xMDFF: molecular dynamics flexible fitting of low-resolution X-ray structures.

PubMed

McGreevy, Ryan; Singharoy, Abhishek; Li, Qufei; Zhang, Jingfen; Xu, Dong; Perozo, Eduardo; Schulten, Klaus

2014-09-01

X-ray crystallography remains the most dominant method for solving atomic structures. However, for relatively large systems, the availability of only medium-to-low-resolution diffraction data often limits the determination of all-atom details. A new molecular dynamics flexible fitting (MDFF)-based approach, xMDFF, for determining structures from such low-resolution crystallographic data is reported. xMDFF employs a real-space refinement scheme that flexibly fits atomic models into an iteratively updating electron-density map. It addresses significant large-scale deformations of the initial model to fit the low-resolution density, as tested with synthetic low-resolution maps of D-ribose-binding protein. xMDFF has been successfully applied to re-refine six low-resolution protein structures of varying sizes that had already been submitted to the Protein Data Bank. Finally, via systematic refinement of a series of data from 3.6 to 7 Å resolution, xMDFF refinements together with electrophysiology experiments were used to validate the first all-atom structure of the voltage-sensing protein Ci-VSP.

Automated structure refinement of macromolecular assemblies from cryo-EM maps using Rosetta.

PubMed

Wang, Ray Yu-Ruei; Song, Yifan; Barad, Benjamin A; Cheng, Yifan; Fraser, James S; DiMaio, Frank

2016-09-26

Cryo-EM has revealed the structures of many challenging yet exciting macromolecular assemblies at near-atomic resolution (3-4.5Å), providing biological phenomena with molecular descriptions. However, at these resolutions, accurately positioning individual atoms remains challenging and error-prone. Manually refining thousands of amino acids - typical in a macromolecular assembly - is tedious and time-consuming. We present an automated method that can improve the atomic details in models that are manually built in near-atomic-resolution cryo-EM maps. Applying the method to three systems recently solved by cryo-EM, we are able to improve model geometry while maintaining the fit-to-density. Backbone placement errors are automatically detected and corrected, and the refinement shows a large radius of convergence. The results demonstrate that the method is amenable to structures with symmetry, of very large size, and containing RNA as well as covalently bound ligands. The method should streamline the cryo-EM structure determination process, providing accurate and unbiased atomic structure interpretation of such maps.

On the temperature dependence of H-U{sub iso} in the riding hydrogen model

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

Lübben, Jens; Volkmann, Christian; Grabowsky, Simon

The temperature dependence of hydrogen U{sub iso} and parent U{sub eq} in the riding hydrogen model is investigated by neutron diffraction, aspherical-atom refinements and QM/MM and MO/MO cluster calculations. Fixed values of 1.2 or 1.5 appear to be underestimated, especially at temperatures below 100 K. The temperature dependence of H-U{sub iso} in N-acetyl-l-4-hydroxyproline monohydrate is investigated. Imposing a constant temperature-independent multiplier of 1.2 or 1.5 for the riding hydrogen model is found to be inaccurate, and severely underestimates H-U{sub iso} below 100 K. Neutron diffraction data at temperatures of 9, 150, 200 and 250 K provide benchmark results for thismore » study. X-ray diffraction data to high resolution, collected at temperatures of 9, 30, 50, 75, 100, 150, 200 and 250 K (synchrotron and home source), reproduce neutron results only when evaluated by aspherical-atom refinement models, since these take into account bonding and lone-pair electron density; both invariom and Hirshfeld-atom refinement models enable a more precise determination of the magnitude of H-atom displacements than independent-atom model refinements. Experimental efforts are complemented by computing displacement parameters following the TLS+ONIOM approach. A satisfactory agreement between all approaches is found.« less

Characterizing the surface roughness of thermomechanical pulp fibers with atomic force microscopy

Treesearch

Rebecca Snell; Leslie H. Groom; Timothy G. Rials

2001-01-01

Loblolly pine, separated into mature and juvenile portions, was refined at various pressures (4, 8 and 12 bar). Fiber surfaces were investigated using a Scanning Electron Microscope (SEM) and an Atomic Force Microscope (AFM). Refiner pressure had a significant effect on the fiber surefaces. SEM images showed an apparent increase in surface roughness with increased...

A full-coordinate model of the polymerase domain of HIV-1 reverse transcriptase and its interaction with a nucleic acid substrate

NASA Technical Reports Server (NTRS)

Setlik, R. F.; Meyer, D. J.; Shibata, M.; Roskwitalski, R.; Ornstein, R. L.; Rein, R.

1994-01-01

We present a full-coordinate model of residues 1-319 of the polymerase domain of HIV-I reverse transcriptase. This model was constructed from the x-ray crystallographic structure of Jacobo-Molina et al. (Jacobo-Molina et al., P.N.A.S. USA 90, 6320-6324 (1993)) which is currently available to the degree of C-coordinates. The backbone and side-chain atoms were constructed using the MAXSPROUT suite of programs (L. Holm and C. Sander, J. Mol. Biol. 218, 183-194 (1991)) and refined through molecular modeling. A seven base pair A-form dsDNA was positioned in the nucleic acid binding cleft to represent the template-primer complex. The orientation of the template-primer complex in the nucleic acid binding cleft was guided by the positions of phosphorus atoms in the crystal structure.

Quantitative Phase Analysis of Plasma-Treated High-Silica Materials

NASA Astrophysics Data System (ADS)

Kosmachev, P. V.; Abzaev, Yu. A.; Vlasov, V. A.

2018-06-01

The paper presents the X-ray diffraction (XRD) analysis of the crystal structure of SiO2 in two modifications, namely quartzite and quartz sand before and after plasma treatment. Plasma treatment enables the raw material to melt and evaporate after which the material quenches and condenses to form nanoparticles. The Rietveld refinement method is used to identify the lattice parameters of SiO2 phases. It is found that after plasma treatment SiO2 oxides are in the amorphous state, which are modeled within the microcanonical ensemble. Experiments show that amorphous phases are stable, and model X-ray reflection intensities approximate the experimental XRD patterns with fine precision. Within the modeling, full information is obtained for SiO2 crystalline and amorphous phases, which includes atom arrangement, structural parameters, atomic population of silicon and oxygen atoms in lattice sites.

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

Charge-density analysis of a protein structure at subatomic resolution: the human aldose reductase case.

PubMed

Guillot, Benoît; Jelsch, Christian; Podjarny, Alberto; Lecomte, Claude

2008-05-01

The valence electron density of the protein human aldose reductase was analyzed at 0.66 angstroms resolution. The methodological developments in the software MoPro to adapt standard charge-density techniques from small molecules to macromolecular structures are described. The deformation electron density visible in initial residual Fourier difference maps was significantly enhanced after high-order refinement. The protein structure was refined after transfer of the experimental library multipolar atom model (ELMAM). The effects on the crystallographic statistics, on the atomic thermal displacement parameters and on the structure stereochemistry are analyzed. Constrained refinements of the transferred valence populations Pval and multipoles Plm were performed against the X-ray diffraction data on a selected substructure of the protein with low thermal motion. The resulting charge densities are of good quality, especially for chemical groups with many copies present in the polypeptide chain. To check the effect of the starting point on the result of the constrained multipolar refinement, the same charge-density refinement strategy was applied but using an initial neutral spherical atom model, i.e. without transfer from the ELMAM library. The best starting point for a protein multipolar refinement is the structure with the electron density transferred from the database. This can be assessed by the crystallographic statistical indices, including Rfree, and the quality of the static deformation electron-density maps, notably on the oxygen electron lone pairs. The analysis of the main-chain bond lengths suggests that stereochemical dictionaries would benefit from a revision based on recently determined unrestrained atomic resolution protein structures.

Hirshfeld atom refinement.

PubMed

Capelli, Silvia C; Bürgi, Hans-Beat; Dittrich, Birger; Grabowsky, Simon; Jayatilaka, Dylan

2014-09-01

Hirshfeld atom refinement (HAR) is a method which determines structural parameters from single-crystal X-ray diffraction data by using an aspherical atom partitioning of tailor-made ab initio quantum mechanical molecular electron densities without any further approximation. Here the original HAR method is extended by implementing an iterative procedure of successive cycles of electron density calculations, Hirshfeld atom scattering factor calculations and structural least-squares refinements, repeated until convergence. The importance of this iterative procedure is illustrated via the example of crystalline ammonia. The new HAR method is then applied to X-ray diffraction data of the dipeptide Gly-l-Ala measured at 12, 50, 100, 150, 220 and 295 K, using Hartree-Fock and BLYP density functional theory electron densities and three different basis sets. All positions and anisotropic displacement parameters (ADPs) are freely refined without constraints or restraints - even those for hydrogen atoms. The results are systematically compared with those from neutron diffraction experiments at the temperatures 12, 50, 150 and 295 K. Although non-hydrogen-atom ADPs differ by up to three combined standard uncertainties (csu's), all other structural parameters agree within less than 2 csu's. Using our best calculations (BLYP/cc-pVTZ, recommended for organic molecules), the accuracy of determining bond lengths involving hydrogen atoms from HAR is better than 0.009 Å for temperatures of 150 K or below; for hydrogen-atom ADPs it is better than 0.006 Å(2) as judged from the mean absolute X-ray minus neutron differences. These results are among the best ever obtained. Remarkably, the precision of determining bond lengths and ADPs for the hydrogen atoms from the HAR procedure is comparable with that from the neutron measurements - an outcome which is obtained with a routinely achievable resolution of the X-ray data of 0.65 Å.

Hirshfeld atom refinement

PubMed Central

Capelli, Silvia C.; Bürgi, Hans-Beat; Dittrich, Birger; Grabowsky, Simon; Jayatilaka, Dylan

2014-01-01

Hirshfeld atom refinement (HAR) is a method which determines structural parameters from single-crystal X-ray diffraction data by using an aspherical atom partitioning of tailor-made ab initio quantum mechanical molecular electron densities without any further approximation. Here the original HAR method is extended by implementing an iterative procedure of successive cycles of electron density calculations, Hirshfeld atom scattering factor calculations and structural least-squares refinements, repeated until convergence. The importance of this iterative procedure is illustrated via the example of crystalline ammonia. The new HAR method is then applied to X-ray diffraction data of the dipeptide Gly–l-Ala measured at 12, 50, 100, 150, 220 and 295 K, using Hartree–Fock and BLYP density functional theory electron densities and three different basis sets. All positions and anisotropic displacement parameters (ADPs) are freely refined without constraints or restraints – even those for hydrogen atoms. The results are systematically compared with those from neutron diffraction experiments at the temperatures 12, 50, 150 and 295 K. Although non-hydrogen-atom ADPs differ by up to three combined standard uncertainties (csu’s), all other structural parameters agree within less than 2 csu’s. Using our best calculations (BLYP/cc-pVTZ, recommended for organic molecules), the accuracy of determining bond lengths involving hydrogen atoms from HAR is better than 0.009 Å for temperatures of 150 K or below; for hydrogen-atom ADPs it is better than 0.006 Å2 as judged from the mean absolute X-ray minus neutron differences. These results are among the best ever obtained. Remarkably, the precision of determining bond lengths and ADPs for the hydrogen atoms from the HAR procedure is comparable with that from the neutron measurements – an outcome which is obtained with a routinely achievable resolution of the X-ray data of 0.65 Å. PMID:25295177

Ab initio structure determination and refinement of a scorpion protein toxin.

PubMed

Smith, G D; Blessing, R H; Ealick, S E; Fontecilla-Camps, J C; Hauptman, H A; Housset, D; Langs, D A; Miller, R

1997-09-01

The structure of toxin II from the scorpion Androctonus australis Hector has been determined ab initio by direct methods using SnB at 0.96 A resolution. For the purpose of this structure redetermination, undertaken as a test of the minimal function and the SnB program, the identity and sequence of the protein was withheld from part of the research team. A single solution obtained from 1 619 random atom trials was clearly revealed by the bimodal distribution of the final value of the minimal function associated with each individual trial. Five peptide fragments were identified from a conservative analysis of the initial E-map, and following several refinement cycles with X-PLOR, a model was built of the complete structure. At the end of the X-PLOR refinement, the sequence was compared with the published sequence and 57 of the 64 residues had been correctly identified. Two errors in sequence resulted from side chains with similar size while the rest of the errors were a result of severe disorder or high thermal motion in the side chains. Given the amino-acid sequence, it is estimated that the initial E-map could have produced a model containing 99% of all main-chain and 81% of side-chain atoms. The structure refinement was completed with PROFFT, including the contributions of protein H atoms, and converged at a residual of 0.158 for 30 609 data with F >or= 2sigma(F) in the resolution range 8.0-0.964 A. The final model consisted of 518 non-H protein atoms (36 disordered), 407 H atoms, and 129 water molecules (43 with occupancies less than unity). This total of 647 non-H atoms represents the largest light-atom structure solved to date.

Improving the accuracy of macromolecular structure refinement at 7 Å resolution.

PubMed

Brunger, Axel T; Adams, Paul D; Fromme, Petra; Fromme, Raimund; Levitt, Michael; Schröder, Gunnar F

2012-06-06

In X-ray crystallography, molecular replacement and subsequent refinement is challenging at low resolution. We compared refinement methods using synchrotron diffraction data of photosystem I at 7.4 Å resolution, starting from different initial models with increasing deviations from the known high-resolution structure. Standard refinement spoiled the initial models, moving them further away from the true structure and leading to high R(free)-values. In contrast, DEN refinement improved even the most distant starting model as judged by R(free), atomic root-mean-square differences to the true structure, significance of features not included in the initial model, and connectivity of electron density. The best protocol was DEN refinement with initial segmented rigid-body refinement. For the most distant initial model, the fraction of atoms within 2 Å of the true structure improved from 24% to 60%. We also found a significant correlation between R(free) values and the accuracy of the model, suggesting that R(free) is useful even at low resolution. Copyright © 2012 Elsevier Ltd. All rights reserved.

RCD+: Fast loop modeling server.

PubMed

López-Blanco, José Ramón; Canosa-Valls, Alejandro Jesús; Li, Yaohang; Chacón, Pablo

2016-07-08

Modeling loops is a critical and challenging step in protein modeling and prediction. We have developed a quick online service (http://rcd.chaconlab.org) for ab initio loop modeling combining a coarse-grained conformational search with a full-atom refinement. Our original Random Coordinate Descent (RCD) loop closure algorithm has been greatly improved to enrich the sampling distribution towards near-native conformations. These improvements include a new workflow optimization, MPI-parallelization and fast backbone angle sampling based on neighbor-dependent Ramachandran probability distributions. The server starts by efficiently searching the vast conformational space from only the loop sequence information and the environment atomic coordinates. The generated closed loop models are subsequently ranked using a fast distance-orientation dependent energy filter. Top ranked loops are refined with the Rosetta energy function to obtain accurate all-atom predictions that can be interactively inspected in an user-friendly web interface. Using standard benchmarks, the average root mean squared deviation (RMSD) is 0.8 and 1.4 Å for 8 and 12 residues loops, respectively, in the challenging modeling scenario in where the side chains of the loop environment are fully remodeled. These results are not only very competitive compared to those obtained with public state of the art methods, but also they are obtained ∼10-fold faster. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

Production of a Powder Metallurgical Hot Work Tool Steel with Harmonic Structure by Mechanical Milling and Spark Plasma Sintering

NASA Astrophysics Data System (ADS)

Deirmina, Faraz; Pellizzari, Massimo; Federici, Matteo

2017-04-01

Commercial AISI-H13 gas atomized powders (AT) were mechanically milled (MM) to refine both the particle size and the microstructure. Different volume fractions of coarser grained (CG) AT powders were mixed with the ultra-fine grained (UFG) MM and consolidated by spark plasma sintering to obtain bulks showing a harmonic structure ( i.e. a 3D interconnected network of UFG areas surrounding the CG atomized particles). The low sintering temperature, 1373.15 K (1100 °C) and the short sintering time (30 minutes) made it possible to obtain near full density samples while preserving the refined microstructure induced by MM. A combination of high hardness and significantly improved fracture toughness is achieved by the samples containing 50 to 80 vol pct MM, essentially showing harmonic structure. The design allows to easily achieve specific application oriented properties by varying the MM volume fraction in the initial mixture. Hardness is governed by the fine-grained MM matrix and improved toughening is due to (1) deviatory effect of AT particles and (2) energy dissipation as a result of the decohesion in MM regions or AT and MM interface.

Advanced Structural Analyses by Third Generation Synchrotron Radiation Powder Diffraction

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

Sakata, M.; Aoyagi, S.; Ogura, T.

2007-01-19

Since the advent of the 3rd generation Synchrotron Radiation (SR) sources, such as SPring-8, the capabilities of SR powder diffraction increased greatly not only in an accurate structure refinement but also ab initio structure determination. In this study, advanced structural analyses by 3rd generation SR powder diffraction based on the Large Debye-Scherrer camera installed at BL02B2, SPring-8 is described. Because of high angular resolution and high counting statistics powder data collected at BL02B2, SPring-8, ab initio structure determination can cope with a molecular crystals with 65 atoms including H atoms. For the structure refinements, it is found that a kindmore » of Maximum Entropy Method in which several atoms are omitted in phase calculation become very important to refine structural details of fairy large molecule in a crystal. It should be emphasized that until the unknown structure is refined very precisely, the obtained structure by Genetic Algorithm (GA) or some other ab initio structure determination method using real space structural knowledge, it is not possible to tell whether the structure obtained by the method is correct or not. In order to determine and/or refine crystal structure of rather complicated molecules, we cannot overemphasize the importance of the 3rd generation SR sources.« less

Sparsity of the normal matrix in the refinement of macromolecules at atomic and subatomic resolution.

PubMed

Jelsch, C

2001-09-01

The normal matrix in the least-squares refinement of macromolecules is very sparse when the resolution reaches atomic and subatomic levels. The elements of the normal matrix, related to coordinates, thermal motion and charge-density parameters, have a global tendency to decrease rapidly with the interatomic distance between the atoms concerned. For instance, in the case of the protein crambin at 0.54 A resolution, the elements are reduced by two orders of magnitude for distances above 1.5 A. The neglect a priori of most of the normal-matrix elements according to a distance criterion represents an approximation in the refinement of macromolecules, which is particularly valid at very high resolution. The analytical expressions of the normal-matrix elements, which have been derived for the coordinates and the thermal parameters, show that the degree of matrix sparsity increases with the diffraction resolution and the size of the asymmetric unit.

Electrostatic properties of the pyrimethamine-2,4-dihydroxybenzoic acid cocrystal in methanol studied using transferred electron-density parameters.

PubMed

Faroque, Muhammad Umer; Noureen, Sajida; Ahmed, Maqsood; Tahir, Muhammad Nawaz

2018-01-01

The crystal structure of the cocrystal salt form of the antimalarial drug pyrimethamine with 2,4-dihydroxybenzoic acid in methanol [systematic name: 2,4-diamino-5-(4-chlorophenyl)-6-ethylpyrimidin-1-ium 2,4-dihydroxybenzoate methanol monosolvate, C 12 H 14 ClN 4 + ·C 7 H 5 O 4 - ·CH 3 OH] has been studied using X-ray diffraction data collected at room temperature. The crystal structure was refined using the classical Independent Atom Model (IAM) and the Multipolar Atom Model by transferring electron-density parameters from the ELMAM2 database. The Cl atom was refined anharmonically. The results of both refinement methods have been compared. The intermolecular interactions have been characterized on the basis of Hirshfeld surface analysis and topological analysis using Bader's theory of Atoms in Molecules. The results show that the molecular assembly is built primarily on the basis of charge transfer between 2,4-dihydroxybenzoic acid and pyrimethamine, which results in strong intermolecular hydrogen bonds. This fact is further validated by the calculation of the electrostatic potential based on transferred electron-density parameters.

Solving the scalability issue in quantum-based refinement: Q|R#1.

PubMed

Zheng, Min; Moriarty, Nigel W; Xu, Yanting; Reimers, Jeffrey R; Afonine, Pavel V; Waller, Mark P

2017-12-01

Accurately refining biomacromolecules using a quantum-chemical method is challenging because the cost of a quantum-chemical calculation scales approximately as n m , where n is the number of atoms and m (≥3) is based on the quantum method of choice. This fundamental problem means that quantum-chemical calculations become intractable when the size of the system requires more computational resources than are available. In the development of the software package called Q|R, this issue is referred to as Q|R#1. A divide-and-conquer approach has been developed that fragments the atomic model into small manageable pieces in order to solve Q|R#1. Firstly, the atomic model of a crystal structure is analyzed to detect noncovalent interactions between residues, and the results of the analysis are represented as an interaction graph. Secondly, a graph-clustering algorithm is used to partition the interaction graph into a set of clusters in such a way as to minimize disruption to the noncovalent interaction network. Thirdly, the environment surrounding each individual cluster is analyzed and any residue that is interacting with a particular cluster is assigned to the buffer region of that particular cluster. A fragment is defined as a cluster plus its buffer region. The gradients for all atoms from each of the fragments are computed, and only the gradients from each cluster are combined to create the total gradients. A quantum-based refinement is carried out using the total gradients as chemical restraints. In order to validate this interaction graph-based fragmentation approach in Q|R, the entire atomic model of an amyloid cross-β spine crystal structure (PDB entry 2oNA) was refined.

DiffPy-CMI-Python libraries for Complex Modeling Initiative

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

Billinge, Simon; Juhas, Pavol; Farrow, Christopher

2014-02-01

Software to manipulate and describe crystal and molecular structures and set up structural refinements from multiple experimental inputs. Calculation and simulation of structure derived physical quantities. Library for creating customized refinements of atomic structures from available experimental and theoretical inputs.

Overview of refinement procedures within REFMAC5: utilizing data from different sources.

PubMed

Kovalevskiy, Oleg; Nicholls, Robert A; Long, Fei; Carlon, Azzurra; Murshudov, Garib N

2018-03-01

Refinement is a process that involves bringing into agreement the structural model, available prior knowledge and experimental data. To achieve this, the refinement procedure optimizes a posterior conditional probability distribution of model parameters, including atomic coordinates, atomic displacement parameters (B factors), scale factors, parameters of the solvent model and twin fractions in the case of twinned crystals, given observed data such as observed amplitudes or intensities of structure factors. A library of chemical restraints is typically used to ensure consistency between the model and the prior knowledge of stereochemistry. If the observation-to-parameter ratio is small, for example when diffraction data only extend to low resolution, the Bayesian framework implemented in REFMAC5 uses external restraints to inject additional information extracted from structures of homologous proteins, prior knowledge about secondary-structure formation and even data obtained using different experimental methods, for example NMR. The refinement procedure also generates the `best' weighted electron-density maps, which are useful for further model (re)building. Here, the refinement of macromolecular structures using REFMAC5 and related tools distributed as part of the CCP4 suite is discussed.

Protein Structure and Function Prediction Using I-TASSER

PubMed Central

Yang, Jianyi; Zhang, Yang

2016-01-01

I-TASSER is a hierarchical protocol for automated protein structure prediction and structure-based function annotation. Starting from the amino acid sequence of target proteins, I-TASSER first generates full-length atomic structural models from multiple threading alignments and iterative structural assembly simulations followed by atomic-level structure refinement. The biological functions of the protein, including ligand-binding sites, enzyme commission number, and gene ontology terms, are then inferred from known protein function databases based on sequence and structure profile comparisons. I-TASSER is freely available as both an on-line server and a stand-alone package. This unit describes how to use the I-TASSER protocol to generate structure and function prediction and how to interpret the prediction results, as well as alternative approaches for further improving the I-TASSER modeling quality for distant-homologous and multi-domain protein targets. PMID:26678386

Probing the accuracy and precision of Hirshfeld atom refinement with HARt interfaced with Olex2.

PubMed

Fugel, Malte; Jayatilaka, Dylan; Hupf, Emanuel; Overgaard, Jacob; Hathwar, Venkatesha R; Macchi, Piero; Turner, Michael J; Howard, Judith A K; Dolomanov, Oleg V; Puschmann, Horst; Iversen, Bo B; Bürgi, Hans-Beat; Grabowsky, Simon

2018-01-01

Hirshfeld atom refinement (HAR) is a novel X-ray structure refinement technique that employs aspherical atomic scattering factors obtained from stockholder partitioning of a theoretically determined tailor-made static electron density. HAR overcomes many of the known limitations of independent atom modelling (IAM), such as too short element-hydrogen distances, r ( X -H), or too large atomic displacement parameters (ADPs). This study probes the accuracy and precision of anisotropic hydrogen and non-hydrogen ADPs and of r ( X -H) values obtained from HAR. These quantities are compared and found to agree with those obtained from (i) accurate neutron diffraction data measured at the same temperatures as the X-ray data and (ii) multipole modelling (MM), an established alternative method for interpreting X-ray diffraction data with the help of aspherical atomic scattering factors. Results are presented for three chemically different systems: the aromatic hydro-carbon rubrene (orthorhombic 5,6,11,12-tetra-phenyl-tetracene), a co-crystal of zwitterionic betaine, imidazolium cations and picrate anions (BIPa), and the salt potassium hydrogen oxalate (KHOx). The non-hydrogen HAR-ADPs are as accurate and precise as the MM-ADPs. Both show excellent agreement with the neutron-based values and are superior to IAM-ADPs. The anisotropic hydrogen HAR-ADPs show a somewhat larger deviation from neutron-based values than the hydrogen SHADE-ADPs used in MM. Element-hydrogen bond lengths from HAR are in excellent agreement with those obtained from neutron diffraction experiments, although they are somewhat less precise. The residual density contour maps after HAR show fewer features than those after MM. Calculating the static electron density with the def2-TZVP basis set instead of the simpler def2-SVP one does not improve the refinement results significantly. All HARs were performed within the recently introduced HARt option implemented in the Olex2 program. They are easily launched inside its graphical user interface following a conventional IAM.

Probing the accuracy and precision of Hirshfeld atom refinement with HARt interfaced with Olex2

PubMed Central

Fugel, Malte; Hathwar, Venkatesha R.; Turner, Michael J.; Howard, Judith A. K.

2018-01-01

Hirshfeld atom refinement (HAR) is a novel X-ray structure refinement technique that employs aspherical atomic scattering factors obtained from stockholder partitioning of a theoretically determined tailor-made static electron density. HAR overcomes many of the known limitations of independent atom modelling (IAM), such as too short element–hydrogen distances, r(X—H), or too large atomic displacement parameters (ADPs). This study probes the accuracy and precision of anisotropic hydrogen and non-hydrogen ADPs and of r(X—H) values obtained from HAR. These quantities are compared and found to agree with those obtained from (i) accurate neutron diffraction data measured at the same temperatures as the X-ray data and (ii) multipole modelling (MM), an established alternative method for interpreting X-ray diffraction data with the help of aspherical atomic scattering factors. Results are presented for three chemically different systems: the aromatic hydro­carbon rubrene (orthorhombic 5,6,11,12-tetra­phenyl­tetracene), a co-crystal of zwitterionic betaine, imidazolium cations and picrate anions (BIPa), and the salt potassium hydrogen oxalate (KHOx). The non-hydrogen HAR-ADPs are as accurate and precise as the MM-ADPs. Both show excellent agreement with the neutron-based values and are superior to IAM-ADPs. The anisotropic hydrogen HAR-ADPs show a somewhat larger deviation from neutron-based values than the hydrogen SHADE-ADPs used in MM. Element–hydrogen bond lengths from HAR are in excellent agreement with those obtained from neutron diffraction experiments, although they are somewhat less precise. The residual density contour maps after HAR show fewer features than those after MM. Calculating the static electron density with the def2-TZVP basis set instead of the simpler def2-SVP one does not improve the refinement results significantly. All HARs were performed within the recently introduced HARt option implemented in the Olex2 program. They are easily launched inside its graphical user interface following a conventional IAM. PMID:29354269

Analysis of macromolecules, ligands and macromolecule-ligand complexes

DOEpatents

Von Dreele, Robert B [Los Alamos, NM

2008-12-23

A method for determining atomic level structures of macromolecule-ligand complexes through high-resolution powder diffraction analysis and a method for providing suitable microcrystalline powder for diffraction analysis are provided. In one embodiment, powder diffraction data is collected from samples of polycrystalline macromolecule and macromolecule-ligand complex and the refined structure of the macromolecule is used as an approximate model for a combined Rietveld and stereochemical restraint refinement of the macromolecule-ligand complex. A difference Fourier map is calculated and the ligand position and points of interaction between the atoms of the macromolecule and the atoms of the ligand can be deduced and visualized. A suitable polycrystalline sample of macromolecule-ligand complex can be produced by physically agitating a mixture of lyophilized macromolecule, ligand and a solvent.

Norman Ramsey and the Separated Oscillatory Fields Method

Science.gov Websites

methods of investigation; in particular, he contributed many refinements of the molecular beam method for the study of atomic and molecular properties, he invented the separated oscillatory field method of atomic and molecular spectroscopy and it is the practical basis for the most precise atomic clocks

Statistical radii associated with amino acids to determine the contact map: fixing the structure of a type I cohesin domain in the Clostridium thermocellum cellulosome

NASA Astrophysics Data System (ADS)

Chwastyk, Mateusz; Poma Bernaola, Adolfo; Cieplak, Marek

2015-07-01

We propose to improve and simplify protein refinement procedures through consideration of which pairs of amino acid residues should form native contacts. We first consider 11 330 proteins from the CATH database to determine statistical distributions of contacts associated with a given type of amino acid. The distributions are set across the distances between the α-C atoms that are in contact. Based on this data, we determine typical radii of effective spheres that can be placed on the α-C atoms in order to reconstruct the distribution of the contact lengths. This is done by checking for overlaps with enlarged van der Waals spheres associated with heavy atoms on other amino acids. The resulting contacts can be used to identify non-native contacts that may arise during the time evolution of structure-based models. Here, the radii are used to guide reconstruction of nine missing side chains in a type I cohesin domain with the Protein Data Bank code 1AOH. We first identify the likely missing contacts and then sculpt the corresponding side chains by standard refinement tools to achieve consistency with the expected contact map. One ambiguity in refinement is resolved by determining all-atom conformational energies.

Aspherical-atom modeling of coordination compounds by single-crystal X-ray diffraction allows the correct metal atom to be identified.

PubMed

Dittrich, Birger; Wandtke, Claudia M; Meents, Alke; Pröpper, Kevin; Mondal, Kartik Chandra; Samuel, Prinson P; Amin Sk, Nurul; Singh, Amit Pratap; Roesky, Herbert W; Sidhu, Navdeep

2015-02-02

Single-crystal X-ray diffraction (XRD) is often considered the gold standard in analytical chemistry, as it allows element identification as well as determination of atom connectivity and the solid-state structure of completely unknown samples. Element assignment is based on the number of electrons of an atom, so that a distinction of neighboring heavier elements in the periodic table by XRD is often difficult. A computationally efficient procedure for aspherical-atom least-squares refinement of conventional diffraction data of organometallic compounds is proposed. The iterative procedure is conceptually similar to Hirshfeld-atom refinement (Acta Crystallogr. Sect. A- 2008, 64, 383-393; IUCrJ. 2014, 1,61-79), but it relies on tabulated invariom scattering factors (Acta Crystallogr. Sect. B- 2013, 69, 91-104) and the Hansen/Coppens multipole model; disordered structures can be handled as well. Five linear-coordinate 3d metal complexes, for which the wrong element is found if standard independent-atom model scattering factors are relied upon, are studied, and it is shown that only aspherical-atom scattering factors allow a reliable assignment. The influence of anomalous dispersion in identifying the correct element is investigated and discussed. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

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

PubMed

Prill, Dragica; Juhás, Pavol; Billinge, Simon J L; Schmidt, Martin U

2016-01-01

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

Polarizable atomic multipole X-ray refinement: application to peptide crystals

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

Schnieders, Michael J.; Fenn, Timothy D.; Howard Hughes Medical Institute

2009-09-01

A method to accelerate the computation of structure factors from an electron density described by anisotropic and aspherical atomic form factors via fast Fourier transformation is described for the first time. Recent advances in computational chemistry have produced force fields based on a polarizable atomic multipole description of biomolecular electrostatics. In this work, the Atomic Multipole Optimized Energetics for Biomolecular Applications (AMOEBA) force field is applied to restrained refinement of molecular models against X-ray diffraction data from peptide crystals. A new formalism is also developed to compute anisotropic and aspherical structure factors using fast Fourier transformation (FFT) of Cartesian Gaussianmore » multipoles. Relative to direct summation, the FFT approach can give a speedup of more than an order of magnitude for aspherical refinement of ultrahigh-resolution data sets. Use of a sublattice formalism makes the method highly parallelizable. Application of the Cartesian Gaussian multipole scattering model to a series of four peptide crystals using multipole coefficients from the AMOEBA force field demonstrates that AMOEBA systematically underestimates electron density at bond centers. For the trigonal and tetrahedral bonding geometries common in organic chemistry, an atomic multipole expansion through hexadecapole order is required to explain bond electron density. Alternatively, the addition of interatomic scattering (IAS) sites to the AMOEBA-based density captured bonding effects with fewer parameters. For a series of four peptide crystals, the AMOEBA–IAS model lowered R{sub free} by 20–40% relative to the original spherically symmetric scattering model.« less

Programming new geometry restraints: Parallelity of atomic groups

DOE PAGES

Sobolev, Oleg V.; Afonine, Pavel V.; Adams, Paul D.; ...

2015-08-01

Improvements in structural biology methods, in particular crystallography and cryo-electron microscopy, have created an increased demand for the refinement of atomic models against low-resolution experimental data. One way to compensate for the lack of high-resolution experimental data is to use a priori information about model geometry that can be utilized in refinement in the form of stereochemical restraints or constraints. Here, the definition and calculation of the restraints that can be imposed on planar atomic groups, in particular the angle between such groups, are described. Detailed derivations of the restraint targets and their gradients are provided so that they canmore » be readily implemented in other contexts. Practical implementations of the restraints, and of associated data structures, in the Computational Crystallography Toolbox( cctbx) are presented.« less

Quantum crystallographic charge density of urea

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

Wall, Michael E.

Standard X-ray crystallography methods use free-atom models to calculate mean unit-cell charge densities. Real molecules, however, have shared charge that is not captured accurately using free-atom models. To address this limitation, a charge density model of crystalline urea was calculated using high-level quantum theory and was refined against publicly available ultra-high-resolution experimental Bragg data, including the effects of atomic displacement parameters. The resulting quantum crystallographic model was compared with models obtained using spherical atom or multipole methods. Despite using only the same number of free parameters as the spherical atom model, the agreement of the quantum model with the datamore » is comparable to the multipole model. The static, theoretical crystalline charge density of the quantum model is distinct from the multipole model, indicating the quantum model provides substantially new information. Hydrogen thermal ellipsoids in the quantum model were very similar to those obtained using neutron crystallography, indicating that quantum crystallography can increase the accuracy of the X-ray crystallographic atomic displacement parameters. Lastly, the results demonstrate the feasibility and benefits of integrating fully periodic quantum charge density calculations into ultra-high-resolution X-ray crystallographic model building and refinement.« less

Quantum crystallographic charge density of urea

DOE PAGES

Wall, Michael E.

2016-06-08

Standard X-ray crystallography methods use free-atom models to calculate mean unit-cell charge densities. Real molecules, however, have shared charge that is not captured accurately using free-atom models. To address this limitation, a charge density model of crystalline urea was calculated using high-level quantum theory and was refined against publicly available ultra-high-resolution experimental Bragg data, including the effects of atomic displacement parameters. The resulting quantum crystallographic model was compared with models obtained using spherical atom or multipole methods. Despite using only the same number of free parameters as the spherical atom model, the agreement of the quantum model with the datamore » is comparable to the multipole model. The static, theoretical crystalline charge density of the quantum model is distinct from the multipole model, indicating the quantum model provides substantially new information. Hydrogen thermal ellipsoids in the quantum model were very similar to those obtained using neutron crystallography, indicating that quantum crystallography can increase the accuracy of the X-ray crystallographic atomic displacement parameters. Lastly, the results demonstrate the feasibility and benefits of integrating fully periodic quantum charge density calculations into ultra-high-resolution X-ray crystallographic model building and refinement.« less

Theoretical investigation of the oxidation pathways of the Cl-initiated reaction of 2-methyl-3-buten-2-ol

NASA Astrophysics Data System (ADS)

Zhang, Weichao; Zhang, Dongju

2012-12-01

The mechanism and products of the reaction of 2-methyl-3-buten-2-ol (MBO232) with Cl atoms in the presence of O2 have been elucidated by performing high-level quantum chemistry calculations. The geometries of the reactants, intermediates, transition states, and products are optimized at the MP2(full)/6-311G(d, p) level, and their single-point energies are refined at the CCSD(T)/6-311 + G(d, p) level. The potential energy surface profiles have been constructed at the CCSD(T)/6-311 + G(d, p)//MP2(full)/6-311G(d, p) + 0.95 × ZPE level of theory, and the possible channels involved in the reaction are also discussed. The calculations indicate that the reaction predominantly proceeds via the addition of Cl atoms to the double bond rather than the direct abstraction of the H atoms in MBO232. The nascent adducts (CH3)2C(OH)CHCH2Cl (IM1) and (CH3)2C(OH)CHClCH2 (IM2) do not undergo subsequent isomerization and dissociation reactions, but rather react with O2. The theoretical results show that the major products are CH2ClCHO and CH3C(O)CH3 for the reaction of MBO232 + Cl in the presence of O2, which is in good agreement with the experimental finding.

Real-space refinement in PHENIX for cryo-EM and crystallography

DOE PAGES

Afonine, Pavel V.; Poon, Billy K.; Read, Randy J.; ...

2018-06-01

This work describes the implementation of real-space refinement in the phenix.real_space_refine program from the PHENIX suite. The use of a simplified refinement target function enables very fast calculation, which in turn makes it possible to identify optimal data-restraint weights as part of routine refinements with little runtime cost. Refinement of atomic models against low-resolution data benefits from the inclusion of as much additional information as is available. In addition to standard restraints on covalent geometry, phenix.real_space_refine makes use of extra information such as secondary-structure and rotamer-specific restraints, as well as restraints or constraints on internal molecular symmetry. The re-refinement ofmore » 385 cryo-EM-derived models available in the Protein Data Bank at resolutions of 6 Å or better shows significant improvement of the models and of the fit of these models to the target maps.« less

Real-space refinement in PHENIX for cryo-EM and crystallography

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

Afonine, Pavel V.; Poon, Billy K.; Read, Randy J.

This work describes the implementation of real-space refinement in the phenix.real_space_refine program from the PHENIX suite. The use of a simplified refinement target function enables very fast calculation, which in turn makes it possible to identify optimal data-restraint weights as part of routine refinements with little runtime cost. Refinement of atomic models against low-resolution data benefits from the inclusion of as much additional information as is available. In addition to standard restraints on covalent geometry, phenix.real_space_refine makes use of extra information such as secondary-structure and rotamer-specific restraints, as well as restraints or constraints on internal molecular symmetry. The re-refinement ofmore » 385 cryo-EM-derived models available in the Protein Data Bank at resolutions of 6 Å or better shows significant improvement of the models and of the fit of these models to the target maps.« less

Sensitivity and Limitations of Structures from X-ray and Neutron-Based Diffraction Analyses of Transition Metal Oxide Lithium-Battery Electrodes

DOE PAGES

Liu, Hao; Liu, Haodong; Lapidus, Saul H.; ...

2017-06-21

Lithium transition metal oxides are an important class of electrode materials for lithium-ion batteries. Binary or ternary (transition) metal doping brings about new opportunities to improve the electrode’s performance and often leads to more complex stoichiometries and atomic structures than the archetypal LiCoO 2. Rietveld structural analyses of X-ray and neutron diffraction data is a widely-used approach for structural characterization of crystalline materials. But, different structural models and refinement approaches can lead to differing results, and some parameters can be difficult to quantify due to the inherent limitations of the data. Here, through the example of LiNi 0.8Co 0.15Al 0.05Omore » 2 (NCA), we demonstrated the sensitivity of various structural parameters in Rietveld structural analysis to different refinement approaches and structural models, and proposed an approach to reduce refinement uncertainties due to the inexact X-ray scattering factors of the constituent atoms within the lattice. Furthermore, this refinement approach was implemented for electrochemically-cycled NCA samples and yielded accurate structural parameters using only X-ray diffraction data. The present work provides the best practices for performing structural refinement of lithium transition metal oxides.« less

Sensitivity and Limitations of Structures from X-ray and Neutron-Based Diffraction Analyses of Transition Metal Oxide Lithium-Battery Electrodes

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

Liu, Hao; Liu, Haodong; Lapidus, Saul H.

Lithium transition metal oxides are an important class of electrode materials for lithium-ion batteries. Binary or ternary (transition) metal doping brings about new opportunities to improve the electrode’s performance and often leads to more complex stoichiometries and atomic structures than the archetypal LiCoO 2. Rietveld structural analyses of X-ray and neutron diffraction data is a widely-used approach for structural characterization of crystalline materials. But, different structural models and refinement approaches can lead to differing results, and some parameters can be difficult to quantify due to the inherent limitations of the data. Here, through the example of LiNi 0.8Co 0.15Al 0.05Omore » 2 (NCA), we demonstrated the sensitivity of various structural parameters in Rietveld structural analysis to different refinement approaches and structural models, and proposed an approach to reduce refinement uncertainties due to the inexact X-ray scattering factors of the constituent atoms within the lattice. Furthermore, this refinement approach was implemented for electrochemically-cycled NCA samples and yielded accurate structural parameters using only X-ray diffraction data. The present work provides the best practices for performing structural refinement of lithium transition metal oxides.« less

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

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

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

2016-01-01

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

Exploiting structure similarity in refinement: automated NCS and target-structure restraints in BUSTER.

PubMed

Smart, Oliver S; Womack, Thomas O; Flensburg, Claus; Keller, Peter; Paciorek, Włodek; Sharff, Andrew; Vonrhein, Clemens; Bricogne, Gérard

2012-04-01

Maximum-likelihood X-ray macromolecular structure refinement in BUSTER has been extended with restraints facilitating the exploitation of structural similarity. The similarity can be between two or more chains within the structure being refined, thus favouring NCS, or to a distinct 'target' structure that remains fixed during refinement. The local structural similarity restraints (LSSR) approach considers all distances less than 5.5 Å between pairs of atoms in the chain to be restrained. For each, the difference from the distance between the corresponding atoms in the related chain is found. LSSR applies a restraint penalty on each difference. A functional form that reaches a plateau for large differences is used to avoid the restraints distorting parts of the structure that are not similar. Because LSSR are local, there is no need to separate out domains. Some restraint pruning is still necessary, but this has been automated. LSSR have been available to academic users of BUSTER since 2009 with the easy-to-use -autoncs and -target target.pdb options. The use of LSSR is illustrated in the re-refinement of PDB entries 5rnt, where -target enables the correct ligand-binding structure to be found, and 1osg, where -autoncs contributes to the location of an additional copy of the cyclic peptide ligand.

Resolution Quality and Atom Positions in Sub-Angstrom Electron Microscopy

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

O'Keefe, Michael A.; Allard, Lawrence F.; Blom, Douglas A.

2005-02-15

Ability to determine whether an image peak represents one single atom or several depends on resolution of the HR-(S)TEM. Rayleigh's resolution criterion, an accepted standard in optics, was derived as a means for judging when two image intensity peaks from two sources of light (stars) are distinguishable from a single source. Atom spacings closer than the Rayleigh limit have been resolved in HR-TEM, suggesting that it may be useful to consider other limits, such as the Sparrow resolution criterion. From the viewpoint of the materials scientist, it is important to be able to use the image to determine whether anmore » image feature represents one or more atoms (resolution), and where the atoms (or atom columns) are positioned relative to one another (resolution quality). When atoms and the corresponding image peaks are separated by more than the Rayleigh limit of the HR-(S)TEM, it is possible to adjust imaging parameters so that relative peak positions in the image correspond to relative atom positions in the specimen. When atoms are closer than the Rayleigh limit, we must find the relationship of the peak position to the atom position by peak fitting or, if we have a suitable model, by image simulation. Our Rayleigh-Sparrow parameter QRS reveals the ''resolution quality'' of a microscope image. QRS values greater than 1 indicate a clearly resolved twin peak, while values between 1 and 0 mean a lower-quality resolution and an image with peaks displaced from the relative atom positions. The depth of the twin-peak minimum can be used to determine the value of QRS and the true separation of the atom peaks that sum to produce the twin peak in the image. The Rayleigh-Sparrow parameter can be used to refine relative atom positions in defect images where atoms are closer than the Rayleigh limit of the HR-(S)TEM, reducing the necessity for full image simulations from large defect models.« less

The two-dimensional tunnel structures of K3Sb5O14 and K2Sb4O11

NASA Technical Reports Server (NTRS)

Hong, H. Y.-P.

1974-01-01

The structures of K3Sb5O14 and K2Sb4O11 have been solved by the single-crystal X-ray direct method and the heavy-atom method, respectively. The structure of K3Sb5O14 is orthorhombic, with space group Pbam and cell parameters a = 24.247 (4), b = 7.157 (2), c = 7.334 (2) A, Z = 4. The structure of K2Sb4O11 is monoclinic, with space group C2/m and cell parameters a = 19.473 (4), b = 7.542 (1), c = 7.198 (1) A, beta = 94.82 (2) deg, Z = 4. A full-matrix least-squares refinement gave R = 0.072 and R = 0.067, respectively. In both structures, oxygen atoms form an octahedron around each Sb atom and an irregular polyhedron around each K atom. By sharing corners and edges, the octahedra form a skeleton network having intersecting b-axis and c-axis tunnels. The K(+) ions, which have more than ten oxygen near neighbors, are located in these tunnels. Evidence for K(+)-ion transport within and between tunnels comes from ion exchange of the alkali ions in molten salts and anisotropic temperature factors that are anomalously large in the direction of the tunnels.

Deformable complex network for refining low-resolution X-ray structures

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

Zhang, Chong; Wang, Qinghua; Ma, Jianpeng, E-mail: jpma@bcm.edu

2015-10-27

A new refinement algorithm called the deformable complex network that combines a novel angular network-based restraint with a deformable elastic network model in the target function has been developed to aid in structural refinement in macromolecular X-ray crystallography. In macromolecular X-ray crystallography, building more accurate atomic models based on lower resolution experimental diffraction data remains a great challenge. Previous studies have used a deformable elastic network (DEN) model to aid in low-resolution structural refinement. In this study, the development of a new refinement algorithm called the deformable complex network (DCN) is reported that combines a novel angular network-based restraint withmore » the DEN model in the target function. Testing of DCN on a wide range of low-resolution structures demonstrated that it constantly leads to significantly improved structural models as judged by multiple refinement criteria, thus representing a new effective refinement tool for low-resolution structural determination.« less

Enhanced rigid-bond restraints

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

Thorn, Andrea; Dittrich, Birger; Sheldrick, George M., E-mail: gsheldr@shelx.uni-ac.gwdg.de

2012-07-01

An extension is proposed to the rigid-bond description of atomic thermal motion in crystals. The rigid-bond model [Hirshfeld (1976 ▶). Acta Cryst. A32, 239–244] states that the mean-square displacements of two atoms are equal in the direction of the bond joining them. This criterion is widely used for verification (as intended by Hirshfeld) and also as a restraint in structure refinement as suggested by Rollett [Crystallographic Computing (1970 ▶), edited by F. R. Ahmed et al., pp. 167–181. Copenhagen: Munksgaard]. By reformulating this condition, so that the relative motion of the two atoms is required to be perpendicular to themore » bond, the number of restraints that can be applied per anisotropic atom is increased from about one to about three. Application of this condition to 1,3-distances in addition to the 1,2-distances means that on average just over six restraints can be applied to the six anisotropic displacement parameters of each atom. This concept is tested against very high resolution data of a small peptide and employed as a restraint for protein refinement at more modest resolution (e.g. 1.7 Å)« less

Incorporation of rare earth elements in titanite: Stabilization of the A2/a dimorph by creation of antiphase boundaries

USGS Publications Warehouse

Hughes, J.M.; Bloodaxe, E.S.; Hanchar, J.M.; Foord, E.E.

1997-01-01

The atomic arrangement of a natural rare-earth-rich titanite and two synthetic rare-earth-doped titanites have been refined in space group A2/a, and the atomic arrangement of an undoped P21/a synthetic titanite was also refined for comparison. Previous work has shown that titanite possesses a domain structure, with domains formed of like-displaced Ti atoms in the [100] octahedral chains. P21/a titanite results when the crystal is formed of a single domain, but as Ti-reversal sites occur in the octahedral chain the apparent A2/a structure results from the average of antiphase domains. Antiphase boundaries occur at O1, which is alternately overbonded or underbonded at the boundaries, depending on the displacement of the neighboring Ti atoms. Type 2 antiphase boundaries exist where two Ti atoms are displaced away from the intervening O1 atom and are energetically unfavorable because of underbonding of that O1 atom. However, substitution of a trivalent rare earth element in the adjacent Ca2+ site relieves that underbonding, favoring the creation of type 2 antiphase boundaries and stabilization of the A2/a dimorph. The results of high-precision crystal structure analyses demonstrate that rare earth substituents for Ca stabilize the A2/a dimorph at lower substitution levels than required for octahedral substitutions.

Liquid Alumina: Detailed Atomic Coordination Determined from Neutron Diffraction Data Using Empirical Potential Structure Refinement

NASA Astrophysics Data System (ADS)

Landron, C.; Hennet, L.; Jenkins, T. E.; Greaves, G. N.; Coutures, J. P.; Soper, A. K.

2001-05-01

The neutron scattering structure factor SN\\(Q\\) for a 40 mg drop of molten alumina ( Al2O3) held at 2500 K, using a laser-heated aerodynamic levitation furnace, is measured for the first time. A 1700 atom model of liquid alumina is generated from these data using the technique of empirical potential structural refinement. About 62% of the aluminum sites are 4-fold coordinated, matching the mostly triply coordinated oxygen sites, but some 24% of the aluminum sites are 5-fold coordinated. The octahedral aluminum sites found in crystalline α-Al2O3 occur only at the 2% level in liquid alumina.

Unambiguous determination of H-atom positions: comparing results from neutron and high-resolution X-ray crystallography.

PubMed

Gardberg, Anna S; Del Castillo, Alexis Rae; Weiss, Kevin L; Meilleur, Flora; Blakeley, Matthew P; Myles, Dean A A

2010-05-01

The locations of H atoms in biological structures can be difficult to determine using X-ray diffraction methods. Neutron diffraction offers a relatively greater scattering magnitude from H and D atoms. Here, 1.65 A resolution neutron diffraction studies of fully perdeuterated and selectively CH(3)-protonated perdeuterated crystals of Pyrococcus furiosus rubredoxin (D-rubredoxin and HD-rubredoxin, respectively) at room temperature (RT) are described, as well as 1.1 A resolution X-ray diffraction studies of the same protein at both RT and 100 K. The two techniques are quantitatively compared in terms of their power to directly provide atomic positions for D atoms and analyze the role played by atomic thermal motion by computing the sigma level at the D-atom coordinate in simulated-annealing composite D-OMIT maps. It is shown that 1.65 A resolution RT neutron data for perdeuterated rubredoxin are approximately 8 times more likely overall to provide high-confidence positions for D atoms than 1.1 A resolution X-ray data at 100 K or RT. At or above the 1.0sigma level, the joint X-ray/neutron (XN) structures define 342/378 (90%) and 291/365 (80%) of the D-atom positions for D-rubredoxin and HD-rubredoxin, respectively. The X-ray-only 1.1 A resolution 100 K structures determine only 19/388 (5%) and 8/388 (2%) of the D-atom positions above the 1.0sigma level for D-rubredoxin and HD-rubredoxin, respectively. Furthermore, the improved model obtained from joint XN refinement yielded improved electron-density maps, permitting the location of more D atoms than electron-density maps from models refined against X-ray data only.

Combining density functional theory (DFT) and pair distribution function (PDF) analysis to solve the structure of metastable materials: the case of metakaolin.

