screening of the space charge field.

Structural variations of single and tandem mismatches in RNA duplexes: a joint MD simulation and crystal structure database analysis.

PubMed

Halder, Sukanya; Bhattacharyya, Dhananjay

2012-10-04

Internal loops within RNA duplex regions are formed by single or tandem basepairing mismatches with flanking canonical Watson-Crick basepairs on both sides. They are the most common motif observed in RNA secondary structures and play integral functional and structural roles. In this report, we have studied the structural features of 1 × 1, 2 × 2, and 3 × 3 internal loops using all-atom molecular dynamics (MD) simulation technique with explicit solvent model. As MD simulation is intricately dependent on the choice of force-field and these are often rather approximate, we have used both the most popular force-fields for nucleic acids-CHARMM27 and AMBER94-for a comparative analysis. We find that tandem noncanonical basepairs forming 2 × 2 and 3 × 3 internal loops are considerably more stable than the single mismatches forming 1 × 1 internal loops, irrespective of the force field. We have also analyzed crystal structure database to study the conservation of these helical fragments in the corresponding sets of RNA structures. We observe that the nature of stability in MD simulations mimic their fluctuating natures in crystal data sets also, probably indicating reliable natures of both the force fields to reproduce experimental results. We also notice significant structural changes in the wobble G:U basepairs present in these double helical stretches, leading to a biphasic stability for these wobble pairs to release the deformational strains introduced by internal loops within duplex regions.

A unified relation for the solid-liquid interface free energy of pure FCC, BCC, and HCP metals.

PubMed

Wilson, S R; Mendelev, M I

2016-04-14

We study correlations between the solid-liquid interface (SLI) free energy and bulk material properties (melting temperature, latent heat, and liquid structure) through the determination of SLI free energies for bcc and hcp metals from molecular dynamics (MD) simulation. Values obtained for the bcc metals in this study were compared to values predicted by the Turnbull, Laird, and Ewing relations on the basis of previously published MD simulation data. We found that of these three empirical relations, the Ewing relation better describes the MD simulation data. Moreover, whereas the original Ewing relation contains two constants for a particular crystal structure, we found that the first coefficient in the Ewing relation does not depend on crystal structure, taking a common value for all three phases, at least for the class of the systems described by embedded-atom method potentials (which are considered to provide a reasonable approximation for metals).

A unified relation for the solid-liquid interface free energy of pure FCC, BCC, and HCP metals

NASA Astrophysics Data System (ADS)

Wilson, S. R.; Mendelev, M. I.

2016-04-01

We study correlations between the solid-liquid interface (SLI) free energy and bulk material properties (melting temperature, latent heat, and liquid structure) through the determination of SLI free energies for bcc and hcp metals from molecular dynamics (MD) simulation. Values obtained for the bcc metals in this study were compared to values predicted by the Turnbull, Laird, and Ewing relations on the basis of previously published MD simulation data. We found that of these three empirical relations, the Ewing relation better describes the MD simulation data. Moreover, whereas the original Ewing relation contains two constants for a particular crystal structure, we found that the first coefficient in the Ewing relation does not depend on crystal structure, taking a common value for all three phases, at least for the class of the systems described by embedded-atom method potentials (which are considered to provide a reasonable approximation for metals).

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.

Highly robust crystalsome via directed polymer crystallization at curved liquid/liquid interface

PubMed Central

Wang, Wenda; Qi, Hao; Zhou, Tian; Mei, Shan; Han, Lin; Higuchi, Takeshi; Jinnai, Hiroshi; Li, Christopher Y.

2016-01-01

Lipids and amphiphilic block copolymers spontaneously self-assemble in water to form a plethora of micelles and vesicles. They are typically fluidic in nature and often mechanically weak for applications such as drug delivery and gene therapeutics. Mechanical properties of polymeric materials could be improved by forming crystalline structures. However, most of the self-assembled micelles and vesicles have curved surfaces and precisely tuning crystallization within a nanoscale curved space is challenging, as the curved geometry is incommensurate with crystals having three-dimensional translational symmetry. Herein, we report using a miniemulsion crystallization method to grow nanosized, polymer single-crystal-like capsules. We coin the name crystalsome to describe this unique structure, because they are formed by polymer lamellar crystals and their structure mimics liposomes and polymersomes. Using poly(L-lactic acid) (PLLA) as the model polymer, we show that curved water/p-xylene interface formed by the miniemulsion process can guide the growth of PLLA single crystals. Crystalsomes with the size ranging from ∼148 nm to over 1 μm have been formed. Atomic force microscopy measurement demonstrate a two to three orders of magnitude increase in bending modulus compared with conventional polymersomes. We envisage that this novel structure could shed light on investigating spherical crystallography and drug delivery. PMID:26837260

Synthesis, structure and luminescence of novel co-crystals based on bispyridyl-substituted α,β-unsaturated ketones with coformers

NASA Astrophysics Data System (ADS)

Li, Hong-Juan; Wang, Lei; Zhao, Juan-Juan; Sun, Ju-Feng; Sun, Ji-Liang; Wang, Chun-Hua; Hou, Gui-Ge

2015-01-01

Based on 2,6-bis((pyridin-4-yl)methylene)cyclohexanone (A) and N-methyl-3,5-bis((pyridin-4-yl)methylene)-4-piperidone (B) with coformers, three novel macrocyclic co-crystals, (A)ṡ(resorcinol) (1), (A)ṡ(1,3,5-benzenetriol) (2), (B)2ṡ(1,3,5-benzenetriol)2 (3) and three chain co-crystals, (A)ṡ(hydroquinone) (4), (A)ṡ(isophthalic acid) (5), (B)ṡ(isophthalic acid) (6) have been synthesized and structurally characterized by IR, 1H NMR and X-ray crystal structure analysis. Structural analysis indicates that four-component macrocycles in 1-3 are generated from "clip-like" resorcinol templates and building blocks, while 4-6 show infinite H-bonding chains. In addition, the luminescent properties of A, B and 1-6 are investigated primarily in the solid state. Compared with free building blocks, 1-6 are blue-shifted 55-60 nm with decreasing emission intensities in spite of the enhancement in 6. The change of luminescent properties might be caused mainly by incorporation of coformers into co-crystals, including H-bonds, molecular conformations, arranging dispositions and π-π characteristics. It might have potential applications for crystal engineering to construct patentable crystals with interesting luminescent properties.

Crystal and molecular structure of 2,2’-(quinoxaline-2,3-diyl)dipyridinium dinitrate (H{sub 2}L)(NO{sub 3}){sub 2}

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

Egorova, O. A.; Polyakova, I. N., E-mail: polyakova@igic.ras.ru; Sergienko, V. S.

2016-07-15

The crystal structure of 2,2’-(quinoxaline-2,3-diyl)dipyridinium dinitrate (H{sub 2}L)(NO{sub 3}){sub 2} is studied by X-ray diffraction (T = 150 K, R1 = 0.0467). The H{sub 2}L{sup 2+} cation is located on the twofold rotation axis and connected with two NO{sub 3}{sup −} anions by strong N–H···O hydrogen bonds. Planar quinoxaline fragments of cations form stacks with the interplanar spacing of 3.308 Å. The structure of the diprotonated H{sub 2}L{sup 2+} cation is compared with those of the monoprotonated H{sub 2}L{sup 2+} cation and neutral L molecule.

Structural and vibrational properties of solid nitromethane under high pressure by density functional theory.

PubMed

Liu, Hong; Zhao, Jijun; Wei, Dongqing; Gong, Zizheng

2006-03-28

The structural, vibrational, and electronic properties of solid nitromethane under hydrostatic pressure of up to 20 GPa have been studied using density functional theory. The changes of cell volume, the lattice constants, and the molecular geometry of solid nitromethane under hydrostatic loading are examined, and the bulk modulus B0 and its pressure derivative B0' are fitted from the volume-pressure relation. Our theoretical results are compared with available experiments. The change of electron band gap of nitromethane under high pressure is also discussed. Based on the optimized crystal structures, the vibrational frequencies for the internal and lattice modes of the nitromethane crystal at ambient and high pressures are computed, and the pressure-induced frequency shifts of these modes are discussed.

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.

Structural and conformational analysis of pentostatin (2'-deoxycoformycin), a potent inhibitor of adenosine deaminase.

PubMed

Cox, M B; Arjunan, P; Arora, S K

1990-08-01

X-ray, NMR and molecular mechanics studies on pentostatin (C11H16N4O4), a potent inhibitor of the enzyme adenosine deaminase, have been carried out to study the structure and conformation. The crystals belong to the monoclinic space group P21 with the cell dimensions of a = 4.960(1), b = 10.746(3), c = 11.279(4)A, beta = 101.18(2) degrees and Z = 2. The structure was solved by direct methods and difference Fourier methods and refined to an R value of 0.047 for 997 reflections. The trihydrodiazepine ring is nonplanar and adopts a distorted sofa conformation with C(7) deviated from the mean plane by 0.66A. The deoxyribose ring adopts a C3'-endo conformation, different from coformycin where the sugar has a C2'-endo conformation. The observed glycosidic torsion angle (chi = -119.5 degrees) is in the anti range. The conformation about the C(4')-C(5') bond is gauche+. The conformation of the molecule is compared with that of coformycin and 2-azacoformycin. 1 and 2D NMR studies have been carried out and the dihedral angles obtained from coupling constants have been compared with those obtained from the crystal structure. The conformation of deoxyribose in solution is approximately 70% S and 30% N. Molecular mechanics studies were performed to obtain the energy minimized conformation, which is compared with X-ray and NMR results.

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.

Computational Modeling of Bloch Surface Waves in One-Dimensional Periodic and Aperiodic Multilayer Structures

NASA Astrophysics Data System (ADS)

Koju, Vijay

Photonic crystals and their use in exciting Bloch surface waves have received immense attention over the past few decades. This interest is mainly due to their applications in bio-sensing, wave-guiding, and other optical phenomena such as surface field enhanced Raman spectroscopy. Improvement in numerical modeling techniques, state of the art computing resources, and advances in fabrication techniques have also assisted in growing interest in this field. The ability to model photonic crystals computationally has benefited both the theoretical as well as experimental communities. It helps the theoretical physicists in solving complex problems which cannot be solved analytically and helps to acquire useful insights that cannot be obtained otherwise. Experimentalists, on the other hand, can test different variants of their devices by changing device parameters to optimize performance before fabrication. In this dissertation, we develop two commonly used numerical techniques, namely transfer matrix method, and rigorous coupled wave analysis, in C++ and MATLAB, and use two additional software packages, one open-source and another commercial, to model one-dimensional photonic crystals. Different variants of one-dimensional multilayered structures such as perfectly periodic dielectric multilayers, quasicrystals, aperiodic multilayer are modeled, along with one-dimensional photonic crystals with gratings on the top layer. Applications of Bloch surface waves, along with new and novel aperiodic dielectric multilayer structures that support Bloch surface waves are explored in this dissertation. We demonstrate a slow light configuration that makes use of Bloch Surface Waves as an intermediate excitation in a double-prism tunneling configuration. This method is simple compared to the more usual techniques for slowing light using the phenomenon of electromagnetically induced transparency in atomic gases or doped ionic crystals operated at temperatures below 4K. Using a semi-numerical approach, we show that a 1D photonic crystal, a multilayer structure composed of alternating layers of TiO2 and SiO2 , can be used to slow down light by a factor of up to 400. The results also show that better control of the speed of light can be achieved by changing the number of bilayers and the air-gap thickness appropriately. The existence of Bloch surface waves in periodic dielectric multilayer structures with a surface defect is well-known. Not yet recognized is that quasi-crystals and aperiodic dielectric multilayers can also support Bloch-like surface waves. We numerically show the excitation of Bloch-like surface waves in Fibonacci quasi-crystals, Thue-Morse aperiodic dielectric multilayers using the prism coupling method. We report improved surface electric field intensity and penetration depth of Bloch-like surface waves in the air side in such structures compared to their periodic counterparts. Bloch surface waves have also demonstrated significant potential in the field of bios-ensing technology. We further extend our study into a new type of multilayer structure based on Maximal-length sequence, which is a pseudo random sequence. We study the characteristics of Bloch surface waves in a 32 layered Maximal-length sequence multilayer and perform angular, as well as spectral sensitivity analysis for refractive index change detection. We demonstrate numerically that Maximal-length sequence multilayers significantly enhance the sensitivity of Bloch surface waves. Another type of structure that support Bloch surface waves are dielectric multilayer structures with a grating profile on the top-most layer. The grating profile adds an additional degree of freedom to the phase matching conditions for Bloch surface wave excitation. In such structures, the conditions for Bloch surface wave coupling can also be achieved by rotating both polar and azimuthal angles. The generation of Bloch surface waves as a function of azimuthal angle have similar characteristics to conventional grating coupled Bloch surface waves. However, azimuthal generated Bloch surface waves have enhanced angular sensitivity compared to conventional polar angle coupled modes, which makes them appropriate for detecting tiny variations in surface refractive index due to the addition of nano-particles such as protein molecules.

Phormidium phycoerythrin forms hexamers in crystals: a crystallographic study

PubMed Central

Sonani, Ravi Raghav; Sharma, Mahima; Gupta, Gagan Deep; Kumar, Vinay; Madamwar, Datta

2015-01-01

The crystallographic analysis of a marine cyanobacterium (Phormidium sp. A09DM) phycoerythrin (PE) that shows distinct sequence features compared with known PE structures from cyanobacteria and red algae is reported. Phormidium PE was crystallized using the sitting-drop vapour-diffusion method with ammonium sulfate as a precipitant. Diffraction data were collected on the protein crystallography beamline at the Indus-2 synchrotron. The crystals diffracted to about 2.1 Å resolution at 100 K. The crystals, with an apparent hexagonal morphology, belonged to space group P1, with unit-cell parameters a = 108.3, b = 108.4 Å, c = 116.6 Å, α = 78.94, β = 82.50, γ = 60.34°. The molecular-replacement solution confirmed the presence of 12 αβ monomers in the P1 cell. The Phormidium PE elutes as an (αβ)3 trimer of αβ monomers from a molecular-sieve column and exists as [(αβ)3]2 hexamers in the crystal lattice. Unlike red algal PE proteins, the hexamers of Phormidium PE do not form higher-order structures in the crystals. The existence of only one characteristic visual absorption band at 564 nm suggests the presence of phycoerythrobilin chromophores, and the absence of any other types of bilins, in the Phormidium PE assembly. PMID:26249689

Structural evolution of gypsum under high pressure: single-crystal X-ray experiments revisited

NASA Astrophysics Data System (ADS)

Li, Tsung-Lung; Lee, Pei-Lun

2018-05-01

The structures of gypsum at pressures up to approximately 4 GPa are studied with density functional theory (DFT) and thoroughly compared with single-crystal X-ray diffraction experiments reported in the literature [Comodi et al. in (Am Miner 93:1530-1537, 2008)]. It is found that the exchange-correlation density functional revPBE (revised Perdew-Burke-Ernzerhof) in conjunction with a nonlocal van der Waals (vdW) correction is capable of modeling the lattice constants, axial compressibility, and bulk modulus with good accuracy, suggesting that the inclusion of the vdW functional is crucially important for understanding the structure of hydrous minerals. To gain further physical insights, the geometric parameters associated with the constituting components of gypsum (water molecules, SO4 tetrahedra, and CaO8 polyhedra) are analyzed and compared with the experimental values. DFT simulations show that, under pressure, the polyhedral layers remain as nearly planar sheets of interconnecting SO4 tetrahedra and CaO8 polyhedra without further crinkling. DFT analysis on the layer compressibility along the major crystal axis reveals that, in contrast to experimental reports, the hydrous interlayer is less compressible than the polyhedral layer. Squeezed by the lateral pressure, the water molecules in the hydrous interlayer become better affixed along the major axis, making the interlayer harder to compress along this axis.

THE CRYSTALLOGRAPHIC INVESTIGATION OF AuCl /center dot/ PCl$sub 3$ AND IBOGAINE /center dot/ HBr

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

Arai-wessel, G.J.

1960-01-01

The structure of the two compounds is completely dlfferent, one being an inorganic complex and the other being an organic alkaloid complex. The difference in crystal constitution caused a difference in behavior with regard to radiation, requiring the use of specific crysthllographic methods for each. Interferences involved in determining their crystal structure are compared and discussed. (N.W.R.)

Single crystal plastic behavior of a single-phase, face-center-cubic-structured, equiatomic FeNiCrCo alloy

DOE PAGES

Wu, Zhenggang; Gao, Y. F.; Bei, Hongbin

2015-07-25

To understand the fundamental deformation mechanisms of compositionally complex alloys, single crystals of a multi-component equiatomic FeNiCoCr alloy with face-centered cubic (FCC) structure were grown for mechanical studies. Similarly to typical FCC pure metals, slip trace analyses indicate that dislocation slips take place on (1 1 1) planes along [11¯0] directions. The critical resolved shear stress (CRSS) obeys the Schmid law at both 77 and 293 K, and tension–compression asymmetry is not observed. Although this material slips in a normal FCC manner both at 293 and 77 K, compared to typical FCC metals the CRSS’s strong temperature dependence is abnormal.

Grand canonical ensemble Monte Carlo simulation of the dCpG/proflavine crystal hydrate.

PubMed Central

Resat, H; Mezei, M

1996-01-01

The grand canonical ensemble Monte Carlo molecular simulation method is used to investigate hydration patterns in the crystal hydrate structure of the dCpG/proflavine intercalated complex. The objective of this study is to show by example that the recently advocated grand canonical ensemble simulation is a computationally efficient method for determining the positions of the hydrating water molecules in protein and nucleic acid structures. A detailed molecular simulation convergence analysis and an analogous comparison of the theoretical results with experiments clearly show that the grand ensemble simulations can be far more advantageous than the comparable canonical ensemble simulations. Images FIGURE 5 FIGURE 7 PMID:8873992

Synthesis, crystal structures, molecular docking and urease inhibition studies of Ni(II) and Cu(II) Schiff base complexes

NASA Astrophysics Data System (ADS)

Sangeeta, S.; Ahmad, K.; Noorussabah, N.; Bharti, S.; Mishra, M. K.; Sharma, S. R.; Choudhary, M.

2018-03-01

[Ni(L)2] 1 and [Cu(L)2] 2 [HL = 2-((E)-(2-methoxyphenylimino)methyl)-4,6-dichlorophenol] Schiff base complexes have been successfully synthesized and were characterized by FT-IR, UV-Vis, fluorescence spectroscopy and thermogravimetric analysis. The crystal structures of the two complexes were determined through X-ray crystallography. Its inhibitory activity against Helicobacter pylori urease was evaluated in vitro and showed strong inhibitory activity against H. pylori urease compared with acetohydroxamic acid (IC50 = 42.12 μmolL-1), which is a positive reference. A docking analysis using the AutoDock 4.0 program could explain the inhibitory activity of the complex against urease.

Analysis of band structure, transmission properties, and dispersion behavior of THz wave in one-dimensional parabolic plasma photonic crystal

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

Askari, Nasim; Eslami, Esmaeil, E-mail: eeslami@iust.ac.ir; Mirzaie, Reza

2015-11-15

The photonic band gap of obliquely incident terahertz electromagnetic waves in a one-dimensional plasma photonic crystal is studied. The periodic structure consists of lossless dielectric and inhomogeneous plasma with a parabolic density profile. The dispersion relation and the THz wave transmittance are analyzed based on the electromagnetic equations and transfer matrix method. The dependence of effective plasma frequency and photonic band gap characteristics on dielectric and plasma thickness, plasma density, and incident angle are discussed in detail. A theoretical calculation for effective plasma frequency is presented and compared with numerical results. Results of these two methods are in good agreement.

Rapid crystallization and morphological adjustment of zeolite ZSM-5 in nonionic emulsions

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

Zhang Ying, E-mail: yingzh1977@163.co; Jin Chao; Research Institute of Petroleum Processing, Beijing 100083

2011-01-15

Zeolite ZSM-5 was synthesized for the first time in a nonionic emulsion composed of polyoxyethylated alkylphenol, butanol, cyclohexane and tetraethylammonium hydroxide (TEAOH)-containing zeolite synthesis mixture. The crystallization kinetics in the emulsion was investigated and the ZSM-5 product was characterized in detail by XRD, SEM, FT-IR, TG, N{sub 2} adsorption and CHN analysis techniques. Compared with the conventionally hydrothermal synthesis with the same structure directing agent TEAOH, the emulsion system allows rapid crystallization of ZSM-5. The ZSM-5 product exhibits unusual agglomerated structure and possesses larger specific surface area. The FT-IR, TG results plus CHN analysis show the encapsulation of a tracemore » of emulsion components in the emulsion ZSM-5. Control experiments show the emulsion system exerts the crystallization induction and morphological adjustment effects mainly during the aging period. The effects are tentatively attributed to the confined space domains, surfactant-water interaction as well as surfactant-growing crystals interaction existing in the emulsion. -- Graphical abstract: The nonionic emulsion synthesis allows rapid crystallization and morphological adjustment of zeolite ZSM-5 compared with the conventional hydrothermal synthesis. Display Omitted« less

Sun protection enhancement of titanium dioxide crystals by the use of carnauba wax nanoparticles: the synergistic interaction between organic and inorganic sunscreens at nanoscale.

PubMed

Villalobos-Hernández, J R; Müller-Goymann, C C

2006-09-28

Carnauba wax is partially composed of cinnamates. The rational combination of cinnamates and titanium dioxide has shown a synergistic effect to improve the sun protection factor (SPF) of cosmetic preparations. However, the mechanism of this interaction has not been fully understood. In this study, an ethanolic extract of the carnauba wax and an ethanolic solution of a typical cinnamate derivative, ethylcinnamate, were prepared and their UV absorption and SPF either alone or in the presence of titanium dioxide were compared. The titanium dioxide crystals and the cinnamates solutions were also distributed into a matrix composed of saturated fatty acids to emulate the structure of the crystallized carnauba wax. SPF, differential scanning calorimetry (DSC) and X-ray studies of these matrices were performed. Additionally, carnauba wax nanosuspensions containing titanium dioxide either in the lipid phase or in the aqueous phase were prepared to evaluate their SPFs and their physical structure. Strong UV absorption was observed in diluted suspensions of titanium dioxide after the addition of cinnamates. The saturated fatty acid matrices probably favored the adsorption of the cinnamates at the surface of titanium dioxide crystals, which was reflected by an increase in the SPF. No modification of the crystal structure of the fatty acid matrices was observed after the addition of cinnamates or titanium dioxide. The distribution of the titanium dioxide inside the lipid phase of the nanosuspensions was more effective to reach higher SPFs than that at the aqueous phase. The close contact between the carnauba wax and the titanium dioxide crystals after the high-pressure homogenization process was confirmed by transmission electron microscopy (TEM).

Effect of crystals and fibrous network polymer additives on cellular morphology of microcellular foams

NASA Astrophysics Data System (ADS)

Miyamoto, Ryoma; Utano, Tatsumi; Yasuhara, Shunya; Ishihara, Shota; Ohshima, Masahiro

2015-05-01

In this study, the core-back foam injection molding was used for preparing microcelluar polypropylene (PP) foam with either a 1,3:2,4 bis-O-(4-methylbenzylidene)-D-sorbitol gelling agent (Gel-all MD) or a fibros network polymer additive (Metablen 3000). Both agent and addiive could effectively control the celluar morphology in foams but somehow different ways. In course of cooling the polymer with Gel-all MD in the mold caity, the agent enhanced the crystal nucleation and resulted in the large number of small crystals. The crystals acted as effective bubble nucleation agent in foaming process. Thus, the agent reduced the cell size and increased the cell density, drastically. Furthermore, the small crystals provided an inhomogenuity to the expanding cell wall and produced the high open cell content with nano-scale fibril structure. Gell-all as well as Metablene 3000 formed a gel-like fibrous network in melt. The network increased the elongational viscosity and tended to prevent the cell wall from breaking up. The foaming temperature window was widened by the presence of the network. Especially, the temperature window where the macro-fibrous structure was formed was expanded to the higher temperature. The effects of crystal nucleating agent and PTFE on crystals' size and number, viscoelsticity, rheological propreties of PP and cellular morphology were compared and thorougly investigated.

Study of Polymer Crystallization by Physical Vapor Deposition

NASA Astrophysics Data System (ADS)

Jeong, Hyuncheol

When a polymer is confined under the submicron length scale, confinement size and interfaces can significantly impact the crystallization kinetics and resulting morphology. The ability to tune the morphology of confined polymer systems is of critical importance for the development of high-performance polymer microelectronics. The wisdom from the research on confined crystallization suggests that it would be beneficial to have a processing route in which the crystallization of polymers is driven by interface and temperature effects at a nanometer-scale confinement. In practice, for atomic and small-molecular systems, physical vapor deposition (PVD) has been recognized as the most successful processing route for the precise control of the film structure at surface utilizing confinement effects. While standard PVD technologies are not generally applicable to the deposition of the chemically fragile macromolecules, the development of matrix-assisted pulsed laser evaporation (MAPLE) now enables the non-destructive PVD of high-molecular weight polymers. In this thesis work, we investigated the use of MAPLE for the precise control of the crystallization of polymer films at a molecular level. We also sought to decipher the rules governing the crystallization of confined polymers, by using MAPLE as a tool to form confined polymer systems onto substrates with a controlled temperature. We first explored the early stages of film growth and crystallization of poly(ethylene oxide) (PEO) at the substrate surface formed by MAPLE. The unique mechanism of film formation in MAPLE, the deposition of submicron-sized polymer droplets, allowed for the manifestation of confinement and substrate effects in the crystallization of MAPLE-deposited PEO. Furthermore, we also focused on the property of the amorphous PEO film formed by MAPLE, showing the dependence of polymer crystallization kinetics on the thermal history of the amorphous phase. Lastly, we probed how MAPLE processing affected the semi-crystalline structure in MAPLE-deposited polyethylene (PE) films. Depositing PE at various temperatures remarkably allowed for the tunability of the melting temperature and crystallinity of the PE films, thus manipulating the semi-crystalline structure. By comparing the structure of PE formed by different processing routes, i.e., MAPLE and melt-crystallization, we discussed how processing routes affect the development of semi-crystalline phase in polymer films.

[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.

Phase transition studied by 7Li nuclear magnetic resonance in LiXSO4 (X = K, Rb, Cs and NH4) single crystals

NASA Astrophysics Data System (ADS)

Lim, Ae Ran; Choh, Sung Ho; Jeong, Se-Young

2000-11-01

The temperature dependences of 7Li nuclear magnetic resonance in LiXSO4 (X = K, Rb, Cs, and NH4) single crystals grown by the slow evaporation method have been investigated by employing a Bruker FT NMR spectrometer. From the experimental data, the nuclear quadrupole constant, the asymmetry parameter and the principal axes of the EFG tensor were determined, and the results were compared with the crystal structure. The temperature dependences of the quadrupole parameters were explained with a single torsional mode of the Li-O bond by the Bayer theory. All the LiO4 tetrahedra in four different crystals showed torsional motion about the X-axis of the EFG tensor. Based on these results, the differences in atomic weight of X in the LiXSO4 single crystals are responsible for the differences in the torsional angular frequencies.

