Fine refinement of solid-state molecular structures of Leu- and Met-enkephalins by NMR crystallography.

PubMed

Pawlak, Tomasz; Potrzebowski, Marek J

2014-03-27

This paper presents a methodology that allows the fine refinement of the crystal and molecular structure for compounds for which the data deposited in the crystallographic bases are of poor quality. Such species belong to the group of samples with molecular disorder. In the Cambridge Crystallographic Data Center (CCDC), there are approximately 22,000 deposited structures with an R-factor over 10. The powerful methodology we present employs crystal data for Leu-enkephalin (two crystallographic forms) with R-factor values of 14.0 and 8.9 and for Met-enkephalin (one form) with an R-factor of 10.5. NMR crystallography was employed in testing the X-ray data and the quality of the structure refinement. The GIPAW (gauge invariant projector augmented wave) method was used to optimize the coordinates of the enkephalins and to compute NMR parameters. As we reveal, this complementary approach makes it possible to generate a reasonable set of new coordinates that better correlate to real samples. This methodology is general and can be employed in the study of each compound possessing magnetically active nuclei.

Physical nature of ethidium and proflavine interactions with nucleic acid bases in the intercalation plane.

PubMed

Langner, Karol M; Kedzierski, Pawel; Sokalski, W Andrzej; Leszczynski, Jerzy

2006-05-18

On the basis of the crystallographic structures of three nucleic acid intercalation complexes involving ethidium and proflavine, we have analyzed the interaction energies between intercalator chromophores and their four nearest bases, using a hybrid variation-perturbation method at the second-order Møller-Plesset theory level (MP2) with a 6-31G(d,p) basis set. A total MP2 interaction energy minimum precisely reproduces the crystallographic position of the ethidium chromophore in the intercalation plane between UA/AU bases. The electrostatic component constitutes the same fraction of the total energy for all three studied structures. The multipole electrostatic interaction energy, calculated from cumulative atomic multipole moments (CAMMs), was found to converge only after including components above the fifth order. CAMM interaction surfaces, calculated on grids in the intercalation planes of these structures, reasonably reproduce the alignment of intercalators in crystal structures; they exhibit additional minima in the direction of the DNA grooves, however, which also need to be examined at higher theory levels if no crystallographic data are given.

Coupling of Crystal Structure and Magnetism in the Layered, Ferromagnetic Insulator CrI 3

DOE PAGES

McGuire, Michael A.; Dixit, Hemant; Cooper, Valentino R.; ...

2014-12-23

Here, we examine the crystallographic and magnetic properties of single crystals of CrI 3, an easily cleavable, layered and insulating ferromagnet with a Curie temperature of 61 K. Our X-ray diffraction studies reveal a first-order crystallographic phase transition occurring near 210–220 K upon warming, with significant thermal hysteresis. The low-temperature structure is rhombohedral (Rmore » $$\\bar{3}$$, BiI 3-type) and the high-temperature structure is monoclinic (C2/m, AlCl 3-type). Evidence for coupling between the crystallographic and magnetic degrees of freedom in CrI 3 was found; we observed an anomaly in the interlayer spacing at the Curie temperature and an anomaly in the magnetic susceptibility at the structural transition. First-principles calculations reveal the importance of proper treatment of the long-ranged interlayer forces, and van der Waals density functional theory does an excellent job of predicting the crystal structures and their relative stability. Our calculations suggest that the ferromagnetic order found in the bulk material may persist into monolayer form, suggesting that CrI 3 and other chromium trihalides may be promising materials for spintronic and magnetoelectronic research.« less

Recombinant production, crystallization and X-ray crystallographic structure determination of the peptidyl-tRNA hydrolase of Pseudomonas aeruginosa

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

Hughes, Ronny C.; McFeeters, Hana; Coates, Leighton

The peptidyl-tRNA hydrolase enzyme from the pathogenic bacterium Pseudomonas aeruginosa (Pth; EC 3.1.1.29) has been cloned, expressed in Escherichia coli and crystallized for X-ray structural analysis. Suitable crystals were grown using the sitting-drop vapour-diffusion method after one week of incubation against a reservoir solution consisting of 20% polyethylene glycol 4000, 100 mM Tris pH 7.5, 10%(v/v) isopropyl alcohol. The crystals were used to obtain the three-dimensional structure of the native protein at 1.77 Å resolution. The structure was determined by molecular replacement of the crystallographic data processed in space group P6122 with unit-cell parameters a = b = 63.62,c =more » 155.20 Å, α = β = 90, γ = 120°. The asymmetric unit of the crystallographic lattice was composed of a single copy of the enzyme molecule with a 43% solvent fraction, corresponding to a Matthews coefficient of 2.43 Å3 Da-1. The crystallographic structure reported here will serve as the foundation for future structure-guided efforts towards the development of novel small-molecule inhibitors specific to bacterial Pths.« less

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

PubMed

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

2016-01-01

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

Homology‐based hydrogen bond information improves crystallographic structures in the PDB

PubMed Central

van Beusekom, Bart; Touw, Wouter G.; Tatineni, Mahidhar; Somani, Sandeep; Rajagopal, Gunaretnam; Luo, Jinquan; Gilliland, Gary L.; Perrakis, Anastassis

2017-01-01

Abstract The Protein Data Bank (PDB) is the global archive for structural information on macromolecules, and a popular resource for researchers, teachers, and students, amassing more than one million unique users each year. Crystallographic structure models in the PDB (more than 100,000 entries) are optimized against the crystal diffraction data and geometrical restraints. This process of crystallographic refinement typically ignored hydrogen bond (H‐bond) distances as a source of information. However, H‐bond restraints can improve structures at low resolution where diffraction data are limited. To improve low‐resolution structure refinement, we present methods for deriving H‐bond information either globally from well‐refined high‐resolution structures from the PDB‐REDO databank, or specifically from on‐the‐fly constructed sets of homologous high‐resolution structures. Refinement incorporating HOmology DErived Restraints (HODER), improves geometrical quality and the fit to the diffraction data for many low‐resolution structures. To make these improvements readily available to the general public, we applied our new algorithms to all crystallographic structures in the PDB: using massively parallel computing, we constructed a new instance of the PDB‐REDO databank (https://pdb-redo.eu). This resource is useful for researchers to gain insight on individual structures, on specific protein families (as we demonstrate with examples), and on general features of protein structure using data mining approaches on a uniformly treated dataset. PMID:29168245

Homology-based hydrogen bond information improves crystallographic structures in the PDB.

PubMed

van Beusekom, Bart; Touw, Wouter G; Tatineni, Mahidhar; Somani, Sandeep; Rajagopal, Gunaretnam; Luo, Jinquan; Gilliland, Gary L; Perrakis, Anastassis; Joosten, Robbie P

2018-03-01

The Protein Data Bank (PDB) is the global archive for structural information on macromolecules, and a popular resource for researchers, teachers, and students, amassing more than one million unique users each year. Crystallographic structure models in the PDB (more than 100,000 entries) are optimized against the crystal diffraction data and geometrical restraints. This process of crystallographic refinement typically ignored hydrogen bond (H-bond) distances as a source of information. However, H-bond restraints can improve structures at low resolution where diffraction data are limited. To improve low-resolution structure refinement, we present methods for deriving H-bond information either globally from well-refined high-resolution structures from the PDB-REDO databank, or specifically from on-the-fly constructed sets of homologous high-resolution structures. Refinement incorporating HOmology DErived Restraints (HODER), improves geometrical quality and the fit to the diffraction data for many low-resolution structures. To make these improvements readily available to the general public, we applied our new algorithms to all crystallographic structures in the PDB: using massively parallel computing, we constructed a new instance of the PDB-REDO databank (https://pdb-redo.eu). This resource is useful for researchers to gain insight on individual structures, on specific protein families (as we demonstrate with examples), and on general features of protein structure using data mining approaches on a uniformly treated dataset. © 2017 The Protein Society.

Solution NMR and molecular dynamics reveal a persistent alpha helix within the dynamic region of PsbQ from photosystem II of higher plants.

PubMed

Rathner, Petr; Rathner, Adriana; Horničáková, Michaela; Wohlschlager, Christian; Chandra, Kousik; Kohoutová, Jaroslava; Ettrich, Rüdiger; Wimmer, Reinhard; Müller, Norbert

2015-09-01

The extrinsic proteins of photosystem II of higher plants and green algae PsbO, PsbP, PsbQ, and PsbR are essential for stable oxygen production in the oxygen evolving center. In the available X-ray crystallographic structure of higher plant PsbQ residues S14-Y33 are missing. Building on the backbone NMR assignment of PsbQ, which includes this "missing link", we report the extended resonance assignment including side chain atoms. Based on nuclear Overhauser effect spectra a high resolution solution structure of PsbQ with a backbone RMSD of 0.81 Å was obtained from torsion angle dynamics. Within the N-terminal residues 1-45 the solution structure deviates significantly from the X-ray crystallographic one, while the four-helix bundle core found previously is confirmed. A short α-helix is observed in the solution structure at the location where a β-strand had been proposed in the earlier crystallographic study. NMR relaxation data and unrestrained molecular dynamics simulations corroborate that the N-terminal region behaves as a flexible tail with a persistent short local helical secondary structure, while no indications of forming a β-strand are found. © 2015 The Authors. Proteins: Structure, Function, and Bioinformatics Published by Wiley Periodicals, Inc.

Open Access Internet Resources for Nano-Materials Physics Education

NASA Astrophysics Data System (ADS)

Moeck, Peter; Seipel, Bjoern; Upreti, Girish; Harvey, Morgan; Garrick, Will

2006-05-01

Because a great deal of nano-material science and engineering relies on crystalline materials, materials physicists have to provide their own specific contributions to the National Nanotechnology Initiative. Here we briefly review two freely accessible internet-based crystallographic databases, the Nano-Crystallography Database (http://nanocrystallography.research.pdx.edu) and the Crystallography Open Database (http://crystallography.net). Information on over 34,000 full structure determinations are stored in these two databases in the Crystallographic Information File format. The availability of such crystallographic data on the internet in a standardized format allows for all kinds of web-based crystallographic calculations and visualizations. Two examples of which that are dealt with in this paper are: interactive crystal structure visualizations in three dimensions and calculations of lattice-fringe fingerprints for the identification of unknown nanocrystals from their atomic-resolution transmission electron microscopy images.

Local atomic and magnetic structure of dilute magnetic semiconductor (Ba ,K ) (Zn,Mn ) 2As2

NASA Astrophysics Data System (ADS)

Frandsen, Benjamin A.; Gong, Zizhou; Terban, Maxwell W.; Banerjee, Soham; Chen, Bijuan; Jin, Changqing; Feygenson, Mikhail; Uemura, Yasutomo J.; Billinge, Simon J. L.

2016-09-01

We have studied the atomic and magnetic structure of the dilute ferromagnetic semiconductor system (Ba ,K )(Zn ,Mn )2As2 through atomic and magnetic pair distribution function analysis of temperature-dependent x-ray and neutron total scattering data. We detected a change in curvature of the temperature-dependent unit cell volume of the average tetragonal crystallographic structure at a temperature coinciding with the onset of ferromagnetic order. We also observed the existence of a well-defined local orthorhombic structure on a short length scale of ≲5 Å , resulting in a rather asymmetrical local environment of the Mn and As ions. Finally, the magnetic PDF revealed ferromagnetic alignment of Mn spins along the crystallographic c axis, with robust nearest-neighbor ferromagnetic correlations that exist even above the ferromagnetic ordering temperature. We discuss these results in the context of other experiments and theoretical studies on this system.

Crystallographic changes in lead zirconate titanate due to neutron irradiation

DOE PAGES

Henriques, Alexandra; Graham, Joseph T.; Landsberger, Sheldon; ...

2014-11-17

Piezoelectric and ferroelectric materials are useful as the active element in non-destructive monitoring devices for high-radiation areas. Here, crystallographic structural refinement (i.e., the Rietveld method) is used to quantify the type and extent of structural changes in PbZr 0 .5Ti 0 .5O 3 after exposure to a 1 MeV equivalent neutron fluence of 1.7 × 10 15 neutrons/cm 2. The results show a measurable decrease in the occupancy of Pb and O due to irradiation, with O vacancies in the tetragonal phase being created preferentially on one of the two O sites. The results demonstrate a method by which themore » effects of radiation on crystallographic structure may be investigated.« less

Rheed Investigation of Pd/Al Bimetallic System on KCl(001) Substrate

NASA Astrophysics Data System (ADS)

Masek, K.; Moroz, V.; Matolín, V.

Pd/Al alloys have very interesting properties from the point of view of their possible application in heterogeneous catalysis. Preparation of small heteroepitaxial Pd/Al alloy particles opens a new way in studies of the influence of Pd/Al crystallographic structure on the alloy catalytic properties. Pd/Al alloy particles were grown by the molecular beam epitaxy method. Their crystallographical structure was controlled by reflection high energy electron diffraction (RHEED). It was found that Pd deposited on epitaxial 3D Al particles grown on KCl is intermixing with Al. This process is accompanied by the variation of lattice parameter from the Al value to the Pd one.

Surface crystallographic structures of cellulose nanofiber films and overlayers of pentacene

NASA Astrophysics Data System (ADS)

Nakayama, Yasuo; Mori, Toshiaki; Tsuruta, Ryohei; Yamanaka, Soichiro; Yoshida, Koki; Imai, Kento; Koganezawa, Tomoyuki; Hosokai, Takuya

2018-03-01

Cellulose nanofibers or nanocellulose is a promising recently developed biomass and biodegradable material used for various applications. In order to utilize this material as a substrate in organic electronic devices, thorough understanding of the crystallographic structures of the surfaces of the nanocellulose composites and of their interfaces with organic semiconductor molecules is essential. In this work, surface crystallographic structures of nanocellulose films (NCFs) and overlayers of pentacene were investigated by two-dimensional grazing-incidence X-ray diffraction. The NCFs are found to crystallize on solid surfaces with the crystal lattice preserving the same structure of the known bulk phase, whereas distortion of interchain packing toward the surface normal direction is suggested. The pentacene overlayers on the NCFs are found to form the thin-film phase with an in-plane mean crystallite size of over 10 nm.

Development of Specific Inhibitors for Breast Cancer-Associated Variants of ErbB2

DTIC Science & Technology

2015-10-01

Produce ErbB2 structures for drug-lead identification Months 1-12 Milestone #2: Production of computationally-derived pdb files of the structures of...crystallographic structures of the kinase domain of ErbB2 and its close relative EGFR (ErbB1). The kinase domains of ErbB2 and EGFR are highly...homologous as indicated by a sequence identity of ~ 78%. There are two currently available crystallographic structures of the ErbB2 kinase domain. One is

Using cryoEM Reconstruction and Phase Extension to Determine Crystal Structure of Bacteriophage $${\\Phi}$$6 Major Capsid Protein

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

Nemecek, Daniel; Plevka, Pavel; Boura, Evzen

2013-11-29

Bacteriophagemore » $${\\Phi}$$6 is a double-stranded RNA virus that has been extensively studied as a model organism. In this paper we describe structure determination of $${\\Phi}$$6 major capsid protein P1. The protein crystallized in base centered orthorhombic space group C2221. Matthews’s coefficient indicated that the crystals contain from four to seven P1 subunits in the crystallographic asymmetric unit. The self-rotation function had shown presence of fivefold axes of non-crystallographic symmetry in the crystals. Thus, electron density map corresponding to a P1 pentamer was excised from a previously determined cryoEM reconstruction of the $${\\Phi}$$6 procapsid at 7 Å resolution and used as a model for molecular replacement. The phases for reflections at higher than 7 Å resolution were obtained by phase extension employing the fivefold non-crystallographic symmetry present in the crystal. Lastly, the averaged 3.6 Å-resolution electron density map was of sufficient quality to allow model building.« less

Production, purification, crystallization and preliminary X-ray analysis of adeno-associated virus serotype 8

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

Lane, Michael Douglas; Nam, Hyun-Joo; Padron, Eric

2005-06-01

The production, purification, crystallization and preliminary X-ray crystallographic analysis of adeno-associated virus serotype 8 is reported. Adeno-associated viruses (AAVs) are actively being developed for clinical gene-therapy applications and the efficiencies of the vectors could be significantly improved by a detailed understanding of their viral capsid structures and the structural determinants of their tissue-transduction interactions. AAV8 is ∼80% identical to the more widely studied AAV2, but its liver-transduction efficiency is significantly greater than that of AAV2 and other serotypes. The production, purification, crystallization and preliminary X-ray crystallographic analysis of AAV8 viral capsids are reported. The crystals diffract X-rays to 3.0 Åmore » resolution using synchrotron radiation and belong to the hexagonal space group P6{sub 3}22, with unit-cell parameters a = 257.5, c = 443.5 Å. The unit cell contains two viral particles, with ten capsid viral protein monomers per crystallographic asymmetric unit.« less

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

Controlled synthesis of nanostructured molybdenum oxide electrodes for high performance supercapacitor devices

NASA Astrophysics Data System (ADS)

Maheswari, Nallappan; Muralidharan, Gopalan

2017-09-01

Well defined crystallographic and one dimensional morphological structure of molybdenum oxide were successfully synthesized by adjusting the duration of hydrothermal treatment. The prepared molybdenum oxide was examined through XRD, SEM, FTIR, TEM, BET and electrochemical studies. The XRD patterns illustrate that MoOx prepared by variying the hydrothermal reaction time are in different crystallographic structure of MoyOx (Mo8O23 and MoO3). SEM studies reveal the different morphological structures ranging from flake like morphology to nanorods. TEM images confirm the excellent nanorod structure. The nanorod structure ensures good cyclic behaviour with maximum capacitance of 1080 F g-1 at a current density of 2 A g-1. This large capacity of the MoO3 nanostructures enabled fabrication of symmetric and asymmertic supercapacitor devices. The asymmertic device exhibits a maximum specific capacitance of 145 F g-1 at 2 mV s-1 with highest energy density of 38.6 W h kg-1 at 374.7 W kg-1 power density.

Identification, display, and use of symmetry elements in atomic and electronic structure models.

PubMed

Khosrovani, N; Kung, P W; Freeman, C M; Gorman, A M; Kölmel, C M; Levine, S M; Newsam, J M

1999-01-01

Crystallographic symmetry plays an important role in structure determination from diffraction or scattering data, in spectroscopy and in simulations. It is convenient and insightful to integrate the display and use of such symmetry data with data analysis and modeling methods. We outline the integration of a suite of crystallographic algorithms, closely coupled with interactive graphical displays. These include techniques for identifying the unit cell of a solid, for automatically determining space and point group symmetries, for generalized displays of symmetry elements overlaid on structural models, and for construction, editing, and transformation of models subject to symmetry constraints. In addition, electron densities derived from periodic density functional calculations can be symmetrized and displayed with the corresponding symmetry elements. Applications of these various capabilities in crystallographic research are illustrated by topical examples.

A crystallographic perspective on sharing data and knowledge

NASA Astrophysics Data System (ADS)

Bruno, Ian J.; Groom, Colin R.

2014-10-01

The crystallographic community is in many ways an exemplar of the benefits and practices of sharing data. Since the inception of the technique, virtually every published crystal structure has been made available to others. This has been achieved through the establishment of several specialist data centres, including the Cambridge Crystallographic Data Centre, which produces the Cambridge Structural Database. Containing curated structures of small organic molecules, some containing a metal, the database has been produced for almost 50 years. This has required the development of complex informatics tools and an environment allowing expert human curation. As importantly, a financial model has evolved which has, to date, ensured the sustainability of the resource. However, the opportunities afforded by technological changes and changing attitudes to sharing data make it an opportune moment to review current practices.

A general way for quantitative magnetic measurement by transmitted electrons

NASA Astrophysics Data System (ADS)

Song, Dongsheng; Li, Gen; Cai, Jianwang; Zhu, Jing

2016-01-01

EMCD (electron magnetic circular dichroism) technique opens a new door to explore magnetic properties by transmitted electrons. The recently developed site-specific EMCD technique makes it possible to obtain rich magnetic information from the Fe atoms sited at nonequivalent crystallographic planes in NiFe2O4, however it is based on a critical demand for the crystallographic structure of the testing sample. Here, we have further improved and tested the method for quantitative site-specific magnetic measurement applicable for more complex crystallographic structure by using the effective dynamical diffraction effects (general routine for selecting proper diffraction conditions, making use of the asymmetry of dynamical diffraction for design of experimental geometry and quantitative measurement, etc), and taken yttrium iron garnet (Y3Fe5O12, YIG) with more complex crystallographic structure as an example to demonstrate its applicability. As a result, the intrinsic magnetic circular dichroism signals, spin and orbital magnetic moment of iron with site-specific are quantitatively determined. The method will further promote the development of quantitative magnetic measurement with high spatial resolution by transmitted electrons.

Inheritance of Crystallographic Orientation during Lithiation/Delithiation Processes of Single-Crystal α-Fe2O3 Nanocubes in Lithium-Ion Batteries.

PubMed

Ma, Xiaowei; Zhang, Manyu; Liang, Chongyun; Li, Yuesheng; Wu, Jingjing; Che, Renchao

2015-11-04

Iron oxides are very promising anode materials based on conversion reactions for lithium-ion batteries (LIBs). During conversion processes, the crystal structure and composition of the electrode material are drastically changed. Surprisingly, in our study, inheritance of a crystallographic orientation was found during lithiation/delithiation processes of single-crystal α-Fe2O3 nanocubes by ex situ transmission electron microscopy. Single-crystal α-Fe2O3 was first transformed into numerous Fe nanograins embedded in a Li2O matrix, and then the conversion between Fe and FeO nanograins became the main reversible electrochemical reaction for energy storage. Interestingly, these Fe/FeO nanograins had almost the same crystallographic orientation, indicating that the lithiated/delithiated products can inherit the crystallographic orientation of single-crystal α-Fe2O3. This finding is important for understanding the detailed electrochemical conversion processes of iron oxides, and this feature may also exist during lithiation/delithiation processes of other transition-metal oxides.

Strain-Detecting Composite Materials

NASA Technical Reports Server (NTRS)

Wallace, Terryl A. (Inventor); Smith, Stephen W. (Inventor); Piascik, Robert S. (Inventor); Horne, Michael R. (Inventor); Messick, Peter L. (Inventor); Alexa, Joel A. (Inventor); Glaessgen, Edward H. (Inventor); Hailer, Benjamin T. (Inventor)

2016-01-01

A composite material includes a structural material and a shape-memory alloy embedded in the structural material. The shape-memory alloy changes crystallographic phase from austenite to martensite in response to a predefined critical macroscopic average strain of the composite material. In a second embodiment, the composite material includes a plurality of particles of a ferromagnetic shape-memory alloy embedded in the structural material. The ferromagnetic shape-memory alloy changes crystallographic phase from austenite to martensite and changes magnetic phase in response to the predefined critical macroscopic average strain of the composite material. A method of forming a composite material for sensing the predefined critical macroscopic average strain includes providing the shape-memory alloy having an austenite crystallographic phase, changing a size and shape of the shape-memory alloy to thereby form a plurality of particles, and combining the structural material and the particles at a temperature of from about 100-700.degree. C. to form the composite material.

Mineralogical, crystallographic and morphological characteristics of natural kaolins from the Ivory Coast (West Africa)

NASA Astrophysics Data System (ADS)

Sei, J.; Morato, F.; Kra, G.; Staunton, S.; Quiquampoix, H.; Jumas, J. C.; Olivier-Fourcade, J.

2006-10-01

Thirteen clay samples from four deposits in the Ivory Coast (West Africa) were studied using X-ray diffraction, thermogravimetric analysis and chemical analysis. Mineralogical, crystallographic and morphological characteristics of these samples are given. Kaolinite is the principal mineral but other minerals are present in small quantities: illite, quartz, anatase and iron oxides (oxides and oxyhydroxides). The crystallographic, morphological and surface characteristics are influenced by the presence of these impurities. In particular, the presence of iron oxides was associated with reduced structural ordering and thermal stability of kaolinite and increased specific surface area. These clays could be used in the ceramics industry to make tiles and bricks, and also in agronomy as supports for chemical fertilizers or for environmental protection by immobilising potentially toxic waste products.

Ensemble MD simulations restrained via crystallographic data: Accurate structure leads to accurate dynamics

PubMed Central

Xue, Yi; Skrynnikov, Nikolai R

2014-01-01

Currently, the best existing molecular dynamics (MD) force fields cannot accurately reproduce the global free-energy minimum which realizes the experimental protein structure. As a result, long MD trajectories tend to drift away from the starting coordinates (e.g., crystallographic structures). To address this problem, we have devised a new simulation strategy aimed at protein crystals. An MD simulation of protein crystal is essentially an ensemble simulation involving multiple protein molecules in a crystal unit cell (or a block of unit cells). To ensure that average protein coordinates remain correct during the simulation, we introduced crystallography-based restraints into the MD protocol. Because these restraints are aimed at the ensemble-average structure, they have only minimal impact on conformational dynamics of the individual protein molecules. So long as the average structure remains reasonable, the proteins move in a native-like fashion as dictated by the original force field. To validate this approach, we have used the data from solid-state NMR spectroscopy, which is the orthogonal experimental technique uniquely sensitive to protein local dynamics. The new method has been tested on the well-established model protein, ubiquitin. The ensemble-restrained MD simulations produced lower crystallographic R factors than conventional simulations; they also led to more accurate predictions for crystallographic temperature factors, solid-state chemical shifts, and backbone order parameters. The predictions for 15N R1 relaxation rates are at least as accurate as those obtained from conventional simulations. Taken together, these results suggest that the presented trajectories may be among the most realistic protein MD simulations ever reported. In this context, the ensemble restraints based on high-resolution crystallographic data can be viewed as protein-specific empirical corrections to the standard force fields. PMID:24452989

XAS Characterization of the Zn Site of Non-structural Protein 3 (NS3) from Hepatitis C Virus

NASA Astrophysics Data System (ADS)

Ascone, I.; Nobili, G.; Benfatto, M.; Congiu-Castellano, A.

2007-02-01

XANES spectra of non structural protein 3 (NS3) have been calculated using 4 Zn coordination models from three crystallographic structures in the Protein Data Base (PDB): 1DY9, subunit B, 1CU1 subunit A and B, and 1JXP subunit B. Results indicate that XANES is an appropriate tool to distinguish among them. Experimental XANES spectra have been simulated refining crystallographic data. The model obtained by XAS is compared with the PDB models.

PRISM-EM: template interface-based modelling of multi-protein complexes guided by cryo-electron microscopy density maps.

PubMed

Kuzu, Guray; Keskin, Ozlem; Nussinov, Ruth; Gursoy, Attila

2016-10-01

The structures of protein assemblies are important for elucidating cellular processes at the molecular level. Three-dimensional electron microscopy (3DEM) is a powerful method to identify the structures of assemblies, especially those that are challenging to study by crystallography. Here, a new approach, PRISM-EM, is reported to computationally generate plausible structural models using a procedure that combines crystallographic structures and density maps obtained from 3DEM. The predictions are validated against seven available structurally different crystallographic complexes. The models display mean deviations in the backbone of <5 Å. PRISM-EM was further tested on different benchmark sets; the accuracy was evaluated with respect to the structure of the complex, and the correlation with EM density maps and interface predictions were evaluated and compared with those obtained using other methods. PRISM-EM was then used to predict the structure of the ternary complex of the HIV-1 envelope glycoprotein trimer, the ligand CD4 and the neutralizing protein m36.

X-ray crystallographic data for minerals

USGS Publications Warehouse

Robie, Richard A.; Bethke, Philip M.; Toulmin, M.S.; Edwards, Jerry L.

1963-01-01

X-ray crystallographic data are of particular importance to the mineralogist. Beyond the considerations of structural chemistry they provide. one of the most accurate methods for phase and/or compositional determination and for obtaining _the molar volumes and densities of minerals {Robie and Bethke, 1962).

Local atomic and magnetic structure of dilute magnetic semiconductor ( Ba , K ) ( Zn , Mn ) 2 As 2

DOE PAGES

Frandsen, Benjamin A.; Gong, Zizhou; Terban, Maxwell W.; ...

2016-09-06

We studied the atomic and magnetic structure of the dilute ferromagnetic semiconductor system (Ba,K)(Zn,Mn) 2As 2 through atomic and magnetic pair distribution function analysis of temperature-dependent x-ray and neutron total scattering data. Furthermore, we detected a change in curvature of the temperature-dependent unit cell volume of the average tetragonal crystallographic structure at a temperature coinciding with the onset of ferromagnetic order. We also observed the existence of a well-defined local orthorhombic structure on a short length scale of ≲5Å, resulting in a rather asymmetrical local environment of the Mn and As ions. Finally, the magnetic PDF revealed ferromagnetic alignment ofmore » Mn spins along the crystallographic c axis, with robust nearest-neighbor ferromagnetic correlations that exist even above the ferromagnetic ordering temperature. Finally, we discuss these results in the context of other experiments and theoretical studies on this system.« less

Investigation of Parent Austenite Grains from Martensite Structure Using EBSD in a Wear Resistant Steel

PubMed Central

Gyhlesten Back, Jessica; Engberg, Göran

2017-01-01

Crystallographic reconstruction of parent austenite grain boundaries from the martensitic microstructure in a wear resistant steel was carried out using electron backscattered diffraction (EBSD). The present study mainly aims to investigate the parent austenite grains from the martensitic structure in an as-rolled (reference) steel sample and samples obtained by quenching at different cooling rates with corresponding dilatometry. Subsequently, this study is to correlate the nearest cooling rate by the dilatometer which yields a similar orientation relationship and substructure as the reference sample. The Kurdjumov-Sachs orientation relationship was used to reconstruct the parent austenite grain boundaries from the martensite boundaries in both reference and dilatometric samples using EBSD crystallographic data. The parent austenite grain boundaries were successfully evaluated from the EBSD data and the corresponding grain sizes were measured. The parent austenite grain boundaries of the reference sample match the sample quenched at 100 °C/s (CR100). Also the martensite substructures and crystallographic textures are similar in these two samples. The results from hardness measurements show that the reference sample exhibits higher hardness than the CR100 sample due to the presence of carbides in the reference sample. PMID:28772813

Investigation of Parent Austenite Grains from Martensite Structure Using EBSD in a Wear Resistant Steel.

PubMed

Gyhlesten Back, Jessica; Engberg, Göran

2017-04-26

Crystallographic reconstruction of parent austenite grain boundaries from the martensitic microstructure in a wear resistant steel was carried out using electron backscattered diffraction (EBSD). The present study mainly aims to investigate the parent austenite grains from the martensitic structure in an as-rolled (reference) steel sample and samples obtained by quenching at different cooling rates with corresponding dilatometry. Subsequently, this study is to correlate the nearest cooling rate by the dilatometer which yields a similar orientation relationship and substructure as the reference sample. The Kurdjumov-Sachs orientation relationship was used to reconstruct the parent austenite grain boundaries from the martensite boundaries in both reference and dilatometric samples using EBSD crystallographic data. The parent austenite grain boundaries were successfully evaluated from the EBSD data and the corresponding grain sizes were measured. The parent austenite grain boundaries of the reference sample match the sample quenched at 100 °C/s (CR100). Also the martensite substructures and crystallographic textures are similar in these two samples. The results from hardness measurements show that the reference sample exhibits higher hardness than the CR100 sample due to the presence of carbides in the reference sample.

Three sets of crystallographic sub-planar structures in quartz formed by tectonic deformation

NASA Astrophysics Data System (ADS)

Derez, Tine; Pennock, Gill; Drury, Martyn; Sintubin, Manuel

2016-05-01

In quartz, multiple sets of fine planar deformation microstructures that have specific crystallographic orientations parallel to planes with low Miller-Bravais indices are commonly considered as shock-induced planar deformation features (PDFs) diagnostic of shock metamorphism. Using polarized light microscopy, we demonstrate that up to three sets of tectonically induced sub-planar fine extinction bands (FEBs), sub-parallel to the basal, γ, ω, and π crystallographic planes, are common in vein quartz in low-grade tectonometamorphic settings. We conclude that the observation of multiple (2-3) sets of fine scale, closely spaced, crystallographically controlled, sub-planar microstructures is not sufficient to unambiguously distinguish PDFs from tectonic FEBs.

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.

Automatic rebuilding and optimization of crystallographic structures in the Protein Data Bank

PubMed Central

Joosten, Robbie P.; Joosten, Krista; Cohen, Serge X.; Vriend, Gert; Perrakis, Anastassis

2011-01-01

Motivation: Macromolecular crystal structures in the Protein Data Bank (PDB) are a key source of structural insight into biological processes. These structures, some >30 years old, were constructed with methods of their era. With PDB_REDO, we aim to automatically optimize these structures to better fit their corresponding experimental data, passing the benefits of new methods in crystallography on to a wide base of non-crystallographer structure users. Results: We developed new algorithms to allow automatic rebuilding and remodeling of main chain peptide bonds and side chains in crystallographic electron density maps, and incorporated these and further enhancements in the PDB_REDO procedure. Applying the updated PDB_REDO to the oldest, but also to some of the newest models in the PDB, corrects existing modeling errors and brings these models to a higher quality, as judged by standard validation methods. Availability and Implementation: The PDB_REDO database and links to all software are available at http://www.cmbi.ru.nl/pdb_redo. Contact: r.joosten@nki.nl; a.perrakis@nki.nl Supplementary Information: Supplementary data are available at Bioinformatics online. PMID:22034521

Development of machine learning models to predict inhibition of 3-dehydroquinate dehydratase.

PubMed

de Ávila, Maurício Boff; de Azevedo, Walter Filgueira

2018-04-20

In this study, we describe the development of new machine learning models to predict inhibition of the enzyme 3-dehydroquinate dehydratase (DHQD). This enzyme is the third step of the shikimate pathway and is responsible for the synthesis of chorismate, which is a natural precursor of aromatic amino acids. The enzymes of shikimate pathway are absent in humans, which make them protein targets for the design of antimicrobial drugs. We focus our study on the crystallographic structures of DHQD in complex with competitive inhibitors, for which experimental inhibition constant data is available. Application of supervised machine learning techniques was able to elaborate a robust DHQD-targeted model to predict binding affinity. Combination of high-resolution crystallographic structures and binding information indicates that the prevalence of intermolecular electrostatic interactions between DHQD and competitive inhibitors is of pivotal importance for the binding affinity against this enzyme. The present findings can be used to speed up virtual screening studies focused on the DHQD structure. © 2018 John Wiley & Sons A/S.

The X-ray system of crystallographic programs for any computer having a PIDGIN FORTRAN compiler

NASA Technical Reports Server (NTRS)

Stewart, J. M.; Kruger, G. J.; Ammon, H. L.; Dickinson, C.; Hall, S. R.

1972-01-01

A manual is presented for the use of a library of crystallographic programs. This library, called the X-ray system, is designed to carry out the calculations required to solve the structure of crystals by diffraction techniques. It has been implemented at the University of Maryland on the Univac 1108. It has, however, been developed and run on a variety of machines under various operating systems. It is considered to be an essentially machine independent library of applications programs. The report includes definition of crystallographic computing terms, program descriptions, with some text to show their application to specific crystal problems, detailed card input descriptions, mass storage file structure and some example run streams.

Magnetic transition temperatures follow crystallographic symmetry in Samarium under high-pressures and low-temperatures

DOE PAGES

Vohra, Yogesh K.; Tsoi, Georgiy M.; Johnson, Craig R.

2016-12-21

Magnetic ordering temperatures in rare earth metal samarium (Sm) have been studied using an ultrasensitive electrical transport measurement technique in a designer diamond anvil cell to high-pressure up to 47 GPa and low-temperature to 10 K. The two magnetic transitions at 106 K and 14 K in the α-Sm phase, attributed to antiferromagnetic ordering on hexagonal and cubic layers respectively, collapse in to one magnetic transition near 10 GPa when Sm assumes a double hexagonal close packed (dhcp) phase. On further increase in pressure above 34 GPa, the magnetic transitions split again as Sm adopts a hexagonal-hP3 structure indicating differentmore » magnetic transition temperatures for different crystallographic sites. A model for magnetic ordering for the hexagonal-hP3 phase in samarium has been proposed based on the experimental data. The magnetic transition temperatures closely follow the crystallographic symmetry during α-Sm → dhcp → fcc/dist.fcc → hP3 structure sequence at high-pressures and low-temperatures.« less

Magnetic transition temperatures follow crystallographic symmetry in Samarium under high-pressures and low-temperatures

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

Vohra, Yogesh K.; Tsoi, Georgiy M.; Johnson, Craig R.

Magnetic ordering temperatures in rare earth metal samarium (Sm) have been studied using an ultrasensitive electrical transport measurement technique in a designer diamond anvil cell to high-pressure up to 47 GPa and low-temperature to 10 K. The two magnetic transitions at 106 K and 14 K in the α-Sm phase, attributed to antiferromagnetic ordering on hexagonal and cubic layers respectively, collapse in to one magnetic transition near 10 GPa when Sm assumes a double hexagonal close packed (dhcp) phase. On further increase in pressure above 34 GPa, the magnetic transitions split again as Sm adopts a hexagonal-hP3 structure indicating differentmore » magnetic transition temperatures for different crystallographic sites. A model for magnetic ordering for the hexagonal-hP3 phase in samarium has been proposed based on the experimental data. The magnetic transition temperatures closely follow the crystallographic symmetry during α-Sm → dhcp → fcc/dist.fcc → hP3 structure sequence at high-pressures and low-temperatures.« less

Magnetic transition temperatures follow crystallographic symmetry in samarium under high-pressures and low-temperatures

NASA Astrophysics Data System (ADS)

Johnson, Craig R.; Tsoi, Georgiy M.; Vohra, Yogesh K.

2017-02-01

Magnetic ordering temperatures in rare earth metal samarium (Sm) have been studied using an ultrasensitive electrical transport measurement technique in a designer diamond anvil cell to high-pressure up to 47 GPa and low-temperature to 10 K. The two magnetic transitions at 106 K and 14 K in the α-Sm phase, attributed to antiferromagnetic ordering on hexagonal and cubic layers respectively, collapse in to one magnetic transition near 10 GPa when Sm assumes a double hexagonal close packed (dhcp) phase. On further increase in pressure above 34 GPa, the magnetic transitions split again as Sm adopts a hexagonal-hP3 structure indicating different magnetic transition temperatures for different crystallographic sites. A model for magnetic ordering for the hexagonal-hP3 phase in samarium has been proposed based on the experimental data. The magnetic transition temperatures closely follow the crystallographic symmetry during α-Sm  →  dhcp  →  fcc/dist.fcc  →  hP3 structure sequence at high-pressures and low-temperatures.

Magnetic transition temperatures follow crystallographic symmetry in samarium under high-pressures and low-temperatures.

PubMed

Johnson, Craig R; Tsoi, Georgiy M; Vohra, Yogesh K

2017-02-15

Magnetic ordering temperatures in rare earth metal samarium (Sm) have been studied using an ultrasensitive electrical transport measurement technique in a designer diamond anvil cell to high-pressure up to 47 GPa and low-temperature to 10 K. The two magnetic transitions at 106 K and 14 K in the α-Sm phase, attributed to antiferromagnetic ordering on hexagonal and cubic layers respectively, collapse in to one magnetic transition near 10 GPa when Sm assumes a double hexagonal close packed (dhcp) phase. On further increase in pressure above 34 GPa, the magnetic transitions split again as Sm adopts a hexagonal-hP3 structure indicating different magnetic transition temperatures for different crystallographic sites. A model for magnetic ordering for the hexagonal-hP3 phase in samarium has been proposed based on the experimental data. The magnetic transition temperatures closely follow the crystallographic symmetry during α-Sm  →  dhcp  →  fcc/dist.fcc  →  hP3 structure sequence at high-pressures and low-temperatures.

Tunable and laser-reconfigurable 2D heterocrystals obtained by epitaxial stacking of crystallographically incommensurate Bi2Se3 and MoS2 atomic layers

PubMed Central

Vargas, Anthony; Liu, Fangze; Lane, Christopher; Rubin, Daniel; Bilgin, Ismail; Hennighausen, Zachariah; DeCapua, Matthew; Bansil, Arun; Kar, Swastik

2017-01-01

Vertical stacking is widely viewed as a promising approach for designing advanced functionalities using two-dimensional (2D) materials. Combining crystallographically commensurate materials in these 2D stacks has been shown to result in rich new electronic structure, magnetotransport, and optical properties. In this context, vertical stacks of crystallographically incommensurate 2D materials with well-defined crystallographic order are a counterintuitive concept and, hence, fundamentally intriguing. We show that crystallographically dissimilar and incommensurate atomically thin MoS2 and Bi2Se3 layers can form rotationally aligned stacks with long-range crystallographic order. Our first-principles theoretical modeling predicts heterocrystal electronic band structures, which are quite distinct from those of the parent crystals, characterized with an indirect bandgap. Experiments reveal striking optical changes when Bi2Se3 is stacked layer by layer on monolayer MoS2, including 100% photoluminescence (PL) suppression, tunable transmittance edge (1.1→0.75 eV), suppressed Raman, and wide-band evolution of spectral transmittance. Disrupting the interface using a focused laser results in a marked the reversal of PL, Raman, and transmittance, demonstrating for the first time that in situ manipulation of interfaces can enable “reconfigurable” 2D materials. We demonstrate submicrometer resolution, “laser-drawing” and “bit-writing,” and novel laser-induced broadband light emission in these heterocrystal sheets. PMID:28740860

Tiopronin Gold Nanoparticle Precursor Forms Aurophilic Ring Tetramer

PubMed Central

Simpson, Carrie A.; Farrow, Christopher L.; Tian, Peng; Billinge, Simon J.L.; Huffman, Brian J.; Harkness, Kellen M.; Cliffel, David E.

2010-01-01

In the two step synthesis of thiolate-monolayer protected clusters (MPCs), the first step of the reaction is a mild reduction of gold(III) by thiols that generates gold(I) thiolate complexes as intermediates. Using tiopronin (Tio) as the thiol reductant, the characterization of the intermediate Au4Tio4 complex was accomplished with various analytical and structural techniques. Nuclear magnetic resonance (NMR), elemental analysis, thermogravimetric analysis (TGA), and matrix-assisted laser desorption/ionization-mass spectrometry (MALDI-MS) were all consistent with a cyclic gold(I)-thiol tetramer structure, and final structural analysis was gathered through the use of powder diffraction and pair distribution functions (PDF). Crystallographic data has proved challenging for almost all previous gold(I)-thiolate complexes. Herein, a novel characterization technique when combined with standard analytical assessment to elucidate structure without crystallographic data proved invaluable to the study of these complexes. This in conjunction with other analytical techniques, in particular mass spectrometry, can elucidate a structure when crystallographic data is unavailable. In addition, luminescent properties provided evidence of aurophilicity within the molecule. The concept of aurophilicity has been introduced to describe a select group of gold-thiolate structures, which possess unique characteristics, mainly red photoluminescence and a distinct Au-Au intramolecular distance indicating a weak metal-metal bond as also evidenced by the structural model of the tetramer. Significant features of both the tetrameric and aurophilic properties of the intermediate gold(I) tiopronin complex are retained after borohydride reduction to form the MPC, including gold(I) tiopronin partial rings as capping motifs, or “staples”, and weak red photoluminescence that extends into the Near Infrared region. PMID:21067183

Insights into Fanconi Anaemia from the structure of human FANCE

PubMed Central

Nookala, Ravi K.; Hussain, Shobbir; Pellegrini, Luca

2007-01-01

Fanconi Anaemia (FA) is a cancer predisposition disorder characterized by spontaneous chromosome breakage and high cellular sensitivity to genotoxic agents. In response to DNA damage, a multi-subunit assembly of FA proteins, the FA core complex, monoubiquitinates the downstream FANCD2 protein. The FANCE protein plays an essential role in the FA process of DNA repair as the FANCD2-binding component of the FA core complex. Here we report a crystallographic and biological study of human FANCE. The first structure of a FA protein reveals the presence of a repeated helical motif that provides a template for the structural rationalization of other proteins defective in Fanconi Anaemia. The portion of FANCE defined by our crystallographic analysis is sufficient for interaction with FANCD2, yielding structural information into the mode of FANCD2 recruitment to the FA core complex. Disease-associated mutations disrupt the FANCE–FANCD2 interaction, providing structural insight into the molecular mechanisms of FA pathogenesis. PMID:17308347

You are lost without a map: Navigating the sea of protein structures.

PubMed

Lamb, Audrey L; Kappock, T Joseph; Silvaggi, Nicholas R

2015-04-01

X-ray crystal structures propel biochemistry research like no other experimental method, since they answer many questions directly and inspire new hypotheses. Unfortunately, many users of crystallographic models mistake them for actual experimental data. Crystallographic models are interpretations, several steps removed from the experimental measurements, making it difficult for nonspecialists to assess the quality of the underlying data. Crystallographers mainly rely on "global" measures of data and model quality to build models. Robust validation procedures based on global measures now largely ensure that structures in the Protein Data Bank (PDB) are largely correct. However, global measures do not allow users of crystallographic models to judge the reliability of "local" features in a region of interest. Refinement of a model to fit into an electron density map requires interpretation of the data to produce a single "best" overall model. This process requires inclusion of most probable conformations in areas of poor density. Users who misunderstand this can be misled, especially in regions of the structure that are mobile, including active sites, surface residues, and especially ligands. This article aims to equip users of macromolecular models with tools to critically assess local model quality. Structure users should always check the agreement of the electron density map and the derived model in all areas of interest, even if the global statistics are good. We provide illustrated examples of interpreted electron density as a guide for those unaccustomed to viewing electron density. Copyright © 2014 Elsevier B.V. All rights reserved.

Data-driven high-throughput prediction of the 3-D structure of small molecules: review and progress. A response to the letter by the Cambridge Crystallographic Data Centre.

PubMed

Baldi, Pierre

2011-12-27

A response is presented to sentiments expressed in "Data-Driven High-Throughput Prediction of the 3-D Structure of Small Molecules: Review and Progress. A Response from The Cambridge Crystallographic Data Centre", recently published in the Journal of Chemical Information and Modeling, (1) which may give readers a misleading impression regarding significant impediments to scientific research posed by the CCDC.

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

Discovery of novel DAPY-IAS hybrid derivatives as potential HIV-1 inhibitors using molecular hybridization based on crystallographic overlays.

PubMed

Huang, Boshi; Wang, Xueshun; Liu, Xinhao; Chen, Zihui; Li, Wanzhuo; Sun, Songkai; Liu, Huiqing; Daelemans, Dirk; De Clercq, Erik; Pannecouque, Christophe; Zhan, Peng; Liu, Xinyong

2017-08-15

Crystallographic overlap studies and pharmacophoric analysis indicated that diarylpyrimidine (DAPY)-based HIV-1 NNRTIs showed a similar binding mode and pharmacophoric features as indolylarylsulfones (IASs), another class of potent NNRTIs. Thus, a novel series of DAPY-IAS hybrid derivatives were identified as newer NNRTIs using structure-based molecular hybridization. Some target compounds exhibited moderate activities against HIV-1 IIIB strain, among which the two most potent inhibitors possessed EC 50 values of 1.48μM and 1.61μM, respectively. They were much potent than the reference drug ddI (EC 50 =76.0μM) and comparable to 3TC (EC 50 =2.54μM). Compound 7a also exhibited the favorable selectivity index (SI=80). Preliminary structure-activity relationships (SARs), structure-cytotoxicity relationships, molecular modeling studies, and in silico calculation of physicochemical properties of these new inhibitors were also discussed. Copyright © 2017 Elsevier Ltd. All rights reserved.

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

PubMed Central

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

2011-01-01

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

From direct-space discrepancy functions to crystallographic least squares.

PubMed

Giacovazzo, Carmelo

2015-01-01

Crystallographic least squares are a fundamental tool for crystal structure analysis. In this paper their properties are derived from functions estimating the degree of similarity between two electron-density maps. The new approach leads also to modifications of the standard least-squares procedures, potentially able to improve their efficiency. The role of the scaling factor between observed and model amplitudes is analysed: the concept of unlocated model is discussed and its scattering contribution is combined with that arising from the located model. Also, the possible use of an ancillary parameter, to be associated with the classical weight related to the variance of the observed amplitudes, is studied. The crystallographic discrepancy factors, basic tools often combined with least-squares procedures in phasing approaches, are analysed. The mathematical approach here described includes, as a special case, the so-called vector refinement, used when accurate estimates of the target phases are available.

Structures of endothiapepsin-fragment complexes from crystallographic fragment screening using a novel, diverse and affordable 96-compound fragment library.

PubMed

Huschmann, Franziska U; Linnik, Janina; Sparta, Karine; Ühlein, Monika; Wang, Xiaojie; Metz, Alexander; Schiebel, Johannes; Heine, Andreas; Klebe, Gerhard; Weiss, Manfred S; Mueller, Uwe

2016-05-01

Crystallographic screening of the binding of small organic compounds (termed fragments) to proteins is increasingly important for medicinal chemistry-oriented drug discovery. To enable such experiments in a widespread manner, an affordable 96-compound library has been assembled for fragment screening in both academia and industry. The library is selected from already existing protein-ligand structures and is characterized by a broad ligand diversity, including buffer ingredients, carbohydrates, nucleotides, amino acids, peptide-like fragments and various drug-like organic compounds. When applied to the model protease endothiapepsin in a crystallographic screening experiment, a hit rate of nearly 10% was obtained. In comparison to other fragment libraries and considering that no pre-screening was performed, this hit rate is remarkably high. This demonstrates the general suitability of the selected compounds for an initial fragment-screening campaign. The library composition, experimental considerations and time requirements for a complete crystallographic fragment-screening campaign are discussed as well as the nine fully refined obtained endothiapepsin-fragment structures. While most of the fragments bind close to the catalytic centre of endothiapepsin in poses that have been observed previously, two fragments address new sites on the protein surface. ITC measurements show that the fragments bind to endothiapepsin with millimolar affinity.

Structures of endothiapepsin–fragment complexes from crystallographic fragment screening using a novel, diverse and affordable 96-compound fragment library

PubMed Central

Huschmann, Franziska U.; Linnik, Janina; Sparta, Karine; Ühlein, Monika; Wang, Xiaojie; Metz, Alexander; Schiebel, Johannes; Heine, Andreas; Klebe, Gerhard; Weiss, Manfred S.; Mueller, Uwe

2016-01-01

Crystallographic screening of the binding of small organic compounds (termed fragments) to proteins is increasingly important for medicinal chemistry-oriented drug discovery. To enable such experiments in a widespread manner, an affordable 96-compound library has been assembled for fragment screening in both academia and industry. The library is selected from already existing protein–ligand structures and is characterized by a broad ligand diversity, including buffer ingredients, carbohydrates, nucleotides, amino acids, peptide-like fragments and various drug-like organic compounds. When applied to the model protease endothiapepsin in a crystallographic screening experiment, a hit rate of nearly 10% was obtained. In comparison to other fragment libraries and considering that no pre-screening was performed, this hit rate is remarkably high. This demonstrates the general suitability of the selected compounds for an initial fragment-screening campaign. The library composition, experimental considerations and time requirements for a complete crystallographic fragment-screening campaign are discussed as well as the nine fully refined obtained endothiapepsin–fragment structures. While most of the fragments bind close to the catalytic centre of endothiapepsin in poses that have been observed previously, two fragments address new sites on the protein surface. ITC measurements show that the fragments bind to endothiapepsin with millimolar affinity. PMID:27139825

Defect structure of web silicon ribbon

NASA Technical Reports Server (NTRS)

Cunningham, B.; Strunk, H.; Ast, D.

1980-01-01

The results of a preliminary study of two dendritic web samples are presented. The structure and electrical activity of the defects in the silicon webs were studied. Optical microscopy of chemically etched specimens was used to determine dislocation densities. Samples were mechanically polished, then Secco etched for approximately 5 minutes. High voltage transmission electron microscopy was used to characterize the crystallographic nature of the defects.

Crystallographic Mapping of Guided Nanowires by Second Harmonic Generation Polarimetry

PubMed Central

2017-01-01

The growth of horizontal nanowires (NWs) guided by epitaxial and graphoepitaxial relations with the substrate is becoming increasingly attractive owing to the possibility of controlling their position, direction, and crystallographic orientation. In guided NWs, as opposed to the extensively characterized vertically grown NWs, there is an increasing need for understanding the relation between structure and properties, specifically the role of the epitaxial relation with the substrate. Furthermore, the uniformity of crystallographic orientation along guided NWs and over the substrate has yet to be checked. Here we perform highly sensitive second harmonic generation (SHG) polarimetry of polar and nonpolar guided ZnO NWs grown on R-plane and M-plane sapphire. We optically map large areas on the substrate in a nondestructive way and find that the crystallographic orientations of the guided NWs are highly selective and specific for each growth direction with respect to the substrate lattice. In addition, we perform SHG polarimetry along individual NWs and find that the crystallographic orientation is preserved along the NW in both polar and nonpolar NWs. While polar NWs show highly uniform SHG along their axis, nonpolar NWs show a significant change in the local nonlinear susceptibility along a few micrometers, reflected in a reduction of 40% in the ratio of the SHG along different crystal axes. We suggest that these differences may be related to strain accumulation along the nonpolar wires. We find SHG polarimetry to be a powerful tool to study both selectivity and uniformity of crystallographic orientations of guided NWs with different epitaxial relations. PMID:28094977

Crystallographic Mapping of Guided Nanowires by Second Harmonic Generation Polarimetry.

PubMed

Neeman, Lior; Ben-Zvi, Regev; Rechav, Katya; Popovitz-Biro, Ronit; Oron, Dan; Joselevich, Ernesto

2017-02-08

The growth of horizontal nanowires (NWs) guided by epitaxial and graphoepitaxial relations with the substrate is becoming increasingly attractive owing to the possibility of controlling their position, direction, and crystallographic orientation. In guided NWs, as opposed to the extensively characterized vertically grown NWs, there is an increasing need for understanding the relation between structure and properties, specifically the role of the epitaxial relation with the substrate. Furthermore, the uniformity of crystallographic orientation along guided NWs and over the substrate has yet to be checked. Here we perform highly sensitive second harmonic generation (SHG) polarimetry of polar and nonpolar guided ZnO NWs grown on R-plane and M-plane sapphire. We optically map large areas on the substrate in a nondestructive way and find that the crystallographic orientations of the guided NWs are highly selective and specific for each growth direction with respect to the substrate lattice. In addition, we perform SHG polarimetry along individual NWs and find that the crystallographic orientation is preserved along the NW in both polar and nonpolar NWs. While polar NWs show highly uniform SHG along their axis, nonpolar NWs show a significant change in the local nonlinear susceptibility along a few micrometers, reflected in a reduction of 40% in the ratio of the SHG along different crystal axes. We suggest that these differences may be related to strain accumulation along the nonpolar wires. We find SHG polarimetry to be a powerful tool to study both selectivity and uniformity of crystallographic orientations of guided NWs with different epitaxial relations.

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

The quaternary architecture of RARβ–RXRα heterodimer facilitates domain–domain signal transmission

DOE PAGES

Chandra, Vikas; Wu, Dalei; Li, Sheng; ...

2017-10-11

Assessing the physical connections and allosteric communications in multi-domain nuclear receptor (NR) polypeptides has remained challenging, with few crystal structures available to show their overall structural organizations. Here we report the quaternary architecture of multi-domain retinoic acid receptor beta-retinoic X receptor alpha (RAR beta-RXR alpha) heterodimer bound to DNA, ligands and coactivator peptides, examined through crystallographic, hydrogen-deuterium exchange mass spectrometry, mutagenesis and functional studies. The RAR beta ligand-binding domain (LBD) and DNA-binding domain (DBD) are physically connected to foster allosteric signal transmission between them. Direct comparisons among all the multi-domain NRs studied crystallographically to date show significant variations within theirmore » quaternary architectures, rather than a common architecture adhering to strict rules. RXR remains flexible and adaptive by maintaining loosely organized domains, while its hetero-dimerization partners use a surface patch on their LBDs to form domain-domain interactions with DBDs.« less

The quaternary architecture of RARβ–RXRα heterodimer facilitates domain–domain signal transmission

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

Chandra, Vikas; Wu, Dalei; Li, Sheng

Assessing the physical connections and allosteric communications in multi-domain nuclear receptor (NR) polypeptides has remained challenging, with few crystal structures available to show their overall structural organizations. Here we report the quaternary architecture of multi-domain retinoic acid receptor beta-retinoic X receptor alpha (RAR beta-RXR alpha) heterodimer bound to DNA, ligands and coactivator peptides, examined through crystallographic, hydrogen-deuterium exchange mass spectrometry, mutagenesis and functional studies. The RAR beta ligand-binding domain (LBD) and DNA-binding domain (DBD) are physically connected to foster allosteric signal transmission between them. Direct comparisons among all the multi-domain NRs studied crystallographically to date show significant variations within theirmore » quaternary architectures, rather than a common architecture adhering to strict rules. RXR remains flexible and adaptive by maintaining loosely organized domains, while its hetero-dimerization partners use a surface patch on their LBDs to form domain-domain interactions with DBDs.« less

A transmission Kikuchi diffraction study of cementite in a quenched and tempered steel

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

Saleh, Ahmed A., E-mail: asaleh@uow.edu.au; Casillas, Gilberto; Pereloma, Elena V.

2016-04-15

This is the first transmission Kikuchi diffraction (TKD) study to report the indexing of nano-sized cementite as distinct structures and its orientation relationship with the body-centered cubic matrix in a quenched and tempered steel. Crystallographic analysis via TKD and selected area diffraction returned the well-known Bagaryatskii and Isaichev orientation relationships. However, the indexing of nano-sized cementite via TKD was sensitive to the thickness of the electron transparent region such that TEM remains the most precise method to characterise such precipitates. - Highlights: • Nano-sized cementite in a QT steel has been investigated by TKD and TEM. • Cementite has beenmore » indexed as distinct structures via TKD. • Crystallographic analysis returned the Bagaryatskii and Isaichev ORs. • Success of TKD is sensitive to the thickness of the electron transparent region. • TEM remains the most precise technique to characterise nano-sized precipitates.« less

AFM Studies of Salt Concentration Effects on the (110) Surface Structure of Tetragonal Lysozyme Crystals

NASA Technical Reports Server (NTRS)

Pusey, Marc Lee; Gorti, Sridhar; Forsythe, Elizabeth; Konnert, John

2002-01-01

Previous high resolution AFM studies of the (110) surface of tetragonal chicken egg white lysozyme crystals had shown that only one of two possible molecular surfaces is present, those constituting the completed 43 helices. These suggested that the crystal growth process was by the solution-phase assembly of the growth units, which then attach to the surface. However, the best fit for the imaged surfaces, vs. those predicted based upon the bulk crystallographic coordinates, were obtained when the packing about the 43 helices was "tightened up", while maintaining the underlying crystallographic unit cell spacing. This results in a widening of the gap between adjacent helices, and the top- most layer(s) may no longer be in contact. We postulated that the tightened packing about the helices is a result of the high salt concentrations in the bulk solution, used to crystallize the protein, driving hydrophobic interactions. Once the crystal surface is sufficiently buried by subsequent growth layers the ratio of salt to protein molecules decreases and the helices relax to their bulk crystallographic coordinates. The crystal surface helix structure is thus a reflection of the solution structure, and the tightness of the packing about the 43 helices would be a function of the bulk salt concentration. AFM images of the (110) surface of tetragonal lysozyme crystals grown under low (2%) and high (5%) NaCl concentrations reveal differences in the packing about the 43 helices consistent with the above proposal.

Structure-Guided Design and Optimization of Dipeptidyl Inhibitors of Norovirus 3CL Protease. Structure–Activity Relationships and Biochemical, X-ray Crystallographic, Cell-Based, and In Vivo Studies

DOE PAGES

Galasiti Kankanamalage, Anushka C.; Kim, Yunjeong; Weerawarna, Pathum M.; ...

2015-04-09

Norovirus infection constitutes the primary cause of acute viral gastroenteritis. There are currently no vaccines or norovirus-specific antiviral therapeutics available for the management of norovirus infection. Norovirus 3C-like protease is essential for viral replication, consequently, inhibition of this enzyme is a fruitful avenue of investigation that may lead to the emergence of antinorovirus therapeutics. We describe herein the optimization of dipeptidyl inhibitors of norovirus 3C-like protease using iterative SAR, X-ray crystallographic, and enzyme and cell-based studies. We also demonstrate herein in vivo efficacy of an inhibitor using the murine model of norovirus infection.

In-situ neutron diffraction of LaCoO3 perovskite under uniaxial compression. I. Crystal structure analysis and texture development

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

Aman, Amjad; Chen, Yan; Lugovy, Mykola

2014-01-01

The dynamics of texture formation, changes in crystal structure and stress accommodation mechanisms are studied in R3c rhombohedral LaCoO3 perovskite during in-situ uniaxial compression experiment by neutron diffraction. The neutron diffraction revealed the complex crystallographic changes causing the texture formation and significant straining along certain crystallographic directions during in-situ compression, which are responsible for the appearance of hysteresis and non-linear ferroelastic deformation in LaCoO3 perovskite. The irreversible strain after the first loading was connected with the appearance of non-recoverable changes in the intensity ratio of certain crystallographic peaks, causing non-reversible texture formation. However in the second loading/unloading cycle the hysteresismore » loop was closed and no irreversible strain appears after deformation. The significant texture formation is responsible for increase in the Young s modulus of LaCoO3 at high compressive loads, where the reported values of Young s modulus increase from 76 GPa measured at the very beginning of the loading to 194 GPa at 900 MPa applied compressive stress measured at the beginning of the unloading curve.« less

Cluster Analysis of Time-Dependent Crystallographic Data: Direct Identification of Time-Independent Structural Intermediates

PubMed Central

Kostov, Konstantin S.; Moffat, Keith

2011-01-01

The initial output of a time-resolved macromolecular crystallography experiment is a time-dependent series of difference electron density maps that displays the time-dependent changes in underlying structure as a reaction progresses. The goal is to interpret such data in terms of a small number of crystallographically refinable, time-independent structures, each associated with a reaction intermediate; to establish the pathways and rate coefficients by which these intermediates interconvert; and thereby to elucidate a chemical kinetic mechanism. One strategy toward achieving this goal is to use cluster analysis, a statistical method that groups objects based on their similarity. If the difference electron density at a particular voxel in the time-dependent difference electron density (TDED) maps is sensitive to the presence of one and only one intermediate, then its temporal evolution will exactly parallel the concentration profile of that intermediate with time. The rationale is therefore to cluster voxels with respect to the shapes of their TDEDs, so that each group or cluster of voxels corresponds to one structural intermediate. Clusters of voxels whose TDEDs reflect the presence of two or more specific intermediates can also be identified. From such groupings one can then infer the number of intermediates, obtain their time-independent difference density characteristics, and refine the structure of each intermediate. We review the principles of cluster analysis and clustering algorithms in a crystallographic context, and describe the application of the method to simulated and experimental time-resolved crystallographic data for the photocycle of photoactive yellow protein. PMID:21244840

Busting out of crystallography's Sisyphean prison: from pencil and paper to structure solving at the press of a button: past, present and future of crystallographic software development, maintenance and distribution.

PubMed

Cranswick, Lachlan Michael David

2008-01-01

The history of crystallographic computing and use of crystallographic software is one which traces the escape from the drudgery of manual human calculations to a world where the user delegates most of the travail to electronic computers. In practice, this involves practising crystallographers communicating their thoughts to the crystallographic program authors, in the hope that new procedures will be implemented within their software. Against this background, the development of small-molecule single-crystal and powder diffraction software is traced. Starting with the analogue machines and the use of Hollerith tabulators of the late 1930's, it is shown that computing developments have been science led, with new technologies being harnessed to solve pressing crystallographic problems. The development of software is also traced, with a final caution that few of the computations now performed daily are really understood by the program users. Unless a sufficient body of people continues to dismantle and re-build programs, the knowledge encoded in the old programs will become as inaccessible as the knowledge of how to build the Great Pyramid at Giza.

Fitmunk: improving protein structures by accurate, automatic modeling of side-chain conformations.

PubMed

Porebski, Przemyslaw Jerzy; Cymborowski, Marcin; Pasenkiewicz-Gierula, Marta; Minor, Wladek

2016-02-01

Improvements in crystallographic hardware and software have allowed automated structure-solution pipelines to approach a near-`one-click' experience for the initial determination of macromolecular structures. However, in many cases the resulting initial model requires a laborious, iterative process of refinement and validation. A new method has been developed for the automatic modeling of side-chain conformations that takes advantage of rotamer-prediction methods in a crystallographic context. The algorithm, which is based on deterministic dead-end elimination (DEE) theory, uses new dense conformer libraries and a hybrid energy function derived from experimental data and prior information about rotamer frequencies to find the optimal conformation of each side chain. In contrast to existing methods, which incorporate the electron-density term into protein-modeling frameworks, the proposed algorithm is designed to take advantage of the highly discriminatory nature of electron-density maps. This method has been implemented in the program Fitmunk, which uses extensive conformational sampling. This improves the accuracy of the modeling and makes it a versatile tool for crystallographic model building, refinement and validation. Fitmunk was extensively tested on over 115 new structures, as well as a subset of 1100 structures from the PDB. It is demonstrated that the ability of Fitmunk to model more than 95% of side chains accurately is beneficial for improving the quality of crystallographic protein models, especially at medium and low resolutions. Fitmunk can be used for model validation of existing structures and as a tool to assess whether side chains are modeled optimally or could be better fitted into electron density. Fitmunk is available as a web service at http://kniahini.med.virginia.edu/fitmunk/server/ or at http://fitmunk.bitbucket.org/.

Protein Ligation of the Photosynthetic Oxygen-Evolving Center

PubMed Central

Debus, Richard J.

2008-01-01

Photosynthetic water oxidation is catalyzed by a unique Mn4Ca cluster in Photosystem II. The ligation environment of the Mn4Ca cluster optimizes the cluster’s reactivity at each step in the catalytic cycle and minimizes the release of toxic, partly oxidized intermediates. However, our understanding of the cluster’s ligation environment remains incomplete. Although the recent X-ray crystallographic structural models have provided great insight and are consistent with most conclusions of earlier site-directed mutagenesis studies, the ligation environments of the Mn4Ca cluster in the two available structural models differ in important respects. Furthermore, while these structural models and the earlier mutagenesis studies agree on the identity of most of the Mn4Ca cluster’s amino acid ligands, they disagree on the identity of others. This review describes mutant characterizations that have been undertaken to probe the ligation environment of the Mn4Ca cluster, some of which have been inspired by the recent X-ray crystallographic structural models. Many of these characterizations have involved Fourier Transform Infrared (FTIR) difference spectroscopy because of the extreme sensitivity of this form of spectroscopy to the dynamic structural changes that occur during an enzyme’s catalytic cycle. PMID:18496594

Crystallographic control of surface structure on the sectoral zoning of iron in a diopside from Orford nickel mine (Quebec), Canada

NASA Astrophysics Data System (ADS)

Paquette, J.; Zangooi, A.; Thornton, K.