PubMed

White, Claire E; Provis, John L; Proffen, Thomas; Riley, Daniel P; van Deventer, Jannie S J

2010-04-07

Understanding the atomic structure of complex metastable (including glassy) materials is of great importance in research and industry, however, such materials resist solution by most standard techniques. Here, a novel technique combining thermodynamics and local structure is presented to solve the structure of the metastable aluminosilicate material metakaolin (calcined kaolinite) without the use of chemical constraints. The structure is elucidated by iterating between least-squares real-space refinement using neutron pair distribution function data, and geometry optimisation using density functional modelling. The resulting structural representation is both energetically feasible and in excellent agreement with experimental data. This accurate structural representation of metakaolin provides new insight into the local environment of the aluminium atoms, with evidence of the existence of tri-coordinated aluminium. By the availability of this detailed chemically feasible atomic description, without the need to artificially impose constraints during the refinement process, there exists the opportunity to tailor chemical and mechanical processes involving metakaolin and other complex metastable materials at the atomic level to obtain optimal performance at the macro-scale.

Entangling two unequal atoms through a common bath

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

Benatti, F.; Marzolino, U.; Istituto Nazionale di Fisica Nucleare, Sezione di Trieste, I-34014 Trieste

The evolution of two, noninteracting, two-level atoms immersed in a weakly coupled bath can be described by a refined, time-coarse-grained Markovian evolution, still preserving complete positivity. We find that this improved, reduced dynamics is able to entangle the two atoms even when their internal frequencies are unequal, an effect that appears impossible in the standard weak-coupling-limit approach. We study in detail this phenomenon for an environment made of quantum fields.

Exploiting structure similarity in refinement: automated NCS and target-structure restraints in BUSTER

PubMed Central

Smart, Oliver S.; Womack, Thomas O.; Flensburg, Claus; Keller, Peter; Paciorek, Włodek; Sharff, Andrew; Vonrhein, Clemens; Bricogne, Gérard

2012-01-01

Maximum-likelihood X-ray macromolecular structure refinement in BUSTER has been extended with restraints facilitating the exploitation of structural similarity. The similarity can be between two or more chains within the structure being refined, thus favouring NCS, or to a distinct ‘target’ structure that remains fixed during refinement. The local structural similarity restraints (LSSR) approach considers all distances less than 5.5 Å between pairs of atoms in the chain to be restrained. For each, the difference from the distance between the corresponding atoms in the related chain is found. LSSR applies a restraint penalty on each difference. A functional form that reaches a plateau for large differences is used to avoid the restraints distorting parts of the structure that are not similar. Because LSSR are local, there is no need to separate out domains. Some restraint pruning is still necessary, but this has been automated. LSSR have been available to academic users of BUSTER since 2009 with the easy-to-use -autoncs and -­target target.pdb options. The use of LSSR is illustrated in the re-refinement of PDB entries 5rnt, where -target enables the correct ligand-binding structure to be found, and 1osg, where -autoncs contributes to the location of an additional copy of the cyclic peptide ligand. PMID:22505257

Free kick instead of cross-validation in maximum-likelihood refinement of macromolecular crystal structures

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

Pražnikar, Jure; University of Primorska,; Turk, Dušan, E-mail: dusan.turk@ijs.si

2014-12-01

The maximum-likelihood free-kick target, which calculates model error estimates from the work set and a randomly displaced model, proved superior in the accuracy and consistency of refinement of crystal structures compared with the maximum-likelihood cross-validation target, which calculates error estimates from the test set and the unperturbed model. The refinement of a molecular model is a computational procedure by which the atomic model is fitted to the diffraction data. The commonly used target in the refinement of macromolecular structures is the maximum-likelihood (ML) function, which relies on the assessment of model errors. The current ML functions rely on cross-validation. Theymore » utilize phase-error estimates that are calculated from a small fraction of diffraction data, called the test set, that are not used to fit the model. An approach has been developed that uses the work set to calculate the phase-error estimates in the ML refinement from simulating the model errors via the random displacement of atomic coordinates. It is called ML free-kick refinement as it uses the ML formulation of the target function and is based on the idea of freeing the model from the model bias imposed by the chemical energy restraints used in refinement. This approach for the calculation of error estimates is superior to the cross-validation approach: it reduces the phase error and increases the accuracy of molecular models, is more robust, provides clearer maps and may use a smaller portion of data for the test set for the calculation of R{sub free} or may leave it out completely.« less

Simulation of Auger electron emission from nanometer-size gold targets using the Geant4 Monte Carlo simulation toolkit

NASA Astrophysics Data System (ADS)

Incerti, S.; Suerfu, B.; Xu, J.; Ivantchenko, V.; Mantero, A.; Brown, J. M. C.; Bernal, M. A.; Francis, Z.; Karamitros, M.; Tran, H. N.

2016-04-01

A revised atomic deexcitation framework for the Geant4 general purpose Monte Carlo toolkit capable of simulating full Auger deexcitation cascades was implemented in June 2015 release (version 10.2 Beta). An overview of this refined framework and testing of its capabilities is presented for the irradiation of gold nanoparticles (NP) with keV photon and MeV proton beams. The resultant energy spectra of secondary particles created within and that escape the NP are analyzed and discussed. It is anticipated that this new functionality will improve and increase the use of Geant4 in the medical physics, radiobiology, nanomedicine research and other low energy physics fields.

Rhombohedrally Distorted γ-Au 5–x Zn 8+y Phases in the Au–Zn System

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

Thimmaiah, Srinivasa; Miller, Gordon J.

2013-02-04

The region of the Au–Zn phase diagram encompassing γ-brass-type phases has been studied experimentally from 45 to 85 atom % Zn. The γ phases were obtained directly from the pure elements by heating to 680 °C in evacuated silica tubes, followed by annealing at 300 °C. Powder X-ray and single-crystal diffraction studies show that γ-“Au5Zn8” phases adopt a rhombohedrally distorted Cr5Al8 structure type rather than the cubic Cu5Zn8 type. The refined compositions from two single crystals extracted from the Zn- and Au-rich loadings are Au4.27(3)Zn8.26(3)γ0.47 (I) and Au4.58(3)Zn8.12(3)γ0.3 (II), respectively (γ = vacancy). These (I and II) refinements indicated bothmore » nonstatistical mixing of Au and Zn atoms as well as partially ordered vacancy distributions. The structures of these γ phases were solved in the acentric space group R3m (No. 160, Z = 6), and the observed lattice parameters from powder patterns were found to be a = 13.1029(6) and 13.1345(8) Å and c = 8.0410(4) and 8.1103(6) Å for crystals I and II, respectively. According to single-crystal refinements, the vacancies were found on the outer tetrahedron (OT) and octahedron (OH) of the 26-atom cluster. Single-crystal structural refinement clearly showed that the vacancy content per unit cell increases with increasing Zn, or valence-electron concentration. Electronic structure calculations, using the tight-binding linear muffin-tin orbital method with the atomic-sphere approximation (TB-LMTO-ASA) method, indicated the presence of a well-pronounced pseudogap at the Fermi level for “Au5Zn8” as the representative composition, an outcome that is consistent with the Hume–Rothery interpretation of γ brass.« less

Refined potentials for rare gas atom adsorption on rare gas and alkali-halide surfaces

NASA Technical Reports Server (NTRS)

Wilson, J. W.; Heinbockel, J. H.; Outlaw, R. A.

1985-01-01

The utilization of models of interatomic potential for physical interaction to estimate the long range attractive potential for rare gases and ions is discussed. The long range attractive force is calculated in terms of the atomic dispersion properties. A data base of atomic dispersion parameters for rare gas atoms, alkali ion, and halogen ions is applied to the study of the repulsive core; the procedure for evaluating the repulsive core of ion interactions is described. The interaction of rare gas atoms on ideal rare gas solid and alkali-halide surfaces is analyzed; zero coverage absorption potentials are derived.

GalaxyRefineComplex: Refinement of protein-protein complex model structures driven by interface repacking.

PubMed

Heo, Lim; Lee, Hasup; Seok, Chaok

2016-08-18

Protein-protein docking methods have been widely used to gain an atomic-level understanding of protein interactions. However, docking methods that employ low-resolution energy functions are popular because of computational efficiency. Low-resolution docking tends to generate protein complex structures that are not fully optimized. GalaxyRefineComplex takes such low-resolution docking structures and refines them to improve model accuracy in terms of both interface contact and inter-protein orientation. This refinement method allows flexibility at the protein interface and in the overall docking structure to capture conformational changes that occur upon binding. Symmetric refinement is also provided for symmetric homo-complexes. This method was validated by refining models produced by available docking programs, including ZDOCK and M-ZDOCK, and was successfully applied to CAPRI targets in a blind fashion. An example of using the refinement method with an existing docking method for ligand binding mode prediction of a drug target is also presented. A web server that implements the method is freely available at http://galaxy.seoklab.org/refinecomplex.

Gyre and gimble: a maximum-likelihood replacement for Patterson correlation refinement.

PubMed

McCoy, Airlie J; Oeffner, Robert D; Millán, Claudia; Sammito, Massimo; Usón, Isabel; Read, Randy J

2018-04-01

Descriptions are given of the maximum-likelihood gyre method implemented in Phaser for optimizing the orientation and relative position of rigid-body fragments of a model after the orientation of the model has been identified, but before the model has been positioned in the unit cell, and also the related gimble method for the refinement of rigid-body fragments of the model after positioning. Gyre refinement helps to lower the root-mean-square atomic displacements between model and target molecular-replacement solutions for the test case of antibody Fab(26-10) and improves structure solution with ARCIMBOLDO_SHREDDER.

Structural refinement of vitreous silica bilayers

NASA Astrophysics Data System (ADS)

Sadjadi, Mahdi; Wilson, Mark; Thorpe, M. F.

The importance of glasses resides not only in their applications but in fundamental questions that they put forth. The continuous random network model can successfully describe the glass structure, but determining details, like ring statistics, has always been difficult using only diffraction data. But recent atomic images of 2D vitreous silica bilayers can offer valuable new insights which are hard to be observed directly in 3D silica models/experiments (for references see). However, the experimental results are prone to uncertainty in atomic positions, systematic errors, and being finite. We employ special boundary conditions developed for such networks to refine the experimental structures. We show the best structure can be found by using various potentials to maximize information gained from the experimental samples. We find a range of densities, the so-called flexibility window, in which tetrahedra are perfect. We compare results from simulations using harmonic potentials, MD with atomic polarizabilities included and DFT. We should thank David Drabold and Bishal Bhattarai for useful discussions. Support through NSF Grant # DMS 1564468 is gratefully acknowledged.

Refined tip preparation by electrochemical etching and ultrahigh vacuum treatment to obtain atomically sharp tips for scanning tunneling microscope and atomic force microscope.

PubMed

Hagedorn, Till; El Ouali, Mehdi; Paul, William; Oliver, David; Miyahara, Yoichi; Grütter, Peter

2011-11-01

A modification of the common electrochemical etching setup is presented. The described method reproducibly yields sharp tungsten tips for usage in the scanning tunneling microscope and tuning fork atomic force microscope. In situ treatment under ultrahigh vacuum (p ≤10(-10) mbar) conditions for cleaning and fine sharpening with minimal blunting is described. The structure of the microscopic apex of these tips is atomically resolved with field ion microscopy and cross checked with field emission. © 2011 American Institute of Physics

Direct Observation of Charge Transfer at a MgO(111) Surface

NASA Astrophysics Data System (ADS)

Subramanian, A.; Marks, L. D.; Warschkow, O.; Ellis, D. E.

2004-01-01

Transmission electron diffraction (TED) combined with direct methods have been used to study the √(3)×√(3)R30° reconstruction on the polar (111) surface of MgO and refine the valence charge distribution. The surface is nonstoichiometric and is terminated by a single magnesium atom. A charge-compensating electron hole is localized in the next oxygen layer and there is a nominal charge transfer from the oxygen atoms to the top magnesium atom. The partial charges that we obtain for the surface atoms are in reasonable agreement with empirical bond-valence estimations.

Hydrogen positions in single nanocrystals revealed by electron diffraction

NASA Astrophysics Data System (ADS)

Palatinus, L.; Brázda, P.; Boullay, P.; Perez, O.; Klementová, M.; Petit, S.; Eigner, V.; Zaarour, M.; Mintova, S.

2017-01-01

The localization of hydrogen atoms is an essential part of crystal structure analysis, but it is difficult because of their small scattering power. We report the direct localization of hydrogen atoms in nanocrystalline materials, achieved using the recently developed approach of dynamical refinement of precession electron diffraction tomography data. We used this method to locate hydrogen atoms in both an organic (paracetamol) and an inorganic (framework cobalt aluminophosphate) material. The results demonstrate that the technique can reliably reveal fine structural details, including the positions of hydrogen atoms in single crystals with micro- to nanosized dimensions.

Exploiting structure similarity in refinement: automated NCS and target-structure restraints in BUSTER

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

Smart, Oliver S., E-mail: osmart@globalphasing.com; Womack, Thomas O.; Flensburg, Claus

2012-04-01

Local structural similarity restraints (LSSR) provide a novel method for exploiting NCS or structural similarity to an external target structure. Two examples are given where BUSTER re-refinement of PDB entries with LSSR produces marked improvements, enabling further structural features to be modelled. Maximum-likelihood X-ray macromolecular structure refinement in BUSTER has been extended with restraints facilitating the exploitation of structural similarity. The similarity can be between two or more chains within the structure being refined, thus favouring NCS, or to a distinct ‘target’ structure that remains fixed during refinement. The local structural similarity restraints (LSSR) approach considers all distances less thanmore » 5.5 Å between pairs of atoms in the chain to be restrained. For each, the difference from the distance between the corresponding atoms in the related chain is found. LSSR applies a restraint penalty on each difference. A functional form that reaches a plateau for large differences is used to avoid the restraints distorting parts of the structure that are not similar. Because LSSR are local, there is no need to separate out domains. Some restraint pruning is still necessary, but this has been automated. LSSR have been available to academic users of BUSTER since 2009 with the easy-to-use -autoncs and @@target target.pdb options. The use of LSSR is illustrated in the re-refinement of PDB entries http://scripts.iucr.org/cgi-bin/cr.cgi?rm, where -target enables the correct ligand-binding structure to be found, and http://scripts.iucr.org/cgi-bin/cr.cgi?rm, where -autoncs contributes to the location of an additional copy of the cyclic peptide ligand.« less

Rietveld refinement of the crystal structures of Rb2 XSi5O12 (X = Ni, Mn).

PubMed

Bell, Anthony M T; Henderson, C Michael B

2016-02-01

The synthetic leucite silicate framework mineral analogues Rb2 XSi5O12 {X = Ni [dirubidium nickel(II) penta-silicate] and Mn [dirubidium manganese(II) penta-silicate]} have been prepared by high-temperature solid-state synthesis. The results of Rietveld refinements, using X-ray powder diffraction data collected using Cu Kα X-rays, show that the title compounds crystallize in the space group Pbca and adopt the cation-ordered structure of Cs2CdSi5O12 and other leucites. The structures consist of tetra-hedral SiO4 and XO4 units sharing corners to form a partially substituted silicate framework. Extraframework Rb(+) cations sit in channels in the framework. All atoms occupy the 8c general position for this space group. In these refined structures, silicon and X atoms are ordered onto separate tetra-hedrally coordinated sites (T-sites). However, the Ni displacement parameter and the Ni-O bond lengths suggest that for the X = Ni sample, there may actually be some T-site cation disorder.

Rietveld refinement of the crystal structures of Rb2 XSi5O12 (X = Ni, Mn)

PubMed Central

Bell, Anthony M. T.; Henderson, C. Michael B.

2016-01-01

The synthetic leucite silicate framework mineral analogues Rb2 XSi5O12 {X = Ni [dirubidium nickel(II) penta­silicate] and Mn [dirubidium manganese(II) penta­silicate]} have been prepared by high-temperature solid-state synthesis. The results of Rietveld refinements, using X-ray powder diffraction data collected using Cu Kα X-rays, show that the title compounds crystallize in the space group Pbca and adopt the cation-ordered structure of Cs2CdSi5O12 and other leucites. The structures consist of tetra­hedral SiO4 and XO4 units sharing corners to form a partially substituted silicate framework. Extraframework Rb+ cations sit in channels in the framework. All atoms occupy the 8c general position for this space group. In these refined structures, silicon and X atoms are ordered onto separate tetra­hedrally coordinated sites (T-sites). However, the Ni displacement parameter and the Ni—O bond lengths suggest that for the X = Ni sample, there may actually be some T-site cation disorder. PMID:26958399

Structure resolution by electron diffraction tomography of the complex layered iron-rich Fe-2234-type Sr{sub 5}Fe{sub 6}O{sub 15.4}

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

Lepoittevin, Christophe, E-mail: christophe.lepoittevin@neel.cnrs.fr

2016-10-15

The crystal structure of the strontium ferrite Sr{sub 5}Fe{sub 6}O{sub 15.4}, was solved by direct methods on electron diffraction tomography data acquired on a transmission electron microscope. The refined cell parameters are a=27.4047(3) Å, b=5.48590(7) Å and c=42.7442(4) Å in Fm2m symmetry. Its structure is built up from the intergrowth sequence between a quadruple perovskite-type layer with a complex rock-salt (RS)-type block. In the latter iron atoms are found in two different environments : tetragonal pyramid and tetrahedron. The structural model was refined by Rietveld method based on the powder X-ray diffraction pattern. - Highlights: • Complex structure of Sr{submore » 5}Fe{sub 6}O{sub 15.4} solved by electron diffraction tomography. • Observed Fourier maps allow determining missing oxygen atoms in the structure. • Structural model refined from powder X-ray diffraction data. • Intergrowth between quadruple perovskite layer with double rock-salt-type layer.« less

Simulation of Auger electron emission from nanometer-size gold targets using the Geant4 Monte Carlo simulation toolkit

DOE PAGES

Incerti, S.; Suerfu, B.; Xu, J.; ...

2016-02-16

We report that a revised atomic deexcitation framework for the Geant4 general purpose Monte Carlo toolkit capable of simulating full Auger deexcitation cascades was implemented in June 2015 release (version 10.2 Beta). An overview of this refined framework and testing of its capabilities is presented for the irradiation of gold nanoparticles (NP) with keV photon and MeV proton beams. The resultant energy spectra of secondary particles created within and that escape the NP are analyzed and discussed. It is anticipated that this new functionality will improve and increase the use of Geant4 in the medical physics, radiobiology, nanomedicine research andmore » other low energy physics fields.« less

PROGEN: An automated modelling algorithm for the generation of complete protein structures from the α-carbon atomic coordinates

NASA Astrophysics Data System (ADS)

Mandal, Chhabinath; Linthicum, D. Scott

1993-04-01

A modelling algorithm (PROGEN) for the generation of complete protein atomic coordinates from only the α-carbon coordinates is described. PROGEN utilizes an optimal geometry parameter (OGP) database for the positioning of atoms for each amino acid of the polypeptide model. The OGP database was established by examining the statistical correlations between 23 different intra-peptide and inter-peptide geometric parameters relative to the α-carbon distances for each amino acid in a library of 19 known proteins from the Brookhaven Protein Database (BPDB). The OGP files for specific amino acids and peptides were used to generate the atomic positions, with respect to α-carbons, for main-chain and side-chain atoms in the modelled structure. Refinement of the initial model was accomplished using energy minimization (EM) and molecular dynamics techniques. PROGEN was tested using 60 known proteins in the BPDB, representing a wide spectrum of primary and secondary structures. Comparison between PROGEN models and BPDB crystal reference structures gave r.m.s.d. values for peptide main-chain atoms between 0.29 and 0.76 Å, with a grand average of 0.53 Å for all 60 models. The r.m.s.d. for all non-hydrogen atoms ranged between 1.44 and 1.93 Å for the 60 polypeptide models. PROGEN was also able to make the correct assignment of cis- or trans-proline configurations in the protein structures examined. PROGEN offers a fully automatic building and refinement procedure and requires no special or specific structural considerations for the protein to be modelled.

REFINING FLUORINATED COMPOUNDS

DOEpatents

Linch, A.L.

1963-01-01

This invention relates to the method of refining a liquid perfluorinated hydrocarbon oil containing fluorocarbons from 12 to 28 carbon atoms per molecule by distilling between 150 deg C and 300 deg C at 10 mm Hg absolute pressure. The perfluorinated oil is washed with a chlorinated lower aliphatic hydrocarbon, which mairtains a separate liquid phase when mixed with the oil. Impurities detrimental to the stability of the oil are extracted by the chlorinated lower aliphatic hydrocarbon. (AEC)

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.

REFMAC5 for the refinement of macromolecular crystal structures

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

Murshudov, Garib N., E-mail: garib@ysbl.york.ac.uk; Skubák, Pavol; Lebedev, Andrey A.

The general principles behind the macromolecular crystal structure refinement program REFMAC5 are described. This paper describes various components of the macromolecular crystallographic refinement program REFMAC5, which is distributed as part of the CCP4 suite. REFMAC5 utilizes different likelihood functions depending on the diffraction data employed (amplitudes or intensities), the presence of twinning and the availability of SAD/SIRAS experimental diffraction data. To ensure chemical and structural integrity of the refined model, REFMAC5 offers several classes of restraints and choices of model parameterization. Reliable models at resolutions at least as low as 4 Å can be achieved thanks to low-resolution refinement toolsmore » such as secondary-structure restraints, restraints to known homologous structures, automatic global and local NCS restraints, ‘jelly-body’ restraints and the use of novel long-range restraints on atomic displacement parameters (ADPs) based on the Kullback–Leibler divergence. REFMAC5 additionally offers TLS parameterization and, when high-resolution data are available, fast refinement of anisotropic ADPs. Refinement in the presence of twinning is performed in a fully automated fashion. REFMAC5 is a flexible and highly optimized refinement package that is ideally suited for refinement across the entire resolution spectrum encountered in macromolecular crystallography.« less

Polarizable Force Field for DNA Based on the Classical Drude Oscillator: I. Refinement Using Quantum Mechanical Base Stacking and Conformational Energetics.

PubMed

Lemkul, Justin A; MacKerell, Alexander D

2017-05-09

Empirical force fields seek to relate the configuration of a set of atoms to its energy, thus yielding the forces governing its dynamics, using classical physics rather than more expensive quantum mechanical calculations that are computationally intractable for large systems. Most force fields used to simulate biomolecular systems use fixed atomic partial charges, neglecting the influence of electronic polarization, instead making use of a mean-field approximation that may not be transferable across environments. Recent hardware and software developments make polarizable simulations feasible, and to this end, polarizable force fields represent the next generation of molecular dynamics simulation technology. In this work, we describe the refinement of a polarizable force field for DNA based on the classical Drude oscillator model by targeting quantum mechanical interaction energies and conformational energy profiles of model compounds necessary to build a complete DNA force field. The parametrization strategy employed in the present work seeks to correct weak base stacking in A- and B-DNA and the unwinding of Z-DNA observed in the previous version of the force field, called Drude-2013. Refinement of base nonbonded terms and reparametrization of dihedral terms in the glycosidic linkage, deoxyribofuranose rings, and important backbone torsions resulted in improved agreement with quantum mechanical potential energy surfaces. Notably, we expand on previous efforts by explicitly including Z-DNA conformational energetics in the refinement.

Periodic Density Functional Theory Study of the Structure, Raman Spectrum, and Mechanical Properties of Schoepite Mineral.

PubMed

Colmenero, Francisco; Cobos, Joaquín; Timón, Vicente

2018-04-16

The structure and Raman spectrum of schoepite mineral, [(UO 2 ) 8 O 2 (OH) 12 ]·12H 2 O, was studied by means of theoretical calculations. The computations were carried out by using density functional theory with plane waves and pseudopotentials. A norm-conserving pseudopotential specific for the U atom developed in a previous work was employed. Because it was not possible to locate H atoms directly from X-ray diffraction (XRD) data by structure refinement in previous experimental studies, all of the positions of the H atoms in the full unit cell were determined theoretically. The structural results, including the lattice parameters, bond lengths, bond angles, and powder XRD pattern, were found to be in good agreement with their experimental counterparts. However, the calculations performed using the unit cell designed by Ostanin and Zeller in 2007, involving half of the atoms of the full unit cell, led to significant errors in the computed powder XRD pattern. Furthermore, Ostanin and Zeller's unit cell contains hydronium ions, H 3 O + , which are incompatible with the experimental information. Therefore, while the use of this schoepite model may be a very useful approximation requiring a much smaller amount of computational effort, the full unit cell should be used to study this mineral accurately. The Raman spectrum was also computed by means of density functional perturbation theory and compared with the experimental spectrum. The results were also in agreement with the experimental data. A normal-mode analysis of the theoretical spectra was performed to assign the main bands of the Raman spectrum. This assignment significantly improved the current empirical assignment of the bands of the Raman spectrum of schoepite mineral. In addition, the equation of state and elastic properties of this mineral were determined. The crystal structure of schoepite was found to be stable mechanically and dynamically. Schoepite can be described as a brittle material exhibiting small anisotropy and large compressibility in the direction perpendicular to the layers, which characterize its structure. The calculated bulk modulus, B, was ∼35 GPa.

Conformational study and structure of N-(2,5-methylphenyl)salicylaldimine

NASA Astrophysics Data System (ADS)

Elmali, A.; Elerman, Y.; Zeyrek, C. T.

1998-02-01

N-(2,5-methylphenyl)salicylaldimine (C 15H 15NO) has been investigated by X-ray analysis and AM1 semi-empirical quantum mechanical method. The crystal is in the orthorhombic space group P2 12 12 1 with a = 6.839(1), b = 7.720(4), c = 23.183(3) Å, V = 1224.1(2) Å3, Z = 4, Dc = 1.222 g cm -3 and μ(Mo K α) = 0.076 mm -1. The title structure was solved by direct methods and refined to R = 0.0364 for 1489 reflections [ I > 2 σ( I)] by full-matrix anisotropic least-squares methods. The title compound is photochromic and the molecule is not planar. There is a strong intramolecular hydrogen bond of distance 2.604(2) Å between the hydroxyl oxygen atom and imine nitrogen atom, the hydrogen atom essentially being bonded to the oxygen atom. Minimum energy conformations from AM1 were calculated as a function of three torsion angles, θ1 (C8N1C7C6), θ2 (C9C8N1C7) and θ3 (N1C7C6C5), varied every 10°. The optimized geometry of the crystal structure corresponding to non-planar conformation is the most stable conformation in all calculations. The results strongly indicate that the minimum energy conformation is primarily determined by non-bonded hydrogen-hydrogen repulsions.

Atomic structure of unligated laccase from Cerrena maxima at 1.76 A with molecular oxygen and hydrogen peroxide

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

Zhukova, Yu. N., E-mail: amm@ns.crys.ras.ru; Lyashenko, A. V.; Lashkov, A. A.

2010-05-15

The three-dimensional structure of unligated laccase from Cerrena maxima was established by X-ray diffraction at 1.76-A resolution; R{sub work} = 18.07%, R{sub free} = 21.71%, rmsd of bond lengths, bond angles, and chiral angles are 0.008 A, 1.19{sup o}, and 0.077{sup o}, respectively. The coordinate error for the refined structure estimated from the Luzzati plot is 0.195 A. The maximum average error in the atomic coordinates is 0.047 A. A total of 99.4% of amino-acid residues of the polypeptide chain are in the most favorable, allowable, and accessible regions of the Ramachandran plot. The three-dimensional structures of the complexes ofmore » laccase from C. maxima with molecular oxygen and hydrogen peroxide were determined by the molecular simulation. These data provide insight into the structural aspect of the mechanism of the enzymatic cycle. The structure factors and the refined atomic coordinates were deposited in the Protein Data Bank (PDB-ID code is 3DIV).« less

Empirical mass formula with proton-neutron interaction

NASA Astrophysics Data System (ADS)

Tachibana, Takahiro; Uno, Masahiro; Yamada, So; Yamada, Masami

1987-12-01

An atomic mass formula consisting of a gross part, and averge even-odd part and an empirical shell part is studied. The gross part is, apart from a small atomic term, taken to be the sum of nucleon rest masses. Coulomb energies and a polynomial in A1/3 and ‖N-Z‖/A. The shell part includes, in addition to proton and neutron support of nuclear magicities and the cooperative deformation effect. After the first construction of such a formula, refinements have been made in two respects. One is a separate treatment of Z=N odd-odd nuclei suggested by a quartet model, and the other is an improvement of the proton neutron interaction term. By these refinements the root-mean-square deviation of calculated masses from the 1986 Audi-Wapstra masses has been reduced from 538 keV to 460 keV.

Structural analysis according to reduced data: VIII. Refinement of the extended model of aspherical atoms

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

Dudka, A. P.

A program for the refinement of the model of aspherical atoms within the Stewart-Hansen-Coppens formalism has been developed. Deformation scattering up to the 8th expansion order in multipoles has been taken into account for the first time. The program was tested for 11 crystals. The effect of the result of interpolation of radial scattering curves on the model parameters is considered. The importance of introduction of multipoles of high (5th-8th) orders into the model for a number of crystals is shown. The use of the extended multipole model for a silicon crystal revealed some new specific features of the electronicmore » structure: consideration of multipoles up to the 7th order makes it possible to explain the intensity of the forbidden 222 reflection.« less

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

Bernander, O.; Haga, I.; Segerberg, F.

BS>From international nuclear industries fair; Basel, Switzerland (16 Oct 1972). Although the present status of the boiling water reactor is one of proven technology, design refinements and technical innovations are still being made to further improve reliability, economy and safety. The new standard ASEA- ATOM BWR features a number of such refinements and design improvements involving main circulation punips, containment design, refuelling system and off-gas treatment plant. In some respects the nuclear and hydraulic design of the ASEA- ATOM BWR differs from that adopted by other BWR manufacturers. Since the Oskarshamn I plant was the first nuclear power station havingmore » these features an extensive physics and hydraulics test program was made during the reactor start- up. The results of these tests have fully confirmed the ability of calculation methods to predict the behavior of the reactor. (auth)« less

Hydrogen bonding in goldichite, KFe(SO4)2ṡ4H2O: structure refinement

NASA Astrophysics Data System (ADS)

Yang, Zhuming; Giester, Gerald

2018-02-01

The crystal structure of goldichite KFe(SO4)2ṡ4H2O was determined on a single crystal from the Baiyinchang copper deposit, Gansu, China. [ P121/ c1, a = 10.395(2), b = 10.475(2), c = 9.0875(18) Å, β = 101.65(3)°, V = 969.1(3) Å3, Z = 4]. All non-H atoms were refined with anisotropic displacement parameters and positions of H-atoms were determined by difference Fourier methods and refined from X-ray diffraction data. The crystal structure of goldichite consists of corrugated sheets parallel to the (100) plane by sharing corners between FeO6 octahedra and SO4 tetrahedra. The interstitial potassium atom exhibits a [KO7(H2O)2] nine-fold coordination, which shares edges to form a column parallel to the c-axis and to build a slab with the corrugated sheet. These slabs are linked in the [100] direction through a network of hydrogen bonds. Three types of hydrogen bonds involve links of slabs: Ow(3)-H(3B)···O(1), Ow(6)-H(6B)···O(11) and Ow(9)-H(9B)···O(11). The FTIR spectrum of goldichite shows a strong absorption between 3384 cm-1 and 3592 cm-1, which is in accordance with the O-H···O distances derived from structure data.

AceDRG: a stereochemical description generator for ligands

PubMed Central

Emsley, Paul; Gražulis, Saulius; Merkys, Andrius; Vaitkus, Antanas

2017-01-01

The program AceDRG is designed for the derivation of stereochemical information about small molecules. It uses local chemical and topological environment-based atom typing to derive and organize bond lengths and angles from a small-molecule database: the Crystallography Open Database (COD). Information about the hybridization states of atoms, whether they belong to small rings (up to seven-membered rings), ring aromaticity and nearest-neighbour information is encoded in the atom types. All atoms from the COD have been classified according to the generated atom types. All bonds and angles have also been classified according to the atom types and, in a certain sense, bond types. Derived data are tabulated in a machine-readable form that is freely available from CCP4. AceDRG can also generate stereochemical information, provided that the basic bonding pattern of a ligand is known. The basic bonding pattern is perceived from one of the computational chemistry file formats, including SMILES, mmCIF, SDF MOL and SYBYL MOL2 files. Using the bonding chemistry, atom types, and bond and angle tables generated from the COD, AceDRG derives the ‘ideal’ bond lengths, angles, plane groups, aromatic rings and chirality information, and writes them to an mmCIF file that can be used by the refinement program REFMAC5 and the model-building program Coot. Other refinement and model-building programs such as PHENIX and BUSTER can also use these files. AceDRG also generates one or more coordinate sets corresponding to the most favourable conformation(s) of a given ligand. AceDRG employs RDKit for chemistry perception and for initial conformation generation, as well as for the interpretation of SMILES strings, SDF MOL and SYBYL MOL2 files. PMID:28177307

Polder maps: Improving OMIT maps by excluding bulk solvent

DOE PAGES

Liebschner, Dorothee; Afonine, Pavel V.; Moriarty, Nigel W.; ...

2017-02-01

The crystallographic maps that are routinely used during the structure-solution workflow are almost always model-biased because model information is used for their calculation. As these maps are also used to validate the atomic models that result from model building and refinement, this constitutes an immediate problem: anything added to the model will manifest itself in the map and thus hinder the validation. OMIT maps are a common tool to verify the presence of atoms in the model. The simplest way to compute an OMIT map is to exclude the atoms in question from the structure, update the corresponding structure factorsmore » and compute a residual map. It is then expected that if these atoms are present in the crystal structure, the electron density for the omitted atoms will be seen as positive features in this map. This, however, is complicated by the flat bulk-solvent model which is almost universally used in modern crystallographic refinement programs. This model postulates constant electron density at any voxel of the unit-cell volume that is not occupied by the atomic model. Consequently, if the density arising from the omitted atoms is weak then the bulk-solvent model may obscure it further. A possible solution to this problem is to prevent bulk solvent from entering the selected OMIT regions, which may improve the interpretative power of residual maps. This approach is called a polder (OMIT) map. Polder OMIT maps can be particularly useful for displaying weak densities of ligands, solvent molecules, side chains, alternative conformations and residues both in terminal regions and in loops. As a result, the tools described in this manuscript have been implemented and are available in PHENIX.« less

Cellular Imaging | Center for Cancer Research

Cancer.gov

Innovative imaging methods developed and refined within CCR revealed atomic-level structures of biological molecules and unveiled dynamic views of a cell’s interior that are driving the design of new treatments and diagnostics for cancer.

Collection of X-ray diffraction data from macromolecular crystals

PubMed Central

Dauter, Zbigniew

2017-01-01

Diffraction data acquisition is the final experimental stage of the crystal structure analysis. All subsequent steps involve mainly computer calculations. Optimally measured and accurate data make the structure solution and refinement easier and lead to more faithful interpretation of the final models. Here, the important factors in data collection from macromolecular crystals are discussed and strategies appropriate for various applications, such as molecular replacement, anomalous phasing, atomic-resolution refinement etc., are presented. Criteria useful for judging the diffraction data quality are also discussed. PMID:28573573

Synthesis, crystal structure, and electrical and magnetic properties of BaMo{sub 6}Te{sub 6}: A novel reduced molybdenum telluride containing infinite chains of trans-face shared Mo{sub 6} octahedra

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

Gall, Philippe; Guizouarn, Thierry; Potel, Michel

Powder samples and single crystals of the new ternary compound BaMo{sub 6}Te{sub 6} were obtained by solid state reaction. The structure was determined by single-crystal X-ray diffraction. BaMo{sub 6}Te{sub 6} crystallizes in the hexagonal space group P6{sub 3}/m (No. 176) with unit-cell parameters a=9.3941(2) Å, c=4.5848(1) Å and Z=1. Full-matrix least-squares refinement on F{sup 2} using 452 independent reflections for 17 refinable parameters resulted in R1=0.0208 and wR2=0.0539. The structure consists of one-dimensional infinite chains of trans-face shared Mo{sub 6} octahedra capped by Se atoms. These chains that are running along the c axis are separated from each other bymore » nine-coordinate Ba atoms. Resistivity measurements on a single crystal indicated that the BaMo{sub 6}Te{sub 6} compound is metallic down to 160 K and semiconductor below. Magnetic susceptibility measurements showed that BaMo{sub 6}Te{sub 6} is weakly diamagnetic with no anomaly at the metal–semiconductor transition. - Graphical abstract: We present here the synthesis, the crystal structure, and the electrical and magnetic properties of the new compound BaMo{sub 6}Te{sub 6} containing infinite chains of trans-face shared Mo{sub 6} octahedra. - Highlights: • BaMo{sub 6}Te{sub 6} contains infinite chains of trans-face-sharing Mo{sub 6} octahedra |Mo{sub 6/2}|{sub ∞}{sup 1}. • Synthesis by solid state reaction. • Single-crystal X-ray study. • Continuous metal–nonmetal transition. • Anderson localization.« less

Empirical mass formula with proton-neutron interaction

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

Tachibana, T.; Uno, M.; Yamada, S.

An atomic mass formula consisting of a gross part, and averge even-odd part and an empirical shell part is studied. The gross part is, apart from a small atomic term, taken to be the sum of nucleon rest masses. Coulomb energies and a polynomial in A/sup 1/3/ and chemically bondN-Zchemically bond/A. The shell part includes, in addition to proton and neutron support of nuclear magicities and the cooperative deformation effect. After the first construction of such a formula, refinements have been made in two respects. One is a separate treatment of Z = N odd-odd nuclei suggested by a quartetmore » model, and the other is an improvement of the proton neutron interaction term. By these refinements the root-mean-square deviation of calculated masses from the 1986 Audi-Wapstra masses has been reduced from 538 keV to 460 keV.« less

Intrinsic stress response of low and high mobility solute additions to Cu thin films

NASA Astrophysics Data System (ADS)

Kaub, Tyler; Anthony, Ryan; Thompson, Gregory B.

2017-12-01

Thin film stress is frequently controlled through adjustments applied to the processing parameters used during film deposition. In this work, we explore how the use of solutes with different intrinsic growth properties influences the residual growth stress development for a common solvent Cu film. The findings demonstrated that the addition of a high atomic mobility solute, Ag, or a low atomic mobility solute, V, results in both alloy films undergoing grain refinement that scaled with increases in the solute content. This grain refinement was associated with solute segregation and was more pronounced in the Cu(Ag) system. The grain size reduction was also associated with an increase in the tensile stresses observed in both alloy sets. These findings indicate that solutes can be used to control the grain size under the same deposition conditions, as well as alter the stress evolution of a growing thin film.

An Embedded Statistical Method for Coupling Molecular Dynamics and Finite Element Analyses

NASA Technical Reports Server (NTRS)

Saether, E.; Glaessgen, E.H.; Yamakov, V.

2008-01-01

The coupling of molecular dynamics (MD) simulations with finite element methods (FEM) yields computationally efficient models that link fundamental material processes at the atomistic level with continuum field responses at higher length scales. The theoretical challenge involves developing a seamless connection along an interface between two inherently different simulation frameworks. Various specialized methods have been developed to solve particular classes of problems. Many of these methods link the kinematics of individual MD atoms with FEM nodes at their common interface, necessarily requiring that the finite element mesh be refined to atomic resolution. Some of these coupling approaches also require simulations to be carried out at 0 K and restrict modeling to two-dimensional material domains due to difficulties in simulating full three-dimensional material processes. In the present work, a new approach to MD-FEM coupling is developed based on a restatement of the standard boundary value problem used to define a coupled domain. The method replaces a direct linkage of individual MD atoms and finite element (FE) nodes with a statistical averaging of atomistic displacements in local atomic volumes associated with each FE node in an interface region. The FEM and MD computational systems are effectively independent and communicate only through an iterative update of their boundary conditions. With the use of statistical averages of the atomistic quantities to couple the two computational schemes, the developed approach is referred to as an embedded statistical coupling method (ESCM). ESCM provides an enhanced coupling methodology that is inherently applicable to three-dimensional domains, avoids discretization of the continuum model to atomic scale resolution, and permits finite temperature states to be applied.

A New Concurrent Multiscale Methodology for Coupling Molecular Dynamics and Finite Element Analyses

NASA Technical Reports Server (NTRS)

Yamakov, Vesselin; Saether, Erik; Glaessgen, Edward H/.

2008-01-01

The coupling of molecular dynamics (MD) simulations with finite element methods (FEM) yields computationally efficient models that link fundamental material processes at the atomistic level with continuum field responses at higher length scales. The theoretical challenge involves developing a seamless connection along an interface between two inherently different simulation frameworks. Various specialized methods have been developed to solve particular classes of problems. Many of these methods link the kinematics of individual MD atoms with FEM nodes at their common interface, necessarily requiring that the finite element mesh be refined to atomic resolution. Some of these coupling approaches also require simulations to be carried out at 0 K and restrict modeling to two-dimensional material domains due to difficulties in simulating full three-dimensional material processes. In the present work, a new approach to MD-FEM coupling is developed based on a restatement of the standard boundary value problem used to define a coupled domain. The method replaces a direct linkage of individual MD atoms and finite element (FE) nodes with a statistical averaging of atomistic displacements in local atomic volumes associated with each FE node in an interface region. The FEM and MD computational systems are effectively independent and communicate only through an iterative update of their boundary conditions. With the use of statistical averages of the atomistic quantities to couple the two computational schemes, the developed approach is referred to as an embedded statistical coupling method (ESCM). ESCM provides an enhanced coupling methodology that is inherently applicable to three-dimensional domains, avoids discretization of the continuum model to atomic scale resolution, and permits finite temperature states to be applied.

Monitoring the refinement of crystal structures with {sup 15}N solid-state NMR shift tensor data

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

Kalakewich, Keyton; Eloranta, Harriet; Harper, James K.

The {sup 15}N chemical shift tensor is shown to be extremely sensitive to lattice structure and a powerful metric for monitoring density functional theory refinements of crystal structures. These refinements include lattice effects and are applied here to five crystal structures. All structures improve based on a better agreement between experimental and calculated {sup 15}N tensors, with an average improvement of 47.0 ppm. Structural improvement is further indicated by a decrease in forces on the atoms by 2–3 orders of magnitude and a greater similarity in atom positions to neutron diffraction structures. These refinements change bond lengths by more thanmore » the diffraction errors including adjustments to X–Y and X–H bonds (X, Y = C, N, and O) of 0.028 ± 0.002 Å and 0.144 ± 0.036 Å, respectively. The acquisition of {sup 15}N tensors at natural abundance is challenging and this limitation is overcome by improved {sup 1}H decoupling in the FIREMAT method. This decoupling dramatically narrows linewidths, improves signal-to-noise by up to 317%, and significantly improves the accuracy of measured tensors. A total of 39 tensors are measured with shifts distributed over a range of more than 400 ppm. Overall, experimental {sup 15}N tensors are at least 5 times more sensitive to crystal structure than {sup 13}C tensors due to nitrogen’s greater polarizability and larger range of chemical shifts.« less

GRID: a high-resolution protein structure refinement algorithm.

PubMed

Chitsaz, Mohsen; Mayo, Stephen L

2013-03-05

The energy-based refinement of protein structures generated by fold prediction algorithms to atomic-level accuracy remains a major challenge in structural biology. Energy-based refinement is mainly dependent on two components: (1) sufficiently accurate force fields, and (2) efficient conformational space search algorithms. Focusing on the latter, we developed a high-resolution refinement algorithm called GRID. It takes a three-dimensional protein structure as input and, using an all-atom force field, attempts to improve the energy of the structure by systematically perturbing backbone dihedrals and side-chain rotamer conformations. We compare GRID to Backrub, a stochastic algorithm that has been shown to predict a significant fraction of the conformational changes that occur with point mutations. We applied GRID and Backrub to 10 high-resolution (≤ 2.8 Å) crystal structures from the Protein Data Bank and measured the energy improvements obtained and the computation times required to achieve them. GRID resulted in energy improvements that were significantly better than those attained by Backrub while expending about the same amount of computational resources. GRID resulted in relaxed structures that had slightly higher backbone RMSDs compared to Backrub relative to the starting crystal structures. The average RMSD was 0.25 ± 0.02 Å for GRID versus 0.14 ± 0.04 Å for Backrub. These relatively minor deviations indicate that both algorithms generate structures that retain their original topologies, as expected given the nature of the algorithms. Copyright © 2012 Wiley Periodicals, Inc.

Bimetallic Catalysts.

ERIC Educational Resources Information Center

Sinfelt, John H.

1985-01-01

Chemical reaction rates can be controlled by varying composition of miniscule clusters of metal atoms. These bimetallic catalysts have had major impact on petroleum refining, where work has involved heterogeneous catalysis (reacting molecules in a phase separate from catalyst.) Experimentation involving hydrocarbon reactions, catalytic…

Prediction of protein loop conformations using multiscale modeling methods with physical energy scoring functions.

PubMed

Olson, Mark A; Feig, Michael; Brooks, Charles L

2008-04-15

This article examines ab initio methods for the prediction of protein loops by a computational strategy of multiscale conformational sampling and physical energy scoring functions. Our approach consists of initial sampling of loop conformations from lattice-based low-resolution models followed by refinement using all-atom simulations. To allow enhanced conformational sampling, the replica exchange method was implemented. Physical energy functions based on CHARMM19 and CHARMM22 parameterizations with generalized Born (GB) solvent models were applied in scoring loop conformations extracted from the lattice simulations and, in the case of all-atom simulations, the ensemble of conformations were generated and scored with these models. Predictions are reported for 25 loop segments, each eight residues long and taken from a diverse set of 22 protein structures. We find that the simulations generally sampled conformations with low global root-mean-square-deviation (RMSD) for loop backbone coordinates from the known structures, whereas clustering conformations in RMSD space and scoring detected less favorable loop structures. Specifically, the lattice simulations sampled basins that exhibited an average global RMSD of 2.21 +/- 1.42 A, whereas clustering and scoring the loop conformations determined an RMSD of 3.72 +/- 1.91 A. Using CHARMM19/GB to refine the lattice conformations improved the sampling RMSD to 1.57 +/- 0.98 A and detection to 2.58 +/- 1.48 A. We found that further improvement could be gained from extending the upper temperature in the all-atom refinement from 400 to 800 K, where the results typically yield a reduction of approximately 1 A or greater in the RMSD of the detected loop. Overall, CHARMM19 with a simple pairwise GB solvent model is more efficient at sampling low-RMSD loop basins than CHARMM22 with a higher-resolution modified analytical GB model; however, the latter simulation method provides a more accurate description of the all-atom energy surface, yet demands a much greater computational cost. (c) 2007 Wiley Periodicals, Inc.

From deep TLS validation to ensembles of atomic models built from elemental motions

DOE PAGES

Urzhumtsev, Alexandre; Afonine, Pavel V.; Van Benschoten, Andrew H.; ...

2015-07-28

The translation–libration–screw model first introduced by Cruickshank, Schomaker and Trueblood describes the concerted motions of atomic groups. Using TLS models can improve the agreement between calculated and experimental diffraction data. Because the T, L and S matrices describe a combination of atomic vibrations and librations, TLS models can also potentially shed light on molecular mechanisms involving correlated motions. However, this use of TLS models in mechanistic studies is hampered by the difficulties in translating the results of refinement into molecular movement or a structural ensemble. To convert the matrices into a constituent molecular movement, the matrix elements must satisfy severalmore » conditions. Refining the T, L and S matrix elements as independent parameters without taking these conditions into account may result in matrices that do not represent concerted molecular movements. Here, a mathematical framework and the computational tools to analyze TLS matrices, resulting in either explicit decomposition into descriptions of the underlying motions or a report of broken conditions, are described. The description of valid underlying motions can then be output as a structural ensemble. All methods are implemented as part of the PHENIX project.« less

Structure refinement of the δ1p phase in the Fe-Zn system by single-crystal X-ray diffraction combined with scanning transmission electron microscopy.

PubMed

Okamoto, Norihiko L; Tanaka, Katsushi; Yasuhara, Akira; Inui, Haruyuki

2014-04-01

The structure of the δ1p phase in the iron-zinc system has been refined by single-crystal synchrotron X-ray diffraction combined with scanning transmission electron microscopy. The large hexagonal unit cell of the δ1p phase with the space group of P63/mmc comprises more or less regular (normal) Zn12 icosahedra, disordered Zn12 icosahedra, Zn16 icosioctahedra and dangling Zn atoms that do not constitute any polyhedra. The unit cell contains 52 Fe and 504 Zn atoms so that the compound is expressed with the chemical formula of Fe13Zn126. All Fe atoms exclusively occupy the centre of normal and disordered icosahedra. Iron-centred normal icosahedra are linked to one another by face- and vertex-sharing forming two types of basal slabs, which are bridged with each other by face-sharing with icosioctahedra, whereas disordered icosahedra with positional disorder at their vertex sites are isolated from other polyhedra. The bonding features in the δ1p phase are discussed in comparison with those in the Γ and ζ phases in the iron-zinc system.

On contribution of known atomic partial charges of protein backbone in electrostatic potential density maps.

PubMed

Wang, Jimin

2017-06-01

Partial charges of atoms in a molecule and electrostatic potential (ESP) density for that molecule are known to bear a strong correlation. In order to generate a set of point-field force field parameters for molecular dynamics, Kollman and coworkers have extracted atomic partial charges for each of all 20 amino acids using restrained partial charge-fitting procedures from theoretical ESP density obtained from condensed-state quantum mechanics. The magnitude of atomic partial charges for neutral peptide backbone they have obtained is similar to that of partial atomic charges for ionized carboxylate side chain atoms. In this study, the effect of these known atomic partial charges on ESP is examined using computer simulations and compared with the experimental ESP density recently obtained for proteins using electron microscopy. It is found that the observed ESP density maps are most consistent with the simulations that include atomic partial charges of protein backbone. Therefore, atomic partial charges are integral part of atomic properties in protein molecules and should be included in model refinement. © 2017 The Protein Society.

On contribution of known atomic partial charges of protein backbone in electrostatic potential density maps

PubMed Central

2017-01-01

Abstract Partial charges of atoms in a molecule and electrostatic potential (ESP) density for that molecule are known to bear a strong correlation. In order to generate a set of point‐field force field parameters for molecular dynamics, Kollman and coworkers have extracted atomic partial charges for each of all 20 amino acids using restrained partial charge‐fitting procedures from theoretical ESP density obtained from condensed‐state quantum mechanics. The magnitude of atomic partial charges for neutral peptide backbone they have obtained is similar to that of partial atomic charges for ionized carboxylate side chain atoms. In this study, the effect of these known atomic partial charges on ESP is examined using computer simulations and compared with the experimental ESP density recently obtained for proteins using electron microscopy. It is found that the observed ESP density maps are most consistent with the simulations that include atomic partial charges of protein backbone. Therefore, atomic partial charges are integral part of atomic properties in protein molecules and should be included in model refinement. PMID:28370507

Adaptive h -refinement for reduced-order models: ADAPTIVE h -refinement for reduced-order models

DOE PAGES

Carlberg, Kevin T.