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

Study of Fluid Flow Control in Protein Crystallization using Strong Magnetic Fields

NASA Astrophysics Data System (ADS)

Ramachandran, Narayanan; Leslie, Fred; Ciszak, Ewa

2002-11-01

An important component in biotechnology, particularly in the area of protein engineering and rational drug design is the knowledge of the precise three-dimensional molecular structure of proteins. The quality of structural information obtained from X-ray diffraction methods is directly dependent on the degree of perfection of the protein crystals. As a consequence, the growth of high quality macromolecular crystals for diffraction analyses has been the central focus for biochemists, biologists, and bioengineers. Macromolecular crystals are obtained from solutions that contain the crystallizing species in equilibrium with higher aggregates, ions, precipitants, other possible phases of the protein, foreign particles, the walls of the container, and a likely host of other impurities. By changing transport modes in general, i.e., reduction of convection and sedimentation, as is achieved in "microgravity", researchers have been able to dramatically affect the movement and distribution of macromolecules in the fluid, and thus their transport, formation of crystal nuclei, and adsorption to the crystal surface. While a limited number of high quality crystals from space flights have been obtained, as the recent National Research Council (NRC) review of the NASA microgravity crystallization program pointed out, the scientific approach and research in crystallization of proteins has been mainly empirical yielding inconclusive results. We postulate that we can reduce convection in ground-based experiments and we can understand the different aspects of convection control through the use of strong magnetic fields and field gradients. Whether this limited convection in a magnetic field will provide the environment for the growth of high quality crystals is still a matter of conjecture that our research will address. The approach exploits the variation of fluid magnetic susceptibility with concentration for this purpose and the convective damping is realized by appropriately positioning the crystal growth cell so that the magnetic susceptibility force counteracts terrestrial gravity. The general objective is to test the hypothesis of convective control using a strong magnetic field and magnetic field gradient and to understand the nature of the various forces that come into play. Specifically we aim to delineate causative factors and to quantify them through experiments, analysis and numerical modeling. Once the basic understanding is obtained, the study will focus on testing the hypothesis on proteins of pyruvate dehydrogenase complex (PDC), proteins E1 and E3. Obtaining high crystal quality of these proteins is of great importance to structural biologists since their structures need to be determined. Specific goals for the investigation are: 1. To develop an understanding of convection control in diamagnetic fluids with concentration gradients through experimentation and numerical modeling. Specifically solutal buoyancy driven convection due to crystal growth will be considered. 2. To develop predictive measures for successful crystallization in a magnetic field using analyses and numerical modeling for use in future protein crystal growth experiments. This will establish criteria that can be used to estimate the efficacy of magnetic field flow damping on crystallization of candidate proteins. 3. To demonstrate the understanding of convection damping by high magnetic fields to a class of proteins that is of interest and whose structure is as yet not determined. 4. To compare quantitatively, the quality of the grown crystals with and without a magnetic field. X-ray diffraction techniques will be used for the comparative studies. In a preliminary set of experiments, we studied crystal dissolution effects in a 5 Tesla magnet available at NASA Marshall Space Flight Center (MSFC). Using a Schlieren setup, a 1mm crystal of Alum (Aluminum-Potassium Sulfate) was introduced in a 75% saturated solution and the resulting dissolution plume was observed. The experiment was conducted both in the presence and absence of a magnetic field gradient. The magnet produces a gradient field of approx. 1 Tesla2/cm. Image analysis of the recorded images indicated an enhanced plume velocity that was of the order of the measurement limit. For this experiment, both the gradient and gravity fields are in the same direction resulting in an enhanced effective gravity that tends to accelerate the observed plume velocity. While the results are not conclusive, pending further tests, it clearly points out the inadequacy of the MSFC magnet for conducting protein crystallization experiments and the need for a stronger magnet. In spacebased experiments, however, where the gravitational effects are small, only a weak magnetic field will be required to control or mitigate the effects of convective contamination.

Study of Fluid Flow Control in Protein Crystallization using Strong Magnetic Fields

NASA Technical Reports Server (NTRS)

Ramachandran, Narayanan; Leslie, Fred; Ciszak, Ewa

2002-01-01

An important component in biotechnology, particularly in the area of protein engineering and rational drug design is the knowledge of the precise three-dimensional molecular structure of proteins. The quality of structural information obtained from X-ray diffraction methods is directly dependent on the degree of perfection of the protein crystals. As a consequence, the growth of high quality macromolecular crystals for diffraction analyses has been the central focus for biochemists, biologists, and bioengineers. Macromolecular crystals are obtained from solutions that contain the crystallizing species in equilibrium with higher aggregates, ions, precipitants, other possible phases of the protein, foreign particles, the walls of the container, and a likely host of other impurities. By changing transport modes in general, i.e., reduction of convection and sedimentation, as is achieved in "microgravity", researchers have been able to dramatically affect the movement and distribution of macromolecules in the fluid, and thus their transport, formation of crystal nuclei, and adsorption to the crystal surface. While a limited number of high quality crystals from space flights have been obtained, as the recent National Research Council (NRC) review of the NASA microgravity crystallization program pointed out, the scientific approach and research in crystallization of proteins has been mainly empirical yielding inconclusive results. We postulate that we can reduce convection in ground-based experiments and we can understand the different aspects of convection control through the use of strong magnetic fields and field gradients. Whether this limited convection in a magnetic field will provide the environment for the growth of high quality crystals is still a matter of conjecture that our research will address. The approach exploits the variation of fluid magnetic susceptibility with concentration for this purpose and the convective damping is realized by appropriately positioning the crystal growth cell so that the magnetic susceptibility force counteracts terrestrial gravity. The general objective is to test the hypothesis of convective control using a strong magnetic field and magnetic field gradient and to understand the nature of the various forces that come into play. Specifically we aim to delineate causative factors and to quantify them through experiments, analysis and numerical modeling. Once the basic understanding is obtained, the study will focus on testing the hypothesis on proteins of pyruvate dehydrogenase complex (PDC), proteins E1 and E3. Obtaining high crystal quality of these proteins is of great importance to structural biologists since their structures need to be determined. Specific goals for the investigation are: 1. To develop an understanding of convection control in diamagnetic fluids with concentration gradients through experimentation and numerical modeling. Specifically solutal buoyancy driven convection due to crystal growth will be considered. 2. To develop predictive measures for successful crystallization in a magnetic field using analyses and numerical modeling for use in future protein crystal growth experiments. This will establish criteria that can be used to estimate the efficacy of magnetic field flow damping on crystallization of candidate proteins. 3. To demonstrate the understanding of convection damping by high magnetic fields to a class of proteins that is of interest and whose structure is as yet not determined. 4. To compare quantitatively, the quality of the grown crystals with and without a magnetic field. X-ray diffraction techniques will be used for the comparative studies. In a preliminary set of experiments, we studied crystal dissolution effects in a 5 Tesla magnet available at NASA Marshall Space Flight Center (MSFC). Using a Schlieren setup, a 1mm crystal of Alum (Aluminum-Potassium Sulfate) was introduced in a 75% saturated solution and the resulting dissolution plume was observed. The experiment was conducted both in the presence and absence of a magnetic field gradient. The magnet produces a gradient field of approx. 1 Tesla2/cm. Image analysis of the recorded images indicated an enhanced plume velocity that was of the order of the measurement limit. For this experiment, both the gradient and gravity fields are in the same direction resulting in an enhanced effective gravity that tends to accelerate the observed plume velocity. While the results are not conclusive, pending further tests, it clearly points out the inadequacy of the MSFC magnet for conducting protein crystallization experiments and the need for a stronger magnet. In spacebased experiments, however, where the gravitational effects are small, only a weak magnetic field will be required to control or mitigate the effects of convective contamination.

Evolution of molecular crystal optical phonons near structural phase transitions

NASA Astrophysics Data System (ADS)

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

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

Mechanisms for Improved Hygroscopicity of L-Arginine Valproate Revealed by X-Ray Single Crystal Structure Analysis.

PubMed

Ito, Masataka; Nambu, Kaori; Sakon, Aya; Uekusa, Hidehiro; Yonemochi, Etsuo; Noguchi, Shuji; Terada, Katsuhide

2017-03-01

Valproic acid is widely used as an antiepileptic agent. Valproic acid is in liquid phase while sodium valproate is in solid phase at room temperature. Sodium valproate is hard to manufacture because of its hygroscopic and deliquescent properties. To improve these, cocrystal and salt screening for valproic acid was employed in this study. Two solid salt forms, l-arginine valproate and l-lysine valproate, were obtained and characterized. By using dynamic vapor sorption method, the critical relative humidity of sodium valproate, l-arginine valproate, and l-lysine valproate were measured. Critical relative humidity of sodium valproate was 40%, of l-lysine valproate was 60%, and of l-arginine valproate was 70%. Single-crystal X-ray structure determination of l-arginine valproate was employed. l-Lysine valproate was of low diffraction quality, and l-arginine valproate formed a 1:1 salt. Crystal l-arginine valproate has a disorder in the methylene carbon chain that creates 2 conformations. The carboxylate group of valproic acid is connected to the amino group of l-arginine. Crystalline morphologies were calculated from its crystal structure. Adsorption of water molecules to crystal facets was simulated by Material Studio. When comparing adsorption energy per site of these salts, sodium valproate is more capable of adsorption of water molecule than l-arginine valproate. Copyright © 2017 American Pharmacists Association®. Published by Elsevier Inc. All rights reserved.

Aging-driven decomposition in zolpidem hemitartrate hemihydrate and the single-crystal structure of its decomposition products.

PubMed

Vega, Daniel R; Baggio, Ricardo; Roca, Mariana; Tombari, Dora

2011-04-01

The "aging-driven" decomposition of zolpidem hemitartrate hemihydrate (form A) has been followed by X-ray powder diffraction (XRPD), and the crystal and molecular structures of the decomposition products studied by single-crystal methods. The process is very similar to the "thermally driven" one, recently described in the literature for form E (Halasz and Dinnebier. 2010. J Pharm Sci 99(2): 871-874), resulting in a two-phase system: the neutral free base (common to both decomposition processes) and, in the present case, a novel zolpidem tartrate monohydrate, unique to the "aging-driven" decomposition. Our room-temperature single-crystal analysis gives for the free base comparable results as the high-temperature XRPD ones already reported by Halasz and Dinnebier: orthorhombic, Pcba, a = 9.6360(10) Å, b = 18.2690(5) Å, c = 18.4980(11) Å, and V = 3256.4(4) Å(3) . The unreported zolpidem tartrate monohydrate instead crystallizes in monoclinic P21 , which, for comparison purposes, we treated in the nonstandard setting P1121 with a = 20.7582(9) Å, b = 15.2331(5) Å, c = 7.2420(2) Å, γ = 90.826(2)°, and V = 2289.73(14) Å(3) . The structure presents two complete moieties in the asymmetric unit (z = 4, z' = 2). The different phases obtained in both decompositions are readily explained, considering the diverse genesis of both processes. Copyright © 2010 Wiley-Liss, Inc.

Mapping the conformational space accessible to BACE2 using surface mutants and cocrystals with Fab fragments, Fynomers and Xaperones.

PubMed

Banner, David W; Gsell, Bernard; Benz, Jörg; Bertschinger, Julian; Burger, Dominique; Brack, Simon; Cuppuleri, Simon; Debulpaep, Maja; Gast, Alain; Grabulovski, Dragan; Hennig, Michael; Hilpert, Hans; Huber, Walter; Kuglstatter, Andreas; Kusznir, Eric; Laeremans, Toon; Matile, Hugues; Miscenic, Christian; Rufer, Arne C; Schlatter, Daniel; Steyaert, Jan; Stihle, Martine; Thoma, Ralf; Weber, Martin; Ruf, Armin

2013-06-01

The aspartic protease BACE2 is responsible for the shedding of the transmembrane protein Tmem27 from the surface of pancreatic β-cells, which leads to inactivation of the β-cell proliferating activity of Tmem27. This role of BACE2 in the control of β-cell maintenance suggests BACE2 as a drug target for diabetes. Inhibition of BACE2 has recently been shown to lead to improved control of glucose homeostasis and to increased insulin levels in insulin-resistant mice. BACE2 has 52% sequence identity to the well studied Alzheimer's disease target enzyme β-secretase (BACE1). High-resolution BACE2 structures would contribute significantly to the investigation of this enzyme as either a drug target or anti-target. Surface mutagenesis, BACE2-binding antibody Fab fragments, single-domain camelid antibody VHH fragments (Xaperones) and Fyn-kinase-derived SH3 domains (Fynomers) were used as crystallization helpers to obtain the first high-resolution structures of BACE2. Eight crystal structures in six different packing environments define an ensemble of low-energy conformations available to the enzyme. Here, the different strategies used for raising and selecting BACE2 binders for cocrystallization are described and the crystallization success, crystal quality and the time and resources needed to obtain suitable crystals are compared.

Superhyperfine Structure of the EPR Spectra of Nd3+ Impurity Ions in Fluorite CaF2

NASA Astrophysics Data System (ADS)

Aminov, L. K.; Gafurov, M. R.; Kurkin, I. N.; Malkin, B. Z.; Rodionov, A. A.

2018-05-01

EPR spectra of a CaF2 single crystal that was grown from melt containing a small addition of NdF3 were studied. Signals corresponding to tetragonal centers of Nd3+ ions and cubic centers of Er3+ and Yb3+ ions were found. Superhyperfine structure (SHFS) in the spectra of the Nd3+ ions was observed for the first time in this crystal; parameters of the superhyperfine interaction of the Nd3+ ions with the nearest nine fluorine ions were determined. The dependence of the resolution of the Nd3+ EPR spectrum SHFS on the incident microwave power at the temperature of T ≈ 6 K was studied. Obtained results are discussed and compared with the literature data.

A strategic approach to physico-chemical analysis of bis (thiourea) lead chloride - A reliable semi-organic nonlinear optical crystal

NASA Astrophysics Data System (ADS)

Rajagopalan, N. R.; Krishnamoorthy, P.; Jayamoorthy, K.

2017-03-01

Good quality crystals of bis thiourea lead chloride (BTLC) have been grown by slow evaporation method from aqueous solution. Orthorhombic structure and Pna21 space group of the crystals have been identified by single crystal X-ray diffraction. Studies on nucleation kinetics of grown BTLC has been carried out from which meta-stable zone width, induction period, free energy change, critical radius, critical number and growth rate have been calculated. The experimental values of interfacial surface energy for the crystal growth process have been compared with theoretical models. Ultra violet transmittance studies resulted in a high transmittance and wide band gap energy suggested the required optical transparency of the crystal. The second harmonic generation (SHG) and phase matching nature of the crystal have been justified by Kurtz-Perry method. The SHG nature of the crystal has been further attested by the higher values of theoretical hyper polarizability. The dielectric nature of the crystals at different temperatures with varying frequencies has been thoroughly studied. The activation energy values of the electrical process have been calculated from ac conductivity study. Solid state parameters including valence electron plasma energy, Penn gap, Fermi energy and polarisability have been unveiled by theoretical approach and correlated with the crystal's SHG efficiency. The values of hardness number, elastic stiffness constant, Meyer's Index, minimum level of indentation load, load dependent constant, fracture toughness, brittleness index and corrected hardness obtained from Vicker's hardness test clearly showed that the BTLC crystal has good mechanical stability required for NLO device fabrication.

Preferential Stereocomplex Crystallization in Enantiomeric Blends of Cellulose Acetate-g-Poly(lactic acid)s with Comblike Topology.

PubMed

Bao, Jianna; Han, Lili; Shan, Guorong; Bao, Yongzhong; Pan, Pengju

2015-10-01

Although stereocomplex (sc) crystallization is highly effective for improving the thermal resistance of poly(lactic acid) (PLA), it is much less predominant than homocrystallization in high-molecular-weight (HMW) poly(l-lactic acid)/ poly(d-lactic acid) (PLLA/PDLA) racemic blends. In this contribution, the sc crystallization of HMW PLLA/PDLA racemic blends was facilitated by using comblike PLAs with cellulose acetate as the backbone. Competing crystallization kinetics, polymorphic crystalline structure, and structural transition of comblike PLLA/PDLA blends with a wide range of MWs were investigated and compared with the corresponding linear/comblike and linear blends. The HMW comblike blend is preferentially crystallized in sc polymorphs and exhibits a faster crystallization rate than does the corresponding linear blend. The sc crystallites are predominantly formed in nonisothermal cold crystallization and isothermal crystallization at temperatures above 120 °C for the comblike blends. Except for the facilitated sc formation in primary crystallization, synchrotron radiation WAXD analysis indicates that the presence of a comblike component also facilitates the transition or recrystallization from homocrystallite (hc) to sc crystallite upon heating. Preferential sc formation of comblike blends is probably attributable to the favorable interdigitation between enantiomeric branches and the increased mobility of polymer segments. After crystallization under the same temperature, the comblike blends, which mainly contain sc crystallites, show smaller long periods and thinner crystalline lamellae than do the corresponding PLLA with homocrystalline structures.

Anisotropy of electrical resistivity in PVT grown WSe2-x crystals

NASA Astrophysics Data System (ADS)

Solanki, G. K.; Patel, Y. A.; Agarwal, M. K.

2018-05-01

Single crystals of p-type WSe2 and WSe1.9 were grown by a physical vapour transport technique. The anisotropy in d.c. electrical resistivity was investigated in these grown crystals. The off-stoichiometric WSe1.9 exhibited a higher anisotropy ratio as compared to WSe2 crystals. The electron microscopic examination revealed the presence of a large number of stacking faults in these crystals. The resistivity enhancement along the c-axis and anisotropic effective mass ratio explained on the basis of structural disorder introduced due to off-stoichiometry.

Synthesis, crystal structure and DFT studies of a dual fluorescent ketamine: Structural changes in the ground and excited states

NASA Astrophysics Data System (ADS)

Latha, V.; Balakrishnan, C.; Neelakantan, M. A.

2015-07-01

A fluorescent probe 2Z,2‧Z-3,3‧-(4,4‧-methylenebis(4,1-phenylene) bis(azanediyl))bis (1,3-diphenylprop-2-en-1-one) (L) was synthesized and characterized by IR, 1H NMR, ESI-mass, UV-visible and fluorescence spectral techniques. The single crystal analysis illustrates the existence of L in ketamine form. The crystal structure is stabilized by intramolecular and intermolecular hydrogen bonding. The thermal stability of L was studied by TG analysis. The fluorescence spectrum of L shows dual emission, and is due to excited state intramolecular proton transfer (ESIPT) process. This is supported by the high Stokes shift value. Electronic structure calculations of L in the ground and excited state have been carried out using DFT and TD-DFT at B3LYP/6-31G (d,p) level, respectively. The vibrational spectrum was computed at this level and compared with experimental values. Major orbital contributions for the electronic transitions were assigned with the help of TD-DFT. The changes in the Mulliken charge, bond lengths and bond angles between the ground and excited states of the tautomers demonstrate that twisted intramolecular charge transfer (TICT) process occurs along with ESIPT in the excited state.

Crystal structure, stoichiometry, and dielectric relaxation in Bi 3.32Nb 7.09O 22.7 and structurally related ternary phases

NASA Astrophysics Data System (ADS)

Grey, I. E.; Vanderah, T. A.; Mumme, W. G.; Roth, R. S.; Guzman, J.; Nino, J. C.; Levin, I.

2008-03-01

The crystal structure of the phase previously reported to occur at 4:9 Bi 2O 3:Nb 2O 5 has been determined using single-crystal X-ray and powder neutron diffraction ( P6 3/ mmc; a=7.4363(1) Å, c=19.7587(5) Å; Z=2). The structural study combined with phase equilibrium analyses indicate that the actual composition is Bi 3.32Nb 7.09O 22.7. This binary compound is the end-member of a family of four phases which form along a line between it and the pyrochlore phase field in the Bi 2O 3:Fe 2O 3:Nb 2O 5 system. The structures are derived from the parent pyrochlore end-member by chemical twinning, and can also be described as unit-cell intergrowths of the pyrochlore and hexagonal tungsten bronze (HTB) structures. The dielectric properties of the three chemically twinned pyrochlore phases, Bi 3.32Nb 7.09O 22.7, Bi 9.3Fe 1.1Nb 16.9O 57.8 and Bi 5.67FeNb 10O 35, were characterized. All exhibit low-temperature, broad dielectric relaxation similar to that of the Bi-Fe-Nb-O pyrochlore. At 1 MHz and ≈175 K the observed relative permittivites were 345, 240, and 205, respectively, compared to 125 for the Bi-Fe-Nb-O pyrochlore. The higher relative permittivities observed for the chemically twinned pyrochlore derivatives are ascribed to the presence of HTB blocks in their structures: The Bi atoms located in the HTB blocks feature highly asymmetric coordination environments compared to pyrochlore, and the magnitude of the relative permittivity increases with the proportion of Bi located within the HTB portions of the structures.

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.

Continuous-wave mid-infrared photonic crystal light emitters at room temperature

NASA Astrophysics Data System (ADS)

Weng, Binbin; Qiu, Jijun; Shi, Zhisheng

2017-01-01

Mid-infrared photonic crystal enhanced lead-salt light emitters operating under continuous-wave mode at room temperature were investigated in this work. For the device, an active region consisting of 9 pairs of PbSe/Pb0.96Sr0.04Se quantum wells was grown by molecular beam epitaxy method on top of a Si(111) substrate which was initially dry-etched with a two-dimensional photonic crystal structure in a pattern of hexagonal holes. Because of the photonic crystal structure, an optical band gap between 3.49 and 3.58 µm was formed, which matched with the light emission spectrum of the quantum wells at room temperature. As a result, under optical pumping, using a near-infrared continuous-wave semiconductor laser, the device exhibited strong photonic crystal band-edge mode emissions and delivered over 26.5 times higher emission efficiency compared to the one without photonic crystal structure. The output power obtained was up to 7.68 mW (the corresponding power density was 363 mW/cm2), and a maximum quantum efficiency reached to 1.2%. Such photonic crystal emitters can be used as promising light sources for novel miniaturized gas-sensing systems.

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.

Structure of CPV17 polyhedrin determined by the improved analysis of serial femtosecond crystallographic data

DOE PAGES

Ginn, Helen M.; Messerschmidt, Marc; Ji, Xiaoyun; ...

2015-03-09

The X-ray free-electron laser (XFEL) allows the analysis of small weakly diffracting protein crystals, but has required very many crystals to obtain good data. Here we use an XFEL to determine the room temperature atomic structure for the smallest cytoplasmic polyhedrosis virus polyhedra yet characterized, which we failed to solve at a synchrotron. These protein microcrystals, roughly a micron across, accrue within infected cells. We use a new physical model for XFEL diffraction, which better estimates the experimental signal, delivering a high-resolution XFEL structure (1.75 Å), using fewer crystals than previously required for this resolution. The crystal lattice and proteinmore » core are conserved compared with a polyhedrin with less than 10% sequence identity. We explain how the conserved biological phenotype, the crystal lattice, is maintained in the face of extreme environmental challenge and massive evolutionary divergence. Our improved methods should open up more challenging biological samples to XFEL analysis.« less

Synthesis, crystal structure and electrical properties of the tetrahedral quaternary chalcogenides CuM{sub 2}InTe{sub 4} (M=Zn, Cd)

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

Nolas, George S., E-mail: gnolas@usf.edu; Hassan, M. Shafiq; Dong, Yongkwan

Quaternary chalcogenides form a large class of materials that continue to be of interest for energy-related applications. Certain compositions have recently been identified as possessing good thermoelectric properties however these materials typically have the kesterite structure type with limited variation in composition. In this study we report on the structural, optical and electrical properties of the quaternary chalcogenides CuZn{sub 2}InTe{sub 4} and CuCd{sub 2}InTe{sub 4} which crystallize in the modified zinc-blende crystal structure, and compare their properties with that of CuZn{sub 2}InSe{sub 4}. These p-type semiconductors have direct band gaps of about 1 eV resulting in relatively high Seebeck coefficientmore » and resistivity values. This work expands on the research into quaternary chalcogenides with new compositions and structure types in order to further the fundamental investigation of multinary chalcogenides for potential thermoelectrics applications. - Graphical abstract: The structural, optical and electrical properties of the quaternary chalcogenides CuZn{sub 2}InTe{sub 4} and CuCd{sub 2}InTe{sub 4} are reported for the first time. The unique crystal structure allows for relatively good electrical transports and therefore potential for thermoelectric applications. - Highlights: • The physical properties of CuZn{sub 2}InTe{sub 4} and CuCd{sub 2}InTe{sub 4} are reported for the first time. • These materials have potential for thermoelectric applications. • Their direct band gaps also suggest potential for photovoltaics applications.« less

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.

Superconductivity and valence state in layered single-crystal HfAs1.67Te0.12

NASA Astrophysics Data System (ADS)

Peng, Jian; Yu, Jia; Zhang, Shuai; Chen, Genfu

2018-01-01

We report a detailed study on single crystals of HfAs1.67Te0.12 within a PbFCl-type layered structure. The single crystals of the title compound were successfully grown using a chemical transport reaction. The temperature dependence of electrical resistivity ρ (T), AC magnetic susceptibility {χ }{AC}(T) and specific heat C(T) show a bulk superconductivity with transition temperature T c = 1.67 K. The jump of C/T at T c is comparable to the traditional BCS weak-coupling model. A full H-T phase diagram is established using the results of ρ (T,H) and C(T) under fields, suggesting a rather weak anisotropy [({H}c2\\parallel {ab}(0)/{H}c2\\parallel c(0)] of 1.8 in orbital limit dominated three-dimension-like superconducting system. The mixed-valence states of Hf and As observed in the binding energy from x-ray photoelectron spectroscopy are consistent with the single-crystal x-ray diffraction analysis, indicating that the As-Te disorder prefers to occur in the [HfAs] layer and a large amount of vacancies are present in tetragonal As layer. As compared to HfAs1.7Se0.2 (T c = 0.52 K), a positive-like vacancy effect on T c has been confirmed in HfAs1.67Te0.12. The analysis of the Hall coefficient implies that the hole-type carriers dominate the transport properties, which is in good agreement with the hole pockets at Fermi surface obtained in a band structure calculation. The detailed study of single-crystal HfAs1.67Te0.12 provides a possible candidate to discuss the non-magnetic Kondo effect.

Structure-function relationship of avian eggshell matrix proteins: a comparative study of two major eggshell matrix proteins, ansocalcin and OC-17.

PubMed

Lakshminarayanan, Rajamani; Joseph, Jeremiah S; Kini, R Manjunatha; Valiyaveettil, Suresh

2005-01-01

The role of individual matrix proteins in avian eggshell calcification is poorly understood despite numerous attempts to characterize and localize their presence in the eggshell matrix. Ansocalcin, the major matrix protein from goose eggshell, was found to induce the formation of calcite crystal aggregates under in vitro. Owing to its high similarity with the chicken eggshell matrix protein ovocleidin 17 (OC-17), a comparative investigation has been carried out to understand the structure-function relationship. RP-HPLC shows that ansocalcin is the major component in extracts of goose eggshells before and after bleach treatment. However, OC-17 was observed in minute quantities in the extract of bleach-treated chicken eggshells. In vitro crystal growth experiments showed that OC-17 and ansocalcin interact differently with the calcite crystals formed. Circular dichroism, intrinsic tryptophan fluorescence, and dynamic light scattering studies showed that, under the conditions used in our experiments, OC-17 does not aggregate in solution or induce the nucleation of calcite aggregates in the concentration range used. These observations indicate that OC-17 and ansocalcin play different roles in the eggshell calcification. To our knowledge, this is the first report on the comparison of properties of homologous eggshell proteins that belong to the same phylogeny.

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.

The crystal structure of human GDP-L-fucose synthase.