2004-05-01

The influence of surface structure on partitioning between mineral and melt (or solution) has been noted by other workers in a handful of minerals, including calcite, dolomite, apatite, topaz and diamond. Each one of these minerals displays at least one crystallographic face where steps present during crystal growth are not equivalent by symmetry. When this is the case, sectors grown at the edge of these steps commonly show differential incorporation of minor or trace elements. In the diopside investigated here, electron probe microanalyses performed on the as-grown (100) surface of several crystals show concentric and sectoral zoning defined by variations in Fe content. Atomic force microscopy (AFM) was used to study the surfaces of the three crystallographic forms present on the diopside crystals, with the goal of relating the compositional zoning to the surface structure of the faces. The dominant {100} faces are covered with growth hillocks consisting of four vicinal faces defined by steps parallel to [010] and [001]. The steps are often bunched into macrosteps and the resulting hillocks are visible optically. The steps along the two crystallographic directions show significant differences in straightness and smoothness that indicate non-equivalent kinetics. The wavier steps correspond to Fe-enriched areas within the {100} sectors. The {010} faces, next in morphological importance, are dominated by a single step orientation and show no differential incorporation. They display topography related to polysynthetic twinning. The {110} faces are much smaller and very few show resolvable steps. Sector zoning (i.e. diffential partitioning among non-equivalent crystallographic faces) has been described in the past from pyroxenes. Explanations have invoked either differences in surface structure among non-equivalent faces or their unequal growth rates. This particular occurrence indicates that trace element incorporation is, in fact, highly site-specific and that significant compositioinal zoning can be induced on a single face without invoking the effect of growth rate. The natural diopside crystals from the Orford nickel mine (Brompton, Quebec) show a unusual bladed habit flattened on {100} faces. Exceptional fluid chemistry during crystallization may therefore be required for the persistence of steps responsible for differential incorporation. Nevertheless, whenever this zoning is present, the trace element involved cannot be expected to reflect thermodynamic equilibrium between the solid and the fluid from which it crystallized.

Sparkle/AM1 Parameters for the Modeling of Samarium(III) and Promethium(III) Complexes.

PubMed

Freire, Ricardo O; da Costa, Nivan B; Rocha, Gerd B; Simas, Alfredo M

2006-01-01

The Sparkle/AM1 model is extended to samarium(III) and promethium(III) complexes. A set of 15 structures of high crystallographic quality (R factor < 0.05 Å), with ligands chosen to be representative of all samarium complexes in the Cambridge Crystallographic Database 2004, CSD, with nitrogen or oxygen directly bonded to the samarium ion, was used as a training set. In the validation procedure, we used a set of 42 other complexes, also of high crystallographic quality. The results show that this parametrization for the Sm(III) ion is similar in accuracy to the previous parametrizations for Eu(III), Gd(III), and Tb(III). On the other hand, promethium is an artificial radioactive element with no stable isotope. So far, there are no promethium complex crystallographic structures in CSD. To circumvent this, we confirmed our previous result that RHF/STO-3G/ECP, with the MWB effective core potential (ECP), appears to be the most efficient ab initio model chemistry in terms of coordination polyhedron crystallographic geometry predictions from isolated lanthanide complex ion calculations. We thus generated a set of 15 RHF/STO-3G/ECP promethium complex structures with ligands chosen to be representative of complexes available in the CSD for all other trivalent lanthanide cations, with nitrogen or oxygen directly bonded to the lanthanide ion. For the 42 samarium(III) complexes and 15 promethium(III) complexes considered, the Sparkle/AM1 unsigned mean error, for all interatomic distances between the Ln(III) ion and the ligand atoms of the first sphere of coordination, is 0.07 and 0.06 Å, respectively, a level of accuracy comparable to present day ab initio/ECP geometries, while being hundreds of times faster.

Dynamic crystallography reveals early signalling events in ultraviolet photoreceptor UVR8

DOE PAGES

Zeng, Xiaoli; Ren, Zhong; Wu, Qi; ...

2015-01-08

Arabidopsis thaliana UVR8 (AtUVR8) is a long-sought-after photoreceptor that undergoes dimer dissociation in response to UV-B light. Crystallographic and mutational studies have identified two crucial tryptophan residues for UV-B responses in AtUVR8. However, the mechanism of UV-B perception and structural events leading up to dimer dissociation remain elusive at the molecular level. We applied dynamic crystallography to capture light-induced structural events in photoactive AtUVR8 crystals. Here we report two intermediate structures at 1.67Å resolution. At the epicenter of UV-B signaling, concerted motions associated with Trp285/Trp233 lead to ejection of a water molecule, which weakens an intricate network of hydrogen bondsmore » and salt bridges at the dimer interface. Partial opening of the β-propeller structure due to thermal relaxation of conformational strains originating in the epicenter further disrupts the dimer interface and leads to dimer dissociation. Ultimately, these dynamic crystallographic observations provide structural insights into the photo-perception and signaling mechanism of UVR8.« less

Automated crystallographic system for high-throughput protein structure determination.

PubMed

Brunzelle, Joseph S; Shafaee, Padram; Yang, Xiaojing; Weigand, Steve; Ren, Zhong; Anderson, Wayne F

2003-07-01

High-throughput structural genomic efforts require software that is highly automated, distributive and requires minimal user intervention to determine protein structures. Preliminary experiments were set up to test whether automated scripts could utilize a minimum set of input parameters and produce a set of initial protein coordinates. From this starting point, a highly distributive system was developed that could determine macromolecular structures at a high throughput rate, warehouse and harvest the associated data. The system uses a web interface to obtain input data and display results. It utilizes a relational database to store the initial data needed to start the structure-determination process as well as generated data. A distributive program interface administers the crystallographic programs which determine protein structures. Using a test set of 19 protein targets, 79% were determined automatically.

Crystal Quality, the Long and the Short of It

NASA Technical Reports Server (NTRS)

Snell, Eddie H.

2004-01-01

The term "crystal quality" is ambiguous and implies different meanings to different crystallographers. For the physical crystallographer who aims to understand long-range aspects of crystal growth mosaicity is one of the leading measures of perfection. For the structural crystallographer and those seeking to understand growth at a short-range, molecular level, the detail in the resulting structure is a key goal. Different quality measures have been developed due to different needs. Each of the measures has advantages and each has limitations. In this talk a sample of these measures will be discussed with particular emphasis applied to their application in the analysis of microgravity grown crystals. The advantages and limitations of each will be discussed. Ultimately, the choice of crystal quality measurement lies in the nature of the question asked. It is scfill to remember that beauty is often in the eye of the beholder.

Distributed computing for macromolecular crystallography

PubMed Central

Krissinel, Evgeny; Uski, Ville; Lebedev, Andrey; Ballard, Charles

2018-01-01

Modern crystallographic computing is characterized by the growing role of automated structure-solution pipelines, which represent complex expert systems utilizing a number of program components, decision makers and databases. They also require considerable computational resources and regular database maintenance, which is increasingly more difficult to provide at the level of individual desktop-based CCP4 setups. On the other hand, there is a significant growth in data processed in the field, which brings up the issue of centralized facilities for keeping both the data collected and structure-solution projects. The paradigm of distributed computing and data management offers a convenient approach to tackling these problems, which has become more attractive in recent years owing to the popularity of mobile devices such as tablets and ultra-portable laptops. In this article, an overview is given of developments by CCP4 aimed at bringing distributed crystallographic computations to a wide crystallographic community. PMID:29533240

Distributed computing for macromolecular crystallography.

PubMed

Krissinel, Evgeny; Uski, Ville; Lebedev, Andrey; Winn, Martyn; Ballard, Charles

2018-02-01

Modern crystallographic computing is characterized by the growing role of automated structure-solution pipelines, which represent complex expert systems utilizing a number of program components, decision makers and databases. They also require considerable computational resources and regular database maintenance, which is increasingly more difficult to provide at the level of individual desktop-based CCP4 setups. On the other hand, there is a significant growth in data processed in the field, which brings up the issue of centralized facilities for keeping both the data collected and structure-solution projects. The paradigm of distributed computing and data management offers a convenient approach to tackling these problems, which has become more attractive in recent years owing to the popularity of mobile devices such as tablets and ultra-portable laptops. In this article, an overview is given of developments by CCP4 aimed at bringing distributed crystallographic computations to a wide crystallographic community.

The effects of deposition parameters on surface morphology and crystallographic orientation of electroless Ni-B coatings

NASA Astrophysics Data System (ADS)

Bulbul, Ferhat

2011-02-01

Electroless Ni-B coatings were deposited on AISI 304 stainless steels by electroless deposition method, which was performed for nine different test conditions at various levels of temperature, concentration of NaBH4, concentration of NiCl2, and time, using the Taguchi L9(34) experimental method. The effects of deposition parameters on the crystallographic orientation of electroless Ni-B coatings were investigated using SEM and XRD equipment. SEM analysis revealed that the Ni-B coatings developed six types (pea-like, maize-like, primary nodular, blackberry-like or grapes-like, broccoli-like, and cauliflower-like) of morphological structures depending on the deposition parameters. XRD results also showed that these structures exhibited different levels of amorphous character. The concentration of NaBH4 had the most dominant effect on the morphological and crystallographic development of electroless Ni-B coatings.

Computational Insights into the O2-evolving complex of photosystem II

PubMed Central

Sproviero, Eduardo M.; McEvoy, James P.; Gascón, José A.; Brudvig, Gary W.; Batista, Victor S.

2009-01-01

Mechanistic investigations of the water-splitting reaction of the oxygen-evolving complex (OEC) of photosystem II (PSII) are fundamentally informed by structural studies. Many physical techniques have provided important insights into the OEC structure and function, including X-ray diffraction (XRD) and extended X-ray absorption fine structure (EXAFS) spectroscopy as well as mass spectrometry (MS), electron paramagnetic resonance (EPR) spectroscopy and Fourier transform infrared spectroscopy applied in conjunction with mutagenesis studies. However, experimental studies have yet to yield consensus as to the exact configuration of the catalytic metal cluster and its ligation scheme. Computational modeling studies, including density functional (DFT) theory combined with quantum mechanics/molecular mechanics (QM/MM) hybrid methods for explicitly including the influence of the surrounding protein, have proposed chemically satisfactory models of the fully ligated OEC within PSII that are maximally consistent with experimental results. The inorganic core of these models is similar to the crystallographic model upon which they were based but comprises important modifications due to structural refinement, hydration and proteinaceous ligation which improve agreement with a wide range of experimental data. The computational models are useful for rationalizing spectroscopic and crystallographic results and for building a complete structure-based mechanism of water-splitting in PSII as described by the intermediate oxidation states of the OEC. This review summarizes these recent advances in QM/MM modeling of PSII within the context of recent experimental studies. PMID:18483777

Direct methods in protein crystallography.

PubMed

Karle, J

1989-11-01

It is pointed out that the 'direct methods' of phase determination for small-structure crystallography do not have immediate applicability to macromolecular structures. The term 'direct methods in macromolecular crystallography' is suggested to categorize a spectrum of approaches to macromolecular structure determination in which the analyses are characterized by the use of two-phase and higher-order-phase invariants. The evaluation of the invariants is generally obtained by the use of heavy-atom techniques. The results of a number of the more recent algebraic and probabilistic studies involving isomorphous replacement and anomalous dispersion thus become valid subjects for discussion here. These studies are described and suggestions are also presented concerning future applicability. Additional discussion concerns the special techniques of filtering, the use of non-crystallographic symmetry, some features of maximum entropy and attempts to apply phase-determining formulas to the refinement of macromolecular structure. It is noted that, in addition to the continuing remarkable progress in macromolecular crystallography based on the traditional applications of isomorphous replacement and anomalous dispersion, recent valuable advances have been made in the application of non-crystallographic symmetry, in particular, to virus structures and in applications of filtering. Good progress has also been reported in the application of exact linear algebra to multiple-wavelength anomalous-dispersion investigations of structures containing anomalous scatterers of only moderate scattering power.

Tetrahydrocarbazoles are a novel class of potent P-type ATPase inhibitors with antifungal activity

PubMed Central

Bublitz, Maike; Kjellerup, Lasse; Cohrt, Karen O’Hanlon; Gordon, Sandra; Mortensen, Anne Louise; Clausen, Johannes D.; Pallin, Thomas David; Hansen, John Bondo; Fuglsang, Anja Thoe; Dalby-Brown, William

2018-01-01

We have identified a series of tetrahydrocarbazoles as novel P-type ATPase inhibitors. Using a set of rationally designed analogues, we have analyzed their structure-activity relationship using functional assays, crystallographic data and computational modeling. We found that tetrahydrocarbazoles inhibit adenosine triphosphate (ATP) hydrolysis of the fungal H+-ATPase, depolarize the fungal plasma membrane and exhibit broad-spectrum antifungal activity. Comparative inhibition studies indicate that many tetrahydrocarbazoles also inhibit the mammalian Ca2+-ATPase (SERCA) and Na+,K+-ATPase with an even higher potency than Pma1. We have located the binding site for this compound class by crystallographic structure determination of a SERCA-tetrahydrocarbazole complex to 3.0 Å resolution, finding that the compound binds to a region above the ion inlet channel of the ATPase. A homology model of the Candida albicans H+-ATPase based on this crystal structure, indicates that the compounds could bind to the same pocket and identifies pocket extensions that could be exploited for selectivity enhancement. The results of this study will aid further optimization towards selective H+-ATPase inhibitors as a new class of antifungal agents. PMID:29293507

Investigation of ZrO x /ZrC-ZrN/Zr thin-film structural evolution and their degradation using X-ray diffraction and Raman spectrometry

NASA Astrophysics Data System (ADS)

Usmani, B.; Vijay, V.; Chhibber, R.; Dixit, A.

2016-11-01

The thin-film structures of DC/FR magnetron-sputtered ZrO x /ZrC-ZrN/Zr tandem solar-selective coatings are investigated using X-ray diffraction and room-temperature Raman spectroscopic measurements. These studies suggest that the major contribution is coming from h-ZrN0.28, c-ZrC, h-Zr3C2 crystallographic phases in ZrN-ZrC absorber layer, in conjunction with mixed ZrO x crystallographic phases. The change in structure for thermally annealed samples has been examined and observed that cubic and hexagonal ZrO x phase converted partially into tetragonal and monoclinic ZrO x phases, whereas hexagonal and cubic ZrN phases, from absorber layer, have not been observed for these thermally treated samples in air. These studies suggest that thermal treatment may lead to the loss of ZrN phase in absorber, degrading the thermal response for the desired wavelength range in open ambient conditions in contrast to vacuum conditions.

Recent Development in Spectroscopic and Chemical Characterization of Cellulose

DTIC Science & Technology

2005-01-01

specific to the reducing end groups of the polysaccharides , confirmed the parallel alignment of molecular chains within the microfibrils in native...they include primary, secondary, and tertiary structures. And indeed, crystallographic studies of the monosaccharides and of related structures...Two approaches were adopted for this purpose. The first was based on examining the Raman spectra of polysaccharide polymers and oligomers that

Sampling the structure and chemical order in assemblies of ferromagnetic nanoparticles by nuclear magnetic resonance

PubMed Central

Liu, Yuefeng; Luo, Jingjie; Shin, Yooleemi; Moldovan, Simona; Ersen, Ovidiu; Hébraud, Anne; Schlatter, Guy; Pham-Huu, Cuong; Meny, Christian

2016-01-01

Assemblies of nanoparticles are studied in many research fields from physics to medicine. However, as it is often difficult to produce mono-dispersed particles, investigating the key parameters enhancing their efficiency is blurred by wide size distributions. Indeed, near-field methods analyse a part of the sample that might not be representative of the full size distribution and macroscopic methods give average information including all particle sizes. Here, we introduce temperature differential ferromagnetic nuclear resonance spectra that allow sampling the crystallographic structure, the chemical composition and the chemical order of non-interacting ferromagnetic nanoparticles for specific size ranges within their size distribution. The method is applied to cobalt nanoparticles for catalysis and allows extracting the size effect from the crystallographic structure effect on their catalytic activity. It also allows sampling of the chemical composition and chemical order within the size distribution of alloyed nanoparticles and can thus be useful in many research fields. PMID:27156575

Crystal Structure Prediction via Deep Learning.

PubMed

Ryan, Kevin; Lengyel, Jeff; Shatruk, Michael

2018-06-06

We demonstrate the application of deep neural networks as a machine-learning tool for the analysis of a large collection of crystallographic data contained in the crystal structure repositories. Using input data in the form of multi-perspective atomic fingerprints, which describe coordination topology around unique crystallographic sites, we show that the neural-network model can be trained to effectively distinguish chemical elements based on the topology of their crystallographic environment. The model also identifies structurally similar atomic sites in the entire dataset of ~50000 crystal structures, essentially uncovering trends that reflect the periodic table of elements. The trained model was used to analyze templates derived from the known binary and ternary crystal structures in order to predict the likelihood to form new compounds that could be generated by placing elements into these structural templates in combinatorial fashion. Statistical analysis of predictive performance of the neural-network model, which was applied to a test set of structures never seen by the model during training, indicates its ability to predict known elemental compositions with a high likelihood of success. In ~30% of cases, the known compositions were found among top-10 most likely candidates proposed by the model. These results suggest that the approach developed in this work can be used to effectively guide the synthetic efforts in the discovery of new materials, especially in the case of systems composed of 3 or more chemical elements.

Displacive Transformation in Ceramics

DTIC Science & Technology

1994-02-28

product However, the evidence here is thin because no other interface which, during transformation movement, pro - crystallographic data were used other... con - and the parent phase. stants c and a change abruptly and the structure becomles The phenomenological crystallographic theory of cubic. Since the...detectable negative volume change near T,, PbTiO3 Pro * vides a more sensitve indication of the role of lattice vari- Department of Matcrials Science

Intrinsic flexibility of West Nile virus protease in solution characterized using small-angle X-ray scattering.

PubMed

Garces, Andrea P; Watowich, Stanley J

2013-10-01

West Nile virus (WNV) is a mosquito-borne flavivirus with a rapidly expanding global distribution. Infection can cause severe neurological disease and fatality in humans. Efforts are ongoing to develop antiviral drugs that inhibit the WNV protease, a viral enzyme required for polyprotein processing. Unfortunately, little is known about the solution structure of recombinant WNV protease (NS2B-NS3pro) used for antiviral drug discovery and development, although X-ray crystal structures and nuclear magnetic resonance (NMR) studies have provided valuable insights into the interactions between NS2B-NS3pro and peptide-based inhibitors. We completed small-angle X-ray scattering and Fourier transform infrared spectroscopy experiments to determine the solution structure and dynamics of WNV NS2B-NS3pro in the absence of a bound substrate or inhibitor. Importantly, these solution studies suggested that all or most of the NS2B cofactor was highly flexible and formed an ensemble of structures, in contrast to the NS2B tertiary structures observed in crystallographic and NMR studies. The secondary structure of NS2B-NS3pro in solution had high β-content, similar to the secondary structure observed in crystallographic studies. This work provided evidence of the intrinsic flexibility and conformational heterogeneity of the NS2B chain of the WNV protease in the absence of substratelike ligands, which should be considered during antiviral drug discovery and development efforts.

Inherent flexibility of CLIC6 revealed by crystallographic and solution studies.

PubMed

Ferofontov, Alisa; Strulovich, Roi; Marom, Milit; Giladi, Moshe; Haitin, Yoni

2018-05-02

Chloride intracellular channels (CLICs) are a family of unique proteins, that were suggested to adopt both soluble and membrane-associated forms. Moreover, following this unusual metamorphic change, CLICs were shown to incorporate into membranes and mediate ion conduction in vitro, suggesting multimerization upon membrane insertion. Here, we present a 1.8 Å resolution crystal structure of the CLIC domain of mouse CLIC6 (mCLIC6). The structure reveals a monomeric arrangement and shows a high degree of structural conservation with other CLICs. Small-angle X-ray scattering (SAXS) analysis of mCLIC6 demonstrated that the overall solution structure is similar to the crystallographic conformation. Strikingly, further analysis of the SAXS data using ensemble optimization method unveiled additional elongated conformations, elucidating high structural plasticity as an inherent property of the protein. Moreover, structure-guided perturbation of the inter-domain interface by mutagenesis resulted in a population shift towards elongated conformations of mCLIC6. Additionally, we demonstrate that oxidative conditions induce an increase in mCLIC6 hydrophobicity along with mild oligomerization, which was enhanced by the presence of membrane mimetics. Together, these results provide mechanistic insights into the metamorphic nature of mCLIC6.

Mosaic structure in epitaxial thin films having large lattice mismatch

NASA Astrophysics Data System (ADS)

Srikant, V.; Speck, J. S.; Clarke, D. R.

1997-11-01

Epitaxial films having a large lattice mismatch with their substrate invariably form a mosaic structure of slightly misoriented sub-grains. The mosaic structure is usually characterized by its x-ray rocking curve on a surface normal reflection but this is limited to the out-of-plane component unless off-axis or transmission experiments are performed. A method is presented by which the in-plane component of the mosaic misorientation can be determined from the rocking curves of substrate normal and off-axis reflections. Results are presented for two crystallographically distinct heteroepitaxial systems, ZnO, AlN, and GaN (wurtzite crystal structure) on c-plane sapphire and MgO (rock salt crystal structure) on (001) GaAs. The differences in the mosaic structure of these films are attributed to the crystallographic nature of their lattice dislocations.

Crystal structure and electronic properties of a thiolate-protected Au24 nanocluster

NASA Astrophysics Data System (ADS)

Das, Anindita; Li, Tao; Li, Gao; Nobusada, Katsuyuki; Zeng, Chenjie; Rosi, Nathaniel L.; Jin, Rongchao

2014-05-01

Solving the total structures of gold nanoclusters is of critical importance for understanding their electronic, optical and catalytic properties. Herein, we report the X-ray structure of a charge-neutral Au24(SCH2Ph-tBu)20 nanocluster. This structure features a bi-tetrahedral Au8 kernel protected by four tetrameric staple-like motifs. Electronic structure analysis is further carried out and the optical absorption spectrum is interpreted. The Au24(SCH2Ph-tBu)20, Au23(S-c-C6H11)16 and Au25(SCH2CH2Ph)18 nanoclusters constitute the first crystallographically characterized ``trio''.Solving the total structures of gold nanoclusters is of critical importance for understanding their electronic, optical and catalytic properties. Herein, we report the X-ray structure of a charge-neutral Au24(SCH2Ph-tBu)20 nanocluster. This structure features a bi-tetrahedral Au8 kernel protected by four tetrameric staple-like motifs. Electronic structure analysis is further carried out and the optical absorption spectrum is interpreted. The Au24(SCH2Ph-tBu)20, Au23(S-c-C6H11)16 and Au25(SCH2CH2Ph)18 nanoclusters constitute the first crystallographically characterized ``trio''. Electronic supplementary information (ESI) available: Experimental and supporting Fig. S1-S3. CCDC NUMBER(1000102). For ESI and crystallographic data in CIF or other electronic format see DOI: 10.1039/c4nr01350f

Production, purification and preliminary X-ray crystallographic studies of adeno-associated virus serotype 1

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

Miller, Edward B.; Gurda-Whitaker, Brittney; Govindasamy, Lakshmanan

2006-12-01

Crystals of baculovirus-expressed adeno-associated virus serotype 1 (AAV1) capsids have been grown in the rhombohedral space group R32 (unit-cell parameters a = 254.7 Å, α = 62.3°) and shown to diffract X-rays to at least 2.5 Å resolution. Crystals of baculovirus-expressed adeno-associated virus serotype 1 (AAV1) capsids have been grown in the rhombohedral space group R32 (unit-cell parameters a = 254.7 Å, α = 62.3°) and shown to diffract X-rays to at least 2.5 Å resolution. The diffraction data were subsequently processed and reduced with an overall R{sub sym} of 12.3% and a completeness of 89.0%. Based on the unit-cellmore » volume, rotation-function and translation-function results and packing considerations, there is one virus capsid (60 viral proteins) per unit cell and there are ten viral proteins per crystallographic asymmetric unit. The AAV1 capsid shares both the twofold and threefold crystallographic symmetry operators. The AAV1 data have been initially phased using a polyalanine model (based on the crystal structure of AAV4) to 4.0 Å resolution and the structure determination and refinement is in progress using tenfold noncrystallographic symmetry electron-density averaging.« less

Crystallographic snapshots of active site metal shift in E. coli fructose 1,6-bisphosphate aldolase.

PubMed

Tran, Huyen-Thi; Lee, Seon-Hwa; Ho, Thien-Hoang; Hong, Seung-Hye; Huynh, Kim-Hung; Ahn, Yeh-Jin; Oh, Deok-Kun; Kang, Lin-Woo

2016-12-01

Fructose 1,6-bisphosphate aldolase (FBA) is important for both glycolysis and gluconeogenesis in life. Class II (zinc dependent) FBA is an attractive target for the development of antibiotics against protozoa, bacteria, and fungi, and is also widely used to produce various high-value stereoisomers in the chemical and pharmaceutical industry. In this study, the crystal structures of class II Escherichia coli FBA (EcFBA) were determined from four different crystals, with resolutions between 1.8 Å and 2.0 Å. Native EcFBA structures showed two separate sites of Zn1 (interior position) and Zn2 (active site surface position) for Zn2＋ ion. Citrate and TRIS bound EcFBA structures showed Zn2＋ position exclusively at Zn2. Crystallographic snapshots of EcFBA structures with and without ligand binding proposed the rationale of metal shift at the active site, which might be a hidden mechanism to keep the trace metal cofactor Zn2＋ within EcFBA without losing it. [BMB Reports 2016; 49(12): 681-686].

Use of Bayesian Inference in Crystallographic Structure Refinement via Full Diffraction Profile Analysis

PubMed Central

Fancher, Chris M.; Han, Zhen; Levin, Igor; Page, Katharine; Reich, Brian J.; Smith, Ralph C.; Wilson, Alyson G.; Jones, Jacob L.

2016-01-01

A Bayesian inference method for refining crystallographic structures is presented. The distribution of model parameters is stochastically sampled using Markov chain Monte Carlo. Posterior probability distributions are constructed for all model parameters to properly quantify uncertainty by appropriately modeling the heteroskedasticity and correlation of the error structure. The proposed method is demonstrated by analyzing a National Institute of Standards and Technology silicon standard reference material. The results obtained by Bayesian inference are compared with those determined by Rietveld refinement. Posterior probability distributions of model parameters provide both estimates and uncertainties. The new method better estimates the true uncertainties in the model as compared to the Rietveld method. PMID:27550221

HRTEM Analysis of Crystallographic Defects in CdZnTe Single Crystal

NASA Astrophysics Data System (ADS)

Yasar, Bengisu; Ergunt, Yasin; Kabukcuoglu, Merve Pinar; Parlak, Mehmet; Turan, Rasit; Kalay, Yunus Eren

2018-01-01

In recent years, CdZnTe has attracted much attention due to its superior electrical and structural properties for room-temperature operable gamma and x-ray detectors. However, CdZnTe (CZT) material has often suffered from crystallographic defects encountered during the growth and post-growth processes. The identification and structural characterization of these defects is crucial to synthesize defect-free CdZnTe single crystals. In this study, Cd0.95 Zn0.05 Te single crystals were grown using a three-zone vertical Bridgman system. The single crystallinity of the material was ensured by using x-ray diffraction measurements. High-resolution electron microscopy (HRTEM) was used to characterize the nano-scale defects on the CdZnTe matrix. The linear defects oriented along the ⟨211⟩ direction were examined by transmission electron microscopy (TEM) and the corresponding HRTEM image simulations were performed by using a quantitative scanning TEM simulation package.

Supervised machine learning techniques to predict binding affinity. A study for cyclin-dependent kinase 2.

PubMed

de Ávila, Maurício Boff; Xavier, Mariana Morrone; Pintro, Val Oliveira; de Azevedo, Walter Filgueira

2017-12-09

Here we report the development of a machine-learning model to predict binding affinity based on the crystallographic structures of protein-ligand complexes. We used an ensemble of crystallographic structures (resolution better than 1.5 Å resolution) for which half-maximal inhibitory concentration (IC 50 ) data is available. Polynomial scoring functions were built using as explanatory variables the energy terms present in the MolDock and PLANTS scoring functions. Prediction performance was tested and the supervised machine learning models showed improvement in the prediction power, when compared with PLANTS and MolDock scoring functions. In addition, the machine-learning model was applied to predict binding affinity of CDK2, which showed a better performance when compared with AutoDock4, AutoDock Vina, MolDock, and PLANTS scores. Copyright © 2017 Elsevier Inc. All rights reserved.

WebCSD: the online portal to the Cambridge Structural Database

PubMed Central

Thomas, Ian R.; Bruno, Ian J.; Cole, Jason C.; Macrae, Clare F.; Pidcock, Elna; Wood, Peter A.

2010-01-01

WebCSD, a new web-based application developed by the Cambridge Crystallographic Data Centre, offers fast searching of the Cambridge Structural Database using only a standard internet browser. Search facilities include two-dimensional substructure, molecular similarity, text/numeric and reduced cell searching. Text, chemical diagrams and three-dimensional structural information can all be studied in the results browser using the efficient entry summaries and embedded three-dimensional viewer. PMID:22477776

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

Bodenheimer, Annette M.; Meilleur, Flora

Trichoderma reesei Cel7A efficiently hydrolyses cellulose. We report here the crystallographic structures of the wild-type TrCel7A catalytic domain (CD) in an open state and, for the first time, in a closed state. Molecular dynamics (MD) simulations indicate that the loops along the CD tunnel move in concerted motions. Together, the crystallographic and MD data suggest that the CD cycles between the tense and relaxed forms that are characteristic of work producing enzymes. Analysis of the interactions formed by R251 provides a structural rationale for the concurrent decrease in product inhibition and catalytic efficiency measured for product-binding site mutants.

Crystallography Open Databases and Preservation: a World-wide Initiative

NASA Astrophysics Data System (ADS)

Chateigner, Daniel

In 2003, an international team of crystallographers proposed the Crystallography Open Database (COD), a fully-free collection of crystal structure data, in the aim of ensuring their preservation. With nearly 250000 entries, this database represents a large open set of data for crystallographers, academics and industrials, located at five different places world-wide, and included in Thomson-Reuters’ ISI. As a large step towards data preservation, raw data can now be uploaded along with «digested» structure files, and COD can be questioned by most of the crystallography-linked industrial software. The COD initiative work deserves several other open developments.

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

Yu, Qi; Zhu, Fang-Yuan; Cheng, Li-Qian

Crystallographic structure of sol-gel-processed lead-free (K,Na)NbO{sub 3} (KNN) epitaxial films on [100]-cut SrTiO{sub 3} single-crystalline substrates was investigated for a deeper understanding of its piezoelectric response. Lattice parameter measurement by high-resolution X-ray diffraction and transmission electron microscopy revealed that the orthorhombic KNN films on SrTiO{sub 3} (100) surfaces are [010] oriented (b-axis-oriented) rather than commonly identified c-axis orientation. Based on the crystallographic orientation and corresponding ferroelectric domain structure investigated by piezoresponse force microscopy, the superior piezoelectric property along b-axis of epitaxial KNN films than other orientations can be explained.

Solid-state NMR and computational studies of 4-methyl-2-nitroacetanilide.

PubMed

Harris, Robin K; Ghi, Phuong Y; Hammond, Robert B; Ma, Cai Yun; Roberts, Kevin J; Yates, Jonathan R; Pickard, Chris J

2006-03-01

Studies on the solid-state structure of two polymorphs of 4-methyl-2-nitroacetanilide (MNA) were conducted using magic-angle spinning (13)C, (15)N and (1)H NMR spectroscopy, together with first-principles computations of NMR shielding (including use of a program that takes explicit account of the translational symmetry inherent in crystalline structures). The effects on (13)C chemical shifts of side-chain rotations have been explored. Information derived from these studies was then incorporated within a systematic space-search methodology for elucidation of trial crystallographic structures from powder XRD.

Development and Processing Improvement of Aerospace Aluminum Alloys

NASA Technical Reports Server (NTRS)

Lisagor, W. Barry; Bales, Thomas T.

2007-01-01

This final report, in multiple presentation format, describes a comprehensive multi-tasked contract study to improve the overall property response of selected aerospace alloys, explore further a newly-developed and registered alloy, and correlate the processing, metallurgical structure, and subsequent properties achieved with particular emphasis on the crystallographic orientation texture developed. Modifications to plate processing, specifically hot rolling practices, were evaluated for Al-Li alloys 2195 and 2297, for the recently registered Al-Cu-Ag alloy, 2139, and for the Al-Zn-Mg-Cu alloy, 7050. For all of the alloys evaluated, the processing modifications resulted in significant improvements in mechanical properties. Analyses also resulted in an enhanced understanding of the correlation of processing, crystallographic texture, and mechanical properties.

Metrics for comparison of crystallographic maps

DOE PAGES

Urzhumtsev, Alexandre; Afonine, Pavel V.; Lunin, Vladimir Y.; ...

2014-10-01

Numerical comparison of crystallographic contour maps is used extensively in structure solution and model refinement, analysis and validation. However, traditional metrics such as the map correlation coefficient (map CC, real-space CC or RSCC) sometimes contradict the results of visual assessment of the corresponding maps. This article explains such apparent contradictions and suggests new metrics and tools to compare crystallographic contour maps. The key to the new methods is rank scaling of the Fourier syntheses. The new metrics are complementary to the usual map CC and can be more helpful in map comparison, in particular when only some of their aspects,more » such as regions of high density, are of interest.« less

A matrix of heterobimetallic complexes for interrogation of hydrogen evolution reaction electrocatalysts† †Electronic supplementary information (ESI) available: Experimental, spectroscopic, additional electrochemical and computational details, X-ray crystallographic data (CIF) from the structure of the complexes [Ni–Fe]0, [Ni2–Fe2]2+, [Ni2–Fe]+, and computational coordinates are available. CCDC crystallographic data for the complexes [Ni–Fe]0, [Ni2–Fe2]2+ and [Ni2–Fe]+ were deposited in the Cambridge Crystallographic Data Centre. CCDC [Ni–Fe]0 (CCDC 1045461), [Ni2–Fe2]2+ (CCDC 1045460) and [Ni2–Fe]+ (CCDC 1565539). For ESI and crystallographic data in CIF or other electronic format see DOI: 10.1039/c7sc03378h

PubMed Central

Ghosh, Pokhraj; Ding, Shengda; Chupik, Rachel B.; Quiroz, Manuel; Hsieh, Chung-Hung; Bhuvanesh, Nattami; Hall, Michael B.

2017-01-01

Experimental and computational studies address key questions in a structure–function analysis of bioinspired electrocatalysts for the HER. Combinations of NiN2S2 or [(NO)Fe]N2S2 as donors to (η5-C5H5)Fe(CO)+ or [Fe(NO)2]+/0 generate a series of four bimetallics, gradually “softened” by increasing nitrosylation, from 0 to 3, by the non-innocent NO ligands. The nitrosylated NiFe complexes are isolated and structurally characterized in two redox levels, demonstrating required features of electrocatalysis. Computational modeling of experimental structures and likely transient intermediates that connect the electrochemical events find roles for electron delocalization by NO, as well as Fe–S bond dissociation that produce a terminal thiolate as pendant base well positioned to facilitate proton uptake and transfer. Dihydrogen formation is via proton/hydride coupling by internal S–H+···–H–Fe units of the “harder” bimetallic arrangements with more localized electron density, while softer units convert H–···H–via reductive elimination from two Fe–H deriving from the highly delocalized, doubly reduced [Fe2(NO)3]– derivative. Computational studies also account for the inactivity of a Ni2Fe complex resulting from entanglement of added H+ in a pinched –Sδ–···H+···δ–S– arrangement. PMID:29619175

Assessing the Chemical Accuracy of Protein Structures via Peptide Acidity

PubMed Central

Anderson, Janet S.; Hernández, Griselda; LeMaster, David M.

2012-01-01

Although the protein native state is a Boltzmann conformational ensemble, practical applications often require a representative model from the most populated region of that distribution. The acidity of the backbone amides, as reflected in hydrogen exchange rates, is exquisitely sensitive to the surrounding charge and dielectric volume distribution. For each of four proteins, three independently determined X-ray structures of differing crystallographic resolution were used to predict exchange for the static solvent-exposed amide hydrogens. The average correlation coefficients range from 0.74 for ubiquitin to 0.93 for Pyrococcus furiosus rubredoxin, reflecting the larger range of experimental exchange rates exhibited by the latter protein. The exchange prediction errors modestly correlate with the crystallographic resolution. MODELLER 9v6-derived homology models at ~60% sequence identity (36% identity for chymotrypsin inhibitor CI2) yielded correlation coefficients that are ~0.1 smaller than for the cognate X-ray structures. The most recently deposited NOE-based ubiquitin structure and the original NMR structure of CI2 fail to provide statistically significant predictions of hydrogen exchange. However, the more recent RECOORD refinement study of CI2 yielded predictions comparable to the X-ray and homology model-based analyses. PMID:23182463

Probing the dynamic nature of water molecules and their influences on ligand binding in a model binding site.

PubMed

Cappel, Daniel; Wahlström, Rickard; Brenk, Ruth; Sotriffer, Christoph A

2011-10-24

The model binding site of the cytochrome c peroxidase (CCP) W191G mutant is used to investigate the structural and dynamic properties of the water network at the buried cavity using computational methods supported by crystallographic analysis. In particular, the differences of the hydration pattern between the uncomplexed state and various complexed forms are analyzed as well as the differences between five complexes of CCP W191G with structurally closely related ligands. The ability of docking programs to correctly handle the water molecules in these systems is studied in detail. It is found that fully automated prediction of water replacement or retention upon docking works well if some additional preselection is carried out but not necessarily if the entire water network in the cavity is used as input. On the other hand, molecular interaction fields for water calculated from static crystal structures and hydration density maps obtained from molecular dynamics simulations agree very well with crystallographically observed water positions. For one complex, the docking and MD results sensitively depend on the quality of the starting structure, and agreement is obtained only after redetermination of the crystal structure and refinement at higher resolution.

Hyperfine field and electronic structure of magnetite below the Verwey transition

NASA Astrophysics Data System (ADS)

Řezníček, R.; Chlan, V.; Štěpánková, H.; Novák, P.

2015-03-01

Magnetite represents a prototype compound with a mixed valence of iron cations. Its structure and electron ordering below the Verwey transition have been studied for decades. A recently published precise crystallographic structure [Senn et al., Nature (London) 481, 173 (2012), 10.1038/nature10704] accompanied by a suggestion of a "trimeron" model has given a new impulse to magnetite research. Here we investigate hyperfine field anisotropy in the C c phase of magnetite by quantitative reanalysis of published measurements of the dependences of the 57Fe nuclear magnetic resonance frequencies on the external magnetic field direction. Further, ab initio density-functional-theory-based calculations of hyperfine field depending on the magnetization direction using the recently reported crystal structure are carried out, and analogous hyperfine anisotropy data linked to particular crystallographic sites are determined. These two sets of data are compared, and mutually matching groups of the iron B sites in the 8:5:3 ratio are found. Moreover, information on electronic structure is obtained from the ab initio calculations. Our results are compared with the trimeron model and with an alternative analysis [Patterson, Phys. Rev. B 90, 075134 (2014), 10.1103/PhysRevB.90.075134] as well.

PDB_REDO: constructive validation, more than just looking for errors.

PubMed

Joosten, Robbie P; Joosten, Krista; Murshudov, Garib N; Perrakis, Anastassis

2012-04-01

Developments of the PDB_REDO procedure that combine re-refinement and rebuilding within a unique decision-making framework to improve structures in the PDB are presented. PDB_REDO uses a variety of existing and custom-built software modules to choose an optimal refinement protocol (e.g. anisotropic, isotropic or overall B-factor refinement, TLS model) and to optimize the geometry versus data-refinement weights. Next, it proceeds to rebuild side chains and peptide planes before a final optimization round. PDB_REDO works fully automatically without the need for intervention by a crystallographic expert. The pipeline was tested on 12 000 PDB entries and the great majority of the test cases improved both in terms of crystallographic criteria such as R(free) and in terms of widely accepted geometric validation criteria. It is concluded that PDB_REDO is useful to update the otherwise `static' structures in the PDB to modern crystallographic standards. The publically available PDB_REDO database provides better model statistics and contributes to better refinement and validation targets.

PDB_REDO: constructive validation, more than just looking for errors

PubMed Central

Joosten, Robbie P.; Joosten, Krista; Murshudov, Garib N.; Perrakis, Anastassis

2012-01-01

Developments of the PDB_REDO procedure that combine re-refinement and rebuilding within a unique decision-making framework to improve structures in the PDB are presented. PDB_REDO uses a variety of existing and custom-built software modules to choose an optimal refinement protocol (e.g. anisotropic, isotropic or overall B-factor refinement, TLS model) and to optimize the geometry versus data-refinement weights. Next, it proceeds to rebuild side chains and peptide planes before a final optimization round. PDB_REDO works fully automatically without the need for intervention by a crystallographic expert. The pipeline was tested on 12 000 PDB entries and the great majority of the test cases improved both in terms of crystallographic criteria such as R free and in terms of widely accepted geometric validation criteria. It is concluded that PDB_REDO is useful to update the otherwise ‘static’ structures in the PDB to modern crystallographic standards. The publically available PDB_REDO database provides better model statistics and contributes to better refinement and validation targets. PMID:22505269

Probing hydrogen and halogen-oxo interactions in uranyl coordination polymers: a combined crystallographic and computational study

DOE PAGES

Carter, Korey P.; Kalaj, Mark; Kerridge, Andrew; ...

2018-01-01

Four uranyl compounds containing either benzoic acid ( 1 ), m -chlorobenzoic acid ( 2 ), m -bromobenzoic acid ( 3 ), or m -iodobenzoic acid ( 4 ) are described, and the latter two compounds are used to probe non-covalent interaction strengths via structural, vibrational, and computational means.

Crystallographic analysis of human hemoglobin elucidates the structural basis of the potent and dual antisickling activity of pyridyl derivatives of vanillin

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

Abdulmalik, Osheiza; Ghatge, Mohini S.; Musayev, Faik N.

2011-11-01

Pyridyl derivatives of vanillin increase the fraction of the more soluble oxygenated sickle hemoglobin and/or directly increase the solubility of deoxygenated sickle hemoglobin. Crystallographic analysis reveals the structural basis of the potent and dual antisickling activity of these derivatives. Vanillin has previously been studied clinically as an antisickling agent to treat sickle-cell disease. In vitro investigations with pyridyl derivatives of vanillin, including INN-312 and INN-298, showed as much as a 90-fold increase in antisickling activity compared with vanillin. The compounds preferentially bind to and modify sickle hemoglobin (Hb S) to increase the affinity of Hb for oxygen. INN-312 also ledmore » to a considerable increase in the solubility of deoxygenated Hb S under completely deoxygenated conditions. Crystallographic studies of normal human Hb with INN-312 and INN-298 showed that the compounds form Schiff-base adducts with the N-terminus of the α-subunits to constrain the liganded (or relaxed-state) Hb conformation relative to the unliganded (or tense-state) Hb conformation. Interestingly, while INN-298 binds and directs its meta-positioned pyridine-methoxy moiety (relative to the aldehyde moiety) further down the central water cavity of the protein, that of INN-312, which is ortho to the aldehyde, extends towards the surface of the protein. These studies suggest that these compounds may act to prevent sickling of SS cells by increasing the fraction of the soluble high-affinity Hb S and/or by stereospecific inhibition of deoxygenated Hb S polymerization.« less

A CPU benchmark for protein crystallographic refinement.

PubMed

Bourne, P E; Hendrickson, W A

1990-01-01

The CPU time required to complete a cycle of restrained least-squares refinement of a protein structure from X-ray crystallographic data using the FORTRAN codes PROTIN and PROLSQ are reported for 48 different processors, ranging from single-user workstations to supercomputers. Sequential, vector, VLIW, multiprocessor, and RISC hardware architectures are compared using both a small and a large protein structure. Representative compile times for each hardware type are also given, and the improvement in run-time when coding for a specific hardware architecture considered. The benchmarks involve scalar integer and vector floating point arithmetic and are representative of the calculations performed in many scientific disciplines.

Inverse analysis of giant macroscopic negative thermal expansion of Ca2RuO4‑ y ceramics based on elasticity and structural topology optimization

NASA Astrophysics Data System (ADS)

Takezawa, Akihiro; Takenaka, Koshi; Zhang, Xiaopeng

2018-05-01

Ca2RuO4‑ y ceramics exhibit a large volumetric negative thermal expansions (NTE), although the crystallographic volume contraction on heating is much smaller than the NTE. Therefore, we examine the differences in the mechanisms underlying the volumetric thermal expansion for ruthenate ceramics and crystals in the context of the elasticity. We identify the possible microstructure of ruthenate ceramics composed of crystal grains and cavities using structural topology optimization. We conclude that the measured large volumetric NTE of ruthenate ceramics is certainly possible via anisotropic crystallographic thermal expansion through an elastic mechanism.

Crystallographic phases in heavy rare earth metals under megabar pressures

NASA Astrophysics Data System (ADS)

Samudrala, G. K.; Vohra, Y. K.

2012-07-01

Experiments aimed at understanding the crystallographic phases of heavy rare earth metals were carried out in a diamond anvil cell at the Advanced Photon Source, Argonne National Laboratory. Heavy rare earth metals dysprosium (Dy), holmium (Ho), erbium (Er) and thulium (Tm) were compressed to multi-megabar pressures. The rare earth crystal sequence hcp→Sm-type→dhcp→distorted-fcc (dfcc) is observed in all four elements. Upon further compression, a structural transformation to a monoclinic C2/m phase has been observed. We summarize the results from these experiments and present Rietveld structural refinements on high pressure phases for the specific case of dysprosium.

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

NASA Astrophysics Data System (ADS)

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

2008-05-01

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

I Situ Surface X-Ray Diffraction Studies of Electrochemically Deposited Monolayers

NASA Astrophysics Data System (ADS)

Yee, Dennis

1995-01-01

In situ x-ray diffraction has been used to determine the detailed atomic structure of electrochemically deposited lead, thallium, and bismuth monolayers on the silver (111) electrode surface. A review of our previously published lead and thallium monolayer results and the first in situ surface x-ray crystallographic study of the bismuth monolayer structure is presented. The crystallographic analysis of the bismuth Bragg rod intensities and the interference between the bismuth Bragg rod and silver crystal truncation rod scattering were used to determine the detailed atomic structure of the bismuth on silver (111) system at the liquid-solid interface. Our previous in situ x-ray diffraction studies showed that the bismuth monolayer lattice is rectangular and uniaxially incommensurate with the underlying hexagonal silver surface. A crystallographic analysis of the measured structure factor magnitudes reveals that the monolayer forms chains of atoms on the silver surface, similar to the bulk Bi(110)_{rh} plane, with a near neighbor distance of 3.12 +/- 0.01 A and a bond angle of 93 +/- 1^circ, consistent with the bulk Bi(110) _{rh} plane values. The crystallographic refinement also shows that the bismuth monolayer atoms are anisotropically disordered with a rms disorder of 0.25 +/- 0.03 A in the incommensurate direction and 0.09 +/- 0.03 A rms in the commnensurate direction. The interference between the Bi(20) Bragg rod and the Ag(10L)_ {h} crystal truncation rod scattering reveals that one set of bismuth atoms is registered near the bridge sites of the silver (111) surface while another set is registered near the 3-fold hollow sites. In addition, the Bi-Ag d-spacing (3.1 +/- 0.1 A) is found to be consistent with the bulk bismuth near neighbor distance. The bismuth z-direction rms disorder (1.01 +/- 0.08 A) is found to be dominated by the roughness of the underlying silver (sigma_{Ag} = 0.9 +/- 0.1 A rms). Using the estimated bismuth-bismuth spring constant of 1.41 +/- 0.07 eV/A^2 from our measured bismuth two-dimensional compressibility, two simple models are used to try and understand the origin of the anisotropic disorder. A simple two-dimensional isotropic thermal fluctuation model shows that thermal fluctuations are not large enough to account for all of the measured excess disorder in the incommensurate direction. A simple one-dimensional Frenkel-Kontorova model shows that the substrate-induced disorder can account for the anisotropic disorder, assuming a substrate sinusoidal potential strength of 0.35 +/- 0.02 eV.

Maximum likelihood density modification by pattern recognition of structural motifs

DOEpatents

Terwilliger, Thomas C.

2004-04-13

An electron density for a crystallographic structure having protein regions and solvent regions is improved by maximizing the log likelihood of a set of structures factors {F.sub.h } using a local log-likelihood function: (x)+p(.rho.(x).vertline.SOLV)p.sub.SOLV (x)+p(.rho.(x).vertline.H)p.sub.H (x)], where p.sub.PROT (x) is the probability that x is in the protein region, p(.rho.(x).vertline.PROT) is the conditional probability for .rho.(x) given that x is in the protein region, and p.sub.SOLV (x) and p(.rho.(x).vertline.SOLV) are the corresponding quantities for the solvent region, p.sub.H (x) refers to the probability that there is a structural motif at a known location, with a known orientation, in the vicinity of the point x; and p(.rho.(x).vertline.H) is the probability distribution for electron density at this point given that the structural motif actually is present. One appropriate structural motif is a helical structure within the crystallographic structure.

Fine refinement of solid state structure of racemic form of phospho-tyrosine employing NMR Crystallography approach.

PubMed

Paluch, Piotr; Pawlak, Tomasz; Oszajca, Marcin; Lasocha, Wieslaw; Potrzebowski, Marek J

2015-02-01

We present step by step facets important in NMR Crystallography strategy employing O-phospho-dl-tyrosine as model sample. The significance of three major techniques being components of this approach: solid state NMR (SS NMR), X-ray diffraction of powdered sample (PXRD) and theoretical calculations (Gauge Invariant Projector Augmented Wave; GIPAW) is discussed. Each experimental technique provides different set of structural constraints. From the PXRD measurement the size of the unit cell, space group and roughly refined molecular structure are established. SS NMR provides information about content of crystallographic asymmetric unit, local geometry, molecular motion in the crystal lattice and hydrogen bonding pattern. GIPAW calculations are employed for validation of quality of elucidation and fine refinement of structure. Crystal and molecular structure of O-phospho-dl-tyrosine solved by NMR Crystallography is deposited at Cambridge Crystallographic Data Center under number CCDC 1005924. Copyright © 2014 Elsevier Inc. All rights reserved.

Crystallographic features of the approximant H (Mn7Si2V) phase in the Mn-Si-V alloy system

NASA Astrophysics Data System (ADS)

Nakayama, Kei; Komatsuzaki, Takumi; Koyama, Yasumasa

2018-07-01

The intermetallic compound H (Mn7Si2V) phase in the Mn-Si-V alloy system can be regarded as an approximant phase of the dodecagonal quasicrystal as one of the two-dimensional quasicrystals. To understand the features of the approximant H phase, in this study, the crystallographic features of both the H phase and the (σ → H) reaction in Mn-Si-V alloy samples were investigated, mainly by transmission electron microscopy. It was found that, in the H phase, there were characteristic structural disorders with respect to an array of a dodecagonal structural unit consisting of 19 dodecagonal atomic columns. Concretely, penetrated structural units consisting of two dodecagonal structural units were presumed to be typical of such disorders. An interesting feature of the (σ → H) reaction was that regions with a rectangular arrangement of penetrated structural units (RAPU) first appeared in the σ matrix as the initial state, and H regions were then nucleated in contact with RAPU regions. The subsequent conversion of RAPU regions into H regions eventually resulted in the formation of the approximant H state as the final state. Furthermore, atomic positions in both the H structure and the dodecagonal quasicrystal were examined using a simple plane-wave model with 12 plane waves.

Magnetic force microscopy studies in bulk polycrystalline iron

NASA Astrophysics Data System (ADS)

Abuthahir, J.; Kumar, Anish

2018-02-01

The paper presents magnetic force microscopy (MFM) studies on the effect of crystallographic orientation and external magnetic field on magnetic microstructure in a bulk polycrystalline iron specimen. The magneto crystalline anisotropic effect on the domain structure is characterized with the support of electron backscatter diffraction study. The distinct variations in magnetic domain structure are observed based on the crystallographic orientation of the grain surface normal with respect to the cube axis i.e. the easy axis of magnetization. Further, the local magnetization behavior is studied in-situ by MFM in presence of external magnetic field in the range of -2000 to 2000 Oe. Various micro-magnetization phenomena such as reversible and irreversible domain wall movements, expansion and contraction of domains, Barkhausen jump, bowing of a pinned domain wall and nucleation of a spike domain are visualized. The respective changes in the magnetic microstructure are compared with the bulk magnetization obtained using vibrating sample magnetometer. Bowing of a domain wall, pinned at two points, upon application of magnetic field is used to estimate the domain wall energy density. The MFM studies in presence of external field applied in two perpendicular directions are used to reveal the influence of the crystalline anisotropy on the local micro-magnetization.

Acquisition of a Thermophoresis Instrument for Molecular Association Thermodynamic Studies

DTIC Science & Technology

2015-05-20

using NAMD.27 Crystallographic structures of C3d ( PDB code 1C3D) and C3d-CR2 ( PDB code 3OED) were obtained from the protein data bank ( PDB ).28 Missing...This project is funded by DTRA (Defense Threat Reduction Agency) and aims to develop new multienzyme structures for the controlled destruction of...enable detection. Pharmacophore models were developed based on known C3d-ligand interactions and information from computational analysis of structural

Resolving the cofactor-binding site in the proline biosynthetic enzyme human pyrroline-5-carboxylate reductase 1

PubMed Central

Christensen, Emily M.; Patel, Sagar M.; Korasick, David A.; Campbell, Ashley C.; Krause, Kurt L.; Becker, Donald F.; Tanner, John J.

2017-01-01

Pyrroline-5-carboxylate reductase (PYCR) is the final enzyme in proline biosynthesis, catalyzing the NAD(P)H-dependent reduction of Δ1-pyrroline-5-carboxylate (P5C) to proline. Mutations in the PYCR1 gene alter mitochondrial function and cause the connective tissue disorder cutis laxa. Furthermore, PYCR1 is overexpressed in multiple cancers, and the PYCR1 knock-out suppresses tumorigenic growth, suggesting that PYCR1 is a potential cancer target. However, inhibitor development has been stymied by limited mechanistic details for the enzyme, particularly in light of a previous crystallographic study that placed the cofactor-binding site in the C-terminal domain rather than the anticipated Rossmann fold of the N-terminal domain. To fill this gap, we report crystallographic, sedimentation-velocity, and kinetics data for human PYCR1. Structures of binary complexes of PYCR1 with NADPH or proline determined at 1.9 Å resolution provide insight into cofactor and substrate recognition. We see NADPH bound to the Rossmann fold, over 25 Å from the previously proposed site. The 1.85 Å resolution structure of a ternary complex containing NADPH and a P5C/proline analog provides a model of the Michaelis complex formed during hydride transfer. Sedimentation velocity shows that PYCR1 forms a concentration-dependent decamer in solution, consistent with the pentamer-of-dimers assembly seen crystallographically. Kinetic and mutational analysis confirmed several features seen in the crystal structure, including the importance of a hydrogen bond between Thr-238 and the substrate as well as limited cofactor discrimination. PMID:28258219

Expression, purification, crystallization and X-ray crystallographic studies of different redox states of the active site of thioredoxin 1 from the whiteleg shrimp Litopenaeus vannamei

PubMed Central

Campos-Acevedo, Adam A.; Garcia-Orozco, Karina D.; Sotelo-Mundo, Rogerio R.; Rudiño-Piñera, Enrique

2013-01-01

Thioredoxin (Trx) is a 12 kDa cellular redox protein that belongs to a family of small redox proteins which undergo reversible oxidation to produce a cystine disulfide bond through the transfer of reducing equivalents from the catalytic site cysteine residues (Cys32 and Cys35) to a disulfide substrate. In this study, crystals of thioredoxin 1 from the Pacific whiteleg shrimp Litopenaeus vannamei (LvTrx) were successfully obtained. One data set was collected from each of four crystals at 100 K and the three-dimensional structures of the catalytic cysteines in different redox states were determined: reduced and oxidized forms at 2.00 Å resolution using data collected at a synchrotron-radiation source and two partially reduced structures at 1.54 and 1.88 Å resolution using data collected using an in-house source. All of the crystals belonged to space group P3212, with unit-cell parameters a = 57.5 (4), b = 57.5 (4), c = 118.1 (8) Å. The asymmetric unit contains two subunits of LvTrx, with a Matthews coefficient (V M) of 2.31 Å3 Da−1 and a solvent content of 46%. Initial phases were determined by molecular replacement using the crystallographic model of Trx from Drosophila melanogaster as a template. In the present work, LvTrx was overexpressed in Escherichia coli, purified and crystallized. Structural analysis of the different redox states at the Trx active site highlights its reactivity and corroborates the existence of a dimer in the crystal. In the crystallographic structures the dimer is stabilized by several interactions, including a disulfide bridge between Cys73 of each LvTrx monomer, a hydrogen bond between the side chain of Asp60 of each monomer and several hydrophobic interactions, with a noncrystallographic twofold axis. PMID:23695560

Preferred orientation in experimentally deformed stishovite: implications for deformation mechanisms

DOE PAGES

Kaercher, Pamela M.; Zepeda-Alarcon, Eloisa; Prakapenka, Vitali B.; ...

2014-11-07

Although the crystal structure of the high pressure SiO 2 polymorph stishovite has been studied in detail, little is known about the development of crystallographic preferred orientation (CPO) during deformation in stishovite. Insight into CPO and associated deformation mechanics of stishovite would provide important information for understanding subduction of quartz-bearing crustal rocks into the mantle. To study CPO development, we converted a natural sample of flint to stishovite in a laser heated diamond anvil cell and compressed the stishovite aggregate up to 38 GPa. We collected diffraction patterns in radial geometry to examine in situ development of crystallographic preferred orientationmore » and find that (001) poles preferentially align with the compression direction. Viscoplastic self-consistent modeling suggests the most likely slip systems at high pressure and ambient temperature are pyramidal and basal slip.« less

Structural and morphological study of ZrO2 thin films

NASA Astrophysics Data System (ADS)

Kumar, Davinder; Singh, Avtar; Kaur, Manpreet; Rana, Vikrant Singh; Kaur, Raminder

2018-05-01

In this paper we discuss the fabrication of transparent thin films of Zirconium Oxide (ZrO2) deposited on glass substrates by sol-gel dip coating technique. Further these fabricated films were characterized for different annealing temperatures and withdrawal speed. X-ray diffraction is used to study the structural properties of deposited thin films and it reveals the change in crystallographic properties with the change in annealing temperature. Thickness of thin films is estimated by using scanning electron microscope.

Crystallographic studies on complexes of potassium iodide and copper perchlorate with N, Nʹ-dicyclohexylurea tethered to a benzo-12-crown-4

NASA Astrophysics Data System (ADS)

Tripathi, Garima; Ramanathan, Gurunath

2018-03-01

The N, N‧-dicyclohexylurea-capped benzo-12-crown-4 (compound 1) has been synthesized. The coordination behaviour of this compound (1) has been studied by crystallizing it with KI (2) and Cu(ClO4)2 (3) salts. The crystallographic studies were performed with all three compounds. The presence of metal ions significantly affects the crystal packing of the compound 1. The crystal lattice of compound 1 was stabilized by Csbnd H⋯π and Cdbnd O⋯Hsbnd N hydrogen bonding. The presence of KI in compound 2 results in a dimer structure in which iodide anion behaves as a bridging ligand. The K+ forms a perching structure with the crown ring. In the compound 3, Cu2+ ion and ligand molecule (1) crystallized independently. They were connected through hydrogen bonding. Interestingly, Cu2+ adopts two different geometries with the coordination number 5 and 6. The centre Cu2+ (Cu1) adopted an octahedral geometry whereas the terminal Cu2+ (Cu2) acquired square pyramidal geometry. The coordination sphere of Cu2+ contains ClO4- anion and water molecules. Cu2+ ion forms a chain structure through ClO4- anion and water molecules involve in hydrogen bonding with the ligand molecule.

Discovery of covalent inhibitors for MIF tautomerase via cocrystal structures with phantom hits from virtual screening

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

McLean, Larry R.; Zhang, Ying; Li, Hua

Biochemical and X-ray crystallographic studies confirmed that hydroxyquinoline derivatives identified by virtual screening were actually covalent inhibitors of the MIF tautomerase. Adducts were formed by N-alkylation of the Pro-1 at the catalytic site with a loss of an amino group of the inhibitor.

Crystallization and preliminary X-ray crystallographic analysis of agkicetin-C from Deinagkistrodon acutus venom

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

Xu, Gufeng; Departments of Molecular and Cell Biology, School of Life Sciences, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui 230026; Huang, Qingqiu

2005-01-01

The crystallization and preliminary crystallographic analysis of agkicetin-C, a well known platelet glycoprotein Ib (GPIb) antagonist from the venom of Deinagkistrodon acutus found in Anhui Province, China is reported. The crystallization and preliminary crystallographic analysis of agkicetin-C, a well known platelet glycoprotein Ib (GPIb) antagonist from the venom of Deinagkistrodon acutus found in Anhui Province, China is reported. Crystals of agkicetin-C suitable for structure determination were obtained from 1.8 M ammonium sulfate, 40 mM MES pH 6.5 with 2%(v/v) PEG 400. Interestingly, low buffer concentrations of MES seem to be necessary for crystal growth. The crystals of agkicetin-C belong tomore » space group C2, with unit-cell parameters a = 177.5, b = 97.7, c = 106.8 Å, β = 118.5°, and diffract to 2.4 Å resolution. Solution of the phase problem by the molecular-replacement method shows that there are four agkicetin-C molecules in the asymmetric unit, with a V{sub M} value of 3.4 Å{sup 3} Da{sup −1}, which corresponds to a high solvent content of approximately 64%. Self-rotation function calculations show a single well defined non-crystallographic twofold axis with features that may represent additional elements of non-crystallographic symmetry.« less

X-Ray Crystallographic Studies on Acetylcholinesterase and Related Enzymes.

DTIC Science & Technology

1999-10-01

nerve gas intoxication, as well as of insecticide poisoning. Such structures can yield direct information concerning the functional groups and steric...Glyll7His mutant (48). Recent solution of the 3D structures of conjugates of the nerve agents , sarin, soman, DFP and VX with 7cAChE (49, 50) has revealed... pesticides and chemical warfare agents is a topic of considerable environmental and toxicological importance. Hence, a substantial research effort is being

Structural Studies on Dy to 119 GPa and Applications to Lanthanide Systematics

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

Patterson, J; Akella, J

2005-05-31

The Rare Earth elements (REE) are known to undergo crystallographic as well as electronic structure changes with applied pressure. On increasing pressure, the trivalent lanthanides follow the sequence hcp {yields} Sm-type {yields} dhcp {yields} fcc {yields} dfcc. In this report we present room-temperature high-pressure x-ray diffraction data for Dy as well as our observations on the post-dfcc phases and concomitant volume changes in the heavy REE.

Oxide nanoparticles in an Al-alloyed oxide dispersion strengthened steel: crystallographic structure and interface with ferrite matrix

NASA Astrophysics Data System (ADS)

Zhang, Zhenbo; Pantleon, Wolfgang

2017-07-01

Oxide nanoparticles are quintessential for ensuring the extraordinary properties of oxide dispersion strengthened (ODS) steels. In this study, the crystallographic structure of oxide nanoparticles, and their interface with the ferritic steel matrix in an Al-alloyed ODS steel, i.e. PM2000, were systematically investigated by high-resolution transmission electron microscopy. The majority of oxide nanoparticles were identified to be orthorhombic YAlO3. During hot consolidation and extrusion, they develop a coherent interface and a near cuboid-on-cube orientation relationship with the ferrite matrix in the material. After annealing at 1200 °C for 1 h, however, the orientation relationship between the oxide nanoparticles and the matrix becomes arbitrary, and their interface mostly incoherent. Annealing at 1300 °C leads to considerable coarsening of oxide nanoparticles, and a new orientation relationship of pseudo-cube-on-cube between oxide nanoparticles and ferrite matrix develops. The reason for the developing interfaces and orientation relationships between oxide nanoparticles and ferrite matrix under different conditions is discussed.

Crystalline Structure and Physical Properties of UCo2Al3

NASA Astrophysics Data System (ADS)

Verdín, E.; Escudero, R.

Some intermetallic compounds which contain uranium or cerium present heavy fermion characteristics. Take, for example, in the UM2Al3 (M=Pd, Ni) family, superconductivity and magnetism coexist and present heavy fermion behavior. This work presents the crystallographic characteristics and physical properties of a new compound of this family; the intermetallic compound UCo2Al3. Our initial crystallographic studies performed in a small single crystal show that the structure is hexagonal and similar to the UNi2Al3 and UPd2Al3 parent compounds. The space group is P6/mmm with a=5.125 Å and c=4.167 Å crystalline parameters. Measurements of resistivity and magnetization performed on the single crystal reveal that the compound is not superconducting when measured at about 1.8 K. The compound is highly anisotropic and features related to Kondo-like behavior are observed. A weak ferromagnetic transition is observed at a temperature of about 20 K.

Evaluation of crystallographic strain, rotation and defects in functional oxides by the moiré effect in scanning transmission electron microscopy.

PubMed

Naden, A B; O'Shea, K J; MacLaren, D A

2018-04-20

Moiré patterns in scanning transmission electron microscopy (STEM) images of epitaxial perovskite oxides are used to assess strain and defect densities over fields of view extending over several hundred nanometers. The patterns arise from the geometric overlap of the rastered STEM electron beam and the samples' crystal periodicities and we explore the emergence and application of these moiré fringes for rapid strain analysis. Using the epitaxial functional oxide perovskites BiFeO 3 and Pr 1-x Ca x MnO 3 , we discuss the impact of large degrees of strain on the quantification of STEM moiré patterns, identify defects in the fringe patterns and quantify strain and lattice rotation. Such a wide-area analysis of crystallographic strain and defects is crucial for developing structure-function relations of functional oxides and we find the STEM moiré technique to be an attractive means of structural assessment that can be readily applied to low dose studies of damage sensitive crystalline materials.

Evaluation of crystallographic strain, rotation and defects in functional oxides by the moiré effect in scanning transmission electron microscopy

NASA Astrophysics Data System (ADS)

Naden, A. B.; O'Shea, K. J.; MacLaren, D. A.

2018-04-01

Moiré patterns in scanning transmission electron microscopy (STEM) images of epitaxial perovskite oxides are used to assess strain and defect densities over fields of view extending over several hundred nanometers. The patterns arise from the geometric overlap of the rastered STEM electron beam and the samples’ crystal periodicities and we explore the emergence and application of these moiré fringes for rapid strain analysis. Using the epitaxial functional oxide perovskites BiFeO3 and Pr1-x Ca x MnO3, we discuss the impact of large degrees of strain on the quantification of STEM moiré patterns, identify defects in the fringe patterns and quantify strain and lattice rotation. Such a wide-area analysis of crystallographic strain and defects is crucial for developing structure-function relations of functional oxides and we find the STEM moiré technique to be an attractive means of structural assessment that can be readily applied to low dose studies of damage sensitive crystalline materials.