2014-11-05

Our work presents a method to adaptively refine reduced-order models a posteriori without requiring additional full-order-model solves. The technique is analogous to mesh-adaptive h-refinement: it enriches the reduced-basis space online by ‘splitting’ a given basis vector into several vectors with disjoint support. The splitting scheme is defined by a tree structure constructed offline via recursive k-means clustering of the state variables using snapshot data. This method identifies the vectors to split online using a dual-weighted-residual approach that aims to reduce error in an output quantity of interest. The resulting method generates a hierarchy of subspaces online without requiring large-scale operationsmore » or full-order-model solves. Furthermore, it enables the reduced-order model to satisfy any prescribed error tolerance regardless of its original fidelity, as a completely refined reduced-order model is mathematically equivalent to the original full-order model. Experiments on a parameterized inviscid Burgers equation highlight the ability of the method to capture phenomena (e.g., moving shocks) not contained in the span of the original reduced basis.« less

Neutron Diffraction Structure of Melampodin: Its Role in the Reclassification of the Germacranolides

PubMed Central

Watkins, Steven F.; Fischer, Nikolaus H.; Bernal, Ivan

1973-01-01

The precise crystal and molecular structure of melampodin, C21H24O9, was determined from three-dimensional neutron diffraction data collected by counter techniques and phases by direct statistical methods. Crystals are orthorhombic, P212121, a = 8,990(9), b = 14.352(14), c = 16.294(16) Å, V = 2102 Å3, d(calc.) = 1.328 g·cm-3, Z = 4 molecules per unit cell. The structural model was refined by full matrix least-squares of 2303 observed independent reflections, with all 54 atoms treated anisotropically, to R(F) = 5.0%. Hydrogen bonds link melampodin molecules together in the solid state. The conformation of the cyclodeca-1,5-diene ring is such that one intraannular hydrogen atom interacts strongly with one double bond, but there is little or no transannular interaction between double bonds. Strain in the ten-membered ring and in the trans-fused lactone ring is discussed, as are chemical implications of the unsymmetric epoxide in the epoxyangelic acid side chain. The previously suggested reclassification of germacranolide sesquiterpene lactones into four subgroups is supported, and a new convention for configurational representations of the four subgroups is proposed. PMID:16592106

Effect of TiC Nanoparticles Supported by Ti Powders on the Solidification Behavior and Microstructure of Pure Aluminum

NASA Astrophysics Data System (ADS)

Zhao, Bingyi; Cai, Qizhou; Li, Xinwei; Li, Bing; Cheng, Jingfan

2018-03-01

A novel grain refiner consisting of TiC nanoparticles (NPs) supported by Ti powders (abbr. TiC/Ti refiner) was prepared by high-energy milling. The addition of 0.5 wt% TiC/Ti refiner converted the structure of pure Al from coarse dendrites to fine equiaxed grains with the average grain size of 114.7 μm, and it also increased the nucleation temperature of α(Al) from 656.7 to 664.4 °C. When TiC/Ti refiner was introduced into Al melt, the heat released from the Al-Ti reaction promoted the uniform dispersion of TiC NPs. The dissolution of the reaction product TiAl3 released Ti atoms into the melt and thus formed a "Ti-rich transition region" around TiC NPs. The dispersive TiC NPs could act as the heterogeneous nuclei for α(Al) and the "Ti-rich transition region" further improved the lattice orientation relationship between Al (\\bar{1}1\\bar{1} ) and TiC (11\\bar{1} ) planes, which eventually resulted in the refining of α(Al).

Comparison Between Self-Guided Langevin Dynamics and Molecular Dynamics Simulations for Structure Refinement of Protein Loop Conformations

DTIC Science & Technology

2011-01-01

SECURITY CLASSIFICATION OF: 17. LIMITATION OF ABSTRACT Same as Report (SAR) 18 . NUMBER OF PAGES 9 19a. NAME OF RESPONSIBLE PERSON a. REPORT...unclassified b. ABSTRACT unclassified c. THIS PAGE unclassified Standard Form 298 (Rev. 8-98) Prescribed by ANSI Std Z39- 18 sampling is based on...atom distance-scaled ideal-gas reference state (DFIRE-AA) statistical potential func- tion.[ 18 ] The third approach is the Rosetta all-atom energy func

Predicting X-ray diffuse scattering from translation–libration–screw structural ensembles

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

Van Benschoten, Andrew H.; Afonine, Pavel V.; Terwilliger, Thomas C.

2015-07-28

A method of simulating X-ray diffuse scattering from multi-model PDB files is presented. Despite similar agreement with Bragg data, different translation–libration–screw refinement strategies produce unique diffuse intensity patterns. Identifying the intramolecular motions of proteins and nucleic acids is a major challenge in macromolecular X-ray crystallography. Because Bragg diffraction describes the average positional distribution of crystalline atoms with imperfect precision, the resulting electron density can be compatible with multiple models of motion. Diffuse X-ray scattering can reduce this degeneracy by reporting on correlated atomic displacements. Although recent technological advances are increasing the potential to accurately measure diffuse scattering, computational modeling andmore » validation tools are still needed to quantify the agreement between experimental data and different parameterizations of crystalline disorder. A new tool, phenix.diffuse, addresses this need by employing Guinier’s equation to calculate diffuse scattering from Protein Data Bank (PDB)-formatted structural ensembles. As an example case, phenix.diffuse is applied to translation–libration–screw (TLS) refinement, which models rigid-body displacement for segments of the macromolecule. To enable the calculation of diffuse scattering from TLS-refined structures, phenix.tls-as-xyz builds multi-model PDB files that sample the underlying T, L and S tensors. In the glycerophosphodiesterase GpdQ, alternative TLS-group partitioning and different motional correlations between groups yield markedly dissimilar diffuse scattering maps with distinct implications for molecular mechanism and allostery. These methods demonstrate how, in principle, X-ray diffuse scattering could extend macromolecular structural refinement, validation and analysis.« less

PURY: a database of geometric restraints of hetero compounds for refinement in complexes with macromolecular structures.

PubMed

Andrejasic, Miha; Praaenikar, Jure; Turk, Dusan

2008-11-01

The number and variety of macromolecular structures in complex with ;hetero' ligands is growing. The need for rapid delivery of correct geometric parameters for their refinement, which is often crucial for understanding the biological relevance of the structure, is growing correspondingly. The current standard for describing protein structures is the Engh-Huber parameter set. It is an expert data set resulting from selection and analysis of the crystal structures gathered in the Cambridge Structural Database (CSD). Clearly, such a manual approach cannot be applied to the vast and ever-growing number of chemical compounds. Therefore, a database, named PURY, of geometric parameters of chemical compounds has been developed, together with a server that accesses it. PURY is a compilation of the whole CSD. It contains lists of atom classes and bonds connecting them, as well as angle, chirality, planarity and conformation parameters. The current compilation is based on CSD 5.28 and contains 1978 atom classes and 32,702 bonding, 237,068 angle, 201,860 dihedral and 64,193 improper geometric restraints. Analysis has confirmed that the restraints from the PURY database are suitable for use in macromolecular crystal structure refinement and should be of value to the crystallographic community. The database can be accessed through the web server http://pury.ijs.si/, which creates topology and parameter files from deposited coordinates in suitable forms for the refinement programs MAIN, CNS and REFMAC. In the near future, the server will move to the CSD website http://pury.ccdc.cam.ac.uk/.

i3Drefine software for protein 3D structure refinement and its assessment in CASP10.

PubMed

Bhattacharya, Debswapna; Cheng, Jianlin

2013-01-01

Protein structure refinement refers to the process of improving the qualities of protein structures during structure modeling processes to bring them closer to their native states. Structure refinement has been drawing increasing attention in the community-wide Critical Assessment of techniques for Protein Structure prediction (CASP) experiments since its addition in 8(th) CASP experiment. During the 9(th) and recently concluded 10(th) CASP experiments, a consistent growth in number of refinement targets and participating groups has been witnessed. Yet, protein structure refinement still remains a largely unsolved problem with majority of participating groups in CASP refinement category failed to consistently improve the quality of structures issued for refinement. In order to alleviate this need, we developed a completely automated and computationally efficient protein 3D structure refinement method, i3Drefine, based on an iterative and highly convergent energy minimization algorithm with a powerful all-atom composite physics and knowledge-based force fields and hydrogen bonding (HB) network optimization technique. In the recent community-wide blind experiment, CASP10, i3Drefine (as 'MULTICOM-CONSTRUCT') was ranked as the best method in the server section as per the official assessment of CASP10 experiment. Here we provide the community with free access to i3Drefine software and systematically analyse the performance of i3Drefine in strict blind mode on the refinement targets issued in CASP10 refinement category and compare with other state-of-the-art refinement methods participating in CASP10. Our analysis demonstrates that i3Drefine is only fully-automated server participating in CASP10 exhibiting consistent improvement over the initial structures in both global and local structural quality metrics. Executable version of i3Drefine is freely available at http://protein.rnet.missouri.edu/i3drefine/.

Refined views of multi-protein complexes in the erythrocyte membrane

PubMed Central

Mankelow, TJ; Satchwell, TJ; Burton, NM

2015-01-01

The erythrocyte membrane has been extensively studied, both as a model membrane system and to investigate its role in gas exchange and transport. Much is now known about the protein components of the membrane, how they are organised into large multi-protein complexes and how they interact with each other within these complexes. Many links between the membrane and the cytoskeleton have also been delineated and have been demonstrated to be crucial for maintaining the deformability and integrity of the erythrocyte. In this study we have refined previous, highly speculative molecular models of these complexes by including the available data pertaining to known protein-protein interactions. While the refined models remain highly speculative, they provide an evolving framework for visualisation of these important cellular structures at the atomic level. PMID:22465511

Improving precipitation hardening behavior of Mg−Zn based alloys with Ce−Ca microalloying additions

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

Langelier, B., E-mail: langelb@mcmaster.ca

2016-10-15

The precipitation hardening behavior of newly developed Mg−Zn−Ca−Ce alloys, with modified texture and improved ductility, is studied to delineate the microstructural characteristics that lead to effective hardening upon ageing treatments. Advanced electron microscopy and atom probe techniques are used to analyze the structural characteristics in relevance to the hardening potential. It has been found that the formation of a new basal precipitate phase, which evolves from a single atomic layer GP zone, and is finely distributed in both under-aged and peak-aged microstructures, has a significant impact in the improvement of the hardening response compared with the base Mg−Zn alloys. Itmore » has also been found that the β′{sub 1} rod precipitates, commonly formed during ageing treatments of Mg−Zn alloys, have their size and distribution significantly refined in the Ca−Ce containing alloys. The role of alloy chemistry in the formation of the fine basal plate GP zones and the refinement in β′{sub 1} precipitation and their relationships to the hardening behavior are discussed. It is proposed that Ca microalloying governs the formation of the GP zones and the enhancement of hardening, particularly in the under-aged conditions, but that this is aided by a beneficial effect from Ce. - Highlights: • Ce−Ca microalloying additions improve hardening in Mg−Zn, over Ce or Ca alone. • Improved hardening is due to refined β′{sub 1} rods, and fine basal plate precipitates. • Atom probe tomography identifies Ca in both β′{sub 1} and the fine basal plates. • The fine basal plates originate as ordered monolayer GP zones with 1:1 Zn:Ca (at.%). • With ageing GP zones become more Zn-rich and transform to the fine basal plates.« less

Geometrical eigen-subspace framework based molecular conformation representation for efficient structure recognition and comparison

NASA Astrophysics Data System (ADS)

Li, Xiao-Tian; Yang, Xiao-Bao; Zhao, Yu-Jun

2017-04-01

We have developed an extended distance matrix approach to study the molecular geometric configuration through spectral decomposition. It is shown that the positions of all atoms in the eigen-space can be specified precisely by their eigen-coordinates, while the refined atomic eigen-subspace projection array adopted in our approach is demonstrated to be a competent invariant in structure comparison. Furthermore, a visual eigen-subspace projection function (EPF) is derived to characterize the surrounding configuration of an atom naturally. A complete set of atomic EPFs constitute an intrinsic representation of molecular conformation, based on which the interatomic EPF distance and intermolecular EPF distance can be reasonably defined. Exemplified with a few cases, the intermolecular EPF distance shows exceptional rationality and efficiency in structure recognition and comparison.

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

Jiang, Xiujuan; Whalen, Scott A.; Darsell, Jens T.

Soft magnetic materials are often limited in scalability due to conventional processes that do not retain beneficial microstructures, and their associated physical properties, during densification. In this work, friction consolidation (FC) has been studied to fabricate Fe-Si soft magnetic materials from gas-atomized powder precursors. Fe-Si powder is consolidated using variable pressure and tool rotation speed in an effort to evaluate this unique densification approach for potential improvements in magnetic properties. FC, due to the high shear deformation involved, is shown to result in uniform gradual grain structure refinement across the consolidated workpiece from the center nearest the tool to themore » edge. Magnetic properties along different orientations indicate little, if any, textural orientation in the refined grain structure. The effect of annealing on the magnetic properties is evaluated and shown to decrease coercivity. FC processing was able to retain the magnetization of the original gas-atomized powders but further process optimization is needed to reach the optimal coercivity for the soft magnetic materials applications.« less

Structure and atomic correlations in molecular systems probed by XAS reverse Monte Carlo refinement

NASA Astrophysics Data System (ADS)

Di Cicco, Andrea; Iesari, Fabio; Trapananti, Angela; D'Angelo, Paola; Filipponi, Adriano

2018-03-01

The Reverse Monte Carlo (RMC) algorithm for structure refinement has been applied to x-ray absorption spectroscopy (XAS) multiple-edge data sets for six gas phase molecular systems (SnI2, CdI2, BBr3, GaI3, GeBr4, GeI4). Sets of thousands of molecular replicas were involved in the refinement process, driven by the XAS data and constrained by available electron diffraction results. The equilibrated configurations were analysed to determine the average tridimensional structure and obtain reliable bond and bond-angle distributions. Detectable deviations from Gaussian models were found in some cases. This work shows that a RMC refinement of XAS data is able to provide geometrical models for molecular structures compatible with present experimental evidence. The validation of this approach on simple molecular systems is particularly important in view of its possible simple extension to more complex and extended systems including metal-organic complexes, biomolecules, or nanocrystalline systems.

Crystal structure of aqua-1κO-{μ-2-[(2-hydroxy-ethyl)methylamino]ethanolato-2:1κ(4) O (1),N,O (2):O (1)}[μ-2,2'-(methylimino)diethanolato-1:2κ(4) O,N,O':O]dithiocyanato-1κN,2κN-chromium(III)copper(II).

PubMed

Rusanova, Julia A; Semenaka, Valentina V; Dyakonenko, Viktoriya V; Shishkin, Oleg V

2015-09-01

The title compound, [CrCu(C5H11NO2)(C5H12NO2)(NCS)2(H2O)] or [Cr(μ-mdea)Cu(μ-Hmdea)(NCS)2H2O], (where mdeaH2 is N-methylethanolamine, C5H13NO2) is formed as a neutral heterometal Cu(II)/Cr(III) complex. The mol-ecular structure of the complex is based on a binuclear {CuCr(μ-O)2} core. The coordination environment of each metal atom involves the N,O,O atoms of the tridentate ligand, one bridging O atom of the ligand and the N atom of the thio-cyanato ligands. The Cu(II) ion adopts a distorted square-pyramidal coordination while the Cr(III) ion has a distorted octa-hedral coordination geometry completed by the aqua ligand. In the crystal, the binuclear complexes are linked via two pairs of O-H⋯O hydrogen bonds to form inversion dimers, which are arranged in columns parallel to the a axis. In the μ-mdea ligand two -CH2 groups and the methyl group were refined as disordered over two sets of sites with equal occupancies. The structure was refined as a two-component twin with a twin scale factor of 0.242 (1).

Structure Refinement of Protein Low Resolution Models Using the GNEIMO Constrained Dynamics Method

PubMed Central

Park, In-Hee; Gangupomu, Vamshi; Wagner, Jeffrey; Jain, Abhinandan; Vaidehi, Nagara-jan

2012-01-01

The challenge in protein structure prediction using homology modeling is the lack of reliable methods to refine the low resolution homology models. Unconstrained all-atom molecular dynamics (MD) does not serve well for structure refinement due to its limited conformational search. We have developed and tested the constrained MD method, based on the Generalized Newton-Euler Inverse Mass Operator (GNEIMO) algorithm for protein structure refinement. In this method, the high-frequency degrees of freedom are replaced with hard holonomic constraints and a protein is modeled as a collection of rigid body clusters connected by flexible torsional hinges. This allows larger integration time steps and enhances the conformational search space. In this work, we have demonstrated the use of a constraint free GNEIMO method for protein structure refinement that starts from low-resolution decoy sets derived from homology methods. In the eight proteins with three decoys for each, we observed an improvement of ~2 Å in the RMSD to the known experimental structures of these proteins. The GNEIMO method also showed enrichment in the population density of native-like conformations. In addition, we demonstrated structural refinement using a “Freeze and Thaw” clustering scheme with the GNEIMO framework as a viable tool for enhancing localized conformational search. We have derived a robust protocol based on the GNEIMO replica exchange method for protein structure refinement that can be readily extended to other proteins and possibly applicable for high throughput protein structure refinement. PMID:22260550

The atomic arrangement of iimoriite-(Y), Y2(SiO4)(CO3)

USGS Publications Warehouse

Hughes, J.M.; Foord, E.E.; Jai-Nhuknan, J.; Bell, J.M.

1996-01-01

Iimoriite-(Y) from Bokan Mountain, Prince of Wales Island, Alaska has been studied using single-crystal X-ray-diffraction techniques. The mineral, ideally Y2(SiO4)(CO3), crystallizes in space group P1, with a 6.5495(13), b 6.6291(14), c 6.4395(11)A??, ?? 116.364(15), ?? 92.556(15) and ?? 95.506(17)??. The atomic arrangement has been solved and refined to an R value of 0.019. The arrangement of atoms consists of alternating (011) slabs of orthosilicate groups and carbonate groups, with no sharing of oxygen atoms between anionic complexes in adjacent slabs. Y1 atoms separate adjacent tetrahedra along [100] within the orthosilicate slab, and Y2 atoms separate adjacent carbonate groups along [100] within the carbonate slab. Adjacent orthosilicate and carbonate slabs are linked in (100) by bonding Y atoms from each slab to oxygen atoms of adjacent slabs, in the form of YO8 polyhedra. The Y1 atoms exist in Y12O14 dimers in the orthosilicate slab, and the Y2 atoms exist in continuous [011] ribbons of edge-sharing Y2O8 polyhedra in the carbonate slab.

Faculty Member for Research in an Undergraduate Institution Prize Talk: Research and Teaching through high-precision spectroscopy of heavy atoms

NASA Astrophysics Data System (ADS)

Majumder, Tiku

2017-04-01

In recent decades, substantial experimental effort has centered on heavy (high-Z) atomic and molecular systems for atomic-physics-based tests of standard model physics, through (for example) measurements of atomic parity nonconservation and searches for permanent electric dipole moments. In all of this work, a crucial role is played by atomic theorists, whose accurate wave function calculations are essential in connecting experimental observables to tests of relevant fundamental physics parameters. At Williams College, with essential contributions from dozens of undergraduate students, we have pursued a series of precise atomic structure measurements in heavy metal atoms such as thallium, indium, and lead. These include measurements of hyperfine structure, transition amplitudes, and atomic polarizability. This work, involving diode lasers, heated vapor cells, and an atomic beam apparatus, has both tested the accuracy and helped guide the refinement of new atomic theory calculations. I will discuss a number of our recent experimental results, emphasizing the role played by students and the opportunities that have been afforded for research-training in this undergraduate environment. Work supported by Research Corporation, the NIST Precision Measurement Grants program, and the National Science Foundation.

3Drefine: an interactive web server for efficient protein structure refinement

PubMed Central

Bhattacharya, Debswapna; Nowotny, Jackson; Cao, Renzhi; Cheng, Jianlin

2016-01-01

3Drefine is an interactive web server for consistent and computationally efficient protein structure refinement with the capability to perform web-based statistical and visual analysis. The 3Drefine refinement protocol utilizes iterative optimization of hydrogen bonding network combined with atomic-level energy minimization on the optimized model using a composite physics and knowledge-based force fields for efficient protein structure refinement. The method has been extensively evaluated on blind CASP experiments as well as on large-scale and diverse benchmark datasets and exhibits consistent improvement over the initial structure in both global and local structural quality measures. The 3Drefine web server allows for convenient protein structure refinement through a text or file input submission, email notification, provided example submission and is freely available without any registration requirement. The server also provides comprehensive analysis of submissions through various energy and statistical feedback and interactive visualization of multiple refined models through the JSmol applet that is equipped with numerous protein model analysis tools. The web server has been extensively tested and used by many users. As a result, the 3Drefine web server conveniently provides a useful tool easily accessible to the community. The 3Drefine web server has been made publicly available at the URL: http://sysbio.rnet.missouri.edu/3Drefine/. PMID:27131371

Synthesis, Crystal Structure, and Topology-Symmetry Analysis of a New Modification of NaIn[IO3]4

NASA Astrophysics Data System (ADS)

Belokoneva, E. L.; Karamysheva, A. S.; Dimitrova, O. V.; Volkov, A. S.

2018-01-01

Crystals of new iodate NaIn[IO3]4 were prepared by the hydrothermal synthesis. The unit cell parameters are a = 7.2672(2) Å, b = 15.2572(6) Å, c = 15.0208(6) Å, β = 101.517(3)°, sp. gr. P21/ c. The formula was determined during the structure determination and refinement of a twinned crystal based on a set of reflections from the atomic planes of the major individual. The refinement with anisotropic displacement parameters was performed for both twin components to the final R factor of 0.050. The In and Na atoms are in octahedral coordination formed by oxygen atoms. The oxygen octahedra are arranged into columns by sharing edges, and the columns are connected by isolated umbrella-like [IO3]- groups to form layers. The new structure is most similar to the isoformular iodate NaIn[IO3]4, which crystallizes in the same sp. gr. P21/ c and is structurally similar, but has a twice smaller unit cell and is characterized by another direction of the monoclinic axis. The structural similarity and difference between the two phases were studied by topologysymmetry analysis. The formation of these phases is related to different combinations of identical one-dimensional infinite chains of octahedra.

Hydrogen atoms in protein structures: high-resolution X-ray diffraction structure of the DFPase

PubMed Central

2013-01-01

Background Hydrogen atoms represent about half of the total number of atoms in proteins and are often involved in substrate recognition and catalysis. Unfortunately, X-ray protein crystallography at usual resolution fails to access directly their positioning, mainly because light atoms display weak contributions to diffraction. However, sub-Ångstrom diffraction data, careful modeling and a proper refinement strategy can allow the positioning of a significant part of hydrogen atoms. Results A comprehensive study on the X-ray structure of the diisopropyl-fluorophosphatase (DFPase) was performed, and the hydrogen atoms were modeled, including those of solvent molecules. This model was compared to the available neutron structure of DFPase, and differences in the protein and the active site solvation were noticed. Conclusions A further examination of the DFPase X-ray structure provides substantial evidence about the presence of an activated water molecule that may constitute an interesting piece of information as regard to the enzymatic hydrolysis mechanism. PMID:23915572

The active site of hen egg-white lysozyme: flexibility and chemical bonding

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

Held, Jeanette, E-mail: jeanette.netzel@uni-bayreuth.de; Smaalen, Sander van

Chemical bonding at the active site of lysozyme is analyzed on the basis of a multipole model employing transferable multipole parameters from a database. Large B factors at low temperatures reflect frozen-in disorder, but therefore prevent a meaningful free refinement of multipole parameters. Chemical bonding at the active site of hen egg-white lysozyme (HEWL) is analyzed on the basis of Bader’s quantum theory of atoms in molecules [QTAIM; Bader (1994 ▶), Atoms in Molecules: A Quantum Theory. Oxford University Press] applied to electron-density maps derived from a multipole model. The observation is made that the atomic displacement parameters (ADPs) ofmore » HEWL at a temperature of 100 K are larger than ADPs in crystals of small biological molecules at 298 K. This feature shows that the ADPs in the cold crystals of HEWL reflect frozen-in disorder rather than thermal vibrations of the atoms. Directly generalizing the results of multipole studies on small-molecule crystals, the important consequence for electron-density analysis of protein crystals is that multipole parameters cannot be independently varied in a meaningful way in structure refinements. Instead, a multipole model for HEWL has been developed by refinement of atomic coordinates and ADPs against the X-ray diffraction data of Wang and coworkers [Wang et al. (2007), Acta Cryst. D63, 1254–1268], while multipole parameters were fixed to the values for transferable multipole parameters from the ELMAM2 database [Domagala et al. (2012), Acta Cryst. A68, 337–351] . Static and dynamic electron densities based on this multipole model are presented. Analysis of their topological properties according to the QTAIM shows that the covalent bonds possess similar properties to the covalent bonds of small molecules. Hydrogen bonds of intermediate strength are identified for the Glu35 and Asp52 residues, which are considered to be essential parts of the active site of HEWL. Furthermore, a series of weak C—H⋯O hydrogen bonds are identified by means of the existence of bond critical points (BCPs) in the multipole electron density. It is proposed that these weak interactions might be important for defining the tertiary structure and activity of HEWL. The deprotonated state of Glu35 prevents a distinction between the Phillips and Koshland mechanisms.« less

Ultrahigh resolution drug design I: details of interactions in human aldose reductase-inhibitor complex at 0.66 A.

PubMed

Howard, E I; Sanishvili, R; Cachau, R E; Mitschler, A; Chevrier, B; Barth, P; Lamour, V; Van Zandt, M; Sibley, E; Bon, C; Moras, D; Schneider, T R; Joachimiak, A; Podjarny, A

2004-06-01

The first subatomic resolution structure of a 36 kDa protein [aldose reductase (AR)] is presented. AR was cocrystallized at pH 5.0 with its cofactor NADP+ and inhibitor IDD 594, a therapeutic candidate for the treatment of diabetic complications. X-ray diffraction data were collected up to 0.62 A resolution and treated up to 0.66 A resolution. Anisotropic refinement followed by a blocked matrix inversion produced low standard deviations (<0.005 A). The model was very well ordered overall (CA atoms' mean B factor is 5.5 A2). The model and the electron-density maps revealed fine features, such as H-atoms, bond densities, and significant deviations from standard stereochemistry. Other features, such as networks of hydrogen bonds (H bonds), a large number of multiple conformations, and solvent structure were also better defined. Most of the atoms in the active site region were extremely well ordered (mean B approximately 3 A2), leading to the identification of the protonation states of the residues involved in catalysis. The electrostatic interactions of the inhibitor's charged carboxylate head with the catalytic residues and the charged coenzyme NADP+ explained the inhibitor's noncompetitive character. Furthermore, a short contact involving the IDD 594 bromine atom explained the selectivity profile of the inhibitor, important feature to avoid toxic effects. The presented structure and the details revealed are instrumental for better understanding of the inhibition mechanism of AR by IDD 594, and hence, for the rational drug design of future inhibitors. This work demonstrates the capabilities of subatomic resolution experiments and stimulates further developments of methods allowing the use of the full potential of these experiments. Copyright 2004 Wiley-Liss, Inc.

Space Radiation, Understanding the Atom Series.

ERIC Educational Resources Information Center

Corliss, William R.

Described is the protection from space radiation afforded the earth by the atmosphere, ionosphere, and magnetic field. The importance of adequate instruments is emphasized by noting how refinements of radiation detection instruments was necessary for increased understanding of space radiation. The role of controversy and accident in the research…

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

NASA Astrophysics Data System (ADS)

Ni, Yunxiang

1995-01-01

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

Probing hydrogen positions in hydrous compounds: information from parametric neutron powder diffraction studies.

PubMed

Ting, Valeska P; Henry, Paul F; Schmidtmann, Marc; Wilson, Chick C; Weller, Mark T

2012-05-21

We demonstrate the extent to which modern detector technology, coupled with a high flux constant wavelength neutron source, can be used to obtain high quality diffraction data from short data collections, allowing the refinement of the full structures (including hydrogen positions) of hydrous compounds from in situ neutron powder diffraction measurements. The in situ thermodiffractometry and controlled humidity studies reported here reveal that important information on the reorientations of structural water molecules with changing conditions can be easily extracted, providing insight into the effects of hydrogen bonding on bulk physical properties. Using crystalline BaCl2·2H2O as an example system, we analyse the structural changes in the compound and its dehydration intermediates with changing temperature and humidity levels to demonstrate the quality of the dynamic structural information on the hydrogen atoms and associated hydrogen bonding that can be obtained without resorting to sample deuteration.

PDB_REDO: automated re-refinement of X-ray structure models in the PDB.

PubMed

Joosten, Robbie P; Salzemann, Jean; Bloch, Vincent; Stockinger, Heinz; Berglund, Ann-Charlott; Blanchet, Christophe; Bongcam-Rudloff, Erik; Combet, Christophe; Da Costa, Ana L; Deleage, Gilbert; Diarena, Matteo; Fabbretti, Roberto; Fettahi, Géraldine; Flegel, Volker; Gisel, Andreas; Kasam, Vinod; Kervinen, Timo; Korpelainen, Eija; Mattila, Kimmo; Pagni, Marco; Reichstadt, Matthieu; Breton, Vincent; Tickle, Ian J; Vriend, Gert

2009-06-01

Structural biology, homology modelling and rational drug design require accurate three-dimensional macromolecular coordinates. However, the coordinates in the Protein Data Bank (PDB) have not all been obtained using the latest experimental and computational methods. In this study a method is presented for automated re-refinement of existing structure models in the PDB. A large-scale benchmark with 16 807 PDB entries showed that they can be improved in terms of fit to the deposited experimental X-ray data as well as in terms of geometric quality. The re-refinement protocol uses TLS models to describe concerted atom movement. The resulting structure models are made available through the PDB_REDO databank (http://www.cmbi.ru.nl/pdb_redo/). Grid computing techniques were used to overcome the computational requirements of this endeavour.

From average to local structure: a Rietveld and an atomic pair distribution function (PDF) study of selenium clusters in zeolite-NdY.

PubMed

Abeykoon, A M Milinda; Donner, Wolfgang; Brunelli, Michela; Castro-Colin, Miguel; Jacobson, Allan J; Moss, Simon C

2009-09-23

The structure of Se particles in the approximately 13 A diameter alpha-cages of zeolite NdY has been determined by Rietveld refinement and pair distribution function (PDF) analysis of X-ray data. With the diffuse scattering subtracted an average structure comprised of an undistorted framework containing nanoclusters of 20 Se atoms is observed. The intracluster correlations and the cluster-framework correlations which give rise to diffuse scattering were modeled by using PDF analysis.

Synthesis of MAX Phases in the Hf-Al-C System.

PubMed

Lapauw, Thomas; Tunca, Bensu; Cabioc'h, Thierry; Lu, Jun; Persson, Per O Å; Lambrinou, Konstantina; Vleugels, Jozef

2016-11-07

For the first time, MAX phases in the Hf-Al-C system were experimentally synthesized using reactive hot pressing. HfC was observed as the main competing phase. The lattice parameters of Hf 2 AlC and Hf 3 AlC 2 were determined by Rietveld refinement based on the X-ray diffraction data. The atomic stacking sequence was revealed by high-resolution scanning transmission electron microscopy. Mixtures of 211 and 312 stacking were observed within the same grain, including 523 layers. This transition in atomic structure is discussed.

Dichlorido[(S,R(S))-1-diphenylphosphino-2-(ethylsulfanylmethyl)ferrocene]palladium(II).

PubMed

Diab, Lisa; Daran, Jean-Claude; Gouygou, Maryse; Manoury, Eric; Urrutigoïty, Martine

2007-12-01

The reaction of enantiomerically pure planar chiral ferrocene phosphine thioether with bis(acetonitrile)dichloridopalladium yields the title square-planar mononuclear palladium complex as an enantiomerically pure single diastereoisomer, [PdFe(C5H5)(C20H20PS)Cl2]. The planar chirality of the ligand is retained in the complex and fully controls the central chirality on the S atom. The absolute configuration, viz. S for the planar chirality and R for the S atom, is unequivocally determined by refinement of the Flack parameter.

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

Jiang, X., E-mail: Xiujuan.jiang@pnnl.gov

Soft magnetic materials are often limited in scalability due to conventional processes that do not retain beneficial microstructures, and their associated physical properties, during densification. In this work, friction consolidation (FC) has been studied to fabricate Fe−Si soft magnetic materials from gas-atomized powder precursors. Fe−Si powder is consolidated using variable pressure and tool rotation speed in an effort to evaluate this unique densification approach for potential improvements in magnetic properties. FC, due to the high shear deformation involved, is shown to result in uniform gradual grain structure refinement across the consolidated workpiece from the center nearest the tool to themore » edge. Magnetic properties along different orientations indicate little, if any, textural orientation in the refined grain structure. The effect of annealing on the magnetic properties is evaluated and shown to decrease coercivity. FC processing was able to retain the magnetization of the original gas-atomized powders but further process optimization is needed to reach the optimal coercivity for the soft magnetic materials applications. - Highlights: •Friction stir processing was utilized to consolidate Fe−Si soft magnetic powders. •The resultant microstructure and magnetic properties were correlated to the processing conditions. •Friction consolidation refined the grain size of the materials by ~ 40%. •Annealing successfully reduced the coercivity induced by the stress during processing. •The results shine light on the possible scaling up of nanostructured materials.« less

Predicting X-ray diffuse scattering from translation–libration–screw structural ensembles

PubMed Central

Van Benschoten, Andrew H.; Afonine, Pavel V.; Terwilliger, Thomas C.; Wall, Michael E.; Jackson, Colin J.; Sauter, Nicholas K.; Adams, Paul D.; Urzhumtsev, Alexandre; Fraser, James S.

2015-01-01

Identifying the intramolecular motions of proteins and nucleic acids is a major challenge in macromolecular X-ray crystallography. Because Bragg diffraction describes the average positional distribution of crystalline atoms with imperfect precision, the resulting electron density can be compatible with multiple models of motion. Diffuse X-ray scattering can reduce this degeneracy by reporting on correlated atomic displacements. Although recent technological advances are increasing the potential to accurately measure diffuse scattering, computational modeling and validation tools are still needed to quantify the agreement between experimental data and different parameterizations of crystalline disorder. A new tool, phenix.diffuse, addresses this need by employing Guinier’s equation to calculate diffuse scattering from Protein Data Bank (PDB)-formatted structural ensembles. As an example case, phenix.diffuse is applied to translation–libration–screw (TLS) refinement, which models rigid-body displacement for segments of the macromolecule. To enable the calculation of diffuse scattering from TLS-refined structures, phenix.tls_as_xyz builds multi-model PDB files that sample the underlying T, L and S tensors. In the glycerophos­phodiesterase GpdQ, alternative TLS-group partitioning and different motional correlations between groups yield markedly dissimilar diffuse scattering maps with distinct implications for molecular mechanism and allostery. These methods demonstrate how, in principle, X-ray diffuse scattering could extend macromolecular structural refinement, validation and analysis. PMID:26249347

Predicting X-ray diffuse scattering from translation–libration–screw structural ensembles

DOE PAGES

Van Benschoten, Andrew H.; Afonine, Pavel V.; Terwilliger, Thomas C.; ...

2015-07-28

Identifying the intramolecular motions of proteins and nucleic acids is a major challenge in macromolecular X-ray crystallography. Because Bragg diffraction describes the average positional distribution of crystalline atoms with imperfect precision, the resulting electron density can be compatible with multiple models of motion. Diffuse X-ray scattering can reduce this degeneracy by reporting on correlated atomic displacements. Although recent technological advances are increasing the potential to accurately measure diffuse scattering, computational modeling and validation tools are still needed to quantify the agreement between experimental data and different parameterizations of crystalline disorder. A new tool, phenix.diffuse, addresses this need by employing Guinier'smore » equation to calculate diffuse scattering from Protein Data Bank (PDB)-formatted structural ensembles. As an example case, phenix.diffuse is applied to translation–libration–screw (TLS) refinement, which models rigid-body displacement for segments of the macromolecule. To enable the calculation of diffuse scattering from TLS-refined structures, phenix.tls_as_xyz builds multi-model PDB files that sample the underlying T, L and S tensors. In the glycerophosphodiesterase GpdQ, alternative TLS-group partitioning and different motional correlations between groups yield markedly dissimilar diffuse scattering maps with distinct implications for molecular mechanism and allostery. In addition, these methods demonstrate how, in principle, X-ray diffuse scattering could extend macromolecular structural refinement, validation and analysis.« less

Crystallographic perturbations to valence charge density and hydrogen-surface interactions

NASA Astrophysics Data System (ADS)

Ciston, James W.

The subject of surfaces has been the epicenter of numerous studies in recent years, particularly with respect to applications in catalysis, thin films, and self-assembly of nanostructures where the surface-to-volume ratio is large. Understanding how the atomic structure of materials differs at surfaces where the atoms are far less constrained can yield fundamental insight into these interesting nanoscale phenomena. Quantum surface crystallography takes this one step further in an attempt to experimentally measure the structure of the electrons themselves, which is of greater importance than atomic positions in determining material properties. We report a procedure for obtaining a much better initial parameterization of the charge density than what is possible from a neutral atom model. This procedure involves the parameterization of a bulk charge density model in terms of simple variables such as bond lengths, which can then be transferred to the problem of interest, for instance a surface. Parameterization is accomplished through the fitting of Density Functional Theory calculations of a variety of crystal distortions to a bond-centered pseudoatom (BCPA) model. This parameterized model can then be applied to surfaces or for other problems where an initial higher-order model is needed without the addition of any extra fitted parameters. Through the use of the BCPA model, we report a three-dimensional charge density refinement from x-ray diffraction intensities of the Si (001) 2x1H surface. By properly accounting for the covalent bonding effects in the silicon structure, we were able to stably refine the positions of hydrogen atoms at this surface in three dimensions, which had never before been accomplished for any surface. In addition, we found experimentally an increased, slightly localized bond density of approximately 0.31 electrons between each Si atom pair at the surface. Both the atomic positions and the charge density were found to be in remarkably good agreement with density functional theory (DFT) calculations. The BCPA model was also applied to an experimental refinement of the local charge density at the Si (111) 7x7 surface utilizing a combination of x-ray and high energy electron diffraction. By perturbing about the bond-centered pseudoatom model, we found experimentally that the adatoms were in an anti-bonding state with the atoms directly below. We were also able to experimentally refine a charge transfer of 0.26+/-0.04 e- from each adatom site to the underlying layers. This was the first statistically significant refinement of site-specific bonding information at any surface utilizing x-ray diffraction data. Precession electron diffraction (PED) is a technique which is gaining increasing interest due to its ease of use and reduction of the dynamical scattering problem in electron diffraction. To further investigate the usefulness of this technique, we performed a systematic study of the effect of precession angle on the mineral andalusite where the semiangle was varied from 6.5 to 32 mrad in five discrete steps. We have shown that the intensities of kinematically forbidden reflections decayed exponentially as the precession semiangle (ϕ) was increased. Additionally, we have determined that charge density effects were best observed at moderately low angles (6.5-13 mrad) even though PED patterns became more kinematical in nature as the precession angle was increased further. We have also shown that the amount of interpretable information provided by direct methods phase inversion of the diffraction data increases monotonically but non-systematically as ϕ increases. We report an experimental and theoretical analysis of the ✓3x✓3-R30° and 2x2 reconstructions on the MgO (111) surface combining transmission electron microscopy, x-ray photoelectron spectroscopy, and reasonably accurate density functional calculations using the meta-GGA functional TPSS. We have not only conclusively solved the atomic structures of these reconstructions, but have developed a kinetic model for an evolutionary pathway between structures driven entirely by exchange of water molecules between the surface and the environment that does not require the cations to move when the structure transforms. This is the first time an experimentally and theoretically supported kinetic model has described not only all of the structures in a series on a single oxide surface, but also describes why none of the structures pass through the thermodynamically most stable configuration. Lastly, we have investigated the observability of valence bonding effects in aberration-corrected high resolution electron microscopy (HREM) images along the [010] projection of the mineral Forsterite (Mg2SiO 4). Direct observability of bonding effects would be both faster and less ambiguous than the refinement of similar features against diffraction data. Through analysis of simulated high resolution electron microscopy images, we have determined that bonding effects should be observable at levels approaching 20% of the total contrast. Initial experimental results for this material system have also been presented.

Chemical Reduction of Nd 1.85 Ce 0.15 CuO 4− δ Powders in Supercritical Sodium Ammonia Solutions

DOE PAGES

Dias, Yasmin; Wang, Hui; Zhou, Haiqing; ...

2015-01-01

Nd 1.85 Ce 0.15 CuO 4− δ powders are chemically reduced in supercritical sodium ammonia solutions from room temperature to 350°C. The crystallographic structure of the reduced powders is investigated from Rietveld refinement of X-ray powder diffraction. The atomic positions are maintained constant within experimental errors while temperature factors of all atoms increase significantly after the chemical treatments, especially of Nd/Ce atoms. The ammonothermally reduced Nd 1.85 Ce 0.15 CuO 4− δ powders show diamagnetic below 24 K which is contributed to the lower oxygen content and higher temperature factors of atoms in the treated compound. Themore » ammonothermal method paves a new way to reduce oxides in supercritical solutions near room temperature.« less

Morphology and topography study of graphene synthesized from plant oil

NASA Astrophysics Data System (ADS)

Robaiah, M.; Rusop, M.; Abdullah, S.; Khusaimi, Z.; Azhan, H.; Laila, M. O.; Salifairus, M. J.; Asli, N. A.

2018-05-01

The graphene is material consists of bonded atom carbon atoms in sheet form one atom thick. The different types of carbon sources which are refined corn oil, palm oil and waste cooking palm oil were used as carbon feedstock to supply carbon atom for synthesizing graphene on the nickel substrate by thermal chemical vapour deposition. The substrate and carbon sources were placed in double zone furnaces. The carbon sources and the substrate were heated at 300 °C and 900 °C respectively. The both furnaces were switched off after synthesis time for cooling process finish. The formation of the graphene on the Ni surface appears due to segregation and precipitation of a high amount of carbon from the source material during the cooling process. FESEM, AFM, UV-VIS Spectroscopy and Raman Spectroscopy were used to characterize and synthesized graphene.

Structural hierarchy as a key to complex phase selection in Al-Sm

NASA Astrophysics Data System (ADS)

Ye, Z.; Zhang, F.; Sun, Y.; Nguyen, M. C.; Zhou, S. H.; Zhou, L.; Meng, F.; Ott, R. T.; Park, E.; Besser, M. F.; Kramer, M. J.; Ding, Z. J.; Mendelev, M. I.; Wang, C. Z.; Napolitano, R. E.; Ho, K. M.

2017-10-01

Investigating the unknown structure of the complex cubic phase, previously observed to crystallize from melt-spun amorphous Al-10 at.% Sm alloy, we determine the structure in full site-occupancy detail, highlighting several critical structural features that govern the far-from-equilibrium phase selection pathway. Using an efficient genetic algorithm combining molecular dynamics, density functional theory, and x-ray diffraction, the structure is clearly identified as body-centered cubic I m 3 ¯m (No. 229) with ˜140 atoms per cubic unit cell and a lattice parameter of 1.4 nm. The complex structure is further refined to elucidate the detailed site occupancy, revealing full Sm occupancy on 6b sites and split Sm/Al occupancy on 16f sites. Based on the refined site occupancy associated with the experimentally observed phase, we term this phase ɛ -A l60S m11 (bcc), corresponding to the limiting situation when all 16f sites are occupied by Sm. However, it should be recognized that the range of solubility enabled by split occupancy at Sm sites is an important feature in phase selection under experimental conditions, permitting an avenue for transition with little or no chemical partitioning. Our analysis shows that the ɛ -A l60S m11 (bcc) exhibits a "3-6-6-1" first-shell packing around Sm centers on 16f sites, the same dominant motif exhibited by the undercooled liquid. The coincident motif supports the notion that liquid/glass ordering at high undercooling may give rise to topological invariants between the noncrystalline and crystalline states that provide kinetic pathways to metastable phases that are not accessible during near-equilibrium processing.

Structural hierarchy as a key to complex phase selection in Al-Sm

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

Ye, Z.; Zhang, F.; Sun, Y.

Investigating the unknown structure of the complex cubic phase, previously observed to crystallize from melt-spun amorphous Al–10 at.% Sm alloy, we determine the structure in full site-occupancy detail, highlighting several critical structural features that govern the far-from-equilibrium phase selection pathway. Using an efficient genetic algorithm combining molecular dynamics, density functional theory, and x-ray diffraction, the structure is clearly identified as body-centered cubic Im¯3m (No. 229) with ~140 atoms per cubic unit cell and a lattice parameter of 1.4 nm. The complex structure is further refined to elucidate the detailed site occupancy, revealing full Sm occupancy on 6b sites and splitmore » Sm/Al occupancy on 16f sites. Based on the refined site occupancy associated with the experimentally observed phase, we term this phase ε–Al 60Sm 11(bcc), corresponding to the limiting situation when all 16f sites are occupied by Sm. However, it should be recognized that the range of solubility enabled by split occupancy at Sm sites is an important feature in phase selection under experimental conditions, permitting an avenue for transition with little or no chemical partitioning. Our analysis shows that the ε–Al 60Sm 11(bcc) exhibits a “3-6-6-1” first-shell packing around Sm centers on 16f sites, the same dominant motif exhibited by the undercooled liquid. Here, the coincident motif supports the notion that liquid/glass ordering at high undercooling may give rise to topological invariants between the noncrystalline and crystalline states that provide kinetic pathways to metastable phases that are not accessible during near-equilibrium processing.« less

Structural hierarchy as a key to complex phase selection in Al-Sm

DOE PAGES

Ye, Z.; Zhang, F.; Sun, Y.; ...

2017-10-12

Investigating the unknown structure of the complex cubic phase, previously observed to crystallize from melt-spun amorphous Al–10 at.% Sm alloy, we determine the structure in full site-occupancy detail, highlighting several critical structural features that govern the far-from-equilibrium phase selection pathway. Using an efficient genetic algorithm combining molecular dynamics, density functional theory, and x-ray diffraction, the structure is clearly identified as body-centered cubic Im¯3m (No. 229) with ~140 atoms per cubic unit cell and a lattice parameter of 1.4 nm. The complex structure is further refined to elucidate the detailed site occupancy, revealing full Sm occupancy on 6b sites and splitmore » Sm/Al occupancy on 16f sites. Based on the refined site occupancy associated with the experimentally observed phase, we term this phase ε–Al 60Sm 11(bcc), corresponding to the limiting situation when all 16f sites are occupied by Sm. However, it should be recognized that the range of solubility enabled by split occupancy at Sm sites is an important feature in phase selection under experimental conditions, permitting an avenue for transition with little or no chemical partitioning. Our analysis shows that the ε–Al 60Sm 11(bcc) exhibits a “3-6-6-1” first-shell packing around Sm centers on 16f sites, the same dominant motif exhibited by the undercooled liquid. Here, the coincident motif supports the notion that liquid/glass ordering at high undercooling may give rise to topological invariants between the noncrystalline and crystalline states that provide kinetic pathways to metastable phases that are not accessible during near-equilibrium processing.« less

Gary Refining Company emerges from Chapter 11 bankruptcy

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

Not Available

1986-09-01

On July 24, 1986 Gary Refining Company, Inc. announced that the Reorganization Plan for Gary Refining Company, Inc., Gary Refining Company, and Mesa Refining, Inc. has been approved by the United States bankruptcy Court (District of Colorado). The companies filed for protection from creditors on March 4, 1985 under Chapter 11 of the United States Bankruptcy Code. Payments to creditors are expected to begin upon start-up of the Gary Refining Company (GRC) refinery in Fruita, Colorado after delivery of shale oil from Union Oil's Parachute Creek plant. In the interim, GRC will continue to explore options for possible startup (onmore » a full scale or partial basis) prior to that time.« less

HAADF-STEM atom counting in atom probe tomography specimens: Towards quantitative correlative microscopy.

PubMed

Lefebvre, W; Hernandez-Maldonado, D; Moyon, F; Cuvilly, F; Vaudolon, C; Shinde, D; Vurpillot, F

2015-12-01

The geometry of atom probe tomography tips strongly differs from standard scanning transmission electron microscopy foils. Whereas the later are rather flat and thin (<20 nm), tips display a curved surface and a significantly larger thickness. As far as a correlative approach aims at analysing the same specimen by both techniques, it is mandatory to explore the limits and advantages imposed by the particular geometry of atom probe tomography specimens. Based on simulations (electron probe propagation and image simulations), the possibility to apply quantitative high angle annular dark field scanning transmission electron microscopy to of atom probe tomography specimens has been tested. The influence of electron probe convergence and the benefice of deconvolution of electron probe point spread function electron have been established. Atom counting in atom probe tomography specimens is for the first time reported in this present work. It is demonstrated that, based on single projections of high angle annular dark field imaging, significant quantitative information can be used as additional input for refining the data obtained by correlative analysis of the specimen in APT, therefore opening new perspectives in the field of atomic scale tomography. Copyright © 2015 Elsevier B.V. All rights reserved.

Crystal structure of aqua-1κO-{μ-2-[(2-hydroxy­ethyl)methylamino]ethanolato-2:1κ4 O 1,N,O 2:O 1}[μ-2,2′-(methylimino)diethanolato-1:2κ4 O,N,O′:O]dithiocyanato-1κN,2κN-chromium(III)copper(II)

PubMed Central

Rusanova, Julia A.; Semenaka, Valentina V.; Dyakonenko, Viktoriya V.; Shishkin, Oleg V.

2015-01-01

The title compound, [CrCu(C5H11NO2)(C5H12NO2)(NCS)2(H2O)] or [Cr(μ-mdea)Cu(μ-Hmdea)(NCS)2H2O], (where mdeaH2 is N-methylethanolamine, C5H13NO2) is formed as a neutral heterometal CuII/CrIII complex. The mol­ecular structure of the complex is based on a binuclear {CuCr(μ-O)2} core. The coordination environment of each metal atom involves the N,O,O atoms of the tridentate ligand, one bridging O atom of the ligand and the N atom of the thio­cyanato ligands. The CuII ion adopts a distorted square-pyramidal coordination while the CrIII ion has a distorted octa­hedral coordination geometry completed by the aqua ligand. In the crystal, the binuclear complexes are linked via two pairs of O—H⋯O hydrogen bonds to form inversion dimers, which are arranged in columns parallel to the a axis. In the μ-mdea ligand two –CH2 groups and the methyl group were refined as disordered over two sets of sites with equal occupancies. The structure was refined as a two-component twin with a twin scale factor of 0.242 (1). PMID:26396853

Peptide crystal simulations reveal hidden dynamics

PubMed Central

Janowski, Pawel A.; Cerutti, David S.; Holton, James; Case, David A.

2013-01-01

Molecular dynamics simulations of biomolecular crystals at atomic resolution have the potential to recover information on dynamics and heterogeneity hidden in the X-ray diffraction data. We present here 9.6 microseconds of dynamics in a small helical peptide crystal with 36 independent copies of the unit cell. The average simulation structure agrees with experiment to within 0.28 Å backbone and 0.42 Å all-atom rmsd; a model refined against the average simulation density agrees with the experimental structure to within 0.20 Å backbone and 0.33 Å all-atom rmsd. The R-factor between the experimental structure factors and those derived from this unrestrained simulation is 23% to 1.0 Å resolution. The B-factors for most heavy atoms agree well with experiment (Pearson correlation of 0.90), but B-factors obtained by refinement against the average simulation density underestimate the coordinate fluctuations in the underlying simulation where the simulation samples alternate conformations. A dynamic flow of water molecules through channels within the crystal lattice is observed, yet the average water density is in remarkable agreement with experiment. A minor population of unit cells is characterized by reduced water content, 310 helical propensity and a gauche(−) side-chain rotamer for one of the valine residues. Careful examination of the experimental data suggests that transitions of the helices are a simulation artifact, although there is indeed evidence for alternate valine conformers and variable water content. This study highlights the potential for crystal simulations to detect dynamics and heterogeneity in experimental diffraction data, as well as to validate computational chemistry methods. PMID:23631449

i3Drefine Software for Protein 3D Structure Refinement and Its Assessment in CASP10

PubMed Central

Bhattacharya, Debswapna; Cheng, Jianlin

2013-01-01

Protein structure refinement refers to the process of improving the qualities of protein structures during structure modeling processes to bring them closer to their native states. Structure refinement has been drawing increasing attention in the community-wide Critical Assessment of techniques for Protein Structure prediction (CASP) experiments since its addition in 8th CASP experiment. During the 9th and recently concluded 10th CASP experiments, a consistent growth in number of refinement targets and participating groups has been witnessed. Yet, protein structure refinement still remains a largely unsolved problem with majority of participating groups in CASP refinement category failed to consistently improve the quality of structures issued for refinement. In order to alleviate this need, we developed a completely automated and computationally efficient protein 3D structure refinement method, i3Drefine, based on an iterative and highly convergent energy minimization algorithm with a powerful all-atom composite physics and knowledge-based force fields and hydrogen bonding (HB) network optimization technique. In the recent community-wide blind experiment, CASP10, i3Drefine (as ‘MULTICOM-CONSTRUCT’) was ranked as the best method in the server section as per the official assessment of CASP10 experiment. Here we provide the community with free access to i3Drefine software and systematically analyse the performance of i3Drefine in strict blind mode on the refinement targets issued in CASP10 refinement category and compare with other state-of-the-art refinement methods participating in CASP10. Our analysis demonstrates that i3Drefine is only fully-automated server participating in CASP10 exhibiting consistent improvement over the initial structures in both global and local structural quality metrics. Executable version of i3Drefine is freely available at http://protein.rnet.missouri.edu/i3drefine/. PMID:23894517

Model-based local density sharpening of cryo-EM maps

PubMed Central

Jakobi, Arjen J; Wilmanns, Matthias

2017-01-01

Atomic models based on high-resolution density maps are the ultimate result of the cryo-EM structure determination process. Here, we introduce a general procedure for local sharpening of cryo-EM density maps based on prior knowledge of an atomic reference structure. The procedure optimizes contrast of cryo-EM densities by amplitude scaling against the radially averaged local falloff estimated from a windowed reference model. By testing the procedure using six cryo-EM structures of TRPV1, β-galactosidase, γ-secretase, ribosome-EF-Tu complex, 20S proteasome and RNA polymerase III, we illustrate how local sharpening can increase interpretability of density maps in particular in cases of resolution variation and facilitates model building and atomic model refinement. PMID:29058676

Ab initio relativistic effective potentials with spin--orbit operators. III. Rb through Xe

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

LaJohn, L.A.; Christiansen, P.A.; Ross, R.B.