PubMed

Zhou, Huan; Sun, Lihua; Li, Jian; Xu, Chunyan; Yu, Feng; Liu, Yahui; Ji, Chaoneng; He, Jianhua

2013-09-01

Human GDP-l-fucose synthase, also known as FX protein, synthesizes GDP-l-fucose from its substrate GDP-4-keto-6-deoxy-d-mannose. The reaction involves epimerization at both C-3 and C-5 followed by an NADPH-dependent reduction of the carbonyl at C-4. In this paper, the first crystal structure of human FX protein was determined at 2.37 Å resolution. The asymmetric unit of the crystal structure contains four molecules which form two homodimers. Each molecule consists of two domains, a Rossmann-fold NADPH-binding motif and a carboxyl terminal domain. Compared with the Escherichia coli GDP-l-fucose synthase, the overall structures of these two enzymes have four major differences. There are four loops in the structure of human FX protein corresponding to two α-helices and two β-sheets in that of the E. coli enzyme. Besides, there are seven different amino acid residues binding with NAPDH comparing human FX protein with that from E. coli. The structure of human FX reveals the key catalytic residues and could be useful for the design of drugs for the treatment of inflammation, auto-immune diseases, and possibly certain types of cancer.

Effects of molecular geometry on the properties of compressed diamondoid crystals

DOE PAGES

Yang, Fan; Lin, Yu; Baldini, Maria; ...

2016-11-01

Diamondoids are an intriguing group of carbon-based nanomaterials, which combine desired properties of inorganic nanomaterials and small hydrocarbon molecules with atomic-level uniformity. In this Letter, we report the first comparative study on the effect of pressure on a series of diamondoid crystals with systematically varying molecular geometries and shapes, including zero-dimensional (0D) adamantane; one-dimensional (1D) diamantane, [121]tetramantane, [123]tetramantane, and [1212]pentamantane; two-dimensional (2D) [12312]hexamantane; and three-dimensional (3D) triamantane and [1(2,3)4]pentamantane. We find the bulk moduli of these diamondoid crystals are strongly dependent on the diamondoids’ molecular geometry with 3D [1(2,3)4]pentamantane being the least compressible and 0D adamantane being the most compressible.more » These diamondoid crystals possess excellent structural rigidity and are able to sustain large volume deformation without structural failure even after repetitive pressure loading cycles. These properties are desirable for constructing cushioning devices. Furthermore, we also demonstrate that lower diamondoids outperform the conventional cushioning materials in both the working pressure range and energy absorption density.« less

Effect of structural defects on the magnetic properties of the EuBaCo1.90O5.36 single crystal

NASA Astrophysics Data System (ADS)

Arbuzova, T. I.; Naumov, S. V.; Telegin, S. V.

2018-01-01

The effect of structural defects in cobalt and oxygen sublattices with the constant average oxidation level 3+ of all cobalt ions on the magnetic properties of the EuBaCo1.90O5.36 single crystal has been studied. The magnetic properties of the single crystal and the polycrystalline sample of the corresponding composition are compared in the range T = 200-650 K. The results show that the cobalt-deficient EuBaCo2- x O5.5-δ samples demonstrate a three-dimensional XY ferromagnetic ordering of magnetic sublattices. The values of the effective magnetic moment at T > 480 K indicate the existence of the IS and HS states of Co3+ ions. The large difference of values of μeff of the EuBaCo1.90O5.36 single crystal and polycrystal can be due to that the magnetic ion spins lie in plane ab. The magnetic field directed along plane ab substantially influences the magnetic ordering at T < 300 K.

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.

Origins of contrasting copper coordination geometries in crystalline copper sulfate pentahydrate.

PubMed

Ruggiero, Michael T; Erba, Alessandro; Orlando, Roberto; Korter, Timothy M

2015-12-14

Metal-aqua ion ([M(H2O)n](X+)) formation is a fundamental step in mechanisms that are central to enzymatic and industrial catalysis. Past investigations of such ions have yielded a wealth of information regarding their properties, however questions still exist involving the exact structures of these complexes. A prominent example of this is hexaaqua copper(II) ([Cu(H2O)6](2+)), with the solution versus gas-phase configurations under debate. The differences are often attributed to the intermolecular interactions between the bulk solvent and the aquated complex, resulting in structures stabilized by extended hydrogen-bonding networks. Yet solution phase systems are difficult to study due to the lack of atomic-level positional details. Crystalline solids are ideal models for comparative study, as they contain fixed structures that can be fully characterized using diffraction techniques. Here, crystalline copper sulfate pentahydrate (CuSO4·5H2O), which contains two unique copper-water geometries, was studied in order to elucidate the origin of these contrasting hydrated metal envrionments. A combination of solid-state density functional theory and low-temperature X-ray diffraction was used to probe the electronic origins of this phenomenon. This was accomplished through implementation of crystal orbital overlap population and crystal orbital Hamiltonian population analyses into a developmental version of the CRYSTAL14 software. These new computational methods help highlight the delicate interplay between electronic structure and metal-water geometries.

Growth of InAs/InP core-shell nanowires with various pure crystal structures.

PubMed

Gorji Ghalamestani, Sepideh; Heurlin, Magnus; Wernersson, Lars-Erik; Lehmann, Sebastian; Dick, Kimberly A

2012-07-20

We have studied the epitaxial growth of an InP shell on various pure InAs core nanowire crystal structures by metal-organic vapor phase epitaxy. The InP shell is grown on wurtzite (WZ), zinc-blende (ZB), and {111}- and {110}-type faceted ZB twin-plane superlattice (TSL) structures by tuning the InP shell growth parameters and controlling the shell thickness. The growth results, particularly on the WZ nanowires, show that homogeneous InP shell growth is promoted at relatively high temperatures (∼500 °C), but that the InAs nanowires decompose under the applied conditions. In order to protect the InAs core nanowires from decomposition, a short protective InP segment is first grown axially at lower temperatures (420-460 °C), before commencing the radial growth at a higher temperature. Further studies revealed that the InP radial growth rate is significantly higher on the ZB and TSL nanowires compared to WZ counterparts, and shows a strong anisotropy in polar directions. As a result, thin shells were obtained during low temperature InP growth on ZB structures, while a higher temperature was used to obtain uniform thick shells. In addition, a schematic growth model is suggested to explain the basic processes occurring during the shell growth on the TSL crystal structures.

Hot Views on Cold Crystals: The Application of Thermal Imaging in Cryocrystallography

NASA Technical Reports Server (NTRS)

Snell, Eddie

2003-01-01

We have used thermal imaging techniques to visualize the cryocooling processes of macromolecular crystals. Cryocooling is a common technique used for structural data collection to reduce radiation damage in intense X-ray beams and decrease the thermal motion of the atoms. From the thermal images it was clear that during cryocooling a cold wave progresses through a crystal starting at the face closest to the origin of the cold stream and ending at the point furthest away. As an extension to this work, we used thermal imaging to study small crystals, held in a cryo-loop, in the presence of vitrified mother liquor. The different infrared transmission and reflectance properties of the crystal in comparison to the mother liquor surrounding it are thought to be the parameter that produces the contrast that makes the crystal visible. An application of this technology may be the determination of the exact location of small crystals in a cryo-loop for automated structural genomics studies. Data from initial tests in support of application development was recorded for lysozyme crystals and for bFGF/dna complex crystals, which were cryocooled and imaged in large loops, both with visible light and with infrared radiation. The crystals were clearly distinguished from the vitrified solution in the infrared spectrum, while in the case of the bFGF/dna complex the illumination had to be carefully manipulated to make the crystal visible in the visible spectrum. These results suggest that the thermal imaging may be more sensitive than visual imaging for automated location of small crystals. However, further work on small crystals robotically mounted at SSRL did not clearly visualize those crystals. The depth of field of the camera proved to be limiting and a different cooling geometry was used, compared to the previous, successful experiments. Analysis to exploit multiple images to improve depth of field and experimental work to understand cooling geometry effects is ongoing. These results will be presented along with advantages and disadvantages of the technique and a discussion of how it might be applied.

Synthesis, crystal structure, spectroscopic characterization, docking simulation and density functional studies of 1-(3,4-dimethoxyphenyl) -3-(4-flurophenyl)-propan-1-one

NASA Astrophysics Data System (ADS)

Khamees, Hussien Ahmed; Jyothi, Mahima; Khanum, Shaukath Ara; Madegowda, Mahendra

2018-06-01

The compound 1-(3,4-dimethoxyphenyl)-3-(4-flurophenyl)-propan-1-one (DFPO) was synthesized by Claisen-Schmidt condensation reaction and the single crystals were obtained by slow evaporation method. Three-dimensional structure was confirmed by single crystal X-ray diffraction method and exhibiting the triclinic crystal system with space group P-1. The crystal structure is stabilized by Csbnd H⋯O intermolecular and weak interactions. Computed molecular geometry has been obtained by density functional theory (DFT) and compared with experimental results. The spectra of both FT-IR in the range (4000-400 cm-1) and FT- Raman (3500-50 cm-1) of DFPO were recorded experimentally and computed by (DFT) using B3LYP/6-311G (d,p) as basis sets. Intramolecular charge transfer has been scanned using natural bond orbital (NBO) analysis and revealed the various contribution of bonding and lone pair to the stabilization of molecule. Nonlinear optical activity (NLO) of the title compound has been determined by second harmonic generation (SHG) and computed using DFT method. Hyperpolarizability, HOMO-LUMO energy gap, hardness, softness electronegativity and others Global reactivity descriptors of DFPO has been calculated and revealed complete picture of chemical reactivity of DFPO. Hirshfeld surface analyses were applied to investigate the intermolecular interactions and revealed that more than two-thirds of the inter contacts are associated with O⋯H, C⋯H and H⋯H interactions. Docking studies of DFPO showed inhibition of Vascular endothelial growth Factor human receptor (VEGFR-2) signalling pathway, which indicates DFPO as anti-angiogenesis, that play pivotal role in cancer, so we suggest it for clinical studies to evaluate its potential to treat human cancers.

DBR, Sub-wavelength grating, and Photonic crystal slab Fabry-Perot cavity design using phase analysis by FDTD.

PubMed

Kim, Jae Hwan Eric; Chrostowski, Lukas; Bisaillon, Eric; Plant, David V

2007-08-06

We demonstrate a Finite-Difference Time-Domain (FDTD) phase methodology to estimate resonant wavelengths in Fabry-Perot (FP) cavity structures. We validate the phase method in a conventional Vertical-Cavity Surface-Emitting Laser (VCSEL) structure using a transfer-matrix method, and compare results with a FDTD reflectance method. We extend this approach to a Sub-Wavelength Grating (SWG) and a Photonic Crystal (Phc) slab, either of which may replace one of the Distributed Bragg Reflectors (DBRs) in the VCSEL, and predict resonant conditions with varying lithographic parameters. Finally, we compare the resonant tunabilities of three different VCSEL structures, taking quality factors into account.

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.

Release of the cyano moiety in the crystal structure of N-cyanomethyl-N-(2-methoxyethyl)-daunomycin complexed with d(CGATCG).

PubMed

Saminadin, P; Dautant, A; Mondon, M; Langlois D'estaintot, B; Courseille, C; Précigoux, G

2000-01-01

Doxorubicin is among the most widely used anthracycline in cancer chemotherapy. In an attempt to avoid the cardiotoxicity and drug resistance of doxorubicin therapy, several analogues were synthesized. The cyanomorpholinyl derivative is the most cytotoxic. They differ greatly from their parent compound in their biological and pharmacological properties, inducing cross-links in drug DNA complexes. The present study concerns N-cyanomethyl-N-(2-methoxyethyl)-daunomycin (CMDa), a synthetic analogue of cyanomorpholino-daunomycin. Compared to doxorubicin, CMDa displays a cytotoxic activity on L1210 leukemia cells at higher concentration but is effective on doxorubicin resistant cells. The results of fluorescence quenching experiments as well as the melting temperature (DeltaTm = 7.5 degrees C) studies are consistent with a drug molecule which intercalates between the DNA base pairs and stabilizes the DNA double helix. The crystal structure of CMDa complexed to the hexanucleotide d(CGATCG) has been determined at 1.5 A resolution. The complex crystallizes in the space group P41212 and is similar to other anthracycline-hexanucleotide complexes. In the crystal state, the observed densities indicate the formation of N-hydroxymethyl-N-(2-methoxyethyl)-daunomycin (HMDa) with the release of the cyano moiety without DNA alkylation. The formation of this degradation compound is discussed in relation with other drug modifications when binding to DNA. Comparison with two other drug-DNA crystal structures suggests a correlation between a slight change in DNA conformation and the nature of the amino sugar substituents at the N3' position located in the minor groove.

Hydrogen bonding interactions and supramolecular assemblies in 2-amino guanidinium 4-methyl benzene sulphonate crystal structure: Hirshfeld surfaces and computational calculations

NASA Astrophysics Data System (ADS)

Muthuraja, P.; Joselin Beaula, T.; Balachandar, S.; Bena Jothy, V.; Dhandapani, M.

2017-10-01

2-aminoguanidinium 4-methyl benzene sulphonate (AGMS), an organic compound with big assembly of hydrogen bonding interactions was crystallized at room temperature. The structure of the compound was confirmed by FT-IR, NMR and single crystal X-ray diffraction analysis. Numerous hydrogen bonded interactions were found to form supramolecular assemblies in the molecular structure. Fingerprint plots of Hirshfeld surface analysis spells out the interactions in various directions. The molecular structure of AGMS was optimised by HF, MP2 and DFT (B3LYP and CAM-B3LYP) methods at 6-311G (d,p) basis set and the geometrical parameters were compared. Electrostatic potential calculations of the reactants and product confirm the transfer of proton. Optical properties of AGMS were ascertained by UV-Vis absorbance and reflectance spectra. The band gap of AGMS is found to be 2.689 eV. Due to numerous hydrogen bonds, the crystal is thermally stable up to 200 °C. Hyperconjugative interactions which are responsible for the second hyperpolarizabilities were accounted by NBO analysis. Static and frequency dependent optical properties were calculated at HF and DFT methods. The hyperpolarizabilities of AGMS increase rapidly at frequencies 0.0428 and 0.08 a.u. compared to static one. The compound exhibits violet and blue emission.

Probing the pH sensitivity of R-phycoerythrin: investigations of active conformational and functional variation.

PubMed

Liu, Lu-Ning; Su, Hai-Nan; Yan, Shi-Gan; Shao, Si-Mi; Xie, Bin-Bin; Chen, Xiu-Lan; Zhang, Xi-Ying; Zhou, Bai-Cheng; Zhang, Yu-Zhong

2009-07-01

Crystal structures of phycobiliproteins have provided valuable information regarding the conformations and amino acid organizations of peptides and chromophores, and enable us to investigate their structural and functional relationships with respect to environmental variations. In this work, we explored the pH-induced conformational and functional dynamics of R-phycoerythrin (R-PE) by means of absorption, fluorescence and circular dichroism spectra, together with analysis of its crystal structure. R-PE presents stronger functional stability in the pH range of 3.5-10 compared to the structural stability. Beyond this range, pronounced functional and structural changes occur. Crystal structure analysis shows that the tertiary structure of R-PE is fixed by several key anchoring points of the protein. With this specific association, the fundamental structure of R-PE is stabilized to present physiological spectroscopic properties, while local variations in protein peptides are also allowed in response to environmental disturbances. The functional stability and relative structural sensitivity of R-PE allow environmental adaptation.

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.

Comparative analysis of spatial organization of laccases from Cerrena maxima and Coriolus zonatus

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

Zhukova, Yu. N.; Zhukhlistova, N. E.; Lyashenko, A. V.

2007-09-15

Laccase (oxygen oxidoreductase, EC 1.10.3.2) belongs to the multicopper oxidase family. The main function of this enzyme is to perform electron transfer from the oxidized substrate through the mononuclear copper-containing site T1 to the oxygen molecule bound to the site T3 in the trinuclear T2/T3 cluster. The structures of two new fungal laccases from C. maxima and C. zonatus were solved on the basis of synchrotron X-ray diffraction data. Both laccases show high structural homology with laccases from other sources. The role of the carbohydrate component of laccases in structure stabilization and formation of ordered protein crystals was demonstrated. Inmore » the structures of C. maxima and C. zonatus laccases, two water channels of functional importance were found and characterized. The structural results reported in the present study characterize one of the functional states of the enzyme fixed in the crystal structure.« less

A comparative study of the spectroscopic properties of Mn4+ in the garnet Y2Mg3Ge3O12 and the commercial Mg28Ge7.55O32F15.04 phosphor

NASA Astrophysics Data System (ADS)

Srivastava, A. M.

2018-05-01

The spectroscopic properties of Mn4+ (3 d3) ions in the garnet Y2Mg3Ge3O12 and in the commercial Mg28Ge7.55O32F15.04 (MFG) phosphors are compared. We find that despite the differences in host crystal composition and crystal structures, the 4A2g→ 4T1g and 2Eg→4A2g optical transitions of the Mn4+ ion occur at similar energies. We provide some insights into the nature of chemical bonding that is responsible for the observed similarity in the spectroscopic data. Additionally, discussion is given to the site preference of the Mn4+ ion in the MFG host crystal.

Growth, structural, spectroscopic, thermal, dielectric and optical study of cobalt sulphide-doped ADP crystals

NASA Astrophysics Data System (ADS)

Kochuparampil, A. P.; Joshi, J. H.; Joshi, M. J.

2017-09-01

As ammonium dihydrogen phosphate (ADP) is a popular nonlinear optical crystal, to engineer its linear and nonlinear optical properties, the chalcogenide compound cobalt sulphide (CoS) was doped and the crystals were grown by the slow solvent evaporation method. To increase the solubility of CoS in water, its nanoparticles were synthesized by wet chemical technique using ethylene diamine as the capping agent followed by microwave irradiation. The nanoparticle sample exhibited finite solubility in water and was used to dope in ADP crystals. The powder XRD patterns showed the single phase nature of the doped crystals. The FTIR spectra confirmed the presence of various functional groups and EDAX gave the estimation of Co and S elements. The EPR spectroscopy also confirmed the presence of cobalt in the doped samples. TGA indicated slightly less thermal stability of the doped crystals compared to the pure ADP. The dielectric study was carried out at room temperature in the frequency range from 100Hz to 1MHz. Also, various linear optical parameters were evaluated for pure and doped crystals using UV-Vis spectroscopy. The second harmonic generation (SHG) efficiency of Nd:YAG laser was evaluated by the Kurtz and Parry method for the doped samples, it was found to be slightly lesser than that of the pure ADP crystals.

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.

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.

Mechanochemical synthesis of N-salicylidene­aniline: thermosalient effect of polymorphic crystals

PubMed Central

Mittapalli, Sudhir; Sravanakumar Perumalla, D.

2017-01-01

Polymorphs of the dichloro derivative of N-salicylideneaniline exhibit mechanical responses such as jumping (Forms I and III) and exploding (Form II) in its three polymorphs. The molecules are connected via the amide N—H⋯O dimer synthon and C—Cl⋯O halogen bond in the three crystal structures. A fourth high-temperature Form IV was confirmed by variable-temperature single-crystal X-ray diffraction at 180°C. The behaviour of jumping exhibited by the polymorphic crystals of Forms I and III is due to the layered sheet morphology and the transmission of thermal stress in a single direction, compared with the corrugated sheet structure of Form II such that heat dissipation is more isotropic causing blasting. The role of weak C—Cl⋯O interactions in the thermal response of molecular crystals is discussed. PMID:28512571

Synthesis, characterization, crystal structure and quantum chemical investigations of three novel coumarin-benzenesulfonohydrazide derivatives

NASA Astrophysics Data System (ADS)

Chethan Prathap, K. N.; Lokanath, N. K.

2018-04-01

Coumarin derivatives are an important class of heterocyclic compounds due to their physical and biological properties. Coumarin derivatives have been identified with many significant electro-optical properties and biological activities. Three novel coumarin derivatives containing benzene sulfonohydrazide group were synthesized by condensation reaction. The synthesized compounds were characterized by various spectroscopic techniques (Mass, 1H/13C NMR and FTIR). Thermal and optical properties were investigated by thermogravimetric analysis (TGA), differential scanning calorimetry (DSC) and UV-Vis spectroscopic studies. Finally their structures were confirmed by single crystal X-ray diffraction (XRD) studies. The three compounds exhibit diverse intermolecular interactions, as observed by the crystal packing and Hirshfeld surface analysis. Further, their structures were optimized by density functional theory (DFT) calculations using B3LYP hybrid functionals with 6-311G+(d,p) level basis set. The Mulliken charge, molecular electrostatic potential (MEP), frontier molecular orbitals (HOMO-LUMO) were investigated. The experimentally determined parameters were compared with those calculated theoretically and they complement each other with a very good correlation. The transitions among the molecular orbitals were investigated using time-dependent density functional theory (TD-DFT) and the electronic absorption spectra obtained showed very good agreement with the experimentally measured UV-Vis spectra. Furthermore, non-linear optical (NLO) properties were investigated by calculating polarizabilities and hyperpolarizabilities. All three compounds exhibit significantly high hyperpolarizabilities compared to the reference material urea, which makes them potential candidates for NLO applications.

Vibrational, DFT, and thermal analysis of 2,4,6-triamino-1,3,5-triazin-1-ium 3-(prop-2-enoyloxy) propanoate acrylic acid monosolvate monohydrate

NASA Astrophysics Data System (ADS)

Sangeetha, V.; Govindarajan, M.; Kanagathara, N.; Marchewka, M. K.; Drozd, M.; Anbalagan, G.

2013-12-01

New organic crystals of 2,4,6-triamino-1,3,5-triazin-1-ium 3-(prop-2-enoyloxy) propanoate acrylic acid monosolvate monohydrate (MAC) have been obtained from aqueous solution by the slow solvent evaporation method at room temperature. Single crystal X-ray diffraction analysis reveals that the compound crystallises in the triclinic system with centrosymmetric space group P-1. FT-IR and FT-Raman spectra of MAC have been recorded and analyzed. The molecular geometry and vibrational frequencies and intensity of the vibrational bands are interpreted with the aid of structure optimization based on density functional theory (DFT) B3LYP method with 6-31G(d,p) basis set. The results of the optimized molecular structure are presented and compared with the experimental X-ray diffraction data. The theoretical results show that the optimized geometry can well reproduce the crystal structure, and the calculated vibrational frequency values show good agreement with experimental values. A study of the electronic properties, such as HOMO and LUMO energies and Molecular electrostatic potential (MEP) were performed. Mulliken charges and NBO charges of the title molecule were also calculated and interpreted. Thermogravimetric analysis has been done to study the thermal behaviour of MAC. The 13C and 1H nuclear magnetic resonance (NMR) chemical shifts of the molecule are calculated by the gauge independent atomic orbital (GIAO) method and compared with experimental results.

Absolute configuration and crystal packing for three chiral drugs prone to spontaneous resolution: Guaifenesin, methocarbamol and mephenesin

NASA Astrophysics Data System (ADS)

Bredikhin, Alexander A.; Gubaidullin, Aidar T.; Bredikhina, Zemfira A.; Krivolapov, Dmitry B.; Pashagin, Alexander V.; Litvinov, Igor A.

2009-02-01

Popular chiral drugs, guaifenesin, methocarbamol, and mephenesin were investigated by single-crystal X-ray analysis both for enantiopure and racemic samples. The absolute configurations for all substances were established through Flack parameter method. The conglomerate-forming nature for the compounds was confirmed by equivalence of crystal characteristics of enantiopure and racemic samples. The molecular structures and crystal packing details were evaluated and compared with one another for all three investigated substances.

Reduction of oxygen concentration by heater design during Czochralski Si growth

NASA Astrophysics Data System (ADS)

Zhou, Bing; Chen, Wenliang; Li, Zhihui; Yue, Ruicun; Liu, Guowei; Huang, Xinming

2018-02-01

Oxygen is one of the highest-concentration impurities in single crystals grown by the Czochralski (CZ) process, and seriously impairs the quality of the Si wafer. In this study, computer simulations were applied to design a new CZ system. A more appropriate thermal field was acquired by optimization of the heater structure. The simulation results showed that, compared with the conventional system, the oxygen concentration in the newly designed CZ system was reduced significantly throughout the entire CZ process because of the lower crucible wall temperature and optimized convection. To verify the simulation results, experiments were conducted on an industrial single-crystal furnace. The experimental results showed that the oxygen concentration was reduced significantly, especially at the top of the CZ-Si ingot. Specifically, the oxygen concentration was 6.19 × 1017 atom/cm3 at the top of the CZ-Si ingot with the newly designed CZ system, compared with 9.22 × 1017 atom/cm3 with the conventional system. Corresponding light-induced degradation of solar cells based on the top of crystals from the newly designed CZ system was 1.62%, a reduction of 0.64% compared with crystals from the conventional system (2.26%).

Anisotropy of Single-Crystal Silicon in Nanometric Cutting.

PubMed

Wang, Zhiguo; Chen, Jiaxuan; Wang, Guilian; Bai, Qingshun; Liang, Yingchun

2017-12-01

The anisotropy exhibited by single-crystal silicon in nanometric cutting is very significant. In order to profoundly understand the effect of crystal anisotropy on cutting behaviors, a large-scale molecular dynamics model was conducted to simulate the nanometric cutting of single-crystal silicon in the (100)[0-10], (100)[0-1-1], (110)[-110], (110)[00-1], (111)[-101], and (111)[-12-1] crystal directions in this study. The simulation results show the variations of different degrees in chip, subsurface damage, cutting force, and friction coefficient with changes in crystal plane and crystal direction. Shear deformation is the formation mechanism of subsurface damage, and the direction and complexity it forms are the primary causes that result in the anisotropy of subsurface damage. Structurally, chips could be classified into completely amorphous ones and incompletely amorphous ones containing a few crystallites. The formation mechanism of the former is high-pressure phase transformation, while the latter is obtained under the combined action of high-pressure phase transformation and cleavage. Based on an analysis of the material removal mode, it can be found that compared with the other crystal direction on the same crystal plane, the (100)[0-10], (110)[-110], and (111)[-101] directions are more suitable for ductile cutting.

Nanoparticles Incorporated inside Single-Crystals: Enhanced Fluorescent Properties

DOE PAGES

Liu, Yujing; Zang, Huidong; Wang, Ling; ...

2016-09-25

Incorporation of guest materials inside single-crystalline hosts leads to single-crystal composites that have become more and more frequently seen in both biogenic and synthetic crystals. The unique composite structure together with long-range ordering promises special properties that are, however, less often demonstrated. In this study, we examine the fluorescent properties of quantum dots (QDs) and polymer dots (Pdots) encapsulated inside the hosts of calcite single-crystals. Two CdTe QDs and two Pdots are incorporated into growing calcite crystals, as the QDs and Pdots are dispersed in the crystallization media of agarose gels. As a result, enhanced fluorescent properties are obtained frommore » the QDs and Pdots inside calcite single-crystals with greatly improved photostability and significantly prolonged fluorescence lifetime, compared to those in solutions and gels. Particularly, the fluorescence lifetime increases by 0.5-1.6 times after the QDs or Pdots are incorporated. The enhanced fluorescent properties indicate the advantages of encapsulation by single-crystal hosts that provide dense shells to isolate the fluorescent nanoparticles from atmosphere. As such, this work has implications for advancing the research of single-crystal composites toward their functional design.« less

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

NASA Astrophysics Data System (ADS)

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

2018-01-01

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

Approaches to automated protein crystal harvesting

PubMed Central

Deller, Marc C.; Rupp, Bernhard

2014-01-01

The harvesting of protein crystals is almost always a necessary step in the determination of a protein structure using X-ray crystallographic techniques. However, protein crystals are usually fragile and susceptible to damage during the harvesting process. For this reason, protein crystal harvesting is the single step that remains entirely dependent on skilled human intervention. Automation has been implemented in the majority of other stages of the structure-determination pipeline, including cloning, expression, purification, crystallization and data collection. The gap in automation between crystallization and data collection results in a bottleneck in throughput and presents unfortunate opportunities for crystal damage. Several automated protein crystal harvesting systems have been developed, including systems utilizing microcapillaries, microtools, microgrippers, acoustic droplet ejection and optical traps. However, these systems have yet to be commonly deployed in the majority of crystallography laboratories owing to a variety of technical and cost-related issues. Automation of protein crystal harvesting remains essential for harnessing the full benefits of fourth-generation synchrotrons, free-electron lasers and microfocus beamlines. Furthermore, automation of protein crystal harvesting offers several benefits when compared with traditional manual approaches, including the ability to harvest microcrystals, improved flash-cooling procedures and increased throughput. PMID:24637746

One-dimensional, two-dimensional, and three-dimensional photonic crystals fabricated with interferometric techniques on ultrafine-grain silver halide emulsions

NASA Astrophysics Data System (ADS)

Ulibarrena, Manuel; Carretero, Luis; Acebal, Pablo; Madrigal, Roque; Blaya, Salvador; Fimia, Antonio

2004-09-01

Holographic techniques have been used for manufacturing multiple band one-dimensional, two-dimensional, and three-dimensional photonic crystals with different configurations, by multiplexing reflection and transmission setups on a single layer of holographic material. The recording material used for storage is an ultra fine grain silver halide emulsion, with an average grain size around 20 nm. The results are a set of photonic crystals with the one-dimensional, two-dimensional, and three-dimensional index modulation structure consisting of silver halide particles embedded in the gelatin layer of the emulsion. The characterisation of the fabricated photonic crystals by measuring their transmission band structures has been done and compared with theoretical calculations.