Control of Polarization of Vertical-Cavity Surface - Lasers

NASA Astrophysics Data System (ADS)

Sun, Decai

1995-01-01

To date, most vertical-cavity surface-emitting lasers (VCSELs) have been fabricated from structures grown on GaAs (InP) substrates oriented in the (001) crystallographic axis. For the most part, these devices have exhibited linear, but random polarization states with no definite relationship to the in-plane crystallographic axes. The control of the polarization states of these devices is important for polarization-sensitive applications. Such applications include magneto-optic disk recording and coherent detection in advanced communication systems. In this thesis, a novel approach for controlling the polarization eigen-states of VCSELs is investigated. The approach utilizes anisotropic optical properties found in quantum wells (QW) oriented in directions other than the (001) to stabilize their polarization states. Specifically, the (110) direction is chosen for this work. An analysis of the in-plane optical matrix element connected with the gain coefficient of (In,Ga)As/GaAs QW structures grown on (110) GaAs substrates is conducted. It is found that the in-plane gain distribution is elliptically anisotropic--with a maximum directed along the (110) - (110) crystallographic axis. The design and growth of (In,Ga)As/GaAs QW VCSEL structures is studied in this work. The transition wavelengths of the (001) - and (110) -oriented (In,Ga)As/GaAs QW structures are calculated using a finite QW model. Distributed Bragg reflector mirrors consisting of GaAs/AlAs quarter wave layers are modeled using a characteristic matrix method. Threshold gain, internal and differential quantum efficiencies are analyzed. The growth of III-V compounds on (110) GaAs substrates by molecular beam epitaxy is investigated. High quality materials are successfully grown on the misoriented (110) GaAs substrates tilted by 6^circ toward the (111)B surface. (In,Ga)As/GaAs QW VCSEL structures are grown on (001) and (110) GaAs substrates. (In,Ga)As/GaAs QW VCSELs are fabricated from structures grown on the (001) and (110) surfaces. Experimental characterization shows that the devices fabricated from the (110) surface exhibit stable, well-defined polarization states at room temperature; this is in contrast to the random polarization characteristics observed from the VCSELs fabricated from the (001) surface. This stability is believed to be a consequence of the predicted anisotropic gain distribution on the (110) surface. Of the two orthogonal eigen-polarizations observed, the one with the higher optical intensity is found to be aligned along the (110) - (110) crystallographic axis; this is in agreement with theoretical predictions.

Crystal structure and magnetic properties of Mn substituted ludwigite Co 3O 2BO 3

NASA Astrophysics Data System (ADS)

Knyazev, Yu. V.; Ivanova, N. B.; Kazak, N. V.; Platunov, M. S.; Bezmaternykh, L. N.; Velikanov, D. А.; Vasiliev, А. D.; Ovchinnikov, S. G.; Yurkin, G. Yu.

2012-03-01

The needle shape single crystals Co3-x MnxO2BO3 with ludwigite structure have been prepared. According to the X-ray diffraction data the preferable character of distinct crystallographic positions occupation by Mn ions is established. Magnetization field and temperature dependencies are measured. Paramagnetic Curie temperature value Θ=-100 K points out the predominance of antiferromagnetic interactions. Spin-glass magnetic ordering takes the onset at TN=41 K. The crystallographic and magnetic properties of Co3O2BO3:Mn are compared with the same for the isostructural analogs Co3O2BO3 and CoO2BO3:Fe.

Nanoparticle Superlattice Engineering with DNA

NASA Astrophysics Data System (ADS)

Macfarlane, Robert J.; Lee, Byeongdu; Jones, Matthew R.; Harris, Nadine; Schatz, George C.; Mirkin, Chad A.

2011-10-01

A current limitation in nanoparticle superlattice engineering is that the identities of the particles being assembled often determine the structures that can be synthesized. Therefore, specific crystallographic symmetries or lattice parameters can only be achieved using specific nanoparticles as building blocks (and vice versa). We present six design rules that can be used to deliberately prepare nine distinct colloidal crystal structures, with control over lattice parameters on the 25- to 150-nanometer length scale. These design rules outline a strategy to independently adjust each of the relevant crystallographic parameters, including particle size (5 to 60 nanometers), periodicity, and interparticle distance. As such, this work represents an advance in synthesizing tailorable macroscale architectures comprising nanoscale materials in a predictable fashion.

Phasing via pure crystallographic least squares: an unexpected feature.

PubMed

Burla, Maria Cristina; Carrozzini, Benedetta; Cascarano, Giovanni Luca; Giacovazzo, Carmelo; Polidori, Giampiero

2018-03-01

Crystallographic least-squares techniques, the main tool for crystal structure refinement of small and medium-size molecules, are for the first time used for ab initio phasing. It is shown that the chief obstacle to such use, the least-squares severe convergence limits, may be overcome by a multi-solution procedure able to progressively recognize and discard model atoms in false positions and to include in the current model new atoms sufficiently close to correct positions. The applications show that the least-squares procedure is able to solve many small structures without the use of important ancillary tools: e.g. no electron-density map is calculated as a support for the least-squares procedure.

Low Loss Substrates for Microwave Applications and Sol-Gel Processing of Superconductors

DTIC Science & Technology

1994-03-31

crystallographic axis normal to solid state technology, in the growth of ferrimagnetic garnets the substrate plane) or. better, in "epitaxial" films (i.e...hay- by liquid phase epitaxy ( LPE ). is from a melt using a para- ing their three crystallographic axes related to those of a magnetic garnet structure...yttrium barium cuprate (YBCO) films and their microwave applications have been carried out. Several promising new hosts such as Sr(All/2Tal/2)03, Sr(Al1

Crystallographic Orientation Effect on Electromigration in Ni-Sn Microbump

NASA Astrophysics Data System (ADS)

Huang, Yi-Ting; Chen, Chih-Hao; Chakroborty, Subhendu; Wu, Albert T.

2017-09-01

This article addresses the reliability challenges regarding electromigration in developing three-dimensional integrated circuits (3D-ICs). The line-type sandwich structure of Ni/Sn3.5Ag(15 μm)/Ni was used to simulate microbumps to examine the reliability of electromigration in 3D-IC technology. The solder strip of Ni/Sn3.5Ag(15 μm)/Ni was stressed with a current density of 1.0 × 104 A/cm2 at 150°C. The current stressing enhanced the reaction between the solder and Ni to form Ni3Sn4, which occupied the entire joint and transformed into a Ni/Ni3Sn4/Ni structure when the solder was completely consumed. Electron backscatter diffraction was used to analyze the crystallographic characteristics of Sn and Ni3Sn4 as related to the electromigration effect. The results indicated that the crystallographic orientation of Sn plays a significant role in the Ni/Sn3.5Ag/Ni, whereas the orientation of Ni3Sn4 is the dominant factor of diffusion behavior in the Ni/Ni3Sn4/Ni.

NMR crystallography of oxybuprocaine hydrochloride, Modification II degrees.

PubMed

Harris, Robin K; Cadars, Sylvian; Emsley, Lyndon; Yates, Jonathan R; Pickard, Chris J; Jetti, Ram K R; Griesser, Ulrich J

2007-01-21

The (13)C CPMAS spectrum is presented for the polymorph of oxybuprocaine hydrochloride which is stable at room temperature, i.e. Mod. II degrees . It shows crystallographic splittings arising from the fact that there are two molecules, with substantially different conformations, in the asymmetric unit. An INADEQUATE two-dimensional experiment was used to link signals for the same independent molecule. The chemical shifts are discussed in relation to the crystal structure. Of the four ethyl groups attached to NH(+) nitrogens, one gives rise to unusually low chemical shifts, very different from those of the other three ethyl groups. This is attributed empirically to gamma-gauche conformational effects, as is confirmed by shielding computations. These considerations allow (13)C signals to be assigned to specific carbons in the two crystallographically inequivalent molecules in the crystal structure. Indeed, information about the conformations is inherent in the NMR spectrum, which thus provides data of crystallographic significance. A (13)C/(1)H HETCOR experiment enabled resolution to be obtained in the (1)H dimension and allowed (1)H and (13)C signals for the same independent molecule to be linked.

Advantages of Crystallographic Fragment Screening: Functional and Mechanistic Insights from a Powerful Platform for Efficient Drug Discovery

PubMed Central

Patel, Disha; Bauman, Joseph D.; Arnold, Eddy

2015-01-01

X-ray crystallography has been an under-appreciated screening tool for fragment-based drug discovery due to the perception of low throughput and technical difficulty. Investigators in industry and academia have overcome these challenges by taking advantage of key factors that contribute to a successful crystallographic screening campaign. Efficient cocktail design and soaking methodologies have evolved to maximize throughput while minimizing false positives/negatives. In addition, technical improvements at synchrotron beamlines have dramatically increased data collection rates thus enabling screening on a timescale comparable to other techniques. The combination of available resources and efficient experimental design has resulted in many successful crystallographic screening campaigns. The three-dimensional crystal structure of the bound fragment complexed to its target, a direct result of the screening effort, enables structure-based drug design while revealing insights regarding protein dynamics and function not readily obtained through other experimental approaches. Furthermore, this “chemical interrogation” of the target protein crystals can lead to the identification of useful reagents for improving diffraction resolution or compound solubility. PMID:25117499

Advantages of crystallographic fragment screening: functional and mechanistic insights from a powerful platform for efficient drug discovery.

PubMed

Patel, Disha; Bauman, Joseph D; Arnold, Eddy

2014-01-01

X-ray crystallography has been an under-appreciated screening tool for fragment-based drug discovery due to the perception of low throughput and technical difficulty. Investigators in industry and academia have overcome these challenges by taking advantage of key factors that contribute to a successful crystallographic screening campaign. Efficient cocktail design and soaking methodologies have evolved to maximize throughput while minimizing false positives/negatives. In addition, technical improvements at synchrotron beamlines have dramatically increased data collection rates thus enabling screening on a timescale comparable to other techniques. The combination of available resources and efficient experimental design has resulted in many successful crystallographic screening campaigns. The three-dimensional crystal structure of the bound fragment complexed to its target, a direct result of the screening effort, enables structure-based drug design while revealing insights regarding protein dynamics and function not readily obtained through other experimental approaches. Furthermore, this "chemical interrogation" of the target protein crystals can lead to the identification of useful reagents for improving diffraction resolution or compound solubility. Copyright © 2014. Published by Elsevier Ltd.

RCrane: semi-automated RNA model building.

PubMed

Keating, Kevin S; Pyle, Anna Marie

2012-08-01

RNA crystals typically diffract to much lower resolutions than protein crystals. This low-resolution diffraction results in unclear density maps, which cause considerable difficulties during the model-building process. These difficulties are exacerbated by the lack of computational tools for RNA modeling. Here, RCrane, a tool for the partially automated building of RNA into electron-density maps of low or intermediate resolution, is presented. This tool works within Coot, a common program for macromolecular model building. RCrane helps crystallographers to place phosphates and bases into electron density and then automatically predicts and builds the detailed all-atom structure of the traced nucleotides. RCrane then allows the crystallographer to review the newly built structure and select alternative backbone conformations where desired. This tool can also be used to automatically correct the backbone structure of previously built nucleotides. These automated corrections can fix incorrect sugar puckers, steric clashes and other structural problems.

In-plane isotropic magnetic and electrical properties of MnAs/InAs/GaAs (111) B hybrid structure

NASA Astrophysics Data System (ADS)

Islam, Md. Earul; Akabori, Masashi

2018-03-01

We characterized in-plane magnetic and electrical properties of MnAs/InAs/GaAs (111) B hybrid structure grown by molecular beam epitaxy (MBE). We observed isotropic easy magnetization in two crystallographic in-plane directions, [ 2 ̅ 110 ] and [ 0 1 ̅ 10 ] of hexagonal MnAs i.e. [ 1 ̅ 10 ] and [ 11 2 ̅ ] of cubic InAs. We also fabricated transmission line model (TLM) devices, and observed almost isotropic electrical properties in two crystallographic in-plane directions, [ 1 ̅ 10 ] and [ 11 2 ̅ ] of cubic InAs. Also we tried to fabricate and characterize lateral spin-valve (LSV) devices from the hybrid structure. We could roughly estimate the spin injection efficiency and the spin diffusion length at room temperature in [ 11 2 ̅ ] direction. We believe that the hybrid structures are helpful to design spintronic device with good flexibility in-plane.

Understanding pre-mRNA splicing through crystallography.

PubMed

Espinosa, Sara; Zhang, Lingdi; Li, Xueni; Zhao, Rui

2017-08-01

Crystallography is a powerful tool to determine the atomic structures of proteins and RNAs. X-ray crystallography has been used to determine the structure of many splicing related proteins and RNAs, making major contributions to our understanding of the molecular mechanism and regulation of pre-mRNA splicing. Compared to other structural methods, crystallography has its own advantage in the high-resolution structural information it can provide and the unique biological questions it can answer. In addition, two new crystallographic methods - the serial femtosecond crystallography and 3D electron crystallography - were developed to overcome some of the limitations of traditional X-ray crystallography and broaden the range of biological problems that crystallography can solve. This review discusses the theoretical basis, instrument requirements, troubleshooting, and exciting potential of these crystallographic methods to further our understanding of pre-mRNA splicing, a critical event in gene expression of all eukaryotes. Copyright © 2017 Elsevier Inc. All rights reserved.

Unraveling the Origin of Structural Disorder in High Temperature Transition Al2O3: Structure of θ-Al2O3

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

Kovarik, Libor; Bowden, Mark E.; Shi, Dachuan

The crystallography of transition Al2O3 has been extensively studied in the past due to the advantageous properties of the oxide in catalytic and a range of other technological applications. However, existing crystallographic models are insufficient to describe the structure of many important Al2O3 polymorphs due to their highly disordered nature. In this work, we investigate structure and disorder in high-temperature treated transition Al2O3, and provide a structural description for θ-Al2O3 by using a suite of complementary imaging, spectroscopy and quantum calculation techniques. Contrary to current understanding, our high-resolution imaging shows that θ-Al2O3 is a disordered composite phase of at leastmore » two different end members. By correlating imaging and spectroscopy results with DFT calculations, we propose a model that describes θ-Al2O3 as a disordered intergrowth of two crystallographic variants at the unit cell level. One variant is based on β-Ga2O3, and the other on a monoclinic phase that is closely-related to δ-Al2O3. The overall findings and interpretations afford new insight into the origin of poor crystallinity in transition Al2O3, and also provide new perspectives on structural complexity that can emerge from intergrowth of closely related structural polymorphs.« less

Data to knowledge: how to get meaning from your result.

PubMed

Berman, Helen M; Gabanyi, Margaret J; Groom, Colin R; Johnson, John E; Murshudov, Garib N; Nicholls, Robert A; Reddy, Vijay; Schwede, Torsten; Zimmerman, Matthew D; Westbrook, John; Minor, Wladek

2015-01-01

Structural and functional studies require the development of sophisticated 'Big Data' technologies and software to increase the knowledge derived and ensure reproducibility of the data. This paper presents summaries of the Structural Biology Knowledge Base, the VIPERdb Virus Structure Database, evaluation of homology modeling by the Protein Model Portal, the ProSMART tool for conformation-independent structure comparison, the LabDB 'super' laboratory information management system and the Cambridge Structural Database. These techniques and technologies represent important tools for the transformation of crystallographic data into knowledge and information, in an effort to address the problem of non-reproducibility of experimental results.

Structural characterization of framework–gas interactions in the metal–organic framework Co2(dobdc) by in situ single-crystal X-ray diffraction† †Electronic supplementary information (ESI) available: Supplementary figures, crystallographic information, adsorption isotherms and fits, CCDC 1530119–1530126. For ESI and crystallographic data in CIF or other electronic format. See DOI: 10.1039/c7sc00449d Click here for additional data file. Click here for additional data file.

PubMed Central

Gonzalez, Miguel I.; Mason, Jarad A.; Bloch, Eric D.; Teat, Simon J.; Gagnon, Kevin J.; Morrison, Gregory Y.; Queen, Wendy L.

2017-01-01

The crystallographic characterization of framework–guest interactions in metal–organic frameworks allows the location of guest binding sites and provides meaningful information on the nature of these interactions, enabling the correlation of structure with adsorption behavior. Here, techniques developed for in situ single-crystal X-ray diffraction experiments on porous crystals have enabled the direct observation of CO, CH4, N2, O2, Ar, and P4 adsorption in Co2(dobdc) (dobdc4– = 2,5-dioxido-1,4-benzenedicarboxylate), a metal–organic framework bearing coordinatively unsaturated cobalt(ii) sites. All these molecules exhibit such weak interactions with the high-spin cobalt(ii) sites in the framework that no analogous molecular structures exist, demonstrating the utility of metal–organic frameworks as crystalline matrices for the isolation and structural determination of unstable species. Notably, the Co–CH4 and Co–Ar interactions observed in Co2(dobdc) represent, to the best of our knowledge, the first single-crystal structure determination of a metal–CH4 interaction and the first crystallographically characterized metal–Ar interaction. Analysis of low-pressure gas adsorption isotherms confirms that these gases exhibit mainly physisorptive interactions with the cobalt(ii) sites in Co2(dobdc), with differential enthalpies of adsorption as weak as –17(1) kJ mol–1 (for Ar). Moreover, the structures of Co2(dobdc)·3.8N2, Co2(dobdc)·5.9O2, and Co2(dobdc)·2.0Ar reveal the location of secondary (N2, O2, and Ar) and tertiary (O2) binding sites in Co2(dobdc), while high-pressure CO2, CO, CH4, N2, and Ar adsorption isotherms show that these binding sites become more relevant at elevated pressures. PMID:28966783

Refolding, crystallization and preliminary X-ray crystallographic studies of the β-barrel domain of BamA, a membrane protein essential for outer membrane protein biogenesis.

PubMed

Ni, Dongchun; Yang, Kun; Huang, Yihua

2014-03-01

In Gram-negative bacteria, the assembly of outer membrane proteins (OMPs) requires a five-protein β-barrel assembly machinery (BAM) complex, of which BamA is an essential and evolutionarily conserved integral outer membrane protein. Here, the refolding, crystallization and preliminary X-ray crystallographic characterization of the β-barrel domain of BamA from Escherichia coli (EcBamA) are reported. Native and selenomethionine-substituted EcBamA proteins were crystallized at 16°C and X-ray diffraction data were collected to 2.6 and 3.7 Å resolution, respectively. The native crystals belonged to space group P21212, with unit-cell parameters a = 118.492, b = 159.883, c = 56.000 Å and two molecules in one asymmetric unit; selenomethionine-substituted protein crystals belonged to space group P4322, with unit-cell parameters a = b = 163.162, c = 46.388 Å and one molecule in one asymmetric unit. Initial phases for EcBamA β-barrel domain were obtained from a SeMet SAD data set. These preliminary X-ray crystallographic studies paved the way for further structural determination of the β-barrel domain of EcBamA.

The role of crystallographic texture in achieving low friction zinc oxide nanolaminate films

NASA Astrophysics Data System (ADS)

Mojekwu, Nneoma

Metal oxide nanolaminate films are potential high temperature solid lubricants due to their ability to exhibit significant plasticity when grain size is reduced to the nanometer scale, and defective growth structure is achieved by condensation of oxygen vacancies to form intrinsic stacking faults. This is in contrast to conventional microcrystalline and single crystal oxides that exhibit brittle fracture during loading in a sliding contact. This study emphasizes the additional effect of growth orientation, in particular crystallographic texture, on determining the sliding friction behavior in nanocolumnar grain zinc oxide films grown by atomic layer deposition. It was determined that zinc oxide low (0002) versus higher (101¯3) surface energy crystallographic planes influenced the sliding friction coefficient. Texturing of the (0002) grains resulted in a decreased adhesive component of friction thereby lowering the sliding friction coefficient to ˜0.25, while the friction coefficient doubled to ˜0.5 with increasing contribution of surface (101¯3) grains. In addition, the variation of the x-ray grazing incident angle from 0.5° to 5° was studied to better understand the surface grain orientation as a function of ZnO layer thickness in one versus four bilayer nanolaminates where the under layer (seed layer) was load-bearing Zn(Ti,Zr)O3.

Does the choice of the crystal structure influence the results of the periodic DFT calculations? A case of glycine alpha polymorph GIPAW NMR parameters computations.

PubMed

Szeleszczuk, Łukasz; Pisklak, Dariusz Maciej; Zielińska-Pisklak, Monika

2018-05-30

Glycine is a common amino acid with relatively complex chemistry in solid state. Although several polymorphs (α, β, δ, γ, ε) of crystalline glycine are known, for NMR spectroscopy the most important is a polymorph, which is used as a standard for calibration of spectrometer performance and therefore it is intensively studied by both experimental methods and theoretical computation. The great scientific interest in a glycine results in a large number of crystallographic information files (CIFs) deposited in Cambridge Structural Database (CSD). The aim of this study was to evaluate the influence of the chosen crystal structure of α glycine obtained in different crystallographic experimental conditions (temperature, pressure and source of radiation of α glycine) on the results of periodic DFT calculation. For this purpose the total of 136 GIPAW calculations of α glycine NMR parameters were performed, preceded by the four approaches ("SP", "only H", "full", "full+cell") of structure preparation. The analysis of the results of those computations performed on the representative group of 34 structures obtained at various experimental conditions revealed that though the structures were generally characterized by good accuracy (R < 0.05 for most of them) the results of the periodic DFT calculations performed using the unoptimized structures differed significantly. The values of the standard deviations of the studied NMR parameters were in most cases decreasing with the number of optimized parameters. The most accurate results (of the calculations) were in most cases obtained using the structures with solely hydrogen atoms positions optimized. © 2018 Wiley Periodicals, Inc. © 2018 Wiley Periodicals, Inc.

Structural and stereoelectronic insights into oxygenase-catalyzed formation of ethylene from 2-oxoglutarate.

PubMed

Zhang, Zhihong; Smart, Tristan J; Choi, Hwanho; Hardy, Florence; Lohans, Christopher T; Abboud, Martine I; Richardson, Melodie S W; Paton, Robert S; McDonough, Michael A; Schofield, Christopher J

2017-05-02

Ethylene is important in industry and biological signaling. In plants, ethylene is produced by oxidation of 1-aminocyclopropane-1-carboxylic acid, as catalyzed by 1-aminocyclopropane-1-carboxylic acid oxidase. Bacteria catalyze ethylene production, but via the four-electron oxidation of 2-oxoglutarate to give ethylene in an arginine-dependent reaction. Crystallographic and biochemical studies on the Pseudomonas syringae ethylene-forming enzyme reveal a branched mechanism. In one branch, an apparently typical 2-oxoglutarate oxygenase reaction to give succinate, carbon dioxide, and sometimes pyrroline-5-carboxylate occurs. Alternatively, Grob-type oxidative fragmentation of a 2-oxoglutarate-derived intermediate occurs to give ethylene and carbon dioxide. Crystallographic and quantum chemical studies reveal that fragmentation to give ethylene is promoted by binding of l-arginine in a nonoxidized conformation and of 2-oxoglutarate in an unprecedented high-energy conformation that favors ethylene, relative to succinate formation.

Protein stability: a crystallographer’s perspective

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

Deller, Marc C., E-mail: mdeller@stanford.edu; Kong, Leopold; Rupp, Bernhard

An understanding of protein stability is essential for optimizing the expression, purification and crystallization of proteins. In this review, discussion will focus on factors affecting protein stability on a somewhat practical level, particularly from the view of a protein crystallographer. Protein stability is a topic of major interest for the biotechnology, pharmaceutical and food industries, in addition to being a daily consideration for academic researchers studying proteins. An understanding of protein stability is essential for optimizing the expression, purification, formulation, storage and structural studies of proteins. In this review, discussion will focus on factors affecting protein stability, on a somewhatmore » practical level, particularly from the view of a protein crystallographer. The differences between protein conformational stability and protein compositional stability will be discussed, along with a brief introduction to key methods useful for analyzing protein stability. Finally, tactics for addressing protein-stability issues during protein expression, purification and crystallization will be discussed.« less

Experimental and first principle studies on electronic structure of BaTiO{sub 3}

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

Sagdeo, Archna, E-mail: archnaj@rrcat.gov.in; Ghosh, Haranath, E-mail: archnaj@rrcat.gov.in; Chakrabarti, Aparna, E-mail: archnaj@rrcat.gov.in

2014-04-24

We have carried out photoemission experiments to obtain valence band spectra of various crystallographic symmetries of BaTiO{sub 3} system which arise as a function of temperature. We also present results of a detailed first principle study of these symmetries of BaTiO{sub 3} using generalized gradient approximation for the exchange-correlation potential. Here we present theoretical results of density of states obtained from DFT based simulations to compare with the experimental valence band spectra. Further, we also perform calculations using post density functional approaches like GGA + U method as well as non-local hybrid exchange-correlation potentials like PBE0, B3LYP, HSE in ordermore » to understand the extent of effect of correlation on band gaps of different available crystallographic symmetries (5 in number) of BaTiO{sub 3}.« less

Quantum mechanics models of the methanol dimer: O-H…O hydrogen bonds of ß-D-glucose moieties from crystallographic data.

USDA-ARS?s Scientific Manuscript database

In this study, a survey of the Cambridge Crystal Structure Database for all donor-acceptor interactions in ß-D-glucose moieties was performed to examine the similarities and differences among the different hydroxyl groups and ether oxygen atoms that participate in hydrogen bonds. Comparable behavior...

CIF2Cell: Generating geometries for electronic structure programs

NASA Astrophysics Data System (ADS)

Björkman, Torbjörn

2011-05-01

The CIF2Cell program generates the geometrical setup for a number of electronic structure programs based on the crystallographic information in a Crystallographic Information Framework (CIF) file. The program will retrieve the space group number, Wyckoff positions and crystallographic parameters, make a sensible choice for Bravais lattice vectors (primitive or principal cell) and generate all atomic positions. Supercells can be generated and alloys are handled gracefully. The code currently has output interfaces to the electronic structure programs ABINIT, CASTEP, CPMD, Crystal, Elk, Exciting, EMTO, Fleur, RSPt, Siesta and VASP. Program summaryProgram title: CIF2Cell Catalogue identifier: AEIM_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEIM_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: GNU GPL version 3 No. of lines in distributed program, including test data, etc.: 12 691 No. of bytes in distributed program, including test data, etc.: 74 933 Distribution format: tar.gz Programming language: Python (versions 2.4-2.7) Computer: Any computer that can run Python (versions 2.4-2.7) Operating system: Any operating system that can run Python (versions 2.4-2.7) Classification: 7.3, 7.8, 8 External routines: PyCIFRW [1] Nature of problem: Generate the geometrical setup of a crystallographic cell for a variety of electronic structure programs from data contained in a CIF file. Solution method: The CIF file is parsed using routines contained in the library PyCIFRW [1], and crystallographic as well as bibliographic information is extracted. The program then generates the principal cell from symmetry information, crystal parameters, space group number and Wyckoff sites. Reduction to a primitive cell is then performed, and the resulting cell is output to suitably named files along with documentation of the information source generated from any bibliographic information contained in the CIF file. If the space group symmetries is not present in the CIF file the program will fall back on internal tables, so only the minimal input of space group, crystal parameters and Wyckoff positions are required. Additional key features are handling of alloys and supercell generation. Additional comments: Currently implements support for the following general purpose electronic structure programs: ABINIT [2,3], CASTEP [4], CPMD [5], Crystal [6], Elk [7], exciting [8], EMTO [9], Fleur [10], RSPt [11], Siesta [12] and VASP [13-16]. Running time: The examples provided in the distribution take only seconds to run.

Crystallographic and magnetic structure of UCu{sub 1.5}Sn{sub 2}

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

Purwanto, A.; Robinson, R.A.; Nakotte, H.

1996-04-01

We report on the crystallographic and magnetic structures of the antiferromagnet UCu{sub 1.5}Sn{sub 2}, as determined by x-ray and neutron powder diffraction. It crystallizes in the tetragonal CaBe{sub 2}Ge{sub 2} structure type, with space group P/4nmm, and we find no site disorder between two different Sn2{ital c} sites, in contrast with a previous report. UCu{sub 1.5}Sn{sub 2} orders antiferromagnetically with a N{acute e}el temperature of about 110 K. This is unusually high among uranium intermetallics. The uranium moments align along the {ital c} axis in a collinear arrangement but alternating along the {ital c} axis. The low-temperature uranium moment ismore » 2.01{mu}{sub {ital B}}. {copyright} {ital 1996 American Institute of Physics.}« less

Mapping intermolecular interactions and active site conformations: from human MMP-1 crystal structure to molecular dynamics free energy calculations.

PubMed

Nash, Anthony; Birch, Helen L; de Leeuw, Nora H

2017-02-01

The zinc-dependent Matrix Metalloproteinases (MMPs) found within the extracellular matrix (ECM) of vertebrates are linked to pathological processes such as arthritis, skin ulceration and cancer. Although a general backbone proteolytic mechanism is understood, crystallographic data continue to suggest an active site that is too narrow to encompass the respective substrate. We present a fully parameterised Molecular Dynamics (MD) study of the structural properties of an MMP-1-collagen crystallographic structure (Protein Data Bank - 4AUO), followed by an exploration of the free energy surface of a collagen polypeptide chain entering the active site, using a combined meta-dynamics and umbrella sampling (MDUS) approach. We conclude that the interactions between MMP-1 and the collagen substrate are in good agreement with a number of experimental studies. As such, our unrestrained MD simulations and our MDUS results, which indicate an energetic barrier for a local uncoiling and insertion event, can inform future investigations of the collagen-peptide non-bonded association steps with the active site prior to proteolytic mechanisms. The elucidation of such free energy barriers provides a better understanding of the role of the enzyme in the ECM and is important in the design of future MMP inhibitors.

Combustion synthesis of LaFeO{sub 3} sensing nanomaterial

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

Zaza, F., E-mail: fabio.zaza@enea.it; Serra, E.; Pallozzi, V.

2015-06-23

Since industrial revolution, human activities drive towards unsustainable global economy due to the overexploitation of natural resources and the unacceptable emissions of pollution and greenhouse gases. In order to address that issue, engineering research has been focusing on gas sensors development for monitoring gas emissions and controlling the combustion process sustainability. Semiconductors metal oxides sensors are attractive technology because they require simple design and fabrication, involving high accessibility, small size and low cost. Perovskite oxides are the most promising sensing materials because sensitivity, selectivity, stability and speed-response can be modulated and optimized by changing the chemical composition. One of themore » most convenient synthesis process of perovskite is the citrate-nitrate auto-combustion method, in which nitrate is the oxidizing agent and citrate is the fuel and the chelating argent in the same time. Since the sensibility of perovskite oxides depends on the defective crystallographic structure and the nanomorphology, the experimental was designed in order to study the dependence of powder properties on the synthesis conditions, such as the solution acidity and the relative amount of metals, nitrates and citric acid. Crystalline structure was studied in depth for defining the effects of synthesis conditions on size, morphology and crystallographic structure of nanopowders of LaFeO{sub 3}.« less

Combustion synthesis of LaFeO3 sensing nanomaterial

NASA Astrophysics Data System (ADS)

Zaza, F.; Pallozzi, V.; Serra, E.; Pasquali, M.

2015-06-01

Since industrial revolution, human activities drive towards unsustainable global economy due to the overexploitation of natural resources and the unacceptable emissions of pollution and greenhouse gases. In order to address that issue, engineering research has been focusing on gas sensors development for monitoring gas emissions and controlling the combustion process sustainability. Semiconductors metal oxides sensors are attractive technology because they require simple design and fabrication, involving high accessibility, small size and low cost. Perovskite oxides are the most promising sensing materials because sensitivity, selectivity, stability and speed-response can be modulated and optimized by changing the chemical composition. One of the most convenient synthesis process of perovskite is the citrate-nitrate auto-combustion method, in which nitrate is the oxidizing agent and citrate is the fuel and the chelating argent in the same time. Since the sensibility of perovskite oxides depends on the defective crystallographic structure and the nanomorphology, the experimental was designed in order to study the dependence of powder properties on the synthesis conditions, such as the solution acidity and the relative amount of metals, nitrates and citric acid. Crystalline structure was studied in depth for defining the effects of synthesis conditions on size, morphology and crystallographic structure of nanopowders of LaFeO3.

Magnetic behavior and spin-lattice coupling in cleavable van der Waals layered CrCl 3 crystals

DOE PAGES

McGuire, Michael A.; Clark, Genevieve; KC, Santosh; ...

2017-06-19

CrCl 3 is a layered insulator that undergoes a crystallographic phase transition below room temperature and orders antiferromagnetically at low temperature. Weak van der Waals bonding between the layers and ferromagnetic in-plane magnetic order make it a promising material for obtaining atomically thin magnets and creating van der Waals heterostructures. In this work we have grown crystals of CrCl 3, revisited the structural and thermodynamic properties of the bulk material, and explored mechanical exfoliation of the crystals. We find two distinct anomalies in the heat capacity at 14 and 17 K confirming that the magnetic order develops in two stagesmore » on cooling, with ferromagnetic correlations forming before long-range antiferromagnetic order develops between them. This scenario is supported by magnetization data. A magnetic phase diagram is constructed from the heat capacity and magnetization results. We also find an anomaly in the magnetic susceptibility at the crystallographic phase transition, indicating some coupling between the magnetism and the lattice. First-principles calculations accounting for van der Waals interactions also indicate spin-lattice coupling, and find multiple nearly degenerate crystallographic and magnetic structures consistent with the experimental observations. Lastly, we demonstrate that monolayer and few-layer CrCl 3 specimens can be produced from the bulk crystals by exfoliation, providing a path for the study of heterostructures and magnetism in ultrathin crystals down to the monolayer limit.« less

Magnetic behavior and spin-lattice coupling in cleavable van der Waals layered CrCl 3 crystals

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

McGuire, Michael A.; Clark, Genevieve; KC, Santosh

CrCl 3 is a layered insulator that undergoes a crystallographic phase transition below room temperature and orders antiferromagnetically at low temperature. Weak van der Waals bonding between the layers and ferromagnetic in-plane magnetic order make it a promising material for obtaining atomically thin magnets and creating van der Waals heterostructures. In this work we have grown crystals of CrCl 3, revisited the structural and thermodynamic properties of the bulk material, and explored mechanical exfoliation of the crystals. We find two distinct anomalies in the heat capacity at 14 and 17 K confirming that the magnetic order develops in two stagesmore » on cooling, with ferromagnetic correlations forming before long-range antiferromagnetic order develops between them. This scenario is supported by magnetization data. A magnetic phase diagram is constructed from the heat capacity and magnetization results. We also find an anomaly in the magnetic susceptibility at the crystallographic phase transition, indicating some coupling between the magnetism and the lattice. First-principles calculations accounting for van der Waals interactions also indicate spin-lattice coupling, and find multiple nearly degenerate crystallographic and magnetic structures consistent with the experimental observations. Lastly, we demonstrate that monolayer and few-layer CrCl 3 specimens can be produced from the bulk crystals by exfoliation, providing a path for the study of heterostructures and magnetism in ultrathin crystals down to the monolayer limit.« less

Crystallographic and Computational Analyses of AUUCU Repeating RNA That Causes Spinocerebellar Ataxia Type 10 (SCA10).

PubMed

Park, HaJeung; González, Àlex L; Yildirim, Ilyas; Tran, Tuan; Lohman, Jeremy R; Fang, Pengfei; Guo, Min; Disney, Matthew D

2015-06-23

Spinocerebellar ataxia type 10 (SCA10) is caused by a pentanucleotide repeat expansion of r(AUUCU) within intron 9 of the ATXN10 pre-mRNA. The RNA causes disease by a gain-of-function mechanism in which it inactivates proteins involved in RNA biogenesis. Spectroscopic studies showed that r(AUUCU) repeats form a hairpin structure; however, there were no high-resolution structural models prior to this work. Herein, we report the first crystal structure of model r(AUUCU) repeats refined to 2.8 Å and analysis of the structure via molecular dynamics simulations. The r(AUUCU) tracts adopt an overall A-form geometry in which 3 × 3 nucleotide (5')UCU(3')/(3')UCU(5') internal loops are closed by AU pairs. Helical parameters of the refined structure as well as the corresponding electron density map on the crystallographic model reflect dynamic features of the internal loop. The computational analyses captured dynamic motion of the loop closing pairs, which can form single-stranded conformations with relatively low energies. Overall, the results presented here suggest the possibility for r(AUUCU) repeats to form metastable A-from structures, which can rearrange into single-stranded conformations and attract proteins such as heterogeneous nuclear ribonucleoprotein K (hnRNP K). The information presented here may aid in the rational design of therapeutics targeting this RNA.

Crystallographic and Computational Analyses of AUUCU Repeating RNA That Causes Spinocerebellar Ataxia Type 10 (SCA10)

PubMed Central

Park, HaJeung; González, Àlex L.; Yildirim, Ilyas; Tran, Tuan; Lohman, Jeremy R.; Fang, Pengfei; Guo, Min; Disney, Matthew D.

2016-01-01

Spinocerebellar ataxia type 10 (SCA10) is caused by a pentanucleotide repeat expansion of r(AUUCU) within intron 9 of the ATXN10 pre-mRNA. The RNA causes disease by a gain-of-function mechanism in which it inactivates proteins involved in RNA biogenesis. Spectroscopic studies showed that r(AUUCU) repeats form a hairpin structure; however, there were no high-resolution structural models prior to this work. Herein, we report the first crystal structure of model r(AUUCU) repeats refined to 2.8 Å and analysis of the structure via molecular dynamics simulations. The r(AUUCU) tracts adopt an overall A-form geometry in which 3 × 3 nucleotide 5′UCU3′/3′UCU5′ internal loops are closed by AU pairs. Helical parameters of the refined structure as well as the corresponding electron density map on the crystallographic model reflect dynamic features of the internal loop. The computational analyses captured dynamic motion of the loop closing pairs, which can form single-stranded conformations with relatively low energies. Overall, the results presented here suggest the possibility for r(AUUCU) repeats to form metastable A-from structures, which can rearrange into single-stranded conformations and attract proteins such as heterogeneous nuclear ribonucleoprotein K (hnRNP K). The information presented here may aid in the rational design of therapeutics targeting this RNA. PMID:26039897

Two Crystallographic Laboratory and Computational Exercises for Undergraduates.

ERIC Educational Resources Information Center

Lessinger, Leslie

1988-01-01

Describes two introductory exercises designed to teach the fundamental ideas and methods of crystallography, and to convey some important features of inorganic and organic crystal structures to students in an advanced laboratory course. Exercises include "The Crystal Structure of NiO" and "The Crystal Structure of Beta-Fumaric Acid." (CW)

Modeling the characteristic etch morphologies along specific crystallographic orientations by anisotropic chemical etching

NASA Astrophysics Data System (ADS)

Li, Kun-Dar; Miao, Jin-Ru

2018-02-01

To improve the advanced manufacturing technology for functional materials, a sophisticated control of chemical etching process is highly demanded, especially in the fields of environment and energy related applications. In this study, a phase-field-based model is utilized to investigate the etch morphologies influenced by the crystallographic characters during anisotropic chemical etching. Three types of etching modes are inspected theoretically, including the isotropic, <100> and <111> preferred oriented etchings. Owing to the specific etching behavior along the crystallographic directions, different characteristic surface structures are presented in the simulations, such as the pimple-like, pyramidal hillock and ridge-like morphologies. In addition, the processing parameters affecting the surface morphological formation and evolution are also examined systematically. According to the numerical results, the growth mechanism of surface morphology in a chemical etching is revealed distinctly. While the etching dynamics plays a dominant role on the surface formation, the characteristic surface morphologies corresponding to the preferred etching direction become more apparent. As the atomic diffusion turned into a determinative factor, a smoothened surface would appear, even under the anisotropic etching conditions. These simulation results provide fundamental information to enhance the development and application of anisotropic chemical etching techniques.

Three-dimensional Structures of Carotenoids by X-ray Crystallography

NASA Astrophysics Data System (ADS)

Helliwell, Madeleine

The number of crystal structures of carotenoid molecules and carotenoid derivatives deposited in the Cambridge Crystallographic Data Centre [1] is still relatively small, but has increased compared with the previous survey [2]. The list is summarized in Table 1.

Analysis of Substrate Access to Active Sites in Bacterial Multicomponent Monooxygenase Hydroxylases: X-ray Crystal Structure of Xenon-Pressurized Phenol Hydroxylase from Pseudomonas sp. OX1†,‡

PubMed Central

McCormick, Michael S.; Lippard, Stephen J.

2011-01-01

In all structurally characterized bacterial multicomponent monooxygenase (BMM) hydroxylase proteins, a series of hydrophobic cavities in the α-subunit trace a conserved path from the protein exterior to the carboxylate-bridged diiron active site. The present study examines these cavities as a potential route for dioxygen transport to the active site by crystallographic characterization of a xenon-pressurized sample of the hydroxylase component of phenol hydroxylase from Pseudomonas sp. OX1. Computational analyses of the hydrophobic cavities in the hydroxylase α-subunits of phenol hydroxylase (PHH), toluene/o-xylene monooxygenase (ToMOH), and soluble methane monooxygenase (sMMOH) are also presented. The results, together with previous findings from crystallographic studies of xenon-pressurized sMMO hydroxylase, clearly identify the propensity for these cavities to bind hydrophobic gas molecules in the protein interior. This proposed functional role is supported by recent stopped flow kinetic studies of ToMOH variants (Song, et al., 2011). In addition to information about the Xe sites, the structure determination revealed significantly reduced regulatory protein binding to the hydroxylase in comparison to the previously reported structure of PHH, as well as the presence of a newly identified metal binding site in the α-subunit that adopts a linear coordination environment consistent with Cu(I), and a glycerol molecule bound to Fe1 in a fashion that is unique among hydrocarbon-diiron site adducts reported to date in BMM hydroxylase structures. Finally, a comparative analysis of the α-subunit structures of MMOH, ToMOH, and PHH details proposed routes for the other three BMM substrates, the hydrocarbon, electrons, and protons, comprising cavities, channels, hydrogen-bonding networks, and pores in the structures of their α-subunits. PMID:22136180

Giant voltage-controlled magnetic anisotropy effect in a crystallographically strained CoFe system

NASA Astrophysics Data System (ADS)

Kato, Yushi; Yoda, Hiroaki; Saito, Yoshiaki; Oikawa, Soichi; Fujii, Keiko; Yoshiki, Masahiko; Koi, Katsuhiko; Sugiyama, Hideyuki; Ishikawa, Mizue; Inokuchi, Tomoaki; Shimomura, Naoharu; Shimizu, Mariko; Shirotori, Satoshi; Altansargai, Buyandalai; Ohsawa, Yuichi; Ikegami, Kazutaka; Tiwari, Ajay; Kurobe, Atsushi

2018-05-01

We experimentally demonstrate a giant voltage-controlled magnetic anisotropy (VCMA) coefficient in a crystallographically strained CoFe layer (∼15 monolayers in thickness) in a MgO/CoFe/Ir system. We observed a strong applied voltage dependence of saturation field and an asymmetric concave behavior with giant VCMA coefficients of ‑758 and 1043 fJ V‑1 m‑1. The result of structural analysis reveals epitaxial growth in MgO/CoFe/Ir layers and the orientation relationship MgO(001)[110] ∥ CoFe(001)[100] ∥ Ir(001)[110]. The CoFe layer has a bcc structure and a tetragonal distortion due to the lattice mismatch; therefore, the CoFe layer has a large perpendicular magnetic anisotropy.

Raman investigation with group theoretical method on structural polymorphism of the nonlinear optical hexamine: p-nitrophenol cocrystals

NASA Astrophysics Data System (ADS)

Vijayalakshmi, S.; Kalyanaraman, S.; Ravindran, T. R.

2014-09-01

We have synthesized organic non-centrosymmetric cocrystals of 1:1 and 1:2 mole ratios of non-proton-transferred hexamine and p-nitrophenol complexes by using a slow evaporation method. The cocrystal with different stoichiometric variation gets crystallized into different crystallographic structures. The non-proton-transfer process of the complexes and the charge transfer (CT) interaction are established through Fourier transform infrared (FTIR) spectroscopy. The contribution of the water molecule in the 1:2 adduct is explained through FTIR analysis. The result has an important bearing in our present study. Existence of two different crystallographic structures (polymorphism) is confirmed by the lower frequency modes that appeared in Raman spectra. The variation in the Raman active modes at lower frequencies that arise on account of polymorphism is addressed through factor group analysis. From the UV-vis analysis, the interesting result of hyperchromic and hypochromic shifts being observed in the 1:1 and 1:2 adducts, respectively, supports the polymorphic behavior. On seeing the variation in properties, particularly nonlinear optical properties, the higher second harmonic generation (SHG) efficiency compared with KDP is observed by using the Kurtz-Perry method for both complexes.

Evolution of LiFePO4 thin films interphase with electrolyte

NASA Astrophysics Data System (ADS)

Dupré, N.; Cuisinier, M.; Zheng, Y.; Fernandez, V.; Hamon, J.; Hirayama, M.; Kanno, R.; Guyomard, D.

2018-04-01

Many parameters may control the growth and the characteristics of the interphase, such as surface structure and morphology, structural defects, grain boundaries, surface reactions, etc. However, polycrystalline surfaces contain these parameters simultaneously, resulting in a quite complicated system to study. Working with model electrode surfaces using crystallographically oriented crystalline thin films appears as a novel and unique approach to understand contributions of preferential orientation and rugosity of the surface. In order to rebuild the interphase architecture along electrochemical cycling, LiFePO4 epitaxial films offering ideal 2D (100) interfaces are here investigated through the use of non-destructive depth profiling by Angular Resolved X-ray Photoelectron Spectroscopy (ARXPS). The composition and structure of the interphase is then monitored upon cycling for samples stopped at the end of charge and discharge for various numbers of cycles, and discussed in the light of combined XPS and X-ray reflectivity (XRR) measurements. Such an approach allows describing the interphase evolution on a specific model LiFePO4 crystallographic orientation and helps understanding the nature and evolution of the LiFePO4/electrolyte interphase forming on the surface of LiFePO4 poly-crystalline powder.

Structure solution of network materials by solid-state NMR without knowledge of the crystallographic space group.

PubMed

Brouwer, Darren H

2013-01-01

An algorithm is presented for solving the structures of silicate network materials such as zeolites or layered silicates from solid-state (29)Si double-quantum NMR data for situations in which the crystallographic space group is not known. The algorithm is explained and illustrated in detail using a hypothetical two-dimensional network structure as a working example. The algorithm involves an atom-by-atom structure building process in which candidate partial structures are evaluated according to their agreement with Si-O-Si connectivity information, symmetry restraints, and fits to (29)Si double quantum NMR curves followed by minimization of a cost function that incorporates connectivity, symmetry, and quality of fit to the double quantum curves. The two-dimensional network material is successfully reconstructed from hypothetical NMR data that can be reasonably expected to be obtained for real samples. This advance in "NMR crystallography" is expected to be important for structure determination of partially ordered silicate materials for which diffraction provides very limited structural information. Copyright © 2013 Elsevier Inc. All rights reserved.

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

Structure and crystallography of foliated and chalk shell microstructures of the oyster Magallana: the same materials grown under different conditions.

PubMed

Checa, Antonio G; Harper, Elizabeth M; González-Segura, Alicia

2018-05-14

Oyster shells are mainly composed of layers of foliated microstructure and lenses of chalk, a highly porous, apparently poorly organized and mechanically weak material. We performed a structural and crystallographic study of both materials, paying attention to the transitions between them. The morphology and crystallography of the laths comprising both microstructures are similar. The main differences were, in general, crystallographic orientation and texture. Whereas the foliated microstructure has a moderate sheet texture, with a defined 001 maximum, the chalk has a much weaker sheet texture, with a defined 011 maximum. This is striking because of the much more disorganized aspect of the chalk. We hypothesize that part of the unanticipated order is inherited from the foliated microstructure by means of, possibly, [Formula: see text] twinning. Growth line distribution suggests that during chalk formation, the mantle separates from the previous shell several times faster than for the foliated material. A shortage of structural material causes the chalk to become highly porous and allows crystals to reorient at a high angle to the mantle surface, with which they continue to keep contact. In conclusion, both materials are structurally similar and the differences in orientation and aspect simply result from differences in growth conditions.

Effect of defects, magnetocrystalline anisotropy, and shape anisotropy on magnetic structure of iron thin films by magnetic force microscopy

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

Xu, Ke; Schreiber, Daniel K.; Li, Yulan

Microstructures of magnetic materials, including defects and crystallographic orientations, are known to strongly influence magnetic domain structures. Measurement techniques such as magnetic force microscopy (MFM) thus allow study of correlations between microstructural and magnetic properties. The present work probes effects of anisotropy and artificial defects on the evolution of domain structure with applied field. Single crystal iron thin films on MgO substrates were milled by Focused Ion Beam (FIB) to create different magnetically isolated squares and rectangles in [110] crystallographic orientations, having their easy axis 45° from the sample edge. To investigate domain wall response on encountering non-magnetic defects, amore » 150 nm diameter hole was created in the center of some samples. By simultaneously varying crystal orientation and shape, both magnetocrystalline anisotropy and shape anisotropy, as well as their interaction, could be studied. Shape anisotropy was found to be important primarily for the longer edge of rectangular samples, which exaggerated the FIB edge effects and provided nucleation sites for spike domains in non-easy axis oriented samples. Center holes acted as pinning sites for domain walls until large applied magnetic fields. The present studies are aimed at deepening the understanding of the propagation of different types of domain walls in the presence of defects and different crystal orientations.« less

Effect of defects, magnetocrystalline anisotropy, and shape anisotropy on magnetic structure of iron thin films by magnetic force microscopy

DOE PAGES

Xu, Ke; Schreiber, Daniel K.; Li, Yulan; ...

2017-02-10

Microstructures of magnetic materials, including defects and crystallographic orientations, are known to strongly influence magnetic domain structures. Measurement techniques such as magnetic force microscopy (MFM) thus allow study of correlations between microstructural and magnetic properties. The present work probes effects of anisotropy and artificial defects on the evolution of domain structure with applied field. Single crystal iron thin films on MgO substrates were milled by Focused Ion Beam (FIB) to create different magnetically isolated squares and rectangles in [110] crystallographic orientations, having their easy axis 45° from the sample edge. To investigate domain wall response on encountering non-magnetic defects, amore » 150 nm diameter hole was created in the center of some samples. By simultaneously varying crystal orientation and shape, both magnetocrystalline anisotropy and shape anisotropy, as well as their interaction, could be studied. Shape anisotropy was found to be important primarily for the longer edge of rectangular samples, which exaggerated the FIB edge effects and provided nucleation sites for spike domains in non-easy axis oriented samples. Center holes acted as pinning sites for domain walls until large applied magnetic fields. The present studies are aimed at deepening the understanding of the propagation of different types of domain walls in the presence of defects and different crystal orientations.« less

Crystallography: past and present

NASA Astrophysics Data System (ADS)

Hodeau, J.-L.; Guinebretiere, R.

2007-12-01

In the 19th century, crystallography referred to the study of crystal shapes. Such studies by Haüy and Bravais allowed the establishment of important hypotheses such as (i) “les molécules intégrantes qui sont censées être les plus petits solides que l’on puisse extraire d’un minéral” [1], (ii) the definition of the crystal lattice and (iii) “le cristal est clivable parallèlement à deux ou trois formes cristallines” [2]. This morphological crystallography defined a crystal like “a chemically homogeneous solid, wholly or partly bounded by natural planes that intersect at predetermined angles” [3]. It described the main symmetry elements and operations, nomenclatures of different crystal forms and also the theory of twinning. A breakthrough appeared in 1912 with the use of X-rays by M. von Laue and W.H. and W.L. Bragg. This experimental development allowed the determination of the atomic content of each unit cell constituting the crystal and defined a crystal as “any solid in which an atomic pattern is repeated periodically in three dimensions, that is, any solid that “diffracts” an incident X-ray beam” [3]. Mathematical tools like the Patterson methods, the direct methods, were developed. The way for solving crystalline structure was opened first for simple compounds and at that time crystallography was associated mainly with perfect crystals. In the fifties, crystallographers already had most apparatus and fundamental methods at their disposal; however, we had to wait for the development of computers to see the full use of these tools. Furthermore the development of new sources of neutrons, electrons and synchrotron X-rays allowed the studies of complex compounds like large macromolecules in biology. Nowadays, one of the new frontiers for crystallographers is to relate the crystal structure to its physical-chemical-biological properties, this means that an accurate structural determination is needed to focus on a selective part of the structure (chemical order, anisotropy, charge transfer, magnetic order) versus an external parameter like temperature, pressure, magnetic or electric field. Modern crystallography is also extended to the study of very small crystals, powders, ill-ordered or non-crystallized materials. Thus presently, crystallography is concerned with any solid that “scatters” an incident beam. Nevertheless, as quoted by A. Guinier, “the problems facing crystallographers have only changed, ... new ones have appeared which require reflection and imagination, ... and which in turn may still bring much joy to all those who like crystallography” [4]. Such developments open up crystallography to modern materials like artificial ones and nanostructures with low- and/or multi-scaled-periodicities and/or extremely small “crystal size” and to materials of the “real world”, with mixtures of phases and/or amorphous contribution and/or defects, a common characteristic of ancient materials analysed in patrimonial research. In our contribution we will show by selected examples that these improvements were allowed (i) by the use of powerful sources, apparatus and detectors which allow micro-diffraction, in-situ diffraction, spectroscopy, resonant scattering, inelastic scattering, coherent scattering, (ii) by the development of methods like diffraction anomalous fine structure (DAFS), pair distribution function (PDF), simulated annealing, single object reconstruction, (iii) by combination of scattering and spectroscopy and by combination of scattering and microscopy. Such combination of different approaches is very efficient and, as said by H. Curien at the IUCr Bordeaux Congress in 1990, “in crystallography, there is a constant alternation between the crystal space and its associated reciprocal space, ... the alternation between experiment and model building is another feature of crystallography activity ..., the crystallographer relies both on his computer and on his diffractometer ..., all these dualistic complementarities are responsible for the fact that crystallographers tend to waver between the description of atomic structures and the explanation of macroscopic properties of solid matter” [5].

Inorganic Crystal Structure Database (ICSD) and Standardized Data and Crystal Chemical Characterization of Inorganic Structure Types (TYPIX)—Two Tools for Inorganic Chemists and Crystallographers

PubMed Central

Fluck, Ekkehard

1996-01-01

The two databases ICSD and TYPIX are described. ICSD is a comprehensive compilation of crystal structure data of inorganic compounds (about 39 000 entries). TYPIX contains 3600 critically evaluated data sets representative of structure types formed by inorganic compounds. PMID:27805158

Molecular Syntheses of Extended Materials

NASA Astrophysics Data System (ADS)

Paley, Daniel W.

Bottom-up molecular synthesis is a route to chemically and crystallographically uniform polymers and solid-state materials. Through the use of molecular precursors, we gain atomic-level control of functionality and fine-tuning of the collective properties of materials. This dissertation presents two studies that demonstrate this approach. Ring-opening alkyne metathesis polymerization is a possible approach to monodisperse conjugated polymers, but its applications have been limited by difficult syntheses and high air sensitivity of known organometallic ROAMP initiators. We designed a dimeric, air-stable molybdenum alkylidyne with a tris(phenolate) supporting ligand. The precatalyst is activated by addition of methanol and polymerizes cyclooctynes with excellent chemical selectivity and functional group tolerance. The Nuckolls and Roy groups have introduced a new family of solid-state compounds synthesized from cobalt chalcogenide clusters Co6Q 8(PR3)6 and fullerenes. The first examples of these materials crystallized in superatom lattices with the symmetry of simple inorganic solids CdI2 (P-3m1) and NaCl (Fm-3m). This dissertation reveals that further members of the family feature extraordinary diversity of structure, including a pseudo-trigonal array of fulleride dimers in [Co 6Te8(PEt3)6]2[C140 ][C70]2 and a heterolayered van der Waals cocrystal [Co6Se8(PEt2phen)6][C 60]5. In addition to these unusual crystal structures, this dissertation presents a method for assigning redox states from crystallographic data in Co6Q8 clusters. Finally, a detailed guide to the collection and solution of single-crystal X-ray data is presented. The guide is intended for independent study by new crystallographers.

Structural and dielectric studies on Ag doped nano ZnSnO3

NASA Astrophysics Data System (ADS)

Deepa, K.; Angel, S. Lilly; Rajamanickam, N.; Jayakumar, K.; Ramachandran, K.

2018-04-01

Undoped and Ag-doped nano Zinc Stannate (ZSO) ternary oxide were prepared by co-precipitation method. The crystallographic, morphological and optical properties of the synthesized nanoparticles were studied using X-ray diffraction (XRD) and UV-Visible spectroscopy (UV-Vis) and Scanning electron microscopy (SEM). The electrical properties of the synthesized samples were studied by dielectric measurements. Higher concentration Ag doped ZSO nanoparticles exhibit higher dielectric constant at low frequency.

Data to knowledge: how to get meaning from your result

PubMed Central

Berman, Helen M.; Gabanyi, Margaret J.; Groom, Colin R.; Johnson, John E.; Murshudov, Garib N.; Nicholls, Robert A.; Reddy, Vijay; Schwede, Torsten; Zimmerman, Matthew D.; Westbrook, John; Minor, Wladek

2015-01-01

Structural and functional studies require the development of sophisticated ‘Big Data’ technologies and software to increase the knowledge derived and ensure reproducibility of the data. This paper presents summaries of the Structural Biology Knowledge Base, the VIPERdb Virus Structure Database, evaluation of homology modeling by the Protein Model Portal, the ProSMART tool for conformation-independent structure comparison, the LabDB ‘super’ laboratory information management system and the Cambridge Structural Database. These techniques and technologies represent important tools for the transformation of crystallographic data into knowledge and information, in an effort to address the problem of non-reproducibility of experimental results. PMID:25610627

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.

Solvent-induced chirality control in the enantioseparation of 1-phenylethylamine via diastereomeric salt formation.

PubMed

Kodama, Koichi; Kimura, Yuria; Shitara, Hiroaki; Yasutake, Mikio; Sakurai, Rumiko; Hirose, Takuji

2011-04-01

Solvent-induced chirality control in the enantioseparation of 1-phenylethylamine 1 by N-(p-toluenesulfonyl)-(S)-phenylalanine 2 via diastereomeric salt formation was studied. (S)-1·(S)-2 was preferentially crystallized as a less-soluble salt from aqueous alcohol, while (R)-1·(S)-2 salt was mainly obtained by addition of solvents with a six-membered ring such as dioxane, cyclohexane, tetrahydropyran, and cyclohexene to 2-propanol. Further investigations were carried out from the viewpoints of molecular structures, optical rotation measurement, and X-ray crystallographic analyses. Crystallographic analyses have revealed that incorporation of the six-membered ring solvent molecule in (R)-1·(S)-2 without hydrogen bonds changed the molecular conformation of (S)-2 to stabilize the salt, which changed the selectivity of 1 in the enantioseparation. Copyright © 2010 Wiley-Liss, Inc.

Ionotropic glutamate receptors made crystal clear.

PubMed

Bowie, Derek

2014-12-01

Two recent crystallographic studies of the full-length GluA2 AMPA receptor provide our first insights into how the modular domains of the tetrameric complex coordinate the process of activation. These findings herald a new era in the structure-function analyses of neurotransmitter receptors, a fitting achievement for the 'International Year of Crystallography'. Copyright © 2014 Elsevier Ltd. All rights reserved.

3D-Printing Crystallographic Unit Cells for Learning Materials Science and Engineering

ERIC Educational Resources Information Center

Rodenbough, Philip P.; Vanti, William B.; Chan, Siu-Wai

2015-01-01

Introductory materials science and engineering courses universally include the study of crystal structure and unit cells, which are by their nature highly visual 3D concepts. Traditionally, such topics are explored with 2D drawings or perhaps a limited set of difficult-to-construct 3D models. The rise of 3D printing, coupled with the wealth of…

Reactivity of 12-tungstophosphoric acid and its inhibitor potency toward Na+/K+-ATPase: A combined 31P NMR study, ab initio calculations and crystallographic analysis.

PubMed

Bošnjaković-Pavlović, Nada; Bajuk-Bogdanović, Danica; Zakrzewska, Joanna; Yan, Zeyin; Holclajtner-Antunović, Ivanka; Gillet, Jean-Michel; Spasojević-de Biré, Anne

2017-11-01

Influence of 12-tungstophosphoric acid (WPA) on conversion of adenosine triphosphate (ATP) to adenosine diphosphate (ADP) in the presence of Na + /K + -ATPase was monitored by 31 P NMR spectroscopy. It was shown that WPA exhibits inhibitory effect on Na + /K + -ATPase activity. In order to study WPA reactivity and intermolecular interactions between WPA oxygen atoms and different proton donor types (D=O, N, C), we have considered data for WPA based compounds from the Cambridge Structural Database (CSD), the Crystallographic Open Database (COD) and the Inorganic Crystal Structure Database (ICSD). Binding properties of Keggin's anion in biological systems are illustrated using Protein Data Bank (PDB). This work constitutes the first determination of theoretical Bader charges on polyoxotungstate compound via the Atom In Molecule theory. An analysis of electrostatic potential maps at the molecular surface and charge of WPA, resulting from DFT calculations, suggests that the preferred protonation site corresponds to WPA bridging oxygen. These results enlightened WPA chemical reactivity and its potential biological applications such as the inhibition of the ATPase activity. Copyright © 2017 Elsevier Inc. All rights reserved.

The fourth crystallographic closest packing unveiled in the gold nanocluster crystal

NASA Astrophysics Data System (ADS)

Gan, Zibao; Chen, Jishi; Wang, Juan; Wang, Chengming; Li, Man-Bo; Yao, Chuanhao; Zhuang, Shengli; Xu, An; Li, Lingling; Wu, Zhikun

2017-03-01

Metal nanoclusters have recently attracted extensive interest not only for fundamental scientific research, but also for practical applications. For fundamental scientific research, it is of major importance to explore the internal structure and crystallographic arrangement. Herein, we synthesize a gold nanocluster whose composition is determined to be Au60S6(SCH2Ph)36 by using electrospray ionization mass spectrometry and single crystal X-ray crystallography (SCXC). SCXC also reveals that Au60S6(SCH2Ph)36 consists of a fcc-like Au20 kernel protected by a pair of giant Au20S3(SCH2Ph)18 staple motifs, which contain 6 tetrahedral-coordinate μ4-S atoms not previously reported in the Au-S interface. Importantly, the fourth crystallographic closest-packed pattern, termed 6H left-handed helical (6HLH) arrangement, which results in the distinct loss of solid photoluminescence of amorphous Au60S6(SCH2Ph)36, is found in the crystals of Au60S6(SCH2Ph)36. The solvent-polarity-dependent solution photoluminescence is also demonstrated. Overall, this work provides important insights about the structure, Au-S bonding and solid photoluminescence of gold nanoclusters.

Quantitative Phase Composition of TiO 2-Coated Nanoporous-Au Monoliths by X-ray Absorption Spectroscopy and Correlations to Catalytic

DOE PAGES

Bagge-Hansen, Michael; Wichmann, Andre; Wittstock, Arne; ...

2014-02-03

Porous titania/metal composite materials have many potential applications in the fields of green catalysis, energy harvesting, and storage in which both the overall morphology of the nanoporous host material and the crystallographic phase of the titania (TiO 2) guest determine the material’s performance. New insights into the structure–function relationships of these materials were obtained by near-edge X-ray absorption fine structure (NEXAFS) spectroscopy that, for example, provides quantitative crystallographic phase composition from ultrathin, nanostructured titania films, including sensitivity to amorphous components. We demonstrate that crystallographic phase, morphology, and catalytic activity of TiO 2-functionalized nanoporous gold (np-Au) can be controlled by amore » simple annealing procedure (T < 1300 K). The material was prepared by atomic layer deposition of ~2 nm thick TiO 2 on millimeter-sized samples of np-Au (40–50 nm mean ligament size) and catalytically investigated with respect to aerobic CO oxidation. Moreover, the annealing-induced changes in catalytic activity are correlated with concurrent morphology and phase changes as provided by cross-sectional scanning electron microscopy, transmission electron microscopy, and near-edge X-ray absorption fine structure (NEXAFS) spectroscopy.« less

Crystallographic structure and superconductive properties of Nb-Ti films with an artificially layered structure

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

Sato, N.

1990-06-15

Artificially layered niobium-titanium (Nb-Ti) films with various thickness ratios (3/1--1/3) and periodicities (2--100 A) are made in an argon or in a mixed argon/nitrogen atmosphere by a dc magnetron sputtering method. Films with small periodicities (less than 30 A) have an artificial superlattice structure (ASL) with crystallographic coherence between constituent layers, where Nb and Ti grow epitaxially on the closest planes. The crystallographic structures of films are bcc with the (110) plane parallel to the film for films with the same or a thicker Nb layer than a Ti layer, and hcp with the (001) plane parallel to the filmmore » for films with a thinner Nb layer than a Ti layer. Films with large periodicities have an artificial superstructure (ASS) with only periodic stacking of constituent layers. Films deposited in the Ar/N atmosphere also have the artificially layered structures of ASL or ASS. The artificially layered structure is thermally stable at temperatures up to 500 {degree}C. The superconducting properties of the films depend strongly on the periodicity and thickness ratio of Nb and Ti layers. The dependence of the transition temperature on the periodicity and thickness ratio is qualitatively explained by a proximity effect with a three-region model. Films with periodicities less than 20 A, composed of the same or a thicker Nb layer than a Ti layer, show high transition temperatures (above 9.3 K). The highest {ital T}{sub {ital c}} of about 13.6 K is obtained in the film composed of monatomic layers of constituents deposited in an Ar atmosphere including 30 vol % N.« less

Magnetic structure of Ho0.5Y0.5Mn6Sn6 compound studied by powder neutron diffraction

NASA Astrophysics Data System (ADS)

Li, X.-Y.; Peng, L.-C.; He, L.-H.; Zhang, S.-Y.; Yao, J.-L.; Zhang, Y.; Wang, F.-W.

2018-05-01

The crystallographic and magnetic structures of the HfFe6Ge6-type compound Ho0.5Y0.5Mn6Sn6 have been studied by powder neutron diffraction and in-situ Lorentz transmission electron microscopy. Besides the nonlinear thermal expansion of lattice parameters, an incommensurate conical spiral magnetic structure was determined in the temperature interval of 2-340 K. A spin reorientation transition has been observed from 50 to 300 K, where the alignment of the c-axis component of magnetic moments of the Ho sublattice and the Mn sublattice transfers from ferrimagnetic to ferromagnetic.

Comparison of a homology model and the crystallographic structure of human 11β-hydroxysteroid dehydrogenase type 1 (11βHSD1) in a structure-based identification of inhibitors

NASA Astrophysics Data System (ADS)

Miguet, Laurence; Zhang, Ziding; Barbier, Maryse; Grigorov, Martin G.

2006-02-01

Human 11β-hydroxysteroid dehydrogenase type 1 (11βHSD1) catalyzes the interconversion of cortisone into active cortisol. 11βHSD1 inhibition is a tempting target for the treatment of a host of human disorders that might benefit from blockade of glucocorticoid action, such as obesity, metabolic syndrome, and diabetes type 2. Here, we report an in silico screening study aimed at identifying new selective inhibitors of human 11βHSD1 enzyme. In the first step, homology modeling was employed to build the 3D structure of 11βHSD1. Further, molecular docking was used to validate the predicted model by showing that it was able to discriminate between known 11βHSD1 inhibitors or substrates and non-inhibitors. The homology model was found to reproduce closely the crystal structure that became publicly available in the final stages of this work. Finally, we carried out structure-based virtual screening experiments on both the homology model and the crystallographic structure with a database of 114'000 natural molecules. Among these, 15 molecules were consistently selected as inhibitors based on both the model and crystal structures of the enzyme, implying a good quality for the homology model. Among these putative 11βHSD1 inhibitors, two were flavonone derivatives that have already been shown to be potent inhibitors of the enzyme.

Crystal Structure of a Ube2S-Ubiquitin Conjugate

PubMed Central

Lorenz, Sonja; Bhattacharyya, Moitrayee; Feiler, Christian; Rape, Michael; Kuriyan, John

2016-01-01

Protein ubiquitination occurs through the sequential formation and reorganization of specific protein-protein interfaces. Ubiquitin-conjugating (E2) enzymes, such as Ube2S, catalyze the formation of an isopeptide linkage between the C-terminus of a “donor” ubiquitin and a primary amino group of an “acceptor” ubiquitin molecule. This reaction involves an intermediate, in which the C-terminus of the donor ubiquitin is thioester-bound to the active site cysteine of the E2 and a functionally important interface is formed between the two proteins. A docked model of a Ube2S-donor ubiquitin complex was generated previously, based on chemical shift mapping by NMR, and predicted contacts were validated in functional studies. We now present the crystal structure of a covalent Ube2S-ubiquitin complex. The structure contains an interface between Ube2S and ubiquitin in trans that resembles the earlier model in general terms, but differs in detail. The crystallographic interface is more hydrophobic than the earlier model and is stable in molecular dynamics (MD) simulations. Remarkably, the docked Ube2S-donor complex converges readily to the configuration seen in the crystal structure in 3 out of 8 MD trajectories. Since the crystallographic interface is fully consistent with mutational effects, this indicates that the structure provides an energetically favorable representation of the functionally critical Ube2S-donor interface. PMID:26828794

Structure of glutathione reductase from Escherichia coli at 1.86 A resolution: comparison with the enzyme from human erythrocytes.