A refined version of the ''shape consistent'' effective potential procedure of Christiansen, Lee, and Pitzer was used to compute averaged relativistic effective potentials (AREP) and spin--orbit operators for the elements Rb through Xe. Particular attention was given to the partitioning of the core and valence space and, where appropriate, more than one set of potentials is provided. These are tabulated in analytic form. Gaussian basis sets with contraction coefficients for the lowest energy state of each atom are given. The reliability of the transition metal AREPs was examined by comparing computed atomic excitation energies with accurate all-electron relativistic values. Themore » spin--orbit operators were tested in calculations on selected atoms.« less

Rietveld-refinement and optical study of the Fe doped ZnO thin film by RF magnetron sputtering

NASA Astrophysics Data System (ADS)

Kumar, Arun; Dhiman, Pooja; Singh, M.

2017-05-01

Fe Doped ZnO Dilute Magnetic Semiconductor thin film prepared by RF magnetron sputtering on glass substrate and Influence of 3% Fe-doping on structural and Optical properties has been studied. The Rietveld-refinement analysis shows that Fe doping has a significant effect on crystalline structure, grain size and strain in the thin film. Two dimensional and three-dimensional atom probe tomography of the thin film shows that Fe ions are randomly distributed which is supported by Xray Diffraction (XRD). Fe-doping is found to effectively modify the band gap energy up to 3.5 eV.

3Drefine: an interactive web server for efficient protein structure refinement.

PubMed

Bhattacharya, Debswapna; Nowotny, Jackson; Cao, Renzhi; Cheng, Jianlin

2016-07-08

3Drefine is an interactive web server for consistent and computationally efficient protein structure refinement with the capability to perform web-based statistical and visual analysis. The 3Drefine refinement protocol utilizes iterative optimization of hydrogen bonding network combined with atomic-level energy minimization on the optimized model using a composite physics and knowledge-based force fields for efficient protein structure refinement. The method has been extensively evaluated on blind CASP experiments as well as on large-scale and diverse benchmark datasets and exhibits consistent improvement over the initial structure in both global and local structural quality measures. The 3Drefine web server allows for convenient protein structure refinement through a text or file input submission, email notification, provided example submission and is freely available without any registration requirement. The server also provides comprehensive analysis of submissions through various energy and statistical feedback and interactive visualization of multiple refined models through the JSmol applet that is equipped with numerous protein model analysis tools. The web server has been extensively tested and used by many users. As a result, the 3Drefine web server conveniently provides a useful tool easily accessible to the community. The 3Drefine web server has been made publicly available at the URL: http://sysbio.rnet.missouri.edu/3Drefine/. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

Refining Students' Explanations of an Unfamiliar Physical Phenomenon-Microscopic Friction

NASA Astrophysics Data System (ADS)

Corpuz, Edgar De Guzman; Rebello, N. Sanjay

2017-08-01

The first phase of this multiphase study involves modeling of college students' thinking of friction at the microscopic level. Diagnostic interviews were conducted with 11 students with different levels of physics backgrounds. A phenomenographic approach of data analysis was used to generate categories of responses which subsequently were used to generate a model of explanation. Most of the students interviewed consistently used mechanical interactions in explaining microscopic friction. According to these students, friction is due to the interlocking or rubbing of atoms. Our data suggest that students' explanations of microscopic friction are predominantly influenced by their macroscopic experiences. In the second phase of the research, teaching experiment was conducted with 18 college students to investigate how students' explanations of microscopic friction can be refined by a series of model-building activities. Data were analyzed using Redish's two-level transfer framework. Our results show that through sequences of hands-on and minds-on activities, including cognitive dissonance and resolution, it is possible to facilitate the refinement of students' explanations of microscopic friction. The activities seemed to be productive in helping students activate associations that refine their ideas about microscopic friction.

Refining glass structure in two dimensions

NASA Astrophysics Data System (ADS)

Sadjadi, Mahdi; Bhattarai, Bishal; Drabold, D. A.; Thorpe, M. F.; Wilson, Mark

2017-11-01

Recently determined atomistic scale structures of near-two dimensional bilayers of vitreous silica (using scanning probe and electron microscopy) allow us to refine the experimentally determined coordinates to incorporate the known local chemistry more precisely. Further refinement is achieved by using classical potentials of varying complexity: one using harmonic potentials and the second employing an electrostatic description incorporating polarization effects. These are benchmarked against density functional calculations. Our main findings are that (a) there is a symmetry plane between the two disordered layers, a nice example of an emergent phenomena, (b) the layers are slightly tilted so that the Si-O-Si angle between the two layers is not 180∘ as originally thought but rather 175 ±2∘ , and (c) while interior areas that are not completely imagined can be reliably reconstructed, surface areas are more problematic. It is shown that small crystallites that appear are just as expected statistically in a continuous random network. This provides a good example of the value that can be added to disordered structures imaged at the atomic level by implementing computer refinement.

Evaluation of unrestrained replica-exchange simulations using dynamic walkers in temperature space for protein structure refinement.

PubMed

Olson, Mark A; Lee, Michael S

2014-01-01

A central problem of computational structural biology is the refinement of modeled protein structures taken from either comparative modeling or knowledge-based methods. Simulations are commonly used to achieve higher resolution of the structures at the all-atom level, yet methodologies that consistently yield accurate results remain elusive. In this work, we provide an assessment of an adaptive temperature-based replica exchange simulation method where the temperature clients dynamically walk in temperature space to enrich their population and exchanges near steep energetic barriers. This approach is compared to earlier work of applying the conventional method of static temperature clients to refine a dataset of conformational decoys. Our results show that, while an adaptive method has many theoretical advantages over a static distribution of client temperatures, only limited improvement was gained from this strategy in excursions of the downhill refinement regime leading to an increase in the fraction of native contacts. To illustrate the sampling differences between the two simulation methods, energy landscapes are presented along with their temperature client profiles.

Accurate X-ray diffraction studies of KTiOPO{sub 4} single crystals doped with niobium

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

Novikova, N. E., E-mail: natnov@ns.crys.ras.ru; Sorokina, N. I.; Alekseeva, O. A.

2017-01-15

Single crystals of potassium titanyl phosphate doped with 4% of niobium (КТР:4%Nb) and 6% of niobium (KTP:6%Nb) are studied by accurate X-ray diffraction at room temperature. The niobium atoms are localized near the Ti1 and Ti2 atomic positions, and their positions are for the first time refined independent of the titanium atomic positions. Maps of difference electron density in the vicinity of K1 and K2 atomic positions are analyzed. It is found that in the structure of crystal КТР:4%Nb, additional positions of K atoms are located farther from the main positions and from each other than in КТР and KTP:6%Nbmore » crystals. The nonuniform distribution of electron density found in the channels of the КТР:4%Nb structure is responsible for ~20% increase in the signal of second harmonic generation.« less

DFT energy optimization of a large carbohydrate: cyclomaltohexaicosaose (CA-26)

USDA-ARS?s Scientific Manuscript database

CA-26 is the largest cyclodextrin (546 atoms) for which refined X-ray structural data is available. Because of its size, 26 D-glucose residues, it is beyond the scope of study of most ab initio or density functional methods, and to date has only been computationally examined using empirical force fi...

Sources of Nuclear Fuel, Understanding the Atom Series.

ERIC Educational Resources Information Center

Singleton, Arthur L., Jr.

A brief outline of the historical landmarks in nuclear physics leading to the use of nuclear energy for peaceful purposes introduces this illustrated booklet. The distribution of known sources of uranium ores is mapped and some details about the geology of each geographical area given. Methods of prospective, mining, milling, refining, and fuel…

Proteopedia Entry: The Large Ribosomal Subunit of "Haloarcula Marismortui"

ERIC Educational Resources Information Center

Decatur, Wayne A.

2010-01-01

This article presents a "Proteopedia" page that shows the refined version of the structure of the "Haloarcula" large ribosomal subunit as solved by the laboratories of Thomas Steitz and Peter Moore. The landmark structure is of great impact as it is the first atomic-resolution structure of the highly conserved ribosomal subunit which harbors…

GIRAF: a method for fast search and flexible alignment of ligand binding interfaces in proteins at atomic resolution

PubMed Central

Kinjo, Akira R.; Nakamura, Haruki

2012-01-01

Comparison and classification of protein structures are fundamental means to understand protein functions. Due to the computational difficulty and the ever-increasing amount of structural data, however, it is in general not feasible to perform exhaustive all-against-all structure comparisons necessary for comprehensive classifications. To efficiently handle such situations, we have previously proposed a method, now called GIRAF. We herein describe further improvements in the GIRAF protein structure search and alignment method. The GIRAF method achieves extremely efficient search of similar structures of ligand binding sites of proteins by exploiting database indexing of structural features of local coordinate frames. In addition, it produces refined atom-wise alignments by iterative applications of the Hungarian method to the bipartite graph defined for a pair of superimposed structures. By combining the refined alignments based on different local coordinate frames, it is made possible to align structures involving domain movements. We provide detailed accounts for the database design, the search and alignment algorithms as well as some benchmark results. PMID:27493524

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

PubMed

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

2016-07-15

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

Accelerator mass spectrometry of strontium-90 for homeland security, environmental monitoring and human health

NASA Astrophysics Data System (ADS)

Tumey, Scott J.; Brown, Thomas A.; Hamilton, Terry E.; Hillegonds, Darren J.

2008-05-01

Strontium-90 is one of the most hazardous materials managed by agencies charged with protecting the public from radiation. Traditional radiometric methods have been limited by low sample throughput and slow turnaround times. Mass spectrometry offers the advantage of shorter analysis times and the ability to measure samples immediately after processing, however conventional mass spectrometric techniques are susceptible to molecular isobaric interferences that limit their overall sensitivity. In contrast, accelerator mass spectrometry is insensitive to molecular interferences and we have therefore begun developing a method for determination of 90Sr by accelerator mass spectrometry. Despite a pervasive interference from 90Zr, our initial development has yielded an instrumental background of ∼108 atoms (75 mBq) per sample. Further refinement of our system (e.g. redesign of our detector, use of alternative target materials) is expected to push the background below 106 atoms, close to the theoretical limit for AMS. Once we have refined our system and developed suitable sample preparation protocols, we will utilize our capability in applications to homeland security, environmental monitoring and human health.

Searching for the rules that govern hadron construction

DOE PAGES

Shepherd, Matthew R.; Dudek, Jozef J.; Mitchell, Ryan E.

2016-06-22

Just as quantum electrodynamics describes how electrons are bound in atoms by the electromagnetic force, mediated by the exchange of photons, quantum chromodynamics (QCD) describes how quarks are bound inside hadrons by the strong force, mediated by the exchange of gluons. QCD seems to allow hadrons constructed from increasingly many quarks to exist, just as atoms with increasing numbers of electrons exist, yet such complex constructions seemed, until recently, not to be present in nature. In this paper, we describe advances in the spectroscopy of mesons that are refining our understanding of the rules for predicting hadron structure from QCD.

Visualization of drug-nucleic acid interactions at atomic resolution v. structure of two aminoacridine/dinucleoside monophosphate crystalline complexes, proflavine: 5-iodocytidylyl(3'-5') guanosine and acridine orange: 5-iodocytidylyl(3'-5') guanosine

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

Reddy, B.S.; Seshadri, T.P.; Sakore, T.D.

1979-01-01

Acridine orange and proflavine form complexes with the dinucleoside monophosphate, 5-iodocytidylyl(3'-5') guanosine (iodoCpG). The acridine orange-iodoCpG crystals are monoclinic, space group P2/sub 1/, with unit cell dimensions a = 14.36 A, b = 19.64 A, c = 20.67 A, ..beta.. = 102.5. The proflavine-iodoCpG crystals are monoclinic, space group C2, with unit cell dimensions a = 32.14 A, b = 22.23 A, c = 18.42 A, ..beta.. = 123.3. Both structures have been solved to atomic resolution by Patterson and Fourier methods, and refined by full matrix least squares. Acridine orange forms an intercalative structure with iodoCpG but the acridinemore » nucleus lies asymmetrically in the intercalation site. This asymmetric intercalation is accompanied by a sliding of base-pairs upon the acridine nucleus. Base-pairs above and below the drug are separated by about 6.8 A and are twisted about 10/sup 0/. Proflavine demonstrates symmetric intercalation with iodoCpG. Hydrogen bonds connect amino- groups on proflavine with phosphate oxygen atoms on the dinucleotide. Base-pairs above and below the intercalative proflavine molecule are twisted about 36/sup 0/. The altered magnitude of this angular twist reflects the sugar puckering pattern that is observed. We propose a proflavine-DNA and an acridine orange-DNA binding model. We will describe these models in detail in this paper.« less

A revised partiality model and post-refinement algorithm for X-ray free-electron laser data

DOE PAGES

Ginn, Helen Mary; Brewster, Aaron S.; Hattne, Johan; ...

2015-05-23

Research towards using X-ray free-electron laser (XFEL) data to solve structures using experimental phasing methods such as sulfur single-wavelength anomalous dispersion (SAD) has been hampered by shortcomings in the diffraction models for X-ray diffraction from FELs. Owing to errors in the orientation matrix and overly simple partiality models, researchers have required large numbers of images to converge to reliable estimates for the structure-factor amplitudes, which may not be feasible for all biological systems. Here, data for cytoplasmic polyhedrosis virus type 17 (CPV17) collected at 1.3 Å wavelength at the Linac Coherent Light Source (LCLS) are revisited. A previously published definitionmore » of a partiality model for reflections illuminated by self-amplified spontaneous emission (SASE) pulses is built upon, which defines a fraction between 0 and 1 based on the intersection of a reflection with a spread of Ewald spheres modelled by a super-Gaussian wavelength distribution in the X-ray beam. A method of post-refinement to refine the parameters of this model is suggested. This has generated a merged data set with an overall discrepancy (by calculating theR splitvalue) of 3.15% to 1.46 Å resolution from a 7225-image data set. The atomic numbers of C, N and O atoms in the structure are distinguishable in the electron-density map. There are 13 S atoms within the 237 residues of CPV17, excluding the initial disordered methionine. These only possess 0.42 anomalous scattering electrons each at 1.3 Å wavelength, but the 12 that have single predominant positions are easily detectable in the anomalous difference Fourier map. It is hoped that these improvements will lead towards XFEL experimental phase determination and structure determination by sulfur SAD and will generally increase the utility of the method for difficult cases.« less

Refinement of protein termini in template-based modeling using conformational space annealing.

PubMed

Park, Hahnbeom; Ko, Junsu; Joo, Keehyoung; Lee, Julian; Seok, Chaok; Lee, Jooyoung

2011-09-01

The rapid increase in the number of experimentally determined protein structures in recent years enables us to obtain more reliable protein tertiary structure models than ever by template-based modeling. However, refinement of template-based models beyond the limit available from the best templates is still needed for understanding protein function in atomic detail. In this work, we develop a new method for protein terminus modeling that can be applied to refinement of models with unreliable terminus structures. The energy function for terminus modeling consists of both physics-based and knowledge-based potential terms with carefully optimized relative weights. Effective sampling of both the framework and terminus is performed using the conformational space annealing technique. This method has been tested on a set of termini derived from a nonredundant structure database and two sets of termini from the CASP8 targets. The performance of the terminus modeling method is significantly improved over our previous method that does not employ terminus refinement. It is also comparable or superior to the best server methods tested in CASP8. The success of the current approach suggests that similar strategy may be applied to other types of refinement problems such as loop modeling or secondary structure rearrangement. Copyright © 2011 Wiley-Liss, Inc.

The solvent component of macromolecular crystals

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

Weichenberger, Christian X.; Afonine, Pavel V.; Kantardjieff, Katherine

2015-04-30

On average, the mother liquor or solvent and its constituents occupy about 50% of a macromolecular crystal. Ordered as well as disordered solvent components need to be accurately accounted for in modelling and refinement, often with considerable complexity. The mother liquor from which a biomolecular crystal is grown will contain water, buffer molecules, native ligands and cofactors, crystallization precipitants and additives, various metal ions, and often small-molecule ligands or inhibitors. On average, about half the volume of a biomolecular crystal consists of this mother liquor, whose components form the disordered bulk solvent. Its scattering contributions can be exploited in initialmore » phasing and must be included in crystal structure refinement as a bulk-solvent model. Concomitantly, distinct electron density originating from ordered solvent components must be correctly identified and represented as part of the atomic crystal structure model. Herein, are reviewed (i) probabilistic bulk-solvent content estimates, (ii) the use of bulk-solvent density modification in phase improvement, (iii) bulk-solvent models and refinement of bulk-solvent contributions and (iv) modelling and validation of ordered solvent constituents. A brief summary is provided of current tools for bulk-solvent analysis and refinement, as well as of modelling, refinement and analysis of ordered solvent components, including small-molecule ligands.« less

Three-dimensional structure of porcine pancreatic carboxypeptidase B with an acetate ion and two zinc atoms in the active site

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

Akparov, V. Kh., E-mail: valery@akparov.ru; Timofeev, V. I., E-mail: tostars@mail.ru; Maghsoudi, N. N., E-mail: maghsudi@yahoo.com

2017-03-15

Crystals of porcine pancreatic carboxypeptidase B (CPB) were grown by the capillary counter-diffusion method in the presence of polyethylene glycol and zinc acetate. The three-dimensional structure of CPB was determined at 1.40 Å resolution using the X-ray diffraction data set collected from the crystals of the enzyme at the SPring 8 synchrotron facility and was refined to R{sub fact} = 17.19%, R{sub free} = 19.78%. The structure contains five zinc atoms, two of which are present in the active site of the enzyme, and an acetate ion. The arrangement of an additional zinc atom in the active site and themore » acetate ion is different from that reported by Yoshimoto et al.« less

The cluster compound In{sub 4}Ti{sub 1.5}Mo{sub 0.5}Mo{sub 14}O{sub 26} containing Mo{sub 14} clusters and the new mono- and bi-capped trioctahedral Mo{sub 15} and Mo{sub 16} clusters: Synthesis, crystal structure, and electrical and magnetic properties

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

Gall, Philippe; Guizouarn, Thierry; Gougeon, Patrick, E-mail: Patrick.Gougeon@univ-rennes1.fr

2015-07-15

Single crystals of the new quaternary compound In{sub 4}Ti{sub 1.5}Mo{sub 0.5}Mo{sub 14}O{sub 26} were obtained by solid state reaction. The crystal structure was determined by single-crystal X-ray diffraction. In{sub 4}Ti{sub 1.5}Mo{sub 0.5}Mo{sub 14}O{sub 26} crystallizes in the orthorhombic space group Pbca with unit-cell parameters a=9.4432(14) Å, b=11.4828(12) Å, c=20.299(4) Å and Z=4. Full-matrix least-squares refinement on F{sup 2} using 3807 independent reflections for 219 refinable parameters resulted in R{sub 1}=0.0259 and wR{sub 2}=0.0591. The crystal structure contains in addition to Mo{sub 14} clusters the first examples of mono- and bi-capped trioctahedral Mo{sub 14} i.e. Mo{sub 15} and Mo{sub 16} clusters.more » The oxygen framework derives from a stacking along the a direction of close-packed layers with sequence (…ABAC…). The Mo–Mo distances range between 2.6938(5) and 2.8420(6) Å and the Mo–O distances between 1.879(5) and 2.250(3) Å, as usually observed in molybdenum oxide clusters. The indium atoms form In{sub 4}{sup 6+} bent chains with In–In distances of 2.6682(5) and 2.6622(8) Å and the Ti atoms are in highly distorted octahedral sites of oxygen atoms with Ti–O distances ranging between 1.865(4) and 2.161(4) Å. Magnetic susceptibility measurements confirm the presence of Ti{sup 4+} cations and the absence of localized moments on the Mo network. Electrical resistivity measurements on a single crystal of In{sub 4}Ti{sub 1.5}Mo{sub 0.5}Mo{sub 14}O{sub 26} show a semimetallic behavior. - Graphical abstract: We present here the synthesis, the crystal structure, and the electrical and magnetic properties of the new compound In{sub 4}Ti{sub 1.5}Mo{sub 0.5}Mo{sub 14}O{sub 26} in which Mo{sub 14} clusters coexist statistically with mono- and bi-capped trioctahedral Mo{sub 14} that is Mo{sub 15} and Mo{sub 16} clusters. - Highlights: • Single crystals of In{sub 4}Ti{sub 1.5}Mo{sub 0.5}Mo{sub 14}O{sub 26} were obtained by solid state reaction. • The crystal structure contains Mo{sub 14}, Mo{sub 15} and Mo{sub 16} clusters. • The indium atoms form In{sub 4}{sup 6+} bent chains. • Poorly metallic behavior. • Absence of localized moments on the Mo network as well as on the Ti atoms.« less

Revision of the Li13Si4 structure.

PubMed

Zeilinger, Michael; Fässler, Thomas F

2013-11-06

Besides Li17Si4, Li16.42Si4, and Li15Si4, another lithium-rich representative in the Li-Si system is the phase Li13Si4 (trideca-lithium tetra-silicide), the structure of which has been determined previously [Frank et al. (1975 ▶). Z. Naturforsch. Teil B, 30, 10-13]. A careful analysis of X-ray diffraction patterns of Li13Si4 revealed discrepancies between experimentally observed and calculated Bragg positions. Therefore, we redetermined the structure of Li13Si4 on the basis of single-crystal X-ray diffraction data. Compared to the previous structure report, decisive differences are (i) the introduction of a split position for one Li site [occupancy ratio 0.838 (7):0.162 (7)], (ii) the anisotropic refinement of atomic displacement parameters for all atoms, and (iii) a high accuracy of atom positions and unit-cell parameters. The asymmetric unit of Li13Si4 contains two Si and seven Li atoms. Except for one Li atom situated on a site with symmetry 2/m, all other atoms are on mirror planes. The structure consists of isolated Si atoms as well as Si-Si dumbbells surrounded by Li atoms. Each Si atom is either 12- or 13-coordinated. The isolated Si atoms are situated in the ab plane at z = 0 and are strictly separated from the Si-Si dumbbells at z = 0.5.

Purification of selenium by zone refining

NASA Astrophysics Data System (ADS)

Burger, A.; Henderson, D. O.; Morgan, S. H.; Feng, J.; Silberman, E.

1990-11-01

We studied the purification of Se using zone refining, with emphasis on the efficiency of this technique in removing the Cu impurity, which is known to be related to a trapping center in CdSe. After 78 passes it was found that Cu accumulates at one end section of the ingot, while at the opposite end the level was below the detection limit of the atomic absorption spectroscopic analysis employed. Infrared spectroscopic data, differential solubility and differential scanning calorimetry measurements also indicate that the effective distribution coefficient, k, for the Cu solute, is less than 1. A model for the various phases present during zone melting is presented and the possibility of segregating impurities having k>1 is discussed.

The comparison of approaches to the solid-state NMR-based structural refinement of vitamin B1 hydrochloride and of its monohydrate

NASA Astrophysics Data System (ADS)

Czernek, Jiří; Pawlak, Tomasz; Potrzebowski, Marek J.; Brus, Jiří

2013-01-01

The 13C and 15N CPMAS SSNMR measurements were accompanied by the proper theoretical description of the solid-phase environment, as provided by the density functional theory in the pseudopotential plane-wave scheme, and employed in refining the atomic coordinates of the crystal structures of thiamine chloride hydrochloride and of its monohydrate. Thus, using the DFT functionals PBE, PW91 and RPBE, the SSNMR-consistent solid-phase structures of these compounds are derived from the geometrical optimization, which is followed by an assessment of the fits of the GIPAW-predicted values of the chemical shielding parameters to their experimental counterparts.

Local structural and chemical ordering of nanosized Pt3±δCo probed by multiple-scattering x-ray absorption spectroscopy

NASA Astrophysics Data System (ADS)

Greco, Giorgia; Witkowska, Agnieszka; Principi, Emiliano; Minicucci, Marco; di Cicco, Andrea

2011-04-01

This work reports a detailed investigation of the local structure and chemical disorder of a Pt3±δCo thin film and Pt3±δCo nanoparticles. We have used a combination of techniques including x-ray absorption spectroscopy (XAS), x-ray diffraction (XRD), and high-resolution transmission electron microscopy (TEM). High-quality XAS spectra at the Co K edge and Pt L3 edge have been analyzed using double-edge multiple-scattering data analysis. Structural extended x-ray absorption fine structure (EXAFS) refinements have been performed accounting for the reduction of the coordination numbers and degeneracy of three-atom configurations, resulting from the measured size distribution and stoichiometry. The important effect of chemical ordering on pair and three-atom configurations has been studied using computer simulations based on a simple model accounting for substitutional disorder, defined by an order parameter s. It has been found that individual EXAFS signals related to the minority species (Co) are extremely sensitive to substitutional disorder so their intensities, especially those of the collinear three-atom configurations, can be used as a measure of the ordering level. The thin film has been found to be chemically disordered (s⩽0.4), in agreement with previous estimates. The Pt3±δCo nanoalloy has been found to be partially ordered (s=0.6±0.1) while the local structure around Co atoms is characterized by a higher level of structural disorder as compared to the bulk-like thin film. The robust approach for nanomaterial characterization used in this work combining different techniques can, in principle, be applied for structural refinements of any binary nanocrystalline functional system.

Local structure in LaMnO3 and CaMnO3 perovskites: A quantitative structural refinement of Mn K -edge XANES data

NASA Astrophysics Data System (ADS)

Monesi, C.; Meneghini, C.; Bardelli, F.; Benfatto, M.; Mobilio, S.; Manju, U.; Sarma, D. D.

2005-11-01

Hole-doped perovskites such as La1-xCaxMnO3 present special magnetic and magnetotransport properties, and it is commonly accepted that the local atomic structure around Mn ions plays a crucial role in determining these peculiar features. Therefore experimental techniques directly probing the local atomic structure, like x-ray absorption spectroscopy (XAS), have been widely exploited to deeply understand the physics of these compounds. Quantitative XAS analysis usually concerns the extended region [extended x-ray absorption fine structure (EXAFS)] of the absorption spectra. The near-edge region [x-ray absorption near-edge spectroscopy (XANES)] of XAS spectra can provide detailed complementary information on the electronic structure and local atomic topology around the absorber. However, the complexity of the XANES analysis usually prevents a quantitative understanding of the data. This work exploits the recently developed MXAN code to achieve a quantitative structural refinement of the Mn K -edge XANES of LaMnO3 and CaMnO3 compounds; they are the end compounds of the doped manganite series LaxCa1-xMnO3 . The results derived from the EXAFS and XANES analyses are in good agreement, demonstrating that a quantitative picture of the local structure can be obtained from XANES in these crystalline compounds. Moreover, the quantitative XANES analysis provides topological information not directly achievable from EXAFS data analysis. This work demonstrates that combining the analysis of extended and near-edge regions of Mn K -edge XAS spectra could provide a complete and accurate description of Mn local atomic environment in these compounds.

X-ray structure determination at low resolution

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

Brunger, Axel T., E-mail: brunger@stanford.edu; Department of Molecular and Cellular Physiology, Stanford University; Department of Neurology and Neurological Sciences, Stanford University

2009-02-01

Refinement is meaningful even at 4 Å or lower, but with present methodologies it should start from high-resolution crystal structures whenever possible. As an example of structure determination in the 3.5–4.5 Å resolution range, crystal structures of the ATPase p97/VCP, consisting of an N-terminal domain followed by a tandem pair of ATPase domains (D1 and D2), are discussed. The structures were originally solved by molecular replacement with the high-resolution structure of the N-D1 fragment of p97/VCP, whereas the D2 domain was manually built using its homology to the D1 domain as a guide. The structure of the D2 domain alonemore » was subsequently solved at 3 Å resolution. The refined model of D2 and the high-resolution structure of the N-D1 fragment were then used as starting models for re-refinement against the low-resolution diffraction data for full-length p97. The re-refined full-length models showed significant improvement in both secondary structure and R values. The free R values dropped by as much as 5% compared with the original structure refinements, indicating that refinement is meaningful at low resolution and that there is information in the diffraction data even at ∼4 Å resolution that objectively assesses the quality of the model. It is concluded that de novo model building is problematic at low resolution and refinement should start from high-resolution crystal structures whenever possible.« less

Oxygen-storage behavior and local structure in Ti-substituted YMnO3

NASA Astrophysics Data System (ADS)

Levin, I.; Krayzman, V.; Vanderah, T. A.; Tomczyk, M.; Wu, H.; Tucker, M. G.; Playford, H. Y.; Woicik, J. C.; Dennis, C. L.; Vilarinho, P. M.

2017-02-01

Hexagonal manganates RMnO3 (R=Y, Ho, Dy) have been recently shown to exhibit oxygen-storage capacities promising for three-way catalysts, air-separation, and related technologies. Here, we demonstrate that Ti substitution for Mn can be used to chemically tune the oxygen-breathing properties of these materials towards practical applications. Specifically, Y(Mn1-xTix)O3 solid solutions exhibit facile oxygen absorption/desorption via reversible Ti3+↔Ti4+ and Mn3+↔Mn4+ reactions already in ambient air at ≈400 °C and ≈250 °C, respectively. On cooling, the oxidation of both cations is accompanied by oxygen uptake yielding a formula YMn3+1-x-yMn4+yTi4+xO3+δ. The presence of Ti promotes the oxidation of Mn3+ to Mn4+, which is almost negligible for YMnO3 in air, thereby increasing the uptake of oxygen beyond that required for a given Ti4+ concentration. The reversibility of the redox reactions is limited by sluggish kinetics; however, the oxidation process continues, if slowly, even at room temperature. The extra oxygen atoms are accommodated by the large interstices within a triangular lattice formed by the [MnO5] trigonal bipyramids. According to bond distances from Rietveld refinements using the neutron diffraction data, the YMnO3 structure features under-bonded Mn and even more severely under-bonded oxygen atoms that form the trigonal bases of the [MnO5] bipyramids. The tensile bond strain around the 5-fold coordinated Mn site and the strong preference of Ti4+(and Mn4+) for higher coordination numbers likely provide driving forces for the oxidation reaction. Reverse Monte Carlo refinements of the local atomic displacements using neutron total scattering revealed how the excess oxygen atoms are accommodated in the structure by correlated local displacements of the host atoms. Large displacements of the under-bonded host oxygen atoms play a key part in this lattice-relaxation process, facilitating reversible exchange of significant amounts of oxygen with atmosphere.

Oxygen-storage behavior and local structure in Ti-substituted YMnO 3

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

Levin, I.; Krayzman, V.; Vanderah, T. A.

Hexagonal manganates RMnO3 (R=Y, Ho, Dy) have been recently shown to exhibit oxygen-storage capacities promising for three-way catalysts, air-separation, and related technologies. Here, we demonstrate that Ti substitution for Mn can be used to chemically tune the oxygen-breathing properties of these materials towards practical applications. Specifically, Y(Mn1-xTix)O3 solid solutions exhibit facile oxygen absorption/desorption via reversible Ti3+↔Ti4+ and Mn3+↔Mn4+ reactions already in ambient air at ≈400 °C and ≈250 °C, respectively. On cooling, the oxidation of both cations is accompanied by oxygen uptake yielding a formula YMn3+1-x-yMn4+yTi4+xO3+δ. The presence of Ti promotes the oxidation of Mn3+ to Mn4+, which is almostmore » negligible for YMnO3 in air, thereby increasing the uptake of oxygen beyond that required for a given Ti4+ concentration. The reversibility of the redox reactions is limited by sluggish kinetics; however, the oxidation process continues, if slowly, even at room temperature. The extra oxygen atoms are accommodated by the large interstices within a triangular lattice formed by the [MnO5] trigonal bipyramids. According to bond distances from Rietveld refinements using the neutron diffraction data, the YMnO3 structure features under-bonded Mn and even more severely under-bonded oxygen atoms that form the trigonal bases of the [MnO5] bipyramids. The tensile bond strain around the 5-fold coordinated Mn site and the strong preference of Ti4+(and Mn4+) for higher coordination numbers likely provide driving forces for the oxidation reaction. Reverse Monte Carlo refinements of the local atomic displacements using neutron total scattering revealed how the excess oxygen atoms are accommodated in the structure by correlated local displacements of the host atoms. Large displacements of the under-bonded host oxygen atoms play a key part in this lattice-relaxation process, facilitating reversible exchange of significant amounts of oxygen with atmosphere.« less

Structural Refinement of Proteins by Restrained Molecular Dynamics Simulations with Non-interacting Molecular Fragments.

PubMed

Shen, Rong; Han, Wei; Fiorin, Giacomo; Islam, Shahidul M; Schulten, Klaus; Roux, Benoît

2015-10-01

The knowledge of multiple conformational states is a prerequisite to understand the function of membrane transport proteins. Unfortunately, the determination of detailed atomic structures for all these functionally important conformational states with conventional high-resolution approaches is often difficult and unsuccessful. In some cases, biophysical and biochemical approaches can provide important complementary structural information that can be exploited with the help of advanced computational methods to derive structural models of specific conformational states. In particular, functional and spectroscopic measurements in combination with site-directed mutations constitute one important source of information to obtain these mixed-resolution structural models. A very common problem with this strategy, however, is the difficulty to simultaneously integrate all the information from multiple independent experiments involving different mutations or chemical labels to derive a unique structural model consistent with the data. To resolve this issue, a novel restrained molecular dynamics structural refinement method is developed to simultaneously incorporate multiple experimentally determined constraints (e.g., engineered metal bridges or spin-labels), each treated as an individual molecular fragment with all atomic details. The internal structure of each of the molecular fragments is treated realistically, while there is no interaction between different molecular fragments to avoid unphysical steric clashes. The information from all the molecular fragments is exploited simultaneously to constrain the backbone to refine a three-dimensional model of the conformational state of the protein. The method is illustrated by refining the structure of the voltage-sensing domain (VSD) of the Kv1.2 potassium channel in the resting state and by exploring the distance histograms between spin-labels attached to T4 lysozyme. The resulting VSD structures are in good agreement with the consensus model of the resting state VSD and the spin-spin distance histograms from ESR/DEER experiments on T4 lysozyme are accurately reproduced.

Crystal structure and crystal chemistry of melanovanadite, a natural vanadium bronze.

USGS Publications Warehouse

Konnert, J.A.; Evans, H.T.

1987-01-01

The crystal structure of melanovanadite from Minas Ragra, Peru, has been determined in space group P1. The triclinic unit cell (non-standard) has a 6.360(2), b 18.090(9), c 6.276(2) A, alpha 110.18(4)o, beta 101.62(3)o, gamma 82.86(4)o. A subcell with b' = b/2 was found by crystal-structure analysis to contain CaV4O10.5H2O. The subcell has a layer structure in which the vanadate sheet consists of corner-shared tetrahedral VO4 and double square-pyramidal V2O8 groups, similar to that previously found in synthetic CsV2O5. Refinement of the full structure (R = 0.056) showed that the Ca atom, which half-occupies a general position in the subcell, is 90% ordered at one of these sites in the whole unit cell. Bond length-bond strength estimates indicate that the tetrahedra contain V5+, and the square pyramids, V4+.-J.A.Z.

Electron-density descriptors as predictors in quantitative structure--activity/property relationships and drug design.

PubMed

Matta, Chérif F; Arabi, Alya A

2011-06-01

The use of electron density-based molecular descriptors in drug research, particularly in quantitative structure--activity relationships/quantitative structure--property relationships studies, is reviewed. The exposition starts by a discussion of molecular similarity and transferability in terms of the underlying electron density, which leads to a qualitative introduction to the quantum theory of atoms in molecules (QTAIM). The starting point of QTAIM is the topological analysis of the molecular electron-density distributions to extract atomic and bond properties that characterize every atom and bond in the molecule. These atomic and bond properties have considerable potential as bases for the construction of robust quantitative structure--activity/property relationships models as shown by selected examples in this review. QTAIM is applicable to the electron density calculated from quantum-chemical calculations and/or that obtained from ultra-high resolution x-ray diffraction experiments followed by nonspherical refinement. Atomic and bond properties are introduced followed by examples of application of each of these two families of descriptors. The review ends with a study whereby the molecular electrostatic potential, uniquely determined by the density, is used in conjunction with atomic properties to elucidate the reasons for the biological similarity of bioisosteres.

Crystal structure of the tri-ethyl-ammonium salt of 3-[(4-hy-droxy-3-meth-oxy-phen-yl)(4-hy-droxy-2-oxo-2H-chromen-3-yl)meth-yl]-2-oxo-2H-chromen-4-olate.

PubMed

Ikram, Muhammad; Rehman, Sadia; Khan, Afzal; Schulzke, Carola

2018-03-01

The reaction between 3,3'-[(3-meth-oxy-4-hy-droxy-phen-yl)methanedi-yl]bis-(4-hy-droxy-2 H -chromen-2-one) and tri-ethyl-amine in methanol yielded the title compound tri-ethyl-ammonium 3-[(4-hy-droxy-3-meth-oxy-phen-yl)(4-hy-droxy-2-oxo-2 H -chromen-3-yl)meth-yl]-2-oxo-2 H -chromen-4-olate, C 6 H 16 N + ·C 26 H 17 O 8 - or (NHEt 3 ) + (C 26 H 17 O 8 ) - , which crystallized directly from its methano-lic mother liquor. The non-deprotonated coumarol substituent shares its H atom with the deprotonated coumarolate substituent in a short negative charge-assisted hydrogen bond in which the freely refined H atom is moved from its parent O atom towards the acceptor O atom, elongating the covalent O-H bond to 1.18 (3) Å. The respective H atom can therefore be described as being shared by two alcohol O atoms, culminating in the formation of an eight-membered ring.

A theoretical-electron-density databank using a model of real and virtual spherical atoms.

PubMed

Nassour, Ayoub; Domagala, Slawomir; Guillot, Benoit; Leduc, Theo; Lecomte, Claude; Jelsch, Christian

2017-08-01

A database describing the electron density of common chemical groups using combinations of real and virtual spherical atoms is proposed, as an alternative to the multipolar atom modelling of the molecular charge density. Theoretical structure factors were computed from periodic density functional theory calculations on 38 crystal structures of small molecules and the charge density was subsequently refined using a density model based on real spherical atoms and additional dummy charges on the covalent bonds and on electron lone-pair sites. The electron-density parameters of real and dummy atoms present in a similar chemical environment were averaged on all the molecules studied to build a database of transferable spherical atoms. Compared with the now-popular databases of transferable multipolar parameters, the spherical charge modelling needs fewer parameters to describe the molecular electron density and can be more easily incorporated in molecular modelling software for the computation of electrostatic properties. The construction method of the database is described. In order to analyse to what extent this modelling method can be used to derive meaningful molecular properties, it has been applied to the urea molecule and to biotin/streptavidin, a protein/ligand complex.

Influence of attrition milling on nano-grain boundaries

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

Rawers, J.; Cook, D.

1999-03-01

Nanostructured materials have a relatively large proportion of their atoms associated with the grain boundary, and the method used to develop the nano-grains has a strong influence on the resulting grain boundary structure. In this study, attrition milling iron powders and blends of iron powders produced micron-size particles composed of nano-size grains. Mechanical cold-working powder resulted in dislocation generation, multiplication, and congealing that produced grain refinement. As the grain size approached nano-dimensions, dislocations were no longer sustained within the grain and once generated, rapidly diffused to the grain boundary. Dislocations on the grain boundary strained the local lattice structure which,more » as the grain size decreased, became the entire grain. Mechanical alloying of substitutional aluminium atoms into iron powder resulted in the aluminium atoms substituting for iron atoms in the grain boundary cells and providing a grain boundary structure similar to that of the iron powder processed in argon. Attrition milling iron powder in nitrogen gas resulted in nitrogen atoms being adsorbed onto the particle surface. Continued mechanical milling infused the nitrogen atoms into interstitial lattice sites on the grain boundary which also contributed to expanding and straining the local lattice.« less

A method to estimate statistical errors of properties derived from charge-density modelling

PubMed Central

Lecomte, Claude

2018-01-01

Estimating uncertainties of property values derived from a charge-density model is not straightforward. A methodology, based on calculation of sample standard deviations (SSD) of properties using randomly deviating charge-density models, is proposed with the MoPro software. The parameter shifts applied in the deviating models are generated in order to respect the variance–covariance matrix issued from the least-squares refinement. This ‘SSD methodology’ procedure can be applied to estimate uncertainties of any property related to a charge-density model obtained by least-squares fitting. This includes topological properties such as critical point coordinates, electron density, Laplacian and ellipticity at critical points and charges integrated over atomic basins. Errors on electrostatic potentials and interaction energies are also available now through this procedure. The method is exemplified with the charge density of compound (E)-5-phenylpent-1-enylboronic acid, refined at 0.45 Å resolution. The procedure is implemented in the freely available MoPro program dedicated to charge-density refinement and modelling. PMID:29724964

Automated MAD and MIR structure solution

PubMed Central

Terwilliger, Thomas C.; Berendzen, Joel

1999-01-01

Obtaining an electron-density map from X-ray diffraction data can be difficult and time-consuming even after the data have been collected, largely because MIR and MAD structure determinations currently require many subjective evaluations of the qualities of trial heavy-atom partial structures before a correct heavy-atom solution is obtained. A set of criteria for evaluating the quality of heavy-atom partial solutions in macromolecular crystallography have been developed. These have allowed the conversion of the crystal structure-solution process into an optimization problem and have allowed its automation. The SOLVE software has been used to solve MAD data sets with as many as 52 selenium sites in the asymmetric unit. The automated structure-solution process developed is a major step towards the fully automated structure-determination, model-building and refinement procedure which is needed for genomic scale structure determinations. PMID:10089316

Total Scattering Analysis of Disordered Nanosheet Materials

NASA Astrophysics Data System (ADS)

Metz, Peter C.

Two dimensional materials are of increasing interest as building blocks for functional coatings, catalysts, and electrochemical devices. While increasingly sophisticated processing routes have been designed to obtain high-quality exfoliated nanosheets and controlled, self-assembled mesostructures, structural characterization of these materials remains challenging. This work presents a novel method of analyzing pair distribution function (PDF) data for disordered nanosheet ensembles, where supercell stacking models are used to infer atom correlations over as much as 50 A. Hierarchical models are used to reduce the parameter space of the refined model and help eliminate strongly correlated parameters. Three data sets for restacked nanosheet assemblies with stacking disorder are analyzed using these methods: simulated data for graphene-like layers, experimental data for 1 nm thick perovskite layers, and experimental data for highly defective delta-MnO2 layers. In each case, the sensitivity of the PDF to the real-space distribution of layer positions is demonstrated by exploring the fit residual as a function of stacking vectors. The refined models demonstrate that nanosheets tend towards local interlayer ordering, which is hypothesized to be driven by the electrostatic potential of the layer surfaces. Correctly accounting for interlayer atom correlations permits more accurate refinement of local structural details including local structure perturbations and defect site occupancies. In the delta-MnO2 nanosheet material, the new modeling approach identified 14% Mn vacancies while application of 3D periodic crystalline models to the < 7 A PDF region suggests a 25% vacancy concentration. In contrast, the perovskite nanosheet material is demonstrated to exhibit almost negligible structural relaxation in contrast with the bulk crystalline material from which it is derived.

Adaptive Multi-Sensor Interrogation of Targets Embedded in Complex Environments

DTIC Science & Technology

2010-06-09

to efficient refinement of data from distributed networked sensor systems for interpretation by both machines and humans in a low latency and...of a DP draw: Tk^HIltiU-^). Vk*& Beta{l,a), d’k ~ d" H. (19) where 5g - is a point measure concentrated at 9*k (each 9*k is termed an atom

The Collaborative Seismic Earth Model: Generation 1

NASA Astrophysics Data System (ADS)

Fichtner, Andreas; van Herwaarden, Dirk-Philip; Afanasiev, Michael; SimutÄ--, SaulÄ--; Krischer, Lion; ćubuk-Sabuncu, Yeşim; Taymaz, Tuncay; Colli, Lorenzo; Saygin, Erdinc; Villaseñor, Antonio; Trampert, Jeannot; Cupillard, Paul; Bunge, Hans-Peter; Igel, Heiner

2018-05-01

We present a general concept for evolutionary, collaborative, multiscale inversion of geophysical data, specifically applied to the construction of a first-generation Collaborative Seismic Earth Model. This is intended to address the limited resources of individual researchers and the often limited use of previously accumulated knowledge. Model evolution rests on a Bayesian updating scheme, simplified into a deterministic method that honors today's computational restrictions. The scheme is able to harness distributed human and computing power. It furthermore handles conflicting updates, as well as variable parameterizations of different model refinements or different inversion techniques. The first-generation Collaborative Seismic Earth Model comprises 12 refinements from full seismic waveform inversion, ranging from regional crustal- to continental-scale models. A global full-waveform inversion ensures that regional refinements translate into whole-Earth structure.

Nonempirical calculations of the structure and stability of ALi/sub 2k/ lithium clusters of group-two elements

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

Klimenko, N.M.; Musaev, D.G.; Gorbik, A.A.

Nonempirical Hartree-Fock calculations of the geometric and relative energetic characteristics of linear ALi/sub 2/ molecules and square ALi/sub 4/ molecules, where A = Be, Mg, Ca, and Zn, have been performed. The results for BeLi/sup +/, BeLi/sup 2/, BeLi/sub 4/, and MgLi/sub 2/ have been refined with consideration of the electron correlation in the framework of the theory of self-consistent electron pairs (SCEP). It has been shown that the stability of ALi/sub 2k/ increases with increasing size of the cluster and that the energy of the singlet-triplet transitions does not exceed 0.5-1.5 eV in all cases. The interactions between themore » atoms in the clusters have a cooperative character: the overlapping Q(Li-Li) between the Li atoms is no less significant than the overlapping Q(A-Li) between the Li atoms and the central atom A.« less

K(3)TaF(8) from laboratory X-ray powder data.

PubMed

Smrcok, Lubomír; Cerný, Radovan; Boca, Miroslav; Macková, Iveta; Kubíková, Blanka

2010-02-01

The crystal structure of tripotassium octafluoridotantalate, K(3)TaF(8), determined from laboratory powder diffraction data by the simulated annealing method and refined by total energy minimization in the solid state, is built from discrete potassium cations, fluoride anions and monocapped trigonal-prismatic [TaF(7)](2-) ions. All six atoms in the asymmetric unit are in special positions of the P6(3)mc space group: the Ta and one F atom in the 2b (3m) sites, the K and two F atoms in the 6c (m) sites, and one F atom in the 2a (3m) site. The structure consists of face-sharing K(6) octahedra with a fluoride anion at the center of each octahedron, forming chains of composition [FK(3)](2+) running along [001] with isolated [TaF(7)](2-) trigonal prisms in between. The structure of the title compound is different from the reported structure of Na(3)TaF(8) and represents a new structure type.

Effects of Sm addition on electromagnetic interference shielding property of Mg-Zn-Zr alloys

NASA Astrophysics Data System (ADS)

Yang, Chubin; Pan, Fusheng; Chen, Xianhua; Luo, Ning

2017-06-01

The electromagnetic interference (EMI) shielding of Sm-containing magnesium alloys in the 30-1500 MHz testing frequency range was investigated by coaxial cable method. The results demonstrated that Mg-3Zn alloys displayed the best electromagnetic shielding property. When 0.5 wt% of Zr was added for crystal grain refinement, the shielding effectiveness (SE) was apparently reduced. The addition of the rare earth element Sm in ZK magnesium alloys can improve the electromagnetic interference shielding of magnesium alloys. The main reason for the differences in electromagnetic interference shielding of magnesium alloys was the change in conductivity. The addition of Zr in Mg-Zn alloys can refine the grains and consequently improve the grain boundary area significantly. Therefore, the number of irregularly arranged atoms at the grain boundaries increased, decreasing the conductivity of magnesium alloys and leading to a decrease in the electromagnetic interference shielding. Following the Sm addition, the Mg-Zn-Sm phase was precipitated at the grain boundaries and in cores. The precipitation of Sm-containing rare earth phases could consume the solid-soluted Zn atoms within the Mg, resulting in an increase in electrical conductivity and electromagnetic interference shielding improvement.

Gctf: Real-time CTF determination and correction

PubMed Central

Zhang, Kai

2016-01-01

Accurate estimation of the contrast transfer function (CTF) is critical for a near-atomic resolution cryo electron microscopy (cryoEM) reconstruction. Here, a GPU-accelerated computer program, Gctf, for accurate and robust, real-time CTF determination is presented. The main target of Gctf is to maximize the cross-correlation of a simulated CTF with the logarithmic amplitude spectra (LAS) of observed micrographs after background subtraction. Novel approaches in Gctf improve both speed and accuracy. In addition to GPU acceleration (e.g. 10–50×), a fast ‘1-dimensional search plus 2-dimensional refinement (1S2R)’ procedure further speeds up Gctf. Based on the global CTF determination, the local defocus for each particle and for single frames of movies is accurately refined, which improves CTF parameters of all particles for subsequent image processing. Novel diagnosis method using equiphase averaging (EPA) and self-consistency verification procedures have also been implemented in the program for practical use, especially for aims of near-atomic reconstruction. Gctf is an independent program and the outputs can be easily imported into other cryoEM software such as Relion (Scheres, 2012) and Frealign (Grigorieff, 2007). The results from several representative datasets are shown and discussed in this paper. PMID:26592709

Accelerator mass spectrometry of Strontium-90 for homeland security, environmental monitoring, and human health

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

Tumey, S J; Brown, T A; Hamilton, T F

2008-03-03

Strontium-90 is one of the most hazardous materials managed by agencies charged with protecting the public from radiation. Traditional radiometric methods have been limited by low sample throughput and slow turnaround times. Mass spectrometry offers the advantage of shorter analysis times and the ability to measure samples immediately after processing, however conventional mass spectrometric techniques are susceptible to molecular isobaric interferences that limit their overall sensitivity. In contrast, accelerator mass spectrometry is insensitive to molecular interferences and we have therefore begun developing a method for determination of {sup 90}Sr by accelerator mass spectrometry. Despite a pervasive interference from {sup 90}Zr,more » our initial development has yielded an instrumental background of {approx} 10{sup 8} atoms (75 mBq) per sample. Further refinement of our system (e.g., redesign of our detector, use of alternative target materials) is expected to push the background below 10{sup 6} atoms, close to the theoretical limit for AMS. Once we have refined our system and developed suitable sample preparation protocols, we will utilize our capability in applications to homeland security, environmental monitoring, and human health.« less

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.

Redetermination of (2,2'-bipyridine-κN,N')dichlorido-palladium(II) dichloro-methane solvate.