Terahertz Spectroscopy and Solid-State Density Functional Theory Calculations of Cyanobenzaldehyde Isomers.

PubMed

Dash, Jyotirmayee; Ray, Shaumik; Nallappan, Kathirvel; Kaware, Vaibhav; Basutkar, Nitin; Gonnade, Rajesh G; Ambade, Ashootosh V; Joshi, Kavita; Pesala, Bala

2015-07-23

Spectral signatures in the terahertz (THz) frequency region are mainly due to bulk vibrations of the molecules. These resonances are highly sensitive to the relative position of atoms in a molecule as well as the crystal packing arrangement. To understand the variation of THz resonances, THz spectra (2-10 THz) of three structural isomers: 2-, 3-, and 4-cyanobenzaldehyde have been studied. THz spectra obtained from Fourier transform infrared (FTIR) spectrometry of these isomers show that the resonances are distinctly different especially below 5 THz. For understanding the intermolecular interactions due to hydrogen bonds, four molecule cluster simulations of each of the isomers have been carried out using the B3LYP density functional with the 6-31G(d,p) basis set in Gaussian09 software and the compliance constants are obtained. However, to understand the exact reason behind the observed resonances, simulation of each isomer considering the full crystal structure is essential. The crystal structure of each isomer has been determined using X-ray diffraction (XRD) analysis for carrying out crystal structure simulations. Density functional theory (DFT) simulations using CRYSTAL14 software, utilizing the hybrid density functional B3LYP, have been carried out to understand the vibrational modes. The bond lengths and bond angles from the optimized structures are compared with the XRD results in terms of root-mean-square-deviation (RMSD) values. Very low RMSD values confirm the overall accuracy of the results. The simulations are able to predict most of the spectral features exhibited by the isomers. The results show that low frequency modes (<3 THz) are mediated through hydrogen bonds and are dominated by intermolecular vibrations.

Infrared and Raman spectroscopy and DFT calculations of DL amino acids: Valine and lysine hydrochloride

NASA Astrophysics Data System (ADS)

Paiva, F. M.; Batista, J. C.; Rêgo, F. S. C.; Lima, J. A.; Freire, P. T. C.; Melo, F. E. A.; Mendes Filho, J.; de Menezes, A. S.; Nogueira, C. E. S.

2017-01-01

Single crystals of DL-valine and DL-lysine hydrochloride were grown by slow evaporation method and the crystallographic structure were confirmed by X-ray diffraction experiment and Rietveld method. These two crystals have been studied by Raman spectroscopy in the 25-3600 cm-1 spectral range and by infrared spectroscopy through the interval 375-4000 cm-1 at room temperature. Experimental and theoretical vibrational spectra were compared and a complete analysis of the modes was done in terms of the Potential Energy Distribution (PED).

Structure of the mixed-metal carbonate KAgCO₃ revisited: order-disorder (OD) polytypism and allotwinning.

PubMed

Hans, Philipp; Stöger, Berthold; Weil, Matthias; Zobetz, Erich

2015-04-01

Crystals of KAgCO3 belong to an order-disorder (OD) family of structures composed of layers of two kinds. There are two polytypes with a maximum degree of order [MDO1: Pccb; MDO2: Ibca, doubled a-axis compared with MDO1], which are both realised to a different extent in two crystals under investigation [volume fraction MDO1:MDO2 in crystal (I): 0.0216:0.9784 (3) and in crystal (II): 0.9657:0.0343 (3)]. Sharp diffraction spots and the absence of diffuse scattering indicate highly ordered macroscopic domains. The structure of KAgCO3 was refined concurrently against all reflections using an allotwin model (addition of the intensities of both domains). It is shown that a disorder model refined against reflections of only one domain can lead to a significant overestimation of the volume fraction of this domain.

Order-disorder phase transitions and their influence on the structure and vibrational properties of new hybrid material: 2-Amino-4-methyl-3-nitropyridinium trifluoroacetate

NASA Astrophysics Data System (ADS)

Lorenc, J.; Bryndal, I.; Syska, W.; Wandas, M.; Marchewka, M.; Pietraszko, A.; Lis, T.; Mączka, M.; Hermanowicz, K.; Hanuza, J.

2010-08-01

New organic-organic salt, 2-amino-4-methyl-3-nitropyridinium trifluoroacetate, has been synthesised and characterised by FT-IR, FT-Raman, DSC and single crystal X-ray crystallography. The 2-amino-4-methyl-3-nitropyridinium trifluoroacetate undergoes a reversible phase transition at ˜162 K. The X-ray structures, vibrational spectra and quantum chemical DFT calculations (B3LYP/6-31G(d,p) approach) have been analysed for high-temperature and low-temperature modifications of the compound, which both crystallize in orthorhombic space group Pbca with two non-equivalent cations and two anions in the asymmetric unit. Their crystal and molecular structures have been compared and the role of the intermolecular interactions in these crystals has been analysed. The mechanisms of the phase transition have been proposed.

Extended-Range Ultrarefractive 1D Photonic Crystal Prisms

NASA Technical Reports Server (NTRS)

Ting, David Z.

2007-01-01

A proposal has been made to exploit the special wavelength-dispersive characteristics of devices of the type described in One-Dimensional Photonic Crystal Superprisms (NPO-30232) NASA Tech Briefs, Vol. 29, No. 4 (April 2005), page 10a. A photonic crystal is an optical component that has a periodic structure comprising two dielectric materials with high dielectric contrast (e.g., a semiconductor and air), with geometrical feature sizes comparable to or smaller than light wavelengths of interest. Experimental superprisms have been realized as photonic crystals having three-dimensional (3D) structures comprising regions of amorphous Si alternating with regions of SiO2, fabricated in a complex process that included sputtering. A photonic crystal of the type to be exploited according to the present proposal is said to be one-dimensional (1D) because its contrasting dielectric materials would be stacked in parallel planar layers; in other words, there would be spatial periodicity in one dimension only. The processes of designing and fabricating 1D photonic crystal superprisms would be simpler and, hence, would cost less than do those for 3D photonic crystal superprisms. As in 3D structures, 1D photonic crystals may be used in applications such as wavelength-division multiplexing. In the extended-range configuration, it is also suitable for spectrometry applications. As an engineered structure or artificially engineered material, a photonic crystal can exhibit optical properties not commonly found in natural substances. Prior research had revealed several classes of photonic crystal structures for which the propagation of electromagnetic radiation is forbidden in certain frequency ranges, denoted photonic bandgaps. It had also been found that in narrow frequency bands just outside the photonic bandgaps, the angular wavelength dispersion of electromagnetic waves propagating in photonic crystal superprisms is much stronger than is the angular wavelength dispersion obtained by use of conventional prisms and diffraction gratings and is highly nonlinear.

Comparing pharmacophore models derived from crystallography and NMR ensembles

NASA Astrophysics Data System (ADS)

Ghanakota, Phani; Carlson, Heather A.

2017-11-01

NMR and X-ray crystallography are the two most widely used methods for determining protein structures. Our previous study examining NMR versus X-Ray sources of protein conformations showed improved performance with NMR structures when used in our Multiple Protein Structures (MPS) method for receptor-based pharmacophores (Damm, Carlson, J Am Chem Soc 129:8225-8235, 2007). However, that work was based on a single test case, HIV-1 protease, because of the rich data available for that system. New data for more systems are available now, which calls for further examination of the effect of different sources of protein conformations. The MPS technique was applied to Growth factor receptor bound protein 2 (Grb2), Src SH2 homology domain (Src-SH2), FK506-binding protein 1A (FKBP12), and Peroxisome proliferator-activated receptor-γ (PPAR-γ). Pharmacophore models from both crystal and NMR ensembles were able to discriminate between high-affinity, low-affinity, and decoy molecules. As we found in our original study, NMR models showed optimal performance when all elements were used. The crystal models had more pharmacophore elements compared to their NMR counterparts. The crystal-based models exhibited optimum performance only when pharmacophore elements were dropped. This supports our assertion that the higher flexibility in NMR ensembles helps focus the models on the most essential interactions with the protein. Our studies suggest that the "extra" pharmacophore elements seen at the periphery in X-ray models arise as a result of decreased protein flexibility and make very little contribution to model performance.

Local order and crystallization of dense polydisperse hard spheres

NASA Astrophysics Data System (ADS)

Coslovich, Daniele; Ozawa, Misaki; Berthier, Ludovic

2018-04-01

Computer simulations give precious insight into the microscopic behavior of supercooled liquids and glasses, but their typical time scales are orders of magnitude shorter than the experimentally relevant ones. We recently closed this gap for a class of models of size polydisperse fluids, which we successfully equilibrate beyond laboratory time scales by means of the swap Monte Carlo algorithm. In this contribution, we study the interplay between compositional and geometric local orders in a model of polydisperse hard spheres equilibrated with this algorithm. Local compositional order has a weak state dependence, while local geometric order associated to icosahedral arrangements grows more markedly but only at very high density. We quantify the correlation lengths and the degree of sphericity associated to icosahedral structures and compare these results to those for the Wahnström Lennard-Jones mixture. Finally, we analyze the structure of very dense samples that partially crystallized following a pattern incompatible with conventional fractionation scenarios. The crystal structure has the symmetry of aluminum diboride and involves a subset of small and large particles with size ratio approximately equal to 0.5.

Crystal chemistry of KCuMn3(VO4)3 in the context of detailed systematics of the alluaudite family

NASA Astrophysics Data System (ADS)

Yakubovich, O. V.; Kiryukhina, G. V.; Dimitrova, O. V.

2016-07-01

The crystal structure of new manganese potassium copper vanadate KCuMn3(VO4)3, which was prepared by the hydrothermal synthesis in the K2CO3-CuO-MnCl2-V2O5-H2O system, was studied by X-ray diffraction ( R = 0.0355): a = 12.396(1) Å, b = 12.944(1) Å, c = 6.9786(5) Å, β = 112.723(1)°, sp. gr. C2/ c, Z = 4, ρcalc = 3.938 g/cm3. A comparative analysis of the crystal-chemical features of the new representative of the alluaudite family and related structures of minerals and synthetic phosphates, arsenates, and vanadates of the general formula A(1) A(1)' A(1)″ A(2) A(2)' M(1) M(2)2( TO4)3 (where A are sites in the channels of the framework composed of MO6 octahedra and TO4 tetrahedra) was performed. A classification of these structures into subgroups according to the occupancy of A sites is suggested.

Statistical physics of modulated phases in nematic liquid crystals

NASA Astrophysics Data System (ADS)

Shamid, Shaikh M.

Nematic liquid crystals are the state of the matter in which there is no positional order like crystals but it has orientational order of the constituent molecules. In the conventional nematics, the long axes of the rod-like molecules tend to align up or down uniformly along a director n. If the constituent molecules are chiral, they tend to form a modulated structure in one of the space dimensions. They are called the chiral nematics. If the chirality is strong enough we get the modulated structures in all three dimensions called the chiral blue phase. On the other hand, if the molecules are achiral, but an additional polar dipole is attached to the molecules, they also tend to form a modulated structure. In these types of materials we observe an important physical effect called flexoelectric effect, in which the polar order is linearly coupled to the director gradients. This dissertation work presents analytical and simulation studies of that modulated structures using the flexoelectric mechanism. Classic work by R. B. Meyer and further studies by I. Dozov predicted two possible structures, known as twist-bend and splay-bend. One of these predictions, the twist-bend phase, has recently been identified in experiments on bent-shaped liquid crystals. In this recently discovered twist-bend nematic phase the modulation is along one of the space dimensions. If this flexoelectric coupling is strong enough, in addition to twist-bend and splay-bend, here we predict the formation of polar analog of chiral blue phases (in both 2D and 3D) made of achiral polar liquid crystal materials by using Elastic continuum theory-based numerical calculations and computer simulations. This dissertation work also presents the coarse-grained theory of twist-bend phase. This theory predicts normal modes of fluctuation in both sides of nematic to twist-bend transition, which then compared with light scattering experiments. Macroscopic elastic and electric properties of twist-bend nematics can be realized using this coarse-grained description.

Characterization and evaluation of miconazole salts and cocrystals for improved physicochemical properties.

PubMed

Tsutsumi, Shunichirou; Iida, Motoo; Tada, Norio; Kojima, Takashi; Ikeda, Yukihiro; Moriwaki, Toshiya; Higashi, Kenjirou; Moribe, Kunikazu; Yamamoto, Keiji

2011-12-15

Miconazole salts and cocrystals were studied to improve the physicochemical properties of miconazole. Maleate, hemifumarate, and hemisuccinate were prepared and characterized by powder X-ray diffractometry, differential scanning calorimetry, and single crystal X-ray diffractometry. The intrinsic dissolution rate and stability of each miconazole crystal form were compared to those of freebase and nitrate to evaluate the optimal crystal form. Crystal structure analysis indicated that maleate was a salt formed by proton transfer from the acid to the imidazole group of miconazole. Hemifumarate and hemisuccinate were determined to be cocrystals formed by hydrogen bonding between the acids and the base in their crystal lattices. Intrinsic dissolution tests showed that the formation of salts and cocrystals improved the dissolution rate of miconazole. Stability tests of preliminary formulations prepared with each crystal form indicated that maleate and hemifumarate were unstable at 80°C and generated a specific degraded product, i.e., a Michael adduct, between miconazole and the acids. Hemisuccinate had a superior intrinsic dissolution rate and stability, and is thus considered a promising crystal form of miconazole. Copyright © 2011 Elsevier B.V. All rights reserved.

B1 to B2 structural phase transition in LiF under pressure

NASA Astrophysics Data System (ADS)

Jain, Aayushi; Dixit, R. C.

2018-05-01

In the last few decades the alkali halides emerged as crystals with useful applications and their high-pressure behaviour is the most intensively studied subject in high-pressure physics/chemistry, material science, and geosciences. Most alkali halides follow the B1 (NaCl-type)→B2 (CsCl-type) phase-transition route under pressure. In the present paper, we have investigated the characteristics of structural phase transition that occurred in Lithium Florid compound under high pressure. The transition pressure of B1-B2 was calculated using an effective interionic interaction potential (EIOP). The changes of the characteristics of crystals like, Gibbs free energy, cohesive energy, volume collapse, and lattice constant are calculated for the B1 and B2 structures. These data were compared with the available experimental and theoretical data.

Crystal structure and phase stability in Fe{sub 1{minus}x}Co{sub x} from AB initio theory

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

Soederlind, P.; Abrikosov, I.A.; James, P.

1996-06-01

For alloys between Fe and Co, their magnetic properties determine their structure. From the occupation of d states, a phase diagram is expected which depend largely on the spin polarization. A method more elaborate than canonical band models is used to calculate the spin moment and crystal structure energies. This method was the multisublattice generalization of the coherent potential approximation in conjunction with the Linear-Muffin-Tin-Orbital method in the atomic sphere approximation. To treat itinerant magnetism, the Vosko-Wilk-Nusair parameterization was used for the local spin density approximation. The fcc, bcc, and hcp phases were studied as completely random alloys, while themore » {alpha}{prime} phase for off-stoichiometries were considered as partially ordered. Results are compared with experiment and canonical band model.« less

Numerical modeling study of silver nano-filling based on grapefruit-type photonic crystal fiber sensor

NASA Astrophysics Data System (ADS)

Zheng, Yibo; Zhang, Lei; Wang, Yuan

2017-10-01

In this letter, surface plasmon resonance sensors based on grapefruit-type photonic crystal fiber (PCF)with different silver nano-filling structure have been analyzed and compared though the finite element method (FEM). The regularity of the resonant wavelength changing with refractive index of the sample has been numerically simulated. The surface plasmon resonance (SPR) sensing properties have been numerically simulated in both areas of resonant wavelength and intensity detection. Numerical results show that excellent sensor resolution of 4.17×10-5RIU can be achieved as the radius of the filling silver nanowires is 150 nm by spectrum detection method. Comprehensive comparison indicates that the 150 nm silver wire filling structure is suitable for spectrum detection and 30 nm silver film coating structure is suitable for the amplitude detection.

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.

New supramolecular cocrystal of 2-amino-5-chloropyridine with 3-methylbenzoic acids: Syntheses, structural characterization, Hirshfeld surfaces and quantum chemical investigations

NASA Astrophysics Data System (ADS)

Thanigaimani, Kaliyaperumal; Khalib, Nuridayanti Che; Temel, Ersin; Arshad, Suhana; Razak, Ibrahim Abdul

2015-11-01

2-amino-5-chloropyridine: 3-methylbenzoic acid [(2A5CP) (3MBA)] (I) cocrystal was synthesized and its single crystal was grown by slow evaporation technique. The structure of the grown crystal was elucidated by using single crystal X-ray diffraction technique. The cocrystal belongs to the monoclinic crystallographic system with space group P21/c, Z = 4, and a = 13.3155 (5) Å, b = 5.5980 (2) Å, c = 18.3787 (7) Å, β = 110.045 (2)°. The crystal structure is stabilized by Npyridine-H•••Odbnd C, Cdbnd O-H•••Npyridine and C-H⋯O type hydrogen bonding interactions. The presence of unionized -COOH functional group in the cocrystal was identified both by spectral methods and X-ray structural analysis. The experimental studies obtained by using the methods of single crystal X-ray analysis, powder X-ray diffraction (PXRD) analysis, FTIR, 1H NMR and 13C NMR spectroscopies confirmed the predicted cocrystal. The supramolecular assembly of the cocrystal was analyzed and discussed. The molecular geometry, vibrational frequencies of the compound in the ground state were calculated by using the density functional theory (DFT) method with 6-311++G (d,p) basis set and were compared with the experimental data. Additionally, HOMO-LUMO energy gap, natural bond orbital (NBO) analysis and nonlinear optical (NLO) properties of the compound were performed at B3LYP/6-311++G (d,p) level. Hirshfeld surfaces were used to confirm the existence of inter-molecular interactions in the compound.

Purification, characterization and crystallization of the human 80S ribosome

PubMed Central

Khatter, Heena; Myasnikov, Alexander G.; Mastio, Leslie; Billas, Isabelle M. L.; Birck, Catherine; Stella, Stefano; Klaholz, Bruno P.

2014-01-01

Ribosomes are key macromolecular protein synthesis machineries in the cell. Human ribosomes have so far not been studied to atomic resolution because of their particularly complex structure as compared with other eukaryotic or prokaryotic ribosomes, and they are difficult to prepare to high homogeneity, which is a key requisite for high-resolution structural work. We established a purification protocol for human 80S ribosomes isolated from HeLa cells that allows obtaining large quantities of homogenous samples as characterized by biophysical methods using analytical ultracentrifugation and multiangle laser light scattering. Samples prepared under different conditions were characterized by direct single particle imaging using cryo electron microscopy, which helped optimizing the preparation protocol. From a small data set, a 3D reconstruction at subnanometric resolution was obtained showing all prominent structural features of the human ribosome, and revealing a salt concentration dependence of the presence of the exit site tRNA, which we show is critical for obtaining crystals. With these well-characterized samples first human 80S ribosome crystals were obtained from several crystallization conditions in capillaries and sitting drops, which diffract to 26 Å resolution at cryo temperatures and for which the crystallographic parameters were determined, paving the way for future high-resolution work. PMID:24452798

Omnidirectional photonic band gap enlarged by one-dimensional ternary unmagnetized plasma photonic crystals based on a new Fibonacci quasiperiodic structure

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

Zhang Haifeng; Nanjing Artillery Academy, Nanjing 211132; Liu Shaobin

2012-11-15

In this paper, an omnidirectional photonic band gap realized by one-dimensional ternary unmagnetized plasma photonic crystals based on a new Fibonacci quasiperiodic structure, which is composed of homogeneous unmagnetized plasma and two kinds of isotropic dielectric, is theoretically studied by the transfer matrix method. It has been shown that such an omnidirectional photonic band gap originates from Bragg gap in contrast to zero-n gap or single negative (negative permittivity or negative permeability) gap, and it is insensitive to the incidence angle and the polarization of electromagnetic wave. From the numerical results, the frequency range and central frequency of omnidirectional photonicmore » band gap can be tuned by the thickness and density of the plasma but cease to change with increasing Fibonacci order. The bandwidth of omnidirectional photonic band gap can be notably enlarged. Moreover, the plasma collision frequency has no effect on the bandwidth of omnidirectional photonic band gap. It is shown that such new structure Fibonacci quasiperiodic one-dimensional ternary plasma photonic crystals have a superior feature in the enhancement of frequency range of omnidirectional photonic band gap compared with the conventional ternary and conventional Fibonacci quasiperiodic ternary plasma photonic crystals.« less

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.

The electronic structure of RbTiOPO4 and the effects of the A-site cation substitution in KTiOPO4-family crystals

NASA Astrophysics Data System (ADS)

Atuchin, V. V.; Kesler, V. G.; Meng, Guangsi; Lin, Z. S.

2012-10-01

The electronic structure of RbTiOPO4 has been investigated with x-ray photoemission spectroscopy. Detailed photoemission spectra of the element core levels have been recorded under excitation by nonmonochromatic Al Kα radiation (1486.6 eV). The chemical bonding parameters are compared to those reported for complex titanates and phosphates. The band structures of KTiOPO4, RbTiOPO4, K0.535R0.465TiOPO4 and TlTiOPO4 have been calculated by ab initio methods and compared to available experimental results. It is found that the band structure of KTP-type phosphate crystals is weakly dependent on the nature of the A-site (A=K, Rb, Tl) element.

Calcium aluminate in alumina

NASA Astrophysics Data System (ADS)

Altay, Arzu

The properties of ceramic materials are determined not only by the composition and structure of the phases present, but also by the distribution of impurities, intergranular films and second phases. The phase distribution and microstructure both depend on the fabrication techniques, the raw materials used, the phase-equilibrium relations, grain growth and sintering processes. In this dissertation research, various approaches have been employed to understand fundamental phenomena such as grain growth, impurity segregation, second-phase formation and crystallization. The materials system chosen was alumina intentionally doped with calcium. Atomic-scale structural analyses of grain boundaries in alumina were carried on the processed samples. It was found that above certain calcium concentrations, CA6 precipitated as a second phase at all sintering temperatures. The results also showed that abnormal grain growth can occur after precipitation and it is not only related to the calcium level, but it is also temperature dependent. In order to understand the formation mechanism of CA6 precipitates in calcium doped alumina samples, several studies have been carried out using either bulk materials or thin films The crystallization of CA2 and CA6 powders has been studied. Chemical processing techniques were used to synthesize the powders. It was observed that CA2 powders crystallized directly, however CA6 powders crystallized through gamma-Al 2O3 solid solution. The results of energy-loss near-edge spectrometry confirmed that gamma-Al2O3 can dissolve calcium. Calcium aluminate/alumina reaction couples have also been investigated. All reaction couples were heat treated following deposition. It was found that gamma-Al2O3 was formed at the interface as a result of the interfacial reaction between the film and the substrate. gamma-Al 2O3 at the interface was stable at much higher temperatures compared to the bulk gamma-Al2O3 formed prior to the CA6 crystallization. In order to complement the studies carried out on the calcium aluminate phases, energy-loss near-edge structure (ELNES) fingerprints of CA2 and CA6 were obtained. It was shown that it is possible to distinguish these phases from each other by comparing the ELNES fingerprints. Theoretical calculations of ELNES were used to assign spectral features to certain symmetry environments that can later be used to understand the structures of unknown materials.

Hydrogen bonded charge transfer molecular salt (4-chloro anilinium-3-nitrophthalate) for photophysical and pharmacological applications

NASA Astrophysics Data System (ADS)

Singaravelan, K.; Chandramohan, A.; Saravanabhavan, M.; Muthu Vijayan Enoch, I. V.; Suganthi, V. S.

2017-09-01

Radical scavenging activity against DPPH radical and binding properties of a hydrogen bonded charge transfer molecular salt 4-chloro anilinium-3-nitrophthalate(CANP) with calf thymus DNA has been studied by electronic absorption and emission spectroscopy. The molecular structure and crystallinity of the CANP salt have been established by carried out powder and single crystal X-ray diffraction analysis which indicated that cation and anion are linked through strong N+sbnd H…O- type of hydrogen bond. FTIR spectroscopic study was carried out to know the various functional groups present in the crystal. 1H and 13C NMR spectra were recorded to further confirm the molecular structure of the salt crystal. The thermal stability of the title salt was established by TG/DTA analyses simultaneously on the powdered sample of the title crystal. Further, the CANP salt was examined against various bacteria and fungi strains which showed a remarkable antimicrobial activity compared to that of the standards Ciproflaxin and Clotrimazole. The results showed that the CANP salt could interact with CT-DNA through intercalation. Antioxidant studies of the substrates alone and synthesized CANP salt showed that the latter has been better radical scavenging activity than that of the former against DPPH radical. The third order nonlinear susceptibility of the CANP salt was established by the Z-scan study.

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.

Structure and vibrational spectra of melaminium bis(trifluoroacetate) trihydrate: FT-IR, FT-Raman and quantum chemical calculations

NASA Astrophysics Data System (ADS)

Sangeetha, V.; Govindarajan, M.; Kanagathara, N.; Marchewka, M. K.; Gunasekaran, S.; Anbalagan, G.

Melaminium bis(trifluoroacetate) trihydrate (MTFA), an organic material has been synthesized and single crystals of MTFA have been grown by the slow solvent evaporation method at room temperature. X-ray powder diffraction analysis confirms that MTFA crystal belongs to the monoclinic system with space group P2/c. The molecular geometry, vibrational frequencies and intensity of the vibrational bands have been interpreted with the aid of structure optimization based on density functional theory (DFT) B3LYP method with 6-311G(d,p) and 6-311++G(d,p) basis sets. The X-ray diffraction data have been compared with the data of optimized molecular structure. The theoretical results show that the crystal structure can be reproduced by optimized geometry and the vibrational frequencies show good agreement with the experimental values. The nuclear magnetic resonance (NMR) chemical shift of the molecule has been calculated by the gauge independent atomic orbital (GIAO) method and compared with experimental results. HOMO-LUMO, and other related molecular and electronic properties are calculated. The Mulliken and NBO charges have also been calculated and interpreted.