PubMed Central

Mittl, P. R.; Schulz, G. E.

1994-01-01

The crystal structure of the dimeric flavoenzyme glutathione reductase from Escherichia coli was determined and refined to an R-factor of 16.8% at 1.86 A resolution. The molecular 2-fold axis of the dimer is local but very close to a possible crystallographic 2-fold axis; the slight asymmetry could be rationalized from the packing contacts. The 2 crystallographically independent subunits of the dimer are virtually identical, yielding no structural clue on possible cooperativity. The structure was compared with the well-known structure of the homologous enzyme from human erythrocytes with 52% sequence identity. Significant differences were found at the dimer interface, where the human enzyme has a disulfide bridge, whereas the E. coli enzyme has an antiparallel beta-sheet connecting the subunits. The differences at the glutathione binding site and in particular a deformation caused by a Leu-Ile exchange indicate why the E. coli enzyme accepts trypanothione much better than the human enzyme. The reported structure provides a frame for explaining numerous published engineering results in detail and for guiding further ones. PMID:8061609

Synthesis, crystal structures and luminescence properties of the Eu 3+-doped yttrium oxotellurates(IV) Y 2Te 4O 11 and Y 2Te 5O 13

NASA Astrophysics Data System (ADS)

Höss, Patrick; Osvet, Andres; Meister, Frank; Batentschuk, Miroslaw; Winnacker, Albrecht; Schleid, Thomas

2008-10-01

Y 2Te 4O 11:Eu 3+ and Y 2Te 5O 13:Eu 3+ single crystals in sub-millimeter scale were synthesized from the binary oxides (Y 2O 3, Eu 2O 3 and TeO 2) using CsCl as fluxing agent. Crystallographic structures of the undoped yttrium oxotellurates(IV) Y 2Te 4O 11 and Y 2Te 5O 13 have been determined and refined from single-crystal X-ray diffraction data. In Y 2Te 4O 11, a layered structure is present where the reticulated sheets consisting of edge-sharing [YO 8] 13- polyhedra are interconnected by the oxotellurate(IV) units, whereas in Y 2Te 5O 13 only double chains of condensed yttrium-oxygen polyhedra with coordination numbers of 7 and 8 are left, now linked in two crystallographic directions by the oxotellurate(IV) entities. The Eu 3+ luminescence spectra and the decay time from different energy levels of the doped compounds were investigated and all detected emission levels were identified. Luminescence properties of the Eu 3+ cations have been interpreted in consideration of the now accessible detailed crystallographic data of the yttrium compounds, providing the possibility to examine the influence of the local symmetry of the oxygen coordination spheres.

Investigation of the shear response and geometrically necessary dislocation densities in shear localization in high-purity titanium

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

Zhu, Chaoyi; Livescu, Veronica; Harrington, Tyler

The influence of microstructural anisotropy on shear response of high-purity titanium was studied using the compact forced-simple-shear specimen (CFSS) loaded under quasi-static loading conditions. Post-mortem characterization reveals significant difference in shear response of different directions in the same material due to material crystallographic texture anisotropy. Shear bands are narrower in specimens in which the shear zone is aligned along the direction with a strong {0001} basal texture. Twinning was identified as an active mechanism to accommodate strains in the shear region in both orientations. This paper confirms the applicability of the CFSS design for the investigation of differences in themore » shear response of materials as a function of process-induced crystallographic texture. A detailed, systematic approach to quantifying shear band evolution by evaluating geometrically necessary dislocations (GND) associated with crystallographic anisotropy is presented. Finally, the results show that: i) line average GND density profiles, for Ti samples that possess a uniform equiaxed-grain structure, but with strong crystallographic anisotropy, exhibit significant differences in GND density close to the shear band center; ii) GND profiles decrease steadily away from the shear band as the plastic strain diminishes, in agreement with Ashby's theory of work hardening, where the higher GND density in the through-thickness (TT) orientation is a result of restricted < a > type slip in the shear band compared with in-plane (IP) samples; iii) the anisotropy in deformation response is derived from initial crystallographic texture of the materials, where GND density of < a > GNDs are higher adjacent to the shear band in the through-thickness sample oriented away from easy slip, but the density of < c+a > type GNDs are very similar in these two samples; and iv) the increase in grain average GND density was determined to have strong correlation to an increase in the Euler Φ angle of the grain average orientation, indicating an increased misorientation angle evolution.« less

Investigation of the shear response and geometrically necessary dislocation densities in shear localization in high-purity titanium

DOE PAGES

Zhu, Chaoyi; Livescu, Veronica; Harrington, Tyler; ...

2017-03-31

The influence of microstructural anisotropy on shear response of high-purity titanium was studied using the compact forced-simple-shear specimen (CFSS) loaded under quasi-static loading conditions. Post-mortem characterization reveals significant difference in shear response of different directions in the same material due to material crystallographic texture anisotropy. Shear bands are narrower in specimens in which the shear zone is aligned along the direction with a strong {0001} basal texture. Twinning was identified as an active mechanism to accommodate strains in the shear region in both orientations. This paper confirms the applicability of the CFSS design for the investigation of differences in themore » shear response of materials as a function of process-induced crystallographic texture. A detailed, systematic approach to quantifying shear band evolution by evaluating geometrically necessary dislocations (GND) associated with crystallographic anisotropy is presented. Finally, the results show that: i) line average GND density profiles, for Ti samples that possess a uniform equiaxed-grain structure, but with strong crystallographic anisotropy, exhibit significant differences in GND density close to the shear band center; ii) GND profiles decrease steadily away from the shear band as the plastic strain diminishes, in agreement with Ashby's theory of work hardening, where the higher GND density in the through-thickness (TT) orientation is a result of restricted < a > type slip in the shear band compared with in-plane (IP) samples; iii) the anisotropy in deformation response is derived from initial crystallographic texture of the materials, where GND density of < a > GNDs are higher adjacent to the shear band in the through-thickness sample oriented away from easy slip, but the density of < c+a > type GNDs are very similar in these two samples; and iv) the increase in grain average GND density was determined to have strong correlation to an increase in the Euler Φ angle of the grain average orientation, indicating an increased misorientation angle evolution.« less

Evolution of rapidly solidified NiAlCu(B) alloy microstructure.

PubMed

Czeppe, Tomasz; Ochin, Patrick

2006-10-01

This study concerned phase transformations observed after rapid solidification and annealing at 500, 700 and 800 degrees C in 56.3 Ni-39.9 Al-3.8 Cu-0.06 B (E1) and 59.8 Ni-36.0 Al-4.3 Cu-0.06 B (E2) alloys (composition in at.%). Injection casting led to a homogeneous structure of very small, one-phase grains (2-4 microm in size). In both alloys, the phase observed at room temperature was martensite of L1(0) structure. The process of the formation of the Ni(5)Al(3) phase by atomic reordering proceeded at 285-394 degrees C in the case of E1 alloy and 450-550 degrees C in the case of E2 alloy. Further decomposition into NiAl (beta) and Ni(3)Al (gamma') phases, the microstructure and crystallography of the phases depended on the path of transformations, proceeding in the investigated case through the transformation of martensite crystallographic variants. This preserved precise crystallographic orientation between the subsequent phases, very stable plate-like morphology and very small beta + gamma' grains after annealing at 800 degrees C.

Analysis of the bacterial luciferase mobile loop by replica-exchange molecular dynamics.

PubMed

Campbell, Zachary T; Baldwin, Thomas O; Miyashita, Osamu

2010-12-15

Bacterial luciferase contains an extended 29-residue mobile loop. Movements of this loop are governed by binding of either flavin mononucleotide (FMNH2) or polyvalent anions. To understand this process, loop dynamics were investigated using replica-exchange molecular dynamics that yielded conformational ensembles in either the presence or absence of FMNH2. The resulting data were analyzed using clustering and network analysis. We observed the closed conformations that are visited only in the simulations with the ligand. Yet the mobile loop is intrinsically flexible, and FMNH2 binding modifies the relative populations of conformations. This model provides unique information regarding the function of a crystallographically disordered segment of the loop near the binding site. Structures at or near the fringe of this network were compatible with flavin binding or release. Finally, we demonstrate that the crystallographically observed conformation of the mobile loop bound to oxidized flavin was influenced by crystal packing. Thus, our study has revealed what we believe are novel conformations of the mobile loop and additional context for experimentally determined structures. Copyright © 2010 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Orientation relationship between the T structure and the icosahedral quasicrystal in the Zn-Mg-Al alloy system

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

Nakayama, Kei, E-mail: k.n@aoni.waseda.jp; Watanabe, Junya; Koyama, Yasumasa, E-mail: ykoyama@waseda.jp

2016-08-26

To understand the crystallographic relation between the Bergman-type icosahedral quasicrystal and its approximant-T structure, we have investigated the crystallographic features of prepared Zn-Mg-Al alloy samples, mainly by transmission electron microscopy. It was found that there existed three kinds of regions: that is, C14-Laves, approximant-T, and icosahedral-quasicrystal regions, in Zn-Mg-Al alloy samples with the composition of Zn-36at.%Mg-9at.%Al. Among these regions, in particular, we tried to determine an orientation relationship between neighboring icosahedral-quasicrystal and approximant-T regions. Based on the determined relationship, for instance, four threefold rotatory-inversion axes in the T structure were found to be parallel to four of ten threefold rotatory-inversionmore » axes in the icosahedral quasicrystal. It was thus understood that the atomic arrangements of the Bergman-type icosahedral quasicrystal and its approximant-T structure are likely to resemble each other.« less

N-benzoylimido complexes of palladium. Synthesis, structural characterisation and structure-reactivity relationship.

PubMed

Besenyei, Gábor; Párkányi, László; Szalontai, Gábor; Holly, Sándor; Pápai, Imre; Keresztury, Gábor; Nagy, Andrea

2004-07-07

Benzoyl azides, ArC(O)N3, 2, (Ar = phenyl or substituted phenyl), react with [Pd2Cl2(dppm)2], 1, [dppm = bis(diphenylphosphino)methane] with the formation of novel [Pd2Cl2(mu-NC(O)Ar)(dppm)2], 3, benzoylnitrene complexes that were structurally characterised by multinuclear magnetic resonance and IR spectroscopy and, in several instances, by single crystal X-ray diffraction. As shown by crystallographic studies, the C2P4Pd2 rings adopt extended twist-boat conformations with methylene groups bending towards the bridging benzoylimido moieties. X-ray diffraction studies have revealed the chiral nature of the imido complexes, the chiral element being the propeller-like C2P4Pd2 ring. Structural data accumulated on complexes 3 such as short C-N distances (1.32 A), elongated C=O bonds (1.30 A) as well as the outstandingly high barrier to internal rotation around the N-C(O) linkage (88.3 kJ mol(-1)) are in line with extensive ppi-ppi interaction between the bridging nitrogen and the carbonyl carbon atoms. Theoretical calculations indicate an electron shift from the dimer towards the apical nitrogen atom, which, in turn, facilitates the donation of electrons towards the carbonyl moiety. To elucidate the structure-reactivity relationship of benzoyl azides towards 1, crystallographic and solution IR spectroscopic studies were carried out on a series of para-substituted benzoyl azides. The reaction obeys the Hammett equation. The large positive value of the reaction constant indicates that the azides act as electrophiles in the reaction studied. The enhanced reactivity of 2-nitrobenzoyl azide has been attributed to a decreased conjugation of the phenyl and carbonyl moieties in this reagent.

Teaching Three-Dimensional Structural Chemistry Using Crystal Structure Databases. 4. Examples of Discovery-Based Learning Using the Complete Cambridge Structural Database

ERIC Educational Resources Information Center

Battle, Gary M.; Allen, Frank H.; Ferrence, Gregory M.

2011-01-01

Parts 1 and 2 of this series described the educational value of experimental three-dimensional (3D) chemical structures determined by X-ray crystallography and retrieved from the crystallographic databases. In part 1, we described the information content of the Cambridge Structural Database (CSD) and discussed a representative teaching subset of…

Teaching Three-Dimensional Structural Chemistry Using Crystal Structure Databases. 3. The Cambridge Structural Database System: Information Content and Access Software in Educational Applications

ERIC Educational Resources Information Center

Battle, Gary M.; Allen, Frank H.; Ferrence, Gregory M.

2011-01-01

Parts 1 and 2 of this series described the educational value of experimental three-dimensional (3D) chemical structures determined by X-ray crystallography and retrieved from the crystallographic databases. In part 1, we described the information content of the Cambridge Structural Database (CSD) and discussed a representative teaching subset of…

X-ray crystallographic and tungsten-183 nuclear magnetic resonance structural studies of the [M4(H2O)2(XW9O34) 2]10- heteropolyanions (M = COII or Zn, X = P or As)

USGS Publications Warehouse

Evans, H.T.; Tourne, C.M.; Tourne, G.F.; Weakley, T.J.R.

1986-01-01

The crystal structures of K10[Co4(H2O)2(PW9O 34)2]??22H2O (1) and isomorphous K10[Zn4(H2O)2(AsW9O 34)2]??23H2O (2) have been determined {Mo-K?? radiation, space group P21/n, Z = 2; (1) a = 15.794(2), b = 21.360(2), c = 12.312(1) A??, ?? = 91.96??, R = 0.084 for 3 242 observed reflections [I ??? 3??(I)]; (2) a = 15.842(4), b = 21.327(5), c = 12.308(4) A??, ?? = 92.42(4)??, R = 0.066 for 4 675 observed reflections [F ??? 3??(F)]}. The anions have crystallographic symmetry 1 and non-crystallographic symmetry very close to 2/m (C2h). Each consists of two [XW9O34]9- moieties [??-B isomers; X = P (1) or As (2)] linked via four CoIIO6 or ZnO6 groups. Two Co or Zn atoms each carry a water ligand. The 183W n.m.r. spectra of the anions [Zn4(H2O)2(XW9O34) 2]10- (X = P or As) confirm that the anions retain 2/m symmetry in aqueous solution. Homonuclear coupling constants between 183W atoms are 5.8-9.0 Hz for adjacent WO6 octahedra sharing edges, and 19.6-25.0 Hz for octahedra sharing corners.

Molecular driving forces defining lipid positions around aquaporin-0

PubMed Central

Aponte-Santamaría, Camilo; Briones, Rodolfo; Schenk, Andreas D.; Walz, Thomas; de Groot, Bert L.

2012-01-01

Lipid–protein interactions play pivotal roles in biological membranes. Electron crystallographic studies of the lens-specific water channel aquaporin-0 (AQP0) revealed atomistic views of such interactions, by providing high-resolution structures of annular lipids surrounding AQP0. It remained unclear, however, whether these lipid structures are representative of the positions of unconstrained lipids surrounding an individual protein, and what molecular determinants define the lipid positions around AQP0. We addressed these questions by using molecular dynamics simulations and crystallographic refinement, and calculated time-averaged densities of dimyristoyl-phosphatidylcholine lipids around AQP0. Our simulations demonstrate that, although the experimentally determined crystallographic lipid positions are constrained by the crystal packing, they appropriately describe the behavior of unconstrained lipids around an individual AQP0 tetramer, and thus likely represent physiologically relevant lipid positions.While the acyl chains were well localized, the lipid head groups were not. Furthermore, in silico mutations showed that electrostatic interactions do not play a major role attracting these phospholipids towards AQP0. Instead, the mobility of the protein crucially modulates the lipid localization and explains the difference in lipid density between extracellular and cytoplasmic leaflets. Moreover, our simulations support a general mechanism in which membrane proteins laterally diffuse accompanied by several layers of localized lipids, with the positions of the annular lipids being influenced the most by the protein surface. We conclude that the acyl chains rather than the head groups define the positions of dimyristoyl-phosphatidylcholine lipids around AQP0. Lipid localization is largely determined by the mobility of the protein surface, whereas hydrogen bonds play an important but secondary role. PMID:22679286

Diamond-like phases formed from fullerene-like clusters

NASA Astrophysics Data System (ADS)

Belenkov, E. A.; Greshnyakov, V. A.

2015-11-01

The geometrically optimized structure and properties of thirteen diamond-like carbon phases formed by linking or combining fullerene-like clusters (C4, C6, C8, C12, C16, C24, or C48) have been investigated. Atoms in the structures of these phases are located in crystallographically equivalent positions. The calculations have been performed using the density functional theory in the generalized gradient approximation. The calculated values of the structural characteristics and properties (sublimation energies, bulk moduli, band gaps, X-ray diffraction patterns) of the studied diamond-like phases differ significantly from the corresponding values for cubic diamond.

Anion ordering, magnetic structure and properties of the vacancy ordered perovskite Ba{sub 3}Fe{sub 3}O{sub 7}F

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

Clemens, Oliver, E-mail: oliver.clemens@nano.tu-darmstadt.de; Karlsruher Institut für Technologie, Institut für Nanotechnologie, Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen; University of Birmingham, School of Chemistry, Birmingham B152TT

2016-11-15

This article describes a detailed investigation of the crystallographic and magnetic structure of perovskite type Ba{sub 3}Fe{sub 3}O{sub 7}F by a combined analysis of X-ray and neutron powder diffraction data. Complete ordering of vacancies within the perovskite lattice could be confirmed. In addition, the structure of the anion sublattice was studied by means of the valence bond method, which suggested partial ordering of the fluoride ions on two of the six crystallographically different anion sites. Moreover, the compound was found to show G-type antiferromagnetic ordering of Fe moments, in agreement with magnetometric measurements as well as previously recorded {sup 57}Femore » Mössbauer spectroscopy data. - Graphical abstract: The vacancy and anion ordered structure of Ba{sub 3}Fe{sub 3}O{sub 7}F is described together with its magnetic properties. - Highlights: • Ba{sub 3}Fe{sub 3}O{sub 7}F possesses a unique vacancy order not found for other perovskite type compounds. • The valence bond method was used to locate oxide and fluoride ions. • Fluoride ions are distributed only on two of the six anion sites in Ba{sub 3}Fe{sub 3}O{sub 7}F. • The compound shows G-type antiferromagnetic ordering of magnetic moments. • The magnetic structure could be refined in one of the maximal magnetic subgroups of the nuclear structure.« less

Active-site solvent replenishment observed during human carbonic anhydrase II catalysis.

PubMed

Kim, Jin Kyun; Lomelino, Carrie L; Avvaru, Balendu Sankara; Mahon, Brian P; McKenna, Robert; Park, SangYoun; Kim, Chae Un

2018-01-01

Human carbonic anhydrase II (hCA II) is a zinc metalloenzyme that catalyzes the reversible hydration/dehydration of CO 2 /HCO 3 - . Although hCA II has been extensively studied to investigate the proton-transfer process that occurs in the active site, its underlying mechanism is still not fully understood. Here, ultrahigh-resolution crystallographic structures of hCA II cryocooled under CO 2 pressures of 7.0 and 2.5 atm are presented. The structures reveal new intermediate solvent states of hCA II that provide crystallographic snapshots during the restoration of the proton-transfer water network in the active site. Specifically, a new intermediate water (W I ') is observed next to the previously observed intermediate water W I , and they are both stabilized by the five water molecules at the entrance to the active site (the entrance conduit). Based on these structures, a water network-restructuring mechanism is proposed, which takes place at the active site after the nucleophilic attack of OH - on CO 2 . This mechanism explains how the zinc-bound water (W Zn ) and W1 are replenished, which are directly responsible for the reconnection of the His64-mediated proton-transfer water network. This study provides the first 'physical' glimpse of how a water reservoir flows into the hCA II active site during its catalytic activity.

Confocal Raman microscopy as a tool to describe different mineral and organic phases at high spatial resolution within marine biogenic carbonates: case study on Nerita undata (Gastropoda, Neritopsina)

NASA Astrophysics Data System (ADS)

Nehrke, G.; Nouet, J.

2011-06-01

Marine biogenic carbonates formed by invertebrates (e.g. corals and mollusk shells) represent complex composites of one or more mineral phases and organic molecules. This complexity ranges from the macroscopic structures observed with the naked eye down to sub micrometric structures only revealed by micro analytical techniques. Understanding to what extent and how organisms can control the formation of these structures requires that the mineral and organic phases can be identified and their spatial distribution related. Here we demonstrate the capability of confocal Raman microscopy applied to cross sections of a shell of Nerita undata to describe the distribution of calcite and aragonite including their crystallographic orientation with high lateral resolution (∼300 nm). Moreover, spatial distribution of functional groups of organic compounds can be simultaneously acquired, allowing to specifically relate them to the observed microstructures. The data presented in this case study highlights the possible new contributions of this method to the description of modalities of Nerita undata shell formation, and what could be expected of its application to other marine biogenic carbonates. Localization of areas of interest would also allow further investigations using more localized methods, such as TEM that would provide complementary information on the relation between organic molecules and crystallographic lattice.

X-ray Crystallographic, Multifrequency Electron Paramagnetic Resonance, and Density Functional Theory Characterization of the Ni(P(Cy)2N(tBu)2)2(n+) Hydrogen Oxidation Catalyst in the Ni(I) Oxidation State.

PubMed

Niklas, Jens; Westwood, Mark; Mardis, Kristy L; Brown, Tiara L; Pitts-McCoy, Anthony M; Hopkins, Michael D; Poluektov, Oleg G

2015-07-06

The Ni(I) hydrogen oxidation catalyst [Ni(P(Cy)2N(tBu)2)2](+) (1(+); P(Cy)2N(tBu)2 = 1,5-di(tert-butyl)-3,7-dicyclohexyl-1,5-diaza-3,7-diphosphacyclooctane) has been studied using a combination of electron paramagnetic resonance (EPR) techniques (X-, Q-, and D-band, electron-nuclear double resonance, hyperfine sublevel correlation spectroscopy), X-ray crystallography, and density functional theory (DFT) calculations. Crystallographic and DFT studies indicate that the molecular structure of 1(+) is highly symmetrical. EPR spectroscopy has allowed determination of the electronic g tensor and the spin density distribution on the ligands, and revealed that the Ni(I) center does not interact strongly with the potentially coordinating solvents acetonitrile and butyronitrile. The EPR spectra and magnetic parameters of 1(+) are found to be distinctly different from those for the related compound [Ni(P(Ph)2N(Ph)2)2](+) (4(+)). One significant contributor to these differences is that the molecular structure of 4(+) is unsymmetrical, unlike that of 1(+). DFT calculations on derivatives in which the R and R' groups are systematically varied have allowed elucidation of structure/substituent relationships and their corresponding influence on the magnetic resonance parameters.

Structural similarities in tetraaryltins described by virtual non-crystallographic rotations or translations: Kitaigorodskii's morphotropism is revisited.

PubMed

Kálmán, Alajos; Fábián, László

2007-06-01

Recently Kálmán [(2005), Acta Cryst. B61, 536-547] revealed that semirigid molecules or their patterns held together e.g. by hydrogen bonds may perform non-crystallographic rotations (through 180, 90 degrees etc.) around themselves whenever a substitution, ring enlargement or isomerization destroys the existing close packing, i.e. the novel substituent or the enlarged ring can no longer fit in the hollows formed between the molecules. In other words, the old and new arrangements of such chemically similar molecules can be converted into each other by virtual rotations. However, when a semirigid molecule without substitution, but under the influence of solvents, temperature etc., is fully or partly rearranged in the solid state, the corresponding non-crystallographic rotation (hereinafter ncr) is real and gives rise to polymorphism. Such polymorphs are hallmarked by full or partial isostructurality and show that ncrs always occur together with isostructurality. First Kitaigorodskii [(1961), Organic Chemical Crystallography, New York: Consultants Bureau] reported on the structural similarity of three tetraaryltins, (p-RC(6)H(4))(4)Sn, R = H, CH(3), CH(3)O, which is terminated by the larger C(2)H(5)O group. A revisit to these structures revealed that the tetragonal --> monoclinic conversion termed by Kitaigorodskii as a ;morphotropic step' is also performed by an ncr. Similarly, other tetraaryltins in the literature are related by ncrs or the nc translation of the semirigid tetrahedra, or they remain isostructural. Since one of the definitions of morphotropism, a word of Greek origin, is 'turn of form', the ncrs of semirigid molecules can be denoted--following Kitaigorodskii--by this word, whereas its alternative definition in the morphological crystallography of ;unidirectional changes' [applied by Groth (1870). Ber. Chem. Ges. 3, 449-457] covers the non-crystallographic translations described first in this work.

Synthesis and the crystal and molecular structure of the germanium(IV) complex with propylene-1,3-diaminetetraacetic acid [Ge(Pdta)

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

Sergienko, V. S., E-mail: sergienko@igic.ras.ru; Martsinko, E. E.; Seifullina, I. I.

2015-09-15

The germanium(IV) complex with propylene-1,3-diaminetetraacetic acid (H{sub 4}Pdta) is studied by elemental analysis, X-ray diffraction, thermogravimetry, and IR spectroscopy. The X-ray diffraction study reveals two crystallographically independent [Ge(Pdta)] molecules of similar structure. Both Ge atoms are octahedrally coordinated by four O atoms and two N atoms (at the cis positions) of the hexadentate pentachelate Pdta{sup 4–} ligand. An extended system of weak C—H···O hydrogen bonds connects complex molecules into a supramolecular 3D framework.

Synthesis and the crystal and molecular structure of the germanium(IV) complex with propylene-1,3-diaminetetraacetic acid [Ge( Pdta)

NASA Astrophysics Data System (ADS)

Sergienko, V. S.; Martsinko, E. E.; Seifullina, I. I.; Churakov, A. V.; Chebanenko, E. A.

2015-09-01

The germanium(IV) complex with propylene-1,3-diaminetetraacetic acid (H4 Pdta) is studied by elemental analysis, X-ray diffraction, thermogravimetry, and IR spectroscopy. The X-ray diffraction study reveals two crystallographically independent [Ge( Pdta)] molecules of similar structure. Both Ge atoms are octahedrally coordinated by four O atoms and two N atoms (at the cis positions) of the hexadentate pentachelate Pdta 4- ligand. An extended system of weak С—Н···О hydrogen bonds connects complex molecules into a supramolecular 3D framework.

Small-angle X-ray scattering reveals the solution structure of the full-length DNA gyrase a subunit.

PubMed

Costenaro, Lionel; Grossmann, J Günter; Ebel, Christine; Maxwell, Anthony

2005-02-01

DNA gyrase is the topoisomerase uniquely able to actively introduce negative supercoils into DNA. Vital in all bacteria, but absent in humans, this enzyme is a successful target for antibacterial drugs. From biophysical experiments in solution, we report the low-resolution structure of the full-length A subunit (GyrA). Analytical ultracentrifugation shows that GyrA is dimeric, but nonglobular. Ab initio modeling from small-angle X-ray scattering allows us to retrieve the molecular envelope of GyrA and thereby the organization of its domains. The available crystallographic structure of the amino-terminal domain (GyrA59) forms a dimeric core, and two additional pear-shaped densities closely flank it in an unexpected position. Each accommodates very well a carboxyl-terminal domain (GyrA-CTD) built from a homologous crystallographic structure. The uniqueness of gyrase is due to the ability of the GyrA-CTDs to wrap DNA. Their position within the GyrA structure strongly suggests a large conformation change of the enzyme upon DNA binding.

Structure determination of an 11-subunit exosome in complex with RNA by molecular replacement

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

Makino, Debora Lika, E-mail: dmakino@biochem.mpg.de; Conti, Elena

The crystallographic steps towards the structure determination of a complete eukaryotic exosome complex bound to RNA are presented. Phasing of this 11-protein subunit complex was carried out via molecular replacement. The RNA exosome is an evolutionarily conserved multi-protein complex involved in the 3′ degradation of a variety of RNA transcripts. In the nucleus, the exosome participates in the maturation of structured RNAs, in the surveillance of pre-mRNAs and in the decay of a variety of noncoding transcripts. In the cytoplasm, the exosome degrades mRNAs in constitutive and regulated turnover pathways. Several structures of subcomplexes of eukaryotic exosomes or related prokaryoticmore » exosome-like complexes are known, but how the complete assembly is organized to fulfil processive RNA degradation has been unclear. An atomic snapshot of a Saccharomyces cerevisiae 420 kDa exosome complex bound to an RNA substrate in the pre-cleavage state of a hydrolytic reaction has been determined. Here, the crystallographic steps towards the structural elucidation, which was carried out by molecular replacement, are presented.« less

High-pressure Irreversible Amorphization of La1/3NbO3

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

I Halevy; A Hen; A Broide

2011-12-31

The crystallographic structure of La{sub 1/3}NbO{sub 3} perovskite was studied at high pressures using a diamond-anvil cell and synchrotron radiation. High-pressure energy dispersive (EDS) x-ray diffraction and high-pressure angle dispersive (ADS) x-ray diffraction revealed an irreversible amorphization at {approx}10 GPa. A large change in the bulk modulus accompanied the high-pressure amorphization.

Raw diffraction data preservation and reuse: Overview, update on practicalities and metadata requirements

DOE PAGES

Kroon-Batenburg, Loes M. J.; Helliwell, John R.; McMahon, Brian; ...

2017-01-01

A topical review is presented of the rapidly developing interest in and storage options for the preservation and reuse of raw data within the scientific domain of the IUCr and its Commissions, each of which operates within a great diversity of instrumentation. A résumé is included of the case for raw diffraction data deposition. An overall context is set by highlighting the initiatives of science policy makers towards an `Open Science' model within which crystallographers will increasingly work in the future; this will bring new funding opportunities but also new codes of procedure within open science frameworks. Skills education andmore » training for crystallographers will need to be expanded. Overall, there are now the means and the organization for the preservation of raw crystallographic diffraction dataviadifferent types of archive, such as at universities, discipline-specific repositories (Integrated Resource for Reproducibility in Macromolecular Crystallography, Structural Biology Data Grid), general public data repositories (Zenodo, ResearchGate) and centralized neutron and X-ray facilities. Formulation of improved metadata descriptors for the raw data types of each of the IUCr Commissions is in progress; some detailed examples are provided. Lastly, a number of specific case studies are presented, including an example research thread that provides complete open access to raw data.« less

Raw diffraction data preservation and reuse: overview, update on practicalities and metadata requirements

PubMed Central

Kroon-Batenburg, Loes M. J.

2017-01-01

A topical review is presented of the rapidly developing interest in and storage options for the preservation and reuse of raw data within the scientific domain of the IUCr and its Commissions, each of which operates within a great diversity of instrumentation. A résumé is included of the case for raw diffraction data deposition. An overall context is set by highlighting the initiatives of science policy makers towards an ‘Open Science’ model within which crystallographers will increasingly work in the future; this will bring new funding opportunities but also new codes of procedure within open science frameworks. Skills education and training for crystallographers will need to be expanded. Overall, there are now the means and the organization for the preservation of raw crystallographic diffraction data via different types of archive, such as at universities, discipline-specific repositories (Integrated Resource for Reproducibility in Macromol­ecular Crystallography, Structural Biology Data Grid), general public data repositories (Zenodo, ResearchGate) and centralized neutron and X-ray facilities. Formulation of improved metadata descriptors for the raw data types of each of the IUCr Commissions is in progress; some detailed examples are provided. A number of specific case studies are presented, including an example research thread that provides complete open access to raw data. PMID:28250944

Raw diffraction data preservation and reuse: Overview, update on practicalities and metadata requirements

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

Kroon-Batenburg, Loes M. J.; Helliwell, John R.; McMahon, Brian

A topical review is presented of the rapidly developing interest in and storage options for the preservation and reuse of raw data within the scientific domain of the IUCr and its Commissions, each of which operates within a great diversity of instrumentation. A résumé is included of the case for raw diffraction data deposition. An overall context is set by highlighting the initiatives of science policy makers towards an `Open Science' model within which crystallographers will increasingly work in the future; this will bring new funding opportunities but also new codes of procedure within open science frameworks. Skills education andmore » training for crystallographers will need to be expanded. Overall, there are now the means and the organization for the preservation of raw crystallographic diffraction dataviadifferent types of archive, such as at universities, discipline-specific repositories (Integrated Resource for Reproducibility in Macromolecular Crystallography, Structural Biology Data Grid), general public data repositories (Zenodo, ResearchGate) and centralized neutron and X-ray facilities. Formulation of improved metadata descriptors for the raw data types of each of the IUCr Commissions is in progress; some detailed examples are provided. Lastly, a number of specific case studies are presented, including an example research thread that provides complete open access to raw data.« less

Stepwise observation and quantification and mixed matrix membrane separation of CO2 within a hydroxy-decorated porous host† †Electronic supplementary information (ESI) available. CCDC 1504685–1504693. See DOI: 10.1039/c6sc04343g Click here for additional data file. Click here for additional data file.

PubMed Central

Morris, Christopher G.; Jacques, Nicholas M.; Godfrey, Harry G. W.; Mitra, Tamoghna; Fritsch, Detlev; Lu, Zhenzhong; Murray, Claire A.; Potter, Jonathan; Cobb, Tom M.; Yuan, Fajin

2017-01-01

The identification of preferred binding domains within a host structure provides important insights into the function of materials. State-of-the-art reports mostly focus on crystallographic studies of empty and single component guest-loaded host structures to determine the location of guests. However, measurements of material properties (e.g., adsorption and breakthrough of substrates) are usually performed for a wide range of pressure (guest coverage) and/or using multi-component gas mixtures. Here we report the development of a multifunctional gas dosing system for use in X-ray powder diffraction studies on Beamline I11 at Diamond Light Source. This facility is fully automated and enables in situ crystallographic studies of host structures under (i) unlimited target gas loadings and (ii) loading of multi-component gas mixtures. A proof-of-concept study was conducted on a hydroxyl-decorated porous material MFM-300(VIII) under (i) five different CO2 pressures covering the isotherm range and (ii) the loading of equimolar mixtures of CO2/N2. The study has successfully captured the structural dynamics underpinning CO2 uptake as a function of surface coverage. Moreover, MFM-300(VIII) was incorporated in a mixed matrix membrane (MMM) with PIM-1 in order to evaluate the CO2/N2 separation potential of this material. Gas permeation measurements on the MMM show a great improvement over the bare PIM-1 polymer for CO2/N2 separation based on the ideal selectivity. PMID:28507700

Low temperature dielectric relaxation in ordinary perovskite ferroelectrics: enlightenment from high-energy x-ray diffraction

NASA Astrophysics Data System (ADS)

Ochoa, D. A.; Levit, R.; Fancher, C. M.; Esteves, G.; Jones, J. L.; E García, J.

2017-05-01

Ordinary ferroelectrics exhibit a second order phase transition that is characterized by a sharp peak in the dielectric permittivity at a frequency-independent temperature. Furthermore, these materials show a low temperature dielectric relaxation that appears to be a common behavior of perovskite systems. Tetragonal lead zirconate titanate is used here as a model system in order to explore the origin of such an anomaly, since there is no consensus about the physical phenomenon involved in it. Crystallographic and domain structure studies are performed from temperature dependent synchrotron x-ray diffraction measurement. Results indicate that the dielectric relaxation cannot be associated with crystallographic or domain configuration changes. The relaxation process is then parameterized by using the Vogel-Fulcher-Tammann phenomenological equation. Results allow us to hypothesize that the observed phenomenon is due to changes in the dynamic behavior of the ferroelectric domains related to the fluctuation of the local polarization.

Signatures of unfolding in the early stages of protein denaturation

NASA Astrophysics Data System (ADS)

Gray, Harry B.; Winkler, Jay R.; Kozak, John J.

2012-04-01

A comparative study of the early stages of unfolding of five proteins: cyt c, c-b 562, cyt c‧, azurin, and lysozyme is reported. From crystallographic data, helical regions and intervening non-helical (or 'turning') regions are identified in each. Exploiting a previously introduced geometrical model, the paper describes quantitatively the stepwise extension of a polypeptide chain subject to the geometrical constraint that the spatial relationship among the residues of each triplet is fixed by native-state crystallographic data. Despite differences among the above-cited proteins, remarkable universality of behavior is found in the early stages of unfolding. At the very earliest stages, internal residues in each helical region have a common unfolding history; the terminal residues, however, are extraordinarily sensitive to structural perturbations. Residues in non-helical sections of the polypeptide unfold after residues in the internal helical regions, but with increasing steric perturbation playing a dominant role in advancing denaturation.

Preparation, crystallization and preliminary crystallographic analysis of old yellow enzyme from Trypanosoma cruzi

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

Sugiyama, Shigeru; Tokuoka, Keiji; Uchiyama, Nahoko

2007-10-01

Old yellow enzyme from Trypanosoma cruzi, has been crystallized using the hanging-drop vapour-diffusion method. Old yellow enzyme (OYE) is an NADPH oxidoreductase that contains a flavin mononucleotide as a prosthetic group. The OYE from Trypanosoma cruzi, which produces prostaglandin F{sub 2α}, a potent mediator of various physiological and pathological processes, from prostaglandin H2. The protein was recombinantly expressed and purified from Escherichia coli and was crystallized using the hanging-drop vapour-diffusion method. The crystal belongs to the monoclinic space group P2{sub 1}, with unit-cell parameters a = 56.3, b = 78.8, c = 78.8 Å, β = 93.4° and two moleculesmore » per asymmetric unit. The crystals were suitable for X-ray crystallographic studies and diffracted to 1.70 Å resolution. A Patterson search method is in progress using the structure of OYE from Pseudomonas putida as a starting model.« less

Polarized Neutron Study of Ni-Mn-Ga Alloys: Site-Specific Spin Density Affected by Martensitic Transformation.

PubMed

Lázpita, P; Barandiarán, J M; Gutiérrez, J; Mondelli, C; Sozinov, A; Chernenko, V A

2017-10-13

Polarized neutron scattering has been used to obtain the magnetic moment at specific crystallographic sites of the austenitic and martensitic phases of two nonstoichiometric Ni-Mn-Ga single crystals with close composition. These alloys have been chosen because they exhibit different structures in the paramagnetic state and inverse positions of the respective martensitic transformation and Curie temperature. The diffraction analysis revealed a remarkable result: Despite the similar alloy composition, the magnetic moments of Mn are quite different for the two alloys at the same crystallographic position. Furthermore, such a difference enabled us to assess that the exchange coupling between Mn atoms switches from ferro- to antiferromagnetic at a distance between 2.92 and 3.32 Å in the martensite. These results are of great importance to guide first principles calculations that, up to now, have not been contrasted with experiments at the atomic level.

Optical third harmonic generation in the magnetic semiconductor EuSe

NASA Astrophysics Data System (ADS)

Lafrentz, M.; Brunne, D.; Kaminski, B.; Pavlov, V. V.; Pisarev, R. V.; Henriques, A. B.; Yakovlev, D. R.; Springholz, G.; Bauer, G.; Bayer, M.

2012-01-01

Third harmonic generation (THG) has been studied in europium selenide EuSe in the vicinity of the band gap at 2.1-2.6 eV and at higher energies up to 3.7 eV. EuSe is a magnetic semiconductor crystalizing in centrosymmetric structure of rock-salt type with the point group m3m. For this symmetry the crystallographic and magnetic-field-induced THG nonlinearities are allowed in the electric-dipole approximation. Using temperature, magnetic field, and rotational anisotropy measurements, the crystallographic and magnetic-field-induced contributions to THG were unambiguously separated. Strong resonant magnetic-field-induced THG signals were measured at energies in the range of 2.1-2.6 eV and 3.1-3.6 eV for which we assign to transitions from 4f7 to 4f65d1 bands, namely involving 5d(t2g) and 5d(eg) states.

Polarized Neutron Study of Ni-Mn-Ga Alloys: Site-Specific Spin Density Affected by Martensitic Transformation

NASA Astrophysics Data System (ADS)

Lázpita, P.; Barandiarán, J. M.; Gutiérrez, J.; Mondelli, C.; Sozinov, A.; Chernenko, V. A.

2017-10-01

Polarized neutron scattering has been used to obtain the magnetic moment at specific crystallographic sites of the austenitic and martensitic phases of two nonstoichiometric Ni-Mn-Ga single crystals with close composition. These alloys have been chosen because they exhibit different structures in the paramagnetic state and inverse positions of the respective martensitic transformation and Curie temperature. The diffraction analysis revealed a remarkable result: Despite the similar alloy composition, the magnetic moments of Mn are quite different for the two alloys at the same crystallographic position. Furthermore, such a difference enabled us to assess that the exchange coupling between Mn atoms switches from ferro- to antiferromagnetic at a distance between 2.92 and 3.32 Å in the martensite. These results are of great importance to guide first principles calculations that, up to now, have not been contrasted with experiments at the atomic level.

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

Nazareth, A.S.; Sood, D.K.; Zmood, R.B.

A focusing grid broad beam Kaufman source, using argon ions on a target of nominal composition Nd{sub 2}Fe{sub 14}B has been employed to sputter deposit magnetic thin films of thicknesses ranging from 800 {angstrom} to 1300 {angstrom} on silicon-(111) substrates at room temperature. These films were characterized for their composition depth profile by Rutherford Backscattering Spectroscopy, while x-ray diffraction was used to study the crystallographic structure. Due to a close match between (111) Si with (220) Nd{sub 2}Fe{sub 14}B lattice spacings, preferred crystallographic texturing was expected, and experimental results showed a greatly enhanced (220) texture. The degradation in magnetic propertiesmore » was attributed to the presence of oxygen in the films as indicated by concentration depth profiles. It is premised that another significant role of oxygen may be to relieve the misfit strain across the interface by its incorporation within the Nd{sub 2}Fe{sub 14}B phase.« less

Crystallographic structure refinement with quadrupolar nuclei: a combined solid-state NMR and GIPAW DFT example using MgBr(2).

PubMed

Widdifield, Cory M; Bryce, David L

2009-09-07

Solid-state NMR spectroscopy and GIPAW DFT calculations reveal the pronounced sensitivity of (79/81)Br and (25)Mg quadrupolar coupling constants to subtle aspects of solid state structure which were not previously detected by pXRD methods.

Energetic Materials for Bio-Agent Destruction

DTIC Science & Technology

2017-03-01

Delocalization of electrons in 4 The structure of 5 was obtained by X-ray single crystal crystallography . The crystallographic data are summarized in...4 22.2 49.6 - - 8.36 5 18.8 41.7 - - 5.07 The structure of 5 was obtained by X-ray single crystal crystallography . The

Structure of an LiKSO 4 single crystal studied by 7Li and 39K NMR at low temperature

NASA Astrophysics Data System (ADS)

Lim, A. R.; Jeong, S.-Y.

2000-09-01

The 7Li and 39K nuclear magnetic resonances in an LiKSO 4 single crystal grown by the slow evaporation method have been investigated using a Bruker FT nuclear magnetic resonance (NMR) spectrometer. From the experimental data, the quadrapole coupling constant and asymmetry parameter were determined at room temperature and low temperature, respectively. Unlike the case at 300 K, the 7Li NMR line consists of three sets at 180 K, while 39K nucleus exhibits six sets for the rotation around the three crystallographic axes. The three resonance lines of 7Li and 39K at low temperature can be explained by the existence of three kinds of twin domain, rotated with respect to each other by 120° around the c-axis. The three resonance lines are also related to the crystallographic mirror plane. Structure of ferroelastic LiKSO 4 crystals at 180 K can be directly inferred from the domain pattern obtained by 7Li and 39K NMR. The above results show that the equations of the twin boundaries belong to the mm2 F6 mm ferroelastic species. Therefore, the symmetry of phases III and II is given by orthorhombic structure with Cmc2 1 ( mm2) and hexagonal structural with P6 3mc (6 mm), respectively.

Novel Antimicrobial Titanium Dioxide Nanotubes Obtained through a Combination of Atomic Layer Deposition and Electrospinning Technologies.

PubMed

López de Dicastillo, Carol; Patiño, Cristian; Galotto, María Jose; Palma, Juan Luis; Alburquenque, Daniela; Escrig, Juan

2018-02-24

The search for new antimicrobial substances has increased in recent years. Antimicrobial nanostructures are one of the most promising alternatives. In this work, titanium dioxide nanotubes were obtained by an atomic layer deposition (ALD) process over electrospun polyvinyl alcohol nanofibers (PVN) at different temperatures with the purpose of obtaining antimicrobial nanostructures with a high specific area. Electrospinning and ALD parameters were studied in order to obtain PVN with smallest diameter and highest deposition rate, respectively. Chamber temperature was a key factor during ALD process and an appropriate titanium dioxide deposition performance was achieved at 200 °C. Subsequently, thermal and morphological analysis by SEM and TEM microscopies revealed hollow nanotubes were obtained after calcination process at 600 °C. This temperature allowed complete polymer removal and influenced the resulting anatase crystallographic structure of titanium dioxide that positively affected their antimicrobial activities. X-ray analysis confirmed the change of titanium dioxide crystallographic structure from amorphous phase of deposited PVN to anatase crystalline structure of nanotubes. These new nanostructures with very large surface areas resulted in interesting antimicrobial properties against Gram-positive and Gram-negative bacteria. Titanium dioxide nanotubes presented the highest activity against Escherichia coli with 5 log cycles reduction at 200 μg/mL concentration.

Novel Antimicrobial Titanium Dioxide Nanotubes Obtained through a Combination of Atomic Layer Deposition and Electrospinning Technologies

PubMed Central

Patiño, Cristian; Galotto, María Jose; Palma, Juan Luis; Alburquenque, Daniela

2018-01-01

The search for new antimicrobial substances has increased in recent years. Antimicrobial nanostructures are one of the most promising alternatives. In this work, titanium dioxide nanotubes were obtained by an atomic layer deposition (ALD) process over electrospun polyvinyl alcohol nanofibers (PVN) at different temperatures with the purpose of obtaining antimicrobial nanostructures with a high specific area. Electrospinning and ALD parameters were studied in order to obtain PVN with smallest diameter and highest deposition rate, respectively. Chamber temperature was a key factor during ALD process and an appropriate titanium dioxide deposition performance was achieved at 200 °C. Subsequently, thermal and morphological analysis by SEM and TEM microscopies revealed hollow nanotubes were obtained after calcination process at 600 °C. This temperature allowed complete polymer removal and influenced the resulting anatase crystallographic structure of titanium dioxide that positively affected their antimicrobial activities. X-ray analysis confirmed the change of titanium dioxide crystallographic structure from amorphous phase of deposited PVN to anatase crystalline structure of nanotubes. These new nanostructures with very large surface areas resulted in interesting antimicrobial properties against Gram-positive and Gram-negative bacteria. Titanium dioxide nanotubes presented the highest activity against Escherichia coli with 5 log cycles reduction at 200 μg/mL concentration. PMID:29495318

Reinterpretation of the Vibrational Spectroscopy of the Medicinal Bioinorganic Synthon c,c,t-[Pt(NH3)2Cl2(OH)2]†

PubMed Central

Johnstone, Timothy C.

2014-01-01

The Pt(IV) complex c,c,t-[Pt(NH3)2Cl2(OH)2] is an important intermediate in the synthesis of Pt(IV) anticancer prodrugs and has been investigated as an anticancer agent in its own right. An analysis of the vibrational spectroscopy of this molecule was previously reported [Faggiani et al., 1982, Can. J. Chem. 60, 529] in which crystallographic determination of the structure of the complex permitted a site group approach. The space group, however, was incorrectly assigned. In the present study we have redetermined at high resolution crystal structures of c,c,t-[Pt(NH3)2Cl2(OH)2] and c,c,t-[Pt(NH3)2Cl2(OH)2]·H2O2, which enable discussion of the effect of hydrogen bonding on the N–H and O–H vibrational bands. The correct crystallographic site symmetry of the platinum complex in the c,c,t-[Pt(NH3)2Cl2(OH)2] structure is employed to conduct a new vibrational analysis using both group theoretical and modern DFT methods. This analysis reveals the nature and symmetry of the “missing band” described in the original publication and suggests a possible explanation for its disappearance. PMID:24515615

Crystallographic and magnetic properties of nanocrystalline perovskite structure SmFeO3 orthoferrite

NASA Astrophysics Data System (ADS)

Kumar, Ashwini; Shen, Jingdong; Zhao, Huihui; Zhengjian, Qi; Li, Qi

2018-05-01

In this article, we present the structural and magnetic studies of pristine SmFeO3 nanocrystalline ceramic samples as sintered at temperature 850 °C and 1000 °C. X-ray powder diffraction data confirm the existence of single-phase nature with orthorhombic (Pbnm) structure of the samples. The SEM image reveals spherical particles with a size range of 60-130 nm for SFO-850 and SFO-1000 samples. X-ray absorption spectroscopy studies on Fe L3,2 and O K-edges of SmFeO3 sample revealed the homo-valence state of Fe in these materials. From magnetization studies it has been observed the materials exhibit ferromagnetic and antiferromagnetic (canted spin structure) sub-lattices, which results strong magnetic anisotropy in the system.

Pressure induced phase transition and elastic properties of cerium mono-nitride (CeN)

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

Yaduvanshi, Namrata, E-mail: namrata-yaduvanshi@yahoo.com; Singh, Sadhna

2016-05-23

In the present paper, we have investigated the high-pressure structural phase transition and elastic properties of cerium mono-nitride. We studied theoretically the structural properties of this compound (CeN) by using the improved interaction potential model (IIPM) approach. This compound exhibits first order crystallographic phase transition from NaCl (B{sub 1}) to tetragonal (BCT) phase at 37 GPa. The phase transition pressures and associated volume collapse obtained from present potential model (IIPM) show a good agreement with available theoretical data.

Structural and magnetic properties and superconductivity in Ba(Fe 1-xTM x) 2As 2

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

Thaler, Alexander

2012-01-01

We studied the effects on structural and magnetic phase transitions and the emergence of superconductivity in transition metal substituted BaFe 2As 2. We grew four series of Ba(Fe 1-xTM 2) 2As 2 (TM=Ru, Mn, Co+Cr and Co+Mn) and characterized them by crystallographic, magnetic and transport measurements. We also subjected Ba(Fe 1-xCr x) 2As 2 and Ba(Fe 1-xCo x) 2As 2 to heat treatment to explore what changes might be induced.

Analysis of Crystallographic Structure of a Japanese Sword by the Pulsed Neutron Transmission Method

NASA Astrophysics Data System (ADS)

Kino, K.; Ayukawa, N.; Kiyanagi, Y.; Uchida, T.; Uno, S.; Grazzi, F.; Scherillo, A.

We measured two-dimensional transmission spectra of pulsed neutron beams for a Japanese sword sample. Atom density, crystalline size, and preferred orientation of crystals were obtained using the RITS code. The position dependence of the atomic density is consistent with the shape of the sample. The crystalline size is very small and shows position dependence, which is understood by the unique structure of Japanese swords. The preferred orientation has strong position dependence. Our study shows the usefulness of the pulsed neutron transmission method for cultural metal artifacts.

Automated docking of ligands to an artificial active site: augmenting crystallographic analysis with computer modeling

NASA Astrophysics Data System (ADS)

Rosenfeld, Robin J.; Goodsell, David S.; Musah, Rabi A.; Morris, Garrett M.; Goodin, David B.; Olson, Arthur J.

2003-08-01

The W191G cavity of cytochrome c peroxidase is useful as a model system for introducing small molecule oxidation in an artificially created cavity. A set of small, cyclic, organic cations was previously shown to bind in the buried, solvent-filled pocket created by the W191G mutation. We docked these ligands and a set of non-binders in the W191G cavity using AutoDock 3.0. For the ligands, we compared docking predictions with experimentally determined binding energies and X-ray crystal structure complexes. For the ligands, predicted binding energies differed from measured values by ± 0.8 kcal/mol. For most ligands, the docking simulation clearly predicted a single binding mode that matched the crystallographic binding mode within 1.0 Å RMSD. For 2 ligands, where the docking procedure yielded an ambiguous result, solutions matching the crystallographic result could be obtained by including an additional crystallographically observed water molecule in the protein model. For the remaining 2 ligands, docking indicated multiple binding modes, consistent with the original electron density, suggesting disordered binding of these ligands. Visual inspection of the atomic affinity grid maps used in docking calculations revealed two patches of high affinity for hydrogen bond donating groups. Multiple solutions are predicted as these two sites compete for polar hydrogens in the ligand during the docking simulation. Ligands could be distinguished, to some extent, from non-binders using a combination of two trends: predicted binding energy and level of clustering. In summary, AutoDock 3.0 appears to be useful in predicting key structural and energetic features of ligand binding in the W191G cavity.

Identification of N-ethylmethylamine as a novel scaffold for inhibitors of soluble epoxide hydrolase by crystallographic fragment screening.

PubMed

Amano, Yasushi; Tanabe, Eiki; Yamaguchi, Tomohiko

2015-05-15

Soluble epoxide hydrolase (sEH) is a potential target for the treatment of inflammation and hypertension. X-ray crystallographic fragment screening was used to identify fragment hits and their binding modes. Eight fragment hits were identified via soaking of sEH crystals with fragment cocktails, and the co-crystal structures of these hits were determined via individual soaking. Based on the binding mode, N-ethylmethylamine was identified as a promising scaffold that forms hydrogen bonds with the catalytic residues of sEH, Asp335, Tyr383, and Tyr466. Compounds containing this scaffold were selected from an in-house chemical library and assayed. Although the starting fragment had a weak inhibitory activity (IC50: 800μM), we identified potent inhibitors including 2-({[2-(adamantan-1-yl)ethyl]amino}methyl)phenol exhibiting the highest inhibitory activity (IC50: 0.51μM). This corresponded to a more than 1500-fold increase in inhibitory activity compared to the starting fragment. Co-crystal structures of the hit compounds demonstrate that the binding of N-ethylmethylamine to catalytic residues is similar to that of the starting fragment. We therefore consider crystallographic fragment screening to be appropriate for the identification of weak but promising fragment hits. Copyright © 2015 Elsevier Ltd. All rights reserved.

Stress generated modifications of epitaxial ferroelectric SrTiO3 films on sapphire

NASA Astrophysics Data System (ADS)

Hollmann, E.; Schubert, J.; Kutzner, R.; Wördenweber, R.

2009-06-01

The effect of lattice-mismatch induced stress upon the crystallographic structure, strain, strain relaxation, and the generation of different types of defects in heteroepitaxially grown SrTiO3 films on CeO2 buffered sapphire is examined. Depending on the thickness of the SrTiO3 layer, characteristic changes in the structural perfection of the layers, their crystallographic orientation with respect to the substrate system, and their strain is observed. For thin films misfit dislocations partially compensate the stress in the SrTiO3 layer, whereas cracks develop in thicker SrTiO3 films. The cracks are orientated along two predominant crystallographic orientations of the sapphire. The structural modifications and the formation of misfit defects and cracks are explained in a model based on lattice misfit induced stress, on the one hand, and energy considerations taking into account the stress release due to crack formation and the energy necessary for the formation of new surfaces at the crack, on the other hand. The impact of lattice misfit is discussed in two steps, i.e., intrinsic and thermal induced misfits during heteroepitaxial film growth at a given temperature and the subsequent cooling of the sample, respectively. The comparison of the theoretical predictions and the experimental observations demonstrate that intrinsic mismatch and thermal mismatch have to be considered in order to explain strain dependent effects in complex heteroepitaxial layer systems such as induced ferroelectricity of SrTiO3 on sapphire.

Crystallographic tilt and in-plane anisotropies of an a-plane InGaN/GaN layered structure grown by MOCVD on r-plane sapphire using a ZnO buffer

NASA Astrophysics Data System (ADS)

Liu, H. F.; Liu, W.; Guo, S.; Chi, D. Z.

2016-03-01

High-resolution x-ray diffraction (HRXRD) was used to investigate the crystallographic tilts and structural anisotropies in epitaxial nonpolar a-plane InGaN/GaN grown by metal-organic chemical vapor deposition on r-plane sapphire using a ZnO buffer. The substrate had an unintentional miscut of 0.14° towards its [-4 2 2 3] axis. However, HRXRD revealed a tilt of 0.26° (0.20°) between the ZnO (GaN) (11-20) and the Al2O3 (1-102) atomic planes, with the (11-20) axis of ZnO (GaN) tilted towards its c-axis, which has a difference of 163° in azimuth from that of the substrate’s miscut. Excess broadenings in the GaN/ZnO (11-20) rocking curves (RCs) were observed along its c-axis. Specific analyses revealed that partial dislocations and anisotropic in-plane strains, rather than surface-related effects, wafer curvature or stacking faults, are the dominant factors for the structural anisotropy. The orientation of the partial dislocations is most likely affected by the miscut of the substrate, e.g. via tilting of the misfit dislocation gliding planes created during island coalescences. Their Burgers vector components in the growth direction, in turn, gave rise to crystallographic tilts in the same direction as that of the excess RC-broadenings.

Location-Control of Large Si Grains by Dual-Beam Excimer-Laser and Thick Oxide Portion

NASA Astrophysics Data System (ADS)

Ishihara, Ryoichi; Burtsev, Artyom; Alkemade, Paul F. A.

2000-07-01

An array of large Si grains was placed at a predetermined position by dual excimer-laser irradiation of a multi-layer structure of silicon (Si), silicon dioxide (SiO2) with an array of bumps and metal on a glass substrate. We have investigated the effects of irradiating energy density and the topology of the structure on the grain size and crystallographic structure by scanning electron microscopy (SEM) and electron back-scattering pattern (EBSP) analysis. In the low-energy-density regime, numerous small grains and petal shaped grains formed on top of the SiO2 bumps. The number of small grains on the bumps decreased with increasing irradiating energy density. At sufficiently high energy densities, one single Si grain as large as 3.5 μm was positioned at the center of the bumps. Although most of the area of the large Si grain has a single crystallographic orientation, twins and low-angle grain boundaries are often formed at the periphery of the grain. There was no preferred crystallographic orientation in the center of the location-controlled Si grain. Numerical analysis of the temperature profile showed that a temperature drop occurs at the center of the bump, during and immediately after laser irradiation. The diameter of the location-controlled Si grain increased with total thickness of the intermediate SiO2 layer, and took the maximum value of 6.2 μm.

Comparison of the NCI open database with seven large chemical structural databases.

PubMed

Voigt, J H; Bienfait, B; Wang, S; Nicklaus, M C

2001-01-01

Eight large chemical databases have been analyzed and compared to each other. Central to this comparison is the open National Cancer Institute (NCI) database, consisting of approximately 250 000 structures. The other databases analyzed are the Available Chemicals Directory ("ACD," from MDL, release 1.99, 3D-version); the ChemACX ("ACX," from CamSoft, Version 4.5); the Maybridge Catalog and the Asinex database (both as distributed by CamSoft as part of ChemInfo 4.5); the Sigma-Aldrich Catalog (CD-ROM, 1999 Version); the World Drug Index ("WDI," Derwent, version 1999.03); and the organic part of the Cambridge Crystallographic Database ("CSD," from Cambridge Crystallographic Data Center, 1999 Version 5.18). The database properties analyzed are internal duplication rates; compounds unique to each database; cumulative occurrence of compounds in an increasing number of databases; overlap of identical compounds between two databases; similarity overlap; diversity; and others. The crystallographic database CSD and the WDI show somewhat less overlap with the other databases than those with each other. In particular the collections of commercial compounds and compilations of vendor catalogs have a substantial degree of overlap among each other. Still, no database is completely a subset of any other, and each appears to have its own niche and thus "raison d'être". The NCI database has by far the highest number of compounds that are unique to it. Approximately 200 000 of the NCI structures were not found in any of the other analyzed databases.

Protein crystallization studies

NASA Technical Reports Server (NTRS)

Lyne, James Evans

1996-01-01

The Structural Biology laboratory at NASA Marshall Spaceflight Center uses x-ray crystallographic techniques to conduct research into the three-dimensional structure of a wide variety of proteins. A major effort in the laboratory involves an ongoing study of human serum albumin (the principal protein in human plasma) and its interaction with various endogenous substances and pharmaceutical agents. Another focus is on antigenic and functional proteins from several pathogenic organisms including the human immunodeficiency virus (HIV) and the widespread parasitic genus, Schistosoma. My efforts this summer have been twofold: first, to identify clinically significant drug interactions involving albumin binding displacement and to initiate studies of the three-dimensional structure of albumin complexed with these agents, and secondly, to establish collaborative efforts to extend the lab's work on human pathogens.

Self-assembly of Zn(salphen) complexes: steric regulation, stability studies and crystallographic analysis revealing an unexpected dimeric 3,3'-t-Bu-substituted Zn(salphen) complex.

PubMed

Martínez Belmonte, Marta; Wezenberg, Sander J; Haak, Robert M; Anselmo, Daniele; Escudero-Adán, Eduardo C; Benet-Buchholz, Jordi; Kleij, Arjan W

2010-05-21

The self-assembly features of a series of (non)symmetrical Zn(salphen) complexes have been studied in detail by X-ray crystallography, NMR and UV-vis techniques. The combined data demonstrate that the stability of these dimeric assemblies and the relative position of each monomeric unit within the dinuclear structure depend on the location and combination of the aromatic ring substituents.

Fine Structure in Multi-Phase Zr8Ni21-Zr7Ni10-Zr2Ni7 Alloy Revealed by Transmission Electron Microscope

PubMed Central

Shen, Haoting; Bendersky, Leonid A.; Young, Kwo; Nei, Jean

2015-01-01

The microstructure of an annealed alloy with a Zr8Ni21 composition was studied by both scanning electron microscopy (SEM) and transmission electron microscopy (TEM). The presence of three phases, Zr8Ni21, Zr2Ni7, and Zr7Ni10, was confirmed by SEM/X-ray energy dispersive spectroscopy compositional mapping and TEM electron diffraction. Distribution of the phases and their morphology can be linked to a multi-phase structure formed by a sequence of reactions: (1) L → Zr2Ni7 + L’; (2) peritectic Zr2Ni7 + L’ → Zr2Ni7 + Zr8Ni21 + L”; (3) eutectic L” → Zr8Ni21 + Zr7Ni10. The effect of annealing at 960 °C, which was intended to convert a cast structure into a single-phase Zr8Ni21 structure, was only moderate and the resulting alloy was still multi-phased. TEM and crystallographic analysis of the Zr2Ni7 phase show a high density of planar (001) defects that were explained as low-energy boundaries between rotational variants and stacking faults. The crystallographic features arise from the pseudo-hexagonal structure of Zr2Ni7. This highly defective Zr2Ni7 phase was identified as the source of the broad X-ray diffraction peaks at around 38.4° and 44.6° when a Cu-K was used as the radiation source. PMID:28793460

DiSCaMB: a software library for aspherical atom model X-ray scattering factor calculations with CPUs and GPUs.

PubMed

Chodkiewicz, Michał L; Migacz, Szymon; Rudnicki, Witold; Makal, Anna; Kalinowski, Jarosław A; Moriarty, Nigel W; Grosse-Kunstleve, Ralf W; Afonine, Pavel V; Adams, Paul D; Dominiak, Paulina Maria

2018-02-01

It has been recently established that the accuracy of structural parameters from X-ray refinement of crystal structures can be improved by using a bank of aspherical pseudoatoms instead of the classical spherical model of atomic form factors. This comes, however, at the cost of increased complexity of the underlying calculations. In order to facilitate the adoption of this more advanced electron density model by the broader community of crystallographers, a new software implementation called DiSCaMB , 'densities in structural chemistry and molecular biology', has been developed. It addresses the challenge of providing for high performance on modern computing architectures. With parallelization options for both multi-core processors and graphics processing units (using CUDA), the library features calculation of X-ray scattering factors and their derivatives with respect to structural parameters, gives access to intermediate steps of the scattering factor calculations (thus allowing for experimentation with modifications of the underlying electron density model), and provides tools for basic structural crystallographic operations. Permissively (MIT) licensed, DiSCaMB is an open-source C++ library that can be embedded in both academic and commercial tools for X-ray structure refinement.

Crystallographic Study of Itokawa Particle, RA-QD02-0127 by Using Energy-Scanning X-Ray Diffraction Method with Synchrotron Radiation

NASA Astrophysics Data System (ADS)

Hagiya, K.; Ohsumi, K.; Komatsu, M.; Mikouchi, T.; Zolensky, M. E.; Hirata, A.; Yamaguchi, S.; Kurokawa, A.

2016-08-01

Crystallographic study of Itokawa particle, RA-QD02-0127 by using new X-ray diffraction method was performed. The purpose of this study is to understand better the metamorphic and impact shock history of asteroid Itokawa, and other S-class asteroids.

Collaborative Research Program on Seafood Toxins

DTIC Science & Technology

1988-08-14

Crystallographic Structures of Saxitoxins Cl and C2 Appendix C: Collaborative Research Program an Seafcod Toxins Progress Report on Ciguatera and Related...radioimmunoassay for PSP were also evalumted. The Hokama stick test for ciguatera toxin was also evaluated. 4. initiate Studies on the Accumulation...tco•d which caie a form of b-mnn poisoning referred to as ciguatera . The respcnsible toxins originate from ll1ular rine algae of the division

Discrimination between Closely Related Cellular Metabolites by the SAM-I Riboswitch

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

Montange, R.; Mondragon, E; van Tyne, D

2010-01-01

The SAM-I riboswitch is a cis-acting element of genetic control found in bacterial mRNAs that specifically binds S-adenosylmethionine (SAM). We previously determined the 2.9-{angstrom} X-ray crystal structure of the effector-binding domain of this RNA element, revealing details of RNA-ligand recognition. To improve this structure, variations were made to the RNA sequence to alter lattice contacts, resulting in a 0.5-{angstrom} improvement in crystallographic resolution and allowing for a more accurate refinement of the crystallographic model. The basis for SAM specificity was addressed by a structural analysis of the RNA complexed to S-adenosylhomocysteine (SAH) and sinefungin and by measuring the affinity ofmore » SAM and SAH for a series of mutants using isothermal titration calorimetry. These data illustrate the importance of two universally conserved base pairs in the RNA that form electrostatic interactions with the positively charged sulfonium group of SAM, thereby providing a basis for discrimination between SAM and SAH.« less

Timely deposition of macromolecular structures is necessary for peer review

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

Joosten, Robbie P.; Soueidan, Hayssam; Wessels, Lodewyk F. A.

2013-12-01

Deposition of crystallographic structures should be concurrent with or prior to manuscript submission for peer review, enabling validation and increasing reliability of the PDB. Most of the macromolecular structures in the Protein Data Bank (PDB), which are used daily by thousands of educators and scientists alike, are determined by X-ray crystallography. It was examined whether the crystallographic models and data were deposited to the PDB at the same time as the publications that describe them were submitted for peer review. This condition is necessary to ensure pre-publication validation and the quality of the PDB public archive. It was found thatmore » a significant proportion of PDB entries were submitted to the PDB after peer review of the corresponding publication started, and many were only submitted after peer review had ended. It is argued that clear description of journal policies and effective policing is important for pre-publication validation, which is key in ensuring the quality of the PDB and of peer-reviewed literature.« less

Screening of matrix metalloproteinases available from the protein data bank: insights into biological functions, domain organization, and zinc binding groups.