PubMed

Kim, Nam-Ho; Hwang, In-Chul; Ha, Kwang

2009-05-07

In the title compound, [PdCl(2)(C(10)H(8)N(2))]·CH(2)Cl(2), the Pd(2+) ion is four-coordinated in a slightly distorted square-planar environment by two N atoms of the 2,2'-bipyridine (bipy) ligand and two chloride ions. The compound displays intra-molecular C-H⋯Cl hydrogen bonds and pairs of complex mol-ecules are connected by inter-molecular C-H⋯Cl hydrogen bonds. Inter-molecular π-π inter-actions are present between the pyridine rings of the ligand, the shortest centroid-centroid distance being 4.096 (3) Å. As a result of the electronic nature of the chelate ring, it is possible to create π-π inter-actions to its symmetry-related counterpart [3.720 (2) Å] and also with a pyridine ring [3.570 (3) Å] of the bipy unit. The present structure is a redetermination of a previous structure [Vicente et al. (1997 ▶). Private communication (refcode PYCXMN02). CCDC, Cambridge, England]. In the new structure refinement all H atoms were located in a difference Fourier synthesis. Their coordinates were refined freely, together with isotropic displacement parameters.

Stability, surface features, and atom leaching of palladium nanoparticles: toward prediction of catalytic functionality.

PubMed

Ramezani-Dakhel, Hadi; Mirau, Peter A; Naik, Rajesh R; Knecht, Marc R; Heinz, Hendrik

2013-04-21

Surfactant-stabilized metal nanoparticles have shown promise as catalysts although specific surface features and their influence on catalytic performance have not been well understood. We quantify the thermodynamic stability, the facet composition of the surface, and distinct atom types that affect rates of atom leaching for a series of twenty near-spherical Pd nanoparticles of 1.8 to 3.1 nm size using computational models. Cohesive energies indicate higher stability of certain particles that feature an approximate 60/20/20 ratio of {111}, {100}, and {110} facets while less stable particles exhibit widely variable facet composition. Unique patterns of atom types on the surface cause apparent differences in binding energies and changes in reactivity. Estimates of the relative rate of atom leaching as a function of particle size were obtained by the summation of Boltzmann-weighted binding energies over all surface atoms. Computed leaching rates are in good qualitative correlation with the measured catalytic activity of peptide-stabilized Pd nanoparticles of the same shape and size in Stille coupling reactions. The agreement supports rate-controlling contributions by atom leaching in the presence of reactive substrates. The computational approach provides a pathway to estimate the catalytic activity of metal nanostructures of engineered shape and size, and possible further refinements are described.

Revision of the Li13Si4 structure

PubMed Central

Zeilinger, Michael; Fässler, Thomas F.

2013-01-01

Besides Li17Si4, Li16.42Si4, and Li15Si4, another lithium-rich representative in the Li–Si system is the phase Li13Si4 (trideca­lithium tetra­silicide), the structure of which has been determined previously [Frank et al. (1975 ▶). Z. Naturforsch. Teil B, 30, 10–13]. A careful analysis of X-ray diffraction patterns of Li13Si4 revealed discrepancies between experimentally observed and calculated Bragg positions. Therefore, we redetermined the structure of Li13Si4 on the basis of single-crystal X-ray diffraction data. Compared to the previous structure report, decisive differences are (i) the introduction of a split position for one Li site [occupancy ratio 0.838 (7):0.162 (7)], (ii) the anisotropic refinement of atomic displacement parameters for all atoms, and (iii) a high accuracy of atom positions and unit-cell parameters. The asymmetric unit of Li13Si4 contains two Si and seven Li atoms. Except for one Li atom situated on a site with symmetry 2/m, all other atoms are on mirror planes. The structure consists of isolated Si atoms as well as Si–Si dumbbells surrounded by Li atoms. Each Si atom is either 12- or 13-coordinated. The isolated Si atoms are situated in the ab plane at z = 0 and are strictly separated from the Si–Si dumbbells at z = 0.5. PMID:24454148

Simulation optimization of the cathode deposit growth in a coaxial electrolyzer-refiner

NASA Astrophysics Data System (ADS)

Smirnov, G. B.; Fokin, A. A.; Markina, S. E.; Vakhitov, A. I.

2015-08-01

The results of simulation of the cathode deposit growth in a coaxial electrolyzer-refiner are presented. The sizes of the initial cathode matrix are optimized. The data obtained by simulation and full-scale tests of the precipitation of platinum from a salt melt are compared.

A grid-enabled web service for low-resolution crystal structure refinement.

PubMed

O'Donovan, Daniel J; Stokes-Rees, Ian; Nam, Yunsun; Blacklow, Stephen C; Schröder, Gunnar F; Brunger, Axel T; Sliz, Piotr

2012-03-01

Deformable elastic network (DEN) restraints have proved to be a powerful tool for refining structures from low-resolution X-ray crystallographic data sets. Unfortunately, optimal refinement using DEN restraints requires extensive calculations and is often hindered by a lack of access to sufficient computational resources. The DEN web service presented here intends to provide structural biologists with access to resources for running computationally intensive DEN refinements in parallel on the Open Science Grid, the US cyberinfrastructure. Access to the grid is provided through a simple and intuitive web interface integrated into the SBGrid Science Portal. Using this portal, refinements combined with full parameter optimization that would take many thousands of hours on standard computational resources can now be completed in several hours. An example of the successful application of DEN restraints to the human Notch1 transcriptional complex using the grid resource, and summaries of all submitted refinements, are presented as justification.

The Crystal Structure of Ba 17Sm 10Cl 64

NASA Astrophysics Data System (ADS)

Liu, Guo; Eick, Harry A.

1999-08-01

The structure of Ba17Sm10Cl64, prepared by solvolytic extraction of a program-cooled 1:1 BaCl2:SmCl3 molar mixture sealed in a quartz tube and heated to 750°C, was determined from single-crystal X-ray diffraction data. The compound exhibits cubic symmetry, space group Pa3 (No. 205) with a=21.366(2) Å and Z=4. Refinement effected with I>2σ(I) yielded R1= 0.0926 and wR2=0.216. One Ba atom is 12-coordinated by Cl atoms in a distorted icosahedral arrangement; the three other Ba atoms are 10-coordinated in a distorted bicapped cubic arrangement. There are two Sm atom sites. The coordination around one Sm atom is best described as square antiprismatic, but one Sm-Cl distance is too long for effective bonding. The other Sm atom site, occupied statistically by {1}/{3}Ba and {2}/{3}Sm atoms, is 9-coordinated by Cl atoms in a monocapped square antiprismatic arrangement. The two types of Sm sites combine to form an M6Cl37 cuboctahedral cluster of the composition BaSm5Cl37. It is shown that the cβ phase identified previously in the Yb-F and related fluoride systems is probably isostructural with Ba17Sm10Cl64.

Crystal Chemistry and Magnetism of Ternary Actinoid Boron Carbides UB 1- xC 1+ x and U 1- xMxB 2C with M = Sc, Lu, and Th

NASA Astrophysics Data System (ADS)

Rogl, P.; Rupp, B.; Felner, I.; Fischer, P.

1993-06-01

Within the homogeneous range of uranium monocarbide UB 1- xC 1+ x, the crystal structures of stoichiometric UBC and of the carbon-rich solid solution UB 0.78C 1.22, have been refined from single-crystal X-ray counter data. From X-ray analysis crystal symmetry in both cases is consistent with the centro-symmetric space group Cmcm and there are no indications of superstructure formation. In contrast to the fully ordered atom arrangement revealed for stoichiometric UBC ( a = 0.35899(4), b = 1.19781(12), c = 0.33474(3) nm), random occupation by boron and carbon atoms is observed for the boron site in UB 0.78C 1.22 ( a = 0.35752(4), b = 1.18584(3), c = 0.33881(4) nm). For 279(278) reflections (|F 0| > 3σ) the obtained reliability factors R x = ∑|ΔF|/∑| F0| were R x = 0.069 for UBC and R x = 0.050 for UB 0.78C 1.22. Neutron powder diffraction experiments at 9 and 295 K unambiguously revealed full occupancy by the nonmetal atoms in UB 0.78C 1.22 and prove the statistical occupation of B and C atoms in the B-sites. For the orthorhombic symmetry Cmcm, refinement was not better than R1 = 0.044. A model calculation in monoclinic symmetry C12/ m1, however, resulted in a significant reduction of the residual value to R1 = 0.030, releasing spatial constraints on the boron atoms. Thus the boron-boron chain in Cmcm (B-B = 0.1874 nm) is dissolved into boron pairs (B-B = 0.1706 nm) which are loosely bound at a distance of 0.2043 nm. The formation of C-B-B-C groups corresponds to the structure types of ThBC and Th 3B 2C 3. The magnetic behavior has been investigated in the temperature range from 4.2 K to 1000 K for UB 1- xC 1+ x (UBC-type) and U 1- xMxB 2C (ThB 2C-type for the high temperature modification and 1-UB 2C-type for the low temperature modification) with U partially substituted by Th or Sc, Lu. From magnetic susceptibilities, the alloys UB 1- xC 1+ x reveal temperature independent paramagnetism with typical intermediate valence fluctuation behavior ( TSF ˜ 350 K). ThB 2C and 1-UB 2C both are temperature independent paramagnets, whereas h-UB 2C is a ferromagnet with the rather high Curie temperature TM = 80(2) K. TM and the saturation magnetiziation per U atom both successively decrease on substitution of U by Th, Sc, or Lu in UB 2C, whereas the U-moments remain practically unchanged at μ eff(U) ˜ 1.9 μ B. Uranium L 3-XANES (X-ray Absorption Near Edge Structure) spectroscopy revealed increased d-band localization, comparable to uranium-transition metal alloys, in nonmagnetic UB 1- xC 1+ x ( x = 0, 0.22). No superconductivity was observed down to 1.5 K; no hydrogen uptake was observed for UB 2C and ThB 2C even under hydrogen pressures as high as 7 × 10 7 Pa at 670 K.

Yes, one can obtain better quality structures from routine X-ray data collection.

PubMed

Sanjuan-Szklarz, W Fabiola; Hoser, Anna A; Gutmann, Matthias; Madsen, Anders Østergaard; Woźniak, Krzysztof

2016-01-01

Single-crystal X-ray diffraction structural results for benzidine dihydrochloride, hydrated and protonated N,N,N,N-peri(dimethylamino)naphthalene chloride, triptycene, dichlorodimethyltriptycene and decamethylferrocene have been analysed. A critical discussion of the dependence of structural and thermal parameters on resolution for these compounds is presented. Results of refinements against X-ray data, cut off to different resolutions from the high-resolution data files, are compared to structural models derived from neutron diffraction experiments. The Independent Atom Model (IAM) and the Transferable Aspherical Atom Model (TAAM) are tested. The average differences between the X-ray and neutron structural parameters (with the exception of valence angles defined by H atoms) decrease with the increasing 2θmax angle. The scale of differences between X-ray and neutron geometrical parameters can be significantly reduced when data are collected to the higher, than commonly used, 2θmax diffraction angles (for Mo Kα 2θmax > 65°). The final structural and thermal parameters obtained for the studied compounds using TAAM refinement are in better agreement with the neutron values than the IAM results for all resolutions and all compounds. By using TAAM, it is still possible to obtain accurate results even from low-resolution X-ray data. This is particularly important as TAAM is easy to apply and can routinely be used to improve the quality of structural investigations [Dominiak (2015 ▸). LSDB from UBDB. University of Buffalo, USA]. We can recommend that, in order to obtain more adequate (more accurate and precise) structural and displacement parameters during the IAM model refinement, data should be collected up to the larger diffraction angles, at least, for Mo Kα radiation to 2θmax = 65° (sin θmax/λ < 0.75 Å(-1)). The TAAM approach is a very good option to obtain more adequate results even using data collected to the lower 2θmax angles. Also the results of translation-libration-screw (TLS) analysis and vibrational entropy values are more reliable for 2θmax > 65°.

Redetermination of 2-methyl-4-nitro­pyridine N-oxide

PubMed Central

Peukert, Max; Seichter, Wilhelm; Weber, Edwin

2014-01-01

An improved crystal structure of the title compound, C6H6N2O3, is reported. The structure, previously solved [Li et al. (1987 ▶). Jiegou Huaxue (Chin. J. Struct. Chem.), 6, 20–24] in the ortho­rhom­bic space group Pca21 and refined to R = 0.067, has been solved in the ortho­rhom­bic space group Pbcm with data of enhanced quality, giving an improved structure (R = 0.0485). The mol­ecule adopts a planar conformation with all atoms lying on a mirror plane. The crystal structure is composed of mol­ecular sheets extending parallel to the ab plane and connected via C—H⋯O contacts involving ring H atoms and O atoms of the N-oxide and nitro groups, while van der Waals forces consolidate the stacking of the layers. PMID:24826136

Measurements of Excitation Functions and Line Polarizations for Electron Impact Excitation of the n = 2, 3 States of Atomic Hydrogen in the Energy Range 11 - 2000 eV

NASA Technical Reports Server (NTRS)

James, G. K.; Ajello, J. M.; Kanik, I.; Slevin, J.; Franklin, B.; Shemansky, D.

1993-01-01

The electron-atomic hydrogen scattering system is an important testing ground for theoretical models and has received a great deal of attention from experimentalists and theoreticians alike over the years. A complete description of the excitation process requires a knowledge of many different parameters, and experimental measurements of these parameters have been performed in various laboratories around the world. As far as total cross section data are concerned it has been noted that the discrepancy between the data of Long et al. and Williams for n = 2 excitations needs to be resolved in the interests of any further refinement of theory. We report new measurements of total cross sections and atomic line polarizations for both n=2 and n=3 excitations at energies from threshold to 2000 eV...

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.

Use of B4C powder for preparing in situ Al-Ti-B-C inoculant in Al-Ti melt and its refining effect on A356 alloy

NASA Astrophysics Data System (ADS)

Liu, Shuiqing; Cui, Chunxiang; Wang, Xin; Zhao, Lichen; Sun, Yijiao; Shi, Jiejie; Cui, Sen; Ding, Jinhua

2018-01-01

A novel preparation technology of Al-Ti-B-C inoculant with uniform microstructure is prepared using B4C powder instead of graphite in Al-Ti melt reaction method in this study. It is found that the addition of B4C powder improves the wettability between carbon element and liquid aluminum and reduce the tendency to the gravity segregation simultaneously. The result shows that Al-Ti-B-C inoculant using B4C powder presents excellent grain refinement performance than the conventional approach. After T6 heat treatment, the ultimate tensile strength, the yield strength and elongation of A356 alloy are increased to 292 ± 6 MPa, 238 ± 7 MPa and 8.2% ± 0.5% from 260 ± 7 MPa, 218 ± 5 MPa and 4.9% ± 0.6% by addition of Al-Ti-B-C inoculant with a very small ratio of 0.3% in weight. The increase of strength in Al-Ti-B-C refined alloy is attributed to the grain refinement of primary α-Al, while the increase of ductility results from the submicron particles in Al-Ti-B-C inoculant adsorb impurity atoms as well as decreased grain size.

Study of corrosion behavior on the addition of sodium citrate in nickel electroplating on SPCC steel using EIS

NASA Astrophysics Data System (ADS)

Riastuti, R.; Ramadini, C.; Siallagan, S. T.; Rifki, A.; Herdino, F.

2018-04-01

The addition of sodium citrate to nickel electroplating process as additive is useful for refining the grain size of nickel deposit. The refining of grain size in nickel deposit as coating layer can improve surface performance, one of which corrosion resistance. This paper aims to investigate the effect of sodium citrate addition as grain refiner to promote corrosion resistance on SPCC steel. This experiment used Watt’s Bath solution of NiSO4 300 g/L, NiCl4 45 g/L, H3BO3 60 g/L, wetting agent 0.2 cc/L. Sodium citrate was added in composition of 45g/L and 60g/L. Nickel were deposited by direct current using current density on 6 A/dm2 at the acidity level of 5 for 30 minutes by keeping the operating temperature stable at 50°C. The grain size of nickel deposit was observed through Optical Microscope and Atomic Force Microscope (AFM). The corrosion behavior of SPCC was observed by linear polarization and Electrochemical Impedance Spectroscopy (EIS) methods using 3% NaCl solution. Based on the research, the addition of sodium citrate as grain refiner will increasing corrosion resistance on SPCC steel from 0.35 to 0.05 mm/year.

The combination of activated natural zeolite-bentonite to reduce Fe and Cu in refined bleached palm oil (RBPO) by using atomic absorption spectrophotometer method

NASA Astrophysics Data System (ADS)

Zakwan; Raja, PM; Giyanto

2018-02-01

Indonesia is one of the crude palm oil (CPO) production country in the world. As many products are derivated from the CPO, the quality must be increased continuously. One of the things that influence the quality of palm oil is the Fe and Cu content. The objective of this research was to reduce Fe and Cu content in Refined Bleached Palm Oil (RBPO). In processing CPO or Refined Bleachead Palm Oil (RBPO) may be contaminated by Fe and Cu from metal tank and pipe in the factory. The zeolite and bentonite was activated by maceration method using hydrochloric acid (0,1 N). Four batch reactions consisting of refined palm oil (RPO), activated natural zeolite-bentonite (ANZB) was bleached by heating and stirring them at about 105°C and 1200 rpm for 30 minutes. The results showed that all combinations of ANZB can reduce the Fe content. Thereafter, the optimal combination of ANZB was obtained in K1, K2 and K4 with Cu content 0.02 ppm. In the future, it is needed to study on the reduction of the Fe and Cu content in palm oil with the other adsorbent.

Likelihood of atom-atom contacts in crystal structures of halogenated organic compounds.

PubMed

Jelsch, Christian; Soudani, Sarra; Ben Nasr, Cherif

2015-05-01

The likelihood of occurrence of intermolecular contacts in crystals of halogenated organic compounds has been analysed statistically using tools based on the Hirshfeld surface. Several families of small halogenated molecules (containing organic F, Cl, Br or I atoms) were analysed, based on chemical composition and aromatic or aliphatic character. The behaviour of crystal contacts was also probed for molecules containing O or N. So-called halogen bonding (a halogen making short interactions with O or N, or a π interaction with C) is generally disfavoured, except when H is scarce on the molecular surface. Similarly, halogen⋯halogen contacts are more rare than expected, except for molecules that are poor in H. In general, the H atom is found to be the preferred partner of organic halogen atoms in crystal structures. On the other hand, C⋯C interactions in parallel π-stacking have a high propensity to occur in halogenated aromatic molecules. The behaviour of the four different halogen species (F, Cl, Br, I) is compared in several chemical composition contexts. The analysis tool can be refined by distinguishing several types for a given chemical species, such as H atoms bound to O or C. Such distinction shows, for instance, that C-H⋯Cl and O-H⋯O are the preferred interactions in compounds containing both O and Cl.

[Can the local energy minimization refine the PDB structures of different resolution universally?].

PubMed

Godzi, M G; Gromova, A P; Oferkin, I V; Mironov, P V

2009-01-01

The local energy minimization was statistically validated as the refinement strategy for PDB structure pairs of different resolution. Thirteen pairs of structures with the only difference in resolution were extracted from PDB, and the structures of 11 identical proteins obtained by different X-ray diffraction techniques were represented. The distribution of RMSD value was calculated for these pairs before and after the local energy minimization of each structure. The MMFF94 field was used for energy calculations, and the quasi-Newton method was used for local energy minimization. By comparison of these two RMSD distributions, the local energy minimization was proved to statistically increase the structural differences in pairs so that it cannot be used for refinement purposes. To explore the prospects of complex refinement strategies based on energy minimization, randomized structures were obtained by moving the initial PDB structures as far as the minimized structures had been moved in a multidimensional space of atomic coordinates. For these randomized structures, the RMSD distribution was calculated and compared with that for minimized structures. The significant differences in their mean values proved the energy surface of the protein to have only few minima near the conformations of different resolution obtained by X-ray diffraction for PDB. Some other results obtained by exploring the energy surface near these conformations are also presented. These results are expected to be very useful for the development of new protein refinement strategies based on energy minimization.

Gradient Echo Quantum Memory in Warm Atomic Vapor

PubMed Central

Pinel, Olivier; Hosseini, Mahdi; Sparkes, Ben M.; Everett, Jesse L.; Higginbottom, Daniel; Campbell, Geoff T.; Lam, Ping Koy; Buchler, Ben C.

2013-01-01

Gradient echo memory (GEM) is a protocol for storing optical quantum states of light in atomic ensembles. The primary motivation for such a technology is that quantum key distribution (QKD), which uses Heisenberg uncertainty to guarantee security of cryptographic keys, is limited in transmission distance. The development of a quantum repeater is a possible path to extend QKD range, but a repeater will need a quantum memory. In our experiments we use a gas of rubidium 87 vapor that is contained in a warm gas cell. This makes the scheme particularly simple. It is also a highly versatile scheme that enables in-memory refinement of the stored state, such as frequency shifting and bandwidth manipulation. The basis of the GEM protocol is to absorb the light into an ensemble of atoms that has been prepared in a magnetic field gradient. The reversal of this gradient leads to rephasing of the atomic polarization and thus recall of the stored optical state. We will outline how we prepare the atoms and this gradient and also describe some of the pitfalls that need to be avoided, in particular four-wave mixing, which can give rise to optical gain. PMID:24300586

Gradient echo quantum memory in warm atomic vapor.

PubMed

Pinel, Olivier; Hosseini, Mahdi; Sparkes, Ben M; Everett, Jesse L; Higginbottom, Daniel; Campbell, Geoff T; Lam, Ping Koy; Buchler, Ben C

2013-11-11

Gradient echo memory (GEM) is a protocol for storing optical quantum states of light in atomic ensembles. The primary motivation for such a technology is that quantum key distribution (QKD), which uses Heisenberg uncertainty to guarantee security of cryptographic keys, is limited in transmission distance. The development of a quantum repeater is a possible path to extend QKD range, but a repeater will need a quantum memory. In our experiments we use a gas of rubidium 87 vapor that is contained in a warm gas cell. This makes the scheme particularly simple. It is also a highly versatile scheme that enables in-memory refinement of the stored state, such as frequency shifting and bandwidth manipulation. The basis of the GEM protocol is to absorb the light into an ensemble of atoms that has been prepared in a magnetic field gradient. The reversal of this gradient leads to rephasing of the atomic polarization and thus recall of the stored optical state. We will outline how we prepare the atoms and this gradient and also describe some of the pitfalls that need to be avoided, in particular four-wave mixing, which can give rise to optical gain.

Large structural modulations in the relaxor ferroelectric and intermediate state of strontium rich members (x>0.6) of the Sr{sub x}Ba{sub 1−x}Nb{sub 2}O{sub 6} (sbn) solid solution series

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

Graetsch, H.A., E-mail: heribert.graetsch@rub.de

The amplitudes of the positional, occupational and adp modulations of sbn mixed crystals are strongly enhanced for high strontium contents. The increase of structural modulations is accompanied by reduced spontaneous electric polarization largely due to smaller off-center shifts of the niobium atoms. Beyond the room temperature ferroelectric – intermediate transition near x=0.77, anomal large U{sub 33} atomic displacement parameters of the niobium atoms indicate static disorder caused by loss of orientational coupling between residual shifts of Nb atoms in neighboring NbO{sub 6} octahedra. Change of satellite intensities show a reduction from two-dimensional to one-dimensional modulation which is not consistent withmore » tetragonal symmetry. The pseudo-tetragonally twinned crystal structure of sbn82 was refined in the orthorhombic super-space group A2mm(½0γ)000. The apparent tetragonal symmetry of the other investigated sbn samples also seems to be due to pseudo tetragonal twinning with equal twin volumes. The modulations mainly consist of cooperatively tilted NbO{sub 6} octahedra and wave-like ordered incomplete occupation of the largest cation sites (Me2a and b) by Ba{sup 2+} and Sr{sup 2+}. Furthermore, the atomic displacement parameters of the Me2 sites are strongly modulated. - Graphical abstract: Satellite reflections and modulation coefficients in the solid solution series Sr{sub x}Ba{sub 1−x}Nb{sub 2}O{sub 6}. - Highlights: • The modulationed structures are refined for the whole composition range of sbn32–sbn82 in tetragonal and orthorhombic setting. • The amplitudes of positional, occupational and adp modulations increase strongly with the strontium content. • Evidence is presented that the sbn crystals are pseudo tetragonally twinned. • The ferroelectric–intermediate paraelectric transition is not accompanied by a change of symmetry. • Anomal adp of intermediate (non-ferroelectric) sbn82 indicate loss of coupling between off-center shifts of neighboring niobium.« less

Average structure and M2 site configurations in C2/c clinopyroxenes along the Di-En join

NASA Astrophysics Data System (ADS)

Tribaudino, M.; Benna, P.; Bruno, E.

1989-12-01

In order to clarify the structural configurations observed in Diss in the Ca-rich region of the Di-En join (in which TEM observations show neither exsolution microstructures nor evidence of spinodal decomposition) single crystals large enough for X-ray diffraction analyses, with composition (Ca0.66Mg0.34)MgSi2O6, have been equilibrated close to the solvus at T=1350° C for 317 h, and quenched at room temperature. The refinement in C2/c space group shows that in the M2 site Ca and Mg are fully ‘ordered’ in two split positions (M2occ: 0.66 Ca; M2'occ: 0.34 Mg). Since the average structure shows a relevant elongation of anisotropic thermal ellipsoids of the O2 and O3 oxygen atoms, the refinement has been carried out according to a split model for O2 and O3 atoms: Ca appears 8-coordinated (as in diopside) and Mg shows a sixfold coordination similar to that of high-pigeonite. This coordination for Mg is significantly different from the fourfold coordination (Zn-like in Zn-cpx) proposed previously and it is a more probable coordination for Mg from a crystalchemical point of view. The same results were obtained refining a Di80En20 cpx, equilibrated at T=1230° C, according to the same O-split model. The data support the coexistence of a Di-like configuration for Ca and of a highPig-like configuration for Mg away from the solvus also. At T very near to T solidus the different configurations, observed at room temperature in the quenched samples, should converge and Ca and Mg should retain a single disordered configuration in the M2 site.

Structure determination in 55-atom Li-Na and Na-K nanoalloys.

PubMed

Aguado, Andrés; López, José M

2010-09-07

The structure of 55-atom Li-Na and Na-K nanoalloys is determined through combined empirical potential (EP) and density functional theory (DFT) calculations. The potential energy surface generated by the EP model is extensively sampled by using the basin hopping technique, and a wide diversity of structural motifs is reoptimized at the DFT level. A composition comparison technique is applied at the DFT level in order to make a final refinement of the global minimum structures. For dilute concentrations of one of the alkali atoms, the structure of the pure metal cluster, namely, a perfect Mackay icosahedron, remains stable, with the minority component atoms entering the host cluster as substitutional impurities. At intermediate concentrations, the nanoalloys adopt instead a core-shell polyicosahedral (p-Ih) packing, where the element with smaller atomic size and larger cohesive energy segregates to the cluster core. The p-Ih structures show a marked prolate deformation, in agreement with the predictions of jelliumlike models. The electronic preference for a prolate cluster shape, which is frustrated in the 55-atom pure clusters due to the icosahedral geometrical shell closing, is therefore realized only in the 55-atom nanoalloys. An analysis of the electronic densities of states suggests that photoelectron spectroscopy would be a sufficiently sensitive technique to assess the structures of nanoalloys with fixed size and varying compositions.

Three-dimensional structure of photosystem II from Thermosynechococcus elongates in complex with terbutryn

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

Gabdulkhakov, A. G., E-mail: azat@vega.protes.ru; Dontsova, M. V.; Saenger, W.

Photosystem II is a key component of the photosynthetic pathway producing oxygen at the thylakoid membrane of cyanobacteria, green algae, and plants. The three-dimensional structure of photosystem II from the cyanobacterium Thermosynechococcus elongates in a complex with herbicide terbutryn (a photosynthesis inhibitor) was determined for the first time by X-ray diffraction and refined at 3.2 Angstrom-Sign resolution (R{sub factor} = 26.9%, R{sub free} = 29.9%, rmsd for bond lengths is 0.013 Angstrom-Sign , and rmsd for bond angles is 2.2 Degree-Sign ). The terbutryn molecule was located in the binding pocket of the mobile plastoquinone. The atomic coordinates of themore » refined structure of photosystem II in a complex with terbutryn were deposited in the Protein Data Bank.« less

Model State Plan Characteristics. A Guide for Refining State Plans for Career Education.

ERIC Educational Resources Information Center

Mitchell, Anita

This guide for refining state plans for career education was developed to assist states in revision of their state plans to satisfy requirements of Public Law 95-207. The guide is divided into fourteen chapters. Chapter 1, the introduction, contains background information on the assessment conducted to develop the guidelines. (A full report of…

Refined Simulation of Satellite Laser Altimeter Full Echo Waveform

NASA Astrophysics Data System (ADS)

Men, H.; Xing, Y.; Li, G.; Gao, X.; Zhao, Y.; Gao, X.

2018-04-01

The return waveform of satellite laser altimeter plays vital role in the satellite parameters designation, data processing and application. In this paper, a method of refined full waveform simulation is proposed based on the reflectivity of the ground target, the true emission waveform and the Laser Profile Array (LPA). The ICESat/GLAS data is used as the validation data. Finally, we evaluated the simulation accuracy with the correlation coefficient. It was found that the accuracy of echo simulation could be significantly improved by considering the reflectivity of the ground target and the emission waveform. However, the laser intensity distribution recorded by the LPA has little effect on the echo simulation accuracy when compared with the distribution of the simulated laser energy. At last, we proposed a refinement idea by analyzing the experimental results, in the hope of providing references for the waveform data simulation and processing of GF-7 satellite in the future.

Hydrogen atom distribution and hydrogen induced site depopulation for the La{sub 2-x}Mg{sub x}Ni{sub 7}-H system

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

Guzik, Matylda N., E-mail: Matylda.Guzik@ife.no; Physics Department, Institute for Energy Technology, P.O. Box 40, NO-2027 Kjeller; Hauback, Bjorn C.

2012-02-15

La{sub 2-x}Mg{sub x}Ni{sub 7} and its hydrides/deuterides were investigated by high resolution synchrotron powder X-ray and neutron diffraction. Upon deuteration the single phase sample of the intermetallic compound with the refined composition La{sub 1.63}Mg{sub 0.37}Ni{sub 7} (space group: P6{sub 3}/mmc) expands isotropically, in contrast to the Mg free phase. The hydrogen uptake, {approx}9 D/f.u., is higher than in La{sub 2}Ni{sub 7}D{sub 6.5}. The refined composition accounts for La{sub 1.63}Mg{sub 0.37}Ni{sub 7}D{sub 8.8} (beta-phase). Rietveld refinements using the neutron and synchrotron diffraction data suggest that deuterium atoms occupy 5 different interstitial sites within both AB{sub 2} and AB{sub 5} slabs, eithermore » in an ordered or a disordered way. All determined D sites have an occupancy >50% and the shortest D-D contact is 1.96(3) A. It is supposed that a competition between the tendency to form directional bonds and repulsive D-D (H-H) interactions is the most important factor that influences the distribution of deuterium atoms in this structure. A hitherto unknown second, alpha-phase with composition La{sub 1.63}Mg{sub 0.37}Ni{sub 7}D{sub 0.56}, crystallizing with the same hexagonal symmetry as La{sub 1.63}Mg{sub 0.37}Ni{sub 7}D{sub 8.8}, has been discovered. The unit cell parameters for this D-poor phase differ slightly from those of the intermetallic. Alpha-phase displays only one D site (4f, space group: P6{sub 3}/mmc) occupied >50%, which is not populated in the D-rich beta-phase. This hydrogen/deuterium induced site depopulation can be explained by repulsive D-D (H-H) interactions that are likely to influence non-occupancy of certain interstices in metal lattice when absorbing hydrogen. - Graphical abstract: The detailed D atoms arrangement in La{sub 1.63}Mg{sub 0.37}Ni{sub 7}D{sub 8.8} differs significantly from the previously reported La{sub 1.5}Mg{sub 0.5}Ni{sub 7}D{sub 8.9(9.1)}. The present model consists of only five deuterium sites as opposed to nine proposed for La{sub 1.5}Mg{sub 0.5}Ni{sub 7}D{sub 8.9(9.1)}. The reported four remaining deuterium atom positions in La{sub 1.5}Mg{sub 0.5}Ni{sub 7}D{sub 8.9(9.1)} were not found in the investigated La{sub 1.63}Mg{sub 0.37}Ni{sub 7}D{sub 8.8}. The five Ni atoms have deuterium among their nearest neighbors, which surround them in a way similar to configurations observed in some complex transition metal hydrides and already reported for metallic hydrides. In the presented deuterium-rich phase, deformed tetrahedron, rigid trigonal pyramids as well as disordered and deformed saddle-like configuration are observed. Highlights: Black-Right-Pointing-Pointer Alpha- and beta-phase for La{sub 2-x}Mg{sub x}Ni{sub 7}-H system have been characterized. Black-Right-Pointing-Pointer Five different interstitial sites are occupied by deuterium/hydrogen atoms in the beta-phase. Black-Right-Pointing-Pointer One D/H site has been determined in the alpha-phase. Black-Right-Pointing-Pointer Deuterium/hydrogen induced site depopulation during phase transformation is observed. Black-Right-Pointing-Pointer Ni atoms tend to have tetrahedral-like D/H atom coordination.« less

Experimental and theoretical charge density studies at subatomic resolution.

PubMed

Fischer, A; Tiana, D; Scherer, W; Batke, K; Eickerling, G; Svendsen, H; Bindzus, N; Iversen, B B

2011-11-17

Analysis of accurate experimental and theoretical structure factors of diamond and silicon reveals that the contraction of the core shell due to covalent bond formation causes significant perturbations of the total charge density that cannot be ignored in precise charge density studies. We outline that the nature and origin of core contraction/expansion and core polarization phenomena can be analyzed by experimental studies employing an extended Hansen-Coppens multipolar model. Omission or insufficient treatment of these subatomic charge density phenomena might yield erroneous thermal displacement parameters and high residual densities in multipolar refinements. Our detailed studies therefore suggest that the refinement of contraction/expansion and population parameters of all atomic shells is essential to the precise reconstruction of electron density distributions by a multipolar model. Furthermore, our results imply that also the polarization of the inner shells needs to be adopted, especially in cases where second row or even heavier elements are involved in covalent bonding. These theoretical studies are supported by direct multipolar refinements of X-ray powder diffraction data of diamond obtained from a third-generation synchrotron-radiation source (SPring-8, BL02B2).

AssignFit: a program for simultaneous assignment and structure refinement from solid-state NMR spectra

PubMed Central

Tian, Ye; Schwieters, Charles D.; Opella, Stanley J.; Marassi, Francesca M.

2011-01-01

AssignFit is a computer program developed within the XPLOR-NIH package for the assignment of dipolar coupling (DC) and chemical shift anisotropy (CSA) restraints derived from the solid-state NMR spectra of protein samples with uniaxial order. The method is based on minimizing the difference between experimentally observed solid-state NMR spectra and the frequencies back calculated from a structural model. Starting with a structural model and a set of DC and CSA restraints grouped only by amino acid type, as would be obtained by selective isotopic labeling, AssignFit generates all of the possible assignment permutations and calculates the corresponding atomic coordinates oriented in the alignment frame, together with the associated set of NMR frequencies, which are then compared with the experimental data for best fit. Incorporation of AssignFit in a simulated annealing refinement cycle provides an approach for simultaneous assignment and structure refinement (SASR) of proteins from solid-state NMR orientation restraints. The methods are demonstrated with data from two integral membrane proteins, one α-helical and one β-barrel, embedded in phospholipid bilayer membranes. PMID:22036904

Comparative study of the physicochemical, nutritional, and antioxidant properties of some commercial refined and non-centrifugal sugars.

PubMed

Lee, Jong Suk; Ramalingam, Srinivasan; Jo, Il Guk; Kwon, Ye Som; Bahuguna, Ashutosh; Oh, Young Sook; Kwon, O-Jun; Kim, Myunghee

2018-07-01

Three refined and four unrefined branded commercial sugars available in Korea were investigated in terms of pH, soluble solids, moisture, ash content, turbidity, color values, microbial profile, reducing power, 2,2-diphenyl-1-picrylhydrazyl and 2,2'-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid) radical scavenging activities, cellular antioxidant activity, and total phytoconstituent (i.e. phenolic, flavonoid, mineral, sucrose, glucose, and fructose) contents using standard analytical protocols such as high-performance liquid chromatography, gas chromatography-flame ionization detector/mass spectrometry, and inductively coupled plasma atomic emission spectroscopy. All tested physicochemical parameters were within the recommended standard levels. Significantly high nutritional and antioxidant properties were observed for the unrefined sugars, especially AUNO® sugar, whereas a high sucrose content was detected for the refined sugars. Hence, this study revealed that the degree of purification affects the nutritional values and antioxidant potentials of sugars. The present findings also indicate that unrefined sugars can be used as sweeteners in sugar-based cuisine to obtain nutritional and antioxidant-rich foodstuff. Copyright © 2018 Elsevier Ltd. All rights reserved.

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.

Intermetallic Growth and Interfacial Properties of the Grain Refiners in Al Alloys.

PubMed

Li, Chunmei; Cheng, Nanpu; Chen, Zhiqian; Xie, Zhongjing; Hui, Liangliang

2018-04-20

Al₃TM(TM = Ti, Zr, Hf, Sc) particles acting as effective grain refiners for Al alloys have been receiving extensive attention these days. In order to judge their nucleation behaviors, first-principles calculations are used to investigate their intermetallic and interfacial properties. Based on energy analysis, Al₃Zr and Al₃Sc are more suitable for use as grain refiners than the other two intermetallic compounds. Interfacial properties show that Al/Al₃TM(TM = Ti, Zr, Hf, Sc) interfaces in I-ter interfacial mode exhibit better interface wetting effects due to larger Griffith rupture work and a smaller interface energy. Among these, Al/Al₃Sc achieves the lowest interfacial energy, which shows that Sc atoms should get priority for occupying interfacial sites. Additionally, Sc-doped Al/Al₃(Zr, Sc) interfacial properties show that Sc can effectively improve the Al/Al₃(Zr, Sc) binding strength with the Al matrix. By combining the characteristics of interfaces with the properties of intermetallics, the core-shell structure with Al₃Zr-core or Al₃Zr(Sc1-1)-core encircled with an Sc-rich shell forms.

Recursive Factorization of the Inverse Overlap Matrix in Linear-Scaling Quantum Molecular Dynamics Simulations.

PubMed

Negre, Christian F A; Mniszewski, Susan M; Cawkwell, Marc J; Bock, Nicolas; Wall, Michael E; Niklasson, Anders M N

2016-07-12

We present a reduced complexity algorithm to compute the inverse overlap factors required to solve the generalized eigenvalue problem in a quantum-based molecular dynamics (MD) simulation. Our method is based on the recursive, iterative refinement of an initial guess of Z (inverse square root of the overlap matrix S). The initial guess of Z is obtained beforehand by using either an approximate divide-and-conquer technique or dynamical methods, propagated within an extended Lagrangian dynamics from previous MD time steps. With this formulation, we achieve long-term stability and energy conservation even under the incomplete, approximate, iterative refinement of Z. Linear-scaling performance is obtained using numerically thresholded sparse matrix algebra based on the ELLPACK-R sparse matrix data format, which also enables efficient shared-memory parallelization. As we show in this article using self-consistent density-functional-based tight-binding MD, our approach is faster than conventional methods based on the diagonalization of overlap matrix S for systems as small as a few hundred atoms, substantially accelerating quantum-based simulations even for molecular structures of intermediate size. For a 4158-atom water-solvated polyalanine system, we find an average speedup factor of 122 for the computation of Z in each MD step.

Crystal structure of the non-stoichiometric argyrodite compound Ag 7- xGeSe 5I 1- x ( x=0.31). A highly disordered silver superionic conducting material

NASA Astrophysics Data System (ADS)

Belin, Renaud; Aldon, Laurent; Zerouale, Abdel; Belin, Claude; Ribes, Michel

2001-03-01

Single crystals of the Ag 6.69GeSe 5I 0.69 phase have been obtained by iodine transport of the iodine-partially substituted stoichiometric argyrodite compound Ag 7GeSe 5I. This phase crystallizes in the cubic space group F4¯3 m (argyrodite γ-phase, a=10.921(2) Å at -100°C, a=10.972(3) Å at 25°C, Z=4). It is highly disordered both at anion and cation sites. Crystal structure refinements were completed by an anharmonic Gram-Charlier development of the atomic displacement factors of iodine and silver atoms. The structure of Ag 6.69GeSe 5I 0.69 was determined at -100°C and +25°C and was refined to R( F) values of 5.80 and 6.51%, respectively. Both iodine and selenium (Se1) anions have been found disordered and iodine is slightly defective on its crystallographic site. This is correlated to the disorder observed for the two Ag1 and Ag2 cations that provides this material with superionic conducting properties. Analysis of the joint probability density function allowed the visualization of the Ag + diffusion paths within the anionic framework.

Diffuse X-ray scattering from benzil, C(14)H(10)O(2): analysis via automatic refinement of a Monte Carlo model.

PubMed

Welberry, T R; Goossens, D J; Edwards, A J; David, W I

2001-01-01

A recently developed method for fitting a Monte Carlo computer-simulation model to observed single-crystal diffuse X-ray scattering has been used to study the diffuse scattering in benzil, diphenylethanedione, C(6)H(5)-CO-CO-C(6)H(5). A model involving 13 parameters consisting of 11 intermolecular force constants, a single intramolecular torsional force constant and a local Debye-Waller factor was refined to give an agreement factor, R = [summation operator omega(Delta I)(2)/summation operator omega I(obs)(2)](1/2), of 14.5% for 101,324 data points. The model was purely thermal in nature. The analysis has shown that the diffuse lines, which feature so prominently in the observed diffraction patterns, are due to strong longitudinal displacement correlations. These are transmitted from molecule to molecule via a network of contacts involving hydrogen bonding of an O atom on one molecule and the para H atom of the phenyl ring of a neighbouring molecule. The analysis also allowed the determination of a torsional force constant for rotations about the single bonds in the molecule. This is the first diffuse scattering study in which measurement of such internal molecular torsion forces has been attempted.

GPU accelerated cell-based adaptive mesh refinement on unstructured quadrilateral grid

NASA Astrophysics Data System (ADS)

Luo, Xisheng; Wang, Luying; Ran, Wei; Qin, Fenghua

2016-10-01

A GPU accelerated inviscid flow solver is developed on an unstructured quadrilateral grid in the present work. For the first time, the cell-based adaptive mesh refinement (AMR) is fully implemented on GPU for the unstructured quadrilateral grid, which greatly reduces the frequency of data exchange between GPU and CPU. Specifically, the AMR is processed with atomic operations to parallelize list operations, and null memory recycling is realized to improve the efficiency of memory utilization. It is found that results obtained by GPUs agree very well with the exact or experimental results in literature. An acceleration ratio of 4 is obtained between the parallel code running on the old GPU GT9800 and the serial code running on E3-1230 V2. With the optimization of configuring a larger L1 cache and adopting Shared Memory based atomic operations on the newer GPU C2050, an acceleration ratio of 20 is achieved. The parallelized cell-based AMR processes have achieved 2x speedup on GT9800 and 18x on Tesla C2050, which demonstrates that parallel running of the cell-based AMR method on GPU is feasible and efficient. Our results also indicate that the new development of GPU architecture benefits the fluid dynamics computing significantly.

Atomic resolution view into the structure–function relationships of the human myelin peripheral membrane protein P2

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

Ruskamo, Salla; University of Oulu, Oulu; Yadav, Ravi P.

2014-01-01

The structure of the human myelin peripheral membrane protein P2 has been refined at 0.93 Å resolution. In combination with functional experiments in vitro, in vivo and in silico, the fine details of the structure–function relationships in P2 are emerging. P2 is a fatty acid-binding protein expressed in vertebrate peripheral nerve myelin, where it may function in bilayer stacking and lipid transport. P2 binds to phospholipid membranes through its positively charged surface and a hydrophobic tip, and accommodates fatty acids inside its barrel structure. The structure of human P2 refined at the ultrahigh resolution of 0.93 Å allows detailed structuralmore » analyses, including the full organization of an internal hydrogen-bonding network. The orientation of the bound fatty-acid carboxyl group is linked to the protonation states of two coordinating arginine residues. An anion-binding site in the portal region is suggested to be relevant for membrane interactions and conformational changes. When bound to membrane multilayers, P2 has a preferred orientation and is stabilized, and the repeat distance indicates a single layer of P2 between membranes. Simulations show the formation of a double bilayer in the presence of P2, and in cultured cells wild-type P2 induces membrane-domain formation. Here, the most accurate structural and functional view to date on P2, a major component of peripheral nerve myelin, is presented, showing how it can interact with two membranes simultaneously while going through conformational changes at its portal region enabling ligand transfer.« less

Rosetta FlexPepDock ab-initio: simultaneous folding, docking and refinement of peptides onto their receptors.

PubMed

Raveh, Barak; London, Nir; Zimmerman, Lior; Schueler-Furman, Ora

2011-04-29

Flexible peptides that fold upon binding to another protein molecule mediate a large number of regulatory interactions in the living cell and may provide highly specific recognition modules. We present Rosetta FlexPepDock ab-initio, a protocol for simultaneous docking and de-novo folding of peptides, starting from an approximate specification of the peptide binding site. Using the Rosetta fragments library and a coarse-grained structural representation of the peptide and the receptor, FlexPepDock ab-initio samples efficiently and simultaneously the space of possible peptide backbone conformations and rigid-body orientations over the receptor surface of a given binding site. The subsequent all-atom refinement of the coarse-grained models includes full side-chain modeling of both the receptor and the peptide, resulting in high-resolution models in which key side-chain interactions are recapitulated. The protocol was applied to a benchmark in which peptides were modeled over receptors in either their bound backbone conformations or in their free, unbound form. Near-native peptide conformations were identified in 18/26 of the bound cases and 7/14 of the unbound cases. The protocol performs well on peptides from various classes of secondary structures, including coiled peptides with unusual turns and kinks. The results presented here significantly extend the scope of state-of-the-art methods for high-resolution peptide modeling, which can now be applied to a wide variety of peptide-protein interactions where no prior information about the peptide backbone conformation is available, enabling detailed structure-based studies and manipulation of those interactions. © 2011 Raveh et al.

Rosetta FlexPepDock ab-initio: Simultaneous Folding, Docking and Refinement of Peptides onto Their Receptors

PubMed Central

Raveh, Barak; London, Nir; Zimmerman, Lior; Schueler-Furman, Ora

2011-01-01

Flexible peptides that fold upon binding to another protein molecule mediate a large number of regulatory interactions in the living cell and may provide highly specific recognition modules. We present Rosetta FlexPepDock ab-initio, a protocol for simultaneous docking and de-novo folding of peptides, starting from an approximate specification of the peptide binding site. Using the Rosetta fragments library and a coarse-grained structural representation of the peptide and the receptor, FlexPepDock ab-initio samples efficiently and simultaneously the space of possible peptide backbone conformations and rigid-body orientations over the receptor surface of a given binding site. The subsequent all-atom refinement of the coarse-grained models includes full side-chain modeling of both the receptor and the peptide, resulting in high-resolution models in which key side-chain interactions are recapitulated. The protocol was applied to a benchmark in which peptides were modeled over receptors in either their bound backbone conformations or in their free, unbound form. Near-native peptide conformations were identified in 18/26 of the bound cases and 7/14 of the unbound cases. The protocol performs well on peptides from various classes of secondary structures, including coiled peptides with unusual turns and kinks. The results presented here significantly extend the scope of state-of-the-art methods for high-resolution peptide modeling, which can now be applied to a wide variety of peptide-protein interactions where no prior information about the peptide backbone conformation is available, enabling detailed structure-based studies and manipulation of those interactions. PMID:21572516

Diffraction pattern simulation of cellulose fibrils using distributed and quantized pair distances

DOE PAGES

Zhang, Yan; Inouye, Hideyo; Crowley, Michael; ...

2016-10-14

Intensity simulation of X-ray scattering from large twisted cellulose molecular fibrils is important in understanding the impact of chemical or physical treatments on structural properties such as twisting or coiling. This paper describes a highly efficient method for the simulation of X-ray diffraction patterns from complex fibrils using atom-type-specific pair-distance quantization. Pair distances are sorted into arrays which are labelled by atom type. Histograms of pair distances in each array are computed and binned and the resulting population distributions are used to represent the whole pair-distance data set. These quantized pair-distance arrays are used with a modified and vectorized Debyemore » formula to simulate diffraction patterns. This approach utilizes fewer pair distances in each iteration, and atomic scattering factors are moved outside the iteration since the arrays are labelled by atom type. As a result, this algorithm significantly reduces the computation time while maintaining the accuracy of diffraction pattern simulation, making possible the simulation of diffraction patterns from large twisted fibrils in a relatively short period of time, as is required for model testing and refinement.« less

Diffraction pattern simulation of cellulose fibrils using distributed and quantized pair distances

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

Zhang, Yan; Inouye, Hideyo; Crowley, Michael

Intensity simulation of X-ray scattering from large twisted cellulose molecular fibrils is important in understanding the impact of chemical or physical treatments on structural properties such as twisting or coiling. This paper describes a highly efficient method for the simulation of X-ray diffraction patterns from complex fibrils using atom-type-specific pair-distance quantization. Pair distances are sorted into arrays which are labelled by atom type. Histograms of pair distances in each array are computed and binned and the resulting population distributions are used to represent the whole pair-distance data set. These quantized pair-distance arrays are used with a modified and vectorized Debyemore » formula to simulate diffraction patterns. This approach utilizes fewer pair distances in each iteration, and atomic scattering factors are moved outside the iteration since the arrays are labelled by atom type. This algorithm significantly reduces the computation time while maintaining the accuracy of diffraction pattern simulation, making possible the simulation of diffraction patterns from large twisted fibrils in a relatively short period of time, as is required for model testing and refinement.« less

Diffraction pattern simulation of cellulose fibrils using distributed and quantized pair distances

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

Zhang, Yan; Inouye, Hideyo; Crowley, Michael

Intensity simulation of X-ray scattering from large twisted cellulose molecular fibrils is important in understanding the impact of chemical or physical treatments on structural properties such as twisting or coiling. This paper describes a highly efficient method for the simulation of X-ray diffraction patterns from complex fibrils using atom-type-specific pair-distance quantization. Pair distances are sorted into arrays which are labelled by atom type. Histograms of pair distances in each array are computed and binned and the resulting population distributions are used to represent the whole pair-distance data set. These quantized pair-distance arrays are used with a modified and vectorized Debyemore » formula to simulate diffraction patterns. This approach utilizes fewer pair distances in each iteration, and atomic scattering factors are moved outside the iteration since the arrays are labelled by atom type. As a result, this algorithm significantly reduces the computation time while maintaining the accuracy of diffraction pattern simulation, making possible the simulation of diffraction patterns from large twisted fibrils in a relatively short period of time, as is required for model testing and refinement.« less

Crystal structures of a novel NNN pincer ligand and its dinuclear titanium(IV) alkoxide pincer complex.