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.

A new multicomponent salt of imidazole and tetrabromoterepthalic acid: structural, optical, thermal, electrical transport properties and antibacterial activity along with Hirshfeld surface analysis.

PubMed

Dey, Sanjoy Kumar; Saha, Rajat; Singha, Soumen; Biswas, Susobhan; Layek, Animesh; Middya, Somnath; Ray, Partha Pratim; Bandhyopadhyay, Debasis; Kumar, Sanjay

2015-06-05

Herein, we report the structural, optical, thermal and electrical transport properties of a new multicomponent salt (TBTA(2-))·2(IM(+))·(water) [TBTA-IM] of tetrabromoterepthalic acid (TBTA) with imidazole (IM). The crystal structure of TBTA-IM is determined by both the single crystal and powder X-ray diffraction techniques. The structural analysis has revealed that the supramolecular charge assisted O(-)⋯HN(+) hydrogen bonding and Br⋯π interactions play the most vital role in formation of this multicomponent supramolecular assembly. The Hirshfeld surface analysis has been carried out to investigate supramolecular interactions and associated 2D fingerprint plots reveal the relative contribution of these interactions in the crystal structure quantitatively. According to theoretical analysis the HOMO-LUMO energy gap of the salt is 2.92 eV. The salt has been characterized by IR, UV-vis and photoluminescence spectroscopic studies. It shows direct optical transition with band gaps of 4.1 eV, which indicates that the salt is insulating in nature. The photoluminescence spectrum of the salt is significantly different from that of TBTA. Further, a comparative study on the antibacterial activity of the salt with respect to imidazole, Gatifloxacin and Ciprofloxacin has been performed. Moreover, the current-voltage (I-V) characteristic of ITO/TBTA-IM/Al sandwich structure exhibits good rectifying property and the electron tunneling process governs the electrical transport mechanism of the device. Copyright © 2015 Elsevier B.V. All rights reserved.

Crystal structure of TBC1D15 GTPase-activating protein (GAP) domain and its activity on Rab GTPases.

PubMed

Chen, Yan-Na; Gu, Xin; Zhou, X Edward; Wang, Weidong; Cheng, Dandan; Ge, Yinghua; Ye, Fei; Xu, H Eric; Lv, Zhengbing

2017-04-01

TBC1D15 belongs to the TBC (Tre-2/Bub2/Cdc16) domain family and functions as a GTPase-activating protein (GAP) for Rab GTPases. So far, the structure of TBC1D15 or the TBC1D15·Rab complex has not been determined, thus, its catalytic mechanism on Rab GTPases is still unclear. In this study, we solved the crystal structures of the Shark and Sus TBC1D15 GAP domains, to 2.8 Å and 2.5 Å resolution, respectively. Shark-TBC1D15 and Sus-TBC1D15 belong to the same subfamily of TBC domain-containing proteins, and their GAP-domain structures are highly similar. This demonstrates the evolutionary conservation of the TBC1D15 protein family. Meanwhile, the newly determined crystal structures display new variations compared to the structures of yeast Gyp1p Rab GAP domain and TBC1D1. GAP assays show that Shark and Sus GAPs both have higher catalytic activity on Rab11a·GTP than Rab7a·GTP, which differs from the previous study. We also demonstrated the importance of arginine and glutamine on the catalytic sites of Shark GAP and Sus GAP. When arginine and glutamine are changed to alanine or lysine, the activities of Shark GAP and Sus GAP are lost. © 2017 The Protein Society.

Experimental and quantum chemical studies on Nsbnd Hsbnd sbnd sbnd O hydrogen bonded helical chain type Morpholinium 2-chloro-4-nitrobenzoate: A phasematchable organic nonlinear optical material

NASA Astrophysics Data System (ADS)

Karthick, S.; Thirupugalmani, K.; Shanmugam, G.; Kannan, V.; Brahadeeswaran, S.

2018-03-01

We report on the studies performed on Morpholinium 2-chloro-4-nitrobenzoate (M2C4N), a second order nonlinear optical (NLO) material, which has been proved to crystallize with chiral structure as compared to its other two variants. The synthesized powder was studied for its composition, crystalline phase and NLO efficiency and phasematchability. The solubility and the metastable zone width (MSZW) of the title compound were measured for the growth of bulk crystals of M2C4N. A smoky pattern observed in the middle region of the crystals that could prevent it from optical applications was greatly reduced, through suitable modifications in the growth process. The optical properties such as luminescence and laser damage threshold resistance were studied for the bulk crystals whereas the molecular vibrations of M2C4N were studied through Fourier transform infrared (FTIR) and FT-Raman spectral analysis using the polycrystalline powders derived from the single crystals. In addition, quantum chemical studies on M2C4N molecule were performed by using density functional theory (DFT) at the B3LYP/6-311++G (d, p) basis set. These studies showed that the M2C4N is a phasematchable NLO crystal and could be used for device fabrication.

Synthesis, spectroscopic characterization, crystal structure, DNA interaction study and invitro biological screenings of 4-(5-chloro-2-hydroxyphenylamino)-4-oxobut-2-enoic acid

NASA Astrophysics Data System (ADS)

Sirajuddin, Muhammad; Nooruddin; Ali, Saqib; McKee, Vickie; Khan, Shahan Zeb; Malook, Khan

2015-01-01

The titled compound, 4-(5-chloro-2-hydroxyphenylamino)-4-oxobut-2-enoic acid was synthesized and characterized by various techniques like elemental analyses, FT-IR, NMR (1H, and 13C) and single crystal X-ray structural analysis. The appearance of the OH peak of the carboxylic acid in the FT-IR and NMR spectra conform the formation of the compound. A good agreement was found between the calculated values of C, H, N and found values in elemental analysis that show the purity of the compound. Protons H2 and H3 are in cis conformation with each other as conformed both from 1H NMR as well as from single crystal X-ray analysis. The molecular structure of the title compound, C10H10NO3Cl, is stabilized by short intramolecular Osbnd H- - -O hydrogen bonds within the molecule. In the crystal structure, intermolecular Nsbnd H- - -O hydrogen bonds link molecules into zigzag chains resulting in a dendrimer like structure. The title compound was screened for biological activities like interaction with DNA, cytotoxicity, antitumor and antioxidant activities. DNA interaction study reveals that the binding mode of interaction of the compound with SS-DNA is intercalative as it results in hypochromism along with significant red shift of 5 nm. It was also found to be effective antioxidant of 2,2-diphenyl-1-picrylhydrazyl radical (DPPH) and show almost comparable antioxidant activity to that of the standard and known antioxidant, ascorbic acid, at higher concentration. The antitumor activity data of the compound shows that it can be used as potent antitumor agent.

Structure-property relationship of 3-(4-substituted benzyl)-1,3-diazaspiro[4.4]nonane-2,4-diones as new potentional anticonvulsant agents. An experimental and theoretical study

NASA Astrophysics Data System (ADS)

Lazić, Anita M.; Božić, Bojan Đ.; Vitnik, Vesna D.; Vitnik, Željko J.; Rogan, Jelena R.; Radovanović, Lidija D.; Valentić, Nataša V.; Ušćumlić, Gordana S.

2017-01-01

The structure-property relationship of newly synthesized 3-(4-substituted benzyl)-1,3-diazaspiro [4.4]nonane-2,4-diones was studied by experimental and calculated methods. The prepared compounds were characterized by UV-Vis, FT-IR, 1H NMR and 13C NMR spectroscopy and elemental analysis. The crystal structure was elucidated by single-crystal X-ray diffraction. The 3-benzyl-1,3-diazaspiro[4.4]nonane-2,4-dione crystallizes in triclinic P-1 space group, with two crystallographically independent molecules in the asymmetric unit. Cyclopentane ring adopts an envelope conformation. A three-dimensional crystal packing is governed by hydrogen N-H⋯O bonds, numerous C-H⋯O/N and C-H … π interactions between neighboring molecules. Density functional theory (DFT) calculations with B3LYP and M06-2X methods using 6-311++G(d,p) basis set were performed to provide structural and spectroscopic information. Comparisons between experimental and calculated UV-Vis spectral properties suggest that the monomeric form of the investigated spirohydantoins is dominant in all used solvents. The effects of substituents on the absorption spectra of spirohydantoins are interpreted by correlation of absorption frequencies with Hammett equation. The lipophilicities of the investigated molecules were estimated by calculation of their log P values. Some of the spirohydantoins synthesized in this work, exhibit the lipophilicities comparable to the standard medicine anticonvulsant drug Phenytoin. The results obtained in this investigation afford guidelines for the preparation of new derivatives of spirohydantoin as potential anticonvulsant agents and for better understanding the structure-activity relationship.

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

Structural and Biophysical Characterization of Cajanus cajan Protease Inhibitor.

PubMed

Shamsi, Tooba Naz; Parveen, Romana; Ahamad, Shahzaib; Fatima, Sadaf

2017-01-01

A large number of studies have proven that Protease inhibitors (PIs), specifically serine protease inhibitors, show immense divergence in regulation of proteolysis by targeting their specific proteases and hence, they play a key role in healthcare. We aimed to access in-vitro anticancer potential of PI from Cajanus cajan (CCPI). Also, crystallization of CCPI was targetted alongwith structure determination and its structure-function relationship. CCPI was purified from Cajanus cajan seeds by chromatographic techniques. The purity and molecular mass was determined by SDS-PAGE. Anticancer potential of CCPI was determined by MTT assay in normal HEK and cancerous A549 cells. The crystallization screening of CCPI was performed by commercially available screens. CCPI sequence was subject to BLASTp with homologous PIs. Progressive multiple alignment was performed using clustalw2 and was modelled using ab initio protocol of I-TASSER. The results showed ~14kDa CCPI was purified in homogeneity. Also, CCPI showed low cytotoxic effects of in HEK i.e., 27% as compared with 51% cytotoxicity in A549 cells. CCPI crystallized at 16°C using 15% PEG 6000 in 0.1M potassium phosphate buffer (pH 6.0) in 2-3weeks as rod or needles visualized as clusters under the microscope. The molecular modelling revealed that it contains 3 beta sheets, 3 beta hairpins, 2 β-bulges, 6 strands, 3 helices, 1helix-helix interaction, 41 β-turns and 27 γ-turns. The results indicate that CCPI may help to treat cancer in vivo aswell. Also, this is the first report on preliminary crystallization and structural studies of CCPI.

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.

Electronic structures of superionic conductor Li3N

NASA Astrophysics Data System (ADS)

Aoki, Masaru; Ode, Yoshiyuki; Tsumuraya, Kazuo

2011-03-01

Lithium nitride is a superionic conductor with high Li conductivity. The compound has been studied extensively because of its potential utility as electrolyte in solid-state batteries. Though the mobility of the cations within the crystalline solid is high comparable to that of molten salts, the mechanism of the high mobility of the cations remains unsolved. To clarify the origin of the mobility we investigate the electronic states of the Li cations in the Li 3 N crystal with the first principles electronic structure analysis, focusing a correlation between the cations and the ionicities of the constituent atoms. We have found the existence of the covalent bonding between the Li atoms in the Li 3 N crystal in spite of the ionized states of the constituent atoms.

Hydrogen Bonding: Between Strengthening the Crystal Packing and Improving Solubility of Three Haloperidol Derivatives.

PubMed

Saluja, Hardeep; Mehanna, Ahmed; Panicucci, Riccardo; Atef, Eman

2016-06-01

The purpose of this study is to confirm the impact of polar functional groups on inter and intra-molecular hydrogen bonding in haloperidol (HP) and droperidol (DP) and, hence, their effects on dissolution using a new approach. To confirm our theory, a new molecule: deshydroxy-haloperidol (DHP) was designed and its synthesis was requested from a contract laboratory. The molecule was then studied and compared to DP and HP. Unlike DHP, both the HP and DP molecules have hydrogen donor groups, therefore, DHP was used to confirm the relative effects of the hydrogen donor group on solubility and crystal packing. The solid dispersions of the three structurally related molecules: HP, DP, and DHP were prepared using PVPK30, and characterized using XRPD and IR. A comparative dissolution study was carried out in aqueous medium. The absence of a hydrogen bonding donor group in DHP resulted in an unexpected increase in its aqueous solubility and dissolution rate from solid dispersion, which is attributed to weaker crystal pack. The increased dissolution rate of HP and DP from solid dispersions is attributed to drug-polymer hydrogen bonding that interferes with the drug-drug intermolecular hydrogen bonding and provides thermodynamic stability of the dispersed drug molecules. The drug-drug intermolecular hydrogen bond is the driving force for precipitation and crystal packing.

Comparative theoretical and experimental study on novel tri-quinoline system and its anticancer studies

NASA Astrophysics Data System (ADS)

Gayathri, Kasirajan; Radhika, Ramachandran; Shankar, Ramasamy; Malathi, Mahalingam; Savithiri, Krishnaswamy; Sparkes, Hazel A.; Howard, Judith A. K.; Mohan, Palathurai Subramaniam

2017-04-01

A novel compound 2-chloro-3,6-bis-(quinolin-8-yloxymethyl)-quinoline 3 bearing a tri-quinoline moiety has been synthesized from 2-chloro-3,6-dimethyl quinoline 1 and 8-hydroxy quinoline 2 using dry acetone and K2CO3 as a base. 3 has been characterized by using FT-IR, FT-Raman, UV-Vis, 1H NMR, 13C NMR spectra and single crystal X-ray diffraction methods. We have also made a combined experimental and theoretical study on the molecular structure, vibrational spectra, NMR, FT-IR, FT-Raman and UV-Vis spectra of 2-chloro-3,6-bis-(quinolin-8-yloxymethyl)-quinoline. The theoretical studies of the title compound have been evaluated by using density functional theory calculations using B3LYP/6-31+G(d,p) and M06-2X/6-31+G(d,p) level of theories. The calculated theoretical values were found to be in good agreement with the experimental findings. The single crystal structure 3 crystallized in the orthorhombic space group Pna21. The compound 3 exhibits higher cytotoxicity in human cervical cancer cell lines (HeLa) than human breast cancer cell lines (MCF7).

Biomineral nanoparticles are space-filling.

PubMed

Yang, Li; Killian, Christopher E; Kunz, Martin; Tamura, Nobumichi; Gilbert, P U P A

2011-02-01

Sea urchin biominerals have been shown to form from aggregating nanoparticles of amorphous calcium carbonate (ACC), which then crystallize into macroscopic single crystals of calcite. Here we measure the surface areas of these biominerals and find them to be comparable to those of space-filling macroscopic geologic calcite crystals. These biominerals differ from synthetic mesocrystals, which are invariably porous. We propose that space-filling ACC is the structural precursor for echinoderm biominerals.

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

PubMed

van de Streek, Jacco; Neumann, Marcus A

2014-12-01

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

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

PubMed Central

van de Streek, Jacco; Neumann, Marcus A.

2014-01-01

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

Circularly polarized Raman study on diamond structure crystals

NASA Astrophysics Data System (ADS)

Lee, Je-Ho; Kim, Sera; Seong, Maeng-Je

2018-01-01

Circularly polarized Raman and/or photoluminescence (PL) analyses have recently been very important in studying physical properties of many layered materials that were either mechanically exfoliated or grown by chemical-vapor-deposition (CVD) on silicon substrates. Since silicon Raman signal is always accompanied by the circularly polarized Raman and/or PL signal from the layered materials, observation of proper circularly polarized Raman selection rules on silicon substrates would be extremely good indicator that the circularly polarized Raman and/or PL measurements on the layered materials were done properly. We have performed circularly polarized Raman measurements on silicon substrates and compared the results with the Raman intensities calculated by using Raman tensors of the diamond crystal structure. Our experimental results were in excellent agreement with the calculation. Similar circularly polarized Raman analysis done on germanium substrate also showed good agreement.

Raman Spectroscopy Adds Complementary Detail to the High-Resolution X-Ray Crystal Structure of Photosynthetic PsbP from Spinacia oleracea

PubMed Central

Lapkouski, Mikalai; Hofbauerova, Katerina; Sovova, Zofie; Ettrichova, Olga; González-Pérez, Sergio; Dulebo, Alexander; Kaftan, David; Kuta Smatanova, Ivana; Revuelta, Jose L.; Arellano, Juan B.; Carey, Jannette; Ettrich, Rüdiger

2012-01-01

Raman microscopy permits structural analysis of protein crystals in situ in hanging drops, allowing for comparison with Raman measurements in solution. Nevertheless, the two methods sometimes reveal subtle differences in structure that are often ascribed to the water layer surrounding the protein. The novel method of drop-coating deposition Raman spectropscopy (DCDR) exploits an intermediate phase that, although nominally “dry,” has been shown to preserve protein structural features present in solution. The potential of this new approach to bridge the structural gap between proteins in solution and in crystals is explored here with extrinsic protein PsbP of photosystem II from Spinacia oleracea. In the high-resolution (1.98 Å) x-ray crystal structure of PsbP reported here, several segments of the protein chain are present but unresolved. Analysis of the three kinds of Raman spectra of PsbP suggests that most of the subtle differences can indeed be attributed to the water envelope, which is shown here to have a similar Raman intensity in glassy and crystal states. Using molecular dynamics simulations cross-validated by Raman solution data, two unresolved segments of the PsbP crystal structure were modeled as loops, and the amino terminus was inferred to contain an additional beta segment. The complete PsbP structure was compared with that of the PsbP-like protein CyanoP, which plays a more peripheral role in photosystem II function. The comparison suggests possible interaction surfaces of PsbP with higher-plant photosystem II. This work provides the first complete structural picture of this key protein, and it represents the first systematic comparison of Raman data from solution, glassy, and crystalline states of a protein. PMID:23071614

Density functional theory study of dopant effect on formation energy of intrinsic point defects in germanium crystals

NASA Astrophysics Data System (ADS)

Yamaoka, S.; Kobayashi, K.; Sueoka, K.; Vanhellemont, J.

2017-09-01

During the last decade the use of single crystal germanium (Ge) layers and structures in combination with silicon (Si) substrates has led to a revival of defect research on Ge. Ge is used because of the much higher carrier mobility compared to Si, allowing to design devices operating at much higher frequencies. A major issue for the use of Ge single crystal wafers is the fact that all Czochralski-grown Ge (CZ-Ge) crystals are vacancy-rich and contain vacancy clusters that are much larger than the ones in Si. In contrast to Si, control of intrinsic point defect concentrations has not yet been realized at the same level in Ge crystals due to the lack of experimental data especially on dopant effects. In this study, we have evaluated with density functional theory (DFT) calculations the dopant effect on the formation energy (Ef) of the uncharged vacancy (V) and self-interstitial (I) in Ge and compared the results with those for Si. The dependence of the total thermal equilibrium concentrations of point defects (sum of free V or I and V or I paired with dopant atoms) at melting temperature on the type and concentration of various dopants is obtained. It was found that (1) Ge crystals will be more V-rich by Tl, In, Sb, Sn, As and P doping, (2) Ge crystals will be more I-rich by Ga, C and B doping, (3) Si doping has negligible impact. The dopant impact on Ef of V and I in Ge has a narrower range and is smaller than that in Si. The obtained results are useful to control grown-in V and I concentrations, and will perhaps also allow to develop defect-free ;perfect; Ge crystals.

Halogen bonds in some dihalogenated phenols: applications to crystal engineering.

PubMed

Mukherjee, Arijit; Desiraju, Gautam R

2014-01-01

3,4-Dichlorophenol (1) crystallizes in the tetragonal space group I41/a with a short axis of 3.7926 (9) Å. The structure is unique in that both type I and type II Cl⋯Cl interactions are present, these contact types being distinguished by the angle ranges of the respective C-Cl⋯Cl angles. The present study shows that these two types of contacts are utterly different. The crystal structures of 4-bromo-3-chlorophenol (2) and 3-bromo-4-chlorophenol (3) have been determined. The crystal structure of (2) is isomorphous to that of (1) with the Br atom in the 4-position participating in a type II interaction. However, the monoclinic P21/c packing of compound (3) is different; while the structure still has O-H⋯O hydrogen bonds, the tetramer O-H⋯O synthon seen in (1) and (2) is not seen. Rather than a type I Br⋯Br interaction which would have been mandated if (3) were isomorphous to (1) and (2), Br forms a Br⋯O contact wherein its electrophilic character is clearly evident. Crystal structures of the related compounds 4-chloro-3-iodophenol (4) and 3,5-dibromophenol (5) were also determined. A computational survey of the structural landscape was undertaken for (1), (2) and (3), using a crystal structure prediction protocol in space groups P21/c and I41/a with the COMPASS26 force field. While both tetragonal and monoclinic structures are energetically reasonable for all compounds, the fact that (3) takes the latter structure indicates that Br prefers type II over type I contacts. In order to differentiate further between type I and type II halogen contacts, which being chemically distinct are expected to have different distance fall-off properties, a variable-temperature crystallography study was performed on compounds (1), (2) and (4). Length variations with temperature are greater for type II contacts compared with type I. The type II Br⋯Br interaction in (2) is stronger than the corresponding type II Cl⋯Cl interaction in (1), leading to elastic bending of the former upon application of mechanical stress, which contrasts with the plastic deformation of (1). The observation of elastic deformation in (2) is noteworthy; in that it finds an explanation based on the strengths of the respective halogen bonds, it could also be taken as a good starting model for future property design. Cl/Br isostructurality is studied with the Cambridge Structural Database and it is indicated that this isostructurality is based on shape and size similarity of Cl and Br, rather than arising from any chemical resemblance.

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.

Solid dispersions of Myricetin with enhanced solubility: Formulation, characterization and crystal structure of stability-impeding Myricetin monohydrate crystals

NASA Astrophysics Data System (ADS)

Mureşan-Pop, M.; Pop, M. M.; Borodi, G.; Todea, M.; Nagy-Simon, T.; Simon, S.

2017-08-01

Three solid dispersion forms of Myricetin combined with the Polyvinylpyrrolidone were successfully prepared by spray drying method, and characterized by X-ray powder diffraction, thermal analysis, infrared spectroscopy and optical microscopy. Zeta potential measurements provided indications on solid dispersions stability in aqueous suspension related to their storage at elevated temperature and relative humidity, which depends on the Myricetin load. By increase of Myricetin load, the stability of the solid dispersion is impeded due to growth of Myricetin monohydrate crystals. The amorphous dispersions with 10% and 50% Myricetin load are stable and, compared to pure Myricetin, their aqueous solubility is enhanced by a factor of 47 and 13, respectively. The dispersion with 80% Myricetin load is unstable on storage, and this behavior acts in conjunction with the development of Myricetin monohydrate crystals. Single-crystal X-ray diffraction results obtained for Myricetin monohydrate reveal a structure of an infinite 2D network of hydrogen-bonded molecules involving all six hydroxyl groups of Myricetin. The water molecules are positioned in between the infinite chains, and contribute via H-bonds to robust crystal packing. The calculated needle-like morphology of monohydrate form is in agreement with the optical microscopy results. The study shows that the solid amorphous dispersions with up to 50% Myricetin load are a viable option for achieving substantial solubility improvement of Myricetin, and supports their potential use in pharmaceutical applications.

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.

Crystal structures of D-psicose 3-epimerase from Clostridium cellulolyticum H10 and its complex with ketohexose sugars.

PubMed

Chan, Hsiu-Chien; Zhu, Yueming; Hu, Yumei; Ko, Tzu-Ping; Huang, Chun-Hsiang; Ren, Feifei; Chen, Chun-Chi; Ma, Yanhe; Guo, Rey-Ting; Sun, Yuanxia

2012-02-01

D-psicose 3-epimerase (DPEase) is demonstrated to be useful in the bioproduction of D-psicose, a rare hexose sugar, from D-fructose, found plenty in nature. Clostridium cellulolyticum H10 has recently been identified as a DPEase that can epimerize D-fructose to yield D-psicose with a much higher conversion rate when compared with the conventionally used DTEase. In this study, the crystal structure of the C. cellulolyticum DPEase was determined. The enzyme assembles into a tetramer and each subunit shows a (β/α)(8) TIM barrel fold with a Mn(2+) metal ion in the active site. Additional crystal structures of the enzyme in complex with substrates/products (D-psicose, D-fructose, D-tagatose and D-sorbose) were also determined. From the complex structures of C. cellulolyticum DPEase with D-psicose and D-fructose, the enzyme has much more interactions with D-psicose than D-fructose by forming more hydrogen bonds between the substrate and the active site residues. Accordingly, based on these ketohexose-bound complex structures, a C3-O3 proton-exchange mechanism for the conversion between D-psicose and D-fructose is proposed here. These results provide a clear idea for the deprotonation/protonation roles of E150 and E244 in catalysis.

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

Effect of heat treatment on surface hydrophilicity-retaining ability of titanium dioxide nanotubes

NASA Astrophysics Data System (ADS)

Sun, Yu; Sun, Shupei; Liao, Xiaoming; Wen, Jiang; Yin, Guangfu; Pu, Ximing; Yao, Yadong; Huang, Zhongbing

2018-05-01

The aim of this study is to investigate the effect of different annealing temperature and atmosphere on the surface wettability retaining properties of titania nanotubes (TNs) fabricated by anodization. The TNs morphology, crystal phase composition and surface elemental composition and water contact angle (WCA) were investigated by scanning electron microscopy, X-ray diffraction, X-ray photoelectron spectroscopy and contact angle instrument, respectively. After the samples annealed at 200 °C, 450 °C, 850 °C have been stored in air for 28 days, the WCAs increase to 31.7°, 21.1° and 110.5°, respectively. The results indicate that crystal phase composition of TNs plays an important role in surface wettability. Compared with the WCA (21.1°) of the samples annealed in air after 28 days, the WCA of samples annealed in oxygen-deficient atmosphere is lower, suggesting the contribution of oxygen vacancy in the enhanced hydrophilicity-retaining ability. Our study demonstrates that the surface hydrophilicity-retaining ability of TNs is related to the ordered nanotubular structure, crystal structure, the amount of surface hydroxyl group and oxygen vacancy defects.

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.

Design, structural investigation and physicochemical properties of benzotriazolium m-nitrophthalate monohydrate single crystals

NASA Astrophysics Data System (ADS)

Mekala, R.; Mani, Rajaboopathi; Jagdish, P.; Mathammal, R.

2018-04-01

The single crystals of organic salt benzotriazolium m-nitrophthalate monohydrate were grown by slow evaporation technique. It crystallizes in orthorhombic system with space group Pbca. The molecular interactions of the compound have been pictured using Hirshfeld surfaces and fingerprints plots and the results were compared with BZD+·mNPA-. The functional groups were identified by FTIR and FT-Raman spectra. The proton transfer from acid to base was identified from the 1H and 13C NMR spectra. The absorption and emission spectrum of BTA+·mNPA-·H2O was recorded in aqueous solution and different solvents, respectively The HOMO and LUMO energy gap of benzotriazole and BTA+·mNPA-·H2O were calculated using density functional theory (DFT). The thermal stability and melting point of hydrated salt was analysed and compared by TG-DTG/DSC study. The anti-oxidant activity of the title compound was evaluated by DPPH and ABTS+ Radical scavenging assay. The anti-microbial and anti-cancer activity showed a potential impact in the crystal.

Predicting New Materials for Hydrogen Storage Application

PubMed Central

Vajeeston, Ponniah; Ravindran, Ponniah; Fjellvåg, Helmer

2009-01-01

Knowledge about the ground-state crystal structure is a prerequisite for the rational understanding of solid-state properties of new materials. To act as an efficient energy carrier, hydrogen should be absorbed and desorbed in materials easily and in high quantities. Owing to the complexity in structural arrangements and difficulties involved in establishing hydrogen positions by x-ray diffraction methods, the structural information of hydrides are very limited compared to other classes of materials (like oxides, intermetallics, etc.). This can be overcome by conducting computational simulations combined with selected experimental study which can save environment, money, and man power. The predicting capability of first-principles density functional theory (DFT) is already well recognized and in many cases structural and thermodynamic properties of single/multi component system are predicted. This review will focus on possible new classes of materials those have high hydrogen content, demonstrate the ability of DFT to predict crystal structure, and search for potential meta-stable phases. Stabilization of such meta-stable phases is also discussed.