PubMed

Nicolotti, Orazio; Miscioscia, Teresa Fabiola; Leonetti, Francesco; Muncipinto, Giovanni; Carotti, Angelo

2007-01-01

A total of 142 matrix metalloproteinase (MMP) X-ray crystallographic structures were retrieved from the Protein Data Bank (PDB) and analyzed by an automated and efficient routine, developed in-house, with a series of bioinformatic tools. Highly informative heat maps and hierarchical clusterograms provided a reliable and comprehensive representation of the relationships existing among MMPs, enlarging and complementing the current knowledge in the field. Multiple sequence and structural alignments permitted better location and display of key MMP motifs and quantification of the residue consensus at each amino acid position in the most critical binding subsites of MMPs. The MMP active site consensus sequences, the C-alpha root-mean-square deviation (RMSd) analysis of diverse enzymatic subsites, and the examination of the chemical nature, binding topologies, and zinc binding groups (ZBGs) of ligands extracted from crystallographic complexes provided useful insights on the structural arrangements of the most potent MMP inhibitors.

Crystallographic features related to a van der Waals coupling in the layered chalcogenide FePS{sub 3}

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

Murayama, Chisato; Okabe, Momoko; Fukuda, Koichiro

We investigated the crystallographic structure of FePS{sub 3} with a layered structure using transmission electron microscopy and powder X-ray diffraction. We found that FePS{sub 3} forms a rotational twin structure with the common axis along the c*-axis. The high-resolution transmission electron microscopy images revealed that the twin boundaries were positioned at the van der Waals gaps between the layers. The narrow bands of dark contrast were observed in the bright-field transmission electron microscopy images below the antiferromagnetic transition temperature, T{sub N} ≈ 120 K. Low-temperature X-ray diffraction showed a lattice distortion; the a- and b-axes shortened and lengthened, respectively, as the temperature decreasedmore » below T{sub N.} We propose that the narrow bands of dark contrast observed in the bright-field transmission electron microscopy images are caused by the directional lattice distortion with respect to each micro-twin variant in the antiferromagnetic phase.« less

The Introduction of Crystallographic Concepts Using Lap-Dissolve Slide Techniques.

ERIC Educational Resources Information Center

Bodner, George M.; And Others

1980-01-01

Describes a method using lap-dissolve slide techniques with two or more slide projectors focused on a single screen for presenting visual effects that show structural features in extended arrays of atoms, or ions involving up to several hundred atoms. Presents an outline of an introduction to the structures of crystalline solids. (CS)

Antifungal diterpenes from Hypoestes serpens (Acanthaceae).

PubMed

Rasoamiaranjanahary, Lalao; Marston, Andrew; Guilet, David; Schenk, Kurt; Randimbivololona, Fanantenanirainy; Hostettmann, Kurt

2003-02-01

Two new diterpenes, fusicoserpenol A and dolabeserpenoic acid A, with antifungal activity, were isolated from leaves of Hypoestes serpens (Acanthaceae). Their structures were elucidated by means of spectrometric methods including 1D and 2D NMR experiments and MS analysis. X-ray crystallographic analysis confirmed the structure of fusicoserpenol A and established the relative configuration.

How To Use Crystallographic Information in Teaching First-Year Chemistry.

ERIC Educational Resources Information Center

Bevan, D. J. M.; And Others

1988-01-01

Emphasizes the role that crystallography plays and has played in building up the body of chemical fact. Shows how the teaching of much of this material is illuminated by reference to crystal structures and crystallochemical relationships in all areas of chemistry. Discusses close packing, silicate structures, and salt hydrates. (CW)

A synthesis, X-ray crystallographic and vibrational studies of guanidinium o-nitrobenzoate hydrate. New NLO crystal in guanidinium nitrobenzoate family

NASA Astrophysics Data System (ADS)

Drozd, Marek; Daszkiewicz, Marek

2018-06-01

According to literature data the two crystals are known: guanidinium m-nitrobenzoate and guanidinium p-nitrobenzoate. Both compounds belong to noncetrosymmetric crystallographic systems are consider as second order generators in nonlinear optic (NLO). For each of these crystals the detailed crystallographic, theoretical calculations and vibrational studies were performed. It is interesting that nitrobenzoic acid create tree variety of compounds ((2) ortho-, (3) meta- and (4) para-) what any data for third member of guanidinium nitrobenzoate crystal were not known. The guanidinium o-nitrobenzoate hydrate crystal was synthesized first time. The performed X-ray crystallographic study shown that crystal belongs to space group without macroscopic symmetry center. Additionally, the vibrational spectra (intensities, frequencies and PED analysis) of investigated compound are presented. These results are compared with theoretical calculations for equilibrium geometry and vibrational properties. Furthermore, the results of the theoretical approach include HOMO and LUMO energies and first order hyperpolarizability were obtained, also. On the basis of these data the crystal was classified as second order generator. All obtained results are compared with previous literature data of guanidinium m-nitrobenzoate and guanidinium p-nitrobenzoate compounds. Surprisingly, each of examined crystal belongs to different crystallographic system and shows different vibrational properties.

Computational materials science: Think locally, act globally

NASA Astrophysics Data System (ADS)

Rabe, Karin M.

2002-11-01

New first-principles calculations reveal the range of atomic arrangements underlying the average crystallographic structure of a perovskite oxide, PZT. This work opens the door to understanding the exceptional physical behaviour of PZT and related systems.

Influence of different kinds of rolling on the crystallographic texture and magnetic induction of a NOG 3 wt% Si steel

NASA Astrophysics Data System (ADS)

Silva, J. M.; Baêta Júnior, E. S.; Moraes, N. R. D. C.; Botelho, R. A.; Felix, R. A. C.; Brandao, L.

2017-01-01

The purpose of this work was to study the influence of different kinds of rolling on the magnetic properties of NOG steel, an electric steel widely used in electrical motors. These properties are highly correlated with the crystallographic texture of the material, which can be changed by rolling. Three kinds of rolling were examined: conventional rolling, cross-rolling and asymmetrical rolling. The crystallographic texture was determined by X-ray diffraction and the magnetic properties were calculated from a theoretical model that related the magnetic induction to crystallographic texture through the anisotropy energy. The results show that cross-rolling yields higher values of magnetic induction than the other processes.

Observation of a re-entrant phase transition in the molecular complex tris(μ 2-3,5-diisopropyl-1,2,4-triazolato-κ 2 N 1: N 2)trigold(I) under high pressure

DOE PAGES

Woodall, Christopher H.; Christensen, Jeppe; Skelton, Jonathan M.; ...

2016-08-18

We report a molecular crystal that exhibits four successive phase transitions under hydro­static pressure, driven by aurophilic interactions, with the ground-state structure re-emerging at high pressure. The effect of pressure on two polytypes of tris(μ 2-3,5-diiso­propyl-1,2,4-triazolato-κ 2 N 1: N 2)trigold(I) (denoted Form-I and Form-II) has been analysed using luminescence spectroscopy, single-crystal X-ray diffraction and first-principles computation. A unique phase behaviour was observed in Form-I, with a complex sequence of phase transitions between 1 and 3.5 GPa. The ambient C2/c mother cell transforms to a P2 1/n phase above 1 GPa, followed by a P2 1/a phase above 2 GPamore » and a large-volume C2/c supercell at 2.70 GPa, with the previously observed P2 1/n phase then reappearing at higher pressure. The observation of crystallographically identical low- and high-pressure P2 1/n phases makes this a rare example of a re-entrant phase transformation. The phase behaviour has been characterized using detailed crystallographic theory and modelling, and rationalized in terms of molecular structural distortions. The dramatic changes in conformation are correlated with shifts of the luminescence maxima, from a band maximum at 14040 cm –1 at 2.40 GPa, decreasing steeply to 13550 cm –1 at 3 GPa. A similar study of Form-II displays more conventional crystallographic behaviour, indicating that the complex behaviour observed in Form-I is likely to be a direct consequence of the differences in crystal packing between the two polytypes.« less

Observation of a re-entrant phase transition in the molecular complex tris(μ 2-3,5-diisopropyl-1,2,4-triazolato-κ 2 N 1: N 2)trigold(I) under high pressure

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

Woodall, Christopher H.; Christensen, Jeppe; Skelton, Jonathan M.

We report a molecular crystal that exhibits four successive phase transitions under hydro­static pressure, driven by aurophilic interactions, with the ground-state structure re-emerging at high pressure. The effect of pressure on two polytypes of tris(μ 2-3,5-diiso­propyl-1,2,4-triazolato-κ 2 N 1: N 2)trigold(I) (denoted Form-I and Form-II) has been analysed using luminescence spectroscopy, single-crystal X-ray diffraction and first-principles computation. A unique phase behaviour was observed in Form-I, with a complex sequence of phase transitions between 1 and 3.5 GPa. The ambient C2/c mother cell transforms to a P2 1/n phase above 1 GPa, followed by a P2 1/a phase above 2 GPamore » and a large-volume C2/c supercell at 2.70 GPa, with the previously observed P2 1/n phase then reappearing at higher pressure. The observation of crystallographically identical low- and high-pressure P2 1/n phases makes this a rare example of a re-entrant phase transformation. The phase behaviour has been characterized using detailed crystallographic theory and modelling, and rationalized in terms of molecular structural distortions. The dramatic changes in conformation are correlated with shifts of the luminescence maxima, from a band maximum at 14040 cm –1 at 2.40 GPa, decreasing steeply to 13550 cm –1 at 3 GPa. A similar study of Form-II displays more conventional crystallographic behaviour, indicating that the complex behaviour observed in Form-I is likely to be a direct consequence of the differences in crystal packing between the two polytypes.« less

Research Update: Emerging chalcostibite absorbers for thin-film solar cells

DOE PAGES

de Souza Lucas, Francisco Willian; Zakutayev, Andriy

2018-06-04

Copper antimony chalcogenides CuSbCh 2 (Ch=S, Se) are an emerging family of absorbers studied for thin-film solar cells. These non-toxic and Earth-abundant materials show a layered low-dimensional chalcostibite crystal structure, leading to interesting optoelectronic properties for applications in photovoltaic (PV) devices. This research update describes the CuSbCh 2 crystallographic structures, synthesis methods, competing phases, band structures, optoelectronic properties, point defects, carrier dynamics, and interface band offsets, based on experimental and theoretical data. Correlations between these absorber properties and PV device performance are discussed, and opportunities for further increase in the efficiency of the chalcostibite PV devices are highlighted.

Research Update: Emerging chalcostibite absorbers for thin-film solar cells

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

de Souza Lucas, Francisco Willian; Zakutayev, Andriy

Copper antimony chalcogenides CuSbCh 2 (Ch=S, Se) are an emerging family of absorbers studied for thin-film solar cells. These non-toxic and Earth-abundant materials show a layered low-dimensional chalcostibite crystal structure, leading to interesting optoelectronic properties for applications in photovoltaic (PV) devices. This research update describes the CuSbCh 2 crystallographic structures, synthesis methods, competing phases, band structures, optoelectronic properties, point defects, carrier dynamics, and interface band offsets, based on experimental and theoretical data. Correlations between these absorber properties and PV device performance are discussed, and opportunities for further increase in the efficiency of the chalcostibite PV devices are highlighted.

Three oxime ether derivatives: Synthesis, crystallographic study, electronic structure and molecular electrostatic potential calculation

NASA Astrophysics Data System (ADS)

Dey, Tanusri; Praveena, Koduru Sri Shanthi; Pal, Sarbani; Mukherjee, Alok Kumar

2017-06-01

Three oxime ether derivatives, (E)-3-methoxy-4-(prop-2-ynyloxy)-benzaldehyde-O-prop-2-ynyl-oxime (C14H13NO3) (2), benzophenone-O-prop-2-ynyl-oxime (C16H13NO) (3) and (E)-2-chloro-6-methylquinoline-3-carbaldehyde-O-prop-2-ynyl-oxime (C14H11ClN2O) (4), have been synthesized and their crystal structures have been determined. The DFT optimized molecular geometries in 2-4 agree closely with those obtained from the crystallographic study. An interplay of intermolecular Csbnd H⋯O, Csbnd H⋯N, Csbnd H⋯Cl and Csbnd H···π(arene) hydrogen bonds and π···π interactions assembles molecules into a 2D columnar architecture in 2, a 1D molecular ribbon in 3 and a 3D framework in 4. Hirshfeld surface analysis showed that the structures of 2 and 3 are mainly characterized by H⋯H, H⋯C and H⋯O contacts but some contribution of H⋯N and H⋯Cl contacts is also observed in 4. Hydrogen-bond based interactions in 2-4 have been complemented by calculating molecular electrostatic potential (MEP) surfaces. The electronic structures of molecules reveal that the estimated band gap in 3, in which both aldehyde hydrogen atoms of formaldehyde-O-prop-2-ynyl-oxime (1) have been substituted by two benzene rings, is higher than that of 2 and 4 with only one aldehyde hydrogen atom replaced.

Determination of solute site occupancies within γ' precipitates in nickel-base superalloys via orientation-specific atom probe tomography

DOE PAGES

Meher, Subhashish; Rojhirunsakool, Tanaporn; Nandwana, Peeyush; ...

2015-04-28

In this study, the analytical limitations in atom probe tomography such as resolving a desired set of atomic planes, for solving complex materials science problems, have been overcome by employing a well-developed unique and reproducible crystallographic technique, involving synergetic coupling of orientation microscopy with atom probe tomography. The crystallographic information in atom probe reconstructions has been utilized to determine the solute site occupancies in Ni-Al-Cr based superalloys accurately. The structural information in atom probe reveals that both Al and Cr occupy the same sub-lattice within the L1 2-ordered g precipitates to form Ni 3(Al,Cr) precipitates in a Ni-14Al-7Cr(at.%) alloy. Interestingly,more » the addition of Co, which is a solid solution strengthener, to a Ni-14Al-7Cr alloy results in the partial reversal of Al site occupancy within g precipitates to form (Ni,Al) 3(Al,Cr,Co) precipitates. This unique evidence of reversal of Al site occupancy, resulting from the introduction of other solutes within the ordered structures, gives insights into the relative energetics of different sub-lattice sites when occupied by different solutes.« less

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.

Enhanced NMR Discrimination of Pharmaceutically Relevant Molecular Crystal Forms through Fragment-Based Ab Initio Chemical Shift Predictions.

PubMed

Hartman, Joshua D; Day, Graeme M; Beran, Gregory J O

2016-11-02

Chemical shift prediction plays an important role in the determination or validation of crystal structures with solid-state nuclear magnetic resonance (NMR) spectroscopy. One of the fundamental theoretical challenges lies in discriminating variations in chemical shifts resulting from different crystallographic environments. Fragment-based electronic structure methods provide an alternative to the widely used plane wave gauge-including projector augmented wave (GIPAW) density functional technique for chemical shift prediction. Fragment methods allow hybrid density functionals to be employed routinely in chemical shift prediction, and we have recently demonstrated appreciable improvements in the accuracy of the predicted shifts when using the hybrid PBE0 functional instead of generalized gradient approximation (GGA) functionals like PBE. Here, we investigate the solid-state 13 C and 15 N NMR spectra for multiple crystal forms of acetaminophen, phenobarbital, and testosterone. We demonstrate that the use of the hybrid density functional instead of a GGA provides both higher accuracy in the chemical shifts and increased discrimination among the different crystallographic environments. Finally, these results also provide compelling evidence for the transferability of the linear regression parameters mapping predicted chemical shieldings to chemical shifts that were derived in an earlier study.

Enhanced NMR Discrimination of Pharmaceutically Relevant Molecular Crystal Forms through Fragment-Based Ab Initio Chemical Shift Predictions

PubMed Central

2016-01-01

Chemical shift prediction plays an important role in the determination or validation of crystal structures with solid-state nuclear magnetic resonance (NMR) spectroscopy. One of the fundamental theoretical challenges lies in discriminating variations in chemical shifts resulting from different crystallographic environments. Fragment-based electronic structure methods provide an alternative to the widely used plane wave gauge-including projector augmented wave (GIPAW) density functional technique for chemical shift prediction. Fragment methods allow hybrid density functionals to be employed routinely in chemical shift prediction, and we have recently demonstrated appreciable improvements in the accuracy of the predicted shifts when using the hybrid PBE0 functional instead of generalized gradient approximation (GGA) functionals like PBE. Here, we investigate the solid-state 13C and 15N NMR spectra for multiple crystal forms of acetaminophen, phenobarbital, and testosterone. We demonstrate that the use of the hybrid density functional instead of a GGA provides both higher accuracy in the chemical shifts and increased discrimination among the different crystallographic environments. Finally, these results also provide compelling evidence for the transferability of the linear regression parameters mapping predicted chemical shieldings to chemical shifts that were derived in an earlier study. PMID:27829821

Dependence of Crystallographic Orientation on Pitting Corrosion Behavior of Ni-Fe-Cr Alloy 028

NASA Astrophysics Data System (ADS)

Zhang, LiNa; Szpunar, Jerzy A.; Dong, JianXin; Ojo, Olanrewaju A.; Wang, Xu

2018-06-01

The influence of crystallographic orientation on the pitting corrosion behavior of Ni-Fe-Cr alloy 028 was studied using a combination of X-ray diffraction (XRD), electron backscatter diffraction (EBSD), potentiodynamic polarization technique, and atomic force microscopy (AFM). The results show that there is anisotropy of pitting corrosion that strongly depends on crystallographic orientation of the surface plane. The distribution of pit density in a standard stereographic triangle indicates that the crystallographic planes close to {100} are more prone to pitting corrosion compared to planes {110} and {111}. The surface energy calculation of (001) and (111) shows that the plane with a high atomic packing density has a low surface energy with concomitant strong resistance to pitting corrosion. A correlation function between crystallographic orientation and pitting corrosion susceptibility suggests a method that not only predicts the pitting resistance of known textured materials, but also could help to improve corrosion resistance by controlling material texture.

Engineering Encodable Lanthanide-Binding Tags (LBTs) into Loop Regions of Proteins

PubMed Central

Barthelmes, Katja; Reynolds, Anne M.; Peisach, Ezra; Jonker, Hendrik R. A.; DeNunzio, Nicholas J.; Allen, Karen N.; Imperiali, Barbara; Schwalbe, Harald

2011-01-01

Lanthanide-binding-tags (LBTs) are valuable tools for investigation of protein structure, function, and dynamics by NMR spectroscopy, X-ray crystallography and luminescence studies. We have inserted LBTs into three different loop positions (denoted L, R, and S) of the model protein interleukin-1β and varied the length of the spacer between the LBT and the protein (denoted 1-3). Luminescence studies demonstrate that all nine constructs bind Tb3+ tightly in the low nanomolar range. No significant change in the fusion protein occurs from insertion of the LBT, as shown by two X-ray crystallographic structures of the IL1β-S1 and IL1β-L3 constructs and for the remaining constructs by comparing 1H-15N-HSQC NMR spectra with wild-type IL1β. Additionally, binding of LBT-loop IL1β proteins to their native binding partner in vitro remains unaltered. X-ray crystallographic phasing was successful using only the signal from the bound lanthanide. Large residual dipolar couplings (RDCs) could be determined by NMR spectroscopy for all LBT-loop-constructs and revealed that the LBT-2 series were rigidly incorporated into the interleukin-1β structure. The paramagnetic NMR spectra of loop-LBT mutant IL1β-R2 were assigned and the Δχ tensor components were calculated based on RDCs and pseudocontact shifts (PCSs). A structural model of the IL1β-R2 construct was calculated using the paramagnetic restraints. The current data provide support that encodable LBTs serve as versatile biophysical tags when inserted into loop regions of proteins of known structure or predicted via homology modelling. PMID:21182275

Outcome of the First wwPDB/CCDC/D3R Ligand Validation Workshop.

PubMed

Adams, Paul D; Aertgeerts, Kathleen; Bauer, Cary; Bell, Jeffrey A; Berman, Helen M; Bhat, Talapady N; Blaney, Jeff M; Bolton, Evan; Bricogne, Gerard; Brown, David; Burley, Stephen K; Case, David A; Clark, Kirk L; Darden, Tom; Emsley, Paul; Feher, Victoria A; Feng, Zukang; Groom, Colin R; Harris, Seth F; Hendle, Jorg; Holder, Thomas; Joachimiak, Andrzej; Kleywegt, Gerard J; Krojer, Tobias; Marcotrigiano, Joseph; Mark, Alan E; Markley, John L; Miller, Matthew; Minor, Wladek; Montelione, Gaetano T; Murshudov, Garib; Nakagawa, Atsushi; Nakamura, Haruki; Nicholls, Anthony; Nicklaus, Marc; Nolte, Robert T; Padyana, Anil K; Peishoff, Catherine E; Pieniazek, Susan; Read, Randy J; Shao, Chenghua; Sheriff, Steven; Smart, Oliver; Soisson, Stephen; Spurlino, John; Stouch, Terry; Svobodova, Radka; Tempel, Wolfram; Terwilliger, Thomas C; Tronrud, Dale; Velankar, Sameer; Ward, Suzanna C; Warren, Gregory L; Westbrook, John D; Williams, Pamela; Yang, Huanwang; Young, Jasmine

2016-04-05

Crystallographic studies of ligands bound to biological macromolecules (proteins and nucleic acids) represent an important source of information concerning drug-target interactions, providing atomic level insights into the physical chemistry of complex formation between macromolecules and ligands. Of the more than 115,000 entries extant in the Protein Data Bank (PDB) archive, ∼75% include at least one non-polymeric ligand. Ligand geometrical and stereochemical quality, the suitability of ligand models for in silico drug discovery and design, and the goodness-of-fit of ligand models to electron-density maps vary widely across the archive. We describe the proceedings and conclusions from the first Worldwide PDB/Cambridge Crystallographic Data Center/Drug Design Data Resource (wwPDB/CCDC/D3R) Ligand Validation Workshop held at the Research Collaboratory for Structural Bioinformatics at Rutgers University on July 30-31, 2015. Experts in protein crystallography from academe and industry came together with non-profit and for-profit software providers for crystallography and with experts in computational chemistry and data archiving to discuss and make recommendations on best practices, as framed by a series of questions central to structural studies of macromolecule-ligand complexes. What data concerning bound ligands should be archived in the PDB? How should the ligands be best represented? How should structural models of macromolecule-ligand complexes be validated? What supplementary information should accompany publications of structural studies of biological macromolecules? Consensus recommendations on best practices developed in response to each of these questions are provided, together with some details regarding implementation. Important issues addressed but not resolved at the workshop are also enumerated. Copyright © 2016 Elsevier Ltd. All rights reserved.

Outcome of the first wwPDB/CCDC/D3R Ligand Validation Workshop

PubMed Central

Adams, Paul D.; Aertgeerts, Kathleen; Bauer, Cary; Bell, Jeffrey A.; Berman, Helen M.; Bhat, Talapady N.; Blaney, Jeff; Bolton, Evan; Bricogne, Gerard; Brown, David; Burley, Stephen K.; Case, David A.; Clark, Kirk L.; Darden, Tom; Emsley, Paul; Feher, Victoria A.; Feng, Zukang; Groom, Colin R.; Harris, Seth F.; Hendle, Jorg; Holder, Thomas; Joachimiak, Andrzej; Kleywegt, Gerard J.; Krojer, Tobias; Marcotrigiano, Joseph; Mark, Alan E.; Markley, John L.; Miller, Matthew; Minor, Wladek; Montelione, Gaetano T.; Murshudov, Garib; Nakagawa, Atsushi; Nakamura, Haruki; Nicholls, Anthony; Nicklaus, Marc; Nolte, Robert T.; Padyana, Anil K.; Peishoff, Catherine E.; Pieniazek, Susan; Read, Randy J.; Shao, Chenghua; Sheriff, Steven; Smart, Oliver; Soisson, Stephen; Spurlino, John; Stouch, Terry; Svobodova, Radka; Tempel, Wolfram; Terwilliger, Thomas C.; Tronrud, Dale; Velankar, Sameer; Ward, Suzanna; Warren, Gregory L.; Westbrook, John D.; Williams, Pamela; Yang, Huanwang; Young, Jasmine

2016-01-01

Summary Crystallographic studies of ligands bound to biological macromolecules (proteins and nucleic acids) represent an important source of information concerning drug-target interactions, providing atomic level insights into the physical chemistry of complex formation between macromolecules and ligands. Of the more than 115,000 entries extant in the Protein Data Bank archive, ~75% include at least one non-polymeric ligand. Ligand geometrical and stereochemical quality, the suitability of ligand models for in silico drug discovery/design, and the goodness-of-fit of ligand models to electron density maps vary widely across the archive. We describe the proceedings and conclusions from the first Worldwide Protein Data Bank/Cambridge Crystallographic Data Centre/Drug Design Data Resource (wwPDB/CCDC/D3R) Ligand Validation Workshop held at the Research Collaboratory for Structural Bioinformatics at Rutgers University on July 30–31, 2015. Experts in protein crystallography from academe and industry came together with non-profit and for-profit software providers for crystallography and with experts in computational chemistry and data archiving to discuss and make recommendations on best practices, as framed by a series of questions central to structural studies of macromolecule-ligand complexes. What data concerning bound ligands should be archived in the Protein Data Bank? How should the ligands be best represented? How should structural models of macromolecule-ligand complexes be validated? What supplementary information should accompany publications of structural studies of biological macromolecules? Consensus recommendations on best practices developed in response to each of these questions are provided, together with some details regarding implementation. Important issues addressed but not resolved at the workshop are also enumerated. PMID:27050687

Advanced Organic Solid States Materials. Volume 173. Materials Research Society Symposium Proceedings

DTIC Science & Technology

1990-08-08

for their collaboration in synthetic study. We also thank Prof. N. Kasai and Dr. Y. Kai for their collaboration in X - ray crystallographic study. We...substantially with the increasing amount of doping as monitored by the powder x - ray diffraction. After doping the sample was kept for at least one day...physical properties at different oxidation states in solution and in the solid state of tEDTB complexed with TCNQF4. The X ray crystal structure of

A Study of the Cold Resistance of Pipe Coiled Stock Produced at Foundry-Rolling Works. Part 2

NASA Astrophysics Data System (ADS)

Bagmet, O. A.; Naumenko, V. V.; Smetanin, K. S.

2018-03-01

Results of a study of coiled stock from low-carbon steels alloyed with manganese and silicon and different additives of niobium and titanium are presented. The coiled stock is produced at foundry-rolling works by the method of direct rolling of thin slabs right after their continuous casting. The microdeformation of the crystal lattice and the crystallographic texture are determined. The conditions of formation of the most favorable structure and texture in the steels are specified.

X-ray structure determination using low-resolution electron microscopy maps for molecular replacement

DOE PAGES

Jackson, Ryan N.; McCoy, Airlie J.; Terwilliger, Thomas C.; ...

2015-07-30

Structures of multi-subunit macromolecular machines are primarily determined by either electron microscopy (EM) or X-ray crystallography. In many cases, a structure for a complex can be obtained at low resolution (at a coarse level of detail) with EM and at higher resolution (with finer detail) by X-ray crystallography. The integration of these two structural techniques is becoming increasingly important for generating atomic models of macromolecular complexes. A low-resolution EM image can be a powerful tool for obtaining the "phase" information that is missing from an X-ray crystallography experiment, however integration of EM and X-ray diffraction data has been technically challenging.more » Here we show a step-by-step protocol that explains how low-resolution EM maps can be placed in the crystallographic unit cell by molecular replacement, and how initial phases computed from the placed EM density are extended to high resolution by averaging maps over non-crystallographic symmetry. As the resolution gap between EM and Xray crystallography continues to narrow, the use of EM maps to help with X-ray crystal structure determination, as described in this protocol, will become increasingly effective.« less

3D Microstructural Architectures for Metal and Alloy Components Fabricated by 3D Printing/Additive Manufacturing Technologies

NASA Astrophysics Data System (ADS)

Martinez, E.; Murr, L. E.; Amato, K. N.; Hernandez, J.; Shindo, P. W.; Gaytan, S. M.; Ramirez, D. A.; Medina, F.; Wicker, R. B.

The layer-by-layer building of monolithic, 3D metal components from selectively melted powder layers using laser or electron beams is a novel form of 3D printing or additive manufacturing. Microstructures created in these 3D products can involve novel, directional solidification structures which can include crystallographically oriented grains containing columnar arrays of precipitates characteristic of a microstructural architecture. These microstructural architectures are advantageously rendered in 3D image constructions involving light optical microscopy and scanning and transmission electron microscopy observations. Microstructural evolution can also be effectively examined through 3D image sequences which, along with x-ray diffraction (XRD) analysis in the x-y and x-z planes, can effectively characterize related crystallographic/texture variances. This paper compares 3D microstructural architectures in Co-base and Ni-base superalloys, columnar martensitic grain structures in 17-4 PH alloy, and columnar copper oxides and dislocation arrays in copper.

Dehydrogenation of methanol to formaldehyde catalyzed by pristine and defective ceria surfaces

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

Beste, Ariana; Overbury, Steven H.

We have explored the dehydrogenation of methoxy on pristine and defective (111), (100), and (110) ceria surfaces with density functional methods. Methanol conversion is used as a probe reaction to understand structure sensitivity of the oxide catalysis. Differences in reaction selectivity have been observed experimentally as a function of crystallographically exposed faces and degree of reduction. We find that the barrier for carbon-hydrogen cleavage in methoxy is similar for the pristine and defective (111), (100), and (110) surfaces. However, there are large differences in the stability of the surface intermediates on the different surfaces. The variations in experimentally observed productmore » selectivities are a consequence of the interplay between barrier controlled bond cleavage and desorption processes. Ultimately, subtle differences in activation energies for carbon-hydrogen cleavage on the different crystallographic faces of ceria could not be correlated with structural or electronic descriptors.« less

Dehydrogenation of methanol to formaldehyde catalyzed by pristine and defective ceria surfaces

DOE PAGES

Beste, Ariana; Overbury, Steven H.

2016-03-09

We have explored the dehydrogenation of methoxy on pristine and defective (111), (100), and (110) ceria surfaces with density functional methods. Methanol conversion is used as a probe reaction to understand structure sensitivity of the oxide catalysis. Differences in reaction selectivity have been observed experimentally as a function of crystallographically exposed faces and degree of reduction. We find that the barrier for carbon-hydrogen cleavage in methoxy is similar for the pristine and defective (111), (100), and (110) surfaces. However, there are large differences in the stability of the surface intermediates on the different surfaces. The variations in experimentally observed productmore » selectivities are a consequence of the interplay between barrier controlled bond cleavage and desorption processes. Ultimately, subtle differences in activation energies for carbon-hydrogen cleavage on the different crystallographic faces of ceria could not be correlated with structural or electronic descriptors.« less

Dehydrogenation of methanol to formaldehyde catalyzed by pristine and defective ceria surfaces.

PubMed

Beste, Ariana; Overbury, Steven H

2016-04-21

We have explored the dehydrogenation of methoxy on pristine and defective (111), (100), and (110) ceria surfaces with density functional methods. Methanol conversion is used as a probe reaction to understand structure sensitivity of the oxide catalysis. Differences in reaction selectivity have been observed experimentally as a function of crystallographically exposed faces and degree of reduction. We find that the barrier for carbon-hydrogen cleavage in methoxy is similar for the pristine and defective (111), (100), and (110) surfaces. However, there are large differences in the stability of the surface intermediates on the different surfaces. The variations in experimentally observed product selectivities are a consequence of the interplay between barrier controlled bond cleavage and desorption processes. Subtle differences in activation energies for carbon-hydrogen cleavage on the different crystallographic faces of ceria could not be correlated with structural or electronic descriptors.

Cadmium-1,4-cyclohexanedicarboxylato coordination polymers bearing different di-alkyl-2,2'-bipyridines: syntheses, crystal structures and photoluminescence studies.

PubMed

Rosales-Vázquez, Luis D; Sánchez-Mendieta, Víctor; Dorazco-González, Alejandro; Martínez-Otero, Diego; García-Orozco, Iván; Morales-Luckie, Raúl A; Jaramillo-Garcia, Jonathan; Téllez-López, Antonio

2017-09-26

Four coordination polymers have been synthesized using self-assembly solution reactions under ambient conditions, reacting Cd(ii) ions with 1,4-cyclohexanedicarboxylic acid in the presence of different 2,2'-bipyridine co-ligands: {[Cd(H 2 O)(e,a-cis-1,4-chdc)(2,2'-bpy)]·H 2 O} n (1); [Cd 2 (H 2 O) 2 (e,a-cis-1,4-chdc) 2 (4,4'-dmb) 2 ] n (2); {[Cd(e,a-cis-1,4-chdc)(5,5'-dmb)]·H 2 O·CH 3 OH} n (3) and {[Cd(e,e-trans-1,4-chdc)(4,4'-dtbb)]·CH 3 OH} n (4), where 1,4-chdc = 1,4-cyclohexanedicarboxylato, 2,2'-bpy = 2,2'-bipyridine, 4,4'-dmb = 4,4'-dimethyl-2,2'-bipyridine, 5,5'-dmb = 5,5'-dimethyl-2,2'-bipyridine and 4,4'-dtbb = 4,4'-di-tert-butyl-2,2'-bipyridine. Crystallographic studies show that compound 1 has a 1D structure propagating along the crystallographic b-axis; the Cd ion in 1 is six-coordinated with a distorted-octahedral coordination sphere. Compound 2 has two crystallographic different Cd ions and both are six-coordinated with a distorted-octahedral coordination sphere. Compound 3 exhibits a seven-coordinated Cd ion having a distinctive distorted-monocapped trigonal prismatic geometry. In compound 4, the Cd ion is also seven-coordinated in a distorted monocapped octahedral geometry. Compounds 2, 3 and 4 possess rhombic-shaped dinuclear units (Cd 2 O 2 ) as nodes to generate larger cycles made up of four dinuclear units, a Cd 4 motif, bridged by four 1,4-chdc ligands, accomplishing, thus, 2D structures. Remarkably, in compound 4 the 1,4-chdc ligand conformation changes to the equatorial, equatorial trans, unlike the other compounds where the bridging ligand conformation is the more typical equatorial, axial cis. The solid state luminescence properties of 1-4 were investigated; polymers 3 and 4 exhibited a strong blue emission (λ em = 410-414 nm) compared to 1 and 2; structure-related photoluminescence is attributed to the degree of hydration of the compounds. Furthermore, Cd-polymer 3 suspended in acetone allows the fluorescence selective sensing of acetonitrile over common organic solvents such as alcohols and DMF, based on turn-on fluorescence intensity with a limit of 53 μmol L -1 .

HIV Structural Database using Chem BLAST for all classes of AIDS inhibitors

National Institute of Standards and Technology Data Gateway

SRD 155 HIV Structural Database using Chem BLAST for all classes of AIDS inhibitors (Web, free access)   The HIV structural database (HIVSDB) is a comprehensive collection of the structures of HIV protease, both of unliganded enzyme and of its inhibitor complexes. It contains abstracts and crystallographic data such as inhibitor and protein coordinates for 248 data sets, of which only 141 are from the Protein Data Bank (PDB).

Sequence Tolerance of a Highly Stable Single Domain Antibody: Comparison of Computational and Experimental Profiles

DTIC Science & Technology

2016-09-09

evaluating 18 mutants using either the A or B conformer is only r = ~ 0.2. Given the poor performance of approximating the observed experimental ...1    Sequence Tolerance of a Highly Stable Single Domain Antibody: Comparison of Computational and Experimental Profiles Mark A. Olson,1 Patricia...unusually high thermal stability is explored by a combined computational and experimental study. Starting with the crystallographic structure

Crystallographic structure of ChitA, a glycoside hydrolase family 19, plant class IV chitinase from Zea mays

USDA-ARS?s Scientific Manuscript database

Maize ChitA chitinase is composed of a small, hevein-like domain attached to a carboxy-terminal chitinase domain. During fungal ear rot, the hevein-like domain is cleaved by secreted fungal proteases to produce truncated forms of ChitA. Here, we report a structural and biochemical characterization o...

Crystallographic education in the 21st century

PubMed Central

Gražulis, Saulius; Sarjeant, Amy Alexis; Moeck, Peter; Stone-Sundberg, Jennifer; Snyder, Trevor J.; Kaminsky, Werner; Oliver, Allen G.; Stern, Charlotte L.; Dawe, Louise N.; Rychkov, Denis A.; Losev, Evgeniy A.; Boldyreva, Elena V.; Tanski, Joseph M.; Bernstein, Joel; Rabeh, Wael M.; Kantardjieff, Katherine A.

2015-01-01

There are many methods that can be used to incorporate concepts of crystallography into the learning experiences of students, whether they are in elementary school, at university or part of the public at large. It is not always critical that those who teach crystallography have immediate access to diffraction equipment to be able to introduce the concepts of symmetry, packing or molecular structure in an age- and audience-appropriate manner. Crystallography can be used as a tool for teaching general chemistry concepts as well as general research techniques without ever having a student determine a crystal structure. Thus, methods for younger students to perform crystal growth experiments of simple inorganic salts, organic compounds and even metals are presented. For settings where crystallographic instrumentation is accessible (proximally or remotely), students can be involved in all steps of the process, from crystal growth, to data collection, through structure solution and refinement, to final publication. Several approaches based on the presentations in the MS92 Microsymposium at the IUCr 23rd Congress and General Assembly are reported. The topics cover methods for introducing crystallography to undergraduate students as part of a core chemistry curriculum; a successful short-course workshop intended to bootstrap researchers who rely on crystallography for their work; and efforts to bring crystallography to secondary school children and non-science majors. In addition to these workshops, demonstrations and long-format courses, open-format crystallographic databases and three-dimensional printed models as tools that can be used to excite target audiences and inspire them to pursue a deeper understanding of crystallography are described. PMID:26664347

Binary ionic porphyrin nanosheets: electronic and light-harvesting properties regulated by crystal structure

NASA Astrophysics Data System (ADS)

Tian, Yongming; M. Beavers, Christine; Busani, Tito; Martin, Kathleen E.; Jacobsen, John L.; Mercado, Brandon Q.; Swartzentruber, Brian S.; van Swol, Frank; Medforth, Craig J.; Shelnutt, John A.

2012-02-01

Crystalline solids self-assembled from anionic and cationic porphyrins provide a new class of multifunctional optoelectronic micro- and nanomaterials. A 1 : 1 combination of zinc(ii) tetra(4-sulfonatophenyl)porphyrin (ZnTPPS) and tin(iv) tetra(N-methyl-4-pyridiniumyl)porphyrin (SnTNMePyP) gives porphyrin nanosheets with high aspect ratios and varying thickness. The room temperature preparation of the nanosheets has provided the first X-ray crystal structure of a cooperative binary ionic (CBI) solid. The unit cell contains one and one-half molecules of aquo-ZnTPPS4- (an electron donor) and three half molecules of dihydroxy-SnTNMePyP4+ (an electron acceptor). Charge balance in the solid is reached without any non-porphyrinic ions, as previously determined for other CBI nanomaterials by non-crystallographic means. The crystal structure reveals a complicated molecular arrangement with slipped π-π stacking only occurring in isolated dimers of one of the symmetrically unique zinc porphyrins. Consistent with the crystal structure, UV-visible J-aggregate bands indicative of exciton delocalization and extended π-π stacking are not observed. XRD measurements show that the structure of the Zn/Sn nanosheets is distinct from that of Zn/Sn four-leaf clover-like CBI solids reported previously. In contrast with the Zn/Sn clovers that do exhibit J-aggregate bands and are photoconductive, the nanosheets are not photoconductive. Even so, the nanosheets act as light-harvesting structures in an artificial photosynthesis system capable of reducing water to hydrogen but not as efficiently as the Zn/Sn clovers.Crystalline solids self-assembled from anionic and cationic porphyrins provide a new class of multifunctional optoelectronic micro- and nanomaterials. A 1 : 1 combination of zinc(ii) tetra(4-sulfonatophenyl)porphyrin (ZnTPPS) and tin(iv) tetra(N-methyl-4-pyridiniumyl)porphyrin (SnTNMePyP) gives porphyrin nanosheets with high aspect ratios and varying thickness. The room temperature preparation of the nanosheets has provided the first X-ray crystal structure of a cooperative binary ionic (CBI) solid. The unit cell contains one and one-half molecules of aquo-ZnTPPS4- (an electron donor) and three half molecules of dihydroxy-SnTNMePyP4+ (an electron acceptor). Charge balance in the solid is reached without any non-porphyrinic ions, as previously determined for other CBI nanomaterials by non-crystallographic means. The crystal structure reveals a complicated molecular arrangement with slipped π-π stacking only occurring in isolated dimers of one of the symmetrically unique zinc porphyrins. Consistent with the crystal structure, UV-visible J-aggregate bands indicative of exciton delocalization and extended π-π stacking are not observed. XRD measurements show that the structure of the Zn/Sn nanosheets is distinct from that of Zn/Sn four-leaf clover-like CBI solids reported previously. In contrast with the Zn/Sn clovers that do exhibit J-aggregate bands and are photoconductive, the nanosheets are not photoconductive. Even so, the nanosheets act as light-harvesting structures in an artificial photosynthesis system capable of reducing water to hydrogen but not as efficiently as the Zn/Sn clovers. Electronic supplementary information (ESI) available: Details of the crystallographic refinement, tables of refinement parameters and bond distances and NSD analysis, and figures showing SEM images of Zn/Sn nanosheets and clovers, the solid grown at different porphyrin concentrations, SEM images of nanosheets at high and low magnification, an ORTEP image showing the five crystallographically distinct porphyrin molecules and the water molecules, and a view of the crystal structure down the b axis are given in the ESI. CCDC reference number 833006. For ESI and crystallographic data in CIF or other electronic format see DOI: 10.1039/c2nr11826b

Semiautomated model building for RNA crystallography using a directed rotameric approach.

PubMed

Keating, Kevin S; Pyle, Anna Marie

2010-05-04

Structured RNA molecules play essential roles in a variety of cellular processes; however, crystallographic studies of such RNA molecules present a large number of challenges. One notable complication arises from the low resolutions typical of RNA crystallography, which results in electron density maps that are imprecise and difficult to interpret. This problem is exacerbated by the lack of computational tools for RNA modeling, as many of the techniques commonly used in protein crystallography have no equivalents for RNA structure. This leads to difficulty and errors in the model building process, particularly in modeling of the RNA backbone, which is highly error prone due to the large number of variable torsion angles per nucleotide. To address this, we have developed a method for accurately building the RNA backbone into maps of intermediate or low resolution. This method is semiautomated, as it requires a crystallographer to first locate phosphates and bases in the electron density map. After this initial trace of the molecule, however, an accurate backbone structure can be built without further user intervention. To accomplish this, backbone conformers are first predicted using RNA pseudotorsions and the base-phosphate perpendicular distance. Detailed backbone coordinates are then calculated to conform both to the predicted conformer and to the previously located phosphates and bases. This technique is shown to produce accurate backbone structure even when starting from imprecise phosphate and base coordinates. A program implementing this methodology is currently available, and a plugin for the Coot model building program is under development.

Crystal Structure Studies of Low-Ca Pyroxenes from LL-Group Chondritic Meteorites

NASA Astrophysics Data System (ADS)

Artioli, G.; Davoli, G.; Sighinolfi, G. P.

1993-07-01

One orthorhombic (Pbca) and two monoclinic (P2(sub)1/c) single crystals of low-Ca pyroxenes were extracted from unequilibrated chondritic meteorites of the LL-group. The results of the crystal structure refinements performed using x-ray diffraction data indicate that: (1) the intracrystalline Fe-Mg distribution over the M1 and M2 crystallographic sites of the Parnallee (LL-3) orthoenstatite is consistent with a temperature of 960 degrees C for the closure of the exchange equilibrium process; and (2) the structural state and intracristalline Fe-Mg order in the Soko Banja (LL-4) and Jolomba (LL-6) clinoenstatites indicate a closing temperature of at least 1000-1100 degrees C, with no significant reequilibration at lower temperatures. The present data represent the first detailed crystallographic investigation of pyroxenes from LL-chondrites and support the hypothesis that the chondrule pyroxenes bear a distinct memory of rapid cooling in the solar nebular and that thermal metamorphism in the parent body, if present, was totally unsufficient to allow reequilibration of the pyroxene minerals to the low-temperature ordered crystal structures. The data also indicate that, assuming low or mild pressure and shock effects, there is no well-defined correlation between equilibrium temperature of the mineral phases and the alleged petrologic type of the meteorites. This evidence is consistent with a rubble-pile model for the parent body accretional history, or with an onion-shell model with very low thermal-peak metamorphism, as it is assumed for a very small object.

Evolution of magnetic phases in SmCrO3: A neutron diffraction and magnetometric study

NASA Astrophysics Data System (ADS)

Tripathi, Malvika; Choudhary, R. J.; Phase, D. M.; Chatterji, T.; Fischer, H. E.

2017-11-01

The classical belief about the mechanism of spin reorientation phase transition (SRPT) and ground-state magnetic structure in SmCrO3 has become intriguing because of inconsistent bulk magnetization observations. The presence of highly neutron-absorbing Sm atom has so far evaded the determination of microscopic magnetic structure. In the present report, we have utilized very high-energy "hot neutrons" to overcome the Sm absorption and to determine the thermal evolution of magnetic configurations. Unambiguously, three distinct phases are observed: the uncompensated canted antiferromagnetic structure Γ4(Gx,Ay,Fz;FzR) occurring below the Néel temperature (TN=191 K), the collinear antiferromagnetic structure Γ1(Ax,Gy,Cz;CzR) occurring below 10 K, and a nonequilibrium configuration with cooccurring Γ1 and Γ4 phases in the neighborhood of the SRPT (10 K ≤T ≤ 40 K). In differing to the earlier predictions, we divulge the SRPT to be a discontinuous transition where chromium spins switch from the a -b crystallographic plane to the b -c crystallographic plane in a discrete manner with no allowed intermediate configuration. The canting angle of chromium ions in the a -b plane is unusually not a thermal constant, rather it is empirically discerned to follow exponential behavior. The competition between magnetocrystalline anisotropy and free energy derived by isotropic and antisymmetric exchange interactions between different pairs of magnetic ions is observed to govern the mechanism of SRPT.

Crystallographic insight into the evolutionary origins of xyloglucan endo-transglycosylases and endo-hydrolases

PubMed Central

McGregor, Nicholas; Yin, Victor; Tung, Ching-Chieh; Van Petegem, Filip; Brumer, Harry

2016-01-01

SUMMARY The xyloglucan endo-transglycosylase/hydrolase (XTH) gene family encodes enzymes of central importance to plant cell wall remodelling. The evolutionary history of plant XTH gene products is incompletely understood vis-à-vis the larger body of bacterial endo-glycanases in Glycoside Hydrolase Family 16 (GH16). To provide molecular insight into this issue, high-resolution X-ray crystal structures and detailed enzyme kinetics of an extant transitional plant endo-glucanase (EG) were determined. Functionally intermediate between plant XTH gene products and bacterial licheninases of GH16, Vitis vinifera EG16 (VvEG16) effectively catalyzes the hydrolysis of the backbones of two dominant plant cell wall matrix glycans, xyloglucan (XyG) and β(1,3)/β(1,4)-mixed-linkage glucan (MLG). Crystallographic complexes with extended oligosaccharide substrates reveal the structural basis for the accommodation of both unbranched, mixed-linked (MLG) and highly decorated, linear (XyG) polysaccharide chains in a broad, extended active-site cleft. Structural comparison with representative bacterial licheninases, a xyloglucan endo-tranglycosylase (XET), and a xyloglucan endo-hydrolase (XEH) outline the functional ramifications of key sequence deletions and insertions across the phylogenetic landscape of GH16. Although the biological role(s) of EG16 orthologs remains to be fully resolved, the present biochemical and tertiary structural characterization provides key insight into plant cell wall enzyme evolution, which will continue to inform genomic analyses and functional studies across species. PMID:27859885

Structure and binding analysis of Polyporus squamosus lectin in complex with the Neu5Acα2-6Galβ1-4GlcNAc human-type influenza receptor

PubMed Central

Kadirvelraj, Renuka; Grant, Oliver C; Goldstein, Irwin J; Winter, Harry C; Tateno, Hiroaki; Fadda, Elisa; Woods, Robert J

2011-01-01

Glycan chains that terminate in sialic acid (Neu5Ac) are frequently the receptors targeted by pathogens for initial adhesion. Carbohydrate-binding proteins (lectins) with specificity for Neu5Ac are particularly useful in the detection and isolation of sialylated glycoconjugates, such as those associated with pathogen adhesion as well as those characteristic of several diseases including cancer. Structural studies of lectins are essential in order to understand the origin of their specificity, which is particularly important when employing such reagents as diagnostic tools. Here, we report a crystallographic and molecular dynamics (MD) analysis of a lectin from Polyporus squamosus (PSL) that is specific for glycans terminating with the sequence Neu5Acα2-6Galβ. Because of its importance as a histological reagent, the PSL structure was solved (to 1.7 Å) in complex with a trisaccharide, whose sequence (Neu5Acα2-6Galβ1-4GlcNAc) is exploited by influenza A hemagglutinin for viral adhesion to human tissue. The structural data illuminate the origin of the high specificity of PSL for the Neu5Acα2-6Gal sequence. Theoretical binding free energies derived from the MD data confirm the key interactions identified crystallographically and provide additional insight into the relative contributions from each amino acid, as well as estimates of the importance of entropic and enthalpic contributions to binding. PMID:21436237

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.

On the spectra of Pisot-cyclotomic numbers

NASA Astrophysics Data System (ADS)

Hare, Kevin G.; Masáková, Zuzana; Vávra, Tomáš

2018-07-01

We investigate the complex spectra X^A(β )= \\sum _{j=0}^na_jβ ^j : n\\in N, a_j\\in A where β is a quadratic or cubic Pisot-cyclotomic number and the alphabet A is given by 0 along with a finite collection of roots of unity. Such spectra are discrete aperiodic structures with crystallographically forbidden symmetries. We discuss in general terms under which conditions they possess the Delone property required for point sets modeling quasicrystals. We study the corresponding Voronoi tilings and we relate these structures to quasilattices arising from the cut-and-project method.

Formation of the structure and properties of an Mg-Al-Zn-Mn alloy during plastic deformation by rolling

NASA Astrophysics Data System (ADS)

Bozhko, S. A.; Betsofen, S. Ya.; Kolobov, Yu. R.; Vershinina, T. N.

2015-03-01

The laws of formation of an ultrafine structure in an Mg-Al-Zn-Mn alloy (MA5 alloy) under severe plastic deformation have been studied during lengthwise section rolling at a strain e = 1.59. The deformation behavior and the physical factors of anisotropy of yield strength during compression tests in various directions with respect to axis of rolling are analyzed. The role of crystallographic texture and twinning processes in the generation of strength processes and the development of plastic deformation of the alloy is analyzed.

The Structural Biology Center 19ID undulator beamline: facility specifications and protein crystallographic results

PubMed Central

Rosenbaum, Gerd; Alkire, Randy W.; Evans, Gwyndaf; Rotella, Frank J.; Lazarski, Krzystof; Zhang, Rong-Guang; Ginell, Stephan L.; Duke, Norma; Naday, Istvan; Lazarz, Jack; Molitsky, Michael J.; Keefe, Lisa; Gonczy, John; Rock, Larry; Sanishvili, Ruslan; Walsh, Martin A.; Westbrook, Edwin; Joachimiak, Andrzej

2008-01-01

The 19ID undulator beamline of the Structure Biology Center has been designed and built to take full advantage of the high flux, brilliance and quality of X-ray beams delivered by the Advanced Photon Source. The beamline optics are capable of delivering monochromatic X-rays with photon energies from 3.5 to 20 keV (3.5–0.6 Å wavelength) with fluxes up to 8–18 × 1012 photons s−1 (depending on photon energy) onto cryogenically cooled crystal samples. The size of the beam (full width at half-maximum) at the sample position can be varied from 2.2 mm × 1.0 mm (horizontal × vertical, unfocused) to 0.083 mm × 0.020 mm in its fully focused configuration. Specimen-to-detector distances of between 100 mm and 1500 mm can be used. The high flexibility, inherent in the design of the optics, coupled with a κ-geometry goniometer and beamline control software allows optimal strategies to be adopted in protein crystallographic experiments, thus maximizing the chances of their success. A large-area mosaic 3 × 3 CCD detector allows high-quality diffraction data to be measured rapidly to the crystal diffraction limits. The beamline layout and the X-ray optical and endstation components are described in detail, and the results of representative crystallographic experiments are presented. PMID:16371706

Protein crystallography for aspiring crystallographers or how to avoid pitfalls and traps in macromolecular structure determination.

PubMed

Wlodawer, Alexander; Minor, Wladek; Dauter, Zbigniew; Jaskolski, Mariusz

2013-11-01

The number of macromolecular structures deposited in the Protein Data Bank now approaches 100,000, with the vast majority of them determined by crystallographic methods. Thousands of papers describing such structures have been published in the scientific literature, and 20 Nobel Prizes in chemistry or medicine have been awarded for discoveries based on macromolecular crystallography. New hardware and software tools have made crystallography appear to be an almost routine (but still far from being analytical) technique and many structures are now being determined by scientists with very limited experience in the practical aspects of the field. However, this apparent ease is sometimes illusory and proper procedures need to be followed to maintain high standards of structure quality. In addition, many noncrystallographers may have problems with the critical evaluation and interpretation of structural results published in the scientific literature. The present review provides an outline of the technical aspects of crystallography for less experienced practitioners, as well as information that might be useful for users of macromolecular structures, aiming to show them how to interpret (but not overinterpret) the information present in the coordinate files and in their description. A discussion of the extent of information that can be gleaned from the atomic coordinates of structures solved at different resolution is provided, as well as problems and pitfalls encountered in structure determination and interpretation. © 2013 FEBS.

Protein crystallography for aspiring crystallographers or how to avoid pitfalls and traps in macromolecular structure determination

PubMed Central

Wlodawer, Alexander; Minor, Wladek; Dauter, Zbigniew; Jaskolski, Mariusz

2014-01-01

The number of macromolecular structures deposited in the Protein Data Bank now approaches 100 000, with the vast majority of them determined by crystallographic methods. Thousands of papers describing such structures have been published in the scientific literature, and 20 Nobel Prizes in chemistry or medicine have been awarded for discoveries based on macromolecular crystallography. New hardware and software tools have made crystallography appear to be an almost routine (but still far from being analytical) technique and many structures are now being determined by scientists with very limited experience in the practical aspects of the field. However, this apparent ease is sometimes illusory and proper procedures need to be followed to maintain high standards of structure quality. In addition, many noncrystallographers may have problems with the critical evaluation and interpretation of structural results published in the scientific literature. The present review provides an outline of the technical aspects of crystallography for less experienced practitioners, as well as information that might be useful for users of macromolecular structures, aiming to show them how to interpret (but not overinterpret) the information present in the coordinate files and in their description. A discussion of the extent of information that can be gleaned from the atomic coordinates of structures solved at different resolution is provided, as well as problems and pitfalls encountered in structure determination and interpretation. PMID:24034303

Electron crystallography and aquaporins.

PubMed

Schenk, Andreas D; Hite, Richard K; Engel, Andreas; Fujiyoshi, Yoshinori; Walz, Thomas

2010-01-01

Electron crystallography of two-dimensional (2D) crystals can provide information on the structure of membrane proteins at near-atomic resolution. Originally developed and used to determine the structure of bacteriorhodopsin (bR), electron crystallography has recently been applied to elucidate the structure of aquaporins (AQPs), a family of membrane proteins that form pores mostly for water but also other solutes. While electron crystallography has made major contributions to our understanding of the structure and function of AQPs, structural studies on AQPs, in turn, have fostered a number of technical developments in electron crystallography. In this contribution, we summarize the insights electron crystallography has provided into the biology of AQPs, and describe technical advancements in electron crystallography that were driven by structural studies on AQP 2D crystals. In addition, we discuss some of the lessons that were learned from electron crystallographic work on AQPs. Copyright © 2010 Elsevier Inc. All rights reserved.

X-ray absorption fine structure and x-ray diffraction studies of crystallographic grains in nanocrystalline FePd:Cu thin films

NASA Astrophysics Data System (ADS)

Krupinski, M.; Perzanowski, M.; Polit, A.; Zabila, Y.; Zarzycki, A.; Dobrowolska, A.; Marszalek, M.

2011-03-01

FePd alloys have recently attracted considerable attention as candidates for ultrahigh density magnetic storage media. In this paper we investigate FePd thin alloy film with a copper admixture composed of nanometer-sized grains. [Fe(0.9 nm)/Pd(1.1 nm)/Cu(d nm)]×5 multilayers were prepared by thermal deposition at room temperature in UHV conditions on Si(100) substrates covered by 100 nm SiO2. The thickness of the copper layer has been changed from 0 to 0.4 nm. After deposition, the multilayers were rapidly annealed at 600 °C in a nitrogen atmosphere, which resulted in the creation of the FePd:Cu alloy. The structure of alloy films obtained this way was determined by x-ray diffraction (XRD), glancing angle x-ray diffraction, and x-ray absorption fine structure (EXAFS). The measurements clearly showed that the L10 FePd:Cu nanocrystalline phase has been formed during the annealing process for all investigated copper compositions. This paper concentrates on the crystallographic grain features of FePd:Cu alloys and illustrates that the EXAFS technique, supported by XRD measurements, can help to extend the information about grain size and grain shape of poorly crystallized materials. We show that, using an appropriate model of the FePd:Cu grains, the comparison of EXAFS and XRD results gives a reasonable agreement.

Cloning, preparation and preliminary crystallographic studies of penicillin V acylase autoproteolytic processing mutants

PubMed Central

Chandra, P. Manish; Brannigan, James A.; Prabhune, Asmita; Pundle, Archana; Turkenburg, Johan P.; Dodson, G. Guy; Suresh, C. G.

2005-01-01

The crystallization of three catalytically inactive mutants of penicillin V acylase (PVA) from Bacillus sphaericus in precursor and processed forms is reported. The mutant proteins crystallize in different primitive monoclinic space groups that are distinct from the crystal forms for the native enzyme. Directed mutants and clone constructs were designed to study the post-translational autoproteolytic processing of PVA. The catalytically inactive mutants will provide three-dimensional structures of precursor PVA forms, plus open a route to the study of enzyme–substrate complexes for this industrially important enzyme. PMID:16508111

Activator anion binding site in pyridoxal phosphorylase b: the binding of phosphite, phosphate, and fluorophosphate in the crystal.

PubMed Central

Oikonomakos, N. G.; Zographos, S. E.; Tsitsanou, K. E.; Johnson, L. N.; Acharya, K. R.

1996-01-01

It has been established that phosphate analogues can activate glycogen phosphorylase reconstituted with pyridoxal in place of the natural cofactor pyridoxal 5'-phosphate (Change YC. McCalmont T, Graves DJ. 1983. Biochemistry 22:4987-4993). Pyridoxal phosphorylase b has been studied by kinetic, ultracentrifugation, and X-ray crystallographic experiments. In solution, the catalytically active species of pyridoxal phosphorylase b adopts a conformation that is more R-state-like than that of native phosphorylase b, but an inactive dimeric species of the enzyme can be stabilized by activator phosphite in combination with the T-state inhibitor glucose. Co-crystals of pyridoxal phosphorylase b complexed with either phosphite, phosphate, or fluorophosphate, the inhibitor glucose, and the weak activator IMP were grown in space group P4(3)2(1)2, with native-like unit cell dimensions, and the structures of the complexes have been refined to give crystallographic R factors of 18.5-19.2%, for data between 8 and 2.4 A resolution. The anions bind tightly at the catalytic site in a similar but not identical position to that occupied by the cofactor 5'-phosphate group in the native enzyme (phosphorus to phosphorus atoms distance = 1.2 A). The structural results show that the structures of the pyridoxal phosphorylase b-anion-glucose-IMP complexes are overall similar to the glucose complex of native T-state phosphorylase b. Structural comparisons suggest that the bound anions, in the position observed in the crystal, might have a structural role for effective catalysis. PMID:8976550

Thermal unfolding of tetrameric melittin: comparison with the molten globule state of cytochrome c.

PubMed Central

Hagihara, Y.; Oobatake, M.; Goto, Y.

1994-01-01

Whereas melittin at micromolar concentrations is unfolded under conditions of low salt at neutral pH, it transforms to a tetrameric alpha-helical structure under several conditions, such as high peptide concentration, high anion concentration, or alkaline pH. The anion- and pH-dependent stabilization of the tetrameric structure is similar to that of the molten globule state of several acid-denatured proteins, suggesting that tetrameric melittin might be a state similar to the molten globule state. To test this possibility, we studied the thermal unfolding of tetrameric melittin using far-UV CD and differential scanning calorimetry. The latter technique revealed a broad but distinct heat absorption peak. The heat absorption curves were consistent with the unfolding transition observed by CD and were explainable by a 2-state transition mechanism between the tetrameric alpha-helical state and the monomeric unfolded state. From the peptide or salt-concentration dependence of unfolding, the heat capacity change upon unfolding was estimated to be 5 kJ (mol of tetramer)-1 K-1 at 30 degrees C and decreased with increasing temperature. The observed change in heat capacity was much smaller than that predicted from the crystallographic structure (9.2 kJ (mol of tetramer)-1 K-1), suggesting that the hydrophobic residues of tetrameric melittin in solution are exposed in comparison with the crystallographic structure. However, the results also indicate that the structure is more ordered than that of a typical molten globule state. We consider that the conformation is intermediate between the molten globule state and the native state of globular proteins. PMID:7833804

Crystallography of decahedral and icosahedral particles. I - Geometry of twinning

NASA Technical Reports Server (NTRS)

Yang, C. Y.

1979-01-01

The crystal structure of the tetrahedral twins in multiply-twinned particles with decahedral and icosahedral point group symmetries has been examined and correlated with the face-centered cubic structure. Details on the crystal structure as well as the geometrical relationships among twins in each particle are presented. These crystallographic facts serve as a basis for the interpretation of small particle images obtained with advanced methods of transmission electron microscopy.

Possible nucleus of the Bergman cluster in the Zn-Mg-Y alloy system

NASA Astrophysics Data System (ADS)

Nakayama, Kei; Nakagawa, Masaya; Koyama, Yasumasa

2018-01-01

To understand the formation of the Bergman cluster in the F-type icosahedral quasicrystal (IQ), crystallographic relations between the quasicrystal and the intermetallic-compound H and Zn23Y6 phases in the Zn-Mg-Y alloy system were investigated mainly by transmission electron microscopy. It was found that, although sample rotations of about 1° were required to obtain simple crystallographic relations, the orientation relationship was established among the cubic-Fm?m Zn23Y6 structure, the hexagonal-P63/mmc H structure and the F-type IQ; that is, [? 1 3]c // the five-fold axis in the IQ // N(2 ? 0)H, and [1 1 0]c // the two-fold axis in the IQ // N(0 5 ? 3)H, where N(h k m l)H means the normal direction of the (h k m l)H plane in the H structure. The correspondences between atomic positions in the Bergman cluster and in the Zn23Y6 structure and between those in the cluster and in the H structure were investigated on the basis of the established relationship. As a result, an assembly of six short-penetrated-decagonal columns was identified as an appropriate nucleus in the formation of the Bergman cluster from these two structures.

Dielectric and Piezoelectric Properties of Barium-substituted Sr1.9Ca0.1NaNb5O15 Ceramics

NASA Astrophysics Data System (ADS)

Xie, Rong-Jun; Akimune, Yoshio; Wang, Ruiping; Hirosaki, Naoto; Nishimura, Toshiyuki

2003-12-01

Highly dense piezoelectric ceramics of tungsten bronze-type (Sr1.9Ca0.1)1-0.5xBaxNaNb5O15 (where x=0.1--0.8) were prepared by spark plasma sintering. The crystallographic parameters, dielectric behaviors and piezoelectric properties of the sintered ceramics were investigated, and the effects of the Ba substitution on these electrical properties were discussed. The structural analysis and the electrical property measurements indicate a morphotropic phase boundary (MPB)-like phenomenon at x=0.4--0.5. In all compositions, a diffuse phase transition and a relaxor behavior are observed. The electrical properties are found to be crystallographically dependent.

The effect of grooves in amorphous substrates on the orientation of metal deposits. I - Carbon substrates

NASA Technical Reports Server (NTRS)

Anton, R.; Poppa, H.; Flanders, D. C.

1982-01-01

The graphoepitaxial alignment of vapor-deposited discrete metal crystallites is investigated in the nucleation and growth stages and during annealing by in situ UHV/TEM techniques. Various stages of nucleation, growth and coalescence of vapor deposits of Au, Ag, Pb, Sn, and Bi on amorphous, topographically structured C substrates are analyzed by advanced dark-field techniques to detect preferred local orientations. It is found that the topography-induced orientation of metal crystallites depends strongly on their mobility and their respective tendency to develop pronounced crystallographic shapes. Lowering of the average surface free energies and increasing the crystallographic surface energy anisotropies cause generally improved graphoepitaxial alignments.

Low Resolution Refinement of Atomic Models Against Crystallographic Data.

PubMed

Nicholls, Robert A; Kovalevskiy, Oleg; Murshudov, Garib N

2017-01-01

This review describes some of the problems encountered during low-resolution refinement and map calculation. Refinement is considered as an application of Bayes' theorem, allowing combination of information from various sources including crystallographic experimental data and prior chemical and structural knowledge. The sources of prior knowledge relevant to macromolecules include basic chemical information such as bonds and angles, structural information from reference models of known homologs, knowledge about secondary structures, hydrogen bonding patterns, and similarity of non-crystallographically related copies of a molecule. Additionally, prior information encapsulating local conformational conservation is exploited, keeping local interatomic distances similar to those in the starting atomic model. The importance of designing an accurate likelihood function-the only link between model parameters and observed data-is emphasized. The review also reemphasizes the importance of phases, and describes how the use of raw observed amplitudes could give a better correlation between the calculated and "true" maps. It is shown that very noisy or absent observations can be replaced by calculated structure factors, weighted according to the accuracy of the atomic model. This approach helps to smoothen the map. However, such replacement should be used sparingly, as the bias toward errors in the model could be too much to avoid. It is in general recommended that, whenever a new map is calculated, map quality should be judged by inspection of the parts of the map where there is no atomic model. It is also noted that it is advisable to work with multiple blurred and sharpened maps, as different parts of a crystal may exhibit different degrees of mobility. Doing so can allow accurate building of atomic models, accounting for overall shape as well as finer structural details. Some of the results described in this review have been implemented in the programs REFMAC5, ProSMART and LORESTR, which are available as part of the CCP4 software suite.

Density Functional Calculations for Prediction of 57Fe Mössbauer Isomer Shifts and Quadrupole Splittings in β-Diketiminate Complexes

PubMed Central

2017-01-01

The relative ease of Mössbauer spectroscopy and of density functional theory (DFT) calculations encourages the use of Mössbauer parameters as a validation method for calculations, and the use of calculations as a double check on crystallographic structures. A number of studies have proposed correlations between the computationally determined electron density at the iron nucleus and the observed isomer shift, but deviations from these correlations in low-valent iron β-diketiminate complexes encouraged us to determine a new correlation for these compounds. The use of B3LYP/def2-TZVP in the ORCA platform provides an excellent balance of accuracy and speed. We provide here not only this new correlation and a clear guide to its use but also a systematic analysis of the limitations of this approach. We also highlight the impact of crystallographic inaccuracies, DFT model truncation, and spin states, with intent to assist experimentalists to use Mössbauer spectroscopy and calculations together. PMID:28691111

Crystallographic observation of nonenzymatic RNA primer extension.