PubMed

Pedziwiatr, Jakub; Ghiviriga, Ion; Abboud, Khalil A; Veige, Adam S

2017-02-01

This report describes a synthetic protocols and the crystal structures involving a novel pincer-type H 3 [NNN] ligand, namely di-μ-bromido-μ-{2-(2,2-di-methylpropanimido-yl)- N -[2-(2,2-di-methyl-propanimido-yl)-4-methyl-phen-yl]-4-methylaniline}-bis-[(diethyl ether)lithium], [Li 2 Br 2 (C 24 H 33 N 3 )(C 4 H 10 O) 2 ] ( 1 ) and a dinuclear metal complex, namely di-μ-bromido-2:3κ 4 Br : Br -bis-{2-(2,2-di-methylpropanimido-yl)- N -[2-(2,2-di-methyl-propanimido-yl)-4-methyl-phen-yl]-4-methylaniline}-1κ 3 N , N ', N '';4κ 3 N , N ', N ''-tetra-μ-iso-propano-lato-1:2κ 4 O : O ;3:4κ 4 O : O -diiso-propano-lato-1κ O ,4κ O -2,3-dilithium-1,4-dititanium, [Li 2 Ti 2 Br 2 (C 24 H 32 N 3 ) 2 (C 3 H 7 O) 6 ] or {[NHNNH]Ti(O i Pr) 3 (LiBr) 2 } 2 ( 2 ). Complex 1 , which sits on a twofold rotation axis, is a rare example of a pincer-type ligand which bears ketimine side arms. A unique feature of complex 1 is that the ketimine N atoms have an LiBr(Et 2 O) fragment bonded to them, with the Li atom adopting a distorted tetra-hedral geometry. This particular fragment creates an LiBr bridge between the two ketimine sidearms, which leads to a cage-type appearance of the ligand. Complex 2 consists of the previously described ligand and a Ti IV metal atom in an octa-hedral environment, and is located on an inversion center. Complex 2 crystallizes as a dinuclear species with the metal atoms being bridged by an LiBr entity [the Br atoms are disordered and refined in two positions with their site occupation factors refining to 0.674 (12)/0.372 (12)], and the Li cation being bonded to the isopropoxide O atoms (Li having a tetra-hedral coordination as in 1 ). The organic ligand of compound 2 exhibits disorder in its periphery groups; isopropyl and tert -butyl groups (occupation factors fixed at 0.6/0.4). The novel [NNN]H 3 pincer-type ligand was characterized by multinuclear and multidimensional NMR, HRMS and X-ray crystallography. The dinuclear metal complex 2 was characterized by X-ray crystallography. Although each structure exhibits donor N-H groups, no hydrogen bonding is found in either one, perhaps due to the bulky groups around them. One of the ethyl groups of the ether ligand of 1 is disordered and refined in two parts with site-occupation factors of 0.812 (8) and 0.188 (8). One and a half toluene solvent mol-ecules are also present in the asymmetric unit of 2 . The toluene mol-ecules were significantly disordered and could not be modeled properly, thus SQUEEZE [Spek (2015 ▸). Acta Cryst. C 71 , 9-18] was used to remove their contributions to the overall intensity data.

Hydrogen atoms can be located accurately and precisely by x-ray crystallography.

PubMed

Woińska, Magdalena; Grabowsky, Simon; Dominiak, Paulina M; Woźniak, Krzysztof; Jayatilaka, Dylan

2016-05-01

Precise and accurate structural information on hydrogen atoms is crucial to the study of energies of interactions important for crystal engineering, materials science, medicine, and pharmacy, and to the estimation of physical and chemical properties in solids. However, hydrogen atoms only scatter x-radiation weakly, so x-rays have not been used routinely to locate them accurately. Textbooks and teaching classes still emphasize that hydrogen atoms cannot be located with x-rays close to heavy elements; instead, neutron diffraction is needed. We show that, contrary to widespread expectation, hydrogen atoms can be located very accurately using x-ray diffraction, yielding bond lengths involving hydrogen atoms (A-H) that are in agreement with results from neutron diffraction mostly within a single standard deviation. The precision of the determination is also comparable between x-ray and neutron diffraction results. This has been achieved at resolutions as low as 0.8 Å using Hirshfeld atom refinement (HAR). We have applied HAR to 81 crystal structures of organic molecules and compared the A-H bond lengths with those from neutron measurements for A-H bonds sorted into bonds of the same class. We further show in a selection of inorganic compounds that hydrogen atoms can be located in bridging positions and close to heavy transition metals accurately and precisely. We anticipate that, in the future, conventional x-radiation sources at in-house diffractometers can be used routinely for locating hydrogen atoms in small molecules accurately instead of large-scale facilities such as spallation sources or nuclear reactors.

Hydrogen atoms can be located accurately and precisely by x-ray crystallography

PubMed Central

Woińska, Magdalena; Grabowsky, Simon; Dominiak, Paulina M.; Woźniak, Krzysztof; Jayatilaka, Dylan

2016-01-01

Precise and accurate structural information on hydrogen atoms is crucial to the study of energies of interactions important for crystal engineering, materials science, medicine, and pharmacy, and to the estimation of physical and chemical properties in solids. However, hydrogen atoms only scatter x-radiation weakly, so x-rays have not been used routinely to locate them accurately. Textbooks and teaching classes still emphasize that hydrogen atoms cannot be located with x-rays close to heavy elements; instead, neutron diffraction is needed. We show that, contrary to widespread expectation, hydrogen atoms can be located very accurately using x-ray diffraction, yielding bond lengths involving hydrogen atoms (A–H) that are in agreement with results from neutron diffraction mostly within a single standard deviation. The precision of the determination is also comparable between x-ray and neutron diffraction results. This has been achieved at resolutions as low as 0.8 Å using Hirshfeld atom refinement (HAR). We have applied HAR to 81 crystal structures of organic molecules and compared the A–H bond lengths with those from neutron measurements for A–H bonds sorted into bonds of the same class. We further show in a selection of inorganic compounds that hydrogen atoms can be located in bridging positions and close to heavy transition metals accurately and precisely. We anticipate that, in the future, conventional x-radiation sources at in-house diffractometers can be used routinely for locating hydrogen atoms in small molecules accurately instead of large-scale facilities such as spallation sources or nuclear reactors. PMID:27386545

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

Thimmaiah, Srinivasa; Tener, Zachary; Lamichhane, Tej N.

Here, the γ-region of the Mn–Al phase diagram between 45 and 70 at.% Al was re-investigated by a combination of powder and single crystal X-ray diffraction as well as EDS analysis to establish the distribution of Mn and Al atoms. Single crystals of γ-Mn 5–x Al 8+x were grown using Sn-flux at 650 °C. The crystal structure, atomic coordinates and site occupancy parameters of γ-Mn 5–x Al 8+x phases were refined from single crystal X-ray data. The γ-Mn 5-x Al 8+x phase adopts the rhombohedral Cr 5Al 8-type structure rather than a cubic γ-brass structure. The refined compositions from twomore » crystals extracted from the Al-rich and Mn-rich sides are, respectively, Mn 4.76Al 8.24(2) (I) and Mn 6.32Al 6.68(2) (II). The structure was refined in the acentric R3m space group (No.160, Z=6), in order to compare with other reported rhombohedral γ-brasses. In addition, according to X-ray powder diffraction analysis, at the Al-rich side the γ-phase coexists with LT–Mn 4Al 11 and, at the Mn-rich side, with a hitherto unknown phase. The refined lattice parameters from powder patterns fall in the range a=12.6814(7)–12.6012(5) Å and c=7.9444(2)–7.9311(2) Å from Al-rich to Mn-rich loadings, and the corresponding rhombohedral angles distorted from a pseudo-cubic cell were found to be 89.1(1)°–88.9(1)°. Magnetic susceptibility and magnetization studies of Mn 4.92Al 8.08(2) are consistent with moment bearing Mn and suggest a spin glass state below 27 K. Tight-binding electronic structure calculations (LMTO-ASA with LSDA) showed that the calculated Fermi level for γ-“Mn 5Al 8” falls within a pseudogap of the density of states, a result which is in accordance with a Hume-Rothery stabilization mechanism γ-brass type phases.« less

Highly Scalable Matching Pursuit Signal Decomposition Algorithm

NASA Technical Reports Server (NTRS)

Christensen, Daniel; Das, Santanu; Srivastava, Ashok N.

2009-01-01

Matching Pursuit Decomposition (MPD) is a powerful iterative algorithm for signal decomposition and feature extraction. MPD decomposes any signal into linear combinations of its dictionary elements or atoms . A best fit atom from an arbitrarily defined dictionary is determined through cross-correlation. The selected atom is subtracted from the signal and this procedure is repeated on the residual in the subsequent iterations until a stopping criterion is met. The reconstructed signal reveals the waveform structure of the original signal. However, a sufficiently large dictionary is required for an accurate reconstruction; this in return increases the computational burden of the algorithm, thus limiting its applicability and level of adoption. The purpose of this research is to improve the scalability and performance of the classical MPD algorithm. Correlation thresholds were defined to prune insignificant atoms from the dictionary. The Coarse-Fine Grids and Multiple Atom Extraction techniques were proposed to decrease the computational burden of the algorithm. The Coarse-Fine Grids method enabled the approximation and refinement of the parameters for the best fit atom. The ability to extract multiple atoms within a single iteration enhanced the effectiveness and efficiency of each iteration. These improvements were implemented to produce an improved Matching Pursuit Decomposition algorithm entitled MPD++. Disparate signal decomposition applications may require a particular emphasis of accuracy or computational efficiency. The prominence of the key signal features required for the proper signal classification dictates the level of accuracy necessary in the decomposition. The MPD++ algorithm may be easily adapted to accommodate the imposed requirements. Certain feature extraction applications may require rapid signal decomposition. The full potential of MPD++ may be utilized to produce incredible performance gains while extracting only slightly less energy than the standard algorithm. When the utmost accuracy must be achieved, the modified algorithm extracts atoms more conservatively but still exhibits computational gains over classical MPD. The MPD++ algorithm was demonstrated using an over-complete dictionary on real life data. Computational times were reduced by factors of 1.9 and 44 for the emphases of accuracy and performance, respectively. The modified algorithm extracted similar amounts of energy compared to classical MPD. The degree of the improvement in computational time depends on the complexity of the data, the initialization parameters, and the breadth of the dictionary. The results of the research confirm that the three modifications successfully improved the scalability and computational efficiency of the MPD algorithm. Correlation Thresholding decreased the time complexity by reducing the dictionary size. Multiple Atom Extraction also reduced the time complexity by decreasing the number of iterations required for a stopping criterion to be reached. The Course-Fine Grids technique enabled complicated atoms with numerous variable parameters to be effectively represented in the dictionary. Due to the nature of the three proposed modifications, they are capable of being stacked and have cumulative effects on the reduction of the time complexity.

Trisodium citrate, Na 3 (C 6 H 5 O 7 )

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

Rammohan, Alagappa; Kaduk, James A.

2016-05-10

The crystal structure of anhydrous trisodium citrate, Na 3(C 6H 5O 7), has been solved and refined using synchrotron X-ray powder diffraction data, and optimized using density functional theory (DFT). There are two independent five-coordinate Na +and one six-coordinate Na +cations in the asymmetric unit. The [NaO 5] and [NaO 6] polyhedra share edges and corners to form a three-dimensional framework. There are channels parallel to theaandbaxes in which the remainder of the citrate anions reside. The only hydrogen bonds are an intramolecular one between the hydroxy group and one of the terminal carboxylate O atoms and an intermolecular onemore » between a methylene group and the hydroxyl O atom.« less

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

Kalsi, Deepti; Rayaprol, S.; Siruguri, V.

We report the crystallographic properties of RE{sub 2}NiGe{sub 3} (RE=La, Ce) synthesized by arc melting. Rietveld refinement on the powder neutron diffraction (ND) data suggest both compounds are isostructural and crystallize in the non-centrosymmetric Er{sub 2}RhSi{sub 3} type structure having hexagonal space group P6{sup ¯}2c. In the crystal structure of RE{sub 2}NiGe{sub 3}, two dimensional arrangements of nickel and germanium atoms lead to the formation of hexagonal layers with rare earth atoms sandwiched between them. Magnetic susceptibility measurements performed in low fields exhibit antiferromagnetic ordering in cerium compound around (T{sub o}=) 3.2 K. Neutron diffraction measurements at 2.8 K (i.e.,more » at T« less

Atomic pair distribution function at the Brazilian Synchrotron Light Laboratory: application to the Pb 1–x La xZr 0.40Ti 0.60O 3 ferroelectric system

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

Saleta, M. E.; Eleotério, M.; Mesquita, A.

2017-07-29

This work reports the setting up of the X-ray diffraction and spectroscopy beamline at the Brazilian Synchrotron Light Laboratory for performing total scattering experiments to be analyzed by atomic pair distribution function (PDF) studies. The results of a PDF refinement for Al 2O 3 standard are presented and compared with data acquired at a beamline of the Advanced Photon Source, where it is common to perform this type of experiment. A preliminary characterization of the Pb 1–xLa xZr 0.40Ti 0.60O 3 ferroelectric system, withx= 0.11, 0.12 and 0.15, is also shown.

Electronic structure of lead pyrophosphate

NASA Astrophysics Data System (ADS)

Suewattana, Malliga; Singh, David

2007-03-01

Lead Pyrophosphate Pb2P2O7 is of interest for potential radiation detection applications and use in long term waste storage. It forms in triclinic P1 crystals and can also be grown as glasses. We performed electronic structure calculations using the crystal structure which determined by Mullica et. al (J. Solid State Chem (1986)) using x-ray diffraction and found large forces on atoms suggesting that the refined atomic positions were not fully correct. Here we report first principles structure relaxation and a revised crystal structure for this compound. We analyze the resulting structure using pair distribution functions and discuss the implications for the electronic properties. This work was supported by DOE NA22 and the Office of Naval Research.

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

Schafer, Marion; Bobev, Svilen

This paper presents results from our exploratory work in the systems K-Cd-Ge, Rb-Cd-Ge, and Cs-Cd-Ge, which yielded the novel type-I clathrates with refined compositions K 8Cd 3.77(7)Ge 42.23, Rb 8Cd 3.65(7)Ge 42.35, and Cs 7.80(1)Cd 3.65(6)Ge 42.35. The three compounds represent rare examples of clathrates of germanium with the alkali metals, where a d 10 element substitutes a group 14 element. The three structures, established by single-crystal X-ray diffraction, indicate that the framework-building Ge atoms are randomly substituted by Cd atoms on only one of the three possible crystallographic sites. Furthermore, this and several other details of the crystal chemistrymore » are elaborated.« less

Oxygen-storage behavior and local structure in Ti-substituted YMnO{sub 3}

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

Levin, I., E-mail: igor.levin@nist.gov; Krayzman, V.; Vanderah, T.A.

Hexagonal manganates RMnO{sub 3} (R=Y, Ho, Dy) have been recently shown to exhibit oxygen-storage capacities promising for three-way catalysts, air-separation, and related technologies. Here, we demonstrate that Ti substitution for Mn can be used to chemically tune the oxygen-breathing properties of these materials towards practical applications. Specifically, Y(Mn{sub 1−x}Ti{sub x})O{sub 3} solid solutions exhibit facile oxygen absorption/desorption via reversible Ti{sup 3+}↔Ti{sup 4+} and Mn{sup 3+}↔Mn{sup 4+} reactions already in ambient air at ≈400 °C and ≈250 °C, respectively. On cooling, the oxidation of both cations is accompanied by oxygen uptake yielding a formula YMn{sup 3+}{sub 1−x-y}Mn{sup 4+}{sub y}Ti{sup 4+}{sub x}O{submore » 3+δ}. The presence of Ti promotes the oxidation of Mn{sup 3+} to Mn{sup 4+}, which is almost negligible for YMnO{sub 3} in air, thereby increasing the uptake of oxygen beyond that required for a given Ti{sup 4+} concentration. The reversibility of the redox reactions is limited by sluggish kinetics; however, the oxidation process continues, if slowly, even at room temperature. The extra oxygen atoms are accommodated by the large interstices within a triangular lattice formed by the [MnO{sub 5}] trigonal bipyramids. According to bond distances from Rietveld refinements using the neutron diffraction data, the YMnO{sub 3} structure features under-bonded Mn and even more severely under-bonded oxygen atoms that form the trigonal bases of the [MnO{sub 5}] bipyramids. The tensile bond strain around the 5-fold coordinated Mn site and the strong preference of Ti{sup 4+}(and Mn{sup 4+}) for higher coordination numbers likely provide driving forces for the oxidation reaction. Reverse Monte Carlo refinements of the local atomic displacements using neutron total scattering revealed how the excess oxygen atoms are accommodated in the structure by correlated local displacements of the host atoms. Large displacements of the under-bonded host oxygen atoms play a key part in this lattice-relaxation process, facilitating reversible exchange of significant amounts of oxygen with atmosphere. - Graphical abstract: Concurrent redox reactions involving Ti and Mn yield facile absorption/desorption of excess oxygen. - Highlights: • Concurrent redox reactions involving Ti and Mn yield oxygen absorption/desorption. • Excess oxygen is accommodated as interstitials via correlated atomic shifts. • Oxygen breathing is facilitated by the under-bonding of host Mn and O atoms.« less

A new generation of effective core potentials for correlated calculations

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

Bennett, Michael Chandler; Melton, Cody A.; Annaberdiyev, Abdulgani

Here, we outline ideas on desired properties for a new generation of effective core potentials (ECPs) that will allow valence-only calculations to reach the full potential offered by recent advances in many-body wave function methods. The key improvements include consistent use of correlated methods throughout ECP constructions and improved transferability as required for an accurate description of molecular systems over a range of geometries. The guiding principle is the isospectrality of all-electron and ECP Hamiltonians for a subset of valence states. We illustrate these concepts on a few first- and second-row atoms (B, C, N, O, S), and we obtainmore » higher accuracy in transferability than previous constructions while using semi-local ECPs with a small number of parameters. In addition, the constructed ECPs enable many-body calculations of valence properties with higher (or same) accuracy than their all-electron counterparts with uncorrelated cores. This implies that the ECPs include also some of the impacts of core-core and core-valence correlations on valence properties. The results open further prospects for ECP improvements and refinements.« less

A new generation of effective core potentials for correlated calculations

DOE PAGES

Bennett, Michael Chandler; Melton, Cody A.; Annaberdiyev, Abdulgani; ...

2017-12-12

Here, we outline ideas on desired properties for a new generation of effective core potentials (ECPs) that will allow valence-only calculations to reach the full potential offered by recent advances in many-body wave function methods. The key improvements include consistent use of correlated methods throughout ECP constructions and improved transferability as required for an accurate description of molecular systems over a range of geometries. The guiding principle is the isospectrality of all-electron and ECP Hamiltonians for a subset of valence states. We illustrate these concepts on a few first- and second-row atoms (B, C, N, O, S), and we obtainmore » higher accuracy in transferability than previous constructions while using semi-local ECPs with a small number of parameters. In addition, the constructed ECPs enable many-body calculations of valence properties with higher (or same) accuracy than their all-electron counterparts with uncorrelated cores. This implies that the ECPs include also some of the impacts of core-core and core-valence correlations on valence properties. The results open further prospects for ECP improvements and refinements.« less

K-distribution models for gas mixtures in hypersonic nonequilibrium flows

NASA Astrophysics Data System (ADS)

Bansal, Ankit

Calculation of nonequilibrium radiation field in plasmas around a spacecraft entering into an atmosphere at hypersonic velocities is a very complicated and computationally expensive task. The objective of this Dissertation is to collect state-of-the art spectroscopic data for the evaluation of spectral absorption and emission coefficients of atomic and molecular gases, develop efficient and accurate spectral models and databases, and study the effect of radiation on wall heat loads and flowfield around the spacecraft. The most accurate simulation of radiative transport in the shock layer requires calculating the gas properties at a large number of wavelengths and solving the Radiative Transfer Equation (RTE) in a line-by-line (LBL) fashion, which is prohibitively expensive for coupled simulations. A number of k-distribution based spectral models are developed for atomic lines, continuum and molecular bands that allow efficient evaluation of radiative properties and heat loads in hypersonic shock layer plasma. Molecular radiation poses very different challenges than atomic radiation. A molecular spectrum is governed by simultaneous electronic, vibrational and rotational transitions, making the spectrum very strongly dependent on wavelength. In contrast to an atomic spectrum, where line wings play a major role in heat transfer, most of the heat transfer in molecular spectra occurs near line centers. As the first step, k-distribution models are developed separately for atomic and molecular species, taking advantage of the fact that in the Earth's atmosphere the radiative field is dominated by atomic species (N and O) and in Titan's and Mars' atmospheres molecular bands of CN and CO are dominant. There are a number of practical applications where both atomic and molecular species are present, for example, the vacuum-ultra-violet spectrum during Earth's reentry conditions is marked by emission from atomic bound-bound lines and continuum and simultaneous absorption by strong bands of N2. For such cases, a new model is developed for the treatment of gas mixtures containing atomic lines, continuum and molecular bands. Full-spectrum k-distribution (FSK) method provides very accurate results compared to those obtained from the exact line-by-line method. For cases involving more extreme gradients in species concentrations and temperature, full-spectrum k-distribution model is relatively less accurate, and the method is refined by dividing the spectrum into a number of groups or scales, leading to the development of multi-scale models. The detailed methodology of splitting the gas mixture into scales is presented. To utilize the full potential of the k-distribution methods, pre-calculated values of k-distributions are stored in databases, which can later be interpolated at local flow conditions. Accurate and compact part-spectrum k-distribution databases are developed for atomic species and molecular bands. These databases allow users to calculate desired full-spectrum k-distributions through look-up and interpolation. Application of the new spectral models and databases to shock layer plasma radiation is demonstrated by solving the radiative transfer equation along typical one-dimensional flowfields in Earth's, Titan's and Mars' atmospheres. The k-distribution methods are vastly more efficient than the line-by-line method. The efficiency of the method is compared with the line-by-line method by measuring computational times for a number of test problems, showing typical reduction in computational time by a factor of more than 500 for property evaluation and a factor of about 32,000 for the solution of the RTE. A large percentage of radiative energy emitted in the shock-layer is likely to escape the region, resulting in cooling of the shock layer. This may change the flow parameters in the flowfield and, in turn, can affect radiative as well as convective heat loads. A new flow solver is constructed to simulate coupled hypersonic flow-radiation over a reentry vehicle. The flow solver employs a number of existing schemes and tools available in OpenFOAM; along with a number of additional features for high temperature, compressible and chemically reacting flows, and k-distribution models for radiative calculations. The radiative transport is solved with the one-dimensional tangent slab and P1 solvers, and also with the two-dimensional P1 solver. The new solver is applied to simulate flow around an entry vehicle in Martian atmosphere. Results for uncoupled and coupled flow-radiation simulations are presented, highlighting the effects of radiative cooling on flowfield and wall fluxes.

The slip-and-slide algorithm: a refinement protocol for detector geometry

PubMed Central

Ginn, Helen Mary; Stuart, David Ian

2017-01-01

Geometry correction is traditionally plagued by mis-fitting of correlated parameters, leading to local minima which prevent further improvements. Segmented detectors pose an enhanced risk of mis-fitting: even a minor confusion of detector distance and panel separation can prevent improvement in data quality. The slip-and-slide algorithm breaks down effects of the correlated parameters and their associated target functions in a fundamental shift in the approach to the problem. Parameters are never refined against the components of the data to which they are insensitive, providing a dramatic boost in the exploitation of information from a very small number of diffraction patterns. This algorithm can be applied to exploit the adherence of the spot-finding results prior to indexing to a given lattice using unit-cell dimensions as a restraint. Alternatively, it can be applied to the predicted spot locations and the observed reflection positions after indexing from a smaller number of images. Thus, the indexing rate can be boosted by 5.8% using geometry refinement from only 125 indexed patterns or 500 unindexed patterns. In one example of cypovirus type 17 polyhedrin diffraction at the Linac Coherent Light Source, this geometry refinement reveals a detector tilt of 0.3° (resulting in a maximal Z-axis error of ∼0.5 mm from an average detector distance of ∼90 mm) whilst treating all panels independently. Re-indexing and integrating with updated detector geometry reduces systematic errors providing a boost in anomalous signal of sulfur atoms by 20%. Due to the refinement of decoupled parameters, this geometry method also reaches convergence. PMID:29091058

Ultra-high-resolution X-ray structure of proteins.

PubMed

Lecomte, C; Guillot, B; Muzet, N; Pichon-Pesme, V; Jelsch, C

2004-04-01

The constant advances in synchrotron radiation sources and crystallogenesis methods and the impulse of structural genomics projects have brought biocrystallography to a context favorable to subatomic resolution protein and nucleic acid structures. Thus, as soon as such precision can be frequently obtained, the amount of information available in the precise electron density should also be easily and naturally exploited, similarly to the field of small molecule charge density studies. Indeed, the use of a nonspherical model for the atomic electron density in the refinement of subatomic resolution protein structures allows the experimental description of their electrostatic properties. Some methods we have developed and implemented in our multipolar refinement program MoPro for this purpose are presented. Examples of successful applications to several subatomic resolution protein structures, including the 0.66 angstrom resolution human aldose reductase, are described.

Novel model of negative secondary ion formation and its use to refine the electronegativity of almost fifty elements.

PubMed

Wittmaack, Klaus

2014-06-17

This study aimed to examine the recently proposed idea that the ionic contribution to atomic bonds is essential in determining the charge state of sputtered atoms. Use was made of negative secondary ion yields reported by Wilson for a large number of elements implanted in silicon and then sputter profiled by Cs bombardment. The derived normalized ion yields (or fractions) P vary by 6 orders of magnitude, but the expected exponential dependence on the electron affinity EA is evident only vaguely. Remarkably, a correlation of similar quality is observed if the data are presented as a function of the ionization potential IP. With IP being the dominant (if not sole) contributor to the electronegativity χ, one is led to assume that P depends on the sum χ + EA. About 72% of the "nonsaturated" ion yields are in accordance with a dependence of the form P ∝ exp[(χ + EA)/ε], with ε ≅ 0.2 eV, provided the appropriate value of χ is selected from the electronegativity tables of Pauling (read in eV), Mulliken or Allen. However, each of the three sources contributes only about one-third to the favorable electronegativity data. This unsatisfactory situation initiated the idea to derive the "true" electronegativity χSIMS from the measured ion yields P(χ + EA), verified for 48 elements. Significant negative deviations of χSIMS from a smooth increase with increasing atomic number are evident for elements with special outer-shell electron configurations such as (n-1)d(g-1)ns(1) or (n-1)d(10)ns(2)np(1). The results strongly support the new model of secondary ion formation and provide means for refining electronegativity data.

Fullrmc, a rigid body Reverse Monte Carlo modeling package enabled with machine learning and artificial intelligence.

PubMed

Aoun, Bachir

2016-05-05

A new Reverse Monte Carlo (RMC) package "fullrmc" for atomic or rigid body and molecular, amorphous, or crystalline materials is presented. fullrmc main purpose is to provide a fully modular, fast and flexible software, thoroughly documented, complex molecules enabled, written in a modern programming language (python, cython, C and C++ when performance is needed) and complying to modern programming practices. fullrmc approach in solving an atomic or molecular structure is different from existing RMC algorithms and software. In a nutshell, traditional RMC methods and software randomly adjust atom positions until the whole system has the greatest consistency with a set of experimental data. In contrast, fullrmc applies smart moves endorsed with reinforcement machine learning to groups of atoms. While fullrmc allows running traditional RMC modeling, the uniqueness of this approach resides in its ability to customize grouping atoms in any convenient way with no additional programming efforts and to apply smart and more physically meaningful moves to the defined groups of atoms. In addition, fullrmc provides a unique way with almost no additional computational cost to recur a group's selection, allowing the system to go out of local minimas by refining a group's position or exploring through and beyond not allowed positions and energy barriers the unrestricted three dimensional space around a group. © 2016 Wiley Periodicals, Inc.

Fullrmc, a rigid body reverse monte carlo modeling package enabled with machine learning and artificial intelligence

DOE PAGES

Aoun, Bachir

2016-01-22

Here, a new Reverse Monte Carlo (RMC) package ‘fullrmc’ for atomic or rigid body and molecular, amorphous or crystalline materials is presented. fullrmc main purpose is to provide a fully modular, fast and flexible software, thoroughly documented, complex molecules enabled, written in a modern programming language (python, cython ,C and C++ when performance is needed) and complying to modern programming practices. fullrmc approach in solving an atomic or molecular structure is different from existing RMC algorithms and software. In a nutshell, traditional RMC methods and software randomly adjust atom positions until the whole system has the greatest consistency with amore » set of experimental data. In contrast, fullrmc applies smart moves endorsed with reinforcement machine learning to groups of atoms. While fullrmc allows running traditional RMC modelling, the uniqueness of this approach resides in its ability to customize grouping atoms in any convenient way with no additional programming efforts and to apply smart and more physically meaningful moves to the defined groups of atoms. Also fullrmc provides a unique way with almost no additional computational cost to recur a group’s selection, allowing the system to go out of local minimas by refining a group’s position or exploring through and beyond not allowed positions and energy barriers the unrestricted three dimensional space around a group.« less

Fullrmc, a rigid body reverse monte carlo modeling package enabled with machine learning and artificial intelligence

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

Aoun, Bachir

Here, a new Reverse Monte Carlo (RMC) package ‘fullrmc’ for atomic or rigid body and molecular, amorphous or crystalline materials is presented. fullrmc main purpose is to provide a fully modular, fast and flexible software, thoroughly documented, complex molecules enabled, written in a modern programming language (python, cython ,C and C++ when performance is needed) and complying to modern programming practices. fullrmc approach in solving an atomic or molecular structure is different from existing RMC algorithms and software. In a nutshell, traditional RMC methods and software randomly adjust atom positions until the whole system has the greatest consistency with amore » set of experimental data. In contrast, fullrmc applies smart moves endorsed with reinforcement machine learning to groups of atoms. While fullrmc allows running traditional RMC modelling, the uniqueness of this approach resides in its ability to customize grouping atoms in any convenient way with no additional programming efforts and to apply smart and more physically meaningful moves to the defined groups of atoms. Also fullrmc provides a unique way with almost no additional computational cost to recur a group’s selection, allowing the system to go out of local minimas by refining a group’s position or exploring through and beyond not allowed positions and energy barriers the unrestricted three dimensional space around a group.« less

Reconstructing Solvent Density of Myoglobin Unit Cell from Proximal Radial Distribution Functions of Amino Acids

NASA Astrophysics Data System (ADS)

Galbraith, Madeline; Lynch, Gc; Pettitt, Bm

Understanding the solvent density around a protein crystal structure is an important step for refining accurate crystal structures for use in dynamics simulations or in free energy calculations. The free energy of solvation has typically been approximated using an implicit continuum solvent model or an all atom MD simulation, with a trade-off between accuracy and computation time. For proteins, using precomputed proximal radial distribution functions (pRDFs) of the solvent to reconstruct solvent density on a grid is much faster than all atom MD simulations and more accurate than using implicit solvent models. MD simulations were run for the 20 common amino acids and pRDFs were calculated for several atom type data sets with and without hydrogens, using atom types representative of amino acid side chain atoms. Preliminary results from reconstructions suggest using a data set with 15 heavy atoms and 3 hydrogen yields results with the lowest error without a tradeoff on time. The results of using precomputed pRDFs to reconstruct the solvent density of water for the myoglobin (pdb ID 2mgk) unit cell quantifies the accuracy of the method in comparison with the crystallographic data. Funding Acknowledgement: This research was funded by the CPRIT Summer Undergraduate Program in Computational Cancer Biology, training Grant award RP 140113 from the Cancer Prevention & Research Institute of Texas (CPRIT).

MoleCoolQt – a molecule viewer for charge-density research

PubMed Central

Hübschle, Christian B.; Dittrich, Birger

2011-01-01

MoleCoolQt is a molecule viewer for charge-density research. Features include the visualization of local atomic coordinate systems in multipole refinements based on the Hansen and Coppens formalism as implemented, for example, in the XD suite. Residual peaks and holes from XDfft are translated so that they appear close to the nearest atom of the asymmetric unit. Critical points from a topological analysis of the charge density can also be visualized. As in the program MolIso, color-mapped isosurfaces can be generated with a simple interface. Apart from its visualization features the program interactively helps in assigning local atomic coordinate systems and local symmetry, which can be automatically detected and altered. Dummy atoms – as sometimes required for local atomic coordinate systems – are calculated on demand; XD system files are updated after changes. When using the invariom database, potential scattering factor assignment problems can be resolved by the use of an interactive dialog. The following file formats are supported: XD, MoPro, SHELX, GAUSSIAN (com, FChk, cube), CIF and PDB. MoleCoolQt is written in C++ using the Qt4 library, has a user-friendly graphical user interface, and is available for several flavors of Linux, Windows and MacOS. PMID:22477783

ATOMIC RESOLUTION CRYO ELECTRON MICROSCOPY OF MACROMOLECULAR COMPLEXES

PubMed Central

ZHOU, Z. HONG

2013-01-01

Single-particle cryo electron microscopy (cryoEM) is a technique for determining three-dimensional (3D) structures from projection images of molecular complexes preserved in their “native,” noncrystalline state. Recently, atomic or near-atomic resolution structures of several viruses and protein assemblies have been determined by single-particle cryoEM, allowing ab initio atomic model building by following the amino acid side chains or nucleic acid bases identifiable in their cryoEM density maps. In particular, these cryoEM structures have revealed extended arms contributing to molecular interactions that are otherwise not resolved by the conventional structural method of X-ray crystallography at similar resolutions. High-resolution cryoEM requires careful consideration of a number of factors, including proper sample preparation to ensure structural homogeneity, optimal configuration of electron imaging conditions to record high-resolution cryoEM images, accurate determination of image parameters to correct image distortions, efficient refinement and computation to reconstruct a 3D density map, and finally appropriate choice of modeling tools to construct atomic models for functional interpretation. This progress illustrates the power of cryoEM and ushers it into the arsenal of structural biology, alongside conventional techniques of X-ray crystallography and NMR, as a major tool (and sometimes the preferred one) for the studies of molecular interactions in supramolecular assemblies or machines. PMID:21501817

Diaqua­bis­(5-carb­oxy-2-propyl-1H-imidazole-4-carboxyl­ato-κ2 N 3,O 4)cadmium N,N-dimethyl­formamide disolvate

PubMed Central

Tong, Shao-Wei; Li, Shi-Jie; Song, Wen-Dong; Miao, Dong-Liang; An, Jing-Bo

2011-01-01

In the title complex, [Cd(C8H9N2O4)2(H2O)2]·2C3H7NO, the six-coordinate CdII ion is in a slightly distorted octa­hedral environment, defined by two O atoms from two coordinated water mol­ecules and two carboxyl­ate O atoms and two N atoms from two N,O-bidentate 5-carb­oxy-2-propyl-1H-imidazole-4-carboxyl­ate ligands. In the crystal, complex mol­ecules and dimethyl­formamide solvent mol­ecules are linked by O—H⋯O and N—H⋯O hydrogen bonds into a two-dimensional supra­molecular structure. The propyl groups of the ligands are disordered over two conformations with refined occupancies of 0.680 (7) and 0.320 (7). PMID:22199635

Crystal structure refinement of ReSi1.75 with an ordered arrangement of silicon vacancies

NASA Astrophysics Data System (ADS)

Harada, Shunta; Hoshikawa, Hiroaki; Kuwabara, Kosuke; Tanaka, Katsushi; Okunishi, Eiji; Inui, Haruyuki

2011-08-01

The crystal structure and microstructure of ReSi1.75 were investigated by synchrotron X-ray diffraction combined with scanning transmission electron microscopy. ReSi1.75 contains an ordered arrangement of vacancies in Si sites in the underlying tetragonal C11b lattice of the MoSi2-type and the crystal structure is monoclinic with the space group Cm. Atomic positions of Si atoms near vacancies are considerably displaced from the corresponding positions in the parent C11b structure, and they exhibit anomalously large local thermal vibration accompanied by large values of atomic displacement parameter. There are four differently-oriented domains with two of them being related to each other by the 90° rotation about the c-axis of the underlying C11b lattice and the other two being their respective twins. The habit planes for domain boundaries observed experimentally are consistent with those predicted with ferroelastic theory.

Multiscale Modeling of Damage Processes in fcc Aluminum: From Atoms to Grains

NASA Technical Reports Server (NTRS)

Glaessgen, E. H.; Saether, E.; Yamakov, V.

2008-01-01

Molecular dynamics (MD) methods are opening new opportunities for simulating the fundamental processes of material behavior at the atomistic level. However, current analysis is limited to small domains and increasing the size of the MD domain quickly presents intractable computational demands. A preferred approach to surmount this computational limitation has been to combine continuum mechanics-based modeling procedures, such as the finite element method (FEM), with MD analyses thereby reducing the region of atomic scale refinement. Such multiscale modeling strategies can be divided into two broad classifications: concurrent multiscale methods that directly incorporate an atomistic domain within a continuum domain and sequential multiscale methods that extract an averaged response from the atomistic simulation for later use as a constitutive model in a continuum analysis.

High-resolution comparative modeling with RosettaCM.

PubMed

Song, Yifan; DiMaio, Frank; Wang, Ray Yu-Ruei; Kim, David; Miles, Chris; Brunette, Tj; Thompson, James; Baker, David

2013-10-08

We describe an improved method for comparative modeling, RosettaCM, which optimizes a physically realistic all-atom energy function over the conformational space defined by homologous structures. Given a set of sequence alignments, RosettaCM assembles topologies by recombining aligned segments in Cartesian space and building unaligned regions de novo in torsion space. The junctions between segments are regularized using a loop closure method combining fragment superposition with gradient-based minimization. The energies of the resulting models are optimized by all-atom refinement, and the most representative low-energy model is selected. The CASP10 experiment suggests that RosettaCM yields models with more accurate side-chain and backbone conformations than other methods when the sequence identity to the templates is greater than ∼15%. Copyright © 2013 Elsevier Ltd. All rights reserved.

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

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

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

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

Intermetallic Growth and Interfacial Properties of the Grain Refiners in Al Alloys

PubMed Central

Li, Chunmei; Cheng, Nanpu; Chen, Zhiqian; Xie, Zhongjing; Hui, Liangliang

2018-01-01

Al3TM(TM = Ti, Zr, Hf, Sc) particles acting as effective grain refiners for Al alloys have been receiving extensive attention these days. In order to judge their nucleation behaviors, first-principles calculations are used to investigate their intermetallic and interfacial properties. Based on energy analysis, Al3Zr and Al3Sc are more suitable for use as grain refiners than the other two intermetallic compounds. Interfacial properties show that Al/Al3TM(TM = Ti, Zr, Hf, Sc) interfaces in I-ter interfacial mode exhibit better interface wetting effects due to larger Griffith rupture work and a smaller interface energy. Among these, Al/Al3Sc achieves the lowest interfacial energy, which shows that Sc atoms should get priority for occupying interfacial sites. Additionally, Sc-doped Al/Al3(Zr, Sc) interfacial properties show that Sc can effectively improve the Al/Al3(Zr, Sc) binding strength with the Al matrix. By combining the characteristics of interfaces with the properties of intermetallics, the core-shell structure with Al3Zr-core or Al3Zr(Sc1-1)-core encircled with an Sc-rich shell forms. PMID:29677155

Atomic motion from the mean square displacement in a monatomic liquid

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

Wallace, Duane C.; De Lorenzi-Venneri, Giulia; Chisolm, Eric D.

V-T theory is constructed in the many-body Hamiltonian formulation, and is being developed as a novel approach to liquid dynamics theory. In this theory the liquid atomic motion consists of two contributions, normal mode vibrations in a single representative potential energy valley, and transits, which carry the system across boundaries between valleys. The mean square displacement time correlation function (the MSD) is a direct measure of the atomic motion, and our goal is to determine if the V-T formalism can produce a physically sensible account of this motion. We employ molecular dynamics (MD) data for a system representing liquid Na,more » and find the motion evolves in three successive time intervals: on the first 'vibrational' interval, the vibrational motion alone gives a highly accurate account of the MD data; on the second 'crossover' interval, the vibrational MSD saturates to a constant while the transit motion builds up from zero; on the third 'random walk' interval, the transit motion produces a purely diffusive random walk of the vibrational equilibrium positions. Furthermore, this motional evolution agrees with, and adds refinement to, the MSD atomic motion as described by current liquid dynamics theories.« less

Atomic motion from the mean square displacement in a monatomic liquid

DOE PAGES

Wallace, Duane C.; De Lorenzi-Venneri, Giulia; Chisolm, Eric D.

2016-04-08

V-T theory is constructed in the many-body Hamiltonian formulation, and is being developed as a novel approach to liquid dynamics theory. In this theory the liquid atomic motion consists of two contributions, normal mode vibrations in a single representative potential energy valley, and transits, which carry the system across boundaries between valleys. The mean square displacement time correlation function (the MSD) is a direct measure of the atomic motion, and our goal is to determine if the V-T formalism can produce a physically sensible account of this motion. We employ molecular dynamics (MD) data for a system representing liquid Na,more » and find the motion evolves in three successive time intervals: on the first 'vibrational' interval, the vibrational motion alone gives a highly accurate account of the MD data; on the second 'crossover' interval, the vibrational MSD saturates to a constant while the transit motion builds up from zero; on the third 'random walk' interval, the transit motion produces a purely diffusive random walk of the vibrational equilibrium positions. Furthermore, this motional evolution agrees with, and adds refinement to, the MSD atomic motion as described by current liquid dynamics theories.« less

Investigation of non-corrin cobalt(II)-containing sites in protein structures of the Protein Data Bank.

PubMed

Abriata, Luciano Andres

2013-04-01

Protein X-ray structures with non-corrin cobalt(II)-containing sites, either natural or substituting another native ion, were downloaded from the Protein Data Bank and explored to (i) describe which amino acids are involved in their first ligand shells and (ii) analyze cobalt(II)-donor bond lengths in comparison with previously reported target distances, CSD data and EXAFS data. The set of amino acids involved in Co(II) binding is similar to that observed for catalytic Zn(II) sites, i.e. with a large fraction of carboxylate O atoms from aspartate and glutamate and aromatic N atoms from histidine. The computed Co(II)-donor bond lengths were found to depend strongly on structure resolution, an artifact previously detected for other metal-donor distances. Small corrections are suggested for the target bond lengths to the aromatic N atoms of histidines and the O atoms of water and hydroxide. The available target distance for cysteine (Scys) is confirmed; those for backbone O and other donors remain uncertain and should be handled with caution in refinement and modeling protocols. Finally, a relationship between both Co(II)-O bond lengths in bidentate carboxylates is quantified.

Building Complex Kondo Impurities by Manipulating Entangled Spin Chains.

PubMed

Choi, Deung-Jang; Robles, Roberto; Yan, Shichao; Burgess, Jacob A J; Rolf-Pissarczyk, Steffen; Gauyacq, Jean-Pierre; Lorente, Nicolás; Ternes, Markus; Loth, Sebastian

2017-10-11

The creation of molecule-like structures in which magnetic atoms interact controllably is full of potential for the study of complex or strongly correlated systems. Here, we create spin chains in which a strongly correlated Kondo state emerges from magnetic coupling of transition-metal atoms. We build chains up to ten atoms in length by placing Fe and Mn atoms on a Cu 2 N surface with a scanning tunneling microscope. The atoms couple antiferromagnetically via superexchange interaction through the nitrogen atom network of the surface. The emergent Kondo resonance is spatially distributed along the chain. Its strength can be controlled by mixing atoms of different transition metal elements and manipulating their spatial distribution. We show that the Kondo screening of the full chain by the electrons of the nonmagnetic substrate depends on the interatomic entanglement of the spins in the chain, demonstrating the prerequisites to build and probe spatially extended strongly correlated nanostructures.

Crystal structure, quantum mechanical investigation, IR and NMR spectroscopy of two new organic salts: (C8H12NO)·[NO3] (I) and (C8H14N4)·[ClO4]2 (II)

NASA Astrophysics Data System (ADS)

Bayar, I.; Khedhiri, L.; Soudani, S.; Lefebvre, F.; Pereira da Silva, P. S.; Ben Nasr, C.

2018-06-01

Two new organic-inorganic hybrid materials, 4-methoxybenzylammonium nitrate, (C8H12NO)·[NO3] (I), and 2-(1-piperazinyl)pyrimidinium bis(perchlorate), (C8H14N4)·[ClO4]2(II), have been synthesized by an acid/base reaction at room temperature, their structures were determined by single crystal X-ray diffraction. Compound (I) crystallizes in the orthorhombic system and Pnma space group with a = 15.7908 (7), b = 6.8032 (3), c = 8.7091 (4) Å, V = 935.60 (7) Å3 with Z = 4. Full-matrix least-squares refinement converged at R = 0.038 and wR(F2) = 0.115. Compound (II) belongs to the monoclinic system, space group P21/c with the following parameters: a = 10.798(2), b = 7.330(1), c = 21.186(2) Å, β = 120.641 (4)°, V = 1442.7 (3) Å3and Z = 4. The structure was refined to R = 0.044, wR(F2) = 0.132. In the structures of (I) and (II), the anionic and cationic entities are interconnected by hydrogen bonding contacts forming three-dimensional networks. Intermolecular interactions were investigated by Hirshfeld surfaces and the contacts of the four different chloride atoms in (II) were compared. The Molecular Electrostatic Potential (MEP) maps and the HOMO and LUMO energy gaps of both compounds were computed. The vibrational absorption bands were identified by infrared spectroscopy. These compounds were also investigated by solid-state 13C, 35Cl and 15N NMR spectroscopy. DFT calculations allowed the attribution of the IR and NMR bands.

Molecular structures of Se(SCH3)2 and Te(SCH3)2 using gas-phase electron diffraction and ab initio and DFT geometry optimisations.

PubMed

Fleischer, Holger; Wann, Derek A; Hinchley, Sarah L; Borisenko, Konstantin B; Lewis, James R; Mawhorter, Richard J; Robertson, Heather E; Rankin, David W H

2005-10-07

The molecular structures of Se(SCH(3))(2) and Te(SCH(3))(2) were investigated using gas-phase electron diffraction (GED) and ab initio and DFT geometry optimisations. While parameters involving H atoms were refined using flexible restraints according to the SARACEN method, parameters that depended only on heavy atoms could be refined without restraints. The GED-determined geometric parameters (r(h1)) are: rSe-S 219.1(1), rS-C 183.2(1), rC-H 109.6(4) pm; angleS-Se-S 102.9(3), angleSe-S-C 100.6(2), angleS-C-H (mean) 107.4(5), phiS-Se-S-C 87.9(20), phiSe-S-C-H 178.8(19) degrees for Se(SCH(3))(2), and rTe-S 238.1(2), rS-C 184.1(3), rC-H 110.0(6) pm; angleS-Te-S 98.9(6), angleTe-S-C 99.7(4), angleS-C-H (mean) 109.2(9), phiS-Te-S-C 73.0(48), phiTe-S-C-H 180.1(19) degrees for Te(SCH(3))(2). Ab initio and DFT calculations were performed at the HF, MP2 and B3LYP levels, employing either full-electron basis sets [3-21G(d) or 6-31G(d)] or an effective core potential with a valence basis set [LanL2DZ(d)]. The best fit to the GED structures was achieved at the MP2 level. Differences between GED and MP2 results for rS-C and angleS-Te-S were explained by the thermal population of excited vibrational states under the experimental conditions. All theoretical models agreed that each compound exists as two stable conformers, one in which the methyl groups are on the same side (g(+)g(-) conformer) and one in which they are on different sides (g(+)g(+) conformer) of the S-Y-S plane (Y = Se, Te). The conformational composition under the experimental conditions could not be resolved from the GED data. Despite GED R-factors and ab initio and DFT energies favouring the g(+)g(+) conformer, it is likely that both conformers are present, for Se(SCH(3))(2) as well as for Te(SCH(3))(2).

Three-dimensional time-dependent computer modeling of the electrothermal atomizers for analytical spectrometry

NASA Astrophysics Data System (ADS)

Tsivilskiy, I. V.; Nagulin, K. Yu.; Gilmutdinov, A. Kh.

2016-02-01

A full three-dimensional nonstationary numerical model of graphite electrothermal atomizers of various types is developed. The model is based on solution of a heat equation within solid walls of the atomizer with a radiative heat transfer and numerical solution of a full set of Navier-Stokes equations with an energy equation for a gas. Governing equations for the behavior of a discrete phase, i.e., atomic particles suspended in a gas (including gas-phase processes of evaporation and condensation), are derived from the formal equations molecular kinetics by numerical solution of the Hertz-Langmuir equation. The following atomizers test the model: a Varian standard heated electrothermal vaporizer (ETV), a Perkin Elmer standard THGA transversely heated graphite tube with integrated platform (THGA), and the original double-stage tube-helix atomizer (DSTHA). The experimental verification of computer calculations is carried out by a method of shadow spectral visualization of the spatial distributions of atomic and molecular vapors in an analytical space of an atomizer.

Grain refinement of cast zinc through magnesium inoculation: Characterisation and mechanism

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

Liu, Zhilin; Qiu, Dong; Wang, Feng

2015-08-15

It was previously found that peritectic-forming solutes are more favourable for the grain refinement of cast Al alloys than eutectic-forming solutes. In this work, we report that the eutectic-forming solute, Mg, can also significantly grain refine cast Zn. Differential thermal analysis (DTA) of a Zn–Mg alloy, in which efficient grain refinement occurred, evidenced an unexpected peak that appeared before the nucleation of η-Zn grains on the DTA spectrum. Based on extensive examination using X-ray diffraction, high resolution SEM and EDS, it was found that: (a) some faceted Zn–Mg intermetallic particles were reproducibly observed; (b) the particles were located at ormore » near grain centres; (c) the atomic ratio of Mg to Zn in the intermetallic compound was determined to be around 1/2. Using tilting selected area diffraction (SAD) and convergent beam Kikuchi line diffraction pattern (CBKLDP) techniques, these faceted particles were identified as MgZn{sub 2} and an orientation relationship between such grain-centred MgZn{sub 2} particles and the η-Zn matrix was determined. Hence, the unexpected peak on the DTA spectrum is believed to correspond to the formation of MgZn{sub 2} particles, which act as effective heterogeneous nucleation sites in the alloy. Together with the effect of Mg solute on restricting grain growth, such heterogeneous nucleation is cooperatively responsible for the grain size reduction in Zn–Mg alloys. - Highlights: • A new eutectic-based grain refiner for the cast Zn was found. • The formation process of an intermetallic compound (MgZn{sub 2}) was characterised. • MgZn{sub 2} can act as potent heterogeneous nucleation sites above the liquidus. • A new OR between MgZn{sub 2} and η-Zn was determined using the CBKLDP technique.« less

Single-particle cryo-EM using alignment by classification (ABC): the structure of Lumbricus terrestris haemoglobin.

PubMed

Afanasyev, Pavel; Seer-Linnemayr, Charlotte; Ravelli, Raimond B G; Matadeen, Rishi; De Carlo, Sacha; Alewijnse, Bart; Portugal, Rodrigo V; Pannu, Navraj S; Schatz, Michael; van Heel, Marin

2017-09-01

Single-particle cryogenic electron microscopy (cryo-EM) can now yield near-atomic resolution structures of biological complexes. However, the reference-based alignment algorithms commonly used in cryo-EM suffer from reference bias, limiting their applicability (also known as the 'Einstein from random noise' problem). Low-dose cryo-EM therefore requires robust and objective approaches to reveal the structural information contained in the extremely noisy data, especially when dealing with small structures. A reference-free pipeline is presented for obtaining near-atomic resolution three-dimensional reconstructions from heterogeneous ('four-dimensional') cryo-EM data sets. The methodologies integrated in this pipeline include a posteriori camera correction, movie-based full-data-set contrast transfer function determination, movie-alignment algorithms, (Fourier-space) multivariate statistical data compression and unsupervised classification, 'random-startup' three-dimensional reconstructions, four-dimensional structural refinements and Fourier shell correlation criteria for evaluating anisotropic resolution. The procedures exclusively use information emerging from the data set itself, without external 'starting models'. Euler-angle assignments are performed by angular reconstitution rather than by the inherently slower projection-matching approaches. The comprehensive 'ABC-4D' pipeline is based on the two-dimensional reference-free 'alignment by classification' (ABC) approach, where similar images in similar orientations are grouped by unsupervised classification. Some fundamental differences between X-ray crystallography versus single-particle cryo-EM data collection and data processing are discussed. The structure of the giant haemoglobin from Lumbricus terrestris at a global resolution of ∼3.8 Å is presented as an example of the use of the ABC-4D procedure.

Distributed force probe bending model of critical dimension atomic force microscopy bias

NASA Astrophysics Data System (ADS)

Ukraintsev, Vladimir A.; Orji, Ndubuisi G.; Vorburger, Theodore V.; Dixson, Ronald G.; Fu, Joseph; Silver, Rick M.