Mechanistic Study of Oxygen Atom Transfer Catalyzed by Rhenium Compounds

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

Shan, Xiaopeng

2003-01-01

Two ionic and one neutral methyl(oxo)rhenium(V) compounds were synthesized and structurally characterized. They were compared in reactivity towards the ligands triphenylphosphane, pyridines, pyridine N-oxides. Assistance from Broensted bases was found on ligand displacement of ionic rhenium compounds as well as nucleophile assistance on oxidation of all compounds. From the kinetic data, crystal structures, and an analysis of the intermediates, a structural formula of PicH +3 - and mechanisms of ligand displacement and oxidation were proposed.

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.

Distributions of methyl group rotational barriers in polycrystalline organic solids

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

Beckmann, Peter A., E-mail: pbeckman@brynmawr.edu, E-mail: wangxianlong@uestc.edu.cn; Conn, Kathleen G.; Division of Education and Human Services, Neumann University, One Neumann Drive, Aston, Pennsylvania 19014-1298

We bring together solid state {sup 1}H spin-lattice relaxation rate measurements, scanning electron microscopy, single crystal X-ray diffraction, and electronic structure calculations for two methyl substituted organic compounds to investigate methyl group (CH{sub 3}) rotational dynamics in the solid state. Methyl group rotational barrier heights are computed using electronic structure calculations, both in isolated molecules and in molecular clusters mimicking a perfect single crystal environment. The calculations are performed on suitable clusters built from the X-ray diffraction studies. These calculations allow for an estimate of the intramolecular and the intermolecular contributions to the barrier heights. The {sup 1}H relaxation measurements,more » on the other hand, are performed with polycrystalline samples which have been investigated with scanning electron microscopy. The {sup 1}H relaxation measurements are best fitted with a distribution of activation energies for methyl group rotation and we propose, based on the scanning electron microscopy images, that this distribution arises from molecules near crystallite surfaces or near other crystal imperfections (vacancies, dislocations, etc.). An activation energy characterizing this distribution is compared with a barrier height determined from the electronic structure calculations and a consistent model for methyl group rotation is developed. The compounds are 1,6-dimethylphenanthrene and 1,8-dimethylphenanthrene and the methyl group barriers being discussed and compared are in the 2–12 kJ mol{sup −1} range.« less

FCC-HCP coexistence in dense thermo-responsive microgel crystals

NASA Astrophysics Data System (ADS)

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

2017-06-01

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

Colloidal crystals with diamond symmetry at optical lengthscales

NASA Astrophysics Data System (ADS)

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

2017-02-01

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

Molecular dynamics simulation of fast particle irradiation on the single crystal CeO2

NASA Astrophysics Data System (ADS)

Sasajima, Y.; Ajima, N.; Osada, T.; Ishikawa, N.; Iwase, A.

2013-11-01

We used a molecular dynamics method to simulate structural relaxation caused by the high-energy-ion irradiation of single crystal CeO2. As the initial condition, we assumed high thermal energy was supplied to the individual atoms within a cylindrical region of nanometer-order diameter located in the center of the single crystal. The potential proposed by Inaba et al. was utilized to calculate interactions between atoms [H. Inaba, R. Sagawa, H. Hayashi, K. Kawamura, Solid State Ionics 122 (1999) 95-103]. The supplied thermal energy was first spent to change the crystal structure into an amorphous one within a short period of about 0.3 ps, then it was dissipated in the crystal. We compared the obtained results with those of computer simulations for UO2 and found that CeO2 was more stable than UO2 when supplied with high thermal energy.

The Band Structure of Polymers: Its Calculation and Interpretation. Part 2. Calculation.

ERIC Educational Resources Information Center

Duke, B. J.; O'Leary, Brian

1988-01-01

Details ab initio crystal orbital calculations using all-trans-polyethylene as a model. Describes calculations based on various forms of translational symmetry. Compares these calculations with ab initio molecular orbital calculations discussed in a preceding article. Discusses three major approximations made in the crystal case. (CW)

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

Chuvashova, Irina, E-mail: irina.chuvashova@gmail.com; Bayerisches Geoinstitut, University of Bayreuth, D-95440 Bayreuth; Bykova, Elena

In the present study single crystals of rhombohedral α-B were investigated under pressure to 60 GPa by means of single-crystal X-ray diffraction. The bulk modulus of α-B was found to be K=224(7) GPa (K′=3.0(3)). Measurements of interatomic distances as a function of pressure revealed that the intericosahedral two-center two-electron (2c–2e) bonds are almost as stiff as some of intraicosahedral ones. The three-center two-electron (3c–2e) intericosahedral bonds show much higher compliance compared to other bonds in α-B. The vibrational properties of α-B under pressure were investigated by Raman spectroscopy at pressures up to 160 GPa and IR spectroscopy at pressures upmore » to 53 GPa. - Graphical abstract: The rhombohedral α-B is highly incompressible and extremely stable: it maintains its crystal structure up to 160 GPa and its intericosahedral 2e2c bonds are almost as stiff as some of intraicosahedral ones. - Highlights: • Structural stability of α-B has been investigated up to 160 GPa on single crystals. • Single-crystal x-ray diffraction reveals that α-B is highly incompressible. • Compressibility of B{sub 12} icosahedra is considerably lower than that of the bulk material. • Intericosahedral 2e2c bonds are almost as stiff as some of intraicosahedral ones.« less

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.

Biochemical, spectroscopic and X-ray structural analysis of deuterated multicopper oxidase CueO prepared from a new expression construct for neutron crystallography.

PubMed

Akter, Mahfuza; Inoue, Chika; Komori, Hirofumi; Matsuda, Nana; Sakurai, Takeshi; Kataoka, Kunishige; Higuchi, Yoshiki; Shibata, Naoki

2016-10-01

Multicopper oxidases oxidize various phenolic and nonphenolic compounds by using molecular oxygen as an electron acceptor to produce water. A multicopper oxidase protein, CueO, from Escherichia coli is involved in copper homeostasis in the bacterial cell. Although X-ray crystallographic studies have been conducted, the reduction mechanism of oxygen and the proton-transfer pathway remain unclear owing to the difficulty in identifying H atoms from X-ray diffraction data alone. To elucidate the reaction mechanism using neutron crystallography, a preparation system for obtaining large, high-quality single crystals of deuterated CueO was developed. Tiny crystals were obtained from the deuterated CueO initially prepared from the original construct. The X-ray crystal structure of the deuterated CueO showed that the protein contained an incompletely truncated signal sequence at the N-terminus, which resulted in the heterogeneity of the protein sample for crystallization. Here, a new CueO expression system that had an HRV3C cleavage site just after the signal sequence was constructed. Deuterated CueO from the new construct was expressed in cells cultured in deuterated algae-extract medium and the signal sequence was completely eliminated by HRV3C protease. The deuteration level of the purified protein was estimated by MALDI-TOF mass spectrometry to be at least 83.2% compared with nondeuterated protein. Nondeuterated CueO crystallized in space group P2 1 , with unit-cell parameters a = 49.51, b = 88.79, c = 53.95 Å, β = 94.24°, and deuterated CueO crystallized in space group P2 1 2 1 2 1 , with unit-cell parameters a = 49.91, b = 106.92, c = 262.89 Å. The crystallographic parameters for the crystals of the new construct were different from those previously reported for nondeuterated crystals. The nondeuterated and deuterated CueO from the new construct had similar UV-Vis spectra, enzymatic activities and overall structure and geometry of the ligands of the Cu atoms in the active site to those of previously reported CueO structures. These results indicate that the CueO protein prepared using the new construct is suitable for further neutron diffraction studies.

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.

Eu 3Ir 2In 15: A mixed-valent and vacancy-filled variant of the Sc 5Co 4Si 10 structure type with anomalous magnetic properties

DOE PAGES

Sarkar, Sumanta; Jana, Rajkumar; Siva, Ramesh; ...

2015-10-27

Here, a new compound, Eu 3Ir 2In 15 has been synthesized using indium as an active metal flux. The compound crystallizes in tetragonal P4/mbm space group with lattice parameters, a = 14.8580(4) Å, b = 14.8580(4) Å, c = 4.3901(2) Å. It was further characterized by SEM-EDX studies. The temperature dependent magnetic susceptibility suggests that Eu in this compound is exclusively in divalent state. The effective magnetic moment (μ eff) of this compound is 7.35 μ B/Eu ion with paramagnetic Curie temperature (θ p) of -28 K suggesting antiferromagnetic interaction. The mixed valent nature of Eu observed in magnetic measurementsmore » was confirmed by XANES measurements. The compound undergoes demagnetization at a low magnetic field (10 Oe), which is quite unusual for Eu based intermetallic compounds. Temperature dependent resistivity studies reveal that the compound is metallic in nature. A comparative study was made between Eu 3Ir 2In 15 and hypothetical vacancy variant Eu 5Ir 4In 10 which also crystallizes in the same crystal structure However our computational studies along with control experiments suggest that the latter is thermodynamically less feasible compared to the former and hence we proposed that it is highly unlikely that a RE 5T 4X 10 would exist with X as a group 13 elements.« less

A decade of crystallization drops: crystallization of the cbb3 cytochrome c oxidase from Pseudomonas stutzeri.

PubMed

Buschmann, Sabine; Richers, Sebastian; Ermler, Ulrich; Michel, Hartmut

2014-04-01

The cbb3 cytochrome c oxidases are distant members of the superfamily of heme copper oxidases. These terminal oxidases couple O2 reduction with proton transport across the plasma membrane and, as a part of the respiratory chain, contribute to the generation of an electrochemical proton gradient. Compared with other structurally characterized members of the heme copper oxidases, the recently determined cbb3 oxidase structure at 3.2 Å resolution revealed significant differences in the electron supply system, the proton conducting pathways and the coupling of O2 reduction to proton translocation. In this paper, we present a detailed report on the key steps for structure determination. Improvement of the protein quality was achieved by optimization of the number of lipids attached to the protein as well as the separation of two cbb3 oxidase isoenzymes. The exchange of n-dodecyl-β-D-maltoside for a precisely defined mixture of two α-maltosides and decanoylsucrose as well as the choice of the crystallization method had a most profound impact on crystal quality. This report highlights problems frequently encountered in membrane protein crystallization and offers meaningful approaches to improve crystal quality. © 2014 The Protein Society.

A decade of crystallization drops: Crystallization of the cbb3 cytochrome c oxidase from Pseudomonas stutzeri

PubMed Central

Buschmann, Sabine; Richers, Sebastian; Ermler, Ulrich; Michel, Hartmut

2014-01-01

The cbb3 cytochrome c oxidases are distant members of the superfamily of heme copper oxidases. These terminal oxidases couple O2 reduction with proton transport across the plasma membrane and, as a part of the respiratory chain, contribute to the generation of an electrochemical proton gradient. Compared with other structurally characterized members of the heme copper oxidases, the recently determined cbb3 oxidase structure at 3.2 Å resolution revealed significant differences in the electron supply system, the proton conducting pathways and the coupling of O2 reduction to proton translocation. In this paper, we present a detailed report on the key steps for structure determination. Improvement of the protein quality was achieved by optimization of the number of lipids attached to the protein as well as the separation of two cbb3 oxidase isoenzymes. The exchange of n-dodecyl-β-d-maltoside for a precisely defined mixture of two α-maltosides and decanoylsucrose as well as the choice of the crystallization method had a most profound impact on crystal quality. This report highlights problems frequently encountered in membrane protein crystallization and offers meaningful approaches to improve crystal quality. PMID:24488923

Split green fluorescent protein as a modular binding partner for protein crystallization.

PubMed

Nguyen, Hau B; Hung, Li-Wei; Yeates, Todd O; Terwilliger, Thomas C; Waldo, Geoffrey S

2013-12-01

A modular strategy for protein crystallization using split green fluorescent protein (GFP) as a crystallization partner is demonstrated. Insertion of a hairpin containing GFP β-strands 10 and 11 into a surface loop of a target protein provides two chain crossings between the target and the reconstituted GFP compared with the single connection afforded by terminal GFP fusions. This strategy was tested by inserting this hairpin into a loop of another fluorescent protein, sfCherry. The crystal structure of the sfCherry-GFP(10-11) hairpin in complex with GFP(1-9) was determined at a resolution of 2.6 Å. Analysis of the complex shows that the reconstituted GFP is attached to the target protein (sfCherry) in a structurally ordered way. This work opens the way to rapidly creating crystallization variants by reconstituting a target protein bearing the GFP(10-11) hairpin with a variety of GFP(1-9) mutants engineered for favorable crystallization.

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

Investigations of structural defects, crystalline perfection, metallic impurity concentration and optical quality of flat-top KDP crystal

NASA Astrophysics Data System (ADS)

Sharma, S. K.; Verma, Sunil; Singh, Yeshpal; Bartwal, K. S.; Tiwari, M. K.; Lodha, G. S.; Bhagavannarayana, G.

2015-08-01

KDP crystal grown using flat-top technique has been characterized using X-ray and optical techniques with the aim of correlating the defects structure and impurity concentration in the crystal with its optical properties. Crystallographic defects were investigated using X-ray topography revealing linear and arc like chains of dislocations and to conclude that defects do not originate from the flat-top part of the crystal. Etching was performed to quantify dislocation defects density. The crystalline perfection of the crystal was found to be high as the FWHM of the rocking curves measured at several locations was consistently low 6-9 arc s. The concentration of Fe metallic impurity quantified using X-ray fluorescence technique was approximately 5 times lower in the flat-top part which falls in pyramidal growth sector as compared to the region near to the seed which lies in prismatic sector. The spectrophotometric characterization for plates cut normal to different crystallographic directions in the flat-top potassium dihydrogen phosphate (FT-KDP) crystal was performed to understand the influence of metallic impurity distribution and growth sectors on the optical transmittance. The transmittance of the FT-KDP crystal at 1064 nm and its higher harmonics (2nd, 3rd, 4th and 5th) was determined from the measured spectra and the lower transmission in the UV region was attributed to increased absorption by Fe metallic impurity at these wavelengths. The results are in agreement with the results obtained using X-ray fluorescence and X-ray topography. Birefringence and Mach-Zehnder interferometry show that except for the region near to the seed crystal the optical homogeneity of the entire crystal was good. The laser-induced damage threshold (LDT) values are in the range 2.4-3.9 GW/cm2. The LDT of the plate taken from the flat-top region is higher than that from the bottom of the crystal, indicating that the flat-top technique has good optical quality and is comparable to those reported using rapid growth technique. The results indicate that the structural defects, crystalline quality and impurity concentration have a correlation with the optical properties of the FT-KDP crystal.

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

Arginine Kinase. Joint Crystallographic & NMR RDC Analyses link Substrate-Associated Motions to Intrinsic Flexibility

PubMed Central

Niu, Xiaogang; Brüschweiler-Li, Lei; Davulcu, Omar; Skalicky, Jack J.; Brüschweiler, Rafael; Chapman, Michael S.

2010-01-01

The phosphagen kinase family, including creatine and arginine kinases, catalyze the reversible transfer of a “high energy” phosphate between ATP and a phospho-guanidino substrate. They have become a model for the study of both substrate-induced conformational change and intrinsic protein dynamics. Prior crystallographic studies indicated large substrate-induced domain rotations, but differences among a recent set of arginine kinase structures was interpreted as a plastic deformation. Here, the structure of Limulus substrate-free arginine kinase is refined against high resolution crystallographic data and compared quantitatively with NMR chemical shifts and residual dipolar couplings (RDCs). This demonstrates the feasibility of this type of RDC analysis of proteins that are large by NMR standards (42 kDa), and illuminates the solution structure, free from crystal-packing constraints. Detailed comparison of the 1.7 Å resolution substrate-free crystal structure against the 1.2 Å transition state analog complex shows large substrate-induced domain motions which can be broken down into movements of smaller quasi-rigid bodies. The solution state structure of substrate-free arginine kinase is most consistent with an equilibrium of substrate-free and –bound structures, with the substrate-free form dominating, but with varying displacements of the quasi-rigid groups. Rigid-group rotations evident from the crystal structures are about axes previously associated with intrinsic millisecond dynamics using NMR relaxation dispersion. Thus, “substrate-induced” motions are along modes that are intrinsically flexible in the substrate-free enzyme, and likely involve some degree of conformational selection. PMID:21075117

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

A class III chitinase without disulfide bonds from the fern, Pteris ryukyuensis: crystal structure and ligand-binding studies.

PubMed

Kitaoku, Yoshihito; Umemoto, Naoyuki; Ohnuma, Takayuki; Numata, Tomoyuki; Taira, Toki; Sakuda, Shohei; Fukamizo, Tamo

2015-10-01

We first solved the crystal structure of class III catalytic domain of a chitinase from fern (PrChiA-cat), and found a structural difference between PrChiA-cat and hevamine. PrChiA-cat was found to have reduced affinities to chitin oligosaccharides and allosamidin. Plant class III chitinases are subdivided into enzymes with three disulfide bonds and those without disulfide bonds. We here referred to the former enzymes as class IIIa chitinases and the latter as class IIIb chitinases. In this study, we solved the crystal structure of the class IIIb catalytic domain of a chitinase from the fern Pteris ryukyuensis (PrChiA-cat), and compared it with that of hevamine, a class IIIa chitinase from Hevea brasiliensis. PrChiA-cat was found to adopt an (α/β)8 fold typical of GH18 chitinases in a similar manner to that of hevamine. However, PrChiA-cat also had two large loops that extruded from the catalytic site, and the corresponding loops in hevamine were markedly smaller than those of PrChiA-cat. An HPLC analysis of the enzymatic products revealed that the mode of action of PrChiA-cat toward chitin oligosaccharides, (GlcNAc) n (n = 4-6), differed from those of hevamine and the other class IIIa chitinases. The binding affinities of (GlcNAc)3 and (GlcNAc)4 toward the inactive mutant of PrChiA-cat were determined by isothermal titration calorimetry, and were markedly lower than those toward other members of the GH18 family. The affinity and the inhibitory activity of allosamidin toward PrChiA-cat were also lower than those toward the GH18 chitinases investigated to date. Several hydrogen bonds found in the crystal structure of hevamine-allosamidin complex were missing in the modeled structure of PrChiA-cat-allosamidin complex. The structural findings for PrChiA-cat successfully interpreted the functional data presented.

Non-linear thermal evolution of the crystal structure and phase transitions of LaFeO{sub 3} investigated by high temperature X-ray diffraction

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

Selbach, Sverre M.; Tolchard, Julian R.; Fossdal, Anita

2012-12-15

The crystal structure, anisotropic thermal expansion and structural phase transition of the perovskite LaFeO{sub 3} has been studied by high-temperature X-ray diffraction from room temperature to 1533 K. The structural evolution of the orthorhombic phase with space group Pbnm and the rhombohedral phase with R3{sup Macron }c structure of LaFeO{sub 3} is reported in terms of lattice parameters, thermal expansion coefficients, atomic positions, octahedral rotations and polyhedral volumes. Non-linear lattice expansion across the antiferromagnetic to paramagnetic transition of LaFeO{sub 3} at T{sub N}=735 K was compared to the corresponding behavior of the ferroelectric antiferromagnet BiFeO{sub 3} to gain insight tomore » the magnetoelectric coupling in BiFeO{sub 3}, which is also multiferroic. The first order phase transition of LaFeO{sub 3} from Pbnm to R3{sup Macron }c was observed at 1228{+-}9 K, and a subsequent transition to Pm3{sup Macron }m was extrapolated to occur at 2140{+-}30 K. The stability of the Pbnm and R3{sup Macron }c polymorphs of LaFeO{sub 3} is discussed in terms of the competing enthalpy and entropy of the two crystal polymorphs and the thermal evolution of the polyhedral volume ratio V{sub A}/V{sub B}. - Graphical abstract: Aniostropic thermal evolution of the lattice parameters and phase transition of LaFeO{sub 3}. Highlights: Black-Right-Pointing-Pointer The crystal structure of LaFeO{sub 3} is studied by HTXRD from RT to 1533 K. Black-Right-Pointing-Pointer A non-linear expansion across the Neel temperature is observed for LaFeO{sub 3}. Black-Right-Pointing-Pointer The ratio V{sub A}/V{sub B} is used to rationalize the thermal evolution of the structure.« less

Persistent hydrogen bonding in polymorphic crystal structures.

PubMed

Galek, Peter T A; Fábián, László; Allen, Frank H

2009-02-01

The significance of hydrogen bonding and its variability in polymorphic crystal structures is explored using new automated structural analysis methods. The concept of a chemically equivalent hydrogen bond is defined, which may be identified in pairs of structures, revealing those types of bonds that may persist, or not, in moving from one polymorphic form to another. Their frequency and nature are investigated in 882 polymorphic structures from the Cambridge Structural Database. A new method to compare conformations of equivalent molecules is introduced and applied to derive distinct subsets of conformational and packing polymorphs. The roles of chemical functionality and hydrogen-bond geometry in persistent interactions are systematically explored. Detailed structural comparisons reveal a large majority of persistent hydrogen bonds that are energetically crucial to structural stability.

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.

Crystal Structure and Antitumor Activity of the Novel Zwitterionic Complex of tri-n-Butyltin(IV) with 2-Thiobarbituric Acid

PubMed Central

Balas, Vasilios I.; Hadjikakou, Sotiris K.; Hadjiliadis, Nick; Kourkoumelis, Nikolaos; Light, Mark E.; Hursthouse, Mike; Metsios, Apostolos K.; Karkabounas, Spyros

2008-01-01

A novel tri-n-butyl(IV) derivative of 2-thiobarbituric acid (HTBA) of formula [(n-Bu)3Sn(TBA) H2O] (1) has been synthesized and characterized by elemental analysis and 119Sn-NMR and FT-IR spectroscopic techniques. The crystal structure of complex 1 has been determined by single crystal X-ray diffraction analysis at 120(2) K. The geometry around Sn(IV) is trigonal bipyramidal. Three n-butyl groups and one oxygen atom from a deprotonated 2-thiobarbituric ligand are bonded to the metal center. The geometry is completed with one oxygen from a water molecule. Compound 1 exhibits potent, in vitro, cytotoxicity against sarcoma cancer cells (mesenchymal tissue) from the Wistar rat, polycyclic aromatic hydrocarbons (PAH, benzo[a]pyrene) carcinogenesis. In addition, the inhibition caused by 1, in the rate of lipoxygenase (LOX) catalyzed oxidation reaction of linoleic acid to hyperoxolinoleic acid, has been also kinetically and theoretically studied. The results are compared to that of cisplatin. PMID:18401456

Structural defects caused by swift ions in fluorite single crystals

NASA Astrophysics Data System (ADS)

Assylbayev, Ruslan; Lushchik, Aleksandr; Lushchik, Cheslav; Kudryavtseva, Irina; Shablonin, Evgeni; Vasil'chenko, Evgeni; Akilbekov, Abdirash; Zdorovets, Maxim

2018-01-01

A comparative study of radiation damage caused by the irradiation of oxygen-free calcium fluoride single crystals with ∼GeV 132Xe or 209Bi heavy ions, 100-keV light hydrogen ions (protons) or X-rays at room temperature has been performed. Optical absorption in a wide spectral region from NIR to VUV (1.5-10.5 eV), its dependence on stepwise preheating of the irradiated CaF2 crystals to a certain temperature as well as thermally stimulated luminescence accompanying the main annealing stages have been analyzed. It is shown that in addition to different F-type aggregates, Ca colloids and trifluorine quasi-molecules, complex and temperature stable structural defects responsible for VUV absorption (in particular, the 9.8 eV band) are induced in CaF2 only after irradiation with swift heavy ions. The origin and tentative creation mechanisms of such defects as well as the features of the used irradiation types are considered.

Sulfaguanidine cocrystals: Synthesis, structural characterization and their antibacterial and hemolytic analysis.

PubMed

Abidi, Syed Sibte Asghar; Azim, Yasser; Khan, Shahper Nazeer; Khan, Asad U

2018-02-05

Sulfaguanidine (SG), belongs to the class of sulfonamide drug used as an effective antibiotic. In the present work, using crystal engineering approach two novel cocrystals of SG were synthesized (SG-TBA and SG-PT) with thiobarbutaric acid (TBA) and 1,10-phenanthroline (PT), characterized by solid state techniques viz., powder X-ray diffraction (PXRD), fourier transform infrared spectroscopy (FT-IR), differential scanning calorimetry (DSC) and the crystal structures were determined by single crystal X-ray diffraction studies. A comparative antibacterial activity and hemolytic potential was done on SG drug, coformers and their cocrystals. The tested cocrystals formulations showed almost two fold higher antibacterial activity against the tested strains of bacteria Gram-positive bacteria (S. mutans and E. faecalis) and Gram-negative bacteria (E. coli, K. pneumonia and E. clocae) over SG alone and their coformers. Cocrystal SG-TBA showed better antibacterial activity and reduced hemolysis, thereby, reduced cytotoxicity than SG-PT. Copyright © 2017 Elsevier B.V. All rights reserved.

Synthesis, characterization, and pharmacological studies of ferrocene-1H-1,2,3-triazole hybrids

NASA Astrophysics Data System (ADS)

Haque, Ashanul; Hsieh, Ming-Fa; Hassan, Syed Imran; Haque Faizi, Md. Serajul; Saha, Anannya; Dege, Necmi; Rather, Jahangir Ahmad; Khan, Muhammad S.

2017-10-01

A series of ferrocene-1H-1,2,3-triazole hybrids namely 1-(4-nitrophenyl)-4-ferrocenyl-1H-1,2,3-triazole (1), 1-(4,4‧-dinitro-2-biphenyl)-4-ferrocenyl-1H-1,2,3-triazole (2), 1-(3-chloro-4-fluorophenyl)-4-ferrocenyl-1H-1,2,3-triazole (3), 1-(4-bromophenyl)-4-ferrocenyl-1H-1,2,3-triazole (4) and 1-(2-nitrophenyl)-4-ferrocenyl-1H-1,2,3-triazole (5) were designed and synthesized by copper-catalyzed azide alkyne cycloaddition (CuAAC) reaction. All the new hybrids were characterized by microanalyses, NMR (1H and 13C), UV-vis, IR, ESI-MS and electrochemical techniques. Crystal structure of the compound (3) was solved by single crystal X-ray diffraction method. The structural (single crystal) and spectroscopic (UV-Vis. and IR) properties of the compound 3 have been analyzed and compared by complementary quantum modeling. Hybrids 1-5 exhibited low toxicity and demonstrated neuroprotective effect.

Enhanced magnetic hysteresis in Ni-Mn-Ga single crystal and its influence on magnetic shape memory effect

NASA Astrophysics Data System (ADS)

Heczko, O.; Drahokoupil, J.; Straka, L.

2015-05-01

Enhanced magnetic hysteresis due to boron doping in combination with magnetic shape memory effect in Ni-Mn-Ga single crystal results in new interesting functionality of magnetic shape memory (MSM) alloys such as mechanical demagnetization. In Ni50.0Mn28.5Ga21.5 single crystal, the boron doping increased magnetic coercivity from few Oe to 270 Oe while not affecting the transformation behavior and 10 M martensite structure. However, the magnetic field needed for MSM effect also increased in doped sample. The magnetic behavior is compared to undoped single crystal of similar composition. The evidence from the X-ray diffraction, magnetic domain structure, magnetization loops, and temperature evolution of the magnetic coercivity points out that the enhanced hysteresis is caused by stress-induced anisotropy.