PubMed

Zhang, Wen; Walton, Travis; Li, Li; Szostak, Jack W

2018-05-31

The importance of genome replication has inspired detailed crystallographic studies of enzymatic DNA/RNA polymerization. In contrast, the mechanism of nonenzymatic polymerization is less well understood, despite its critical role in the origin of life. Here we report the direct observation of nonenzymatic RNA primer extension through time-resolved crystallography. We soaked crystals of an RNA primer-template-dGMP complex with guanosine-5'-phosphoro-2-aminoimidazolide for increasing times. At early times we see the activated ribonucleotides bound to the template, followed by formation of the imidazolium-bridged dinucleotide intermediate. At later times, we see a new phosphodiester bond forming between the primer and the incoming nucleotide. The intermediate is pre-organized because of the constraints of base-pairing with the template and hydrogen bonding between the imidazole amino group and both flanking phosphates. Our results provide atomic-resolution insight into the mechanism of nonenzymatic primer extension, and set the stage for further structural dissection and optimization of the RNA copying process. © 2018, Zhang et al.

Low temperature dielectric relaxation in ordinary perovskite ferroelectrics: enlightenment from high-energy x-ray diffraction

DOE PAGES

Ochoa, D. A.; Levit, R.; Fancher, C. M.; ...

2017-04-05

We report that ordinary ferroelectrics exhibit a second order phase transition that is characterized by a sharp peak in the dielectric permittivity at a frequency-independent temperature. Furthermore, these materials show a low temperature dielectric relaxation that appears to be a common behavior of perovskite systems. Tetragonal lead zirconate titanate is used here as a model system in order to explore the origin of such an anomaly, since there is no consensus about the physical phenomenon involved in it. Crystallographic and domain structure studies are performed from temperature dependent synchrotron x-ray diffraction measurement. Results indicate that the dielectric relaxation cannot bemore » associated with crystallographic or domain configuration changes. The relaxation process is then parameterized by using the Vogel–Fulcher–Tammann phenomenological equation. Finally, results allow us to hypothesize that the observed phenomenon is due to changes in the dynamic behavior of the ferroelectric domains related to the fluctuation of the local polarization.« less

Rhodanine hydrolysis leads to potent thioenolate mediated metallo-β-lactamase inhibition

NASA Astrophysics Data System (ADS)

Brem, Jürgen; van Berkel, Sander S.; Aik, Weishen; Rydzik, Anna M.; Avison, Matthew B.; Pettinati, Ilaria; Umland, Klaus-Daniel; Kawamura, Akane; Spencer, James; Claridge, Timothy D. W.; McDonough, Michael A.; Schofield, Christopher J.

2014-12-01

The use of β-lactam antibiotics is compromised by resistance, which is provided by β-lactamases belonging to both metallo (MBL)- and serine (SBL)-β-lactamase subfamilies. The rhodanines are one of very few compound classes that inhibit penicillin-binding proteins (PBPs), SBLs and, as recently reported, MBLs. Here, we describe crystallographic analyses of the mechanism of inhibition of the clinically relevant VIM-2 MBL by a rhodanine, which reveal that the rhodanine ring undergoes hydrolysis to give a thioenolate. The thioenolate is found to bind via di-zinc chelation, mimicking the binding of intermediates in β-lactam hydrolysis. Crystallization of VIM-2 in the presence of the intact rhodanine led to observation of a ternary complex of MBL, a thioenolate fragment and rhodanine. The crystallographic observations are supported by kinetic and biophysical studies, including 19F NMR analyses, which reveal the rhodanine-derived thioenolate to be a potent broad-spectrum MBL inhibitor and a lead structure for the development of new types of clinically useful MBL inhibitors.

Solution structure of the isolated Pelle death domain.

PubMed

Moncrieffe, Martin C; Stott, Katherine M; Gay, Nicholas J

2005-07-18

The interaction between the death domains (DDs) of Tube and the protein kinase Pelle is an important component of the Toll pathway. Published crystallographic data suggests that the Pelle-Tube DD interface is plastic and implies that in addition to the two predominant Pelle-Tube interfaces, a third interaction is possible. We present the NMR solution structure of the isolated death domain of Pelle and a study of the interaction between the DDs of Pelle and Tube. Our data suggests the solution structure of the isolated Pelle DD is similar to that of Pelle DD in complex with Tube. Additionally, they suggest that the plasticity observed in the crystal structure may not be relevant in the functioning death domain complex.

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

PubMed

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

2016-06-01

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

Phospholipid component volumes: determination and application to bilayer structure calculations.

PubMed

Armen, R S; Uitto, O D; Feller, S E

1998-08-01

We present a new method for the determination of bilayer structure based on a combination of computational studies and laboratory experiments. From molecular dynamics simulations, the volumes of submolecular fragments of saturated and unsaturated phosphatidylcholines in the liquid crystalline state have been extracted with a precision not available experimentally. Constancy of component volumes, both among different lipids and as a function of membrane position for a given lipid, have been examined. The component volumes were then incorporated into the liquid crystallographic method described by Wiener and White (1992. Biophys. J. 61:434-447, and references therein) for determining the structure of a fluid-phase dioleoylphosphatidylcholine bilayer from x-ray and neutron diffraction experiments.

Phospholipid component volumes: determination and application to bilayer structure calculations.

PubMed Central

Armen, R S; Uitto, O D; Feller, S E

1998-01-01

We present a new method for the determination of bilayer structure based on a combination of computational studies and laboratory experiments. From molecular dynamics simulations, the volumes of submolecular fragments of saturated and unsaturated phosphatidylcholines in the liquid crystalline state have been extracted with a precision not available experimentally. Constancy of component volumes, both among different lipids and as a function of membrane position for a given lipid, have been examined. The component volumes were then incorporated into the liquid crystallographic method described by Wiener and White (1992. Biophys. J. 61:434-447, and references therein) for determining the structure of a fluid-phase dioleoylphosphatidylcholine bilayer from x-ray and neutron diffraction experiments. PMID:9675175

Crystallographic and mutational analyses of tannase from Lactobacillus plantarum.

PubMed

Matoba, Yasuyuki; Tanaka, Naomi; Noda, Masafumi; Higashikawa, Fumiko; Kumagai, Takanori; Sugiyama, Masanori

2013-11-01

Tannin acylhydrolase (EC 3.1.1.20) referred commonly as tannase catalyzes the hydrolysis of the galloyl ester bond of tannins to release gallic acid. Although the enzyme is useful for various industries, the tertiary structure is not yet determined. In this study, we determined the crystal structure of tannase produced by Lactobacillus plantarum. The tannase structure belongs to a member of α/β-hydrolase superfamily with an additional "lid" domain. A glycerol molecule derived from cryoprotectant solution was accommodated into the tannase active site. The binding manner of glycerol to tannase seems to be similar to that of the galloyl moiety in the substrate. Copyright © 2013 Wiley Periodicals, Inc.

Structural Studies of the Intestinal α-Glucosidases, Maltase-glucoamylase and Sucrase-isomaltase.

PubMed

Rose, David R; Chaudet, Marcia M; Jones, Kyra

2018-06-01

Maltase-glucoamylase and sucrase-isomaltase are enzymes in the brush-border membrane of the small intestinal lumen responsible for the breakdown of postamylase starch polysaccharides to release monomeric glucose. As such, they are critical players in healthy nutrition and their malfunction can lead to severe disorders. This review covers investigations of the structures and functions of these enzymes. Each consists of 2 enzyme domains of the glycoside hydrolase family GH31 classification, yet with somewhat differing enzymatic properties. Crystallographic structures of 3 of the domains have been published. Insights into substrate binding and specificity will be discussed, along with future lines of inquiry related to the enzymes' roles in disease and potential avenues for therapeutics.

Modeling the Flow Behavior, Recrystallization, and Crystallographic Texture in Hot-Deformed Fe-30 Wt Pct Ni Austenite

NASA Astrophysics Data System (ADS)

Abbod, M. F.; Sellars, C. M.; Cizek, P.; Linkens, D. A.; Mahfouf, M.

2007-10-01

The present work describes a hybrid modeling approach developed for predicting the flow behavior, recrystallization characteristics, and crystallographic texture evolution in a Fe-30 wt pct Ni austenitic model alloy subjected to hot plane strain compression. A series of compression tests were performed at temperatures between 850 °C and 1050 °C and strain rates between 0.1 and 10 s-1. The evolution of grain structure, crystallographic texture, and dislocation substructure was characterized in detail for a deformation temperature of 950 °C and strain rates of 0.1 and 10 s-1, using electron backscatter diffraction and transmission electron microscopy. The hybrid modeling method utilizes a combination of empirical, physically-based, and neuro-fuzzy models. The flow stress is described as a function of the applied variables of strain rate and temperature using an empirical model. The recrystallization behavior is predicted from the measured microstructural state variables of internal dislocation density, subgrain size, and misorientation between subgrains using a physically-based model. The texture evolution is modeled using artificial neural networks.

Ocean acidification reduces the crystallographic control in juvenile mussel shells.

PubMed

Fitzer, Susan C; Cusack, Maggie; Phoenix, Vernon R; Kamenos, Nicholas A

2014-10-01

Global climate change threatens the oceans as anthropogenic carbon dioxide causes ocean acidification and reduced carbonate saturation. Future projections indicate under saturation of aragonite, and potentially calcite, in the oceans by 2100. Calcifying organisms are those most at risk from such ocean acidification, as carbonate is vital in the biomineralisation of their calcium carbonate protective shells. This study highlights the importance of multi-generational studies to investigate how marine organisms can potentially adapt to future projected global climate change. Mytilus edulis is an economically important marine calcifier vulnerable to decreasing carbonate saturation as their shells comprise two calcium carbonate polymorphs: aragonite and calcite. M. edulis specimens were cultured under current and projected pCO2 (380, 550, 750 and 1000μatm), following 6months of experimental culture, adults produced second generation juvenile mussels. Juvenile mussel shells were examined for structural and crystallographic orientation of aragonite and calcite. At 1000μatm pCO2, juvenile mussels spawned and grown under this high pCO2 do not produce aragonite which is more vulnerable to carbonate under-saturation than calcite. Calcite and aragonite were produced at 380, 550 and 750μatm pCO2. Electron back scatter diffraction analyses reveal less constraint in crystallographic orientation with increased pCO2. Shell formation is maintained, although the nacre crystals appear corroded and crystals are not so closely layered together. The differences in ultrastructure and crystallography in shells formed by juveniles spawned from adults in high pCO2 conditions may prove instrumental in their ability to survive ocean acidification. Copyright © 2014 Elsevier Inc. All rights reserved.

Influence of Sn doping in BaSnxTi1-xO3 ceramics on microstructural and dielectric properties

NASA Astrophysics Data System (ADS)

Ansari, Mohd. Azaj; Sreenivas, K.

2018-05-01

BaSnxTi1-x O3 solid solutions with varying Sn content (x = 0.00, 0.05, 0.15, 0.25) prepared by solid state reaction method have been studied for their structural and dielectric properties. X-ray diffraction and Raman spectroscopic analysis show composition induced modifications in the crystallographic structure, and with increasing Sn content the structure changes from tetragonal to cubic structure. The tetragonal distortion decreases with increasing Sn, and the structure becomes purely cubic for x =0.25. Changes in the structure are reflected in the temperature dependent dielectric properties. For increasing Sn content the peak dielectric constant is found to increase and the phase transition temperature (Tc) decreases to lower temperature. The purely cubic structure with x=0.25 shows a diffused phased transition.

Training HBCU Faculty and Students in Prostate Cancer (PC) Research: Signal Transduction and Receptor-Inhibitor Interactions in the Progress of PC

DTIC Science & Technology

2008-03-01

thiocinnamide, and 4-[(3-bromophenyl) amino ]-6- propionylamidoquinazoline have been completed. We continue to crystallize samples of tyrosine kinase...been developed last year identify the geometric relationship between structural features of a set of molecules known to act as tyrosine kinase...L. Klein Stevens, “A Crystallographic Study of ErbB2 Tyrosine Kinase Inhibitors”, 230th American Chemical Society National Meeting, Washington, DC

A molecular model for proflavine-DNA intercalation.

PubMed Central

Neidle, S; Pearl, L H; Herzyk, P; Berman, H M

1988-01-01

A molecular model has been derived for the intercalation of proflavine into the CpG site of the decamer duplex of d(GATACGATAC). The starting geometry of the intercalation site was taken from previous crystallographic studies on the d(CpG)-proflavine complex, and molecular mechanics used to obtain a stereochemically acceptable structure. This has widened grooves compared to standard A- or B- double helices, as well as distinct conformational, roll, twist and tilt features. PMID:3174439

Some structures of marine natural products

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

Finer-Moore, J.S.

1979-07-01

Applications of x-ray crystallographic methods to marine chemistry are discussed. Results of research on a biosynthetic problem: diterpenes from Dictyotaceae are discussed under the following section headings: history of the problem; dictyoxepin; dictyodial; and dictyolactone. Studies on marine ecology are reported under the following headings: symbiosis and antibiosis; metabolites from opisthobranch molluscs, including, dolabelladiene, 9-isocyanopupukeanane and 2-isocyanopupukeanane, and crispatone; metabolites of goronians and soft corals, including zooxanthellae and the metabolism of coelenterates, ophirin, sinularene, and erectene. (JGB)

Voltage-Gated Potassium Channels: A Structural Examination of Selectivity and Gating

PubMed Central

Kim, Dorothy M.; Nimigean, Crina M.

2016-01-01

Voltage-gated potassium channels play a fundamental role in the generation and propagation of the action potential. The discovery of these channels began with predictions made by early pioneers, and has culminated in their extensive functional and structural characterization by electrophysiological, spectroscopic, and crystallographic studies. With the aid of a variety of crystal structures of these channels, a highly detailed picture emerges of how the voltage-sensing domain reports changes in the membrane electric field and couples this to conformational changes in the activation gate. In addition, high-resolution structural and functional studies of K+ channel pores, such as KcsA and MthK, offer a comprehensive picture on how selectivity is achieved in K+ channels. Here, we illustrate the remarkable features of voltage-gated potassium channels and explain the mechanisms used by these machines with experimental data. PMID:27141052

Protein crystal growth and the International Space Station

NASA Technical Reports Server (NTRS)

DeLucas, L. J.; Moore, K. M.; Long, M. M.

1999-01-01

Protein structural information plays a key role in understanding biological structure-function relationships and in the development of new pharmaceuticals for both chronic and infectious diseases. The Center for Macromolecular Crystallography (CMC) has devoted considerable effort studying the fundamental processes involved in macromolecular crystal growth both in a 1-g and microgravity environment. Results from experiments performed on more than 35 U.S. space shuttle flights have clearly indicated that microgravity can provide a beneficial environment for macromolecular crystal growth. This research has led to the development of a new generation of pharmaceuticals that are currently in preclinical or clinical trials for diseases such as cutaneous T-cell lymphoma, psoriasis, rheumatoid arthritis, AIDS, influenza, stroke and other cardiovascular complications. The International Space Station (ISS) provides an opportunity to have complete crystallographic capability on orbit, which was previously not possible with the space shuttle orbiter. As envisioned, the x-ray Crystallography Facility (XCF) will be a complete facility for growing protein crystals; selecting, harvesting, and mounting sample crystals for x-ray diffraction; cryo-freezing mounted crystals if necessary; performing x-ray diffraction studies; and downlinking the data for use by crystallographers on the ground. Other advantages of such a facility include crystal characterization so that iterations in the crystal growth conditions can be made, thereby optimizing the final crystals produced in a three month interval on the ISS.

Mesocrystals in Biominerals and Colloidal Arrays.

PubMed

Bergström, Lennart; Sturm née Rosseeva, Elena V; Salazar-Alvarez, German; Cölfen, Helmut

2015-05-19

Mesocrystals, which originally was a term to designate superstructures of nanocrystals with a common crystallographic orientation, have now evolved to a materials concept. The discovery that many biominerals are mesocrystals generated a large research interest, and it was suggested that mesocrystals result in better mechanical performance and optical properties compared to single crystalline structures. Mesocrystalline biominerals are mainly found in spines or shells, which have to be mechanically optimized for protection or as a load-bearing skeleton. Important examples include red coral and sea urchin spine as well as bones. Mesocrystals can also be formed from purely synthetic components. Biomimetic mineralization and assembly have been used to produce mesocrystals, sometimes with complex hierarchical structures. Important examples include the fluorapatite mesocrystals with gelatin as the structural matrix, and mesocrystalline calcite spicules with impressive strength and flexibility that could be synthesized using silicatein protein fibers as template for calcium carbonate deposition. Self-assembly of nanocrystals can also result in mesocrystals if the nanocrystals have a well-defined size and shape and the assembly conditions are tuned to allow the nanoparticles to align crystallographically. Mesocrystals formed by assembly of monodisperse metallic, semiconducting, and magnetic nanocrystals are a type of colloidal crystal with a well-defined structure on both the atomic and mesoscopic length scale.Mesocrystals typically are hybrid materials between crystalline nanoparticles and interspacing amorphous organic or inorganic layers. This structure allows to combine disparate materials like hard but brittle nanocrystals with a soft and ductile amorphous material, enabling a mechanically optimized structural design as realized in the sea urchin spicule. Furthermore, mesocrystals can combine the properties of individual nanocrystals like the optical quantum size effect, surface plasmon resonance, and size dependent magnetic properties with a mesostructure and morphology tailored for specific applications. Indeed, mesocrystals composed of crystallographically aligned polyhedral or rodlike nanocrystals with anisotropic properties can be materials with strongly directional properties and novel collective emergent properties. An additional advantage of mesocrystals is that they can combine the properties of nanoparticles with a structure on the micro- or macroscale allowing for much easier handling.

Understanding local degradation of cycled Ni-rich cathode materials at high operating temperature for Li-ion batteries

NASA Astrophysics Data System (ADS)

Hwang, Sooyeon; Kim, Dong Hyun; Chung, Kyung Yoon; Chang, Wonyoung

2014-09-01

We utilize transmission electron microscopy in conjunction with electron energy loss spectroscopy to investigate local degradation that occurs in LixNi0.8Co0.15Al0.05O2 cathode materials (NCA) after 30 cycles with cutoff voltages of 4.3 V and 4.8 V at 55 °C. NCA has a homogeneous crystallographic structure before electrochemical reactions; however, we observed that 30 cycles of charge/discharge reactions induced inhomogeneity in the crystallographic and electronic structures and also introduced porosity particularly at surface area. These changes were more noticeable in samples cycled with higher cutoff voltage of 4.8 V. Effect of operating temperature was further examined by comparing electronic structures of oxygen of the NCA particles cycled at both room temperature and 55 °C. The working temperature has a greater impact on the NCA cathode materials at a cutoff voltage of 4.3 V that is the practical the upper limit voltage in most applications, while a cutoff voltage of 4.8 V is high enough to cause surface degradation even at room temperature.

Simultaneous use of solution NMR and X-ray data in REFMAC5 for joint refinement/detection of structural differences.

PubMed

Rinaldelli, Mauro; Ravera, Enrico; Calderone, Vito; Parigi, Giacomo; Murshudov, Garib N; Luchinat, Claudio

2014-04-01

The program REFMAC5 from CCP4 was modified to allow the simultaneous use of X-ray crystallographic data and paramagnetic NMR data (pseudocontact shifts and self-orientation residual dipolar couplings) and/or diamagnetic residual dipolar couplings. Incorporation of these long-range NMR restraints in REFMAC5 can reveal differences between solid-state and solution conformations of molecules or, in their absence, can be used together with X-ray crystallographic data for structural refinement. Since NMR and X-ray data are complementary, when a single structure is consistent with both sets of data and still maintains reasonably `ideal' geometries, the reliability of the derived atomic model is expected to increase. The program was tested on five different proteins: the catalytic domain of matrix metalloproteinase 1, GB3, ubiquitin, free calmodulin and calmodulin complexed with a peptide. In some cases the joint refinement produced a single model consistent with both sets of observations, while in other cases it indicated, outside the experimental uncertainty, the presence of different protein conformations in solution and in the solid state.

The three-dimensional structure of a T-cell antigen receptor V alpha V beta heterodimer reveals a novel arrangement of the V beta domain.

PubMed Central

Housset, D; Mazza, G; Grégoire, C; Piras, C; Malissen, B; Fontecilla-Camps, J C

1997-01-01

The crystal structure of a mouse T-cell antigen receptor (TCR) Fv fragment complexed to the Fab fragment of a specific anti-clonotypic antibody has been determined to 2.6 A resolution. The polypeptide backbone of the TCR V alpha domain is very similar to those of other crystallographically determined V alphas, whereas the V beta structure is so far unique among TCR V beta domains in that it displays a switch of the c" strand from the inner to the outer beta-sheet. The beta chain variable region of this TCR antigen-binding site is characterized by a rather elongated third complementarity-determining region (CDR3beta) that packs tightly against the CDR3 loop of the alpha chain, without leaving any intervening hydrophobic pocket. Thus, the conformation of the CDR loops with the highest potential diversity distinguishes the structure of this TCR antigen-binding site from those for which crystallographic data are available. On the basis of all these results, we infer that a significant conformational change of the CDR3beta loop found in our TCR is required for binding to its cognate peptide-MHC ligand. PMID:9250664

X-ray diffraction and X-ray standing-wave study of the lead stearate film structure

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

Blagov, A. E.; Dyakova, Yu. A.; Kovalchuk, M. V.

2016-05-15

A new approach to the study of the structural quality of crystals is proposed. It is based on the use of X-ray standing-wave method without measuring secondary processes and considers the multiwave interaction of diffraction reflections corresponding to different harmonics of the same crystallographic reflection. A theory of multiwave X-ray diffraction is developed to calculate the rocking curves in the X-ray diffraction scheme under consideration for a long-period quasi-one-dimensional crystal. This phase-sensitive method is used to study the structure of a multilayer lead stearate film on a silicon substrate. Some specific structural features are revealed for the surface layer ofmore » the thin film, which are most likely due to the tilt of the upper layer molecules with respect to the external normal to the film surface.« less

Resonant soft X-ray scattering on protein solutions

NASA Astrophysics Data System (ADS)

Ye, Dan; Le, Thinh; Wang, Cheng; Zwart, Peter; Gomez, Esther; Gomez, Enrique

Protein structure is crucial for biological function, such that characterizing protein folding and packing is important for the design of therapeutics and enzymes. We propose resonant soft X-ray scattering (RSOXS) as an approach to study proteins and other biological assemblies in solution. Calculations of the scattering contrast suggest that soft X-ray scattering is more sensitive than hard X-ray scattering, because of contrast generated at the absorption edges of constituent elements such as carbon, nitrogen and oxygen. We have examined the structure of bovine serum albumin (BSA) in solution by RSOXS. We find that by varying incident X-ray energies, we are able to achieve higher scattering contrast near the absorption edge. From our RSOXS scattering result we are able to reconstruct the structure of BSA in 3D. These RSOXS results also agree with hard X-ray experiments, including crystallographic data. Our study demonstrates the potential of RSOXS for studying protein structure in solution.

Structural mimicry of O-antigen by a peptide revealed in a complex with an antibody raised against Shigella flexneri serotype 2a.

PubMed

Theillet, François-Xavier; Saul, Frederick A; Vulliez-Le Normand, Brigitte; Hoos, Sylviane; Felici, Franco; Weintraub, Andrej; Mulard, Laurence A; Phalipon, Armelle; Delepierre, Muriel; Bentley, Graham A

2009-05-15

The use of carbohydrate-mimicking peptides to induce immune responses against surface polysaccharides of pathogenic bacteria offers a novel approach to vaccine development. Factors governing antigenic and immunogenic mimicry, however, are complex and poorly understood. We have addressed this question using the anti-lipopolysaccharide monoclonal antibody F22-4, which was raised against Shigella flexneri serotype 2a and shown to protect against homologous infection in a mouse model. In a previous crystallographic study, we described F22-4 in complex with two synthetic fragments of the O-antigen, the serotype-specific saccharide moiety of lipopolysaccharide. Here, we present a crystallographic and NMR study of the interaction of F22-4 with a dodecapeptide selected by phage display using the monoclonal antibody. Like the synthetic decasaccharide, the peptide binds to F22-4 with micromolar affinity. Although the peptide and decasaccharide use very similar regions of the antigen-binding site, indicating good antigenic mimicry, immunogenic mimicry by the peptide was not observed. The F22-4-antigen interaction is significantly more hydrophobic with the peptide than with oligosaccharides; nonetheless, all hydrogen bonds formed between the peptide and F22-4 have equivalents in the oligosaccharide complex. Two bridging water molecules are also in common, adding to partial structural mimicry. Whereas the bound peptide is entirely helical, its structure in solution, as shown by NMR, is helical in the central region only. Moreover, docking the NMR structure into the antigen-binding site shows that steric hindrance would occur, revealing poor complementarity between the major solution conformation and the antibody that could contribute to the absence of immunogenic mimicry.

Crystallographic studies of [NiFe]-hydrogenase mutants: towards consensus structures for the elusive unready oxidized states.

PubMed

Volbeda, Anne; Martin, Lydie; Barbier, Elodie; Gutiérrez-Sanz, Oscar; De Lacey, Antonio L; Liebgott, Pierre-Pol; Dementin, Sébastien; Rousset, Marc; Fontecilla-Camps, Juan C

2015-01-01

Catalytically inactive oxidized O2-sensitive [NiFe]-hydrogenases are characterized by a mixture of the paramagnetic Ni-A and Ni-B states. Upon O2 exposure, enzymes in a partially reduced state preferentially form the unready Ni-A state. Because partial O2 reduction should generate a peroxide intermediate, this species was previously assigned to the elongated Ni-Fe bridging electron density observed for preparations of [NiFe]-hydrogenases known to contain the Ni-A state. However, this proposition has been challenged based on the stability of this state to UV light exposure and the possibility of generating it anaerobically under either chemical or electrochemical oxidizing conditions. Consequently, we have considered alternative structures for the Ni-A species including oxidation of thiolate ligands to either sulfenate or sulfenic acid. Here, we report both new and revised [NiFe]-hydrogenases structures and conclude, taking into account corresponding characterizations by Fourier transform infrared spectroscopy (FTIR), that the Ni-A species contains oxidized cysteine and bridging hydroxide ligands instead of the peroxide ligand we proposed earlier. Our analysis was rendered difficult by the typical formation of mixtures of unready oxidized states that, furthermore, can be reduced by X-ray induced photoelectrons. The present study could be carried out thanks to the use of Desulfovibrio fructosovorans [NiFe]-hydrogenase mutants with special properties. In addition to the Ni-A state, crystallographic results are also reported for two diamagnetic unready states, allowing the proposal of a revised oxidized inactive Ni-SU model and a new structure characterized by a persulfide ion that is assigned to an Ni-'Sox' species.

Theoretical investigation of the structural, elastic, electronic and optical properties of the ternary indium sulfide layered structures AInS2 (A = K, Rb and Cs)

NASA Astrophysics Data System (ADS)

Bouchenafa, M.; Sidoumou, M.; Halit, M.; Benmakhlouf, A.; Bouhemadou, A.; Maabed, S.; Bentabet, A.; Bin-Omran, S.

2018-02-01

Ab initio calculations were performed to investigate the structural, elastic, electronic and optical properties of the ternary layered systems AInS2 (A = K, Rb and Cs). The calculated structural parameters are in good agreement with the existing experimental data. Analysis of the electronic band structure shows that the three studied materials are direct band-gap semiconductors. Density of states, charge transfers and charge density distribution maps were computed and analyzed. Numerical estimations of the elastic moduli and their related properties for single-crystal and polycrystalline aggregates were predicted. The optical properties were calculated for incident radiation polarized along the [100], [010] and [001] crystallographic directions. The studied materials exhibit a noticeable anisotropic behaviour in the elastic and optical properties, which is expected due to the symmetry and the layered nature of these compounds.

Application of Single Crystal Failure Criteria: Theory and Turbine Blade Case Study

NASA Technical Reports Server (NTRS)

Sayyah, Tarek; Swanson, Gregory R.; Schonberg, W. P.

1999-01-01

The orientation of the single crystal material within a structural component is known to affect the strength and life of the part. The first stage blade of the High Pressure Fuel Turbopump (HPFTP)/ Alternative Turbopump Development (ATD), of the Space Shuttle Main Engine (SSME) was used to study the effects of secondary axis'orientation angles on the failure rate of the blade. A new failure criterion was developed based on normal and shear strains on the primary crystallographic planes. The criterion was verified using low cycle fatigue (LCF) specimen data and a finite element model of the test specimens. The criterion was then used to study ATD/HPFTP first stage blade failure events. A detailed ANSYS finite element model of the blade was used to calculate the failure parameter for the different crystallographic orientations. A total of 297 cases were run to cover a wide range of acceptable orientations within the blade. Those orientations are related to the base crystallographic coordinate system that was created in the ANSYS finite element model. Contour plots of the criterion as a function of orientation for the blade tip and attachment were obtained. Results of the analysis revealed a 40% increase in the failure parameter due to changing of the primary and secondary axes of material orientations. A comparison between failure criterion predictions and actual engine test data was then conducted. The engine test data comes from two ATD/HPFTP builds (units F3- 4B and F6-5D), which were ground tested on the SSME at the Stennis Space Center in Mississippi. Both units experienced cracking of the airfoil tips in multiple blades, but only a few cracks grew all the way across the wall of the hollow core airfoil.

A fragmentation and reassembly method for ab initio phasing.

PubMed

Shrestha, Rojan; Zhang, Kam Y J

2015-02-01

Ab initio phasing with de novo models has become a viable approach for structural solution from protein crystallographic diffraction data. This approach takes advantage of the known protein sequence information, predicts de novo models and uses them for structure determination by molecular replacement. However, even the current state-of-the-art de novo modelling method has a limit as to the accuracy of the model predicted, which is sometimes insufficient to be used as a template for successful molecular replacement. A fragment-assembly phasing method has been developed that starts from an ensemble of low-accuracy de novo models, disassembles them into fragments, places them independently in the crystallographic unit cell by molecular replacement and then reassembles them into a whole structure that can provide sufficient phase information to enable complete structure determination by automated model building. Tests on ten protein targets showed that the method could solve structures for eight of these targets, although the predicted de novo models cannot be used as templates for successful molecular replacement since the best model for each target is on average more than 4.0 Å away from the native structure. The method has extended the applicability of the ab initio phasing by de novo models approach. The method can be used to solve structures when the best de novo models are still of low accuracy.

Structure of 2C-Methyl-D-erythritol-2,4-cyclodiphosphate Synthase from Shewanella oneidensis at 1.6 angstrom: Identification of Farnesyl pyrophosphate Trapped in a Hydrophobic Cavity

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

Ni, Shuisong; Robinson, Howard; Marsing, Gregory C.

2004-11-01

1. Introduction Enzymes in the non-mevalonate pathway for isoprenoid synthesis have gained recent attention because of their potential value as targets for antibiotic drug development. 2C-methyl-D-erythritol-2,4 cyclophosphate (MECDP) synthase is the fifth enzyme in the seven enzyme non-mevalonate pathway for synthesis of isopentenyl diphosphate. Four groups have published structures of MECDP synthase at resolutions varying from 1.6Å to 2.8Å, either in the presence or absence of substrate from Escherichia coli (Richard et al., 2002; Kemp et al., 2002; Steinbacher et al., 2002) or from Thermus thermophilus (Kishida et al., 2003). Among these structures, the protein always exists as a homotrimermore » either with a crystallographic or a non-crystallographic three-fold symmetry axis and an active site formed in a cleft between adjacent monomers. While the overall shape of the proteins is highly similar among these structures, each of the four reported structures contain different combinations of metal ions in the active site including a Zn2+ ion only (Steinbacher et al., 2002), a Mn2+ ion only (Richard et al., 2002), Zn2+ and Mn2+ ions (Kemp et al., 2002) or two Mg2+ ions (Kishida et al., 2003). Furthermore, two of the structures are reported to contain a hydrophobic channel along the three-fold symmetry axis that is capped by a cluster of three arginine side chains (one from each monomer) at one end of the cavity and a cluster of three glutamic acid side chains (one from each monomer) at the other side of the cavity. In a 1.8Å resolution structure, Kemp et al. (2002) reported a sulfate ion coordinated to the arginine cap and solvent trapped in a hydrophobic cavity. In a lower 2.8Å resolution structure, Richard et al. (2002) concluded that geranyl diphosphate, GPP, was most likely trapped by the arginine cap and hydrophobic cavity (Richard et al., 2002), however, the low resolution of the data together with the presence of the crystallographic symmetry axis prohibited a definitive analysis of the identity and mode of binding of the bound molecule. Kishida et al. (2003) reported that no cavity existed in a 1.6Å structure of the SO3437 homolog from Thermus thermophilus, presumably due to tighter packing of the protein from the thermophilic organism. Steinbacher et al. (2002) make no description of a hydrophobic cavity in a lower resolution (2.5-3.2Å) of the Escherichia coli protein. Here, we report a high-resolution (1.6Å) structure of MECDP synthase from Shewanella oneidensis in the absence of substrate in the active site. We provide unambiguous data that confirms the presence of Zn2+ in one of the metal binding sites and observe what appears to be farnesyl diphosphate (FPP) bound in the hydrophobic cavity along the non-crystallographic three-fold symmetry axis of the homotrimer. The high-resolution structure clarifies the mode of binding of the pyrophosphate of FPP in the arginine cluster that caps the hydrophobic cavity.« less

Purification, crystallization and preliminary crystallographic study of haemoglobin from camel (Camelus dromedarius): a high oxygen-affinity lowland species.

PubMed

Balasubramanian, M; Moorthy, Pon Sathya; Neelagandan, K; Ponnuswamy, M N

2009-08-01

Haemoglobin is a prototypical allosteric protein that is mainly involved in the transportation of oxygen from the lungs to tissues and of carbon dioxide back to the lungs in an intrinsically coordinated manner to maintain the viability of cells. Haemoglobin from Camelus dromedarius provides an interesting case study of adaptation to life in deserts at extremely high temperatures. An ambition to unravel the integrated structural and functional aspects of the casual survival of this animal at high temperatures led us to specifically work on this problem. The present work reports the preliminary crystallographic study of camel haemoglobin. Camel blood was collected and the haemoglobin was purified by anion-exchange chromatography and crystallized using the hanging-drop vapour-diffusion method under buffered high salt concentration using PEG 3350 as a precipitant. Intensity data were collected using a MAR 345 dtb image-plate detector system. Camel haemoglobin crystallized in the monoclinic space group P2(1), with one whole biological molecule (alpha(2)beta(2)) in the asymmetric unit and unit-cell parameters a = 52.759, b = 116.782, c = 52.807 A, beta = 120.07 degrees .

Structure-energy relationship in barbituric acid: a calorimetric, computational, and crystallographic study.

PubMed

Roux, María Victoria; Temprado, Manuel; Notario, Rafael; Foces-Foces, Concepción; Emel'yanenko, Vladimir N; Verevkin, Sergey P

2008-08-14

This paper reports the value of the standard (p(o) = 0.1 MPa) molar enthalpy of formation in the gas phase at T = 298.15 K for barbituric acid. The enthalpies of combustion and sublimation were measured by static bomb combustion calorimetry and transference (transpiration) method in a saturated N2 stream and a gas-phase enthalpy of formation value of -(534.3 +/- 1.7) kJ x mol(-1) was determined at T = 298.15 K. G3-calculated enthalpies of formation are in very good agreement with the experimental value. The behavior of the sample as a function of the temperature was studied by differential scanning calorimetry, and a new polymorph of barbituric acid at high temperature was found. In the solid state, two anhydrous forms are known displaying two out of the six hydrogen-bonding patterns observed in the alkyl/alkenyl derivatives retrieved from the Cambridge Crystallographic Database. The stability of these motifs has been analyzed by theoretical calculations. X-ray powder diffraction technique was used to establish to which polymorphic form corresponds to the commercial sample used in this study and to characterize the new form at high temperature.

The Workshop on Conductive Polymers: Final Report

DOE R&D Accomplishments Database

1985-10-01

Reports are made by groups on: polyacetylene, polyphenylene, polyaniline, and related systems; molecular, crystallographic, and defect structures in conducting polymers; heterocyclic polymers; synthesis of new and improved conducting polymers; future applications possibilities for conducting polymers; and challenges for improved understanding of properties. (DLC)

A catalytic metal ion interacts with the cleavage site G•U wobble in the HDV ribozyme†

PubMed Central

Chen, Jui-Hui; Gong, Bo; Bevilacqua, Philip C.; Carey, Paul R.; Golden, Barbara L.

2009-01-01

The HDV ribozyme self-cleaves by a chemical mechanism involving general acid-base catalysis to generate a 2′,3′-cyclic phosphate and a 5′-hydroxyl termini. Biochemical studies from several laboratories have implicated C75 as the general acid and hydrated magnesium as the general base. We have previously shown that C75 has a pKa shifted > 2 pH units toward neutrality [Gong, B., Chen, J. H., Chase, E., Chadalavada, D. M., Yajima, R., Golden, B. L., Bevilacqua, P. C., and Carey, P. R. (2007) J. Am. Chem. Soc. 129, 13335–13342.], while in crystal structures, it is well-positioned for proton transfer. However no crystallographic evidence for a hydrated magnesium poised to serve as a general base in the reaction has been observed in high-resolution crystal structures of various reaction states and mutants. Herein, we use solution kinetic experiments and parallel Raman crystallographic studies to examine the effects of pH on rate and Mg2+-binding properties of wild-type and 7-deazaguanosine mutants of the HDV ribozyme. These data suggest that a previously-unobserved hydrated magnesium ion interacts with the N7 of the cleavage site G•U wobble base pair. Integrating this metal ion binding site with the available crystal structures provides a new three-dimensional model for the active site of the ribozyme that accommodates all available biochemical data and appears competent for catalysis. The position of this metal is consistent with a role of a magnesium-bound hydroxide as a general base as dictated by biochemical data. PMID:19178151

Study of nanostructure and ethanol vapor sensing performance of WO3 thin films deposited by e-beam evaporation method under different deposition angles: application in breath analysis devices

NASA Astrophysics Data System (ADS)

Amani, E.; Khojier, K.; Zoriasatain, S.

2018-01-01

This paper studies the effect of deposition angle on the crystallographic structure, surface morphology, porosity and subsequently ethanol vapor sensing performance of e-beam-evaporated WO3 thin films. The WO3 thin films were deposited by e-beam evaporation technique on SiO2/Si substrates under different deposition angles (0°, 30°, and 60°) and then post-annealed at 500 °C with a flow of oxygen for 4 h. Crystallographic structure and surface morphology of the samples were checked using X-ray diffraction method and atomic force microscopy, respectively. Physical adsorption isotherm was also used to measure the porosity and effective surface area of the samples. The electrical response of the samples was studied to different concentrations of ethanol vapor (10-50 ppm) at the temperature range of 140-260 °C and relative humidity of 80%. The results reveal that the WO3 thin film deposited under 30° angle shows more sensitivity to ethanol vapor than the other samples prepared in this work due to the more crystallinity, porosity, and effective surface area. The investigations also show that the sample deposited at 30° can be a good candidate as a breath analysis device at the operating temperature of 240 °C because of its high response, low detection limit, and reliability at high relative humidity.

Crystallographic and Computational Studies of a Class II MHC Complex with a Nonconforming Peptide: HLA-DRA/DRB3*0101

NASA Astrophysics Data System (ADS)

Parry, Christian S.; Gorski, Jack; Stern, Lawrence J.

2003-03-01

The stable binding of processed foreign peptide to a class II major histocompatibility (MHC) molecule and subsequent presentation to a T cell receptor is a central event in immune recognition and regulation. Polymorphic residues on the floor of the peptide binding site form pockets that anchor peptide side chains. These and other residues in the helical wall of the groove determine the specificity of each allele and define a motif. Allele specific motifs allow the prediction of epitopes from the sequence of pathogens. There are, however, known epitopes that do not satisfy these motifs: anchor motifs are not adequate for predicting epitopes as there are apparently major and minor motifs. We present crystallographic studies into the nature of the interactions that govern the binding of these so called nonconforming peptides. We would like to understand the role of the P10 pocket and find out whether the peptides that do not obey the consensus anchor motif bind in the canonical conformation observed in in prior structures of class II MHC-peptide complexes. HLA-DRB3*0101 complexed with peptide crystallized in unit cell 92.10 x 92.10 x 248.30 (90, 90, 90), P41212, and the diffraction data is reliable to 2.2ÅWe are complementing our studies with dynamical long time simulations to answer these questions, particularly the interplay of the anchor motifs in peptide binding, the range of protein and ligand conformations, and water hydration structures.

Elucidation of the structure of retroviral proteases: a reminiscence.

PubMed

Jaskolski, Mariusz; Miller, Maria; Mohana Rao, J K; Gustchina, Alla; Wlodawer, Alexander

2015-11-01

Determinations of only a very few protein structures had consequences comparable to the impact exerted by the structure of the protease encoded by HIV-1, published just over 25 years ago. The structure of this relatively small protein and its cousins from other retroviruses provided a clear target for a spectacularly successful structure-assisted drug design effort that offered new hope for controlling the then-escalating AIDS epidemic. This reminiscence is limited primarily to work conducted at the National Cancer Institute, and is not meant to be a comprehensive history of the field, but is rather an attempt to provide a very personal account of how the structures of this most thoroughly studied crystallographic target were determined. Published 2015. This article is a U.S. Government work and is in the public domain in the USA.

Structural Characterization of the Histone Variant macroH2A

PubMed Central

Chakravarthy, Srinivas; Gundimella, Sampath Kumar Y.; Caron, Cecile; Perche, Pierre-Yves; Pehrson, John R.; Khochbin, Saadi; Luger, Karolin

2005-01-01

macroH2A is an H2A variant with a highly unusual structural organization. It has a C-terminal domain connected to the N-terminal histone domain by a linker. Crystallographic and biochemical studies show that changes in the L1 loop in the histone fold region of macroH2A impact the structure and potentially the function of nucleosomes. The 1.6-Å X-ray structure of the nonhistone region reveals an α/β fold which has previously been found in a functionally diverse group of proteins. This region associates with histone deacetylases and affects the acetylation status of nucleosomes containing macroH2A. Thus, the unusual domain structure of macroH2A integrates independent functions that are instrumental in establishing a structurally and functionally unique chromatin domain. PMID:16107708

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

A method used to overcome polarization effects in semi-polar structures of nitride light-emitting diodes emitting green radiation

NASA Astrophysics Data System (ADS)

Morawiec, Seweryn; Sarzała, Robert P.; Nakwaski, Włodzimierz

2013-11-01

Polarization effects are studied within nitride light-emitting diodes (LEDs) manufactured on standard polar and semipolar substrates. A new theoretical approach, somewhat different than standard ones, is proposed to this end. It is well known that when regular polar GaN substrates are used, strong piezoelectric and spontaneous polarizations create built-in electric fields leading to the quantum-confined Stark effects (QCSEs). These effects may be completely avoided in nonpolar crystallographic orientations, but then there are problems with manufacturing InGaN layers of relatively high Indium contents necessary for the green emission. Hence, a procedure leading to partly overcoming these polarization problems in semi-polar LEDs emitting green radiation is proposed. The (11 22) crystallographic substrate orientation (inclination angle of 58∘ to c plane) seems to be the most promising because it is characterized by low Miller-Bravais indices leading to high-quality and high Indium content smooth growth planes. Besides, it makes possible an increased Indium incorporation efficiency and it is efficient in suppressing QCSE. The In0.3Ga0.7N/GaN QW LED grown on the semipolar (11 22) substrate has been found as currently the optimal LED structure emitting green radiation.

Oligomeric State of Lipocalin-1 (LCN1) by Multiangle Laser Light Scattering and Fluorescence Anisotropy Decay

PubMed Central

Gasymov, Oktay K.; Abduragimov, Adil R.; Merschak, Petra; Redl, Bernhard; Glasgow, Ben J.

2007-01-01

Multiangle laser light scattering and fluorescence anisotropy decay measurements clarified the oligomeric states of native and recombinant tear lipocalin (lipocalin-1, TL). Native TL is monomeric. Recombinant TL (5-68 μM) with or without the histidine tag shows less than 7% dimer formation that is not in equilibrium with the monomeric form. Fluorescence anisotropy decay showed a correlation time of 9-10 ns for TL (10 μM- 1mM). Hydrodynamic calculations based on the crystallographic structure of a monomeric TL mutant closely concur with the observed correlation time. The solution properties calculated with HYDROPRO and SOLPRO programs from the available crystallographic structure of a monomeric TL mutant concur closely with the observed fluorescence anisotropy decay. The resulting model shows that protein topology is the major determinant of rotational correlation time and accounts for deviation from the Stokes-Einstein relation. The data challenge previous gel filtration studies to show that native TL exists predominantly as a monomer in solution rather than as a dimer. Delipidation of TL results in a formation of a complex oligomeric state (up to 25%). These findings are important as the dynamic processes in the tear film are limited by diffusional, translational as well as rotational, properties of the protein. PMID:17869594

Effect of Synthesis Temperature on Structure and Magnetic Properties of (La,Nd)0.7Sr0.3MnO3 Nanoparticles.

PubMed

Shlapa, Yulia; Solopan, Sergii; Bodnaruk, Andrii; Kulyk, Mykola; Kalita, Viktor; Tykhonenko-Polishchuk, Yulia; Tovstolytkin, Alexandr; Belous, Anatolii

2017-12-01

Two sets of Nd-doped La 0.7 Sr 0.3 MnO 3 nanoparticles were synthesized via sol-gel method with further heat treatment at 1073 and 1573 K, respectively. Crystallographic and magnetic properties of obtained nanoparticles were studied, and the effect of synthesis conditions on these properties was investigated. According to X-ray data, all particles crystallized in the distorted perovskite structure. Magnetic parameters, such as saturation magnetization, coercivity, Curie temperature, and specific loss power, which is released on the exposure of an ensemble of nanoparticles to AC magnetic field, were determined for both sets of samples. The correlation between the values of Curie temperature and maximal heating temperature under AC magnetic field was found. It was revealed that for the samples synthesized at 1573 K, the dependences of crystallographic and magnetic parameters on Nd content were monotonous, while for the samples synthesized at 1073 K, they were non-monotonous. It was concluded that Nd-doped La 0.7 Sr 0.3 MnO 3 nanoparticles are promising materials for self-controlled magnetic hyperthermia applications, but the researchers should be aware of the unusual behavior of the particles synthesized at relatively low temperatures.

Yb3+-doped cadmium molybdato-tungstate single crystal - Its structural, optical, magnetic and transport properties

NASA Astrophysics Data System (ADS)

Groń, T.; Tomaszewicz, E.; Berkowski, M.; Głowacki, M.; Oboz, M.; Kusz, J.; Sawicki, B.; Kukuła, Z.; Duda, H.

2018-06-01

Single crystal of new cadmium and ytterbium molybdato-tungstate (Cd0.9706⎕0.0098Yb0.0196(MoO4)0.9706(WO4)0.0294, where ⎕ denotes cationic vacancies) has been successfully grown by the Czochralski method in air and under 1 MPa. X-ray crystallographic analysis reveals that the as-grown single crystal belongs to a scheelite-type structure (a = b = 5.15539(12) and c = 11.1919(3) Å, space group I41/a), in which Yb3+ ions do not show long-range order and are randomly distributed in the unit cell, substituting the Cd2+ ones. The as-grown single crystal does not show anisotropy of optical properties, i.e. its direct band gap reaches Eg = 1.76 or 1.75 eV along (100) and (001) crystallographic directions, respectively. The single crystal exhibits paramagnetic state with short-range antiferromagnetic and long-range ferrimagnetic interactions, a magnetization with zero coercivity and, a remanence that is almost a universal function of H/T, characterizing superparamagnetic-like behaviour. Electrical studies of the new ytterbium-doped cadmium molybdato-tungstate single crystal show a relatively small dielectric constant (εr<12), large lossiness of Joule-Lenz type observed at low frequencies as well as nonlinear I-V characteristics of Schottky or Maxwell-Wagner type.

A new photoactive Ru(II)tris(2,2'-bipyridine) templated Zn(II) benzene-1,4-dicarboxylate metal organic framework: structure and photophysical properties.

PubMed

Whittington, Christi L; Wojtas, Lukasz; Gao, Wen-Yang; Ma, Shengqian; Larsen, Randy W

2015-03-28

It has now been demonstrated that Ru(ii)tris(2,2'-bipyridine) (RuBpy) can be utilized to template the formation of new metal organic framework (MOF) materials containing crystallographically resolved RuBpy clusters with unique photophysical properties. Two such materials, RWLC-1 and RWLC-2, have now been reported from our laboratory and are composed of RuBpy encapsulated in MOFs composed of Zn(ii) ions and 1,3,5-tris(4-carboxyphenyl)benzene ligands (C. L. Whittington, L. Wojtas and R. W. Larsen, Inorg. Chem., 2014, 53, 160-166). Here, a third RuBpy templated photoactive MOF is described (RWLC-3) that is derived from the reaction between Zn(ii) ions and 1,4-dicarboxybenzene in the presence of RuBpy. Single Crystal X-ray diffraction studies determined the position of RuBpy cations within the crystal lattice. The RWLC-3 structure is described as a 2-fold interpenetrated pillared honeycomb network (bnb) containing crystallographically resolved RuBpy clusters. The two bnb networks are weakly interconnected. The encapsulated RuBpy exhibits two emission decay lifetimes (τ-fast = 120 ns, τ-slow = 453 ns) and a bathochromic shift in the steady state emission spectrum relative to RuBpy in ethanol.

Anodes for rechargeable lithium batteries

DOEpatents

Thackeray, Michael M.; Kepler, Keith D.; Vaughey, John T.

2003-01-01

A negative electrode (12) for a non-aqueous electrochemical cell (10) with an intermetallic host structure containing two or more elements selected from the metal elements and silicon, capable of accommodating lithium within its crystallographic host structure such that when the host structure is lithiated it transforms to a lithiated zinc-blende-type structure. Both active elements (alloying with lithium) and inactive elements (non-alloying with lithium) are disclosed. Electrochemical cells and batteries as well as methods of making the negative electrode are disclosed.

Structural variability and the nature of intermolecular interactions in Watson-Crick B-DNA base pairs.

PubMed

Czyznikowska, Z; Góra, R W; Zaleśny, R; Lipkowski, P; Jarzembska, K N; Dominiak, P M; Leszczynski, J

2010-07-29

A set of nearly 100 crystallographic structures was analyzed using ab initio methods in order to verify the effect of the conformational variability of Watson-Crick guanine-cytosine and adenine-thymine base pairs on the intermolecular interaction energy and its components. Furthermore, for the representative structures, a potential energy scan of the structural parameters describing mutual orientation of the base pairs was carried out. The results were obtained using the hybrid variational-perturbational interaction energy decomposition scheme. The electron correlation effects were estimated by means of the second-order Møller-Plesset perturbation theory and coupled clusters with singles and doubles method adopting AUG-cc-pVDZ basis set. Moreover, the characteristics of hydrogen bonds in complexes, mimicking those appearing in B-DNA, were evaluated using topological analysis of the electron density. Although the first-order electrostatic energy is usually the largest stabilizing component, it is canceled out by the associated exchange repulsion in majority of the studied crystallographic structures. Therefore, the analyzed complexes of the nucleic acid bases appeared to be stabilized mainly by the delocalization component of the intermolecular interaction energy which, in terms of symmetry adapted perturbation theory, encompasses the second- and higher-order induction and exchange-induction terms. Furthermore, it was found that the dispersion contribution, albeit much smaller in terms of magnitude, is also a vital stabilizing factor. It was also revealed that the intermolecular interaction energy and its components are strongly influenced by four (out of six) structural parameters describing mutual orientation of bases in Watson-Crick pairs, namely shear, stagger, stretch, and opening. Finally, as a part of a model study, much of the effort was devoted to an extensive testing of the UBDB databank. It was shown that the databank quite successfully reproduces the electrostatic energy determined with the aid of ab initio methods.

Sharing electronic structure and crystallographic data with ETSF_IO

NASA Astrophysics Data System (ADS)

Caliste, D.; Pouillon, Y.; Verstraete, M. J.; Olevano, V.; Gonze, X.

2008-11-01

We present a library of routines whose main goal is to read and write exchangeable files (NetCDF file format) storing electronic structure and crystallographic information. It is based on the specification agreed inside the European Theoretical Spectroscopy Facility (ETSF). Accordingly, this library is nicknamed ETSF_IO. The purpose of this article is to give both an overview of the ETSF_IO library and a closer look at its usage. ETSF_IO is designed to be robust and easy to use, close to Fortran read and write routines. To facilitate its adoption, a complete documentation of the input and output arguments of the routines is available in the package, as well as six tutorials explaining in detail various possible uses of the library routines. Catalogue identifier: AEBG_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEBG_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Gnu Lesser General Public License No. of lines in distributed program, including test data, etc.: 63 156 No. of bytes in distributed program, including test data, etc.: 363 390 Distribution format: tar.gz Programming language: Fortran 95 Computer: All systems with a Fortran95 compiler Operating system: All systems with a Fortran95 compiler Classification: 7.3, 8 External routines: NetCDF, http://www.unidata.ucar.edu/software/netcdf Nature of problem: Store and exchange electronic structure data and crystallographic data independently of the computational platform, language and generating software Solution method: Implement a library based both on NetCDF file format and an open specification (http://etsf.eu/index.php?page=standardization)

Transuranic Hybrid Materials: Crystallographic and Computational Metrics of Supramolecular Assembly

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

Surbella, Robert G.; Ducati, Lucas C.; Pellegrini, Kristi L.

A family of twelve supramolecular [AnO2Cl4]2- (An = U, Np, Pu) containing compounds assembled via hydrogen and halogen bonds donated by substituted 4-X-pyridinium cations (X = H, Cl, Br, I) is reported. These materials were prepared from a room-temperature synthesis wherein crystallization of unhydrolyzed and valence pure [An(VI)O2Cl4]2- (An = U, Np, Pu) tectons are the norm. We present a hierarchy of assembly criteria based on crystallographic observations, and subsequently quantify the strengths of the non-covalent interactions using Kohn-Sham density functional calculations. We provide, for the first time, a detailed description of the electrostatic potentials (ESPs) of the actinyl tetrahalidemore » dianions and reconcile crystallographically observed structural motifs and non-covalent interaction (NCI) acceptor-donor pairings. Our findings indicate that the average electrostatic potential across the halogen ligands (the acceptors) changes by only ~2 kJ mol-1 across the AnO22+ series, indicating the magnitude of the potential is independent of the metal center. The role of the cation is therefore critical in directing structural motifs and dictating the resulting hydrogen and halogen bond strengths, the former being stronger due to the positive charge centralized on the pyridyl nitrogen N-H+. Subsequent analyses using the Quantum theory of atoms in molecules (QTAIM) and natural bond orbital (NBO) approaches support this conclusion and highlight the structure directing role of the cations. Whereas one can infer that the 2 Columbic attraction is the driver for assembly, the contribution of the non-covalent interaction is to direct the molecular-level arrangement (or disposition) of the tectons.« less

Structural, magnetothermal, and magnetotransport properties of single crystal terbium silicon germanide and spontaneous generation of voltage in single crystal gadolinium silicon germanide and gadolinium

NASA Astrophysics Data System (ADS)

Zou, Min

A systematic study of single crystalline Tb5Si2.2Ge1.8, including magnetic field induced crystallographic and magnetic phase transformations, magnetocaloric effect, ferromagnetic short-range correlations, electrical resistivity, magnetoresistance, and spontaneous generation of voltage (SGV) has been presented. A study of SGV in single crystalline Gd5Si2Ge2 and Gd has also been included. The metamagnetic-like transitions and giant magnetocaloric effect were observed with the magnetic field applied parallel to the a- and c-axes, but not the b-axis in a Tb5Si 2.2Ge1.8 single crystal. The in-situ x-ray powder diffraction study indicates that these metamagnetic-like transitions are coupled to a crystallographic phase transformation occurring via strong magnetoelastic interactions. The magnetocrystalline anisotropy plays an important role in this system. Magnetic fields less than 40 kOe can not drive either the magnetic or the crystallographic phase transition to completion for Tb5Si2.2Ge1.8 powder due to the strong single ion anisotropy of Tb. Magnetic field dependencies of the critical temperatures of magnetic phase transitions of Tb5Si2.2Ge1.8 are highly anisotropic for both the main magnetic ordering process occurring around 120 K and a spin reorientation transition at ~70 K. Magnetic-field-induced phase transitions occur with the magnetic field applied isothermally along the a-and b-axes (but not along the c-axis) between 1.8 and 70 K in fields below 70 kOe. Strongly anisotropic thermal irreversibility is observed in the Griffiths phase regime between 120 and 200 K with applied fields ranging from 10 to 1000 Oe. Our data: (1) show that the magnetic and structural phase transitions around 120 K are narrowly decoupled; (2) uncover the anisotropy of ferromagnetic short-range order in the Griffiths phase; and (3) reveal some unusual magnetic domain effects in the long-range ordered state of the Tb5Si2.2Ge1.8 compound. The temperature-magnetic field phase diagrams with field applied along the three major crystallographic directions have been constructed. The positive colossal magnetoresistance (CMR) with a magnitude of ~150% was observed with the magnetic field applied parallel to the a-axis, but not the b- and c-axes in Tb5Si 2.2Ge1.8 single crystals. The electrical resistivity shows a low-temperature high-resistivity behavior (i.e. the resistivity at low temperature is higher after the transformation to the low temperature phase than the resistivity of the phase before the transition) along the a-axis, contrary to those along the b- and c-axes. The positive CMR effect originates from an intrinsic crystallographic phase coexistence state frozen below the Curie Temperature (TC). The differences in the temperature dependencies of electrical resistivities and longitudinal magnetoresistance along the a-axis and those along the b- and c-axes can be explained by the geometry of the phase boundaries at low temperatures, and the inability of the external magnetic field to induce the crystallographic phase transformation along the b- and c-axes. Temperature-induced SGVs were observed along all three principal crystallographic axes of Tb5Si2.2Ge1.8, but not in Gd. Field-induced SGVs were observed with magnetic fields less than 40 kOe applied along the a-axis of Tb5Si2.2Ge1.8, and the c-axis of Gd. The absence of the temperature induced SGV in Gd indicates the key role first-order phase transformations play in the appearance of the effect when temperature varies. The anisotropy of magnetic field induced SGV in Tb5Si2.2Ge1.8 and the existence of field induced SGV in Gd, highlight the importance of the magnetocaloric effect in bringing about the SGV. In single crystal and polycrystalline Gd5Si 2Ge2 during the coupled magneto-structural transformations, reversible and repeatable SGV responses of the materials to the temperature and magnetic field have been observed. The parameters of the response and the magnitude of the signal are anisotropic and rate dependent. The magnitude of the SGV signal, and the critical temperatures and critical magnetic fields at which the SGV occurs vary with the rate of temperature and magnetic field changes.

Structural Genomics of Protein Phosphatases

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

Almo,S.; Bonanno, J.; Sauder, J.

The New York SGX Research Center for Structural Genomics (NYSGXRC) of the NIGMS Protein Structure Initiative (PSI) has applied its high-throughput X-ray crystallographic structure determination platform to systematic studies of all human protein phosphatases and protein phosphatases from biomedically-relevant pathogens. To date, the NYSGXRC has determined structures of 21 distinct protein phosphatases: 14 from human, 2 from mouse, 2 from the pathogen Toxoplasma gondii, 1 from Trypanosoma brucei, the parasite responsible for African sleeping sickness, and 2 from the principal mosquito vector of malaria in Africa, Anopheles gambiae. These structures provide insights into both normal and pathophysiologic processes, including transcriptionalmore » regulation, regulation of major signaling pathways, neural development, and type 1 diabetes. In conjunction with the contributions of other international structural genomics consortia, these efforts promise to provide an unprecedented database and materials repository for structure-guided experimental and computational discovery of inhibitors for all classes of protein phosphatases.« less

New ternary tantalum borides containing boron dumbbells: Experimental and theoretical studies of Ta2OsB2 and TaRuB

NASA Astrophysics Data System (ADS)

Mbarki, Mohammed; Touzani, Rachid St.; Rehorn, Christian W. G.; Gladisch, Fabian C.; Fokwa, Boniface P. T.

2016-10-01

The new ternary transition metal-rich borides Ta2OsB2 and TaRuB have been successfully synthesized by arc-melting the elements in a water-cooled crucible under an argon atmosphere. The crystal structures of both compounds were solved by single-crystal X-ray diffraction and their metal compositions were confirmed by EDX analysis. It was found that Ta2OsB2 and TaRuB crystallize in the tetragonal Nb2OsB2 (space group P4/mnc, no. 128) and the orthorhombic NbRuB (space group Pmma, no. 51) structure types with lattice parameters a=5.878(2) Å, c=6.857(2) Å and a=10.806(2) Å, b=3.196(1) Å, c=6.312(2) Å, respectively. Furthermore, crystallographic, electronic and bonding characteristics have been studied by density functional theory (DFT). Electronic structure relaxation has confirmed the crystallographic parameters while COHP bonding analysis indicates that B2-dummbells are the strongest bonds in both compounds. Moreover, the formation of osmium dumbbells in Ta2OsB2 through a Peierls distortion along the c-axis, is found to be the origin of superstructure formation. Magnetic susceptibility measurements reveal that the two phases are Pauli paramagnets, thus confirming the theoretical DOS prediction of metallic character. Also hints of superconductivity are found in the two phases, however lack of single phase samples has prevented confirmation. Furthermore, the thermodynamic stability of the two modifications of AMB (A=Nb, Ta; M =Ru, Os) are studied using DFT, as new possible phases containing either B4- or B2-units are predicted, the former being the most thermodynamically stable modification.

Automating tasks in protein structure determination with the clipper python module

PubMed Central

McNicholas, Stuart; Croll, Tristan; Burnley, Tom; Palmer, Colin M.; Hoh, Soon Wen; Jenkins, Huw T.; Dodson, Eleanor

2017-01-01

Abstract Scripting programming languages provide the fastest means of prototyping complex functionality. Those with a syntax and grammar resembling human language also greatly enhance the maintainability of the produced source code. Furthermore, the combination of a powerful, machine‐independent scripting language with binary libraries tailored for each computer architecture allows programs to break free from the tight boundaries of efficiency traditionally associated with scripts. In the present work, we describe how an efficient C++ crystallographic library such as Clipper can be wrapped, adapted and generalized for use in both crystallographic and electron cryo‐microscopy applications, scripted with the Python language. We shall also place an emphasis on best practices in automation, illustrating how this can be achieved with this new Python module. PMID:28901669

PDB Editor: a user-friendly Java-based Protein Data Bank file editor with a GUI.

PubMed

Lee, Jonas; Kim, Sung Hou

2009-04-01

The Protein Data Bank file format is the format most widely used by protein crystallographers and biologists to disseminate and manipulate protein structures. Despite this, there are few user-friendly software packages available to efficiently edit and extract raw information from PDB files. This limitation often leads to many protein crystallographers wasting significant time manually editing PDB files. PDB Editor, written in Java Swing GUI, allows the user to selectively search, select, extract and edit information in parallel. Furthermore, the program is a stand-alone application written in Java which frees users from the hassles associated with platform/operating system-dependent installation and usage. PDB Editor can be downloaded from http://sourceforge.net/projects/pdbeditorjl/.

Crystallographic identification of an unexpected by-product in an Ullman's reaction toward biphenyls: 1-(4-hexyloxy-3-hydroxyphenyl)ethanone.

PubMed

Manzano, Veronica E; Baggio, Ricardo; Cukiernik, Fabio D

2015-11-01

The synthesis of 3,3'-diacetoxy-4,4'-bis(hexyloxy)biphenyl following the nickel-modified Ullmann reaction yielded a by-product which was identified successfully by crystallographic analysis as 1-(4-hexyloxy-3-hydroxyphenyl)ethanone, C14H20O3. This unexpected nonbiphenyl by-product exhibited IR, (1)H NMR, (13)C NMR and COSY (correlation spectroscopy) spectra fully consistent with the proposed structure. The compound crystallized in the orthorombic Pbca space group, with two independent formula units in the asymmetric unit (one of which was slightly disordered), and showed a supramolecular architecture in which molecules linked by hydroxy-ethanone O-H···O interactions are organized in columns separated by the aliphatic tails.

Significance of structural changes in proteins: expected errors in refined protein structures.

PubMed Central

Stroud, R. M.; Fauman, E. B.

1995-01-01

A quantitative expression key to evaluating significant structural differences or induced shifts between any two protein structures is derived. Because crystallography leads to reports of a single (or sometimes dual) position for each atom, the significance of any structural change based on comparison of two structures depends critically on knowing the expected precision of each median atomic position reported, and on extracting it for each atom, from the information provided in the Protein Data Bank and in the publication. The differences between structures of protein molecules that should be identical, and that are normally distributed, indicating that they are not affected by crystal contacts, were analyzed with respect to many potential indicators of structure precision, so as to extract, essentially by "machine learning" principles, a generally applicable expression involving the highest correlates. Eighteen refined crystal structures from the Protein Data Bank, in which there are multiple molecules in the crystallographic asymmetric unit, were selected and compared. The thermal B factor, the connectivity of the atom, and the ratio of the number of reflections to the number of atoms used in refinement correlate best with the magnitude of the positional differences between regions of the structures that otherwise would be expected to be the same. These results are embodied in a six-parameter equation that can be applied to any crystallographically refined structure to estimate the expected uncertainty in position of each atom. Structure change in a macromolecule can thus be referenced to the expected uncertainty in atomic position as reflected in the variance between otherwise identical structures with the observed values of correlated parameters. PMID:8563637

Improving Protocols for Protein Mapping through Proper Comparison to Crystallography Data

PubMed Central

Lexa, Katrina W.; Carlson, Heather A.

2013-01-01

Computational approaches to fragment-based drug design (FBDD) can complement experiments and facilitate the identification of potential hot spots along the protein surface. However, the evaluation of computational methods for mapping binding sites frequently focuses upon the ability to reproduce crystallographic coordinates to within a low RMSD threshold. This dependency on the deposited coordinate data overlooks the original electron density from the experiment, thus techniques may be developed based upon subjective - or even erroneous - atomic coordinates. This can become a significant drawback in applications to systems where the location of hot spots is unknown. Based on comparison to crystallographic density, we previously showed that mixed-solvent molecular dynamics (MixMD) accurately identifies the active site for HEWL, with acetonitrile as an organic solvent. Here, we concentrated on the influence of protic solvent on simulation and refined the optimal MixMD approach for extrapolation of the method to systems without established sites. Our results establish an accurate approach for comparing simulations to experiment. We have outlined the most efficient strategy for MixMD, based on simulation length and number of runs. The development outlined here makes MixMD a robust method which should prove useful across a broad range of target structures. Lastly, our results with MixMD match experimental data so well that consistency between simulations and density may be a useful way to aid the identification of probes vs waters during the refinement of future MSCS crystallographic structures. PMID:23327200

Human TTR conformation altered by rhenium tris-carbonyl derivatives.

PubMed

Ciccone, Lidia; Policar, Clotilde; Stura, Enrico A; Shepard, William

2016-09-01

Transthyretin (TTR) is a 54 kDa homotetrameric serum protein that transports thyroxine (T4) and retinol. TTR is potentially amyloidogenic due to homotetramer dissociation into monomeric intermediates that self-assemble as amyloid deposits and insoluble fibrils. Most crystallographic structures, including those of amyloidogenic variants show the same tetramer without major variations in the monomer-monomer interface nor in the volume of the interdimeric cavity. Soaking TTR crystals in a solution containing rhenium tris-carbonyl derivatives yields a TTR conformer never observed before. Only one of the two monomers of the crystallographic dimer is significantly altered, and the inner part of the T4 binding cavity is expanded at one end and shrunk at the other. The result redefines the mechanism of allosteric communication between the two sites, suggesting that negative cooperativity is a function of dimer asymmetry, which can be induced through internal or external binding. An aspect that remains unexplained is why the conformational changes are ubiquitous throughout the crystal although the heavy metal content of the derivatized crystals is relatively low. The conformational changes observed, which include Leu(82), may represent a form of TTR better at scavenging β-Amyloid. At a resolution of 1.69Å, with excellent refinement statistics and well defined electron density for all parts of the structure, it is possible to envisage answering important questions that range from protein cooperative behavior to heavy atom induced protein conformational modifications that can result in crystallographic non-isomorphism. Copyright © 2016 Elsevier Inc. All rights reserved.