2013-04-01

Critical dimension atomic force microscopy (CD-AFM) is a widely used reference metrology technique. To characterize modern semiconductor devices, small and flexible probes, often 15 to 20 nm in diameter, are used. Recent studies have reported uncontrolled and significant probe-to-probe bias variation during linewidth and sidewall angle measurements. To understand the source of these variations, tip-sample interactions between high aspect ratio features and small flexible probes, and their influence on measurement bias, should be carefully studied. Using theoretical and experimental procedures, one-dimensional (1-D) and two-dimensional (2-D) models of cylindrical probe bending relevant to carbon nanotube (CNT) AFM probes were developed and tested. An earlier 1-D bending model was refined, and a new 2-D distributed force (DF) model was developed. Contributions from several factors were considered, including: probe misalignment, CNT tip apex diameter variation, probe bending before snapping, and distributed van der Waals-London force. A method for extracting Hamaker probe-surface interaction energy from experimental probe-bending data was developed. Comparison of the new 2-D model with 1-D single point force (SPF) model revealed a difference of about 28% in probe bending. A simple linear relation between biases predicted by the 1-D SPF and 2-D DF models was found. The results suggest that probe bending can be on the order of several nanometers and can partially explain the observed CD-AFM probe-to-probe variation. New 2-D and three-dimensional CD-AFM data analysis software is needed to take full advantage of the new bias correction modeling capabilities.

Finite-temperature stress calculations in atomic models using moments of position.

PubMed

Parthasarathy, Ranganathan; Misra, Anil; Ouyang, Lizhi

2018-07-04

Continuum modeling of finite temperature mechanical behavior of atomic systems requires refined description of atomic motions. In this paper, we identify additional kinematical quantities that are relevant for a more accurate continuum description as the system is subjected to step-wise loading. The presented formalism avoids the necessity for atomic trajectory mapping with deformation, provides the definitions of the kinematic variables and their conjugates in real space, and simplifies local work conjugacy. The total work done on an atom under deformation is decomposed into the work corresponding to changing its equilibrium position and work corresponding to changing its second moment about equilibrium position. Correspondingly, we define two kinematic variables: a deformation gradient tensor and a vibration tensor, and derive their stress conjugates, termed here as static and vibration stresses, respectively. The proposed approach is validated using MD simulation in NVT ensembles for fcc aluminum subjected to uniaxial extension. The observed evolution of second moments in the MD simulation with macroscopic deformation is not directly related to the transformation of atomic trajectories through the deformation gradient using generator functions. However, it is noteworthy that deformation leads to a change in the second moment of the trajectories. Correspondingly, the vibration part of the Piola stress becomes particularly significant at high temperature and high tensile strain as the crystal approaches the softening limit. In contrast to the eigenvectors of the deformation gradient, the eigenvectors of the vibration tensor show strong spatial heterogeneity in the vicinity of softening. More importantly, the elliptic distribution of local atomic density transitions to a dumbbell shape, before significant non-affinity in equilibrium positions has occurred.

Finite-temperature stress calculations in atomic models using moments of position

NASA Astrophysics Data System (ADS)

Parthasarathy, Ranganathan; Misra, Anil; Ouyang, Lizhi

2018-07-01

Continuum modeling of finite temperature mechanical behavior of atomic systems requires refined description of atomic motions. In this paper, we identify additional kinematical quantities that are relevant for a more accurate continuum description as the system is subjected to step-wise loading. The presented formalism avoids the necessity for atomic trajectory mapping with deformation, provides the definitions of the kinematic variables and their conjugates in real space, and simplifies local work conjugacy. The total work done on an atom under deformation is decomposed into the work corresponding to changing its equilibrium position and work corresponding to changing its second moment about equilibrium position. Correspondingly, we define two kinematic variables: a deformation gradient tensor and a vibration tensor, and derive their stress conjugates, termed here as static and vibration stresses, respectively. The proposed approach is validated using MD simulation in NVT ensembles for fcc aluminum subjected to uniaxial extension. The observed evolution of second moments in the MD simulation with macroscopic deformation is not directly related to the transformation of atomic trajectories through the deformation gradient using generator functions. However, it is noteworthy that deformation leads to a change in the second moment of the trajectories. Correspondingly, the vibration part of the Piola stress becomes particularly significant at high temperature and high tensile strain as the crystal approaches the softening limit. In contrast to the eigenvectors of the deformation gradient, the eigenvectors of the vibration tensor show strong spatial heterogeneity in the vicinity of softening. More importantly, the elliptic distribution of local atomic density transitions to a dumbbell shape, before significant non-affinity in equilibrium positions has occurred.

Probing cluster surface morphology by cryo spectroscopy of N2 on cationic nickel clusters

NASA Astrophysics Data System (ADS)

Dillinger, Sebastian; Mohrbach, Jennifer; Niedner-Schatteburg, Gereon

2017-11-01

We present the cryogenic (26 K) IR spectra of selected [Nin(N2)m]+ (n = 5-20, m = 1 - mmax), which strongly reveal n- and m-dependent features in the N2 stretching region, in conjunction with density functional theory modeling of some of these findings. The observed spectral features allow us to refine the kinetic classification [cf. J. Mohrbach, S. Dillinger, and G. Niedner-Schatteburg, J. Chem. Phys. 147, 184304 (2017)] and to define four classes of structure related surface adsorption behavior: Class (1) of Ni6+, Ni13+, and Ni19+ are highly symmetrical clusters with all smooth surfaces of equally coordinated Ni atoms that entertain stepwise N2 adsorption up to stoichiometric N2:Nisurface saturation. Class (2) of Ni12+ and Ni18+ are highly symmetrical clusters minus one. Their relaxed smooth surfaces reorganize by enhanced N2 uptake toward some low coordinated Ni surface atoms with double N2 occupation. Class (3) of Ni5+ and Ni7+ through Ni11+ are small clusters of rough surfaces with low coordinated Ni surface atoms, and some reveal semi-internal Ni atoms of high next-neighbor coordination. Surface reorganization upon N2 uptake turns rough into rough surface by Ni atom migration and turns octahedral based structures into pentagonal bipyramidal structures. Class (4) of Ni14+ through Ni17+ and Ni20+ are large clusters with rough and smooth surface areas. They possess smooth icosahedral surfaces with some proximate capping atom(s) on one hemisphere of the icosahedron with the other one largely unaffected.

A Comparison of Spectral Element and Finite Difference Methods Using Statically Refined Nonconforming Grids for the MHD Island Coalescence Instability Problem

NASA Astrophysics Data System (ADS)

Ng, C. S.; Rosenberg, D.; Pouquet, A.; Germaschewski, K.; Bhattacharjee, A.

2009-04-01

A recently developed spectral-element adaptive refinement incompressible magnetohydrodynamic (MHD) code [Rosenberg, Fournier, Fischer, Pouquet, J. Comp. Phys. 215, 59-80 (2006)] is applied to simulate the problem of MHD island coalescence instability (\\ci) in two dimensions. \\ci is a fundamental MHD process that can produce sharp current layers and subsequent reconnection and heating in a high-Lundquist number plasma such as the solar corona [Ng and Bhattacharjee, Phys. Plasmas, 5, 4028 (1998)]. Due to the formation of thin current layers, it is highly desirable to use adaptively or statically refined grids to resolve them, and to maintain accuracy at the same time. The output of the spectral-element static adaptive refinement simulations are compared with simulations using a finite difference method on the same refinement grids, and both methods are compared to pseudo-spectral simulations with uniform grids as baselines. It is shown that with the statically refined grids roughly scaling linearly with effective resolution, spectral element runs can maintain accuracy significantly higher than that of the finite difference runs, in some cases achieving close to full spectral accuracy.

Modeling protein-small molecule interactions: structure and thermodynamics of noble gases binding in a cavity in mutant phage T4 lysozyme L99A.

PubMed

Mann, G; Hermans, J

2000-09-29

The complexes of phage T4 lysozyme L99A with noble gases have been studied by molecular dynamics simulation. In a long simulation of the complex with one Xe atom, the structure was found to undergo global conformation change involving a reversible opening and closing of the entrance to the substrate-binding site, during which the conformations of the N and C-terminal domains varied little. The distributions of Xe positions sampled in dynamics simulations were refined in terms of anisotropic Gaussian distributions via least-squares minimization of the difference between Fourier transforms. In addition, molecular transformation simulations have been applied in order to calculate the binding free energies of Xe, Kr and Ar relative to a standard state at a pressure of 1 bar. A single bound Xe is found to assume an equilibrium distribution over three adjacent preferred sites, while in a two-Xe complex, the two Xe atoms preferentially occupy two of these. The positions of the three sites agree closely with the positions of bound Xe determined in the refined crystal structure of a complex formed at a pressure of 8 bar Xe, and the calculated affinities agree well with the observed partial occupancies. At a pressure of 8 bar, a mixture of one-Xe and two-Xe complexes is present, and similarly for complexes with Kr and Ar, with single occupancy relatively more prevalent with Kr and Ar. (Binding of a third Xe atom is found to be quite unfavorable.) A comparison with simulation results for the binding of benzene to the same site leads to the conclusion that binding of Xe within cavities in proteins is common because of several favorable factors: (1) Xe has a large atomic polarizability; (2) Xe can be applied at a relatively high pressure, i.e. high chemical potential; (3) an unfavorable entropic term related to the need to orient the ligand in the binding site is absent. Finally, it is found that the model's binding energy of a water molecule in the cavity is insufficient to overcome the unfavorable binding entropy. Copyright 2000 Academic Press.

Influence of valence electron concentration on Laves phases: Structures and phase stability of pseudo-binary MgZn 2-xPd x

DOE PAGES

Thimmaiah, Srinivasa; Miller, Gordon J.

2015-06-03

A series of pseudo-binary compounds MgZn 2-xPd x (0.15 ≤ x ≤ 1.0) were synthesized and structurally characterized to understand the role of valence electron concentration (vec) on the prototype Laves phase MgZn 2 with Pd-substitution. Three distinctive phase regions were observed with respect to Pd content, all exhibiting fundamental Laves phase structures: 0.1 ≤ x ≤ 0.3 (MgNi 2-type, hP24; MgZn 1.80Pd 0.20(2)), 0.4 ≤ x ≤ 0.6 (MgCu 2-type, cF24; MgZn 1.59Pd 0.41(2)), and 0.62 ≤ x ≤ 0.8 (MgZn 2-type, hP12: MgZn 1.37Pd 0.63(2)). Refinements from single-crystal X-ray diffraction indicated nearly statistical distributions of Pd and Znmore » atoms among the majority atom sites in these structures. Interestingly, the MgZn 2-type structure re-emerges in MgZn 2–xPd x at x ≈ 0.7 with the refined composition MgZn 1.37(2)Pd 0.63 and a c/a ratio of 1.59 compared to 1.64 for binary MgZn 2. Electronic structure calculations on a model “MgZn 1.25Pd 0.75” yielded a density of states (DOS) curve showing enhancement of a pseudogap at the Fermi level as a result of electronic stabilization due to the Pd addition. Moreover, integrated crystal orbital Hamilton population values show significant increases of orbital interactions for (Zn,Pd)–(Zn,Pd) atom pairs within the majority atom substructure, i.e., within the Kagomé nets as well as between a Kagomé net and an apical site, from binary MgZn 2 to the ternary “MgZn 1.25Pd 0.75”. Multi-centered bonding is evident from electron localization function plots for “MgZn 1.25Pd 0.75”, an outcome which is in accordance with analysis of other Laves phases.« less

SFCHECK: a unified set of procedures for evaluating the quality of macromolecular structure-factor data and their agreement with the atomic model.

PubMed

Vaguine, A A; Richelle, J; Wodak, S J

1999-01-01

In this paper we present SFCHECK, a stand-alone software package that features a unified set of procedures for evaluating the structure-factor data obtained from X-ray diffraction experiments and for assessing the agreement of the atomic coordinates with these data. The evaluation is performed completely automatically, and produces a concise PostScript pictorial output similar to that of PROCHECK [Laskowski, MacArthur, Moss & Thornton (1993). J. Appl. Cryst. 26, 283-291], greatly facilitating visual inspection of the results. The required inputs are the structure-factor amplitudes and the atomic coordinates. Having those, the program summarizes relevant information on the deposited structure factors and evaluates their quality using criteria such as data completeness, structure-factor uncertainty and the optical resolution computed from the Patterson origin peak. The dependence of various parameters on the nominal resolution (d spacing) is also given. To evaluate the global agreement of the atomic model with the experimental data, the program recomputes the R factor, the correlation coefficient between observed and calculated structure-factor amplitudes and Rfree (when appropriate). In addition, it gives several estimates of the average error in the atomic coordinates. The local agreement between the model and the electron-density map is evaluated on a per-residue basis, considering separately the macromolecule backbone and side-chain atoms, as well as solvent atoms and heterogroups. Among the criteria are the normalized average atomic displacement, the local density correlation coefficient and the polymer chain connectivity. The possibility of computing these criteria using the omit-map procedure is also provided. The described software should be a valuable tool in monitoring the refinement procedure and in assessing structures deposited in databases.

Decadal climate prediction with a refined anomaly initialisation approach

NASA Astrophysics Data System (ADS)

Volpi, Danila; Guemas, Virginie; Doblas-Reyes, Francisco J.; Hawkins, Ed; Nichols, Nancy K.

2017-03-01

In decadal prediction, the objective is to exploit both the sources of predictability from the external radiative forcings and from the internal variability to provide the best possible climate information for the next decade. Predicting the climate system internal variability relies on initialising the climate model from observational estimates. We present a refined method of anomaly initialisation (AI) applied to the ocean and sea ice components of the global climate forecast model EC-Earth, with the following key innovations: (1) the use of a weight applied to the observed anomalies, in order to avoid the risk of introducing anomalies recorded in the observed climate, whose amplitude does not fit in the range of the internal variability generated by the model; (2) the AI of the ocean density, instead of calculating it from the anomaly initialised state of temperature and salinity. An experiment initialised with this refined AI method has been compared with a full field and standard AI experiment. Results show that the use of such refinements enhances the surface temperature skill over part of the North and South Atlantic, part of the South Pacific and the Mediterranean Sea for the first forecast year. However, part of such improvement is lost in the following forecast years. For the tropical Pacific surface temperature, the full field initialised experiment performs the best. The prediction of the Arctic sea-ice volume is improved by the refined AI method for the first three forecast years and the skill of the Atlantic multidecadal oscillation is significantly increased compared to a non-initialised forecast, along the whole forecast time.

Single-crystal diffraction at megabar conditions by synchrotron radiation

NASA Astrophysics Data System (ADS)

Merlini, Marco; Hanfland, Michael

2013-08-01

Crystal structure determination at extreme pressures is currently possible at synchrotron beamlines optimized for such a purpose. We report the description of the experimental setup available at European Synchrotron Radiation Facility ID09 beamline (Grenoble, France) and, with two examples, we illustrate the state-of-the-art experiments currently performed at third-generation synchrotrons. The first example concerns the determination of the equation of state and the structural behavior of low-spin Fe-bearing siderite in the megabar pressure range. Siderite, in fact, undergoes a first-order isosymmetric transition at 45 GPa, and, above this pressure, it features Fe2+ in electronic low-spin configuration. The local configuration of Fe coordination polyhedra, determined by structural refinements, significantly deviates from a regular octahedron. Nevertheless, no further structural transition is detected up to the maximum pressure reached in our experiments, 135 GPa. The analysis of the Fe-O bond length extrapolated to ambient pressure, which indicates that the difference in ionic radii between the high- and the low-spin state of Fe2+ is 0.172 Å, in excellent agreement with the tabulated data by Shannon and Prewitt [Effective ionic radii in oxides and fluorides. Acta Crystallogr. 1969;B25:925-946]. The second example concerns the determination and refinement of the oP8 structure adopted by sodium in the pressure interval 118-125 GPa, using an experimental dataset collected at 118 GPa. The orthorhombic [a=4.7687(15) Å, b=3.0150(6) Å, c=5.2423(7) Å, V=75.4(3) Å3] oP8 structure is topologically related to the MnP structure, with two non-equivalent atoms in the unit cell. Despite the weak scattering factor of Na atoms, the quality of the data also allows meaningful displacement parameters refinements (R1=4.6%, 14 parameters, 190 diffractions, and 105 unique) demonstrating that the current accuracy of diffraction data at extreme pressures can be comparable with ambient condition measurements.

Strengthening of Cu–Ni–Si alloy using high-pressure torsion and aging

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

Lee, Seungwon, E-mail: chominamlsw@gmail.com; WPI, International Institute for Carbon-Neutral Energy Research; Matsunaga, Hirotaka

2014-04-01

An age-hardenable Cu–2.9%Ni–0.6%Si alloy was subjected to high-pressure torsion. Aging behavior was investigated in terms of hardness, electrical conductivity and microstructural features. Transmission electron microscopy showed that the grain size is refined to ∼ 150 nm and the Vickers microhardness was significantly increased through the HPT processing. Aging treatment of the HPT-processed alloy led to a further increase in the hardness. Electrical conductivity is also improved with the aging treatment. It was confirmed that the simultaneous strengthening by grain refinement and fine precipitation is achieved while maintaining high electrical conductivity. Three dimensional atom probe analysis including high-resolution transmission electron microscopymore » revealed that nanosized precipitates having compositions of a metastable Cu{sub 3}Ni{sub 5}Si{sub 2} phase and a stable NiSi phase were formed in the Cu matrix by aging of the HPT-processed samples and these particles are responsible for the additional increase in strength after the HPT processing. - Highlights: • Grain refinement is achieved in Corson alloy the size of ∼150nm by HPT. • Aging at 300°C after HPT leads to further increase in the mechanical property. • Electrical conductivity reaches 40% IACS after aging for 100 h. • 3D-APT revealed the formation of nanosized-precipitates during aging treatment. • Simultaneous hardening in both grain refinement and precipitation is achieved.« less

EMRinger: side chain–directed model and map validation for 3D cryo-electron microscopy

DOE PAGES

Barad, Benjamin A.; Echols, Nathaniel; Wang, Ray Yu-Ruei; ...

2015-08-17

Advances in high-resolution cryo-electron microscopy (cryo-EM) require the development of validation metrics to independently assess map quality and model geometry. We report that EMRinger is a tool that assesses the precise fitting of an atomic model into the map during refinement and shows how radiation damage alters scattering from negatively charged amino acids. EMRinger (https://github.com/fraser-lab/EMRinger) will be useful for monitoring progress in resolving and modeling high-resolution features in cryo-EM.

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

Grain Refinement of AZ31 Magnesium Alloy Weldments by AC Pulsing Technique

NASA Astrophysics Data System (ADS)

Kishore Babu, N.; Cross, C. E.

2012-11-01

The current study has investigated the influence of alternating current pulsing on the structure and mechanical properties of AZ31 magnesium alloy gas tungsten arc (GTA) weldments. Autogenous full penetration bead-on-plate GTA welds were made under a variety of conditions including variable polarity (VP), variable polarity mixed (VPM), alternating current (AC), and alternating current pulsing (ACPC). AC pulsing resulted in significant refinement of weld metal when compared with the unpulsed conditions. AC pulsing leads to relatively finer and more equiaxed grain structure in GTA welds. In contrast, VP, VPM, and AC welding resulted in predominantly columnar grain structures. The reason for this grain refinement may be attributed to the periodic variations in temperature gradient and solidification rate associated with pulsing as well as weld pool oscillation observed in the ACPC welds. The observed grain refinement was shown to result in an appreciable increase in fusion zone hardness, tensile strength, and ductility.

Getting the chemistry right: protonation, tautomers and the importance of H atoms in biological chemistry.

PubMed

Bax, Ben; Chung, Chun Wa; Edge, Colin

2017-02-01

There are more H atoms than any other type of atom in an X-ray crystal structure of a protein-ligand complex, but as H atoms only have one electron they diffract X-rays weakly and are `hard to see'. The positions of many H atoms can be inferred by our chemical knowledge, and such H atoms can be added with confidence in `riding positions'. For some chemical groups, however, there is more ambiguity over the possible hydrogen placements, for example hydroxyls and groups that can exist in multiple protonation states or tautomeric forms. This ambiguity is far from rare, since about 25% of drugs have more than one tautomeric form. This paper focuses on the most common, `prototropic', tautomers, which are isomers that readily interconvert by the exchange of an H atom accompanied by the switch of a single and an adjacent double bond. Hydrogen-exchange rates and different protonation states of compounds (e.g. buffers) are also briefly discussed. The difference in heavy (non-H) atom positions between two tautomers can be small, and careful refinement of all possible tautomers may single out the likely bound ligand tautomer. Experimental methods to determine H-atom positions, such as neutron crystallography, are often technically challenging. Therefore, chemical knowledge and computational approaches are frequently used in conjugation with experimental data to deduce the bound tautomer state. Proton movement is a key feature of many enzymatic reactions, so understanding the orchestration of hydrogen/proton motion is of critical importance to biological chemistry. For example, structural studies have suggested that, just as a chemist may use heat, some enzymes use directional movement to protonate specific O atoms on phosphates to catalyse phosphotransferase reactions. To inhibit `wriggly' enzymes that use movement to effect catalysis, it may be advantageous to have inhibitors that can maintain favourable contacts by adopting different tautomers as the enzyme `wriggles'.

The Collaborative Seismic Earth Model Project

NASA Astrophysics Data System (ADS)

Fichtner, A.; van Herwaarden, D. P.; Afanasiev, M.

2017-12-01

We present the first generation of the Collaborative Seismic Earth Model (CSEM). This effort is intended to address grand challenges in tomography that currently inhibit imaging the Earth's interior across the seismically accessible scales: [1] For decades to come, computational resources will remain insufficient for the exploitation of the full observable seismic bandwidth. [2] With the man power of individual research groups, only small fractions of available waveform data can be incorporated into seismic tomographies. [3] The limited incorporation of prior knowledge on 3D structure leads to slow progress and inefficient use of resources. The CSEM is a multi-scale model of global 3D Earth structure that evolves continuously through successive regional refinements. Taking the current state of the CSEM as initial model, these refinements are contributed by external collaborators, and used to advance the CSEM to the next state. This mode of operation allows the CSEM to [1] harness the distributed man and computing power of the community, [2] to make consistent use of prior knowledge, and [3] to combine different tomographic techniques, needed to cover the seismic data bandwidth. Furthermore, the CSEM has the potential to serve as a unified and accessible representation of tomographic Earth models. Generation 1 comprises around 15 regional tomographic refinements, computed with full-waveform inversion. These include continental-scale mantle models of North America, Australasia, Europe and the South Atlantic, as well as detailed regional models of the crust beneath the Iberian Peninsula and western Turkey. A global-scale full-waveform inversion ensures that regional refinements are consistent with whole-Earth structure. This first generation will serve as the basis for further automation and methodological improvements concerning validation and uncertainty quantification.

A database of new zeolite-like materials.

PubMed

Pophale, Ramdas; Cheeseman, Phillip A; Deem, Michael W

2011-07-21

We here describe a database of computationally predicted zeolite-like materials. These crystals were discovered by a Monte Carlo search for zeolite-like materials. Positions of Si atoms as well as unit cell, space group, density, and number of crystallographically unique atoms were explored in the construction of this database. The database contains over 2.6 M unique structures. Roughly 15% of these are within +30 kJ mol(-1) Si of α-quartz, the band in which most of the known zeolites lie. These structures have topological, geometrical, and diffraction characteristics that are similar to those of known zeolites. The database is the result of refinement by two interatomic potentials that both satisfy the Pauli exclusion principle. The database has been deposited in the publicly available PCOD database and in www.hypotheticalzeolites.net/database/deem/. This journal is © the Owner Societies 2011

Influences on Distribution of Solute Atoms in Cu-8Fe Alloy Solidification Process Under Rotating Magnetic Field

NASA Astrophysics Data System (ADS)

Zou, Jin; Zhai, Qi-Jie; Liu, Fang-Yu; Liu, Ke-Ming; Lu, De-Ping

2018-05-01

A rotating magnetic field (RMF) was applied in the solidification process of Cu-8Fe alloy. Focus on the mechanism of RMF on the solid solution Fe(Cu) atoms in Cu-8Fe alloy, the influences of RMF on solidification structure, solute distribution, and material properties were discussed. Results show that the solidification behavior of Cu-Fe alloy have influenced through the change of temperature and solute fields in the presence of an applied RMF. The Fe dendrites were refined and transformed to rosettes or spherical grains under forced convection. The solute distribution in Cu-rich phase and Fe-rich phase were changed because of the variation of the supercooling degree and the solidification rate. Further, the variation in solute distribution was impacted the strengthening mechanism and conductive mechanism of the material.

Comparing Ultraviolet Spectra Against Calculations: First Results

NASA Technical Reports Server (NTRS)

Peterson, Ruth C.

2003-01-01

The five-year goal of this effort is to calculate high fidelity mid-UV spectra for individual stars and stellar systems for a wide range of ages, abundances, and abundance ratios. In this first year, the emphasis was placed on revising the list of atomic line parameters used to calculate mid-UV spectra. First, new identifications of atomic lines and measurements of their transition probabilities were obtained for lines of the first and second ionization stages of iron-peak elements. Second, observed mid-UV and optical spectra for standard stars were re-analyzed and compared to new calculations, to refine the determination of transition probabilities and to estimate the identity of lines still missing from the laboratory lists. As evidenced by the figures, a dramatic improvement has resulted in the reproduction of the spectra of standard stars by the calculations.

Improved ligand geometries in crystallographic refinement using AFITT in PHENIX

DOE PAGES

Janowski, Pawel A.; Moriarty, Nigel W.; Kelley, Brian P.; ...

2016-08-31

Modern crystal structure refinement programs rely on geometry restraints to overcome the challenge of a low data-to-parameter ratio. While the classical Engh and Huber restraints work well for standard amino-acid residues, the chemical complexity of small-molecule ligands presents a particular challenge. Most current approaches either limit ligand restraints to those that can be readily described in the Crystallographic Information File (CIF) format, thus sacrificing chemical flexibility and energetic accuracy, or they employ protocols that substantially lengthen the refinement time, potentially hindering rapid automated refinement workflows.PHENIX–AFITTrefinement uses a full molecular-mechanics force field for user-selected small-molecule ligands during refinement, eliminating the potentiallymore » difficult problem of finding or generating high-quality geometry restraints. It is fully integrated with a standard refinement protocol and requires practically no additional steps from the user, making it ideal for high-throughput workflows.PHENIX–AFITTrefinements also handle multiple ligands in a single model, alternate conformations and covalently bound ligands. Here, the results of combiningAFITTand thePHENIXsoftware suite on a data set of 189 protein–ligand PDB structures are presented. Refinements usingPHENIX–AFITTsignificantly reduce ligand conformational energy and lead to improved geometries without detriment to the fit to the experimental data. Finally, for the data presented,PHENIX–AFITTrefinements result in more chemically accurate models for small-molecule ligands.« less

Neutron and X-ray powder diffraction study of skutterudite thermoelectrics

DOE PAGES

Wang, H.; Kirkham, M. J.; Watkins, T. R.; ...

2016-02-17

N- and p-type filled-skutterudite materials prepared for thermoelectric power generation modules were analyzed by neutron diffraction at the POWGEN beam line of the Spallation Neutron Source (SNS) and X-ray diffraction (XRD). The skutterudite powders were processed by melt spinning, followed by ball milling and annealing. The n-type material consists of Ba–Yb–Co–Sb and the p-type material consists of Di–Fe–Ni–Sb or Di–Fe–Co–Sb (Di = didymium, an alloy of Pr and Nd). Powders for prototype module fabrication from General Motors and Marlow Industries were analyzed in this study. XRD and neutron diffraction studies confirm that both the n- and p-type materials have cubicmore » symmetry. Structural Rietveld refinements determined the lattice parameters and atomic parameters of the framework and filler atoms. The cage filling fraction was found to depend linearly on the lattice parameter, which in turn depends on the average framework atom size. Ultimately, this knowledge may allow the filling fraction of these skutterudite materials to be purposefully adjusted, thereby tuning the thermoelectric properties.« less

Testing atomic mass models with radioactive beams

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

Haustein, P.E.

1989-01-01

Significantly increased yields of new or poorly characterized exotic isotopes that lie far from beta-decay stability can be expected when radioactive beams are used to produce these nuclides. Measurements of the masses of these new species are very important. Such measurements are motivated by the general tendency of mass models to diverge from one another upon excursions from the line of beta-stability. Therefore in these regions (where atomic mass data are presently nonexistent or sparse) the models can be tested rigorously to highlight the features that affect the quality of their short-range and long-range extrapolation properties. Selection of systems tomore » study can be guided, in part, by a desire to probe those mass regions where distinctions among mass models are most apparent and where yields of exotic isotopes, produced via radioactive beams, can be optimized. Identification of models in such regions that have good predictive properties will aid materially in guiding the selection of additional experiments which ultimately will provide expansion of the atomic mass database for further refinement of the mass models. 6 refs., 5 figs.« less

Rapid model building of beta-sheets in electron-density maps.

PubMed

Terwilliger, Thomas C

2010-03-01

A method for rapidly building beta-sheets into electron-density maps is presented. beta-Strands are identified as tubes of high density adjacent to and nearly parallel to other tubes of density. The alignment and direction of each strand are identified from the pattern of high density corresponding to carbonyl and C(beta) atoms along the strand averaged over all repeats present in the strand. The beta-strands obtained are then assembled into a single atomic model of the beta-sheet regions. The method was tested on a set of 42 experimental electron-density maps at resolutions ranging from 1.5 to 3.8 A. The beta-sheet regions were nearly completely built in all but two cases, the exceptions being one structure at 2.5 A resolution in which a third of the residues in beta-sheets were built and a structure at 3.8 A in which under 10% were built. The overall average r.m.s.d. of main-chain atoms in the residues built using this method compared with refined models of the structures was 1.5 A.

First-Principles Study of Carbon and Vacancy Structures in Niobium

DOE PAGES

Ford, Denise C.; Zapol, Peter; Cooley, Lance D.

2015-04-03

The interstitial chemical impurities hydrogen, oxygen, nitrogen, and carbon are important for niobium metal production, and particularly for the optimization of niobium SRF technology. These atoms are present in refined sheets and can be absorbed into niobium during processing treatments, resulting in changes to the residual resistance and the performance of SRF cavities. A first-principles approach is taken to study the properties of carbon in niobium, and the results are compared and contrasted with the properties of the other interstitial impurities. The results indicate that C will likely form precipitates or atmospheres around defects rather than strongly bound complexes withmore » other impurities. Based on the analysis of carbon and hydrogen near niobium lattice vacancies and small vacancy chains and clusters, the formation of extended carbon chains and hydrocarbons is not likely to occur. Association of carbon with hydrogen atoms can, however, occur through the strain fields created by interstitial binding of the impurity atoms. In conclusion, calculated electronic densities of states indicate that interstitial C may have a similar effect as interstitial O on the superconducting transition temperature of Nb.« less

The Quasicontinuum Method: Overview, applications and current directions

NASA Astrophysics Data System (ADS)

Miller, Ronald E.; Tadmor, E. B.

2002-10-01

The Quasicontinuum (QC) Method, originally conceived and developed by Tadmor, Ortiz and Phillips [1] in 1996, has since seen a great deal of development and application by a number of researchers. The idea of the method is a relatively simple one. With the goal of modeling an atomistic system without explicitly treating every atom in the problem, the QC provides a framework whereby degrees of freedom are judiciously eliminated and force/energy calculations are expedited. This is combined with adaptive model refinement to ensure that full atomistic detail is retained in regions of the problem where it is required while continuum assumptions reduce the computational demand elsewhere. This article provides a review of the method, from its original motivations and formulation to recent improvements and developments. A summary of the important mechanics of materials results that have been obtained using the QC approach is presented. Finally, several related modeling techniques from the literature are briefly discussed. As an accompaniment to this paper, a website designed to serve as a clearinghouse for information on the QC method has been established at www.qcmethod.com. The site includes information on QC research, links to researchers, downloadable QC code and documentation.

Fully Flexible Docking of Medium Sized Ligand Libraries with RosettaLigand

PubMed Central

DeLuca, Samuel; Khar, Karen; Meiler, Jens

2015-01-01

RosettaLigand has been successfully used to predict binding poses in protein-small molecule complexes. However, the RosettaLigand docking protocol is comparatively slow in identifying an initial starting pose for the small molecule (ligand) making it unfeasible for use in virtual High Throughput Screening (vHTS). To overcome this limitation, we developed a new sampling approach for placing the ligand in the protein binding site during the initial ‘low-resolution’ docking step. It combines the translational and rotational adjustments to the ligand pose in a single transformation step. The new algorithm is both more accurate and more time-efficient. The docking success rate is improved by 10–15% in a benchmark set of 43 protein/ligand complexes, reducing the number of models that typically need to be generated from 1000 to 150. The average time to generate a model is reduced from 50 seconds to 10 seconds. As a result we observe an effective 30-fold speed increase, making RosettaLigand appropriate for docking medium sized ligand libraries. We demonstrate that this improved initial placement of the ligand is critical for successful prediction of an accurate binding position in the ‘high-resolution’ full atom refinement step. PMID:26207742

Radiative, nonradiative, and mixed-decay transitions of rare-earth ions in dielectric media

NASA Astrophysics Data System (ADS)

Burshtein, Zeev

2010-09-01

We present and discuss in a comprehensive, deductive, and simplified manner, issues of nonradiative transitions involvement in fluorescence of ions embedded in dielectric solid matrices. The semiclassical approach is favored over a full quantum description, and empiric quantities are introduced from the start. One issue is nonradiative single-phonon transitions when the energy gap between the adjacent electronic ion states is smaller than the cutoff matrix phonon energy. Another issue is transitions in a complex energy scheme, where some visible and near-visible transitions are radiative and others are nonradiative. A refined Füchtbauer-Ladenburg recipe for calculation of the stimulated emission spectrum on the basis of measurable absorption and fluorescence emission spectra is worked out. The last issue is multiphonon nonradiative transitions occurring when the energy gap between adjacent electronic ion states is larger than the cutoff matrix phonon energy. Transition probabilities were calculated on the basis of anharmonicity of the effective potential supporting the internal atomic basis vibrations. An expression in a closed form is obtained, similar to the empiric ``energy gap'' law, however, with parameters related to specific host material properties and the actual transition in the ion. Comparison to existing experimental evidence is presented and discussed in detail.

A detailed experimental and theoretical study of two novel substituted trifluoromethylchromones. The influence of the bulky bromine atom on the crystal packing.

PubMed

Alcívar León, C D; Echeverría, G A; Piro, O E; Ulic, S E; Jios, J L

2015-02-05

The new 3-methyl-2-trifluoromethylchromone (1) and 3-bromomethyl-2-trifluoromethylchromone (2) compounds were synthesized and characterized by vibrational (IR, Raman), UV-Vis and NMR ((1)H, (13)C and (19)F) spectroscopy and MS spectrometry. The crystal structures of 1 and 2 were determined by X-ray diffraction methods. Both compounds crystallize in the monoclinic P21/c space group with Z=4 molecules per unit cell. The structures were solved from 1423 (1) and 1856 (2) reflections with I>2σ (I) and refined by full-matrix least-squares to agreement R1-values of 0.0403 (1) and 0.0554 (2). Because of π-bonding delocalization, the organic molecular skeletons are planar and the molecular bonding structures can be described by formally single, double and resonant bonds. In 2, the CF3 group revealed a strong rotational disorder around the CCF3 bond, which could be explained in terms of four split positions with about uniform angular distribution. The vibrational, electronic and NMR, spectra were discussed and assigned with the assistance of DFT calculations. Copyright © 2014 Elsevier B.V. All rights reserved.

Crystal structure of [(1,2,3,4,11,12-η)-anthracene]tris­(tri­methyl­stann­yl)cobalt(III)

PubMed Central

Brennessel, William W.; Ellis, John E.

2014-01-01

The asymmetric unit of the title structure, [Co(η6-C14H10){Sn(CH3)3}3], contains two independent mol­ecules. Each anthracene ligand is η6-coordinating to a CoIII cation and is nearly planar [fold angles of 5.4 (3) and 9.7 (3)°], as would be expected for its behaving almost entirely as a donor to a high-oxidation-state metal center. The slight fold in each anthracene ligand gives rise to slightly longer Co—C bond lengths to the ring junction carbon atoms than to the other four. Each CoIII cation is further coordinated by three Sn(CH3)3 ligands, giving each mol­ecule a three-legged piano-stool geometry. In each of the two independent mol­ecules, the trio of SnMe3 ligands are modeled as disordered over two positions, rotated by approximately 30%, such that the C atoms nearly overlap. In one mol­ecule, the disorder ratio refined to 0.9365 (8):0.0635 (8), while that for the other refined to 0.9686 (8):0.0314 (8). The mol­ecules are well separated, and thus no significant inter­molecular inter­actions are observed. The compound is of inter­est as the first structure report of an η6-anthracene cobalt(III) complex. PMID:25484731

Crystallization and X-ray data analysis of the 10 kDa C-terminal lid subdomain from Caenorhabditis elegans Hsp70

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

Worrall, Liam; Walkinshaw, Malcolm D., E-mail: m.walkinshaw@ed.ac.uk

Crystals of the C-terminal 10 kDa lid subdomain from the C. elegans chaperone Hsp70 have been obtained that diffract X-rays to ∼3.5 Å and belong to space group I2{sub 1}2{sub 1}2{sub 1}. Analysis of X-ray data and initial heavy-atom phasing reveals 24 monomers in the asymmetric unit related by 432 non-crystallographic symmetry. Hsp70 is an important molecular chaperone involved in the regulation of protein folding. Crystals of the C-terminal 10 kDa helical lid domain (residues 542–640) from a Caenorhabditis elegans Hsp70 homologue have been produced that diffract X-rays to ∼3.4 Å. Crystals belong to space group I2{sub 1}2{sub 1}2{sub 1},more » with unit-cell parameters a = b = 197, c = 200 Å. The Matthews coefficient, self-rotation function and Patterson map indicate 24 monomers in the asymmetric unit, showing non-crystallographic 432 symmetry. Molecular-replacement studies using the corresponding domain from rat, the only eukaryotic homologue with a known structure, failed and a mercury derivative was obtained. Preliminary MAD phasing using SHELXD and SHARP for location and refinement of the heavy-atom substructure and SOLOMON for density modification produced interpretable maps with a clear protein–solvent boundary. Further density-modification, model-building and refinement are currently under way.« less

Structure determination of Ba5AlF13 by coupling electron, synchrotron and neutron powder diffraction, solid-state NMR and ab initio calculations.

PubMed

Martineau, Charlotte; Allix, Mathieu; Suchomel, Matthew R; Porcher, Florence; Vivet, François; Legein, Christophe; Body, Monique; Massiot, Dominique; Taulelle, Francis; Fayon, Franck

2016-10-04

The room temperature structure of Ba 5 AlF 13 has been investigated by coupling electron, synchrotron and neutron powder diffraction, solid-state high-resolution NMR ( 19 F and 27 Al) and first principles calculations. An initial structural model has been obtained from electron and synchrotron powder diffraction data, and its main features have been confirmed by one- and two-dimensional NMR measurements. However, DFT GIPAW calculations of the 19 F isotropic shieldings revealed an inaccurate location of one fluorine site (F3, site 8a), which exhibited unusual long F-Ba distances. The atomic arrangement was reinvestigated using neutron powder diffraction data. Subsequent Fourier maps showed that this fluorine atom occupies a crystallographic site of lower symmetry (32e) with partial occupancy (25%). GIPAW computations of the NMR parameters validate the refined structural model, ruling out the presence of local static disorder and indicating that the partial occupancy of this F site reflects a local motional process. Visualisation of the dynamic process was then obtained from the Rietveld refinement of neutron diffraction data using an anharmonic description of the displacement parameters to account for the thermal motion of the mobile fluorine. The whole ensemble of powder diffraction and NMR data, coupled with first principles calculations, allowed drawing an accurate structural model of Ba 5 AlF 13 , including site-specific dynamical disorder in the fluorine sub-network.

Could incommensurability in sulfosalts be more common than thought? The case of meneghinite, CuPb13Sb7S24.

PubMed

Bindi, Luca; Petříček, Václav; Biagioni, Cristian; Plášil, Jakub; Moëlo, Yves

2017-06-01

The structure of meneghinite (CuPb 13 Sb 7 S 24 ), from the Bottino mine in the Apuan Alps (Italy), has been solved and refined as an incommensurate structure in four-dimensional superspace. The structure is orthorhombic, superspace group Pnma(0β0)00s, cell parameters a = 24.0549 (3), b = 4.1291 (6), c = 11.3361 (16) Å, modulation vector q = 0.5433 (4)b*. The structure was refined from 6604 reflections to a final R = 0.0479. The model includes modulation of both atomic positions and displacement parameters, as well as occupational waves. The driving forces stabilizing the modulated structure of meneghinite are linked to the occupation modulation of Cu and some of the Pb atoms. As a consequence of the Cu/[] and Pb/Sb modulations, three- to sevenfold coordinations of the M cations (Pb/Sb) occur in different parts of the structure. The almost bimodal distribution of the occupation of Cu/[] and Pb/Sb at M5 conforms with the coupled substitution Sb 3+ + [] → Pb 2+ + Cu + , thus corroborating the hypothesis deduced previously for the incorporation of copper in the meneghinite structure. The very small departure (∼0.54 versus 0.50) from the commensurate value of the modulation raises the question of whether other sulfosalts considered superstructures have been properly described, and, in this light, if incommensurate modulation in sulfosalts could be much more common than thought.

Boundaries of intergrowths between mineral individuals: A zone of secondary mineral formation in aggregates

NASA Astrophysics Data System (ADS)

Brodskaya, R. L.; Bil'Skaya, I. V.; Lyakhnitskaya, V. D.; Markovsky, B. A.; Sidorov, E. G.

2007-12-01

Intergrowth boundaries between mineral individuals in dunite of the Gal’moenan massif in Koryakia was studied in terms of crystal morphology, crystal optics, and ontogenesis. The results obtained allowed us to trace the staged formation of olivine and chromite and four generations of these minerals. Micro-and nanotopography of boundary surfaces between intergrown mineral individuals of different generations was examined with optic, electron, and atomic force microscopes. The boundaries between mineral individuals of different generations are distinguished by their microsculpture for both olivine and chromite grains. Both minerals demonstrate a compositional trend toward refinement from older to younger generations. The decrease in the iron mole fraction in olivine and chromite is accompanied by the crystallization of magnetite along weakened zones in olivine of the first generation and as outer rims around the chromite grains of the second generation observable under optic and electronic microscopes. The subsequent refinement of chromite results in the release of PGE from its lattice, as established by atomic power microscopy. The newly formed PGM are localized at the boundaries between mineral individuals and, thus, mark a special stage in the ontogenetic evolution of mineral aggregates. Further recrystallization is expressed in the spatial redistribution of grain boundaries and the formation of monomineralic intergrowth boundaries, i.e., the glomerogranular structure of rock and substructures of PGM, chromite, and olivine grains as intermediate types of organization of the granular assemblies in the form of reticulate, chain, and cellular structures and substructures of aggregates.

Structure cristalline du composé Hg3-xSbx(S+Se)2+xI2-x (x ≃ 0.1)

PubMed Central

Kars, Mohammed; Herrero, Adrian Gómez; Roisnel, Thierry; Rebbah, Allaoua; Otero-Diáz, L. Carlos

2016-01-01

Single crystals of the mercury chalcohalide Hg3-xSbx(S+Se)2+xI2-x (x ≃ 0.1) (mercury anti­mony sulfide selenide iodide), were grown by a chemical transport reaction. The structure contains three independent A (Hg/Sb) atoms; each atom is strongly covalently bonded with two X (Se/S) atoms to form approximately linear X–A–X units. The X–A–X units link to form A 4 X 4 rings, which are combined into infinite crankshaft-type bands running along the [100] direction. Four equatorial E (I/X = Se,S) atoms at relatively long distances complete the distorted octa­hedral coordination of A (Hg/Sb). The crystal under investigation was twinned by non-merohedry with a refined twin domain fraction of 0.814 (6):0.186 (6). The structure is isotypic with Hg3Se2I2 [Beck & Hedderich (2000 ▸). J. Solid State Chem. 151, 73–76], but the current determination reveals a coupled substitution, with partial replacement of Hg+2 by Sb+3, balanced by the equivalent substitution of I−1 by S−2 and Se−2. Bond-valence calculations are consistent with this relative substitution model. PMID:27006793

Structure and conformation of N-(2-methyl-5-chlorophenyl)salicylaldimine

NASA Astrophysics Data System (ADS)

Elmali, A.; Elerman, Y.

1998-02-01

N-(2-methyl-5-chlorophenyl)salicylaldimine (C 14H 12ClNO) has been studied by X-ray analysis and AM1 molecular orbital methods. It crystallises in the orthorhombic space group P2 12 12 1 with a = 7.474(1) Å, b = 12.155(1) Å, c = 13.378(1) Å, V = 1215.3(2) Å3, Z = 4, Dc = 1.343 g cm -3 and μ(Mo Kα) = 0.296 mm -1. The structure was solved by direct methods and refined to R = 0.0374 for 1689 reflections [ I > 2 σ( I)]. The title compound is photochromic and the molecule is not planar. There is a strong intramolecular hydrogen bond of distance 2.604(3) Å between the hydroxyl oxygen atom and imine nitrogen atom, the hydrogen atom essentially being bonded to the oxygen atom. Minimum energy conformations from AM1 were calculated as a function of the three torsion angles θ1(C8N1C7C6), θ2(C9C8N1C7) and θ3(N1C7C6C5), varied every 10°. The optimised geometry of the crystal structure corresponding to a non-planar conformation is the most stable conformation in all calculations.

Matrix Methods for Solving Hartree-Fock Equations in Atomic Structure Calculations and Line Broadening

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

Gomez, Thomas; Nagayama, Taisuke; Fontes, Chris

Atomic structure of N-electron atoms is often determined by solving the Hartree-Fock equations, which are a set of integro-differential equations. The integral part of the Hartree-Fock equations treats electron exchange, but the Hartree-Fock equations are not often treated as an integro-differential equation. The exchange term is often approximated as an inhomogeneous or an effective potential so that the Hartree-Fock equations become a set of ordinary differential equations (which can be solved using the usual shooting methods). Because the Hartree-Fock equations are an iterative-refinement method, the inhomogeneous term relies on the previous guess of the wavefunction. In addition, there are numericalmore » complications associated with solving inhomogeneous differential equations. This work uses matrix methods to solve the Hartree-Fock equations as an integro-differential equation. It is well known that a derivative operator can be expressed as a matrix made of finite-difference coefficients; energy eigenvalues and eigenvectors can be obtained by using linear-algebra packages. The integral (exchange) part of the Hartree-Fock equation can be approximated as a sum and written as a matrix. The Hartree-Fock equations can be solved as a matrix that is the sum of the differential and integral matrices. We compare calculations using this method against experiment and standard atomic structure calculations. This matrix method can also be used to solve for free-electron wavefunctions, thus improving how the atoms and free electrons interact. Here, this technique is important for spectral line broadening in two ways: it improves the atomic structure calculations, and it improves the motion of the plasma electrons that collide with the atom.« less

Matrix Methods for Solving Hartree-Fock Equations in Atomic Structure Calculations and Line Broadening

DOE PAGES

Gomez, Thomas; Nagayama, Taisuke; Fontes, Chris; ...

2018-04-23

Atomic structure of N-electron atoms is often determined by solving the Hartree-Fock equations, which are a set of integro-differential equations. The integral part of the Hartree-Fock equations treats electron exchange, but the Hartree-Fock equations are not often treated as an integro-differential equation. The exchange term is often approximated as an inhomogeneous or an effective potential so that the Hartree-Fock equations become a set of ordinary differential equations (which can be solved using the usual shooting methods). Because the Hartree-Fock equations are an iterative-refinement method, the inhomogeneous term relies on the previous guess of the wavefunction. In addition, there are numericalmore » complications associated with solving inhomogeneous differential equations. This work uses matrix methods to solve the Hartree-Fock equations as an integro-differential equation. It is well known that a derivative operator can be expressed as a matrix made of finite-difference coefficients; energy eigenvalues and eigenvectors can be obtained by using linear-algebra packages. The integral (exchange) part of the Hartree-Fock equation can be approximated as a sum and written as a matrix. The Hartree-Fock equations can be solved as a matrix that is the sum of the differential and integral matrices. We compare calculations using this method against experiment and standard atomic structure calculations. This matrix method can also be used to solve for free-electron wavefunctions, thus improving how the atoms and free electrons interact. Here, this technique is important for spectral line broadening in two ways: it improves the atomic structure calculations, and it improves the motion of the plasma electrons that collide with the atom.« less

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

PubMed

van de Streek, Jacco; Neumann, Marcus A

2014-12-01

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

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

PubMed Central

van de Streek, Jacco; Neumann, Marcus A.

2014-01-01

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

Grain Refinement by Authigenic Inoculation Inherited from the Medium-Range Order Structure of Ni-Cr-W Superalloy

NASA Astrophysics Data System (ADS)

Gao, Zhongtang; Hu, Rui; Guo, Wei; Zhang, Chuanwei

2018-04-01

The combination of liquidus casting and thermal control solidification furnace was applied to obtain a fine-grained ingot. A rapid quenching method and x-ray diffraction measurement were used to investigate the effect of authigenic inoculation on grain refinement. The structure factor S(Q) of liquid Ni-Cr-W superalloy at 1400 °C (Liquidus temperature) and bright-field image of the microstructures quenched from 1400 °C have been measured by the high-temperature x-ray diffractometer and the transmission electron microscopy (TEM), respectively. The results show that a pre-peak exists on a S(Q) curve at the liquidus temperature. The clusters of atom in rapidly quenched microstructures obtained by isothermal heat treatment at 1400 °C were studied using TEM. Meanwhile, the effect of isothermal different temperatures on rapidly quenched microstructures was studied. The results also show that there are only the globular, equiaxed grains distributed in the solidification structure. These particles are inherited from the medium-range order structure, which is beneficial for grain refinement. The normalized work-hardening rate-strain curve indicates the work-hardening rate of fine grain is higher than that of conventional grain at the same temperature and the same deformation.

Grain Refinement by Authigenic Inoculation Inherited from the Medium-Range Order Structure of Ni-Cr-W Superalloy

NASA Astrophysics Data System (ADS)

Gao, Zhongtang; Hu, Rui; Guo, Wei; Zhang, Chuanwei

2018-05-01

The combination of liquidus casting and thermal control solidification furnace was applied to obtain a fine-grained ingot. A rapid quenching method and x-ray diffraction measurement were used to investigate the effect of authigenic inoculation on grain refinement. The structure factor S( Q) of liquid Ni -Cr-W superalloy at 1400 °C (Liquidus temperature) and bright-field image of the microstructures quenched from 1400 °C have been measured by the high-temperature x-ray diffractometer and the transmission electron microscopy (TEM), respectively. The results show that a pre-peak exists on a S( Q) curve at the liquidus temperature. The clusters of atom in rapidly quenched microstructures obtained by isothermal heat treatment at 1400 °C were studied using TEM. Meanwhile, the effect of isothermal different temperatures on rapidly quenched microstructures was studied. The results also show that there are only the globular, equiaxed grains distributed in the solidification structure. These particles are inherited from the medium-range order structure, which is beneficial for grain refinement. The normalized work-hardening rate-strain curve indicates the work-hardening rate of fine grain is higher than that of conventional grain at the same temperature and the same deformation.

Bayesian refinement of protein structures and ensembles against SAXS data using molecular dynamics

PubMed Central

Shevchuk, Roman; Hub, Jochen S.

2017-01-01

Small-angle X-ray scattering is an increasingly popular technique used to detect protein structures and ensembles in solution. However, the refinement of structures and ensembles against SAXS data is often ambiguous due to the low information content of SAXS data, unknown systematic errors, and unknown scattering contributions from the solvent. We offer a solution to such problems by combining Bayesian inference with all-atom molecular dynamics simulations and explicit-solvent SAXS calculations. The Bayesian formulation correctly weights the SAXS data versus prior physical knowledge, it quantifies the precision or ambiguity of fitted structures and ensembles, and it accounts for unknown systematic errors due to poor buffer matching. The method further provides a probabilistic criterion for identifying the number of states required to explain the SAXS data. The method is validated by refining ensembles of a periplasmic binding protein against calculated SAXS curves. Subsequently, we derive the solution ensembles of the eukaryotic chaperone heat shock protein 90 (Hsp90) against experimental SAXS data. We find that the SAXS data of the apo state of Hsp90 is compatible with a single wide-open conformation, whereas the SAXS data of Hsp90 bound to ATP or to an ATP-analogue strongly suggest heterogenous ensembles of a closed and a wide-open state. PMID:29045407

Improved the microstructures and properties of M3:2 high-speed steel by spray forming and niobium alloying

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

Lu, L.; Hou, L.G., E-mail: lghou@skl.ustb.edu.cn; Zhang, J.X.