Polyamides based on the renewable monomer, 1,13-tridecane diamine I: synthesis and characterization of nylon 13,T

DOE PAGES

He, Jie; Samanta, Satyabrata; Selvakumar, Sermadurai; ...

2013-06-01

Nylon 13,T was successfully synthesized and chemical composition, thermal properties, crystal structure, and moisture absorption characterized. Melting temperature and glass transition temperature were determined to be 263 °C and 90 °C, respectively, while the equilibrium melting temperature was determined to be 289 °C. Characterization of the crystallization kinetics showed that nylon 13,T exhibits very fast crystallization compared to the industrially important nylons, nylon 6 and nylon 6,6. In addition, the moisture absorption of nylon 13,T was dramatically lower than nylon 6 and nylon 6,6 which is consistent with the much lower amide content of nylon 13,T. The crystal structure wasmore » determined to be pseudohexagonal.« less

Crystal Structure and Substrate Specificity of Drosophila 3,4-Dihydroxyphenylalanine Decarboxylase

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

Han, Q.; Ding, H; Robinson, H

2010-01-01

3,4-Dihydroxyphenylalanine decarboxylase (DDC), also known as aromatic L-amino acid decarboxylase, catalyzes the decarboxylation of a number of aromatic L-amino acids. Physiologically, DDC is responsible for the production of dopamine and serotonin through the decarboxylation of 3,4-dihydroxyphenylalanine and 5-hydroxytryptophan, respectively. In insects, both dopamine and serotonin serve as classical neurotransmitters, neuromodulators, or neurohormones, and dopamine is also involved in insect cuticle formation, eggshell hardening, and immune responses. In this study, we expressed a typical DDC enzyme from Drosophila melanogaster, critically analyzed its substrate specificity and biochemical properties, determined its crystal structure at 1.75 Angstrom resolution, and evaluated the roles residues T82more » and H192 play in substrate binding and enzyme catalysis through site-directed mutagenesis of the enzyme. Our results establish that this DDC functions exclusively on the production of dopamine and serotonin, with no activity to tyrosine or tryptophan and catalyzes the formation of serotonin more efficiently than dopamine. The crystal structure of Drosophila DDC and the site-directed mutagenesis study of the enzyme demonstrate that T82 is involved in substrate binding and that H192 is used not only for substrate interaction, but for cofactor binding of drDDC as well. Through comparative analysis, the results also provide insight into the structure-function relationship of other insect DDC-like proteins.« less

Modeling the intermolecular interactions: molecular structure of N-3-hydroxyphenyl-4-methoxybenzamide.

PubMed

Karabulut, Sedat; Namli, Hilmi; Kurtaran, Raif; Yildirim, Leyla Tatar; Leszczynski, Jerzy

2014-03-01

The title compound, N-3-hydroxyphenyl-4-methoxybenzamide (3) was prepared by the acylation reaction of 3-aminophenol (1) and 4-metoxybenzoylchloride (2) in THF and characterized by ¹H NMR, ¹³C NMR and elemental analysis. Molecular structure of the crystal was determined by single crystal X-ray diffraction and DFT calculations. 3 crystallizes in monoclinic P2₁/c space group. The influence of intermolecular interactions (dimerization and crystal packing) on molecular geometry has been evaluated by calculations performed for three different models; monomer (3), dimer (4) and dimer with added unit cell contacts (5). Molecular structure of 3, 4 and 5 was optimized by applying B3LYP method with 6-31G+(d,p) basis set in gas phase and compared with X-ray crystallographic data including bond lengths, bond angles and selected dihedral angles. It has been concluded that although the crystal packing and dimerization have a minor effect on bond lengths and angles, however, these interactions are important for the dihedral angles and the rotational conformation of aromatic rings. Copyright © 2013 Elsevier Inc. All rights reserved.

Typical intellectual engagement and cognition in old age.

PubMed

Dellenbach, Myriam; Zimprich, Daniel

2008-03-01

Typical Intellectual Engagement (TIE) comprises the preference to engage in cognitively demanding activities and has been proposed as a potential explanatory variable of individual differences in cognitive abilities. Little is known, however, about the factorial structure of TIE, its relations to socio-demographic variables, and its influence on intellectual functioning in old age. In the present study, data of 364 adults (65-81 years) from the Zurich Longitudinal Study on Cognitive Aging (ZULU) were used to investigate the factorial structure of TIE and to examine the hypothesis that TIE is associated more strongly with crystallized intelligence than with fluid intelligence in old age. A measurement model of a second order factor based on a structure of four correlated first order factors (Reading, Problem Solving, Abstract Thinking, and Intellectual Curiosity) evinced an excellent fit. After controlling for age, sex, and formal education, TIE was more strongly associated with crystallized intelligence than with fluid intelligence, comparable to results in younger persons. More detailed analyses showed that this association is mostly defined via Reading and Intellectual Curiosity.

A unified relation for the solid-liquid interface free energy of pure FCC, BCC, and HCP metals

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

Wilson, S. R.; Mendelev, M. I., E-mail: mendelev@ameslab.gov

2016-04-14

We study correlations between the solid-liquid interface (SLI) free energy and bulk material properties (melting temperature, latent heat, and liquid structure) through the determination of SLI free energies for bcc and hcp metals from molecular dynamics (MD) simulation. Values obtained for the bcc metals in this study were compared to values predicted by the Turnbull, Laird, and Ewing relations on the basis of previously published MD simulation data. We found that of these three empirical relations, the Ewing relation better describes the MD simulation data. Moreover, whereas the original Ewing relation contains two constants for a particular crystal structure, wemore » found that the first coefficient in the Ewing relation does not depend on crystal structure, taking a common value for all three phases, at least for the class of the systems described by embedded-atom method potentials (which are considered to provide a reasonable approximation for metals).« less

Regulation of Silk Material Structure by Temperature-Controlled Water Vapor Annealing

PubMed Central

Hu, Xiao; Shmelev, Karen; Sun, Lin; Gil, Eun-Seok; Park, Sang-Hyug; Cebe, Peggy; Kaplan, David L.

2011-01-01

We present a simple and effective method to obtain refined control of the molecular structure of silk biomaterials through physical temperature-controlled water vapor annealing (TCWVA). The silk materials can be prepared with control of crystallinity, from a low content using conditions at 4°C (alpha-helix dominated silk I structure), to highest content of ~60% crystallinity at 100°C (beta-sheet dominated silk II structure). This new physical approach covers the range of structures previously reported to govern crystallization during the fabrication of silk materials, yet offers a simpler, green chemistry, approach with tight control of reproducibility. The transition kinetics, thermal, mechanical, and biodegradation properties of the silk films prepared at different temperatures were investigated and compared by Fourier transform infrared spectroscopy (FTIR), differential scanning calorimetry (DSC), uniaxial tensile studies, and enzymatic degradation studies. The results revealed that this new physical processing method accurately controls structure, in turn providing control of mechanical properties, thermal stability, enzyme degradation rate, and human mesenchymal stem cell interactions. The mechanistic basis for the control is through the temperature controlled regulation of water vapor, to control crystallization. Control of silk structure via TCWVA represents a significant improvement in the fabrication of silk-based biomaterials, where control of structure-property relationships is key to regulating material properties. This new approach to control crystallization also provides an entirely new green approach, avoiding common methods which use organic solvents (methanol, ethanol) or organic acids. The method described here for silk proteins would also be universal for many other structural proteins (and likely other biopolymers), where water controls chain interactions related to material properties. PMID:21425769

Photonic crystal microprisms obtained by carving artificial opals

NASA Astrophysics Data System (ADS)

Fenollosa, R.; Ibisate, M.; Rubio, S.; López, C.; Meseguer, F.; Sánchez-Dehesa, J.

2003-01-01

A method for fabrication of photonic crystal prisms is demonstrated. The procedure is based on micromanipulation techniques, here applied to artificial opals. By means of a microgrinder an opal prism comprising a single crystal (several tens of microns in size) has been carved with three different faces: (111), (110), and (100). The faces were morphologically characterized by scanning electron microscopy and their optical reflectance spectra measured and compared with the theoretical band structure.

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.

Single crystal and optical ceramic multicomponent garnet scintillators: A comparative study

NASA Astrophysics Data System (ADS)

Wu, Yuntao; Luo, Zhaohua; Jiang, Haochuan; Meng, Fang; Koschan, Merry; Melcher, Charles L.

2015-04-01

Multicomponent garnet materials can be made in optical ceramic as well as single crystal form due to their cubic crystal structure. In this work, high-quality Gd3Ga3Al2O12:0.2 at% Ce (GGAG:Ce) single crystal and (Gd,Lu)3Ga3Al2O12:1 at% Ce (GLuGAG:Ce) optical ceramics were fabricated by the Czochralski method and a combination of hot isostatic pressing (HIPing) and annealing treatment, respectively. Under optical and X-ray excitation, the GLuGAG:Ce optical ceramic exhibits a broad Ce3+ transition emission centered at 550 nm, while the emission peak of the GGAG:Ce single crystal is centered at 540 nm. A self-absorption effect in GLuGAG:Ce optical ceramic results in this red-shift of the Ce3+ emission peak compared to that in the GGAG:Ce single crystal. The light yield under 662 keV γ-ray excitation was 45,000±2500 photons/MeV and 48,200±2410 photons/MeV for the GGAG:Ce single crystal and GLuGAG:Ce optical ceramic, respectively. An energy resolution of 7.1% for 662 keV γ-rays was achieved in the GLuGAG:Ce optical ceramic with a Hamamatsu R6231 PMT, which is superior to the value of 7.6% for a GGAG:Ce single crystal. Scintillation decay time measurements under 137Cs irradiation show two exponential decay components of 58 ns (47%) and 504 ns (53%) for the GGAG:Ce single crystal, and 84 ns (76%) and 148 ns (24%) for the GLuGAG:Ce optical ceramic. The afterglow level after X-ray cutoff in the GLuGAG:Ce optical ceramic is at least one order of magnitude lower than in the GGAG:Ce single crystal.

Changes in the Electrical Conductivity and Catalytic Property of Vanadium Iron Borophosphate Glasses with Crystallization

NASA Astrophysics Data System (ADS)

Cha, Jaemin; Jeong, Hwajin; Ryu, Bongki

2018-05-01

Glasses were prepared in the V2O5-P2O5-B2O3 system containing Fe2O3 and were crystallized to examine the changes in the structure, as well as the catalytic and the electrical properties. The glasses were annealed in a graphite mold at a temperature above the glass transition temperature for 1 h and were heat-treated at the crystallization temperature for 1 h, 6 h and 12 h, respectively. Fourier-transform infrared spectroscopy (FTIR) was employed to analyze the structural changes of the V-O bonds after crystallization while the X-ray photoelectron spectroscopy (XPS) analysis indicated a decrease in V5+ and an increase in V4+ amounts. The X-ray diffraction (XRD) analysis indicated that a new crystalline phase of non-stoichiometric Fe0.12V2O5 was formed after 1 h of heat treatment. Structural changes induced by the crystallization were analyzed by determining the molecular volume from the sample density. The conductivity and the catalytic property were examined based on the migration of V and Fe ions exhibiting different valence states with crystallization. Both the conductivity and the catalytic property improved after the samples had been crystallized at the crystallization peak temperature ( T p). Furthermore, as compared to the sample heat treated for 1 h, the conductance and catalytic properties were improved for samples crystallized at T p for 6 h and 12 h.

Influence of tartaric acid on linear-nonlinear optical and electrical properties of KH2PO4 crystal

NASA Astrophysics Data System (ADS)

Baig, M. I.; Anis, Mohd; Muley, G. G.

2017-10-01

KH2PO4 (KDOP) is widely demanded technological crystal for applications in laser driven photonic devices. Therefore, present article is focused to investigate the effect of tartaric acid (TA) on laser induced nonlinear optical properties of KDOP crystal. The optically transparent TA doped KDOP crystal of size 15 × 10 × 04 mm3 has been grown by slow solvent evaporation technique at 35 °C. The structural analysis of pure and TA doped KDOP crystal has been achieved by means of single crystal X-ray diffraction technique. The functional groups of TA doped KDOP crystal has been identified by means of Fourier transform infrared spectral analysis. The UV-visible studies have been performed to determine the optical transparency and evaluate the linear optical constants of pure and TA doped KDOP crystal. The Kurtz-Perry test has been employed to confirm the frequency doubling phenomenon of crystal and the SHG efficiency of TA doped KDOP crystal is found to be 5.68 times higher than that of standard KDP material. The Z-scan technique has been employed to explore the third order nonlinear optical (TONLO) refraction (n2), absorption (β) and susceptibility (χ3) of pure and TA doped KDOP crystal at 632.8 nm. The TA facilitated optical switching in TONLO response of KDOP crystal is found to be an interesting effect to examine. The laser damage threshold of TA doped KDOP crystal has been determined at 1064 nm using the Nd:YAG laser. The comparative electrical analysis on pure and TA doped KDOP crystal has been accomplished by means of dielectric and photoconductivity characterization studies.

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.

Amino Acid-Assisted Incorporation of Dye Molecules within Calcite Crystals.

PubMed

Marzec, Bartosz; Green, David C; Holden, Mark A; Coté, Alexander S; Ihli, Johannes; Khalid, Saba; Kulak, Alexander; Walker, Daniel; Tang, Chiu; Duffy, Dorothy M; Kim, Yi-Yeoun; Meldrum, Fiona C

2018-05-23

Biomineralisation processes invariably occur in the presence of multiple organic additives, which act in combination to give exceptional control over structures and properties. However, few synthetic studies have investigated the cooperative effects of soluble additives. This work addresses this challenge and focuses on the combined effects of amino acids and coloured dye molecules. The experiments demonstrate that strongly coloured calcite crystals only form in the presence of Brilliant Blue R (BBR) and four of the seventeen soluble amino acids, as compared with almost colourless crystals using the dye alone. The active amino acids are identified as those which themselves effectively occlude in calcite, suggesting a mechanism where they can act as chaperones for individual molecules or even aggregates of dyes molecules. These results provide new insight into crystal-additive interactions and suggest a novel strategy for generating materials with target properties. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Thermally evaporated hybrid perovskite for hetero-structured green light-emitting diodes

NASA Astrophysics Data System (ADS)

Mariano, Fabrizio; Listorti, Andrea; Rizzo, Aurora; Colella, Silvia; Gigli, Giuseppe; Mazzeo, Marco

2017-10-01

Thermal evaporation of green-light emitting perovskite (MaPbBr3) films is reported. Morphological studies show that a soft thermal treatment is needed to induce an outstanding crystal growth and film organization. Hetero-structured light-emitting diodes, embedding as-deposited and annealed MAPbBr3 films as active layers, are fabricated and their performances are compared, highlighting that the perovskite evolution is strongly dependent on the growing substrate, too.

Crystal structures of pinoresinol-lariciresinol and phenylcoumaran benzylic ether reductases and their relationship to isoflavone reductases

NASA Technical Reports Server (NTRS)

Min, Tongpil; Kasahara, Hiroyuki; Bedgar, Diana L.; Youn, Buhyun; Lawrence, Paulraj K.; Gang, David R.; Halls, Steven C.; Park, HaJeung; Hilsenbeck, Jacqueline L.; Davin, Laurence B.;

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.

Structures of (2E,5E)-2-(4-cyanobenzylidene)-5-(4-dimethylaminobenzylidene)cyclopentanone and (2E,5E)-2-benzylidene-5-cinnamylidenecyclopentanone

NASA Astrophysics Data System (ADS)

Zoto, Christopher A.; MacDonald, John C.

2017-10-01

The X-ray crystal structures of (2E,5E)-2-(4-cyanobenzylidene)-5-(4-dimethylaminobenzylidene)cyclopentanone (I) and (2E,5E)-2-benzylidene-5-cinnamylidenecyclopentanone (II) are presented, compared to the gas phase structures calculated using density functional theory, and discussed in the context of the photophysical behavior exhibited by I and II. Compound I crystallizes in the triclinic space group P 1 bar with a = 6.8743(2) Å, b = 8.8115(2) Å, c = 14.9664(4) Å, α = 77.135(2)°, β = 81.351(2)°, γ = 80.975(2)°, and Z = 2, and exhibits a planar structure. Compound II crystallizes in the monoclinic space group C2/c with a = 33.4281(10) Å, b = 11.9668(4) Å, c = 7.8031(2) Å, β = 92.785(2)°, and Z = 8, and adopts a nonplanar structure in the solid state and calculated structure.

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

Fluid Physics and Macromolecular Crystal Growth in Microgravity

NASA Technical Reports Server (NTRS)

Helliwell, John R.; Snell, Edward H.; Chayen, Naomi E.; Judge, Russell A.; Boggon, Titus J.; Pusey, M. L.; Rose, M. Franklin (Technical Monitor)

2000-01-01

The first protein crystallization experiment in microgravity was launched in April, 1981 and used Germany's Technologische Experimente unter Schwerelosigkeit (TEXUS 3) sounding rocket. The protein P-galactosidase (molecular weight 465Kda) was chosen as the sample with a liquid-liquid diffusion growth method. A sliding device brought the protein, buffer and salt solution into contact when microgravity was reached. The sounding rocket gave six minutes of microgravity time with a cine camera and schlieren optics used to monitor the experiment, a single growth cell. In microgravity a strictly laminar diffusion process was observed in contrast to the turbulent convection seen on the ground. Several single crystals, approx 100micron in length, were formed in the flight which were of inferior but of comparable visual quality to those grown on the ground over several days. A second experiment using the same protocol but with solutions cooled to -8C (kept liquid with glycerol antifreeze) again showed laminar diffusion. The science of macromolecular structural crystallography involves crystallization of the macromolecule followed by use of the crystal for X-ray diffraction experiments to determine the three dimensional structure of the macromolecule. Neutron protein crystallography is employed for elucidation of H/D exchange and for improved definition of the bound solvent (D20). The structural information enables an understanding of how the molecule functions with important potential for rational drug design, improved efficiency of industrial enzymes and agricultural chemical development. The removal of turbulent convection and sedimentation in microgravity, and the assumption that higher quality crystals will be produced, has given rise to the growing number of crystallization experiments now flown. Many experiments can be flown in a small volume with simple, largely automated, equipment - an ideal combination for a microgravity experiment. The term "protein crystal growth" is often historically used to describe these microgravity experiments. This is somewhat inaccurate as the field involves the study of many varied biological molecules including viruses, proteins, DNA, RNA and complexes of those structures. For this reason we use the term macromolecular crystal growth. In this chapter we review a series of diagnostic microgravity crystal growth experiments carried out principally using the European Space Agency (ESA) Advanced Protein Crystallization Facility (APCF). We also review related research, both experimental and theoretical, on the aspects of microgravity fluid physics that affect microgravity protein crystal growth. Our experiments have revealed some surprises that were not initially expected. We discuss them here in the context of practical lessons learnt and how to maximize the limited microgravity opportunities available.

Anharmonic Normal Mode Analysis of Elastic Network Model Improves the Modeling of Atomic Fluctuations in Protein Crystal Structures

PubMed Central

Zheng, Wenjun

2010-01-01

Abstract Protein conformational dynamics, despite its significant anharmonicity, has been widely explored by normal mode analysis (NMA) based on atomic or coarse-grained potential functions. To account for the anharmonic aspects of protein dynamics, this study proposes, and has performed, an anharmonic NMA (ANMA) based on the Cα-only elastic network models, which assume elastic interactions between pairs of residues whose Cα atoms or heavy atoms are within a cutoff distance. The key step of ANMA is to sample an anharmonic potential function along the directions of eigenvectors of the lowest normal modes to determine the mean-squared fluctuations along these directions. ANMA was evaluated based on the modeling of anisotropic displacement parameters (ADPs) from a list of 83 high-resolution protein crystal structures. Significant improvement was found in the modeling of ADPs by ANMA compared with standard NMA. Further improvement in the modeling of ADPs is attained if the interactions between a protein and its crystalline environment are taken into account. In addition, this study has determined the optimal cutoff distances for ADP modeling based on elastic network models, and these agree well with the peaks of the statistical distributions of distances between Cα atoms or heavy atoms derived from a large set of protein crystal structures. PMID:20550915

Nanocrystallography measurements of early stage synthetic malaria pigment

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

Dilanian, Ruben A.; Streltsov, Victor; Coughlan, Hannah D.

The recent availability of extremely intense, femtosecond X-ray free-electron laser (XFEL) sources has spurred the development of serial femtosecond nanocrystallography (SFX). Here, SFX is used to analyze nanoscale crystals of β-hematin, the synthetic form of hemozoin which is a waste by-product of the malaria parasite. This analysis reveals significant differences in β-hematin data collected during SFX and synchrotron crystallography experiments. To interpret these differences two possibilities are considered: structural differences between the nanocrystal and larger crystalline forms of β-hematin, and radiation damage. Simulation studies show that structural inhomogeneity appears at present to provide a better fit to the experimental data.more » If confirmed, these observations will have implications for designing compounds that inhibit hemozoin formation and suggest that, for some systems at least, additional information may be gained by comparing structures obtained from nanocrystals and macroscopic crystals of the same molecule.« less

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

Dilanian, Ruben A.; Streltsov, Victor; Coughlan, Hannah D.

The recent availability of extremely intense, femtosecond X-ray free-electron laser (XFEL) sources has spurred the development of serial femtosecond nanocrystallography (SFX). Here, SFX is used to analyze nanoscale crystals of β-hematin, the synthetic form of hemozoin which is a waste by-product of the malaria parasite. This analysis reveals significant differences in β-hematin data collected during SFX and synchrotron crystallography experiments. To interpret these differences two possibilities are considered: structural differences between the nanocrystal and larger crystalline forms of β-hematin, and radiation damage. Simulation studies show that structural inhomogeneity appears at present to provide a better fit to the experimental data.more » If confirmed, these observations will have implications for designing compounds that inhibit hemozoin formation and suggest that, for some systems at least, additional information may be gained by comparing structures obtained from nanocrystals and macroscopic crystals of the same molecule.« less

Structural, electronic and optical properties of LiNbO3 using GGA-PBE and TB-mBJ functionals: A DFT study

NASA Astrophysics Data System (ADS)

Arshad Javid, M.; Khan, Zafar Ullah; Mehmood, Zahid; Nabi, Azeem; Hussain, Fayyaz; Imran, M.; Nadeem, Muhammad; Anjum, Naeem

2018-06-01

In the present work, first-principles calculations were performed to obtain the structural, electronic and optical properties of lithium niobate crystal using two exchange-correlation functionals (GGA-PBE and TB-mBJ). The calculated structural parameters were very close to the experimental values. TB-mBJ functional was found to be good when compared to LDA and GGA functionals in case of bandgap energy of 3.715 eV of lithium niobate. It was observed that the upper valence and lower conduction bands consist mainly the O-2p and Nb-4d states, respectively. Furthermore, calculations for real and imaginary parts of frequency-dependent dielectric function 𝜀(ω) of lithium niobate crystal were performed using TD-DFT method. The ordinary refractive index no(ω), extraordinary refractive index ne(ω), its birefringence and absorption peaks in imaginary dielectric function 𝜀2(ω) were also calculated.

Al{sub 4}SiC{sub 4} wurtzite crystal: Structural, optoelectronic, elastic, and piezoelectric properties

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

Pedesseau, L., E-mail: laurent.pedesseau@insa-rennes.fr, E-mail: jacky.even@insa-rennes.fr; Even, J., E-mail: laurent.pedesseau@insa-rennes.fr, E-mail: jacky.even@insa-rennes.fr; Durand, O.

New experimental results supported by theoretical analyses are proposed for aluminum silicon carbide (Al{sub 4}SiC{sub 4}). A state of the art implementation of the density functional theory is used to analyze the experimental crystal structure, the Born charges, the elastic properties, and the piezoelectric properties. The Born charge tensor is correlated to the local bonding environment for each atom. The electronic band structure is computed including self-consistent many-body corrections. Al{sub 4}SiC{sub 4} material properties are compared to other wide band gap wurtzite materials. From a comparison between an ellipsometry study of the optical properties and theoretical results, we conclude thatmore » the Al{sub 4}SiC{sub 4} material has indirect and direct band gap energies of about 2.5 eV and 3.2 eV, respectively.« less

Nanocrystallography measurements of early stage synthetic malaria pigment

DOE PAGES

Dilanian, Ruben A.; Streltsov, Victor; Coughlan, Hannah D.; ...

2017-09-28

The recent availability of extremely intense, femtosecond X-ray free-electron laser (XFEL) sources has spurred the development of serial femtosecond nanocrystallography (SFX). Here, SFX is used to analyze nanoscale crystals of β-hematin, the synthetic form of hemozoin which is a waste by-product of the malaria parasite. This analysis reveals significant differences in β-hematin data collected during SFX and synchrotron crystallography experiments. To interpret these differences two possibilities are considered: structural differences between the nanocrystal and larger crystalline forms of β-hematin, and radiation damage. Simulation studies show that structural inhomogeneity appears at present to provide a better fit to the experimental data.more » If confirmed, these observations will have implications for designing compounds that inhibit hemozoin formation and suggest that, for some systems at least, additional information may be gained by comparing structures obtained from nanocrystals and macroscopic crystals of the same molecule.« less

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

Photonic structures based on hybrid nanocomposites

NASA Astrophysics Data System (ADS)

Husaini, Saima

In this thesis, photonic structures embedded with two types of nanomaterials, (i) quantum dots and (ii) metal nanoparticles are studied. Both of these exhibit optical and electronic properties different from their bulk counterpart due to their nanoscale physical structure. By integrating these nanomaterials into photonic structures, in which the electromagnetic field can be confined and controlled via modification of geometry and composition, we can enhance their linear and nonlinear optical properties to realize functional photonic structures. Before embedding quantum dots into photonic structures, we study the effect of various host matrices and fabrication techniques on the optical properties of the colloidal quantum dots. The two host matrices of interest are SU8 and PMMA. It is shown that the emission properties of the quantum dots are significantly altered in these host matrices (especially SU8) and this is attributed to a high rate of nonradiative quenching of the dots. Furthermore, the effects of fabrication techniques on the optical properties of quantum dots are also investigated. Finally a microdisk resonator embedded with quantum dots is fabricated using soft lithography and luminescence from the quantum dots in the disk is observed. We investigate the absorption and effective index properties of silver nanocomposite films. It is shown that by varying the fill factor of the metal nanoparticles and fabrication parameters such as heating time, we can manipulate the optical properties of the metal nanocomposite. Optimizing these parameters, a silver nanocomposite film with a 7% fill factor is prepared. A one-dimensional photonic crystal consisting of alternating layers of the silver nanocomposite and a polymer (Polymethyl methacrylate) is fabricated using spin coating and its linear and nonlinear optical properties are investigated. Using reflectivity measurements we demonstrate that the one-dimensional silver-nanocomposite-dielectric photonic crystal exhibits a 200% enhancement of the reflection band which is attributed to the interplay between the plasmon resonance of the silver nanoparticles and the Bloch modes of the photonic crystal. Nonlinear optical studies on this one-dimensional silver-nanocomposite-dielectric structure using z-scan measurements are conducted. These measurements indicate a three-fold enhancement in the nonlinear absorption coefficient when compared to a single film of comparable metal composite thickness.