On the retrieval of crystallographic information from atom probe microscopy data via signal mapping from the detector coordinate space.

PubMed

Wallace, Nathan D; Ceguerra, Anna V; Breen, Andrew J; Ringer, Simon P

2018-06-01

Atom probe tomography is a powerful microscopy technique capable of reconstructing the 3D position and chemical identity of millions of atoms within engineering materials, at the atomic level. Crystallographic information contained within the data is particularly valuable for the purposes of reconstruction calibration and grain boundary analysis. Typically, analysing this data is a manual, time-consuming and error prone process. In many cases, the crystallographic signal is so weak that it is difficult to detect at all. In this study, a new automated signal processing methodology is demonstrated. We use the affine properties of the detector coordinate space, or the 'detector stack', as the basis for our calculations. The methodological framework and the visualisation tools are shown to be superior to the standard method of crystallographic pole visualisation directly from field evaporation images and there is no requirement for iterations between a full real-space initial tomographic reconstruction and the detector stack. The mapping approaches are demonstrated for aluminium, tungsten, magnesium and molybdenum. Implications for reconstruction calibration, accuracy of crystallographic measurements, reliability and repeatability are discussed. Copyright © 2018 Elsevier B.V. All rights reserved.

Raman and infrared spectroscopic study of the anhydrous carbonate minerals shortite and barytocalcite.

PubMed

Frost, Ray L; Dickfos, Marilla J

2008-11-01

The Raman spectra of shortite and barytocalcite complimented with infrared spectra have been used to characterise the structure of these carbonate minerals. The Raman spectrum of barytocalcite shows a single band at 1086 cm(-1) attributed to the (CO3)(2-) symmetric stretching mode, in contrast to shortite where two bands are observed. The observation of two bands for shortite confirms the concept of more than one crystallographically distinct carbonate unit in the unit cell. Multiple bands are observed for the antisymmetric stretching and bending region for these minerals proving that the carbonate unit is distorted in the structure of both shortite and barytocalcite.

Spacer conformation in biologically active molecules. Part 1. Structure and conformational preferences of 2-substituted benzoxazoles

NASA Astrophysics Data System (ADS)

Czylkowski, R.; Karolak-Wojciechowska, J.; Mrozek, A.; Yalçin, I.; Aki-Şener, E.

2001-12-01

The mutual position of two pharmacophoric elements in flexible biologically active molecules depends on the spacer conformation. This is true even for a two-atomic chain put to use as a spacer. It was established for 2-substituted-benzoxazoles containing two aromatic centres joined by -CH2-X- (X=S or O). From crystallographic studies of four molecules it was found that the role of heteroatom is essential for the whole molecule conformation. The spacer with X=S adopts the (-)synclinal conformation while for X=O the (+)antiperiplanar one. Such preferences were also found in the statistical data from Cambridge Structural Database (CSD).

Withanolides from Jaborosa caulescens var. bipinnatifida

PubMed Central

Zhang, Huaping; Cao, Cong-Mei; Gallagher, Robert J.; Day, Victor W.; Montenegro, Gloria; Timmermann, Barbara N.

2013-01-01

Two new withanolides 2,3-dihydrotrechonolide A (1) and 2,3-dihydro-21-hydroxytrechonolide A (2) were isolated along with two known withanolides trechonolide A (3) and jaborosalactone 39 (4) from Jaborosa caulescens var. bipinnatifida (Solanaceae). The structures of 1-2 were elucidated through 2D NMR and other spectroscopic techniques. In addition, the structure of withanolide 1 was confirmed by X-ray crystallographic analysis. PMID:24314746

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.)

Structural Insight into the Clostridium difficile Ethanolamine Utilisation Microcompartment

PubMed Central

Faulds-Pain, Alexandra; Lewis, Richard J.; Marles-Wright, Jon

2012-01-01

Bacterial microcompartments form a protective proteinaceous barrier around metabolic enzymes that process unstable or toxic chemical intermediates. The genome of the virulent, multidrug-resistant Clostridium difficile 630 strain contains an operon, eut, encoding a bacterial microcompartment with genes for the breakdown of ethanolamine and its utilisation as a source of reduced nitrogen and carbon. The C. difficile eut operon displays regulatory genetic elements and protein encoding regions in common with homologous loci found in the genomes of other bacteria, including the enteric pathogens Salmonella enterica and Enterococcus faecalis. The crystal structures of two microcompartment shell proteins, CD1908 and CD1918, and an uncharacterised protein with potential enzymatic activity, CD1925, were determined by X-ray crystallography. CD1908 and CD1918 display the same protein fold, though the order of secondary structure elements is permuted in CD1908 and this protein displays an N-terminal β-strand extension. These proteins form hexamers with molecules related by crystallographic and non-crystallographic symmetry. The structure of CD1925 has a cupin β-barrel fold and a putative active site that is distinct from the metal-ion dependent catalytic cupins. Thin-section transmission electron microscopy of Escherichia coli over-expressing eut proteins indicates that CD1918 is capable of self-association into arrays, suggesting an organisational role for CD1918 in the formation of this microcompartment. The work presented provides the basis for further study of the architecture and function of the C. difficile eut microcompartment, its role in metabolism and the wider consequences of intestinal colonisation and virulence in this pathogen. PMID:23144756

Capturing the Complexity of Additively Manufactured Microstructures

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

Livescu, Veronica; Bronkhorst, Curt Allan; Vander Wiel, Scott Alan

2016-05-12

The underlying mechanisms and kinetics controlling damage nucleation and growth as a function of material microstructure and loading paths are discussed. These experiments indicate that structural features such as grain boundaries, grain size distribution, grain morphology crystallographic texture are all factors that influence mechanical behavior.

Synthesis and structural characterisation of a novel phosphine-borane-stabilised dicarbanion and an unusual bis(phosphine-borane).

PubMed

Izod, Keith; McFarlane, William; Tyson, Brent V; Clegg, William; Harrington, Ross W

2004-03-07

The reaction between the phosphine-borane-substituted alkene [Pr(n)(2)P(BH(3))](Me(3)Si)C[double bond]CH(2) and elemental lithium in THF yields the complex [(pmdeta)Li[Pr(n)(2)P(BH(3))](Me(3)Si)CCH(2)](2)(2b) after recrystallisation; an X-ray crystallographic study of 2b reveals that the lithium is bound to the BH(3) hydrogens of the ligand, with no Li-C(carbanion) contact.

Phaser crystallographic software.

PubMed

McCoy, Airlie J; Grosse-Kunstleve, Ralf W; Adams, Paul D; Winn, Martyn D; Storoni, Laurent C; Read, Randy J

2007-08-01

Phaser is a program for phasing macromolecular crystal structures by both molecular replacement and experimental phasing methods. The novel phasing algorithms implemented in Phaser have been developed using maximum likelihood and multivariate statistics. For molecular replacement, the new algorithms have proved to be significantly better than traditional methods in discriminating correct solutions from noise, and for single-wavelength anomalous dispersion experimental phasing, the new algorithms, which account for correlations between F(+) and F(-), give better phases (lower mean phase error with respect to the phases given by the refined structure) than those that use mean F and anomalous differences DeltaF. One of the design concepts of Phaser was that it be capable of a high degree of automation. To this end, Phaser (written in C++) can be called directly from Python, although it can also be called using traditional CCP4 keyword-style input. Phaser is a platform for future development of improved phasing methods and their release, including source code, to the crystallographic community.

Crystallization and initial crystallographic characterization of the Corynebacterium glutamicum nitrilotriacetate monooxygenase component A

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

Kim, Kyung-Jin, E-mail: kkj@postech.ac.kr; Kim, Sujin; Lee, Sujin

2006-11-01

The Corynebacterium glutamicum NTA monooxygenase component A protein, which plays the central role in NTA biodegradation, was crystallized. The initial X-ray crystallographic characterization is reported. Safety and environmental concerns have recently dictated the proper disposal of nitrilotriacetate (NTA). Biodegradation of NTA is initiated by NTA monooxygenase, which is composed of two proteins: component A and component B. The NTA monooxygenase component A protein from Corynebacterium glutamicum was crystallized using the sitting-drop vapour-diffusion method in the presence of ammonium sulfate as the precipitant. X-ray diffraction data were collected to a maximum resolution of 2.5 Å on a synchrotron beamline. The crystalmore » belongs to the monoclinic space group C2, with unit-cell parameters a = 111.04, b = 98.51, c = 171.61 Å, β = 101.94°. The asymmetric unit consists of four molecules, corresponding to a packing density of 2.3 Å{sup 3} Da{sup −1}. The structure was solved by molecular replacement. Structure refinement is in progress.« less

Reintroducing electrostatics into macromolecular crystallographic refinement: application to neutron crystallography and DNA hydration.

PubMed

Fenn, Timothy D; Schnieders, Michael J; Mustyakimov, Marat; Wu, Chuanjie; Langan, Paul; Pande, Vijay S; Brunger, Axel T

2011-04-13

Most current crystallographic structure refinements augment the diffraction data with a priori information consisting of bond, angle, dihedral, planarity restraints, and atomic repulsion based on the Pauli exclusion principle. Yet, electrostatics and van der Waals attraction are physical forces that provide additional a priori information. Here, we assess the inclusion of electrostatics for the force field used for all-atom (including hydrogen) joint neutron/X-ray refinement. Two DNA and a protein crystal structure were refined against joint neutron/X-ray diffraction data sets using force fields without electrostatics or with electrostatics. Hydrogen-bond orientation/geometry favors the inclusion of electrostatics. Refinement of Z-DNA with electrostatics leads to a hypothesis for the entropic stabilization of Z-DNA that may partly explain the thermodynamics of converting the B form of DNA to its Z form. Thus, inclusion of electrostatics assists joint neutron/X-ray refinements, especially for placing and orienting hydrogen atoms. Copyright © 2011 Elsevier Ltd. All rights reserved.

Reintroducing Electrostatics into Macromolecular Crystallographic Refinement: Application to Neutron Crystallography and DNA Hydration

PubMed Central

Fenn, Timothy D.; Schnieders, Michael J.; Mustyakimov, Marat; Wu, Chuanjie; Langan, Paul; Pande, Vijay S.; Brunger, Axel T.

2011-01-01

Summary Most current crystallographic structure refinements augment the diffraction data with a priori information consisting of bond, angle, dihedral, planarity restraints and atomic repulsion based on the Pauli exclusion principle. Yet, electrostatics and van der Waals attraction are physical forces that provide additional a priori information. Here we assess the inclusion of electrostatics for the force field used for all-atom (including hydrogen) joint neutron/X-ray refinement. Two DNA and a protein crystal structure were refined against joint neutron/X-ray diffraction data sets using force fields without electrostatics or with electrostatics. Hydrogen bond orientation/geometry favors the inclusion of electrostatics. Refinement of Z-DNA with electrostatics leads to a hypothesis for the entropic stabilization of Z-DNA that may partly explain the thermodynamics of converting the B form of DNA to its Z form. Thus, inclusion of electrostatics assists joint neutron/X-ray refinements, especially for placing and orienting hydrogen atoms. PMID:21481775

Coexisting nanoscale inverse spinel and rock salt crystallographic phases in NiCo2O4 epitaxial thin films grown by pulsed laser deposition

NASA Astrophysics Data System (ADS)

Sharona, H.; Loukya, B.; Bhat, U.; Sahu, R.; Vishal, B.; Silwal, P.; Gupta, A.; Datta, R.

2017-12-01

The origin of alternating wavy dark-bright stripe-like contrast in strain contrast transmission electron microscopy images of NiCo2O4 (NCO) epitaxial thin films grown by pulsed laser deposition has been investigated. The nanoscale stripe-like pattern is determined to be associated with coexisting rock salt (RS) and inverse spinel crystal phases. The presence of two different phases, not addressed in previous reports, is experimentally confirmed by both electron diffraction and high resolution transmission electron microscopy imaging. First principles based calculations, together with compressive strain present in the films, support the formation of such coexisting crystallographic phases in NCO. Similar microstructural patterns and RS structure are not observed in epitaxial films of two other oxides of the spinel family, namely, NiFe2O4 and CoFe2O4. A correlation between the coexisting structures and the macroscopic physical properties of NCO is discussed.

Optical determination of crystal phase in semiconductor nanocrystals

PubMed Central

Lim, Sung Jun; Schleife, André; Smith, Andrew M.

2017-01-01

Optical, electronic and structural properties of nanocrystals fundamentally derive from crystal phase. This is especially important for polymorphic II–VI, III–V and I-III-VI2 semiconductor materials such as cadmium selenide, which exist as two stable phases, cubic and hexagonal, each with distinct properties. However, standard crystallographic characterization through diffraction yields ambiguous phase signatures when nanocrystals are small or polytypic. Moreover, diffraction methods are low-throughput, incompatible with solution samples and require large sample quantities. Here we report the identification of unambiguous optical signatures of cubic and hexagonal phases in II–VI nanocrystals using absorption spectroscopy and first-principles electronic-structure theory. High-energy spectral features allow rapid identification of phase, even in small nanocrystals (∼2 nm), and may help predict polytypic nanocrystals from differential phase contributions. These theoretical and experimental insights provide simple and accurate optical crystallographic analysis for liquid-dispersed nanomaterials, to improve the precision of nanocrystal engineering and improve our understanding of nanocrystal reactions. PMID:28513577

A Study on the Interaction of Rhodamine B with Methylthioadenosine Phosphorylase Protein Sourced from an Antarctic Soil Metagenomic Library

PubMed Central

Bujacz, Anna; Wierzbicka-Woś, Anna; Kur, Józef

2013-01-01

The presented study examines the phenomenon of the fluorescence under UV light excitation (312 nm) of E. coli cells expressing a novel metagenomic-derived putative methylthioadenosine phosphorylase gene, called rsfp, grown on LB agar supplemented with a fluorescent dye rhodamine B. For this purpose, an rsfp gene was cloned and expressed in an LMG194 E. coli strain using an arabinose promoter. The resulting RSFP protein was purified and its UV-VIS absorbance spectrum and emission spectrum were assayed. Simultaneously, the same spectroscopic studies were carried out for rhodamine B in the absence or presence of RSFP protein or native E. coli proteins, respectively. The results of the spectroscopic studies suggested that the fluorescence of E. coli cells expressing rsfp gene under UV illumination is due to the interaction of rhodamine B molecules with the RSFP protein. Finally, this interaction was proved by a crystallographic study and then by site-directed mutagenesis of rsfp gene sequence. The crystal structures of RSFP apo form (1.98 Å) and complex RSFP/RB (1.90 Å) show a trimer of RSFP molecules located on the crystallographic six fold screw axis. The RSFP complex with rhodamine B revealed the binding site for RB, in the pocket located on the interface between symmetry related monomers. PMID:23383268

Crystallographic and magnetic structure of the novel compound ErGe 1.83

NASA Astrophysics Data System (ADS)

Oleksyn, O.; Schobinger-Papamantellos, P.; Ritter, C.; de Groot, C. H.; Buschow, K. H. J.

1997-02-01

The crystal structure and the magnetic ordering of the novel orthorhombic compound ErGe 2-x has been studied by neutron powder diffraction and magnetic measurements. The crystal structure belongs to the DyGe 1.85-type (space group Cmc2 1)·ErGe 2-x ( x = 0.17 (2)) orders antiferromagnetically below TN = 6 K and displays a metamagnetic behaviour. The magnetic cell has the same size as the chemical unit cell ( q = 0 ). The magnetic space group is Cmc2 1 (Sh 36173). At T = 1.5 K the magnetic moments of the two erbium sites have the same ordered magnetic moment values of 7.63 (6) μB/Er and are antiferromagnetically coupled leading to an uniaxial structure along the a direction.

Crystallographic and Molecular Dynamics Analysis of Loop Motions Unmasking the Peptidoglycan-Binding Site in Stator Protein MotB of Flagellar Motor

PubMed Central

Nahar, Musammat F.; Buckle, Ashley M.; Roujeinikova, Anna

2011-01-01

Background The C-terminal domain of MotB (MotB-C) shows high sequence similarity to outer membrane protein A and related peptidoglycan (PG)-binding proteins. It is believed to anchor the power-generating MotA/MotB stator unit of the bacterial flagellar motor to the peptidoglycan layer of the cell wall. We previously reported the first crystal structure of this domain and made a puzzling observation that all conserved residues that are thought to be essential for PG recognition are buried and inaccessible in the crystal structure. In this study, we tested a hypothesis that peptidoglycan binding is preceded by, or accompanied by, some structural reorganization that exposes the key conserved residues. Methodology/Principal Findings We determined the structure of a new crystalline form (Form B) of Helicobacter pylori MotB-C. Comparisons with the existing Form A revealed conformational variations in the petal-like loops around the carbohydrate binding site near one end of the β-sheet. These variations are thought to reflect natural flexibility at this site required for insertion into the peptidoglycan mesh. In order to understand the nature of this flexibility we have performed molecular dynamics simulations of the MotB-C dimer. The results are consistent with the crystallographic data and provide evidence that the three loops move in a concerted fashion, exposing conserved MotB residues that have previously been implicated in binding of the peptide moiety of peptidoglycan. Conclusion/Significance Our structural analysis provides a new insight into the mechanism by which MotB inserts into the peptidoglycan mesh, thus anchoring the power-generating complex to the cell wall. PMID:21533052

On the control of the crystallographic texture in cladding tubes from Zr-based alloys for nuclear reactor

NASA Astrophysics Data System (ADS)

Isaenkova, M.; Perlovich, Yu.; Fesenko, V.

2016-10-01

This paper summarizes researches of authors, directed to the development of the methodological basis of X-ray studies as applied to zirconium alloys and on the systematization of new experimental results obtained using developed methods. The paper describes regularities of crystallographic texture formation in cladding tubes from zirconium alloys and their substructure inhomogeneity at various stages of manufacture, i.e. at hot and cold deformation, recrystallization, phase transformations and interaction of the above processes. The special attention is payed to possibilities of control the crystallographic texture of tubes at successive stages of their technological treatment.

Role of tryptophan 95 in substrate specificity and structural stability of Sulfolobus solfataricus alcohol dehydrogenase.

PubMed

Pennacchio, Angela; Esposito, Luciana; Zagari, Adriana; Rossi, Mosè; Raia, Carlo A

2009-09-01

A mutant of the thermostable NAD(+)-dependent (S)-stereospecific alcohol dehydrogenase from Sulfolobus solfataricus (SsADH) which has a single substitution, Trp95Leu, located at the substrate binding pocket, was fully characterized to ascertain the role of Trp95 in discriminating between chiral secondary alcohols suggested by the wild-type SsADH crystallographic structure. The Trp95Leu mutant displays no apparent activity with short-chain primary and secondary alcohols and poor activity with aromatic substrates and coenzyme. Moreover, the Trp --> Leu substitution affects the structural stability of the archaeal ADH, decreasing its thermal stability without relevant changes in secondary structure. The double mutant Trp95Leu/Asn249Tyr was also purified to assist in crystallographic analysis. This mutant exhibits higher activity but decreased affinity toward aliphatic alcohols, aldehydes as well as NAD(+) and NADH compared to the wild-type enzyme. The crystal structure of the Trp95Leu/Asn249Tyr mutant apo form, determined at 2.0 A resolution, reveals a large local rearrangement of the substrate site with dramatic consequences. The Leu95 side-chain conformation points away from the catalytic metal center and the widening of the substrate site is partially counteracted by a concomitant change of Trp117 side chain conformation. Structural changes at the active site are consistent with the reduced activity on substrates and decreased coenzyme binding.

Three new tetranorditerpenes from aerial parts of acerola cherry (Malpighia emarginata).

PubMed

Liu, Jie-Qing; Deng, Yuan-Yuan; Li, Ting-Zhao; Han, Qiang; Li, Yan; Qiu, Ming-Hua

2014-02-24

Acerola cherry is a world famous fruit which contains abundant antioxidants such as vitamin C, anthocyanins, flavonoids, and phenolics. However, studies concerning bioactivity components from aerial parts of acerola (Malpighia emarginata) are scarce. In view of this, we have examined the constituents of aerial parts of acerola, and three new tetranorditerpenes acerolanins A-C (1-3) with a rare 2H-benz[e]inden-2-one substructure were isolated. Their structures were determined on the basis of spectral studies and acerolanin C was confirmed by X-ray crystallographic analysis. Furthermore, three new compounds have been studied for their cytotoxic activity.

Push-pull quinoidal porphyrins.

PubMed

Smith, Martin J; Blake, Iain M; Clegg, William; Anderson, Harry L

2018-05-01

A family of push-pull quinoidal porphyrin monomers has been prepared from a meso-formyl porphyrin by bromination, thioacetal formation, palladium-catalyzed coupling with malononitrile and oxidation with DDQ. Attempts at extending this synthesis to a push-pull quinoidal/cumulenic porphyrin dimer were not successful. The crystal structures of the quinoidal porphyrins indicate that there is no significant contribution from singlet biradical or zwitterionic resonance forms. The crystal structure of an ethyne-linked porphyrin dimer shows that the torsion angle between the porphyrin units is only about 3°, in keeping with crystallographic results on related compounds, but contrasting with the torsion angle of about 35° predicted by computational studies. The free-base quinoidal porphyrin monomers form tightly π-stacked layer structures, despite their curved geometries and bulky aryl substituents.

Evolution of the mössbauer spectra of ludwigite Co3 - x Fe x O2BO3 with substitution of iron for cobalt

NASA Astrophysics Data System (ADS)

Knyazev, Yu. V.; Ivanova, N. B.; Bayukov, O. A.; Kazak, N. V.; Bezmaternykh, L. N.; Vasiliev, A. D.

2013-06-01

A concentration series of single crystals of iron-cobalt ludwigites Co3 - x Fe x O2BO3 ( x = 0.0125, 0.025, 0.050, 0.10, 1.0) has been synthesized. The structure has been studied using X-ray diffraction and Mössbauer effect. A preferred occupation of nonequivalent crystallographic positions by iron in the ludwigite structure has been revealed. It has been found that the valence of substituting iron ions is three. It has been revealed that the structure of the γ-resonance spectrum of Co2FeO2BO3 is complicated due to a composition disorder in the system.

Building a model of the blue cone pigment based on the wild type rhodopsin structure with QM/MM methods.

PubMed

Frähmcke, Jan S; Wanko, Marius; Elstner, Marcus

2012-03-15

Understanding the mechanism of color tuning of the retinal chromophore by its host protein became one of the key issues in the research on rhodopsins. While early mutation studies addressed its genetic origin, recent studies advanced to investigate its structural origin, based on X-ray crystallographic structures. For the human cone pigments, no crystal structures have been produced, and homology models were employed to elucidate the origin of its blue-shifted absorption. In this theoretical study, we take a different route to establish a structural model for human blue. Starting from the well-resolved structure of bovine rhodopsin, we derive multiple mutant models by stepwise mutation and equilibration using molecular dynamics simulations in a hybrid quantum mechanics/molecular mechanics framework. Our 30fold mutant reproduces the experimental UV-vis absorption shift of 0.45 eV and provides new insights about both structural and genetic factors that affect the excitation energy. Electrostatic effects of individual amino acids and collaborative structural effects are analyzed using semiempirical (OM2/MRCI) and ab initio (SORCI) multireference approaches. © 2012 American Chemical Society

Experimental and theoretical evidence of a supercritical-like transition in an organic semiconductor presenting colossal uniaxial negative thermal expansion† †Electronic supplementary information (ESI) available: Diffraction and crystallography, Cambridge Structural Database survey, DFT computational details, UV spectroscopy, differential scanning calorimetry, and optical microscopy. CCDC 1810678–1810688. For ESI and crystallographic data in CIF or other electronic format see DOI: 10.1039/c8sc00159f

PubMed Central

Roche, Gilles H.; Wantz, Guillaume; Moreau, Joël J. E.; Dautel, Olivier J.; Filhol, Jean-Sébastien

2018-01-01

Thermal expansion coefficients of most materials are usually small, typically up to 50 parts per million per kelvin, and positive, i.e. materials expand when heated. Some materials show an atypical shrinking behavior in one or more crystallographic directions when heated. Here we show that a high mobility thiophene-based organic semiconductor, BHH-BTBT, has an exceptionally large negative expansion between 95 and 295 K (–216 < α2 = αb < –333 MK–1), being compensated by an even larger positive expansion in the perpendicular direction (287 < α1 < 634 MK–1). It is shown that these anomalous expansivities are completely absent in C8-BTBT, a much studied organic semiconductor with a closely related molecular formula and 3D crystallographic structure. Complete theoretical characterization of BHH-BTBT using ab initio molecular dynamics shows that below ∼200 K two different α and β domains exist of which one is dominant but which dynamically exchange around and above 210 K. A supercritical-like transition from an α dominated phase to a β dominated phase is observed using DSC measurements, UV-VIS spectroscopy, and X-ray diffraction. The origin of the extreme negative and positive thermal expansion is related to steric hindrance between adjacent tilted thiophene units and strongly enhanced by attractive S···S and S···C interactions within the highly anharmonic mixed-domain phase. This material could trigger the tailoring of optoelectronic devices highly sensitive to strain and temperature. PMID:29780527

Synthesis, crystal structure, and magnetic characterization of the three-dimensional compound [Co2(cbut)(H2O)3]n (H4cbut = 1,2,3,4-cyclobutanetetracarboxylic acid).

PubMed

Díaz-Gallifa, Pau; Fabelo, Oscar; Pasán, Jorge; Cañadillas-Delgado, Laura; Rodríguez-Carvajal, Juan; Lloret, Francesc; Julve, Miguel; Ruiz-Pérez, Catalina

2014-06-02

A novel cobalt(II) complex of formula [Co2(cbut)(H2O)3]n (1) (H4cbut = 1,2,3,4-cyclobutanetetracarboxylic acid) has been synthesized under hydrothermal conditions and its crystal structure has been determined by means of synchrotron radiation and neutron powder diffraction. The crystal structure of 1 consists of layers of cobalt(II) ions extending in the bc-plane which are pillared along the crystallographic a-axis through the skeleton of the cbut(4-) ligand. Three crystallographically independent cobalt(II) ions [Co(1), Co(2), and Co(3)] occur in 1. They are all six-coordinate with four carboxylate-oxygens [Co(1)-Co(3)] and two cis-[Co(1)] or trans-water molecules [Co(2) and Co(3)] building distorted octahedral surroundings. Regular alternating double oxo(carboxylate) [between Co(1) and Co(1a)] and oxo(carboxylate) plus one aqua and a syn-syn carboxylate bridges [between Co(1) and Co(2)] occur along the crystallographic b-axis, the values of the cobalt-cobalt separation being 3.1259(8) and 3.1555(6) Å, respectively. These chains are connected to the Co(3) atoms through the OCO carboxylate along the [011] direction leading to the organic-inorganic bc-layers with Co(1)-OCO(anti-syn)-Co(3) and Co(2)-OCO(anti-anti)-Co(3) distances of 5.750(2) and 4.872(1) Å. The shortest interlayer cobalt-cobalt separation through the cbut(4-) skeleton along the crystallographic a-axis is 7.028(2) Å. Variable-temperature magnetic susceptibility measurements show the occurrence of antiferromagnetic ordering with a Néel temperature of 5.0 K, followed by a field-induced ferromagnetic transition under applied dc fields larger than 1500 Oe. The magnetic structure of 1 has been elucidated at low temperatures in zero field by neutron powder diffraction measurements and was found to be formed by ferromagnetic chains running along the b-axis which are antiferromagnetically coupled with the Co(3) ions through the c-axis giving rise to noncompensated magnetic moments within each bc-layer (ferrimagnetic plane). The occurrence of an antitranslation operation between these layers produces a weak interlayer antiferromagnetic coupling along the a-axis which is overcome by dc fields greater than 1500 Oe resulting in a phase transition toward a ferromagnetic state (metamagnetic behavior).

Bacterial expression of the phosphodiester-binding site of the cation-independent mannose 6-phosphate receptor for crystallographic and NMR studies

PubMed Central

Olson, Linda J.; Jensen, Davin R.; Volkman, Brian F.; Kim, Jung-Ja P.; Peterson, Francis C.; Gundry, Rebekah L.; Dahms, Nancy M.

2015-01-01

The cation-independent mannose 6-phosphate receptor (CI-MPR) is a multifunctional protein that interacts with diverse ligands and plays central roles in autophagy, development, and tumor suppression. By delivering newly synthesized phosphomannosyl-containing acid hydrolases from the Golgi to endosomal compartments, CI-MPR is an essential component in the generation of lysosomes that are critical for the maintenance of cellular homeostasis. The ability of CI-MPR to interact with ~60 different acid hydrolases is facilitated by its large extracellular region, with four out of its 15 domains binding phosphomannosyl residues. Although the glycan specificity of CI-MPR has been elucidated, the molecular basis of carbohydrate binding has not been determined for two out of these four carbohydrate recognition domains (CRD). Here we report expression of CI-MPR’s CRD located in domain 5 that preferentially binds phosphodiester-containing glycans. Domain 5 of CI-MPR was expressed in Escherichia coli BL21 (DE3) cells as a fusion protein containing an N-terminal histidine tag and the small ubiquitin-like modifier (SUMO) protein. The His6-SUMO-CRD construct was recovered from inclusion bodies, refolded in buffer to facilitate disulfide bond formation, and subjected to Ni-NTA affinity chromatography and size exclusion chromatography. Surface plasmon resonance analyses demonstrated that the purified protein was active and bound phosphorylated glycans. Characterization by NMR spectroscopy revealed high quality 1H–15N HSQC spectra. Additionally, crystallization conditions were identified and a crystallographic data set of the CRD was collected to 1.8 Å resolution. Together, these studies demonstrate the feasibility of producing CI-MPR’s CRD suitable for three-dimensional structure determination by NMR spectroscopic and X-ray crystallographic approaches. PMID:25863146

Synthesis and characterization of 3-acetoxy-2-methyl-N-(phenyl)benzamide and 3-acetoxy-2-methyl-N-(4- methylphenyl)benzamide

NASA Astrophysics Data System (ADS)

Kırca, Başak Koşar; Çakmak, Şükriye; Kütük, Halil; Odabaşoğlu, Mustafa; Büyükgüngör, Orhan

2018-01-01

This study treats about two successfully synthesized secondary amide compounds 3-Acetoxy-2-methyl-N-(phenyl)benzamide, I and 3-Acetoxy-2-methyl-N-(4-methylphenyl)benzamide, II. Compounds were characterized by FTIR, 1H NMR, 13C NMR and X-ray single crystal diffraction analysis techniques. Single crystal X-ray diffraction analyses show that while I crystallized in the orthorhombic system with space group Pbca, II crystallized in the triclinic system with space group P-1 and the asymmetric unit of II consists of two crystallographically independent molecules. Lattice constants are a = 7.9713 (3) Å, b = 9.5059 (3) Å, c = 37.1762 (2) Å, Z = 8 for I and a = 7.5579 (8) Å, b = 8.8601 (8) Å, c = 23.363 (3) Å, α = 97.011 (9) °, β = 96.932 (9)°, γ = 90.051 (8)°, Z = 4 for II. Crystallographic studies also show that the supramolecular structures were stabilized by intramolecular, intermolecular hydrogen bonds and Csbnd H … π interactions for both compounds. Characteristic amide bonds were observed in IR and NMR spectra.

Synthetic, enzyme kinetic, and protein crystallographic studies of C-β-d-glucopyranosyl pyrroles and imidazoles reveal and explain low nanomolar inhibition of human liver glycogen phosphorylase.

PubMed

Kantsadi, Anastassia L; Bokor, Éva; Kun, Sándor; Stravodimos, George A; Chatzileontiadou, Demetra S M; Leonidas, Demetres D; Juhász-Tóth, Éva; Szakács, Andrea; Batta, Gyula; Docsa, Tibor; Gergely, Pál; Somsák, László

2016-11-10

C-β-d-Glucopyranosyl pyrrole derivatives were prepared in the reactions of pyrrole, 2-, and 3-aryl-pyrroles with O-peracetylated β-d-glucopyranosyl trichloroacetimidate, while 2-(β-d-glucopyranosyl) indole was obtained by a cross coupling of O-perbenzylated β-d-glucopyranosyl acetylene with N-tosyl-2-iodoaniline followed by spontaneous ring closure. An improved synthesis of O-perbenzoylated 2-(β-d-glucopyranosyl) imidazoles was achieved by reacting C-glucopyranosyl formimidates with α-aminoketones. The deprotected compounds were assayed with isoforms of glycogen phosphorylase (GP) to show no activity of the pyrroles against rabbit muscle GPb. The imidazoles proved to be the best known glucose derived inhibitors of not only the muscle enzymes (both a and b) but also of the pharmacologically relevant human liver GPa (Ki = 156 and 26 nM for the 4(5)-phenyl and -(2-naphthyl) derivatives, respectively). An X-ray crystallographic study of the rmGPb-imidazole complexes revealed structural features of the strong binding, and also allowed to explain the absence of inhibition for the pyrrole derivatives. Copyright © 2016 Elsevier Masson SAS. All rights reserved.

Crystallization and preliminary X-ray crystallographic study of a 3.8-MDa respiratory supermolecule hemocyanin.

PubMed

Matsuno, Asuka; Gai, Zuoqi; Tanaka, Miyuki; Kato, Koji; Kato, Sanae; Katoh, Tsuyoshi; Shimizu, Takeshi; Yoshioka, Takeya; Kishimura, Hideki; Tanaka, Yoshikazu; Yao, Min

2015-06-01

Many molluscs transport oxygen using a very large cylindrical multimeric copper-containing protein named hemocyanin. The molluscan hemocyanin forms a decamer (cephalopods) or multidecamer (gastropods) of approximately 330-450kDa subunits, resulting in a molecular mass >3.3MDa. Therefore, molluscan hemocyanin is one of the largest proteins. The reason why these organisms use such a large supermolecule for oxygen transport remains unclear. Atomic-resolution X-ray crystallographic analysis is necessary to unveil the detailed molecular structure of this mysterious large molecule. However, its propensity to dissociate in solution has hampered the crystallization of its intact form. In the present study, we successfully obtained the first crystals of an intact decameric molluscan hemocyanin. The diffraction dataset at 3.0-Å resolution was collected by merging the datasets of two isomorphic crystals. Electron microscopy analysis of the dissolved crystals revealed cylindrical particles. Furthermore, self-rotation function analysis clearly showed the presence of a fivefold symmetry with several twofold symmetries perpendicular to the fivefold axis. The absorption spectrum of the crystals showed an absorption peak around 345nm. These results indicated that the crystals contain intact hemocyanin decamers in the oxygen-bound form. Copyright © 2015 Elsevier Inc. All rights reserved.

Influence of buffer-layer construction and substrate orientation on the electron mobilities in metamorphic In{sup 0.70}Al{sup 0.30}As/In{sup 0.76}Ga{sup 0.24}As/In{sup 0.70}Al{sup 0.30}As structures on GaAs substrates

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

Kulbachinskii, V. A., E-mail: kulb@mig.phys.msu.ru; Oveshnikov, L. N.; Lunin, R. A.

The influence of construction of the buffer layer and misorientation of the substrate on the electrical properties of In{sup 0.70}Al{sup 0.30}As/In{sup 0.76}Ga{sup 0.24}As/In{sup 0.70}Al{sup 0.30}As quantum wells on a GaAs substrate is studied. The temperature dependences (in the temperature range of 4.2 K < T < 300 K) and field dependences (in magnetic fields as high as 6 T) of the sample resistances are measured. Anisotropy of the resistances in different crystallographic directions is detected; this anisotropy depends on the substrate orientation and construction of the metamorphic buffer layer. In addition, the Hall effect and the Shubnikov–de Haas effect aremore » studied. The Shubnikov–de Haas effect is used to determine the mobilities of electrons separately in several occupied dimensionally quantized subbands in different crystallographic directions. The calculated anisotropy of mobilities is in agreement with experimental data on the anisotropy of the resistances.« less

CRYSTMET—The NRCC Metals Crystallographic Data File

PubMed Central

Wood, Gordon H.; Rodgers, John R.; Gough, S. Roger; Villars, Pierre

1996-01-01

CRYSTMET is a computer-readable database of critically evaluated crystallographic data for metals (including alloys, intermetallics and minerals) accompanied by pertinent chemical, physical and bibliographic information. It currently contains about 60 000 entries and covers the literature exhaustively from 1913. Scientific editing of the abstracted entries, consisting of numerous automated and manual checks, is done to ensure consistency with related, previously published studies, to assign structure types where necessary and to help guarantee the accuracy of the data and related information. Analyses of the entries and their distribution across key journals as a function of time show interesting trends in the complexity of the compounds studied as well as in the elements they contain. Two applications of CRYSTMET are the identification of unknowns and the prediction of properties of materials. CRYSTMET is available either online or via license of a private copy from the Canadian Scientific Numeric Database Service (CAN/SND). The indexed online search and analysis system is easy and economical to use yet fast and powerful. Development of a new system is under way combining the capabilities of ORACLE with the flexibility of a modern interface based on the Netscape browsing tool. PMID:27805157

Pestaloporonins: Caryophyllene-Derived Sesquiterpenoids from a Fungicolous Isolate of Pestalotiopsis sp.

PubMed

Hwang, In Hyun; Swenson, Dale C; Gloer, James B; Wicklow, Donald T

2015-09-04

Three new sesquiterpenoids (pestaloporonins A-C; 1-3) related to the caryophyllene-derived punctaporonins were isolated from cultures of a fungicolous isolate of Pestalotiopsis sp. The structures of 1-3 were determined by analysis of NMR and HRMS data, and the structure of 1, including its absolute configuration, was confirmed by X-ray crystallographic analysis. Compounds 1 and 2 contain new bicyclic and tricyclic ring systems, respectively.

Electronic structure of Pt-substituted clathrate silicides Ba{sub 8}Pt{sub x}Si{sub 46–x}(x = 4–6)

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

Borshch, N. A., E-mail: n.a.borshch@ya.ru

The results of calculation of the electronic structure of Si-based Pt-substituted clathrates are reported. Calculation is carried out by the linearized-augmented-plane-wave method. The effect of the number of substitutions and their crystallographic position in the unit cell on the electron-energy spectrum and the electronic properties of Pt-substituted clathrates is analyzed.

Discovery and X-ray crystallographic analysis of a spiropiperidine iminohydantoin inhibitor of beta-secretase.

PubMed

Barrow, James C; Stauffer, Shaun R; Rittle, Kenneth E; Ngo, Phung L; Yang, ZhiQiang; Selnick, Harold G; Graham, Samuel L; Munshi, Sanjeev; McGaughey, Georgia B; Holloway, M Katharine; Simon, Adam J; Price, Eric A; Sankaranarayanan, Sethu; Colussi, Dennis; Tugusheva, Katherine; Lai, Ming-Tain; Espeseth, Amy S; Xu, Min; Huang, Qian; Wolfe, Abigail; Pietrak, Beth; Zuck, Paul; Levorse, Dorothy A; Hazuda, Daria; Vacca, Joseph P

2008-10-23

A high-throughput screen at 100 microM inhibitor concentration for the BACE-1 enzyme revealed a novel spiropiperidine iminohydantoin aspartyl protease inhibitor template. An X-ray cocrystal structure with BACE-1 revealed a novel mode of binding whereby the inhibitor interacts with the catalytic aspartates via bridging water molecules. Using the crystal structure as a guide, potent compounds with good brain penetration were designed.

Withanolides from Jaborosa caulescens var. bipinnatifida.

PubMed

Zhang, Huaping; Cao, Cong-Mei; Gallagher, Robert J; Day, Victor W; Montenegro, Gloria; Timmermann, Barbara N

2014-02-01

Withanolides 2,3-dihydrotrechonolide A (1) and 2,3-dihydro-21-hydroxytrechonolide A (2) were isolated along with two known withanolides trechonolide A (3) and jaborosalactone 39 (4) from Jaborosa caulescens var. bipinnatifida (Solanaceae). The structures of 1-2 were elucidated through 2D NMR and other spectroscopic techniques. In addition, the structure of withanolide 1 was confirmed by X-ray crystallographic analysis. Copyright © 2013 Elsevier Ltd. All rights reserved.

A three-dimensional polyhedral unit model for grain boundary structure in fcc metals

NASA Astrophysics Data System (ADS)

Banadaki, Arash Dehghan; Patala, Srikanth

2017-03-01

One of the biggest challenges in developing truly bottom-up models for the performance of polycrystalline materials is the lack of robust quantitative structure-property relationships for interfaces. As a first step in analyzing such relationships, we present a polyhedral unit model to classify the geometrical nature of atomic packing along grain boundaries. While the atomic structure in disordered systems has been a topic of interest for many decades, geometrical analyses of grain boundaries has proven to be particularly challenging because of the wide range of structures that are possible depending on the underlying macroscopic crystallographic character. In this article, we propose an algorithm that can partition the atomic structure into a connected array of three-dimensional polyhedra, and thus, present a three-dimensional polyhedral unit model for grain boundaries. A point-pattern matching algorithm is also provided for quantifying the distortions of the observed grain boundary polyhedral units. The polyhedral unit model is robust enough to capture the structure of high-Σ, mixed character interfaces and, hence, provides a geometric tool for comparing grain boundary structures across the five-parameter crystallographic phase-space. Since the obtained polyhedral units circumscribe the voids present in the structure, such a description provides valuable information concerning segregation sites within the grain boundary. We anticipate that this technique will serve as a powerful tool in the analysis of grain boundary structure. The polyhedral unit model is also applicable to a wide array of material systems as the proposed algorithm is not limited by the underlying lattice structure.

Density functional theory determination of structural and electronic properties of struvite.

PubMed

Romanowski, Zbigniew; Kempisty, Paweł; Prywer, Jolanta; Krukowski, Stanisław; Torzewska, Agnieszka

2010-07-29

Crystallographic structure, total energy, electronic structure, and the most important elastic properties of struvite, NH(4)MgPO(4).6H(2)O, the main component of infectious urinary stones, are presented. The calculations were performed using ab initio full-electron calculations within the density functional theory-generalized gradient approximation (DFT-GGA) framework. The obtained crystallographic symmetry and the calculated lattice parameters and also the elastic constants are in good agreement with the experimental data. The elastic properties are essential for establishing an optimal response of urinary stones during shock-wave lithotripsy. The calculated electronic charge distribution confirms the layered structure of the struvite crystals. The polar character of the crystal, well-known from crystal growth experiments, was also confirmed by the magnitude of spontaneous polarization which was obtained from direct determination of the electrical dipole density. The calculated value of spontaneous polarization is equal to -8.8 microC cm(-2). This feature may play a key role in struvite crystallization, electrically binding the charged active impurities and other active species, and consequently determining urinary stone formation. We also present the results of our own experiment of the mineralization of struvite induced to growth by Proteus bacteria which are mainly isolated from infectious urinary stones.

Crystallographic and kinetic study of riboflavin synthase from Brucella abortus, a chemotherapeutic target with an enhanced intrinsic flexibility

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

Serer, María I.; Bonomi, Hernán R.; Guimarães, Beatriz G.

This work reports crystal structures of trimeric riboflavin synthase from the pathogen B. abortus both as the apo protein and in complex with several ligands of interest. It is shown that ligand binding drives the assembly of the unique active site of the trimer, and these findings are complemented by a detailed kinetic study on this enzyme, in which marked inhibition by substrate and product was observed. Riboflavin synthase (RS) catalyzes the last step of riboflavin biosynthesis in microorganisms and plants, which corresponds to the dismutation of two molecules of 6,7-dimethyl-8-ribityllumazine to yield one molecule of riboflavin and one moleculemore » of 5-amino-6-ribitylamino-2,4(1H,3H)-pyrimidinedione. Owing to the absence of this enzyme in animals and the fact that most pathogenic bacteria show a strict dependence on riboflavin biosynthesis, RS has been proposed as a potential target for antimicrobial drug development. Eubacterial, fungal and plant RSs assemble as homotrimers lacking C{sub 3} symmetry. Each monomer can bind two substrate molecules, yet there is only one active site for the whole enzyme, which is located at the interface between two neighbouring chains. This work reports the crystallographic structure of RS from the pathogenic bacterium Brucella abortus (the aetiological agent of the disease brucellosis) in its apo form, in complex with riboflavin and in complex with two different product analogues, being the first time that the structure of an intact RS trimer with bound ligands has been solved. These crystal models support the hypothesis of enhanced flexibility in the particle and also highlight the role of the ligands in assembling the unique active site. Kinetic and binding studies were also performed to complement these findings. The structural and biochemical information generated may be useful for the rational design of novel RS inhibitors with antimicrobial activity.« less

Rietveld Refinement on X-Ray Diffraction Patterns of Bioapatite in Human Fetal Bones

PubMed Central

Meneghini, Carlo; Dalconi, Maria Chiara; Nuzzo, Stefania; Mobilio, Settimio; Wenk, Rudy H.

2003-01-01

Bioapatite, the main constituent of mineralized tissue in mammalian bones, is a calcium-phosphate-based mineral that is similar in structure and composition to hydroxyapatite. In this work, the crystallographic structure of bioapatite in human fetuses was investigated by synchrotron radiation x-ray diffraction (XRD) and microdiffraction (μ-XRD) techniques. Rietveld refinement analyses of XRD and μ-XRD data allow for quantitative probing of the structural modifications of bioapatite as functions of the mineralization process and gestational age. PMID:12609904

Electromagnetic Characterization Of Metallic Sensory Alloy

NASA Technical Reports Server (NTRS)

Wincheski, Russell A.; Simpson, John; Wallace, Terryl A.; Newman, John A.; Leser, Paul; Lahue, Rob

2012-01-01

Ferromagnetic shape-memory alloy (FSMA) particles undergo changes in both electromagnetic properties and crystallographic structure when strained. When embedded in a structural material, these attributes can provide sensory output of the strain state of the structure. In this work, a detailed characterization of the electromagnetic properties of a FSMA under development for sensory applications is performed. In addition, a new eddy current probe is used to interrogate the electromagnetic properties of individual FSMA particles embedded in the sensory alloy during controlled fatigue tests on the multifunctional material.

Electromagnetic characterization of metallic sensory alloy

NASA Astrophysics Data System (ADS)

Wincheski, Buzz; Simpson, John; Wallace, Terryl; Newman, Andy; Leser, Paul; Lahue, Rob

2013-01-01

Ferromagnetic shape-memory alloy (FSMA) particles undergo changes in both electromagnetic properties and crystallographic structure when strained. When embedded in a structural material, these attributes can provide sensory output of the strain state of the structure. In this work, a detailed characterization of the electromagnetic properties of a FSMA under development for sensory applications is performed. In addition, a new eddy current probe is used to interrogate the electromagnetic properties of individual FSMA particles embedded in the sensory alloy during controlled fatigue tests on the multifunctional material.

Loop conformation and dynamics of the Escherichia coli HPPK apo-enzyme and its binary complex with MgATP.

PubMed

Yang, Rong; Lee, Matthew C; Yan, Honggao; Duan, Yong

2005-07-01

Comparison of the crystallographic and NMR structures of 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase (HPPK) suggests that the enzyme may undergo significant conformational change upon binding to its first substrate, ATP. Two of the three surface loops (loop 2 and loop 3) accounting for most of the conformational differences appear to be confined by crystal contacts, raising questions about the putative large-scale induced-fit conformational change of HPPK and the functional roles of the conserved side-chain residues on the loops. To investigate the loop dynamics in crystal-free environment, we carried out molecular dynamics and locally enhanced sampling simulations of the apo-enzyme and the HPPK.MgATP complex. Our simulations showed that the crystallographic B-factors underestimated the loop dynamics considerably. We found that the open-conformation of loop 3 in the binary complex is accessible to the apo-enzyme and is the favored conformation in solution phase. These results revise our previous view of HPPK-substrate interactions and the associated functional mechanism of conformational change. The lessons learned here offer valuable structural insights into the workings of HPPK and should be useful for structure-based drug design.

ForceGen 3D structure and conformer generation: from small lead-like molecules to macrocyclic drugs

NASA Astrophysics Data System (ADS)

Cleves, Ann E.; Jain, Ajay N.

2017-05-01

We introduce the ForceGen method for 3D structure generation and conformer elaboration of drug-like small molecules. ForceGen is novel, avoiding use of distance geometry, molecular templates, or simulation-oriented stochastic sampling. The method is primarily driven by the molecular force field, implemented using an extension of MMFF94s and a partial charge estimator based on electronegativity-equalization. The force field is coupled to algorithms for direct sampling of realistic physical movements made by small molecules. Results are presented on a standard benchmark from the Cambridge Crystallographic Database of 480 drug-like small molecules, including full structure generation from SMILES strings. Reproduction of protein-bound crystallographic ligand poses is demonstrated on four carefully curated data sets: the ConfGen Set (667 ligands), the PINC cross-docking benchmark (1062 ligands), a large set of macrocyclic ligands (182 total with typical ring sizes of 12-23 atoms), and a commonly used benchmark for evaluating macrocycle conformer generation (30 ligands total). Results compare favorably to alternative methods, and performance on macrocyclic compounds approaches that observed on non-macrocycles while yielding a roughly 100-fold speed improvement over alternative MD-based methods with comparable performance.

Preliminary Crystallographic Study of Hemoglobin from Buffalo (Bubalus bubalis): A Low Oxygen Affinity Species.

PubMed

Balasubramanian, Moovarkumudalvan; Moorthy, Ponnuraj Sathya; Neelagandan, Kamariah; Ponnuswamy, Mondikalipudur Nanjappa Gounder

2009-01-01

Hemoglobin is a tetrameric, iron-containing metalloprotein, which plays a vital role in the transportation of oxygen from lungs to tissues and carbon dioxide back to lungs. Though good amount of work has already been done on hemoglobins, the scarcity of data on three dimensional structures pertaining to low oxygen affinity hemoglobins from mammalian species, motivated our group to work on this problem specifically. Herein, we report the preliminary crystallographic analysis of buffalo hemoglobin, which belongs to low oxygen affinity species. The buffalo blood was collected, purified by anion exchange chromatography and crystallized with PEG 3350 using 50mM phosphate buffer at pH 6.7 as a precipitant by hanging drop vapor diffusion method. Data collection was carried out using mar345dtb image plate detector system. Buffalo hemoglobin crystallizes in orthorhombic space group P2(1)2(1)2(1) with one whole biological molecule (alpha2beta2) in the asymmetric unit with cell dimensions a=63.064A, b=74.677A, c=110.224A.

Solvent and temperature effects on crambin, a hydrophobic protein

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

Llinas, M.; Lecomte, J.T.J.; De Marco, A.

1980-10-01

Crambin, a 5000-mol. wt. water-insoluble protein found in crambe abyssinica seeds is presently being studied by x-ray diffraction to 0.9 A resolution and /sup 1/H-nuclear magnetic resonance (NMR) spectroscopy. Preliminary /sup 1/H-NMR data at 250 and 600 MHz have suggested that this hydrophobic protein retains a similar globular conformation in both glacial acetic acid (AA), a Bronsted acid, and dimethylformamide (DMF), a Lewis base. These observations suggest that the globular conformation observed in these organic solvents is most likely the native structure present in the crystalline state. As suggested by the high intrinsic resolution of the crystallographic x-ray diffraction pattern,more » and demonstrated by the NMR data, crambin is a very rigid protein. Work is in progress to assign the /sup 1/H-resonances and to correlate H and /sup 13/C NMR dynamic data with the crystallographic model. It is hoped that unravelling conformational features of this hydrophobic protein will provide clues to help us understand other membrane-bound functional proteins.« less

High-level expression, purification, crystallization and preliminary X-ray crystallographic studies of the receptor binding domain of botulinum neurotoxin serotype D

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

Zhang, Yanfeng; Gao, Xiaoli; Qin, Lin

2010-12-01

Botulinum neurotoxins (BoNTs) are highly toxic proteins for humans and can cause neuroparalytic disease botulism. Due to the limitations of production and manipulation of holoenzymes, expressing non-toxic heavy chain receptor binding domains (HCR) has become a common strategy for vaccine and antibody development. Meanwhile, large quantities and highly purified soluble proteins are required for research areas such as antibody maturation and structural biology. We present high level expression and purification of the BoNT serotype D HCR in E. coli using a codon-optimized cDNA. By varying expression conditions, especially at low temperature, the protein was expressed at a high level withmore » high solubility. About 150-200 mg protein was purified to >90% purity from 1 L cell culture. The recombinant D_HCR was crystallized and the crystals diffracted to 1.65 Å resolution. The crystals belong to space group P212121 with unit cell dimensions a = 60.8 Å, b = 89.7 Å, c = 93.9 Å. Preliminary crystallographic data analysis revealed one molecule in asymmetric unit.« less

Magnetic exchange bias of more than 1 Tesla in a natural mineral intergrowth.

PubMed

McEnroe, Suzanne A; Carter-Stiglitz, Brian; Harrison, Richard J; Robinson, Peter; Fabian, Karl; McCammon, Catherine

2007-10-01

Magnetic exchange bias is a phenomenon whereby the hysteresis loop of a 'soft' magnetic phase is shifted by an amount H(E) along the applied field axis owing to its interaction with a 'hard' magnetic phase. Since the discovery of exchange bias fifty years ago, the development of a general theory has been hampered by the uncertain nature of the interfaces between the hard and soft phases, commonly between an antiferromagnetic phase and a ferro- or ferrimagnetic phase. Exchange bias continues to be the subject of investigation because of its technological applications and because it is now possible to manipulate magnetic materials at the nanoscale. Here we present the first documented example of exchange bias of significant magnitude (>1 T) in a natural mineral. We demonstrate that exchange bias in this system is due to the interaction between coherently intergrown magnetic phases formed through a natural process of phase separation during slow cooling over millions of years. Transmission electron microscopy studies show that these intergrowths have a known crystallographic orientation with a known crystallographic structure and that the interfaces are coherent.

29Si-NMR study of magnetic anisotropy and hyperfine interactions in the uranium-bsed ferromagnet UNiSi2

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

Sakai, Hironori; Baek, Seung H; Bauer, Eric D

2009-01-01

UNiSi{sub 2} orders ferromagnetically below T{sub Curie} = 95 K. This material crystallizes in the orthorhombic CeNiSi{sub 2}-type structure. The uranium atoms form double-layers, which are stacked along the crystallographic b axis (the longest axis). From magnetization measurement the easy (hard) magnetization axis is found to be the c axis (b axis). {sup 29}Si-NMR measurements have been performed in the paramagnetic state. In UNiSi{sub 2}, two crystallographic Si sites exist with orthorhombic local symmetry. The Knight shifts on each Si site have been estimated from the spectra of random and oriented powders. The transferred hyperfine couplings have been also derived.more » It is found that the transferred hyperfine coupling constants on each Si site are nearly isotropic, and that their Knight shift anisotropy comes from that of the bulk susceptibility. The nuclear-spin lattice relaxation rate 1/T{sub 1} shows temperature-independent behavior, which indicates the existence of localized 5f electron.« less

Atomic structure and chemistry of human serum albumin

NASA Technical Reports Server (NTRS)

He, Xiao M.; Carter, Daniel C.

1992-01-01

The three-dimensional structure of human serum albumin has been determined crystallographically to a resolution of 2.8 A. It comprises three homologous domains that assemble to form a heart-shaped molecule. Each domain is a product of two subdomains that possess common structural motifs. The principal regions of ligand binding to human serum albumin are located in hydrophobic cavities in subdomains IIA and ILIA, which exhibit similar chemistry. The structure explains numerous physical phenomena and should provide insight into future pharmacokinetic and genetically engineered therapeutic applications of serum albumin.

Effect of wet grinding on structural properties of ball clay

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

Purohit, A., E-mail: anuradha.purohit34@gmail.com; Chander, S.; Dhaka, M. S.

2015-05-15

In this paper, the effect of wet grinding on structural properties of ball clay is undertaken. The wet grinding treatment was performed employing ball and vibro mills for different time spells of 2, 4, 8 and 16 hours. The structural properties were carried out using X-ray diffraction (XRD). The structure of ground samples is found to be simple cubic. The crystallographic parameters are calculated and slight change in lattice constant, inter planner spacing and particle size is observed with grinding treatment. The results are in agreement with the available literature.

Atomic structure and chemistry of human serum albumin

NASA Astrophysics Data System (ADS)

He, Xiao Min; Carter, Daniel C.

1992-07-01

The three-dimensional structure of human serum albumin has been determined crystallographically to a resolution of 2.8 Å. It comprises three homologous domains that assemble to form a heart-shaped molecule. Each domain is a product of two subdomains that possess common structural motifs. The principal regions of ligand binding to human serum albumin are located in hydrophobic cavities in subdomains IIA and IIIA, which exhibit similar chemistry. The structure explains numerous physical phenomena and should provide insight into future pharmacokinetic and genetically engineered therapeutic applications of serum albumin.

Correlation of microstructure and thermo-mechanical properties of a novel hydrogen transport membrane

NASA Astrophysics Data System (ADS)

Zhang, Yongjun

A key part of the FutureGen concept is to support the production of hydrogen to fuel a "hydrogen economy," with the use of clean burning hydrogen in power-producing fuel cells, as well as for use as a transportation fuel. One of the key technical barriers to FutureGen deployment is reliable and efficient hydrogen separation technology. Most Hydrogen Transport Membrane (HTM) research currently focuses on separation technology and hydrogen flux characterization. No significant work has been performed on thermo-mechanical properties of HTMs. The objective of the thesis is to understand the structure-property correlation of HTM and to characterize (1) thermo mechanical properties under different reducing environments and thermal cycles (thermal shock), and (2) evaluate the stability of the novel HTM material. A novel HTM cermet bulk sample was characterized for its physical and mechanical properties at both room temperature and at elevated temperature up to 1000°C. Micro-structural properties and residual stresses were evaluated in order to understand the changing mechanism of the microstructure and its effects on the mechanical properties of materials. A correlation of the microstructural and thermo mechanical properties of the HTM system was established for both HTM and the substrate material. Mechanical properties of both selected structural ceramics and the novel HTM cermet bulk sample are affected mainly by porosity and microstructural features, such as grain size and pore size-distribution. The Young's Modulus (E-value) is positively correlated to the flexural strength for materials with similar crystallographic structure. However, for different crystallographic materials, physical properties are independent of mechanical properties. Microstructural properties, particularly, grain size and crystallographic structure, and thermodynamic properties are the main factors affecting the mechanical properties at both room and high temperatures. The HTM cermet behaves more like an elastic material at room temperature and as a ductile material at temperature above 850°C. The oxidation and the plasticity of Pd phase mainly affected the mechanical properties of HTM cermet at high temperature, also as a result of thermal cycling. Residual stress induced in the HTM by thermo cycles also plays a very critical role in defining the thermo-mechanical properties.

Crystal structure of the sweet-tasting protein thaumatin II at 1.27 A

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

Masuda, Tetsuya, E-mail: t2masuda@kais.kyoto-u.ac.jp; Department Natural Resources, Graduate School of Global Environmental Studies, Kyoto University, Uji, Kyoto 611-0011; Ohta, Keisuke

2011-07-08

Highlights: {yields} X-ray crystallographic structure of sweet-tasting protein, thaumatin II, was determined at a resolution of 1.27 A. {yields} The overall structure of thaumatin II is similar to that of thaumatin I, but a slight shift of the C{alpha} atom of G96 in thaumatin II was observed. {yields} The side chain of two critical residues, 67 and 82, for sweetness was modeled in two alternative conformations. {yields} The flexibility and fluctuation of side chains at 67 and 82 seems to be suitable for interaction of thaumatin molecules with sweet receptors. -- Abstract: Thaumatin, an intensely sweet-tasting protein, elicits a sweetmore » taste sensation at 50 nM. Here the X-ray crystallographic structure of one of its variants, thaumatin II, was determined at a resolution of 1.27 A. Overall structure of thaumatin II is similar to thaumatin I, but a slight shift of the C{alpha} atom of G96 in thaumatin II was observed. Furthermore, the side chain of residue 67 in thaumatin II is highly disordered. Since residue 67 is one of two residues critical to the sweetness of thaumatin, the present results suggested that the critical positive charges at positions 67 and 82 are disordered and the flexibility and fluctuation of these side chains would be suitable for interaction of thaumatin molecules with sweet receptors.« less

Prediction of molecular crystal structures by a crystallographic QM/MM model with full space-group symmetry.

PubMed

Mörschel, Philipp; Schmidt, Martin U

2015-01-01

A crystallographic quantum-mechanical/molecular-mechanical model (c-QM/MM model) with full space-group symmetry has been developed for molecular crystals. The lattice energy was calculated by quantum-mechanical methods for short-range interactions and force-field methods for long-range interactions. The quantum-mechanical calculations covered the interactions within the molecule and the interactions of a reference molecule with each of the surrounding 12-15 molecules. The interactions with all other molecules were treated by force-field methods. In each optimization step the energies in the QM and MM shells were calculated separately as single-point energies; after adding both energy contributions, the crystal structure (including the lattice parameters) was optimized accordingly. The space-group symmetry was maintained throughout. Crystal structures with more than one molecule per asymmetric unit, e.g. structures with Z' = 2, hydrates and solvates, have been optimized as well. Test calculations with different quantum-mechanical methods on nine small organic molecules revealed that the density functional theory methods with dispersion correction using the B97-D functional with 6-31G* basis set in combination with the DREIDING force field reproduced the experimental crystal structures with good accuracy. Subsequently the c-QM/MM method was applied to nine compounds from the CCDC blind tests resulting in good energy rankings and excellent geometric accuracies.

Crystallographically Anisotropic Shape of Forsterite: New Probe for Evaluating Dust Formation History from Infrared Spectroscopy

NASA Astrophysics Data System (ADS)

Takigawa, Aki; Tachibana, Shogo

2012-05-01

Crystalline dust has been observed by infrared spectroscopy around dust-enshrouded asymptotic giant branch stars, in protoplanetary disks, and from some comets. Crystalline materials often have a specific shape related to a specific crystallographic orientation (crystallographically anisotropic shape), which reflects the anisotropic nature of crystals, and their infrared spectral features depend on crystallographically anisotropic shapes. The crystallographically anisotropic shape is thus a potentially powerful probe to evaluate circumstellar dust-forming conditions quantitatively. In order to assess the possibility to determine the crystallographically anisotropic shape from infrared spectra, we calculated mass absorption coefficients for ellipsoidal forsterite particles, the most abundant circumstellar crystalline silicate, elongated and flattened along the crystallographic a-, b-, and c-axes with various aspect ratios in the wavelength range of 9-70 μm. It was found that differences in infrared features caused by various crystallographicaly anisotropic shapes are distinguishable from each other irrespective of the effects of temperature, size, chemical composition, and grain edges of forsterite in the range of 9-12 μm and 15-20 μm. We thus concluded that the crystallographically anisotropic shape of forsterite can be deduced from peak features in infrared spectra. We also showed that the crystallographically anisotropic shapes formed by evaporation and condensation of forsterite can be distinguished from each other and the temperature condition for evaporation can be evaluated from the peak features. We applied the present results to the infrared spectrum of a protoplanetary disk HD100546 and found that a certain fraction (~25%) of forsterite dust may have experienced high-temperature evaporation (>1600 K).

Crystallographic studies of gas sorption in metal–organic frameworks

PubMed Central

Carrington, Elliot J.; Vitórica-Yrezábal, Iñigo J.; Brammer, Lee

2014-01-01

Metal–organic frameworks (MOFs) are a class of porous crystalline materials of modular design. One of the primary applications of these materials is in the adsorption and separation of gases, with potential benefits to the energy, transport and medical sectors. In situ crystallography of MOFs under gas atmospheres has enabled the behaviour of the frameworks under gas loading to be investigated and has established the precise location of adsorbed gas molecules in a significant number of MOFs. This article reviews progress in such crystallographic studies, which has taken place over the past decade, but has its origins in earlier studies of zeolites, clathrates etc. The review considers studies by single-crystal or powder diffraction using either X-rays or neutrons. Features of MOFs that strongly affect gas sorption behaviour are discussed in the context of in situ crystallographic studies, specifically framework flexibility, and the presence of (organic) functional groups and unsaturated (open) metal sites within pores that can form specific interactions with gas molecules. PMID:24892587

Presence of a monoclinic (Pm) phase in the morphotropic phase boundary region of multiferroic (1 − x)Bi(Ni{sub 1/2}Ti{sub 1/2})O{sub 3}-xPbTiO{sub 3} solid solution: A Rietveld study

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

Pandey, Rishikesh, E-mail: akhilesh-bhu@yahoo.com, E-mail: aksingh.mst@itbhu.ac.in; Singh, Akhilesh Kumar, E-mail: akhilesh-bhu@yahoo.com, E-mail: aksingh.mst@itbhu.ac.in

2014-07-28

We present here the results of structural studies on multiferroic (1 − x)Bi(Ni{sub 1/2}Ti{sub 1/2})O{sub 3}-xPbTiO{sub 3} solid solution using Rietveld analysis on powder x-ray diffraction data in the composition range 0.35 ≤ x ≤ 0.55. The stability region of various crystallographic phases at room temperature for (1 − x)Bi(Ni{sub 1/2}Ti{sub 1/2})O{sub 3}-xPbTiO{sub 3} is determined precisely. Structural transformation from pseudo-cubic (x ≤ 0.40) to tetragonal (x ≥ 0.50) phase is observed via phase coexistence region demarcating the morphotropic phase boundary. The morphotropic phase boundary region consists of coexisting tetragonal and monoclinic structures with space group P4mm and Pm, respectively, stable in composition range 0.41 ≤ x ≤ 0.49 as confirmed by Rietveld analysis. The resultsmore » of Rietveld analysis completely rule out the coexistence of rhombohedral and tetragonal phases in the morphotropic phase boundary region reported by earlier workers. A comparison between the bond lengths for “B-site cations-oxygen anions” obtained after Rietveld refinement, with the bond length calculated using Shannon-Prewitt ionic radii, reveals the ionic nature of B-O (Ni/Ti-O) bonds for the cubic phase and partial covalent character for the other crystallographic phases.« less

Bivalent ligands derived from Huperzine A as acetylcholinesterase inhibitors.

PubMed

Haviv, H; Wong, D M; Silman, I; Sussman, J L

2007-01-01

The naturally occurring alkaloid Huperzine A (HupA) is an acetylcholinesterase (AChE) inhibitor that has been used for centuries as a Chinese folk medicine in the context of its source plant Huperzia Serrata. The potency and relative safety of HupA rendered it a promising drug for the ameliorative treatment of Alzheimer's disease (AD) vis-à-vis the "cholinergic hypothesis" that attributes the cognitive decrements associated with AD to acetylcholine deficiency in the brain. However, recent evidence supports a neuroprotective role for HupA, suggesting that it could act as more than a mere palliative. Biochemical and crystallographic studies of AChE revealed two potential binding sites in the active-site gorge of AChE, one of which, the "peripheral anionic site" at the mouth of the gorge, was implicated in promoting aggregation of the beta amyloid (Abeta) peptide responsible for the neurodegenerative process in AD. This feature of AChE facilitated the development of dual-site binding HupA-based bivalent ligands, in hopes of concomitantly increasing AChE inhibition potency by utilizing the "chelate effect", and protecting neurons from Abeta toxicity. Crystal structures of AChE allowed detailed modeling and docking studies that were instrumental in enhancing the understanding of underlying principles of bivalent inhibitor-enzyme dynamics. This monograph reviews two categories of HupA-based bivalent ligands, in which HupA and HupA fragments serve as building blocks, with a focus on the recently solved crystallographic structures of Torpedo californica AChE in complex with such bifunctional agents. The advantages and drawbacks of such structured-based drug design, as well as species differences, are highlighted and discussed.