Role of Solvents in Improvement of Dissolution Rate of Drugs: Crystal Habit and Crystal Agglomeration

PubMed Central

Maghsoodi, Maryam

2015-01-01

Crystallization is often used for manufacturing drug substances. Advances of crystallization have achieved control over drug identity and purity, but control over the physical form remains poor. This review discusses the influence of solvents used in crystallization process on crystal habit and agglomeration of crystals with potential implication for dissolution. According to literature it has been known that habit modification of crystals by use of proper solvents may enhance the dissolution properties by changing the size, number and the nature of crystal faces exposed to the dissolution medium. Also, the faster dissolution rate of drug from the agglomerates of crystals compared with the single crystals may be related to porous structure of the agglomerates and consequently their better wettability. It is concluded from this review that in-depth understanding of role of the solvents in crystallization process can be applied to engineering of crystal habit or crystal agglomeration, and predictably dissolution improvement in poorly soluble drugs. PMID:25789214

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.

Characterization of D-glucaric acid using NMR, x-ray crystal structure, and MM3 molecular modeling analyses

USDA-ARS?s Scientific Manuscript database

D-glucaric acid was characterized in solution by comparing NMR spectra from the isotopically unlabeled molecule with those from D-glucaric acid labeled with deuterium or carbon-13 atoms. The NMR studies provided unequivocal assignments for all carbon atoms and non-hydroxyl protons of the molecule. ...

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

Experimental and theoretical studies of the molecular structure of 7-Methyl-3-[(3-methyl-3-mesityl-cyclobutyl]-5-phenyl-5H-thiazolo[3,2-α]pyrimidine-6-carboxylic acid ethyl ester

NASA Astrophysics Data System (ADS)

Acar, Betül; Yilmaz, Ibrahim; Çalışkan, Nezihe; Cukurovali, Alaaddin

2017-07-01

In this work, the title molecule, 7-Methyl-3-[(3-methyl-3-mesityl-cyclobutyl]-5-phenyl-5H-thiazolo[3,2-α]pyrimidine-6-carboxylic acid ethyl ester (C30H34N2O2S1), was synthesized and characterized by FT-IR spectroscopy and single crystal X-ray diffraction. The compound crystallizes in the triclinic space group P21/c. with Z = 4, a = 14.1988(6), b = 19.0893(5), c = 10.1325(4) Å, V = 2674.56(17) A3. The optimized structure parameters of the studied molecule was determined theoretically using HF/6-31G(d) and B3LYP/6-31G(d) methods for ground state, and compared with previously reported experimental findings. The calculated harmonic vibrational frequencies are scaled and they are compared with experimental frequencies obtained by FT-IR spectra. The electronic properties, such as HOMO and LUMO energies, and molecular electrostatic potential (MEP) are also performed.

Raman and IR Spectroscopic Study of Hydrous Pyroxenes

NASA Astrophysics Data System (ADS)

Kung, J.; Li, C.; Stalder, R.; Inoue, T.; Chuang, S.; Balfan-Casanova, N.; Skogby, H.

2017-12-01

Pyroxene group is one of major composed minerals at upper mantle and is nominally anhydrous mineral (NAM), in terms of its crystal chemistry. The analysis of field specimens showed the mantle-derived pyroxene phase containing some amount of hydrogen within crystal structure, the major incorporation mechanism to be as hydroxyl, OH¯, which chemical component treats as `water', H2O. Compared with the other mantle-derived olivine and garnet, the crystal chemistry of pyroxene phases (opx and cpx) is more complex that can result in different OH¯ bonding environments that would greatly affect the geophysics-interested physical properties, for example, elasticity and transport properties. In order to understand how the hydroxyl bonding condition with different composition of opx and cpx in this study, IR and Raman spectroscopies were employed to investigate the lattice modes and hydroxyl-bonding environments with different composition and crystal structures. The studied pyroxene specimens included natural hydrous pyroxenes and synthesized hydrous orthoenstatite (OEN) at high pressure and temperature (4-7 GPa, 1300-1400°C). The measured IR band range was carried out from 2800 to 3600 cm-1 and the Raman range from 50 to 3600 cm-1. The analysis showed that the band of 3600 cm-1 is the major feature in natural opx specimens but its intensity would be varied in different crystal orientation. For synthesized OEN, the number of observed IR band is higher than that reported in previous studies. The common major bands observed in natural cpx are around 3500 cm-1. The Raman measurement of studied specimen is to characterize the variation of Raman mode as function of composition and possible Raman active hydroxyl-related modes. In this meeting the results will be presented and discussed.

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.

Disparate HDV ribozyme crystal structures represent intermediates on a rugged free-energy landscape

PubMed Central

Sripathi, Kamali N.; Tay, Wendy W.; Banáš, Pavel; Otyepka, Michal; Šponer, Jiří; Walter, Nils G.

2014-01-01

The hepatitis delta virus (HDV) ribozyme is a member of the class of small, self-cleaving catalytic RNAs found in a wide range of genomes from HDV to human. Both pre- and post-catalysis (precursor and product) crystal structures of the cis-acting genomic HDV ribozyme have been determined. These structures, together with extensive solution probing, have suggested that a significant conformational change accompanies catalysis. A recent crystal structure of a trans-acting precursor, obtained at low pH and by molecular replacement from the previous product conformation, conforms to the product, raising the possibility that it represents an activated conformer past the conformational change. Here, using fluorescence resonance energy transfer (FRET), we discovered that cleavage of this ribozyme at physiological pH is accompanied by a structural lengthening in magnitude comparable to previous trans-acting HDV ribozymes. Conformational heterogeneity observed by FRET in solution appears to have been removed upon crystallization. Analysis of a total of 1.8 µsec of molecular dynamics (MD) simulations showed that the crystallographically unresolved cleavage site conformation is likely correctly modeled after the hammerhead ribozyme, but that crystal contacts and the removal of several 2′-oxygens near the scissile phosphate compromise catalytic in-line fitness. A cis-acting version of the ribozyme exhibits a more dynamic active site, while a G-1 residue upstream of the scissile phosphate favors poor fitness, allowing us to rationalize corresponding changes in catalytic activity. Based on these data, we propose that the available crystal structures of the HDV ribozyme represent intermediates on an overall rugged RNA folding free-energy landscape. PMID:24854621

Characterization of physicochemical and thermal properties and crystallization behavior of krabok (Irvingia Malayana ) and rambutan seed fats.

PubMed

Sonwai, Sopark; Ponprachanuvut, Punnee

2012-01-01

Fatty acid composition, physicochemical and thermal properties and crystallization behavior of fats extracted from the seeds of krabok (Irvingia Malayana) and rambutan (Nephelium lappaceum L.) trees grown in Thailand were studied and compared with cocoa butter (CB). The krabok seed fat, KSF, consisted of 46.9% lauric and 40.3% myristic acids. It exhibited the highest saponification value and slip melting point but the lowest iodine values. The three fats displayed different crystallization behavior at 25°C. KSF crystallized into a mixture of β' and pseudo-β' structures with a one-step crystallization curve and high solid fat content (SFC). The fat showed simple DSC crystallization and melting thermograms with one distinct peak. The rambutan seed fat, RSF, consisted of 42.5% arachidic and 33.1% oleic acids. Its crystallization behavior was more similar to CB than KSF, displaying a two-step crystallization curve with SFC lower than that of KSF. RSF solidified into a mixture of β' and pseudo-β' before transforming to β after 24 h. The large spherulitic microstructures were observed in both KSF and RSF. According to these results, the Thai KSF and RSF exhibited physicochemical, thermal characteristics and crystallization behavior that could be suitable for specific applications in several areas of the food, cosmetic and pharmaceutical industries.

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.

Three-dimensional electron diffraction as a complementary technique to powder X-ray diffraction for phase identification and structure solution of powders.

PubMed

Yun, Yifeng; Zou, Xiaodong; Hovmöller, Sven; Wan, Wei

2015-03-01

Phase identification and structure determination are important and widely used techniques in chemistry, physics and materials science. Recently, two methods for automated three-dimensional electron diffraction (ED) data collection, namely automated diffraction tomography (ADT) and rotation electron diffraction (RED), have been developed. Compared with X-ray diffraction (XRD) and two-dimensional zonal ED, three-dimensional ED methods have many advantages in identifying phases and determining unknown structures. Almost complete three-dimensional ED data can be collected using the ADT and RED methods. Since each ED pattern is usually measured off the zone axes by three-dimensional ED methods, dynamic effects are much reduced compared with zonal ED patterns. Data collection is easy and fast, and can start at any arbitrary orientation of the crystal, which facilitates automation. Three-dimensional ED is a powerful technique for structure identification and structure solution from individual nano- or micron-sized particles, while powder X-ray diffraction (PXRD) provides information from all phases present in a sample. ED suffers from dynamic scattering, while PXRD data are kinematic. Three-dimensional ED methods and PXRD are complementary and their combinations are promising for studying multiphase samples and complicated crystal structures. Here, two three-dimensional ED methods, ADT and RED, are described. Examples are given of combinations of three-dimensional ED methods and PXRD for phase identification and structure determination over a large number of different materials, from Ni-Se-O-Cl crystals, zeolites, germanates, metal-organic frameworks and organic compounds to intermetallics with modulated structures. It is shown that three-dimensional ED is now as feasible as X-ray diffraction for phase identification and structure solution, but still needs further development in order to be as accurate as X-ray diffraction. It is expected that three-dimensional ED methods will become crucially important in the near future.

Crystallographic site swapping of La3+ ion in BaA'LaTeO6 (A' = Na, K, Rb) double perovskite type compounds: diffraction and photoluminescence evidence for the site swapping.

PubMed

Phatak, R; Gupta, S K; Krishnan, K; Sali, S K; Godbole, S V; Das, A

2014-02-28

Double perovskite type compounds of the formula BaA'LaTeO6 (A' = Na, K, Rb) were synthesized by solid state route and their crystal structures were determined by Rietveld analysis using powder X-ray diffraction and neutron diffraction data. Na compound crystallizes in the monoclinic system with P2₁/n space group whereas, K and Rb compounds crystallize in Fm3m space group. All the three compounds show rock salt type ordering at B site. Crystal structure analysis shows that La ion occupies A site in Na compound whereas, it occupies B site in K and Rb compounds according to the general formula of AA'BB'O6 for a double perovskite type compound. Effect of this crystallographic site swapping of the La ion was also observed in the photoluminescence study by doping Eu(3+) in La(3+) site. The large decrease in the intensity of the electric dipole ((5)D0-(7)F2) transition in the Rb compound compared to the Na compound indicates that Eu(3+) ion resides in the centrosymmetric octahedral environment in the Rb compound.

The effect of ligand substituent on crystal packing: Structural and theoretical studies of two Ga(III) supramolecular compounds

NASA Astrophysics Data System (ADS)

Soleimannejad, Janet; Nazarnia, Esfandiar

2016-07-01

A new Ga(III) supramolecular compound (4,4‧-bipyH2)[Ga(hpydc)2]2·7H2O (2) (where H2hpydc = 4-hydroxy-pyridine-2,6-dicarboxylic acid and 4,4‧-bipy = 4,4‧-bipyridine) was synthesized using the proton transfer reaction. Compound 2 was structurally characterized using single crystal X-ray diffraction, and it was shown that its asymmetric unit consists of two independent anionic Ga(III) complexes, one fully protonated 4,4‧-bipyridine and seven uncoordinated water molecules. In order to understand the effect of pyridine OH substituent on supramolecular interactions and crystal packing, compound 2 was compared with (bipyH2)[Ga(pydc)2]·(H2pydc)·4H2O (1) (where H2pydc = pyridine-2,6-dicarboxylic acid), that does not have an OH group on the pyridine ligand. The Density Functional Theory (DFT) and Natural Bond Orbital (NBO) calculations and also Atoms in Molecules (AIM) analysis were used to analyze the non-covalent interactions in both complexes. The calculation of non-covalent interactions' energy provides a useful means to investigate their effects in the crystal packing.

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.

3D holographic polymer photonic crystal for superprism application

NASA Astrophysics Data System (ADS)

Chen, Jiaqi; Jiang, Wei; Chen, Xiaonan; Wang, Li; Zhang, Sasa; Chen, Ray T.

2007-02-01

Photonic crystal based superprism offers a new way to design new optical components for beam steering and DWDM application. 3D photonic crystals are especially attractive as they could offer more control of the light beam based on the needs. A polygonal prism based holographic fabrication method has been demonstrated for a three-dimensional face-centered-cubic (FCC)-type submicron polymer photonic crystal using SU8 as the photo-sensitive material. Therefore antivibration equipment and complicated optical alignment system are not needed and the requirement for the coherence of the laser source is relaxed compared with the traditional holographic setup. By changing the top-cut prism structure, the polarization of the laser beam, the exposure and development conditions we can achieve different kinds of triclinic or orthorhombic photonic crystals on demand. Special fabrication treatments have been introduced to ensure the survivability of the fabricated large area (cm2) nano-structures. Scanning electron microscopy and diffraction results proved the good uniformity of the fabricated structures. With the proper design of the refraction prism we have achieved a partial bandgap for S+C band (1460-1565nm) in the [111] direction. The transmission and reflection spectra obtained by Fourier transform infrared spectroscopy (FTIR) are in good agreement with simulated band structure. The superprism effects around 1550nm wavelength for the fabricated 3D polymer photonic crystal have been theoretically calculated and such effects can be used for beam steering purpose.

A study of the solvent effect on the morphology of RDX crystal by molecular modeling method.

PubMed

Chen, Gang; Xia, Mingzhu; Lei, Wu; Wang, Fengyun; Gong, Xuedong

2013-12-01

Molecular dynamics simulations have been performed to investigate the effect of acetone solvent on the crystal morphology of RDX. The results show that the growth morphology of RDX crystal in vacuum is dominated by the (111), (020), (200), (002), and (210) faces using the BFDH laws, and (111) face is morphologically the most important. The analysis of surface structures of RDX crystal indicates that (020) face is non-polar, while (210), (111), (002), and (200) faces are polar among which (210) face has the strongest polarity. The interaction between acetone solvent and each RDX crystal face is different, and the order of binding energy on these surfaces is (210) > (111) > (002) > (200) > (020). The analysis of interactions among RDX and acetone molecules reveal that the system nonbond interactions are primary strong van der Waals and electrostatic interactions containing π-hole interactions, the weak hydrogen bond interactions are also existent. The effect of acetone on the growth of RDX crystal can be evaluated by comparing the binding energies of RDX crystalline faces. It can be predicted that compared to that in vacuum, in the process of RDX crystallization from acetone, the morphological importance of (210) face is increased more and (111) face is not the most important among RDX polar surfaces, while the non-polar (020) face probably disappears. The experimentally obtained RDX morphology grown from acetone is in agreement with the theoretical prediction.

Polarization-independent actively tunable colour generation on imprinted plasmonic surfaces

PubMed Central

Franklin, Daniel; Chen, Yuan; Vazquez-Guardado, Abraham; Modak, Sushrut; Boroumand, Javaneh; Xu, Daming; Wu, Shin-Tson; Chanda, Debashis

2015-01-01

Structural colour arising from nanostructured metallic surfaces offers many benefits compared to conventional pigmentation based display technologies, such as increased resolution and scalability of their optical response with structure dimensions. However, once these structures are fabricated their optical characteristics remain static, limiting their potential application. Here, by using a specially designed nanostructured plasmonic surface in conjunction with high birefringence liquid crystals, we demonstrate a tunable polarization-independent reflective surface where the colour of the surface is changed as a function of applied voltage. A large range of colour tunability is achieved over previous reports by utilizing an engineered surface which allows full liquid crystal reorientation while maximizing the overlap between plasmonic fields and liquid crystal. In combination with imprinted structures of varying periods, a full range of colours spanning the entire visible spectrum is achieved, paving the way towards dynamic pixels for reflective displays. PMID:26066375

Diamond family of colloidal supercrystals as phononic metamaterials

NASA Astrophysics Data System (ADS)

Aryana, Kiumars; Zanjani, Mehdi B.

2018-05-01

Colloidal crystals provide a versatile platform for designing phononic metamaterials with exciting applications for sound and heat management. New advances in the synthesis and self-assembly of anisotropic building blocks such as colloidal clusters have expanded the library of available micro- and nano-scale ordered multicomponent structures. Diamond-like supercrystals formed by such clusters and spherical particles are notable examples that include a rich family of crystal symmetries such as diamond, double diamond, zinc-blende, and MgCu2. This work investigates the design of phononic supercrystals by predicting and analyzing phonon transport properties. In addition to size variation and structural diversity, these supercrystals encapsulate different sub-lattice types within one structure. Computational models are used to calculate the effect of various parameters on the phononic spectrum of diamond-like supercrystals. The results show that structures with relatively small or large filling factors (f > 0.65 or f < 0.45) include smaller bandgaps compared to those with medium filling factors (0.65 > f > 0.45). The double diamond and zinc-blende structures render the largest bandgap size compared to the other supercrystals studied in this paper. Additionally, this article discusses the effect of incorporating various configurations of sub-lattices by selecting different material compositions for the building blocks. The results suggest that, for the same structure, there exist multiple phononic variants with drastically different band structures. This study provides a valuable insight for evaluating novel colloidal supercrystals for phononic applications and guides the future experimental work for the synthesis of colloidal structures with desired phononic behavior.

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

PubMed

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

2013-05-01

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

Crystal and NMR Structures of a Peptidomimetic β-Turn That Provides Facile Synthesis of 13-Membered Cyclic Tetrapeptides.

PubMed

Cameron, Alan J; Squire, Christopher J; Edwards, Patrick J B; Harjes, Elena; Sarojini, Vijayalekshmi

2017-12-14

Herein we report the unique conformations adopted by linear and cyclic tetrapeptides (CTPs) containing 2-aminobenzoic acid (2-Abz) in solution and as single crystals. The crystal structure of the linear tetrapeptide H 2 N-d-Leu-d-Phe-2-Abz-d-Ala-COOH (1) reveals a novel planar peptidomimetic β-turn stabilized by three hydrogen bonds and is in agreement with its NMR structure in solution. While CTPs are often synthetically inaccessible or cyclize in poor yield, both 1 and its N-Me-d-Phe analogue (2) adopt pseudo-cyclic frameworks enabling near quantitative conversion to the corresponding CTPs 3 and 4. The crystal structure of the N-methylated peptide (4) is the first reported for a CTP containing 2-Abz and reveals a distinctly planar 13-membered ring, which is also evident in solution. The N-methylation of d-Phe results in a peptide bond inversion compared to the conformation of 3 in solution. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

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

Changes in the quaternary structure of amelogenin when adsorbed onto surfaces

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

Tarasevich, Barbara J.; Lea, Alan S.; Bernt, William

The amelogenin protein is involved in the formation of highly controlled and anisotropic hydroxyapatite crystals in tooth enamel. Amelogenin is unique in that it self assembles to form supramolecular quaternary structures called “nanospheres,” spherical aggregates of amelogenin monomers typically 20-60 nm in diameter. Although nanospheres have been observed in solution, the quaternary structure of amelogenin adsorbed onto surfaces is not well known. A better understanding of the surface structure is of great importance, however, because the function of amelogenin depends on it. We report studies of the adsorption of amelogenin onto self-assembled monolayers (SAMs) containing COOH and CH3 end groupmore » functionality as well as single crystal fluoroapatite (FAP), a biologically relevant surface. The supramolecular structures of the protein in solution as determined by dynamic light scattering (DLS) were compared with the supramolecular structures of the protein physisorbed onto surfaces as studied by atomic force microscopy (AFM). We found that although our solutions contained only nanospheres of narrow size distribution, smaller structures such as monomers and dimers were observed onto both hydrophilic and hydrophobic surfaces. This suggests that amelogenin can adsorb onto surfaces as small structures that peel away or “shed” from the nanospheres that are present in solution.« less

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.

A crystal structure of the bifunctional antibiotic simocyclinone D8, bound to DNA gyrase.

PubMed

Edwards, Marcus J; Flatman, Ruth H; Mitchenall, Lesley A; Stevenson, Clare E M; Le, Tung B K; Clarke, Thomas A; McKay, Adam R; Fiedler, Hans-Peter; Buttner, Mark J; Lawson, David M; Maxwell, Anthony

2009-12-04

Simocyclinones are bifunctional antibiotics that inhibit bacterial DNA gyrase by preventing DNA binding to the enzyme. We report the crystal structure of the complex formed between the N-terminal domain of the Escherichia coli gyrase A subunit and simocyclinone D8, revealing two binding pockets that separately accommodate the aminocoumarin and polyketide moieties of the antibiotic. These are close to, but distinct from, the quinolone-binding site, consistent with our observations that several mutations in this region confer resistance to both agents. Biochemical studies show that the individual moieties of simocyclinone D8 are comparatively weak inhibitors of gyrase relative to the parent compound, but their combination generates a more potent inhibitor. Our results should facilitate the design of drug molecules that target these unexploited binding pockets.

The Effect of Hydrofluoric Acid Etching Duration on the Surface Micromorphology, Roughness, and Wettability of Dental Ceramics

PubMed Central

Ramakrishnaiah, Ravikumar; Alkheraif, Abdulaziz A.; Divakar, Darshan Devang; Matinlinna, Jukka P.; Vallittu, Pekka K.

2016-01-01

The current laboratory study is evaluating the effect of hydrofluoric acid etching duration on the surface characteristics of five silica-based glass ceramics. Changes in the pore pattern, crystal structure, roughness, and wettability were compared and evaluated. Seventy-five rectangularly shaped specimens were cut from each material (IPS e-max™, Dentsply Celtra™, Vita Suprinity™, Vita mark II™, and Vita Suprinity FC™); the sectioned samples were finished, polished, and ultrasonically cleaned. Specimens were randomly assigned into study groups: control (no etching) and four experimental groups (20, 40, 80 and 160 s of etching). The etched surfaces’ microstructure including crystal structure, pore pattern, pore depth, and pore width was studied under a scanning electron microscope, and the surface roughness and wettability were analyzed using a non-contact surface profilometer and a contact angle measuring device, respectively. The results were statistically analyzed using one-way analysis of variance (ANOVA) and the post hoc Tukey’s test. The results showed a significant change in the pore number, pore pattern, crystal structure, surface roughness, and wettability with increased etching duration. Etching for a short time resulted in small pores, and etching for longer times resulted in wider, irregular grooves. A significant increase in the surface roughness and wettability was observed with an increase in the etching duration. The findings also suggested a strong association between the surface roughness and wettability. PMID:27240353

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.

Unique Conformation in a Natural Interruption Sequence of Type XIX Collagen Revealed by Its High-Resolution Crystal Structure.

PubMed

Xu, Tingting; Zhou, Cong-Zhao; Xiao, Jianxi; Liu, Jinsong

2018-02-20

Naturally occurring interruptions in nonfibrillar collagen play key roles in molecular flexibility, collagen degradation, and ligand binding. The structural feature of the interruption sequences and the molecular basis for their functions have not been well studied. Here, we focused on a G5G type natural interruption sequence G-POALO-G from human type XIX collagen, a homotrimer collagen, as this sequence possesses distinct properties compared with those of a pathological similar Gly mutation sequence in collagen mimic peptides. We determined the crystal structures of the host-guest peptide (GPO) 3 -GPOALO-(GPO) 4 to 1.03 Å resolution in two crystal forms. In these structures, the interruption zone brings localized disruptions to the triple helix and introduces a light 6-8° bend with the same directional preference to the whole molecule, which may correspond structurally to the first physiological kink site in type XIX collagen. Furthermore, at the G5G interruption site, the presence of Ala and Leu residues, both with free N-H groups, allows the formation of more direct and water-mediated interchain hydrogen bonds than in the related Gly → Ala structure. These could partly explain the difference in thermal stability between the different interruptions. In addition, our structures provide a detailed view of the dynamic property of such an interrupted zone with respect to hydrogen bonding topology, torsion angles, and helical parameters. Our results, for the first time, also identified the binding of zinc to the end of the triple helix. These findings will shed light on how the interruption sequence influences the conformation of the collagen molecule and provide a structural basis for further functional studies.

Synthesis, crystal structure, superoxide scavenging activity, anticancer and docking studies of novel adamantyl nitroxide derivatives

NASA Astrophysics Data System (ADS)

Zhu, Xiao-he; Sun, Jin; Wang, Shan; Bu, Wei; Yao, Min-na; Gao, Kai; Song, Ying; Zhao, Jin-yi; Lu, Cheng-tao; Zhang, En-hu; Yang, Zhi-fu; Wen, Ai-dong

2016-03-01

A novel adamantyl nitroxide derivatives has been synthesized and characterized by IR, ESI-MS and elemental analysis. Quantum chemical calculations have also been performed to calculate the molecular geometry using density functional theory (B3LYP) with the 6-31G (d,p) basis set. The calculated results showed that the optimized geometry can well reproduce the crystal structure. The antioxidant and antiproliferative activity were evaluated by superoxide (NBT) and MTT assay. The adamantyl nitroxide derivatives exhibited stronger scavenging ability towards O2· - radicals when compared to Vitamin C, and demonstrated a remarked anticancer activity against all the tested cell lines, especially Bel-7404 cells with IC50 of 43.3 μM, compared to the positive control Sorafenib (IC50 = 92.0 μM). The results of molecular docking within EGFR using AutoDock confirmed that the titled compound favorably fitted into the ATP binding site of EGFR and would be a potential anticancer agent.

Comparative Analysis of Hexagonal Solid Silica and Nitro-benzene Filled Hollow Core Photonic Crystal Fiber

NASA Astrophysics Data System (ADS)

Shahiruddin; Singh, Dharmendra K.; Hassan, M. A.

2018-02-01

A comparative study of five ring solid core and nitrobenzene filled hollow core liquid filled photonic crystal fiber (PCF) are presented. Considering the same structure, one is used as solid silica and another one is filled with nitrobenzene in the core. Here the paper elaborates the confinement loss, dispersion properties and birefringence of an index-guiding PCF with asymmetric cladding designed and analyzed by the finite-element method. The proposed structure shows the low confinement loss in case of solid silica, negative dispersion in nitrobenzene filled hollow core PCF and high birefringence in both the cases. The calculated values shows flat zero confinement loss in 0.7 µm to 1.54 µm range, flat zero dispersion is achieved in solid core and -2000 ps/km-nm in nitrobenzene filled hollow core PCF and high birefringence in the range of 10-3 in nitrobenzene filled hollow core PCF. Results show the relative analysis at different air fill fraction.

In-situ USAXS/SAXS Investigation of Tunable Structural Color in Amorphous Photonic Crystals During Electrophoretic Deposition

NASA Astrophysics Data System (ADS)

Bukosky, Scott; Hammons, Joshua; Han, Jinkyu; Freyman, Megan; Lee, Elaine; Cook, Caitlyn; Kuntz, Joshua; Worsley, Marcus; Han, Thomas Yong; Ristenpart, William; Pascall, Andrew

2017-11-01

Amorphous photonic crystals (APCs) formed via electrophoretic deposition (EPD) exhibit non-iridescent, angle-independent, structural colors believed to arise from changes in the particle-particle interactions and inter-particle spacing, representing a potential new paradigm for display technologies. However, particle dynamics on nanometer length scales that govern the displayed color, crystallinity, and other characteristics of the photonic structures, are not well understood. In this work, in-situ USAXS/SAXS studies of three-dimensional colloidal particle arrays were performed in order to identify their structural response to applied external electric fields. These results were compared to simultaneously acquired UV-Vis spectra to tie the overall electrically induced structure of the APCs directly to the observed changes in visible color. The structural evolution of the APCs provides new information regarding the correlation between nano-scale particle-particle interactions and the corresponding optical response. This work was performed under the auspices of the U.S. Department of Energy by Lawrence Livermore National Laboratory under Contract DE-AC52-07NA27344. LLNL-ABS-736068.