A split-beam probe-pump-probe scheme for femtosecond time resolved protein X-ray crystallography

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

van Thor, Jasper J.; Madsen, Anders

In order to exploit the femtosecond pulse duration of X-ray Free-Electron Lasers (XFEL) operating in the hard X-ray regime for ultrafast time-resolved protein crystallography experiments, critical parameters that determine the crystallographic signal-to-noise (I/σI) must be addressed. For single-crystal studies under low absorbed dose conditions, it has been shown that the intrinsic pulse intensity stability as well as mode structure and jitter of this structure, significantly affect the crystallographic signal-to-noise. Here, geometrical parameters are theoretically explored for a three-beam scheme: X-ray probe, optical pump, X-ray probe (or “probe-pump-probe”) which will allow experimental determination of the photo-induced structure factor amplitude differences, ΔF,more » in a ratiometric manner, thereby internally referencing the intensity noise of the XFEL source. In addition to a non-collinear split-beam geometry which separates un-pumped and pumped diffraction patterns on an area detector, applying an additional convergence angle to both beams by focusing leads to integration over mosaic blocks in the case of well-ordered stationary protein crystals. Ray-tracing X-ray diffraction simulations are performed for an example using photoactive yellow protein crystals in order to explore the geometrical design parameters which would be needed. The specifications for an X-ray split and delay instrument that implements both an offset angle and focused beams are discussed, for implementation of a probe-pump-probe scheme at the European XFEL. We discuss possible extension of single crystal studies to serial femtosecond crystallography, particularly in view of the expected X-ray damage and ablation due to the first probe pulse.« less

A split-beam probe-pump-probe scheme for femtosecond time resolved protein X-ray crystallography

DOE PAGES

van Thor, Jasper J.; Madsen, Anders

2015-01-01

In order to exploit the femtosecond pulse duration of X-ray Free-Electron Lasers (XFEL) operating in the hard X-ray regime for ultrafast time-resolved protein crystallography experiments, critical parameters that determine the crystallographic signal-to-noise (I/σI) must be addressed. For single-crystal studies under low absorbed dose conditions, it has been shown that the intrinsic pulse intensity stability as well as mode structure and jitter of this structure, significantly affect the crystallographic signal-to-noise. Here, geometrical parameters are theoretically explored for a three-beam scheme: X-ray probe, optical pump, X-ray probe (or “probe-pump-probe”) which will allow experimental determination of the photo-induced structure factor amplitude differences, ΔF,more » in a ratiometric manner, thereby internally referencing the intensity noise of the XFEL source. In addition to a non-collinear split-beam geometry which separates un-pumped and pumped diffraction patterns on an area detector, applying an additional convergence angle to both beams by focusing leads to integration over mosaic blocks in the case of well-ordered stationary protein crystals. Ray-tracing X-ray diffraction simulations are performed for an example using photoactive yellow protein crystals in order to explore the geometrical design parameters which would be needed. The specifications for an X-ray split and delay instrument that implements both an offset angle and focused beams are discussed, for implementation of a probe-pump-probe scheme at the European XFEL. We discuss possible extension of single crystal studies to serial femtosecond crystallography, particularly in view of the expected X-ray damage and ablation due to the first probe pulse.« less

A split-beam probe-pump-probe scheme for femtosecond time resolved protein X-ray crystallography

PubMed Central

van Thor, Jasper J.; Madsen, Anders

2015-01-01

In order to exploit the femtosecond pulse duration of X-ray Free-Electron Lasers (XFEL) operating in the hard X-ray regime for ultrafast time-resolved protein crystallography experiments, critical parameters that determine the crystallographic signal-to-noise (I/σI) must be addressed. For single-crystal studies under low absorbed dose conditions, it has been shown that the intrinsic pulse intensity stability as well as mode structure and jitter of this structure, significantly affect the crystallographic signal-to-noise. Here, geometrical parameters are theoretically explored for a three-beam scheme: X-ray probe, optical pump, X-ray probe (or “probe-pump-probe”) which will allow experimental determination of the photo-induced structure factor amplitude differences, ΔF, in a ratiometric manner, thereby internally referencing the intensity noise of the XFEL source. In addition to a non-collinear split-beam geometry which separates un-pumped and pumped diffraction patterns on an area detector, applying an additional convergence angle to both beams by focusing leads to integration over mosaic blocks in the case of well-ordered stationary protein crystals. Ray-tracing X-ray diffraction simulations are performed for an example using photoactive yellow protein crystals in order to explore the geometrical design parameters which would be needed. The specifications for an X-ray split and delay instrument that implements both an offset angle and focused beams are discussed, for implementation of a probe-pump-probe scheme at the European XFEL. We discuss possible extension of single crystal studies to serial femtosecond crystallography, particularly in view of the expected X-ray damage and ablation due to the first probe pulse. PMID:26798786

Modeling of protein binary complexes using structural mass spectrometry data

PubMed Central

Kamal, J.K. Amisha; Chance, Mark R.

2008-01-01

In this article, we describe a general approach to modeling the structure of binary protein complexes using structural mass spectrometry data combined with molecular docking. In the first step, hydroxyl radical mediated oxidative protein footprinting is used to identify residues that experience conformational reorganization due to binding or participate in the binding interface. In the second step, a three-dimensional atomic structure of the complex is derived by computational modeling. Homology modeling approaches are used to define the structures of the individual proteins if footprinting detects significant conformational reorganization as a function of complex formation. A three-dimensional model of the complex is constructed from these binary partners using the ClusPro program, which is composed of docking, energy filtering, and clustering steps. Footprinting data are used to incorporate constraints—positive and/or negative—in the docking step and are also used to decide the type of energy filter—electrostatics or desolvation—in the successive energy-filtering step. By using this approach, we examine the structure of a number of binary complexes of monomeric actin and compare the results to crystallographic data. Based on docking alone, a number of competing models with widely varying structures are observed, one of which is likely to agree with crystallographic data. When the docking steps are guided by footprinting data, accurate models emerge as top scoring. We demonstrate this method with the actin/gelsolin segment-1 complex. We also provide a structural model for the actin/cofilin complex using this approach which does not have a crystal or NMR structure. PMID:18042684

Orientational anisotropy and interfacial transport in polycrystals

NASA Astrophysics Data System (ADS)

Moghadam, M. M.; Rickman, J. M.; Harmer, M. P.; Chan, H. M.

2016-04-01

Interfacial diffusion is governed to a large degree by geometric parameters that are determined by crystallographic orientation. In this study, we assess the impact of orientational anisotropy on mass transport at internal interfaces, focusing on the role of preferred crystallographic orientation (i.e., texture) on mass diffusion in a polycrystal. More specifically, we perform both numerical and analytical studies of steady-state diffusion for polycrystals having various grain-orientation distributions. By relating grain misorientation to grain-boundary energies and, via the Borisov relation, to the diffusivity, we link microstructure variability to kinetics. Our aim is to correlate shape features of the orientation distribution, such as the location and shapes of peaks, with the calculated effective diffusivity. Finally, we discuss the role of crystallographic constraints, such as those associated with grain junctions, in determining the effective diffusivity of a polycrystal.

Unexpected ferromagnetic interaction in a new tetranuclear copper(II) complex: synthesis, crystal structure, magnetic properties, and theoretical studies.

PubMed

Fondo, Matilde; García-Deibe, Ana M; Corbella, Monstserrat; Ruiz, Eliseo; Tercero, Javier; Sanmartín, Jesús; Bermejo, Manuel R

2005-07-11

The new tetranuclear carbonate complex [Cu2L)2(CO3)] x 8H2O (1 x 8H2O) (H3L = (2-(2-hydroxyphenyl)-1,3-bis[4-(2-hydroxyphenyl)-3-azabut-3-enyl]-1,3-imidazolidine) has been obtained by two different synthetic routes and fully characterized. Recrystallization of 1 x 8H2O in methanol yields single crystals of {[(Cu2L)2(CO3)]}2 x 12H2O (1 x 6H2O), suitable for X-ray diffraction studies. The crystal structure of 1 x 6H2O shows two crystallographically different tetranuclear molecules in the asymmetric unit, 1a and 1b. Both molecules can be understood as self-assembled from two dinuclear [Cu2L]+ cations, joined by a mu4-eta(2):eta(1):eta(1) carbonate ligand. The copper atoms of each crystallographically different [(Cu2L)2(CO3)] molecule present miscellaneous coordination polyhedra: in both 1a and 1b, two metal centers are in square pyramidal environments, one displays a square planar chromophore and the other one has a geometry that can be considered as an intermediate between square pyramid and trigonal bipyramid. Magnetic studies reveal net intramolecular ferromagnetic coupling between the metal atoms. Density functional calculations allow the assignment of the different magnetic coupling constants and explain the unexpected ferromagnetic behavior, because of the presence of an unusual NCN bridging moiety and countercomplementarity of the phenoxo (or carbonate) and NCN bridges.

Studies of high temperature ternary phases in mixed-metal-rich early transition metal sulfide and phosphide systems

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

Marking, Gregory Allen

1994-01-04

Investigations of ternary mixed early transition metal-rich sulfide and phosphide systems resulted in the discovery of new structures and new phases. A new series of Zr and Hf - group V transition metal - sulfur K-phases was synthesized and crystallographically characterized. When the group V transition metal was Nb or Ta, the unit cell volume was larger than any previously reported K-phase. The presence of adventitious oxygen was determined in two K-phases through a combination of neutron scattering and X-ray diffraction experiments. A compound Hf 10Ta 3S 3 was found to crystallize in a new-structure type similar to the knownmore » gamma brasses. This structure is unique in that it is the only reported "stuffed" gamma-brass type structure. The metal components, Hf and Ta, are larger in size and more electropositive than the metals found in normal gamma brasses (e.g. Cu and Zn) and because of the larger metallic radii, sulfur can be incorporated into the structure where it plays an integral role in stabilizing this phase relative to others. X-ray single-crystal, X-ray powder and neutron powder refinements were performed on this structure. A new structure was found in the ternary Nb-Zr-P system which has characteristics in common with many known early transition metal-rich sulfides, selenides, and phosphides. This structure has the simplest known interconnection of the basic building blocks known for this structural class. Anomalous scattering was a powerful tool for differentiating between Zr and Nb when using Mo Kα X-radiation. The compounds ZrNbP and HfNbP formed in the space group Prima with the simple Co 2Si structure which is among the most common structures found for crystalline solid materials. Solid solution compounds in the Ta-Nb-P, Ta-Zr-P, Nb-Zr-P, Hf-Nb-P, and Hf-Zr-S systems were crystallographically characterized. The structural information corroborated ideas about bonding in metal-rich compounds.« less

Controlling the opto-electronic properties of nc-SiOx:H films by promotion of 〈220〉 orientation in the growth of ultra-nanocrystallites at the grain boundary

NASA Astrophysics Data System (ADS)

Das, Debajyoti; Samanta, Subhashis

2018-01-01

A systematic development of undoped nc-SiOx:H thin films from (SiH4 + CO2) plasma diluted by a combination of H2 and He has been investigated through structural, optical and electrical characterization and correlation. Gradual inclusion of O into a highly crystalline silicon network progressively produces a two-phase structure where Si-nanocrystals (Si-nc) are embedded into the a-SiOx:H matrix. However, at the intermediate grain boundary region the growth of ultra-nanocrystallites controls the effectiveness of the material. The ultra-nanocrystallites are the part and portion of crystallinity accommodating the dominant fraction of thermodynamically preferred 〈220〉 crystallographic orientation, most favourable for stacked layer device performance. Atomic H plays a dominant role in maintaining an improved nanocrystalliny in the network even during O inclusion, while He in its excited state (He*) maintains a good energy balance at the grain boundary and produces a significant fraction of ultra-nanocrystalline component which has been demonstrated to organize the energetically favourable 〈220〉 crystallographic orientation in the network. The nc-SiOx:H films, maintaining proportionally good electrical conductivity over an wide range of optical band gap, remarkably low microstructure factor and simultaneous high crystalline volume fraction dominantly populated by ultra-nanocrystallites of 〈220〉 crystallographic orientation mostly at the grain boundary, have been obtained in technologically most popular 13.56 MHz PECVD SiH4 plasma even at a low substrate temperature ∼250 °C, convenient for device fabrication.

Non-destructive mapping of grain orientations in 3D by laboratory X-ray microscopy

PubMed Central

McDonald, S. A.; Reischig, P.; Holzner, C.; Lauridsen, E. M.; Withers, P. J.; Merkle, A. P.; Feser, M.

2015-01-01

The ability to characterise crystallographic microstructure, non-destructively and in three-dimensions, is a powerful tool for understanding many aspects related to damage and deformation mechanisms in polycrystalline materials. To this end, the technique of X-ray diffraction contrast tomography (DCT) using monochromatic synchrotron and polychromatic laboratory X-ray sources has been shown to be capable of mapping crystal grains and their orientations non-destructively in 3D. Here we describe a novel laboratory-based X-ray DCT modality (LabDCT), enabling the wider accessibility of the DCT technique for routine use and in-depth studies of, for example, temporal changes in crystallographic grain structure non-destructively over time through ‘4D’ in situ time-lapse studies. The capability of the technique is demonstrated by studying a titanium alloy (Ti-β21S) sample. In the current implementation the smallest grains that can be reliably detected are around 40 μm. The individual grain locations and orientations are reconstructed using the LabDCT method and the results are validated against independent measurements from phase contrast tomography and electron backscatter diffraction respectively. Application of the technique promises to provide important insights related to the roles of recrystallization and grain growth on materials properties as well as supporting 3D polycrystalline modelling of materials performance. PMID:26494523

Non-destructive mapping of grain orientations in 3D by laboratory X-ray microscopy

NASA Astrophysics Data System (ADS)

McDonald, S. A.; Reischig, P.; Holzner, C.; Lauridsen, E. M.; Withers, P. J.; Merkle, A. P.; Feser, M.

2015-10-01

The ability to characterise crystallographic microstructure, non-destructively and in three-dimensions, is a powerful tool for understanding many aspects related to damage and deformation mechanisms in polycrystalline materials. To this end, the technique of X-ray diffraction contrast tomography (DCT) using monochromatic synchrotron and polychromatic laboratory X-ray sources has been shown to be capable of mapping crystal grains and their orientations non-destructively in 3D. Here we describe a novel laboratory-based X-ray DCT modality (LabDCT), enabling the wider accessibility of the DCT technique for routine use and in-depth studies of, for example, temporal changes in crystallographic grain structure non-destructively over time through ‘4D’ in situ time-lapse studies. The capability of the technique is demonstrated by studying a titanium alloy (Ti-β21S) sample. In the current implementation the smallest grains that can be reliably detected are around 40 μm. The individual grain locations and orientations are reconstructed using the LabDCT method and the results are validated against independent measurements from phase contrast tomography and electron backscatter diffraction respectively. Application of the technique promises to provide important insights related to the roles of recrystallization and grain growth on materials properties as well as supporting 3D polycrystalline modelling of materials performance.

Non-destructive mapping of grain orientations in 3D by laboratory X-ray microscopy.

PubMed

McDonald, S A; Reischig, P; Holzner, C; Lauridsen, E M; Withers, P J; Merkle, A P; Feser, M

2015-10-23

The ability to characterise crystallographic microstructure, non-destructively and in three-dimensions, is a powerful tool for understanding many aspects related to damage and deformation mechanisms in polycrystalline materials. To this end, the technique of X-ray diffraction contrast tomography (DCT) using monochromatic synchrotron and polychromatic laboratory X-ray sources has been shown to be capable of mapping crystal grains and their orientations non-destructively in 3D. Here we describe a novel laboratory-based X-ray DCT modality (LabDCT), enabling the wider accessibility of the DCT technique for routine use and in-depth studies of, for example, temporal changes in crystallographic grain structure non-destructively over time through '4D' in situ time-lapse studies. The capability of the technique is demonstrated by studying a titanium alloy (Ti-β21S) sample. In the current implementation the smallest grains that can be reliably detected are around 40 μm. The individual grain locations and orientations are reconstructed using the LabDCT method and the results are validated against independent measurements from phase contrast tomography and electron backscatter diffraction respectively. Application of the technique promises to provide important insights related to the roles of recrystallization and grain growth on materials properties as well as supporting 3D polycrystalline modelling of materials performance.

Ribbon structure stabilized by C10 and C12 turns in αγ hybrid peptide.

PubMed

Wani, Naiem Ahmad; Kant, Rajni; Gupta, Vivek Kumar; Aravinda, Subrayashastry; Rai, Rajkishor

2016-04-01

The present study describes the synthesis and crystallographic analysis of αγ hybrid peptides, Boc-Gpn-L-Pro-NHMe (1), Boc-Aib-Gpn-L-Pro-NHMe (2), and Boc-L-Pro-Aib-Gpn-L-Pro-NHMe (3). Peptides 1 and 2 adopt expanded 12-membered (C12 ) helical turn over γα segment. Peptide 3 promotes the ribbon structure stabilized by type II β-turn (C10 ) followed by the expanded C12 helical γα turn. Both right-handed and left-handed helical conformations for Aib residue are observed in peptides 2 and 3, respectively. Copyright © 2016 European Peptide Society and John Wiley & Sons, Ltd.

Effect of Various Material Properties on the Adhesive Stage of Fretting

NASA Technical Reports Server (NTRS)

Buckley, D. H.

1974-01-01

Various properties of metals and alloys were studied with respect to their effect on the initial stage of the fretting process, namely adhesion. Crystallographic orientation, crystal structure, interfacial binding energies of dissimiliar metal, segregation of alloy constituents and the nature and structure of surface films were found to influence adhesion. High atomic density, low surface energy grain orientations exhibited lower adhesion than other orientations. Knowledge of interfacial surface binding energies assists in predicting adhesive transfer and wear. Selective surface segregation of alloy constituents accomplishes both a reduction in adhesion and improved surface oxidation characteristics. Equivalent surface coverages of various adsorbed species indicate that some are markedly more effective in inhibiting adhesion than others.

Effects Of Crystallographic Properties On The Ice Nucleation Properties Of Volcanic Ash Particles

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

Kulkarni, Gourihar R.; Nandasiri, Manjula I.; Zelenyuk, Alla

2015-04-28

Specific chemical and physical properties of volcanic ash particles that could affect their ability to induce ice formation are poorly understood. In this study, the ice nucleating properties of size-selected volcanic ash and mineral dust particles in relation to their surface chemistry and crystalline structure at temperatures ranging from –30 to –38 °C were investigated in deposition mode. Ice nucleation efficiency of dust particles was higher compared to ash particles at all temperature and relative humidity conditions. Particle characterization analysis shows that surface elemental composition of ash and dust particles was similar; however, the structural properties of ash samples weremore » different.« less

Precision and accuracy in smFRET based structural studies—A benchmark study of the Fast-Nano-Positioning System

NASA Astrophysics Data System (ADS)

Nagy, Julia; Eilert, Tobias; Michaelis, Jens

2018-03-01

Modern hybrid structural analysis methods have opened new possibilities to analyze and resolve flexible protein complexes where conventional crystallographic methods have reached their limits. Here, the Fast-Nano-Positioning System (Fast-NPS), a Bayesian parameter estimation-based analysis method and software, is an interesting method since it allows for the localization of unknown fluorescent dye molecules attached to macromolecular complexes based on single-molecule Förster resonance energy transfer (smFRET) measurements. However, the precision, accuracy, and reliability of structural models derived from results based on such complex calculation schemes are oftentimes difficult to evaluate. Therefore, we present two proof-of-principle benchmark studies where we use smFRET data to localize supposedly unknown positions on a DNA as well as on a protein-nucleic acid complex. Since we use complexes where structural information is available, we can compare Fast-NPS localization to the existing structural data. In particular, we compare different dye models and discuss how both accuracy and precision can be optimized.

X-Ray Crystallography as a Tool to Determine Three-Dimensional Structures of Commercial Enzymes Subjected to Treatment in Pressurized Fluids.

PubMed

Feiten, Mirian Cristina; Di Luccio, Marco; Santos, Karine F; de Oliveira, Débora; Oliveira, J Vladimir

2017-06-01

The study of enzyme function often involves a multi-disciplinary approach. Several techniques are documented in the literature towards determining secondary and tertiary structures of enzymes, and X-ray crystallography is the most explored technique for obtaining three-dimensional structures of proteins. Knowledge of three-dimensional structures is essential to understand reaction mechanisms at the atomic level. Additionally, structures can be used to modulate or improve functional activity of enzymes by the production of small molecules that act as substrates/cofactors or by engineering selected mutants with enhanced biological activity. This paper presentes a short overview on how to streamline sample preparation for crystallographic studies of treated enzymes. We additionally revise recent developments on the effects of pressurized fluid treatment on activity and stability of commercial enzymes. Future directions and perspectives on the the role of crystallography as a tool to access the molecular mechanisms underlying enzymatic activity modulation upon treatment in pressurized fluids are also addressed.

Crystallographic Studies of Prion Protein (PrP) Segments Suggest How Structural Changes Encoded by Polymorphism at Residue 129 Modulate Susceptibility to Human Prion Disease

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

Apostol, Marcin I.; Sawaya, Michael R.; Cascio, Duilio

2010-09-23

A single nucleotide polymorphism (SNP) in codon 129 of the human prion gene, leading to a change from methionine to valine at residue 129 of prion protein (PrP), has been shown to be a determinant in the susceptibility to prion disease. However, the molecular basis of this effect remains unexplained. In the current study, we determined crystal structures of prion segments having either Met or Val at residue 129. These 6-residue segments of PrP centered on residue 129 are 'steric zippers,' pairs of interacting {beta}-sheets. Both structures of these 'homozygous steric zippers' reveal direct intermolecular interactions between Met or Valmore » in one sheet and the identical residue in the mating sheet. These two structures, plus a structure-based model of the heterozygous Met-Val steric zipper, suggest an explanation for the previously observed effects of this locus on prion disease susceptibility and progression.« less

Combining H/D exchange mass spectroscopy and computational docking reveals extended DNA-binding surface on uracil-DNA glycosylase

PubMed Central

Roberts, Victoria A.; Pique, Michael E.; Hsu, Simon; Li, Sheng; Slupphaug, Geir; Rambo, Robert P.; Jamison, Jonathan W.; Liu, Tong; Lee, Jun H.; Tainer, John A.; Ten Eyck, Lynn F.; Woods, Virgil L.

2012-01-01

X-ray crystallography provides excellent structural data on protein–DNA interfaces, but crystallographic complexes typically contain only small fragments of large DNA molecules. We present a new approach that can use longer DNA substrates and reveal new protein–DNA interactions even in extensively studied systems. Our approach combines rigid-body computational docking with hydrogen/deuterium exchange mass spectrometry (DXMS). DXMS identifies solvent-exposed protein surfaces; docking is used to create a 3-dimensional model of the protein–DNA interaction. We investigated the enzyme uracil-DNA glycosylase (UNG), which detects and cleaves uracil from DNA. UNG was incubated with a 30 bp DNA fragment containing a single uracil, giving the complex with the abasic DNA product. Compared with free UNG, the UNG–DNA complex showed increased solvent protection at the UNG active site and at two regions outside the active site: residues 210–220 and 251–264. Computational docking also identified these two DNA-binding surfaces, but neither shows DNA contact in UNG–DNA crystallographic structures. Our results can be explained by separation of the two DNA strands on one side of the active site. These non-sequence-specific DNA-binding surfaces may aid local uracil search, contribute to binding the abasic DNA product and help present the DNA product to APE-1, the next enzyme on the DNA-repair pathway. PMID:22492624

A multimodal microcharacterisation of trace-element zonation and crystallographic orientation in natural cassiterite by combining cathodoluminescence, EBSD, EPMA and contribution of confocal Raman-in-SEM imaging.

PubMed

Wille, G; Lerouge, C; Schmidt, U

2018-01-16

In cassiterite, tin is associated with metals (titanium, niobium, tantalum, indium, tungsten, iron, manganese, mercury). Knowledge of mineral chemistry and trace-element distribution is essential for: the understanding of ore formation, the exploration phase, the feasibility of ore treatment, and disposal/treatment of tailings after the exploitation phase. However, the availability of analytical methods make these characterisations difficult. We present a multitechnical approach to chemical and structural data that includes scanning electron microscopy (SEM)-based imaging and microanalysis techniques such as: secondary and backscattered electrons, cathodoluminescence (CL), electron probe microanalyser (EPMA), electron backscattered diffraction (EBSD) and confocal Raman-imaging integrated in a SEM (RISE). The presented results show the complementarity of the used analytical techniques. SEM, CL, EBSD, EPMA provide information from the interaction of an electron beam with minerals, leading to atomistic information about their composition, whereas RISE, Raman spectroscopy and imaging completes the studies with information about molecular vibrations, which are sensitive to structural modifications of the minerals. The correlation of Raman bands with the presence/absence of Nb, Ta, Fe (heterovalent substitution) and Ti (homovalent substitution) is established at a submicrometric scale. Combination of the different techniques makes it possible to establish a direct link between chemical and crystallographic data of cassiterite. © 2018 The Authors Journal of Microscopy © 2018 Royal Microscopical Society.

Structure development in melt processing isotactic polypropylene, polypropylene blends/compounds and dynamically vulcanized polyolefin TPEs

NASA Astrophysics Data System (ADS)

Yu, Yishan

The influence of various fillers, nucleating agents and ethylene propylene diene terpolymer (EPDM) additive on crystalline modification (alpha-, beta- and smectic forms) and crystalline orientation of polypropylene in die extrudates, melt spun filaments, thick rods, blow molded bottles and injection molded parts of isotactic polypropylene (PP), its blends/compounds and dynamically vulcanized polypropylene thermoplastic elastomers (TPEs) were experimentally studied under a range of cooling and processing conditions. The phenomena of crystallization, polymorphism and orientation in processing of both thin and thick samples (filaments, rods, bottles and injection molded parts) were simulated through transport laws incorporating polymer crystallization kinetics. Continuous cooling transformation (CCT) curves for the various material systems investigated were developed under quiescent and uniaxial stress conditions. We applied experimental data on polymorphism of thin sections to predict crystalline structure variation in thick parts. The predictions were consistent with experiments. For filaments, the polypropylene crystalline orientation-spinline stress relationship is generally similar for the neat PP, blends/compounds and TPEs. However, the blends and TPEs have much lower birefringence apparently due to a lack of orientation in the rubber phase. It was shown that the polypropylene contribution to the birefringence for the neat PP and its blends is the same at the same spinline stress. For bottles, the inflation pressures used have little effect on orientation of either polypropylene crystals or disc-shaped talc filler. The talc discs are highly oriented parallel to the bottle surface. For the bottles without talc, the orientation of polypropylene crystallographic axes are low. The polypropylene crystallographic b-axes in the talc filled bottles are more highly oriented. For injection molded parts, it was found that a low orientation layer exists between the part surface and an intermediate highly oriented layer in the parts of neat PP and its blends/compounds. The thickness of this layer increases as the injection pressure decreases. This layer was not formed in the TPE parts. This would seem to be associated with the TPEs exhibiting a yield stress in shear flow and not exhibiting fountain flow in mold filling. For all parts studied, the orientation characteristics of polypropylene crystallographic axes in the highly oriented layer are similar from sample to sample. The strong orientation of the c-axis parallel to the machine direction and the b-axis perpendicular to the machine direction are observed in the highly oriented layer. The talc discs in both the highly oriented layer and the intermediate position are highly oriented parallel to the part face due to melt flow. At intermediate position in the talc-filled parts, the polypropylene crystallographic (040) planes prefer to align themselves parallel to the part surface but are not so well oriented when the talc is absent.

Structure-based analysis of CysZ-mediated cellular uptake of sulfate

PubMed Central

Assur Sanghai, Zahra; Liu, Qun; Clarke, Oliver B; Belcher-Dufrisne, Meagan; Wiriyasermkul, Pattama; Giese, M Hunter; Leal-Pinto, Edgar; Kloss, Brian; Tabuso, Shantelle; Love, James; Punta, Marco; Banerjee, Surajit; Rajashankar, Kanagalaghatta R; Rost, Burkhard; Logothetis, Diomedes; Quick, Matthias; Hendrickson, Wayne A

2018-01-01

Sulfur, most abundantly found in the environment as sulfate (SO42-), is an essential element in metabolites required by all living cells, including amino acids, co-factors and vitamins. However, current understanding of the cellular delivery of SO42- at the molecular level is limited. CysZ has been described as a SO42- permease, but its sequence family is without known structural precedent. Based on crystallographic structure information, SO42- binding and flux experiments, we provide insight into the molecular mechanism of CysZ-mediated translocation of SO42- across membranes. CysZ structures from three different bacterial species display a hitherto unknown fold and have subunits organized with inverted transmembrane topology. CysZ from Pseudomonas denitrificans assembles as a trimer of antiparallel dimers and the CysZ structures from two other species recapitulate dimers from this assembly. Mutational studies highlight the functional relevance of conserved CysZ residues. PMID:29792261

Structure-based analysis of CysZ-mediated cellular uptake of sulfate

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

Assur Sanghai, Zahra; Liu, Qun; Clarke, Oliver B.

Sulfur, most abundantly found in the environment as sulfate (SO42-), is an essential element in metabolites required by all living cells, including amino acids, co-factors and vitamins. However, current understanding of the cellular delivery of SO42- at the molecular level is limited. CysZ has been described as a SO42- permease, but its sequence family is without known structural precedent. Based on crystallographic structure information, SO42- binding and flux experiments, we provide insight into the molecular mechanism of CysZ-mediated translocation of SO42- across membranes. CysZ structures from three different bacterial species display a hitherto unknown fold and have subunits organized withmore » inverted transmembrane topology. CysZ from Pseudomonas denitrificans assembles as a trimer of antiparallel dimers and the CysZ structures from two other species recapitulate dimers from this assembly. Mutational studies highlight the functional relevance of conserved CysZ residues.« less

Topological distribution of four-alpha-helix bundles.

PubMed Central

Presnell, S R; Cohen, F E

1989-01-01

The four-alpha-helix bundle, a common structural motif in globular proteins, provides an excellent forum for the examination of predictive constraints for protein backbone topology. An exhaustive examination of the Brookhaven Crystallographic Protein Data Bank and other literature sources has lead to the discovery of 20 putative four-alpha-helix bundles. Application of an analytical method that examines the difference between solvent-accessible surface areas in packed and partially unpacked bundles reduced the number of structures to 16. Angular requirements further reduced the list of bundles to 13. In 12 of these bundles, all pairs of neighboring helices were oriented in an anti-parallel fashion. This distribution is in accordance with structure types expected if the helix macro dipole effect makes a substantial contribution to the stability of the native structure. The characterizations and classifications made in this study prompt a reevaluation of constraints used in structure prediction efforts. Images PMID:2771946

Role of surface energy on the morphology and optical properties of GaP micro & nano structures grown on polar and non-polar substrates

NASA Astrophysics Data System (ADS)

Roychowdhury, R.; Kumar, Shailendra; Wadikar, A.; Mukherjee, C.; Rajiv, K.; Sharma, T. K.; Dixit, V. K.

2017-10-01

Role of surface energy on the morphology, crystalline quality, electronic structure and optical properties of GaP layer grown on Si (001), Si (111), Ge (111) and GaAs (001) is investigated. GaP layers are grown on four different substrates under identical growth kinetics by metal organic vapour phase epitaxy. The atomic force microscopy images show that GaP layer completely covers the surface of GaAs substrate. On the other hand, the surfaces of Si (001), Si (111), Ge (111) substrates are partially covered with crystallographically morphed GaP island type micro and nano-structures. Origin of these crystallographically morphed GaP island is explained by the theoretical calculation of surface energy of the layer and corresponding substrates respectively. The nature of GaP island type micro and nano-structures and layers are single crystalline with existence of rotational twins on Si and Ge (111) substrates which is confirmed by the phi, omega and omega/2theta scans of high resolution x-ray diffraction. The electronic valence band offsets between the GaP and substrates have been determined from the valence band spectra of ultraviolet photoelectron spectroscopy. The valence electron plasmon of GaP are investigated by studying the energy values of Ga (3d) core level along with loss peaks in the energy dependent photoelectron spectra. The peak observed within the range of 3-6 eV from the Ga (3d) core level in the photoelectron spectra are associated to inter band transitions as their energy values are estimated from the pseudo dielectric function by the spectroscopic ellipsometry.

Assigning crystallographic electron densities with free energy calculations—The case of the fluoride channel Fluc

PubMed Central

2018-01-01

Approximately 90% of the structures in the Protein Data Bank (PDB) were obtained by X-ray crystallography or electron microscopy. Whereas the overall quality of structure is considered high, thanks to a wide range of tools for structure validation, uncertainties may arise from density maps of small molecules, such as organic ligands, ions or water, which are non-covalently bound to the biomolecules. Even with some experience and chemical intuition, the assignment of such disconnected electron densities is often far from obvious. In this study, we suggest the use of molecular dynamics (MD) simulations and free energy calculations, which are well-established computational methods, to aid in the assignment of ambiguous disconnected electron densities. Specifically, estimates of (i) relative binding affinities, for instance between an ion and water, (ii) absolute binding free energies, i.e., free energies for transferring a solute from bulk solvent to a binding site, and (iii) stability assessments during equilibrium simulations may reveal the most plausible assignments. We illustrate this strategy using the crystal structure of the fluoride specific channel (Fluc), which contains five disconnected electron densities previously interpreted as four fluoride and one sodium ion. The simulations support the assignment of the sodium ion. In contrast, calculations of relative and absolute binding free energies as well as stability assessments during free MD simulations suggest that four of the densities represent water molecules instead of fluoride. The assignment of water is compatible with the loss of these densities in the non-conductive F82I/F85I mutant of Fluc. We critically discuss the role of the ion force fields for the calculations presented here. Overall, these findings indicate that MD simulations and free energy calculations are helpful tools for modeling water and ions into crystallographic density maps. PMID:29771936

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

Poletika, T. M., E-mail: poletm@ispms.tsc.ru; Girsova, S. L., E-mail: llm@ispms.tsc.ru; Meisner, L. L., E-mail: girs@ispms.tsc.ru

The structure of the surface and near-surface layers of single crystals of NiTi, differently oriented relative to the direction of ion beam treatment was investigated. The role of the crystallographic orientation in formation of structure of surface layers after ion-plasma alloying was revealed. It was found that the orientation effects of selective sputtering and channeling determine the thickness of the oxide and amorphous layers, the depth of penetration of ions and impurities, the distribution of Ni with depth.

Crystallography Open Database – an open-access collection of crystal structures

PubMed Central

Gražulis, Saulius; Chateigner, Daniel; Downs, Robert T.; Yokochi, A. F. T.; Quirós, Miguel; Lutterotti, Luca; Manakova, Elena; Butkus, Justas; Moeck, Peter; Le Bail, Armel

2009-01-01

The Crystallography Open Database (COD), which is a project that aims to gather all available inorganic, metal–organic and small organic molecule structural data in one database, is described. The database adopts an open-access model. The COD currently contains ∼80 000 entries in crystallographic information file format, with nearly full coverage of the International Union of Crystallography publications, and is growing in size and quality. PMID:22477773

Unusual Thermal Stability of High-Entropy Alloy Amorphous Structure

DTIC Science & Technology

2012-06-20

incident angle X - ray diffractometer (GIAXRD, RIGAKU D/MAX2500) with Cu Kα radiation and at the incident angle of 1°. The surface morphology and...microanalyzer (EPMA, JEOL JAX-8800). The crystallographic structures of as-deposited and annealed metallic films were characterized utilizing a glancing ...field image and selected-area- diffraction (SAD) patterns of (a) 800 °C-, (b) 850 °C- and (c) 900 °C-annealed alloy thin films, respectively. Both

Diterpenoid glycosides from the bitter fern Gleichenia quadripartita.

PubMed

Socolsky, Cecilia; Asakawa, Yoshinori; Bardón, Alicia

2007-12-01

Fifteen new diterpenoid glycosides (1a-n, 2) were isolated from an Argentine collection of the bitter fern Gleichenia quadripartita along with the known flavonoid glycoside afzelin. Structure elucidation was accomplished by 1D and 2D NMR spectroscopy and by high-resolution MS analyses. In addition, X-ray crystallographic analysis of a monocrystal of 1a as well as chemical derivatization of 1h and 1m were performed to confirm their structures.

Structure of the bifunctional aminoglycoside-resistance enzyme AAC(6')-Ie-APH(2'')-Ia revealed by crystallographic and small-angle X-ray scattering analysis.

PubMed

Smith, Clyde A; Toth, Marta; Weiss, Thomas M; Frase, Hilary; Vakulenko, Sergei B

2014-10-01

Broad-spectrum resistance to aminoglycoside antibiotics in clinically important Gram-positive staphylococcal and enterococcal pathogens is primarily conferred by the bifunctional enzyme AAC(6')-Ie-APH(2'')-Ia. This enzyme possesses an N-terminal coenzyme A-dependent acetyltransferase domain [AAC(6')-Ie] and a C-terminal GTP-dependent phosphotransferase domain [APH(2'')-Ia], and together they produce resistance to almost all known aminoglycosides in clinical use. Despite considerable effort over the last two or more decades, structural details of AAC(6')-Ie-APH(2'')-Ia have remained elusive. In a recent breakthrough, the structure of the isolated C-terminal APH(2'')-Ia enzyme was determined as the binary Mg2GDP complex. Here, the high-resolution structure of the N-terminal AAC(6')-Ie enzyme is reported as a ternary kanamycin/coenzyme A abortive complex. The structure of the full-length bifunctional enzyme has subsequently been elucidated based upon small-angle X-ray scattering data using the two crystallographic models. The AAC(6')-Ie enzyme is joined to APH(2'')-Ia by a short, predominantly rigid linker at the N-terminal end of a long α-helix. This α-helix is in turn intrinsically associated with the N-terminus of APH(2'')-Ia. This structural arrangement supports earlier observations that the presence of the intact α-helix is essential to the activity of both functionalities of the full-length AAC(6')-Ie-APH(2'')-Ia enzyme.

Crystallographic isomorphism in the structural type of α-HgI{sub 2} by example of KHgI{sub 3} · H{sub 2}O, β-Ag{sub 2}HgI{sub 4}, and β-Cu{sub 2}HgI{sub 4}

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

Borisov, S. V., E-mail: borisov@niic.nsc.ru; Magarill, S. A.; Pervukhina, N. V.

The structure of KHgI{sub 3} · H{sub 2}O is assigned to the family of crystal structures having the three-layer cubic packing of iodine anions with cations in the tetrahedral voids (the structures of α-HgI{sub 2}, β-Ag{sub 2}HgI{sub 4}, and β-Cu{sub 2}HgI{sub 4} among them). Crystallographic analysis shows that the nodes of the three-layer close packing are populated by iodine anions and K cations in the ratio 3/4: 1/4. Transformation of the structure of α-HgI{sub 2} into the structure of KHgI{sub 3} · H{sub 2}O can be formally represented as the replacement of (HgI){sub n}{sup +} fragments by (KH{sub 2}O){sub n}{supmore » +} fragments: (Hg{sub 2}I{sub 4})–(HgI){sup +} + (KH{sub 2}O){sub n}{sup +} = KHgI{sub 3} · H{sub 2}O. Perforated layers of vertex-sharing HgI{sub 4} tetrahedra break down into parallel isolated chains. Channels formed in place of I–Hg–I–Hg–fragments are occupied by–H{sub 2}O–K–-H{sub 2}-O-K-H{sub 2}O-chains weakly bound to neighbors.« less

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

PubMed Central

Sikic, Kresimir; Tomic, Sanja; Carugo, Oliviero

2010-01-01

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

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

Liu, Z.; Gosser, Y; Baker, P

Cutinases are responsible for hydrolysis of the protective cutin lipid polyester matrix in plants and thus have been exploited for hydrolysis of small molecule esters and polyesters. Here we explore the reactivity, stability, and structure of Aspergillus oryzae cutinase and compare it to the well-studied enzyme from Fusarium solani. Two critical differences are highlighted in the crystallographic analysis of the A. oryzae structure: (i) an additional disulfide bond and (ii) a topologically favored catalytic triad with a continuous and deep groove. These structural features of A. oryzae cutinase are proposed to result in an improved hydrolytic activity and altered substratemore » specificity profile, enhanced thermostability, and remarkable reactivity toward the degradation of the synthetic polyester polycaprolactone. The results presented here provide insight into engineering new cutinase-inspired biocatalysts with tailor-made properties.« less

Cholinesterase Confabs and Cousins: Approaching Forty Years

PubMed Central

Taylor, Palmer; De Jaco, Antonella; Comoletti, Davide; Miller, Meghan; Camp, Shelley

2013-01-01

In the past four decades of cholinesterase (ChE) research, we have seen substantive evolution of the field from one centered around substrate and inhibitor kinetic profiles and compound characterizations to the analysis of ChE structure, first through the gene families and then by x-ray crystallographic determinations of the free enzymes and their complexes and conjugates. Indeed, these endeavors have been facilitated by recombinant DNA technologies, structure determinations and parallel studies in related proteins in the α/β-hydrolase fold family. This approach has not only contributed to a fundamental understanding of structure and function of a large family of hydrolase-like proteins possessing functions other than catalysis, but also has been used to develop new practical strategies for scavenging and antidotal activity in cases of organophosphate insecticide or nerve agent exposure. PMID:23085121

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

PubMed

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

2013-01-01

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

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

PubMed Central

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

2013-01-01

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

Structure solution of DNA-binding proteins and complexes with ARCIMBOLDO libraries

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

Pröpper, Kevin; Instituto de Biologia Molecular de Barcelona; Meindl, Kathrin

2014-06-01

The structure solution of DNA-binding protein structures and complexes based on the combination of location of DNA-binding protein motif fragments with density modification in a multi-solution frame is described. Protein–DNA interactions play a major role in all aspects of genetic activity within an organism, such as transcription, packaging, rearrangement, replication and repair. The molecular detail of protein–DNA interactions can be best visualized through crystallography, and structures emphasizing insight into the principles of binding and base-sequence recognition are essential to understanding the subtleties of the underlying mechanisms. An increasing number of high-quality DNA-binding protein structure determinations have been witnessed despite themore » fact that the crystallographic particularities of nucleic acids tend to pose specific challenges to methods primarily developed for proteins. Crystallographic structure solution of protein–DNA complexes therefore remains a challenging area that is in need of optimized experimental and computational methods. The potential of the structure-solution program ARCIMBOLDO for the solution of protein–DNA complexes has therefore been assessed. The method is based on the combination of locating small, very accurate fragments using the program Phaser and density modification with the program SHELXE. Whereas for typical proteins main-chain α-helices provide the ideal, almost ubiquitous, small fragments to start searches, in the case of DNA complexes the binding motifs and DNA double helix constitute suitable search fragments. The aim of this work is to provide an effective library of search fragments as well as to determine the optimal ARCIMBOLDO strategy for the solution of this class of structures.« less

Fatigue 󈨛. Papers presented at the International Conference on Fatigue and Fatigue Threshold (3rd) Held in Charlottesville, Virginia on June 28-July 3, 1987. Volume 3.

DTIC Science & Technology

1987-10-15

cracks and loss of fiber-matrix bond, leadin, to nonuniform loading (tensile overload) of composite structure. Figures 13 through 15 show the micro...propagation within the matrix, and alon- the interface, leading to a nonuniform load transfer from matrix to fibers, and causing tensile overload failure...long cracks, were attributed to high cyclic strains at crack tips within grains of maximum crystallographic orientation. Ma and Laire (4) studying the

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).

On three-dimensional misorientation spaces.

PubMed

Krakow, Robert; Bennett, Robbie J; Johnstone, Duncan N; Vukmanovic, Zoja; Solano-Alvarez, Wilberth; Lainé, Steven J; Einsle, Joshua F; Midgley, Paul A; Rae, Catherine M F; Hielscher, Ralf

2017-10-01

Determining the local orientation of crystals in engineering and geological materials has become routine with the advent of modern crystallographic mapping techniques. These techniques enable many thousands of orientation measurements to be made, directing attention towards how such orientation data are best studied. Here, we provide a guide to the visualization of misorientation data in three-dimensional vector spaces, reduced by crystal symmetry, to reveal crystallographic orientation relationships. Domains for all point group symmetries are presented and an analysis methodology is developed and applied to identify crystallographic relationships, indicated by clusters in the misorientation space, in examples from materials science and geology. This analysis aids the determination of active deformation mechanisms and evaluation of cluster centres and spread enables more accurate description of transformation processes supporting arguments regarding provenance.

On three-dimensional misorientation spaces

NASA Astrophysics Data System (ADS)

Krakow, Robert; Bennett, Robbie J.; Johnstone, Duncan N.; Vukmanovic, Zoja; Solano-Alvarez, Wilberth; Lainé, Steven J.; Einsle, Joshua F.; Midgley, Paul A.; Rae, Catherine M. F.; Hielscher, Ralf

2017-10-01

Determining the local orientation of crystals in engineering and geological materials has become routine with the advent of modern crystallographic mapping techniques. These techniques enable many thousands of orientation measurements to be made, directing attention towards how such orientation data are best studied. Here, we provide a guide to the visualization of misorientation data in three-dimensional vector spaces, reduced by crystal symmetry, to reveal crystallographic orientation relationships. Domains for all point group symmetries are presented and an analysis methodology is developed and applied to identify crystallographic relationships, indicated by clusters in the misorientation space, in examples from materials science and geology. This analysis aids the determination of active deformation mechanisms and evaluation of cluster centres and spread enables more accurate description of transformation processes supporting arguments regarding provenance.

pH-Dependent reversible crystal transformation of 1-carboxymethyl-1-methyl-pyrrolidinium bromides and their spectroscopic fingerprint

NASA Astrophysics Data System (ADS)

Tong, Ya-yan; Zhang, Heng; Chang, Liang-liang; Xuan, Xiao-peng

2018-03-01

In this work, two 1-carboxymethyl-1-methyl-pyrrolidinium bromides (N-methylpyrrolidine betaine hydrobromides) with the stoichiometry of betaine:hydrobromic acid as 1:1 and 2:1, denoted as CMPRHBr-I and CMPRHBr-II, respectively, were prepared and crystallographically determined. The large difference in these two structures is the type of hydrogen bonds, resulting in the different thermal stability. A strong Osbnd H ⋯ Br hydrogen bond was observed in CMPRHBr-I, whereas O ⋯ H ⋯ O hydrogen bond in CMPRHBr-II. Both these two crystals can mutually transform by changing the pH value of the aqueous solution. Vibrational spectroscopic studies shows that these two structures can be easily distinguished by the characteristic bands such as νCdbnd O stretching vibration and the D-type bands. Our studies indicate that it should be cautious of the structural change as this type of organic salts was purified and recrystallized.

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.

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

NASA Astrophysics Data System (ADS)

Haire, L. F.; Gopal, B.

2001-11-01

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

Structural and biochemical analyses of YvgN and YtbE from Bacillus subtilis

PubMed Central

Lei, Jian; Zhou, Yan-Feng; Li, Lan-Fen; Su, Xiao-Dong

2009-01-01

Bacillus subtilis is one of the most studied gram-positive bacteria. In this work, YvgN and YtbE from B. subtilis, assigned as AKR5G1 and AKR5G2 of aldo-keto reductase (AKR) superfamily. AKR catalyzes the NADPH-dependent reduction of aldehyde or aldose substrates to alcohols. YvgN and YtbE were studied by crystallographic and enzymatic analyses. The apo structures of these proteins were determined by molecular replacement, and the structure of holoenzyme YvgN with NADPH was also solved, revealing the conformational changes upon cofactor binding. Our biochemical data suggest both YvgN and YtbE have preferential specificity for derivatives of benzaldehyde, such as nitryl or halogen group substitution at the 2 or 4 positions. These proteins also showed broad catalytic activity on many standard substrates of AKR, such as glyoxal, dihydroxyacetone, and DL-glyceraldehyde, suggesting a possible role in bacterial detoxification. PMID:19585557

Superresolution microscopy reveals structural mechanisms driving the nanoarchitecture of a viral chromatin tether.

PubMed

Grant, Margaret J; Loftus, Matthew S; Stoja, Aiola P; Kedes, Dean H; Smith, M Mitchell

2018-05-08

By tethering their circular genomes (episomes) to host chromatin, DNA tumor viruses ensure retention and segregation of their genetic material during cell divisions. Despite functional genetic and crystallographic studies, there is little information addressing the 3D structure of these tethers in cells, issues critical for understanding persistent infection by these viruses. Here, we have applied direct stochastic optical reconstruction microscopy (dSTORM) to establish the nanoarchitecture of tethers within cells latently infected with the oncogenic human pathogen, Kaposi's sarcoma-associated herpesvirus (KSHV). Each KSHV tether comprises a series of homodimers of the latency-associated nuclear antigen (LANA) that bind with their C termini to the tandem array of episomal terminal repeats (TRs) and with their N termini to host chromatin. Superresolution imaging revealed that individual KSHV tethers possess similar overall dimensions and, in aggregate, fold to occupy the volume of a prolate ellipsoid. Using plasmids with increasing numbers of TRs, we found that tethers display polymer power law scaling behavior with a scaling exponent characteristic of active chromatin. For plasmids containing a two-TR tether, we determined the size, separation, and relative orientation of two distinct clusters of bound LANA, each corresponding to a single TR. From these data, we have generated a 3D model of the episomal half of the tether that integrates and extends previously established findings from epifluorescent, crystallographic, and epigenetic approaches. Our findings also validate the use of dSTORM in establishing novel structural insights into the physical basis of molecular connections linking host and pathogen genomes.

Taraxacin, a new guaianolide from Taraxacum wallichii.

PubMed

Ahmad, V U; Yasmeen, S; Ali, Z; Khan, M A; Choudhary, M I; Akhtar, F; Miana, G A; Zahid, M

2000-07-01

A new guaianolide, taraxacin (1), and a known sesquiterpene ketolactone (2) have been isolated from an ethyl acetate-soluble part of a methanolic extract of Taraxacum wallichii. The structure of 1 was established using NMR, MS, and X-ray crystallographic methods. The (13)C NMR data of 2 is also being reported for the first time.

A new sesquiterpenoid metabolite from Psilocybe samuiensis.

PubMed

Pornpakakul, Surachai; Suwancharoen, Sunisa; Petsom, Amorn; Roengsumran, Sophon; Muangsin, Nongnuj; Chaichit, Narongsak; Piapukiew, Jittra; Sihanonth, Prakistin; Allen, John W

2009-01-01

A novel 2,3-secoaromadendrane-type sesquiterpenoid metabolite, psilosamuiensin A (1), was isolated from the broth of Psilocybe samuiensis. The structure of psilosamuiensin A was established by spectroscopic data and its configurations were confirmed by single crystal X-ray crystallographic analysis. This is the first report of psilosamuiensin A found in the genus Psilocybes.

Structure and physicochemical characterization of a naproxen–picolinamide cocrystal

PubMed Central

Kerr, Hannah E.; Softley, Lorna K.; Suresh, Kuthuru; Hodgkinson, Paul; Evans, Ivana Radosavljevic

2017-01-01

Naproxen (NPX) is a nonsteroidal anti-inflammatory drug with pain- and fever-relieving properties, currently marketed in the sodium salt form to overcome solubility problems; however, alternative solutions for improving its solubility across all pH values are desirable. NPX is suitable for cocrystal formation, with hydrogen-bonding possibilities via the COOH group. The crystal structure is presented of a 1:1 cocrystal of NPX with picolinamide as a coformer [systematic name: (S)-2-(6-meth­oxy­naphthalen-2-yl)propanoic acid–pyridine-2-carbox­amide (1/1), C14H14O3·C6H6N2O]. The pharmaceutically relevant physical properties were investigated and the intrinsic dissolution rate was found to be essentially the same as that of commercial naproxen. An NMR crystallography approach was used to investigate the H-atom positions in the two crystallographically unique COOH–CONH hydrogen-bonded dimers. 1H solid-state NMR distinguished the two carboxyl protons, despite the very similar crystallographic environments. The nature of the hydrogen bonding was confirmed by solid-state NMR and density functional theory calculations. PMID:28257010

Structure and physicochemical characterization of a naproxen-picolinamide cocrystal.

PubMed

Kerr, Hannah E; Softley, Lorna K; Suresh, Kuthuru; Hodgkinson, Paul; Evans, Ivana Radosavljevic

2017-03-01

Naproxen (NPX) is a nonsteroidal anti-inflammatory drug with pain- and fever-relieving properties, currently marketed in the sodium salt form to overcome solubility problems; however, alternative solutions for improving its solubility across all pH values are desirable. NPX is suitable for cocrystal formation, with hydrogen-bonding possibilities via the COOH group. The crystal structure is presented of a 1:1 cocrystal of NPX with picolinamide as a coformer [systematic name: (S)-2-(6-methoxynaphthalen-2-yl)propanoic acid-pyridine-2-carboxamide (1/1), C 14 H 14 O 3 ·C 6 H 6 N 2 O]. The pharmaceutically relevant physical properties were investigated and the intrinsic dissolution rate was found to be essentially the same as that of commercial naproxen. An NMR crystallography approach was used to investigate the H-atom positions in the two crystallographically unique COOH-CONH hydrogen-bonded dimers. 1 H solid-state NMR distinguished the two carboxyl protons, despite the very similar crystallographic environments. The nature of the hydrogen bonding was confirmed by solid-state NMR and density functional theory calculations.

X-ray crystallographic characterization of rhesus macaque MHC Mamu-A*02 complexed with an immunodominant SIV-Gag nonapeptide

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

Feng, Youjun; Graduate School, Chinese Academy of Sciences, Beijing; Qi, Jianxun

2006-01-01

X-ray crystallographic characterization of rhesus macaque MHC Mamu-A*02 complexed with an immunodominant SIV-Gag nonapeptide. Simian immunodeficiency virus (SIV) in the rhesus macaque is regarded as a classic animal model, playing a crucial role in HIV vaccine strategies and therapeutics by characterizing various cytotoxic T-lymphocyte (CTL) responses in macaque monkeys. However, the availability of well documented structural reports focusing on rhesus macaque major histocompatibility complex class I (MHC I) molecules remains extremely limited. Here, a complex of the rhesus macaque MHC I molecule (Mamu-A*02) with human β{sub 2}m and an immunodominant SIV-Gag nonapeptide, GESNLKSLY (GY9), has been crystallized. The crystal diffractsmore » X-rays to 2.7 Å resolution and belongs to space group C2, with unit-cell parameters a = 124.11, b = 110.45, c = 100.06 Å, and contains two molecules in the asymmetric unit. The availability of the structure, which is being solved by molecular replacement, will provide new insights into rhesus macaque MHC I (Mamu-A*02) presenting pathogenic SIV peptides.« less

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

Marana, S. R.; Cançado, F. C.; Valério, A. A.

The digestive lysozymes 1 and 2 from M. domestica were crystallized by vapour diffusion. The crystallographic data were processed to a maximum resolution of 1.9 Å in both cases. Lysozymes are mostly known for their defensive role against bacteria, but in several animals lysozymes have a digestive function. Here, the initial crystallographic characterization of two digestive lysozymes from Musca domestica are presented. The proteins were crystallized using the sitting-drop vapour-diffusion method in the presence of ammonium sulfate or PEG/2-propanol as the precipitant. X-ray diffraction data were collected to a maximum resolution of 1.9 Å using synchrotron radiation. The lysozyme 1more » and 2 crystals belong to the monoclinic space group P2{sub 1} (unit-cell parameters a = 36.52, b = 79.44, c = 45.20 Å, β = 102.97°) and the orthorhombic space group P2{sub 1}2{sub 1}2 (unit-cell parameters a = 73.90, b = 96.40, c = 33.27 Å), respectively. The crystal structures were solved by molecular replacement and structure refinement is in progress.« less

Research Update: Focused ion beam direct writing of magnetic patterns with controlled structural and magnetic properties

NASA Astrophysics Data System (ADS)

Urbánek, Michal; Flajšman, Lukáš; Křižáková, Viola; Gloss, Jonáš; Horký, Michal; Schmid, Michael; Varga, Peter

2018-06-01

Focused ion beam irradiation of metastable Fe78Ni22 thin films grown on Cu(100) substrates is used to create ferromagnetic, body-centered cubic patterns embedded into paramagnetic, face-centered-cubic surrounding. The structural and magnetic phase transformation can be controlled by varying parameters of the transforming gallium ion beam. The focused ion beam parameters such as the ion dose, number of scans, and scanning direction can be used not only to control a degree of transformation but also to change the otherwise four-fold in-plane magnetic anisotropy into the uniaxial anisotropy along a specific crystallographic direction. This change is associated with a preferred growth of specific crystallographic domains. The possibility to create magnetic patterns with continuous magnetization transitions and at the same time to create patterns with periodical changes in magnetic anisotropy makes this system an ideal candidate for rapid prototyping of a large variety of nanostructured samples. Namely, spin-wave waveguides and magnonic crystals can be easily combined into complex devices in a single fabrication step.

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

NASA Technical Reports Server (NTRS)

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

2001-01-01

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

Synthesis, crystal structure and DFT studies of N-(4-acetyl-5,5-dimethyl-4,5-dihydro-1,3,4-thiadiazol-2-yl)acetamide

NASA Astrophysics Data System (ADS)

Gautam, P.; Gautam, D.; Chaudhary, R. P.

2013-12-01

The title compound N-(4-acetyl-5,5-dimethyl-4,5-dihydro-1,3,4-thiadiazol-2-yl)acetamide ( III) was obtained from the reaction of 2-(propan-2-ylidene)hydrazinecarbothioamide ( II) with acetic anhydride instead of formation of the desired thiosemcarbazide derivative of Meldrum acid. The structures of II and III were established by elemental analysis, IR, NMR, Mass and X-ray crystallographic studies. II crystallizes in triclinic system, sp. gr. Z = 2; III crystallizes in the monoclinic system, sp. gr. P21/ c, Z = 8. Density functional theory (DFT) calculations have been carried out for III. 1H and 13C NMR of III has been calculated and correlated with experimental results.

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

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

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

2008-07-01

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

The role of regioregularity, crystallinity, and chain orientation on electron transport in a high-mobility n-type copolymer.

PubMed

Steyrleuthner, Robert; Di Pietro, Riccardo; Collins, Brian A; Polzer, Frank; Himmelberger, Scott; Schubert, Marcel; Chen, Zhihua; Zhang, Shiming; Salleo, Alberto; Ade, Harald; Facchetti, Antonio; Neher, Dieter

2014-03-19

We investigated the correlation between the polymer backbone structural regularity and the charge transport properties of poly{[N,N'-bis(2-octyldodecyl)-1,4,5,8-naphthalenediimide-2,6-diyl]-alt-5,5'-(2,2'-bithiophene)} [P(NDI2OD-T2)], a widely studied semiconducting polymer exhibiting high electron mobility and an unconventional micromorphology. To understand the influence of the chemical structure and crystal packing of conventional regioregular P(NDI2OD-T2) [RR-P(NDI2OD-T2)] on the charge transport, the corresponding regioirregular polymer RI-P(NDI2OD-T2) was synthesized. By combining optical, X-ray, and transmission electron microscopy data, we quantitatively characterized the aggregation, crystallization, and backbone orientation of all of the polymer films, which were then correlated to the electron mobilities in electron-only diodes. By carefully selecting the preparation conditions, we were able to obtain RR-P(NDI2OD-T2) films with similar crystalline structure along the three crystallographic axes but with different orientations of the polymer chains with respect to the substrate surface. RI-P(NDI2OD-T2), though exhibiting a rather similar LUMO structure and energy compared with the regioregular counterpart, displayed a very different packing structure characterized by the formation of ordered stacks along the lamellar direction without detectible π-stacking. Vertical electron mobilities were extracted from the space-charge-limited currents in unipolar devices. We demonstrate the anisotropy of the charge transport along the different crystallographic directions and how the mobility depends on π-stacking but is insensitive to the degree or coherence of lamellar stacking. The comparison between the regioregular and regioirregular polymers also shows how the use of large planar functional groups leads to improved charge transport, with mobilities that are less affected by chemical and structural disorder with respect to classic semicrystalline polymers such as poly(3-hexylthiophene).

Structural studies in columnar basalts from crystallographic and magnetic fabrics

NASA Astrophysics Data System (ADS)

Tiphaine, Boiron; Jérôme, Bascou; Pierre, Camps; Eric, Ferre; Claire, Maurice; Bernard, Guy; Marie-Christine, Gerbe

2010-05-01

The purpose of this study is to better characterize the columnar and the associated microstructure development in basalt flows. The thermal contraction (O'Reilly, 1879) is the main hypothesis to explain the columnar formation. However, neither the structures which appear in basalt flow constituted of three levels (Tomkeieff, 1940) nor circular and radial structures within the prisms (for which weathering nor fracturing can account for) can be explained by the thermal contraction theory alone. An early structuring process during solidification (Guy and Le Coze, 1990) could play for a part that must be discussed (Guy, 2010). We studied two recent basalt flows (75 000 years) from the French Massif Central, in which the three flow levels are clearly observed. In the first basalt flow (La Palisse, Ardèche), the emission centre and the flow direction are known. In the second one (Saint Arcons d'Allier, Haute Loire), the prismatic columns are particularly well developed. In order to characterize the flow structure at different scales, from the flow to the grain scale, anisotropy of magnetic susceptibility (AMS) measurements were performed. The AMS data were coupled with crystallographic preferred orientation measurements of magnetite, plagioclase and clinopyroxene using Electron Backscattered Diffraction (EBSD) and image analyses from perpendicular thin sections. Magnetic mineralogy studies of the La Palisse basalts, in particular the thermomagnetic curves, indicate that the main carrier of AMS is high-Ti titanomagnetite (Tc≈130°C). AMS measurements of about a hundred samples show a higher degree of AMS (P parameter) in the middle level in comparison to the base. Inversely, the bulk magnetic susceptibility (Km) is higher at the flow base. Distinctive parameters for the different levels of the basaltic flows could be then provided by AMS measurements.. Moreover, the comparison between AMS and EBSD data indicate that the magnetic susceptibility carried by the magnetic grains is controlled by the crystallographic orientation of plagioclase and then related to the direction lava flow. In addition, an AMS study carried out on a prism section shows that Km and P magnetic parameters increase from the core to the rim of the prism. The analysis of hysteresis parameters on the same samples indicates that the magnetic grains are larger in size in the core than on the rim. This suggests processes inducing a magnetic grain size arrangement before the prism formation. References O'Reilly J.P (1879)Explanatory notes and discussion on the nature of the prismatic forms of a group of columnar basalts, Giant's Causeway. Trans. Roy. Irish Acad. Tomkeieff S.I, (1940)The basalt lavas of the Giant's Causeway district of the Northern Ireland. Bull. Volc vol 2, pp 89-146. Guy B. and Le Coze J. (1990) Reflections about columnar jointing in basalts: the instability of the planar solidification front, C.R.Acad.Sc. Paris, 311, II, 943-949. Guy B (2010) Basalt columns: Large scale constitutional supercooling? Comments on the paper by John Gilman (JVGR, 2009) and presentation of some new data, JVG to appear.

Evidence for Coordination and Redox Changes of Iron in Shocked Feldspar from Synchrotron MicroXANES

NASA Technical Reports Server (NTRS)

Delaney, J. S.; Dyar, M. D.; Hoerz, F.; Johnson, J. R.

2003-01-01

Shock modification of feldspar has been documented and experimentally reproduced in many studies since the recognition of maskelynite in Shergotty. Experimentally shocked feldspar samples have been well studied using chemical and crystallographic techniques. The crystallographic, site-specific characterization of major and minor elements is less well documented. We present early x-ray absorption (XAS) spectral data for a suite of albitite samples that were experimentally shocked at pressures between 17 and 50 Gpa.

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

PubMed Central

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

2015-01-01

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

Crystallography, chemistry and structural disorder in the new high-Tc Bi-Ca-Sr-Cu-O superconductor

NASA Technical Reports Server (NTRS)

Veblen, D. R.; Heaney, P. J.; Angel, R. J.; Finger, L. W.; Hazen, R. M.

1988-01-01

Diffraction experiments are reported which indicate that the new Bi-Ca-Sr-Cu-O layer-structure superconductor possesses a primitive orthorhombic unit cell with probable space group Pnnn. The material exhibits severe structural disorder which is primarily related to stacking within the layers. The apparent orthorhombic structure is an average resulting from orthorhombic material mixed with monoclinic domains in two twinned orientations. Two distinct types of structural disorder that are common in materials synthesized to date are also described. This disorder complicates the crystallographic analysis and suggests that X-ray and neutron diffraction methods may yield only an average structure.

From molecule to solid: The prediction of organic crystal structures

NASA Astrophysics Data System (ADS)

Dzyabchenko, A. V.

2008-10-01

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

Manipulating the Lewis antigen specificity of the cholesterol-dependent cytolysin lectinolysin

PubMed Central

Lawrence, Sara L.; Feil, Susanne C.; Holien, Jessica K.; Kuiper, Michael J.; Doughty, Larissa; Dolezal, Olan; Mulhern, Terrence D.; Tweten, Rodney K.; Parker, Michael W.

2012-01-01

The cholesterol-dependent cytolysins (CDCs) attack cells by punching large holes in their membranes. Lectinolysin from Streptococcus mitis is unique among CDCs due to the presence of an N-terminal lectin domain that enhances the pore-forming activity of the toxin. We recently determined the crystal structures of the lectin domain in complex with various glycans. These structures revealed the molecular basis for the Lewis antigen specificity of the toxin. Based on this information we have used in silico molecular modeling to design a mutant toxin, which we predicted would increase its specificity for Lewis y, an antigen found on the surface of cancer cells. Surprisingly, we found by surface plasmon resonance binding experiments that the resultant mutant lectin domain exhibited higher specificity for Lewis b antigens instead. We then undertook comparative crystallographic and molecular dynamics simulation studies of the wild-type and mutant lectin domains to understand the molecular basis for the disparity between the theoretical and experimental results. The crystallographic results revealed that the net number of interactions between Lewis y and wild-type versus mutant was unchanged whereas there was a loss of a hydrogen bond between mutant and Lewis b compared to wild-type. In contrast, the molecular dynamics studies revealed that the Lewis b antigen spent more time in the binding pocket of the mutant compared to wild-type and the reverse was true for Lewis y. The results of these simulation studies are consistent with the conclusions drawn from the surface plasmon resonance studies. This work is part of a program to engineer lectinolysin so that it will target and kill specific cells in human diseases. PMID:23181061

RHEED and EELS study of Pd/Al bimetallic thin film growth on different α-Al 2O 3 substrates

NASA Astrophysics Data System (ADS)

Moroz, V.; Rajs, K.; Mašek, K.

2002-06-01

Pd/Al bimetallic thin films were grown by molecular beam epitaxy on single-crystalline α-Al 2O 3(0 0 0 1) and (1 1 2¯ 0) surfaces. Substrate and deposit crystallographic structures and evolution of deposit lattice parameter during the growth were studied by reflection high-energy electron diffraction. The electron energy loss spectroscopy was used as an auxiliary method for chemical analysis. The bimetallic films were prepared by successive deposition of both Pd and Al metals. The structure of Pd and Al deposits in early stages of the growth and its dependence on the preparation conditions were studied. Two phases of Pd clusters covered by Al overlayer have been found. The formation of Al overlayer strongly influenced the lattice parameter of Pd clusters.