The microstructures and properties of spray formed (SF) high-speed steels (HSSs) with or without niobium (Nb) addition were studied. Particular emphasis was placed on the effect of Nb on the solidification microstructures, decomposition of M{sub 2}C carbides, thermal stability and mechanical properties. The results show that spray forming can refine the cell size of eutectic carbides due to the rapid cooling effect during atomization. With Nb addition, further refinement of the eutectic carbides and primary austenite grains are obtained. Moreover, the Nb addition can accelerate the decomposition of M{sub 2}C carbides and increase the thermal stability of high-speed steel, andmore » also can improve the hardness and bending strength with slightly decrease the impact toughness. The high-speed steel made by spray forming and Nb alloying can give a better tool performance compared with powder metallurgy M3:2 and commercial AISI M2 high-speed steels. - Highlights: • Spray forming can effectively refine the microstructure of M3:2 steel. • Niobium accelerates the decomposition of M{sub 2}C carbides. • Niobium increases the hardness and bending strength of spray formed M3:2 steel. • Spray-formed niobium-containing M3:2 steel has the best tool performance.« less

Segmental Refinement: A Multigrid Technique for Data Locality

DOE PAGES

Adams, Mark F.; Brown, Jed; Knepley, Matt; ...

2016-08-04

In this paper, we investigate a domain decomposed multigrid technique, termed segmental refinement, for solving general nonlinear elliptic boundary value problems. We extend the method first proposed in 1994 by analytically and experimentally investigating its complexity. We confirm that communication of traditional parallel multigrid is eliminated on fine grids, with modest amounts of extra work and storage, while maintaining the asymptotic exactness of full multigrid. We observe an accuracy dependence on the segmental refinement subdomain size, which was not considered in the original analysis. Finally, we present a communication complexity analysis that quantifies the communication costs ameliorated by segmental refinementmore » and report performance results with up to 64K cores on a Cray XC30.« less

Constructing irregular surfaces to enclose macromolecular complexes for mesoscale modeling using the discrete surface charge optimization (DISCO) algorithm.

PubMed

Zhang, Qing; Beard, Daniel A; Schlick, Tamar

2003-12-01

Salt-mediated electrostatics interactions play an essential role in biomolecular structures and dynamics. Because macromolecular systems modeled at atomic resolution contain thousands of solute atoms, the electrostatic computations constitute an expensive part of the force and energy calculations. Implicit solvent models are one way to simplify the model and associated calculations, but they are generally used in combination with standard atomic models for the solute. To approximate electrostatics interactions in models on the polymer level (e.g., supercoiled DNA) that are simulated over long times (e.g., milliseconds) using Brownian dynamics, Beard and Schlick have developed the DiSCO (Discrete Surface Charge Optimization) algorithm. DiSCO represents a macromolecular complex by a few hundred discrete charges on a surface enclosing the system modeled by the Debye-Hückel (screened Coulombic) approximation to the Poisson-Boltzmann equation, and treats the salt solution as continuum solvation. DiSCO can represent the nucleosome core particle (>12,000 atoms), for example, by 353 discrete surface charges distributed on the surfaces of a large disk for the nucleosome core particle and a slender cylinder for the histone tail; the charges are optimized with respect to the Poisson-Boltzmann solution for the electric field, yielding a approximately 5.5% residual. Because regular surfaces enclosing macromolecules are not sufficiently general and may be suboptimal for certain systems, we develop a general method to construct irregular models tailored to the geometry of macromolecules. We also compare charge optimization based on both the electric field and electrostatic potential refinement. Results indicate that irregular surfaces can lead to a more accurate approximation (lower residuals), and the refinement in terms of the electric field is more robust. We also show that surface smoothing for irregular models is important, that the charge optimization (by the TNPACK minimizer) is efficient and does not depend on the initial assigned values, and that the residual is acceptable when the distance to the model surface is close to, or larger than, the Debye length. We illustrate applications of DiSCO's model-building procedure to chromatin folding and supercoiled DNA bound to Hin and Fis proteins. DiSCO is generally applicable to other interesting macromolecular systems for which mesoscale models are appropriate, to yield a resolution between the all-atom representative and the polymer level. Copyright 2003 Wiley Periodicals, Inc. J Comput Chem 24: 2063-2074, 2003

Reference Gauging System for a Small-Scale Liquid Hydrogen Tank

NASA Technical Reports Server (NTRS)

VanDresar, Neil T.; Siegwarth, James D.

2003-01-01

A system to accurately weigh the fluid contents of a small-scale liquid hydrogen test tank has been experimentally verified. It is intended for use as a reference or benchmark system when testing lowgravity liquid quantity gauging concepts in the terrestrial environment. The reference gauging system has shown a repeatable measurement accuracy of better than 0.5 percent of the full tank liquid weight. With further refinement, the system accuracy can be improved to within 0.10 percent of full scale. This report describes the weighing system design, calibration, and operational results. Suggestions are given for further refinement of the system. An example is given to illustrate additional sources of uncertainty when mass measurements are converted to volume equivalents. Specifications of the companion test tank and its multi-layer insulation system are provided.

Chloro-, methyl-, and (tetrahydroborato)tris((hexamethyldisilyl)amido)thorium(IV) and -uranium(IV). Crystal structure of (tetrahydroborato)tris((hexamethyldisilyl)amido)thorium(IV)

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

Turner, H.W.; Andersen, R.A.; Zalkin, A.

1979-05-01

Reaction of sodium (hexamethyldisilyl)amide with thorium tetrachloride or uranium tetrachloride yields chlorotris-((hexamethyldisilyl)amido)thorium(IV) or -uranium(IV), respectively. The chloroamides of thorium or uranium react with dimethylmagnesium or methyllithium yielding the methyl derivatives MeTh(N(SiMe/sub 3/)/sub 2/)/sub 3/ or MeU(N(SiMe/sub 3/)/sub 2/)/sub 3/, respectively. The chloro compounds yield BH/sub 4/M(N(SiMe/sub 3/)/sub 2/)/sub 3/ upon reaction with lithium tetrahydroborate, where M is thorium or uranium. Infrared spectra of the tetrahydroborate derivatives suggest that BH/sub 4/ is bonded in a tridentate fashion in both compounds, the metal atoms being six-coordinate. Single-crystal X-ray analysis of the thorium borohydride confirms the infrared result. The white BH/sub 4/Th(N(Si(CH/sub 3/))/submore » 2/)/sub 3/ crystals are rhombohedral with cell dimensions a/sub r/ = 11.137 A and ..cap alpha../sub r/ = 113.61/sup 0/; the triply primitive hexagonal cell has a/sub h/ = 18.640 (3) A c/sub h/ = 8.604 (1) A, V = 2489 A/sup 3/, Z = 3, and D/sub x/ = 1.40 g/cm/sup 3/, space group R3m. The structure was refined by full-matrix least squares to a conventional R factor of 0.031 for 1014 data. The Th atom is on a threefold axis 2.32 A from three nitrogen atoms and 2.61 A from the boron atom, a distance which represents a triple bridge bond between Th and B. The three (dimethylsilyl)amide ligands are disordered by a mirror plane parallel to the threefold axis. CH/sub 3/Th(N(Si(CH/sub 3/)/sub 3/)/sub 2/)/sub 3/ is isomorphous with BH/sub 4/Th(N(Si(CH/sub 3/)/sub 3/)/sub 2/)/sub 3/ with cell dimensions a/sub h/ = 18.68 (1) A and c/sub h/ = 8.537 (6) A. The diffraction data yielded integral'' = 12.16 +- 0.33 e for the imaginary scattering term for Th with Cu K..cap alpha.. radiation.« less

Phase transformation of Ca{sub 4}[Al{sub 6}O{sub 12}]SO{sub 4} and its disordered crystal structure at 1073 K

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

Kurokawa, Daisuke; R and D Center, Taiheiyo Cement Corporation, Chiba 285-8655; Takeda, Seiya

The phase transformation of Ca{sub 4}[Al{sub 6}O{sub 12}]SO{sub 4} and the crystal structure of its high-temperature phase were investigated by differential thermal analysis, temperature-dependent Raman spectroscopy and high-temperature X-ray powder diffraction (CuKα{sub 1}). We determined the starting temperature of the orthorhombic-to-cubic transformation during heating (=711 K) and that of the reverse transformation during cooling (=742 K). The thermal hysteresis was negative (=−31 K), suggesting the thermoelasticity of the transformation. The space group of the high temperature phase is I4{sup ¯}3m with the unit-cell dimensions of a=0.92426(2) nm and V=0.78955(2) nm{sup 3} (Z=2) at 1073 K. The initial structural model wasmore » derived by the direct methods and further refined by the Rietveld method. The final structural model showed the orientational disordering of SO{sub 4} tetrahedra. The maximum-entropy method-based pattern fitting method was used to confirm the validity of the split-atom model, in which conventional structure bias caused by assuming intensity partitioning was minimized. At around the transformation temperature during heating, the vibrational spectra, corresponding to the Raman-active SO{sub 4} internal stretching mode, showed the continuous and gradual change in the slope of full width at half maximum versus temperature curve. This strongly suggests that the orthorhombic-to-cubic phase transformation would be principally accompanied by the statistical disordering in orientation of the SO{sub 4} tetrahedra, without distinct dynamical reorientation. - Graphical abstract: (Left) Three-dimensional electron-density distributions of the SO{sub 4} tetrahedron with the split-atom model, and (right) a bird's eye view of electron densities on the plane parallel to (111). - Highlights: • Crystal structure of Ca{sub 4}[Al{sub 6}O{sub 12}]SO{sub 4} at 1073 K is determined by powder XRD. • The atom arrangements are represented by the split-atom model. • The MPF method is used to confirm the validity of the model. • The phase transition is accompanied by orientational disordering of SO{sub 4} tetrahedra.« less

On the error in the nucleus-centered multipolar expansion of molecular electron density and its topology: A direct-space computational study.

PubMed

Michael, J Robert; Koritsanszky, Tibor

2017-05-28

The convergence of nucleus-centered multipolar expansion of the quantum-chemical electron density (QC-ED), gradient, and Laplacian is investigated in terms of numerical radial functions derived by projecting stockholder atoms onto real spherical harmonics at each center. The partial sums of this exact one-center expansion are compared with the corresponding Hansen-Coppens pseudoatom (HC-PA) formalism [Hansen, N. K. and Coppens, P., "Testing aspherical atom refinements on small-molecule data sets," Acta Crystallogr., Sect. A 34, 909-921 (1978)] commonly utilized in experimental electron density studies. It is found that the latter model, due to its inadequate radial part, lacks pointwise convergence and fails to reproduce the local topology of the target QC-ED even at a high-order expansion. The significance of the quantitative agreement often found between HC-PA-based (quadrupolar-level) experimental and extended-basis QC-EDs can thus be challenged.

Key structure-activity relationships in the vanadium phosphorus oxide catalyst system

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

Thompson, M.R.; Ebner, J.R.

1990-04-01

The crystal structure of vanadyl pyrophosphate has been redetermined using single crystals obtained from a near solidified melt of a microcrystalline catalyst sample. Crystals that index as vanadyl pyrophosphate obtained from this melt are variable in color. Crystallographic refinement of the single crystal x-ray diffraction data indicates that structural differences among these materials can be described in terms of crystal defects associated with linear disorder of the vanadium atoms. The importance of the disorder is outlined in the context of its effect on the proposed surface topology parallel to (1,0,0). Models of the surface topology simply and intuitively account formore » the non-stoichometric surface atomic P/V ratio exhibited by selective catalysts of this phase. These models also point to the possible role of the excess phosphorus in providing site isolation of reactive centers at the surface. 33 refs., 7 figs.« less

Hydrogen Atomic Positions of O-H···O Hydrogen Bonds in Solution and in the Solid State: The Synergy of Quantum Chemical Calculations with ¹H-NMR Chemical Shifts and X-ray Diffraction Methods.

PubMed

Siskos, Michael G; Choudhary, M Iqbal; Gerothanassis, Ioannis P

2017-03-07

The exact knowledge of hydrogen atomic positions of O-H···O hydrogen bonds in solution and in the solid state has been a major challenge in structural and physical organic chemistry. The objective of this review article is to summarize recent developments in the refinement of labile hydrogen positions with the use of: (i) density functional theory (DFT) calculations after a structure has been determined by X-ray from single crystals or from powders; (ii) ¹H-NMR chemical shifts as constraints in DFT calculations, and (iii) use of root-mean-square deviation between experimentally determined and DFT calculated ¹H-NMR chemical shifts considering the great sensitivity of ¹H-NMR shielding to hydrogen bonding properties.

Sheet, ligament and droplet formation in swirling primary atomization

NASA Astrophysics Data System (ADS)

Shao, Changxiao; Luo, Kun; Chai, Min; Fan, Jianren

2018-04-01

We report direct numerical simulations of swirling liquid atomization to understand the physical mechanism underlying the sheet breakup of a non-turbulent liquid swirling jet which lacks in-depth investigation. The volume-of-fluid (VOF) method coupled with adapted mesh refinement (AMR) technique in GERRIS code is employed in the present simulation. The mechanisms of sheet, ligament and droplet formation are investigated. It is observed that the olive-shape sheet structure is similar to the experimental result qualitatively. The numerical results show that surface tension, pressure difference and swirling effect contribute to the contraction and extension of liquid sheet. The ligament formation is partially at the sheet rim or attributed to the extension of liquid hole. Especially, the movement of hairpin vortex exerts by an anti-radial direction force to the sheet surface and leads to the sheet thinness. In addition, droplet formation is attributed to breakup of ligament and central sheet.

Investigating students' mental models and knowledge construction of microscopic friction. II. Implications for curriculum design and development

NASA Astrophysics Data System (ADS)

Corpuz, Edgar D.; Rebello, N. Sanjay

2011-12-01

Our previous research showed that students’ mental models of friction at the atomic level are significantly influenced by their macroscopic ideas. For most students, friction is due to the meshing of bumps and valleys and rubbing of atoms. The aforementioned results motivated us to further investigate how students can be helped to improve their present models of microscopic friction. Teaching interviews were conducted to study the dynamics of their model construction as they interacted with the interviewer, the scaffolding activities, and/or with each other. In this paper, we present the different scaffolding activities and the variation in the ideas that students generated as they did the hands-on and minds-on scaffolding activities. Results imply that through a series of carefully designed scaffolding activities, it is possible to facilitate the refinement of students’ ideas of microscopic friction.

Single-crystal X-ray diffraction study of SrGeO3 high-pressure perovskite phase at 100 K

NASA Astrophysics Data System (ADS)

Nakatsuka, Akihiko; Arima, Hiroshi; Ohtaka, Osamu; Fujiwara, Keiko; Yoshiasa, Akira

2017-10-01

Single-crystal X-ray diffraction study of SrGeO3 perovskite (cubic; space group Pmɜ¯m) synthesized at 6 GPa and 1223 K was conducted at a low temperature of 100 K. The residual electron density revealed the presence of the bonding electron at the center of the Ge-O bond, in accordance with our previous conclusion that the Ge-O bond is strongly covalent. From comparison with our previous structure-refinement result at 296 K, the mean square displacement (MSD) of the O atom in the direction of the Ge-O bond is suggested to exhibit no significant temperature dependence, in contrast to that in the direction perpendicular to the bond. Thus, the strong covalency of the Ge-O bond can have a large influence on the temperature dependence of thermal vibration of the O atom.

Detection of boron, cobalt, and other weak interstellar lines toward Zeta Ophiuchi

NASA Technical Reports Server (NTRS)

Federman, S. R.; Sheffer, Y.; Lambert, D. L.; Gilliland, R. L.

1993-01-01

Numerous weak lines from interstellar atomic species toward Zeta Ophiuchi were observed with the Goddard High-Resolution Spectrograph. Of particular note are the first interstellar detection of cobalt and the detection of boron in this sight line. These measurements provide estimates for the amount of depletion for the two elements. Boron, a volatile, and cobalt, a refractory element, display the depletion pattern found by Savage et al. (1992). The abundance of phosphorus in the H II region associated with the star was obtained from a detection of P III. Additional weak lines from S I, C I, Ni II, and Cu II were detected for the first time; these lines provide the basis for refinements in oscillator strength and column density. Analysis of the neutral sulfur data indicates that the atomic gas is more widely distributed than the molecular material in the main component.

Crystal structure of (S)-sec-butyl­ammonium l-tartrate monohydrate

PubMed Central

Publicover, Ernlie A.; Kolwich, Jennifer; Stack, Darcie L.; Doué, Alyssa J.; Ylijoki, Kai E. O.

2017-01-01

The title hydrated mol­ecular salt, C4H12N+·C4H5O6 −·H2O, was prepared by deprotonation of enanti­opure l-tartaric acid with racemic sec-butyl­amine in water. Only one enanti­omer was observed crystallographically, resulting from the combination of (S)-sec-butyl­amine with l-tartaric acid. The sec-butyl­ammonium moiety is disordered over two conformations related by rotation around the CH–CH2 bond; the refined occupancy ratio is 0.68 (1):0.32 (1). In the crystal, mol­ecules are linked through a network of O—H⋯O and N—H⋯O hydrogen-bonding inter­actions, between the ammonium H atoms, the tartrate hy­droxy H atoms, and the inter­stitial water, forming a three-dimensional supra­molecular structure. PMID:28529783

On the error in the nucleus-centered multipolar expansion of molecular electron density and its topology: A direct-space computational study

NASA Astrophysics Data System (ADS)

Michael, J. Robert; Koritsanszky, Tibor

2017-05-01

The convergence of nucleus-centered multipolar expansion of the quantum-chemical electron density (QC-ED), gradient, and Laplacian is investigated in terms of numerical radial functions derived by projecting stockholder atoms onto real spherical harmonics at each center. The partial sums of this exact one-center expansion are compared with the corresponding Hansen-Coppens pseudoatom (HC-PA) formalism [Hansen, N. K. and Coppens, P., "Testing aspherical atom refinements on small-molecule data sets," Acta Crystallogr., Sect. A 34, 909-921 (1978)] commonly utilized in experimental electron density studies. It is found that the latter model, due to its inadequate radial part, lacks pointwise convergence and fails to reproduce the local topology of the target QC-ED even at a high-order expansion. The significance of the quantitative agreement often found between HC-PA-based (quadrupolar-level) experimental and extended-basis QC-EDs can thus be challenged.

Correlated high-resolution x-ray diffraction photoluminescence and atom probe tomography analysis of continuous and discontinuous In xGa 1-xN quantum wells

DOE PAGES

Ren, Xiaochen; Riley, James R.; Koleske, Daniel; ...

2015-07-14

In this study, atom probe tomography (APT) is used to characterize the influence of hydrogen dosing duringGaN barrier growth on the indium distribution of In xGa 1-xN quantum wells, and correlatedmicro-photoluminescence is used to measure changes in the emission spectrum and efficiency. We found that relative to the control growth, hydrogen dosing leads to a 50% increase in emission intensity arising from discontinuous quantum wells that are narrower, of lower indium content, and with more abrupt interfaces. Additionally, simulations of carrier distributions based on APT composition profiles indicate that the greater carrier confinement leads to an increased radiative recombination rate.more » Furthermore, APT analysis of quantum well profiles enables refinement of x-ray diffractionanalysis for more accurate nondestructive measurements of composition.« less

Single-particle cryo-EM using alignment by classification (ABC): the structure of Lumbricus terrestris haemoglobin

PubMed Central

Seer-Linnemayr, Charlotte; Ravelli, Raimond B. G.; Matadeen, Rishi; De Carlo, Sacha; Alewijnse, Bart; Portugal, Rodrigo V.; Pannu, Navraj S.; Schatz, Michael; van Heel, Marin

2017-01-01

Single-particle cryogenic electron microscopy (cryo-EM) can now yield near-atomic resolution structures of biological complexes. However, the reference-based alignment algorithms commonly used in cryo-EM suffer from reference bias, limiting their applicability (also known as the ‘Einstein from random noise’ problem). Low-dose cryo-EM therefore requires robust and objective approaches to reveal the structural information contained in the extremely noisy data, especially when dealing with small structures. A reference-free pipeline is presented for obtaining near-atomic resolution three-dimensional reconstructions from heterogeneous (‘four-dimensional’) cryo-EM data sets. The methodologies integrated in this pipeline include a posteriori camera correction, movie-based full-data-set contrast transfer function determination, movie-alignment algorithms, (Fourier-space) multivariate statistical data compression and unsupervised classification, ‘random-startup’ three-dimensional reconstructions, four-dimensional structural refinements and Fourier shell correlation criteria for evaluating anisotropic resolution. The procedures exclusively use information emerging from the data set itself, without external ‘starting models’. Euler-angle assignments are performed by angular reconstitution rather than by the inherently slower projection-matching approaches. The comprehensive ‘ABC-4D’ pipeline is based on the two-dimensional reference-free ‘alignment by classification’ (ABC) approach, where similar images in similar orientations are grouped by unsupervised classification. Some fundamental differences between X-ray crystallography versus single-particle cryo-EM data collection and data processing are discussed. The structure of the giant haemoglobin from Lumbricus terrestris at a global resolution of ∼3.8 Å is presented as an example of the use of the ABC-4D procedure. PMID:28989723

Smiles2Monomers: a link between chemical and biological structures for polymers.

PubMed

Dufresne, Yoann; Noé, Laurent; Leclère, Valérie; Pupin, Maude

2015-01-01

The monomeric composition of polymers is powerful for structure comparison and synthetic biology, among others. Many databases give access to the atomic structure of compounds but the monomeric structure of polymers is often lacking. We have designed a smart algorithm, implemented in the tool Smiles2Monomers (s2m), to infer efficiently and accurately the monomeric structure of a polymer from its chemical structure. Our strategy is divided into two steps: first, monomers are mapped on the atomic structure by an efficient subgraph-isomorphism algorithm ; second, the best tiling is computed so that non-overlapping monomers cover all the structure of the target polymer. The mapping is based on a Markovian index built by a dynamic programming algorithm. The index enables s2m to search quickly all the given monomers on a target polymer. After, a greedy algorithm combines the mapped monomers into a consistent monomeric structure. Finally, a local branch and cut algorithm refines the structure. We tested this method on two manually annotated databases of polymers and reconstructed the structures de novo with a sensitivity over 90 %. The average computation time per polymer is 2 s. s2m automatically creates de novo monomeric annotations for polymers, efficiently in terms of time computation and sensitivity. s2m allowed us to detect annotation errors in the tested databases and to easily find the accurate structures. So, s2m could be integrated into the curation process of databases of small compounds to verify the current entries and accelerate the annotation of new polymers. The full method can be downloaded or accessed via a website for peptide-like polymers at http://bioinfo.lifl.fr/norine/smiles2monomers.jsp.Graphical abstract:.

The crystal structure of calcite III

NASA Astrophysics Data System (ADS)

Smyth, Joseph R.; Ahrens, Thomas J.

The crystal structure of calcite III has been deduced from existing high pressure powder X-ray diffraction patterns, based on the assumption that it is a displacive modification of the calcite I structure. The structure is monoclinic with space group C2 and a Z of 6. There are two Ca and two C positions, and five O positions, and atom coordinates have been refined by distance-least-squares methods to give reasonable octahedral coordination for Ca and parallel, planar CO3 groups. Unit cell parameters refined from a published powder diffraction pattern at 4.1 GPa are: a = 8.746(8)Å b = 4.685(5)Å c = 8.275(8)Å and β= 94.4°. The structure has a calculated density of 2.949 Mg/m³ at 4.1 GPa which is less than that of aragonite at this pressure and consistent with early piston cylinder studies. This implies that calcite III is indeed a metastable intermediary between calcite I and aragonite.

A mass and momentum conserving unsplit semi-Lagrangian framework for simulating multiphase flows

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

Owkes, Mark, E-mail: mark.owkes@montana.edu; Desjardins, Olivier

In this work, we present a computational methodology for convection and advection that handles discontinuities with second order accuracy and maintains conservation to machine precision. This method can transport a variety of discontinuous quantities and is used in the context of an incompressible gas–liquid flow to transport the phase interface, momentum, and scalars. The proposed method provides a modification to the three-dimensional, unsplit, second-order semi-Lagrangian flux method of Owkes & Desjardins (JCP, 2014). The modification adds a refined grid that provides consistent fluxes of mass and momentum defined on a staggered grid and discrete conservation of mass and momentum, evenmore » for flows with large density ratios. Additionally, the refined grid doubles the resolution of the interface without significantly increasing the computational cost over previous non-conservative schemes. This is possible due to a novel partitioning of the semi-Lagrangian fluxes into a small number of simplices. The proposed scheme is tested using canonical verification tests, rising bubbles, and an atomizing liquid jet.« less

Enabling X-ray free electron laser crystallography for challenging biological systems from a limited number of crystals

DOE PAGES

Uervirojnangkoorn, Monarin; Zeldin, Oliver B.; Lyubimov, Artem Y.; ...

2015-03-17

There is considerable potential for X-ray free electron lasers (XFELs) to enable determination of macromolecular crystal structures that are difficult to solve using current synchrotron sources. Prior XFEL studies often involved the collection of thousands to millions of diffraction images, in part due to limitations of data processing methods. We implemented a data processing system based on classical post-refinement techniques, adapted to specific properties of XFEL diffraction data. When applied to XFEL data from three different proteins collected using various sample delivery systems and XFEL beam parameters, our method improved the quality of the diffraction data as well as themore » resulting refined atomic models and electron density maps. Moreover, the number of observations for a reflection necessary to assemble an accurate data set could be reduced to a few observations. In conclusion, these developments will help expand the applicability of XFEL crystallography to challenging biological systems, including cases where sample is limited.« less

Enabling X-ray free electron laser crystallography for challenging biological systems from a limited number of crystals

DOE PAGES

Uervirojnangkoorn, Monarin; Zeldin, Oliver B.; Lyubimov, Artem Y.; ...

2015-03-17

There is considerable potential for X-ray free electron lasers (XFELs) to enable determination of macromolecular crystal structures that are difficult to solve using current synchrotron sources. Prior XFEL studies often involved the collection of thousands to millions of diffraction images, in part due to limitations of data processing methods. We implemented a data processing system based on classical post-refinement techniques, adapted to specific properties of XFEL diffraction data. When applied to XFEL data from three different proteins collected using various sample delivery systems and XFEL beam parameters, our method improved the quality of the diffraction data as well as themore » resulting refined atomic models and electron density maps. Moreover, the number of observations for a reflection necessary to assemble an accurate data set could be reduced to a few observations. These developments will help expand the applicability of XFEL crystallography to challenging biological systems, including cases where sample is limited.« less

Enabling X-ray free electron laser crystallography for challenging biological systems from a limited number of crystals

PubMed Central

Uervirojnangkoorn, Monarin; Zeldin, Oliver B; Lyubimov, Artem Y; Hattne, Johan; Brewster, Aaron S; Sauter, Nicholas K; Brunger, Axel T; Weis, William I

2015-01-01

There is considerable potential for X-ray free electron lasers (XFELs) to enable determination of macromolecular crystal structures that are difficult to solve using current synchrotron sources. Prior XFEL studies often involved the collection of thousands to millions of diffraction images, in part due to limitations of data processing methods. We implemented a data processing system based on classical post-refinement techniques, adapted to specific properties of XFEL diffraction data. When applied to XFEL data from three different proteins collected using various sample delivery systems and XFEL beam parameters, our method improved the quality of the diffraction data as well as the resulting refined atomic models and electron density maps. Moreover, the number of observations for a reflection necessary to assemble an accurate data set could be reduced to a few observations. These developments will help expand the applicability of XFEL crystallography to challenging biological systems, including cases where sample is limited. DOI: http://dx.doi.org/10.7554/eLife.05421.001 PMID:25781634

On the Tetragonal Forms of KMo 4O 6

NASA Astrophysics Data System (ADS)

McCarroll, W. H.; Ramanujachary, K. V.; Greenblatt, M.; Marsh, Richard E.

1995-06-01

A reexamination of the X-ray diffraction data for the tetragonal form of KMo4O6 prepared by fused salt electrolysis leads to the conclusion that the crystal structure is better described by using space group P 4/mbm and not P4¯ as previously reported. However, refinement in the new space group does not result in any significant changes in the atomic arrangement. Possible reasons for the significant difference between the c lattice parameter of this form of KMo4O6 and that prepared at high pressures are also discussed.

Characterization of Arcjet Flows Using Laser-Induced Fluorescence

NASA Technical Reports Server (NTRS)

Bamford, Douglas J.; O'Keefe, Anthony; Babikian, Dikran S.; Stewart, David A.; Strawa, Anthony W.

1995-01-01

A sensor based on laser-induced fluorescence has been installed at the 20-MW NASA Ames Aerodynamic Heating Facility. The sensor has provided new, quantitative, real-time information about properties of the arcjet flow in the highly dissociated, partially ionized, nonequilibrium regime. Number densities of atomic oxygen, flow velocities, heavy particle translational temperatures, and collisional quenching rates have been measured. These results have been used to test and refine computational models of the arcjet flow. The calculated number densities, translational temperatures, and flow velocities are in moderately good agreement with experiment

Triclinic lysozyme at 0.65 angstrom resolution.

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

Wang, J.; Dauter, M.; Alkire, R.

The crystal structure of triclinic hen egg-white lysozyme (HEWL) has been refined against diffraction data extending to 0.65 {angstrom} resolution measured at 100 K using synchrotron radiation. Refinement with anisotropic displacement parameters and with the removal of stereochemical restraints for the well ordered parts of the structure converged with a conventional R factor of 8.39% and an R{sub free} of 9.52%. The use of full-matrix refinement provided an estimate of the variances in the derived parameters. In addition to the 129-residue protein, a total of 170 water molecules, nine nitrate ions, one acetate ion and three ethylene glycol molecules weremore » located in the electron-density map. Eight sections of the main chain and many side chains were modeled with alternate conformations. The occupancies of the water sites were refined and this step is meaningful when assessed by use of the free R factor. A detailed description and comparison of the structure are made with reference to the previously reported triclinic HEWL structures refined at 0.925 {angstrom} (at the low temperature of 120 K) and at 0.95 {angstrom} resolution (at room temperature).« less

Quantum spin dynamics with pairwise-tunable, long-range interactions

PubMed Central

Hung, C.-L.; González-Tudela, Alejandro; Cirac, J. Ignacio; Kimble, H. J.

2016-01-01

We present a platform for the simulation of quantum magnetism with full control of interactions between pairs of spins at arbitrary distances in 1D and 2D lattices. In our scheme, two internal atomic states represent a pseudospin for atoms trapped within a photonic crystal waveguide (PCW). With the atomic transition frequency aligned inside a band gap of the PCW, virtual photons mediate coherent spin–spin interactions between lattice sites. To obtain full control of interaction coefficients at arbitrary atom–atom separations, ground-state energy shifts are introduced as a function of distance across the PCW. In conjunction with auxiliary pump fields, spin-exchange versus atom–atom separation can be engineered with arbitrary magnitude and phase, and arranged to introduce nontrivial Berry phases in the spin lattice, thus opening new avenues for realizing topological spin models. We illustrate the broad applicability of our scheme by explicit construction for several well-known spin models. PMID:27496329

Enhanced Representation of Turbulent Flow Phenomena in Large-Eddy Simulations of the Atmospheric Boundary Layer using Grid Refinement with Pseudo-Spectral Numerics

NASA Astrophysics Data System (ADS)

Torkelson, G. Q.; Stoll, R., II

2017-12-01

Large Eddy Simulation (LES) is a tool commonly used to study the turbulent transport of momentum, heat, and moisture in the Atmospheric Boundary Layer (ABL). For a wide range of ABL LES applications, representing the full range of turbulent length scales in the flow field is a challenge. This is an acute problem in regions of the ABL with strong velocity or scalar gradients, which are typically poorly resolved by standard computational grids (e.g., near the ground surface, in the entrainment zone). Most efforts to address this problem have focused on advanced sub-grid scale (SGS) turbulence model development, or on the use of massive computational resources. While some work exists using embedded meshes, very little has been done on the use of grid refinement. Here, we explore the benefits of grid refinement in a pseudo-spectral LES numerical code. The code utilizes both uniform refinement of the grid in horizontal directions, and stretching of the grid in the vertical direction. Combining the two techniques allows us to refine areas of the flow while maintaining an acceptable grid aspect ratio. In tests that used only refinement of the vertical grid spacing, large grid aspect ratios were found to cause a significant unphysical spike in the stream-wise velocity variance near the ground surface. This was especially problematic in simulations of stably-stratified ABL flows. The use of advanced SGS models was not sufficient to alleviate this issue. The new refinement technique is evaluated using a series of idealized simulation test cases of neutrally and stably stratified ABLs. These test cases illustrate the ability of grid refinement to increase computational efficiency without loss in the representation of statistical features of the flow field.

An Examination of Job Satisfaction among Full-Time Faculty in a Selected Mississippi Community College

ERIC Educational Resources Information Center

Arnold, Dana Martin

2017-01-01

The purpose of this study was to survey the levels of job satisfaction among full-time faculty members at a selected Mississippi community college using the constructs of Herzberg's Motivation-Hygiene Theory as defined by Wood (1973). The researcher used Wood's 1976 refined Faculty Job Satisfaction/Dissatisfaction Scale to discover the…

Crystal chemistry and structure refinement of five hydrated calcium borates

USGS Publications Warehouse

Clark, J.R.; Appleman, D.E.; Christ, C.L.

1964-01-01

The crystal structures of the five known members of the series Ca2B6O11??xH2O (x = 1, 5, 5, 7, 9, and 13) have been refined by full-matrix least-squares techniques, yielding bond distances and angles with standard errors of less than 0??01 A?? and 0??5??, respectively. The results illustrate the crystal chemical principles that govern the structures of hydrated borate compounds. The importance of hydrogen bonding in the ferroelectric transition of colemanite is confirmed by more accurate proton assignments. ?? 1964.

77 FR 75833 - Airworthiness Directives; Airbus Airplanes

Federal Register 2010, 2011, 2012, 2013, 2014

2012-12-26

... accordance with Airbus SB A300-57-6053 (Mod. 10453). Therefore and pending completion of the full analysis using a refined Finite Element Model, EASA [European Aviation Safety Agency] issued AD 2009-0094 [which...

Stabilizing stored PuO2 with addition of metal impurities

NASA Astrophysics Data System (ADS)

Moten, Shafaq; Huda, Muhammad

Plutonium oxides is of widespread significance due its application in nuclear fuels, space missions, as well as the long-termed storage of plutonium from spent fuel and nuclear weapons. The processes to refine and store plutonium bring many other elements in contact with the plutonium metal and thereby affect the chemistry of the plutonium. Pure plutonium metal corrodes to an oxide in air with the most stable form of this oxide is stoichiometric plutonium dioxide, PuO2. Defects such as impurities and vacancies can form in the plutonium dioxide before, during and after the refining processes as well as during storage. An impurity defect manifests itself at the bottom of the conduction band and affects the band gap of the unit cell. Studying the interaction between transition metals and plutonium dioxide is critical for better, more efficient storage plans as well as gaining insights to provide a better response to potential threats of exposure to the environment. Our study explores the interaction of a few metals within the plutonium dioxide structure which have a likelihood of being exposed to the plutonium dioxide powder. Using Density Functional Theory, we calculated a substituted metal impurity in PuO2 supercell. We repeated the calculations with an additional oxygen vacancy. Our results reveal interesting volume contraction of PuO2 supercell when one plutonium atom is substituted with a metal atom. The authors acknowledge the Texas Computing Center (TACC) at The University of Texas at Austin and High Performance Computing (HPC) at The University of Texas at Arlington.

Full-dimensional quantum calculations of ground-state tunneling splitting of malonaldehyde using an accurate ab initio potential energy surface

NASA Astrophysics Data System (ADS)

Wang, Yimin; Braams, Bastiaan J.; Bowman, Joel M.; Carter, Stuart; Tew, David P.

2008-06-01

Quantum calculations of the ground vibrational state tunneling splitting of H-atom and D-atom transfer in malonaldehyde are performed on a full-dimensional ab initio potential energy surface (PES). The PES is a fit to 11 147 near basis-set-limit frozen-core CCSD(T) electronic energies. This surface properly describes the invariance of the potential with respect to all permutations of identical atoms. The saddle-point barrier for the H-atom transfer on the PES is 4.1 kcal/mol, in excellent agreement with the reported ab initio value. Model one-dimensional and ``exact'' full-dimensional calculations of the splitting for H- and D-atom transfer are done using this PES. The tunneling splittings in full dimensionality are calculated using the unbiased ``fixed-node'' diffusion Monte Carlo (DMC) method in Cartesian and saddle-point normal coordinates. The ground-state tunneling splitting is found to be 21.6 cm-1 in Cartesian coordinates and 22.6 cm-1 in normal coordinates, with an uncertainty of 2-3 cm-1. This splitting is also calculated based on a model which makes use of the exact single-well zero-point energy (ZPE) obtained with the MULTIMODE code and DMC ZPE and this calculation gives a tunneling splitting of 21-22 cm-1. The corresponding computed splittings for the D-atom transfer are 3.0, 3.1, and 2-3 cm-1. These calculated tunneling splittings agree with each other to within less than the standard uncertainties obtained with the DMC method used, which are between 2 and 3 cm-1, and agree well with the experimental values of 21.6 and 2.9 cm-1 for the H and D transfer, respectively.

Full-dimensional quantum calculations of ground-state tunneling splitting of malonaldehyde using an accurate ab initio potential energy surface.

PubMed

Wang, Yimin; Braams, Bastiaan J; Bowman, Joel M; Carter, Stuart; Tew, David P

2008-06-14

Quantum calculations of the ground vibrational state tunneling splitting of H-atom and D-atom transfer in malonaldehyde are performed on a full-dimensional ab initio potential energy surface (PES). The PES is a fit to 11 147 near basis-set-limit frozen-core CCSD(T) electronic energies. This surface properly describes the invariance of the potential with respect to all permutations of identical atoms. The saddle-point barrier for the H-atom transfer on the PES is 4.1 kcalmol, in excellent agreement with the reported ab initio value. Model one-dimensional and "exact" full-dimensional calculations of the splitting for H- and D-atom transfer are done using this PES. The tunneling splittings in full dimensionality are calculated using the unbiased "fixed-node" diffusion Monte Carlo (DMC) method in Cartesian and saddle-point normal coordinates. The ground-state tunneling splitting is found to be 21.6 cm(-1) in Cartesian coordinates and 22.6 cm(-1) in normal coordinates, with an uncertainty of 2-3 cm(-1). This splitting is also calculated based on a model which makes use of the exact single-well zero-point energy (ZPE) obtained with the MULTIMODE code and DMC ZPE and this calculation gives a tunneling splitting of 21-22 cm(-1). The corresponding computed splittings for the D-atom transfer are 3.0, 3.1, and 2-3 cm(-1). These calculated tunneling splittings agree with each other to within less than the standard uncertainties obtained with the DMC method used, which are between 2 and 3 cm(-1), and agree well with the experimental values of 21.6 and 2.9 cm(-1) for the H and D transfer, respectively.

Trichlorido(tetra­hydro­furan){(1,2,3,3a,7a-η)-1-[2-(1-trimethyl­silyl-1H-imidazol-2-yl-κN 3)-1-methyl­prop­yl]inden­yl}zirconium(IV)

PubMed Central

Guan, Shengzhou; Nie, Wanli; Borzov, Maxim V.

2011-01-01

The title compound, [ZrCl3(C19H25N2Si)(C4H8O)], was prepared from bis­(N,N-dimethyl­amido-κN)(2-{2-[(1,2,3,3a,7a-η)-inden­yl]-2-methyl­prop­yl}-1H-imidazolido-κN 1)zirconium(IV) [(C16H16N2)Zr(NMe2)] by reaction with excess Me3SiCl in tetra­hydro­furan (THF) at elevated temperature. The crystal studied contained a minor non-merohedral twin contaminant [6.3 (4)%] which was taken into account during the refinement. The coordination polyhedron of the ZrIV atom is a distorted octa­hedron [assuming that the five-membered ring of the indenyl group (Cp) occupies one coordination site], with the Cp group and a THF O atom at the apical positions and the three Cl and ligating N atoms at the equatorial positions. The Zr, Si and the methyl­ene C atoms deviate noticeably from the imidazole ring plane [by −0.197 (5), −0.207 (5) and 0.119 (6) Å, respectively]. The THF ligand adopts an envelope conformation. PMID:21754279

Vanadium K-edge XAS studies on the native and peroxo-forms of vanadium chloroperoxidase from Curvularia inaequalis.

PubMed

Renirie, Rokus; Charnock, John M; Garner, C David; Wever, Ron

2010-06-01

Vanadium K-edge X-ray Absorption Spectra have been recorded for the native and peroxo-forms of vanadium chloroperoxidase from Curvularia inaequalis at pH 6.0. The Extended X-ray Absorption Fine Structure (EXAFS) regions provide a refinement of previously reported crystallographic data; one short V=O bond (1.54A) is present in both forms. For the native enzyme, the vanadium is coordinated to two other oxygen atoms at 1.69A, another oxygen atom at 1.93A and the nitrogen of an imidazole group at 2.02A. In the peroxo-form, the vanadium is coordinated to two other oxygen atoms at 1.67A, another oxygen atom at 1.88A and the nitrogen of an imidazole group at 1.93A. When combined with the available crystallographic and kinetic data, a likely interpretation of the EXAFS distances is a side-on bound peroxide involving V-O bonds of 1.67 and 1.88A; thus, the latter oxygen would be 'activated' for transfer. The shorter V-N bond observed in the peroxo-form is in line with the previously reported stronger binding of the cofactor in this form of the enzyme. Reduction of the enzyme with dithionite has a clear influence on the spectrum, showing a change from vanadium(V) to vanadium(IV).

Conformation and structure of 3-methoxyphenyl-salicylaldimine

NASA Astrophysics Data System (ADS)

Elmali, A.; Kabak, M.; Elerman, Y.

1999-06-01

3-methoxyphenyl-salicylaldimine (C 14H 13NO 2) was studied by X-ray analysis and AM1 molecular orbital methods. It crystallises in the monoclinic space group P2 1/c with a=20.486(4) Å, b=4.7935(8) Å Å, c=12.310(5) Å, β=107.43(2)°, V=1153.3(6) Å 3, Z=4, D 0=1.309 g cm -3, Z=4, and μ(MoK α)=0.088 mm -1. The structure was solved by direct methods and refined to R=0.033 for 1635 reflections [ I<2(( I)]. The title molecule was nearly planar. There was a strong intramolecular hydrogen bond of distance 2.598(2) Å between the hydroxyl oxygen atom and imine nitrogen atom, the hydrogen atom essentially being bonded to the oxygen atom. Minimum energy conformations from AM1 were calculated as a function of the three torsion angles θ1(C8-N1-C7-C6), θ2(N1-C7-C6-C5), and θ3(C9-C8-N1-C7) varied every 10°. The theoretical calculations were carried out to compare with experimental results of the molecular conformations. The optimized geometry of the crystal structure corresponding to a non-planar conformation is the most stable conformation in all theoretical calculations.

An investigation into the role of metastable states on excited populations of weakly ionized argon plasmas, with applications for optical diagnostics

NASA Astrophysics Data System (ADS)

Arnold, Nicholas; Loch, Stuart; Ballance, Connor; Thomas, Ed

2017-10-01

Low temperature plasmas (Te < 10 eV) are ubiquitous in the medical, industrial, basic, and dusty plasma communities, and offer an opportunity for researchers to gain a better understanding of atomic processes in plasmas. Here, we report on a new atomic dataset for neutral and low charge states of argon, from which rate coefficients and cross-sections for the electron-impact excitation of neutral argon are determined. We benchmark by comparing with electron impact excitation cross-sections available in the literature, with very good agreement. We have used the Atomic Data and Analysis Structure (ADAS) code suite to calculate a level-resolved, generalized collisional-radiative (GCR) model for line emission in low temperature argon plasmas. By combining our theoretical model with experimental electron temperature, density, and spectral measurements from the Auburn Linear eXperiment for Instability Studies (ALEXIS), we have developed diagnostic techniques to measure metastable fraction, electron temperature, and electron density. In the future we hope to refine our methods, and extend our model to plasmas other than ALEXIS. Supported by the U.S. Department of Energy. Grant Number: DE-FG02-00ER54476.

Selenium doping NaCl-type superconductor: SnAs1-xSex (x=0-0.13)

NASA Astrophysics Data System (ADS)

He, Jianqiao; Zhang, Xian; Lai, Xiaofang; Huang, Fuqiang

2017-08-01

Selenium doped NaCl-type superconductor SnAs1-xSex (x=0-0.13) were made through solid state reaction. EDS results show that Se content increases with Se doping until over doped in SnAs0.9Se0.1 and SnAs0.87Se0.13 (around 2.7%). PXRD patterns confirmed the main phase of the six doped samples are SnAs. The cell parameters of doped SnAs were calculated using Rietveld refinements. Their cell parameters increase almost linearly with x until x reaches 13%. Single crystal diffraction measurement results show that there are no interstitial atom in doped SnAs. We conclude that Se atoms are substitutional atoms in SnAs. The superconducting onset temperatures (Tconset, under a magnetic field of 10 Oe) of SnAs increased from 3.8 K to 4.5 K by 10% Se doping. ρ-T curves of 1%, 5% and 10% Se doped samples show that all the three samples are metallic. Upper critical field Hc2(0) of 1%, 5% and 10% Se doped samples are 294 Oe, 649 Oe and 1011 Oe, respectively.

cis-(Acetato-κ2 O,O′)(5,5,7,12,12,14-hexa­methyl-1,4,8,11-tetra­aza­cyclo­tetra­decane-κ4 N,N′,N′′,N′′′)nickel(II) perchlorate monohydrate

PubMed Central

Roy, Tapashi G.; Palit, Debashis; Nath, Babul Chandra; Ng, Seik Weng; Tiekink, Edward R. T.

2012-01-01

The complete cation in the title hydrated mol­ecular salt, [Ni(CH3CO2)(C16H36N4)]ClO4·H2O, is generated by the application of crystallographic twofold symmetry; the perchlorate anion and water mol­ecule are each disordered around a twofold axis. The NiII atom exists within a cis-N4O2 donor set based on a strongly distorted octa­hedron and defined by the four N atoms of the macrocyclic ligand and two O atoms of a symmetrically coordinating acetate ligand. In the crystal, hydrogen bonding (water–acetate/perchlorate O—H⋯O and amine–perchlorate N—H⋯O) leads to layers in the ab plane. The layers stack along the c axis, being connected by C—H⋯O(water) inter­actions. The crystal studied was found to be a non-merohedral twin; the minor component refined to 15.9 (6)%. PMID:22589873

Quantifying accessible sites and reactivity on titania–silica (photo)catalysts: Refining TOF calculations

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

Eaton, Todd R.; Campos, Michael P.; Gray, Kimberly A.

2014-01-01

It can be difficult to determine the number of active atoms accessible to the fluid phase in mixed oxide catalysts, as required for obtaining true turnover frequencies (TOF). Here, we utilize the selective titration of surface Ti atoms with phenylphosphonic acid (PPA) on TiO 2–SiO 2 materials to estimate the number of reactant-accessible sites. TiO 2–SiO 2 composites were synthesized over a range of Ti loadings from grafting of titanocene dichloride (Cp 2TiCl 2) or tetraethoxy orthotitanate (TEOT) on SiO 2 and sol–gel co-hydrolysis of Si and Ti alkoxides. The materials were characterized by DRUV–vis, XRD, BET, and XANES. Despitemore » the significant morphological and electronic differences, materials prepared by Cp 2TiCl 2 and TEOT yielded a near-constant TOF of 0.14 h -1 (±0.04) across Ti loadings, for benzyl alcohol photooxidation, when normalizing rates by sites titrated by PPA. The fraction of Ti atoms titrated by PPA was strongly dependent on synthesis method and surface density. PPA titration and benzyl alcohol photooxidation may be useful measures of surface accessibility in other supported oxides.« less

The Atomic Bomb Casualty Commission in retrospect

PubMed Central

Putnam, Frank W.

1998-01-01

For 50 years, the Atomic Bomb Casualty Commission (ABCC) and its successor, the Radiation Effects Research Foundation (RERF), have conducted epidemiological and genetic studies of the survivors of the atomic bombs and of their children. This research program has provided the primary basis for radiation health standards. Both ABCC (1947–1975) and RERF (1975 to date) have been a joint enterprise of the United States (through the National Academy of Sciences) and of Japan. ABCC began in devastated, occupied Japan. Its mission had to be defined and refined. Early research revealed the urgent need for long term study. In 1946, a Directive of President Truman enjoined the National Research Council of the National Academy of Sciences to develop the program. By 1950, ABCC staff exceeded 1,000, and clinical and genetic studies were underway. Budgetary difficulties and other problems almost forced closure in 1953. In 1955, the Francis Report led to a unified epidemiological study. Much progress was made in the next decade, but changing times required founding of a binational nonprofit organization (RERF) with equal participation by Japan and the United States. New programs have been developed and existing ones have been extended in what is the longest continuing health survey ever undertaken. PMID:9576898

Ensemble modeling of very small ZnO nanoparticles.

PubMed

Niederdraenk, Franziska; Seufert, Knud; Stahl, Andreas; Bhalerao-Panajkar, Rohini S; Marathe, Sonali; Kulkarni, Sulabha K; Neder, Reinhard B; Kumpf, Christian

2011-01-14

The detailed structural characterization of nanoparticles is a very important issue since it enables a precise understanding of their electronic, optical and magnetic properties. Here we introduce a new method for modeling the structure of very small particles by means of powder X-ray diffraction. Using thioglycerol-capped ZnO nanoparticles with a diameter of less than 3 nm as an example we demonstrate that our ensemble modeling method is superior to standard XRD methods like, e.g., Rietveld refinement. Besides fundamental properties (size, anisotropic shape and atomic structure) more sophisticated properties like imperfections in the lattice, a size distribution as well as strain and relaxation effects in the particles and-in particular-at their surface (surface relaxation effects) can be obtained. Ensemble properties, i.e., distributions of the particle size and other properties, can also be investigated which makes this method superior to imaging techniques like (high resolution) transmission electron microscopy or atomic force microscopy, in particular for very small nanoparticles. For the particles under study an excellent agreement of calculated and experimental X-ray diffraction patterns could be obtained with an ensemble of anisotropic polyhedral particles of three dominant sizes, wurtzite structure and a significant relaxation of Zn atoms close to the surface.

Joint Sparse Recovery With Semisupervised MUSIC

NASA Astrophysics Data System (ADS)

Wen, Zaidao; Hou, Biao; Jiao, Licheng

2017-05-01

Discrete multiple signal classification (MUSIC) with its low computational cost and mild condition requirement becomes a significant noniterative algorithm for joint sparse recovery (JSR). However, it fails in rank defective problem caused by coherent or limited amount of multiple measurement vectors (MMVs). In this letter, we provide a novel sight to address this problem by interpreting JSR as a binary classification problem with respect to atoms. Meanwhile, MUSIC essentially constructs a supervised classifier based on the labeled MMVs so that its performance will heavily depend on the quality and quantity of these training samples. From this viewpoint, we develop a semisupervised MUSIC (SS-MUSIC) in the spirit of machine learning, which declares that the insufficient supervised information in the training samples can be compensated from those unlabeled atoms. Instead of constructing a classifier in a fully supervised manner, we iteratively refine a semisupervised classifier by exploiting the labeled MMVs and some reliable unlabeled atoms simultaneously. Through this way, the required conditions and iterations can be greatly relaxed and reduced. Numerical experimental results demonstrate that SS-MUSIC can achieve much better recovery performances than other MUSIC extended algorithms as well as some typical greedy algorithms for JSR in terms of iterations and recovery probability.

Effects of Al addition on atomic structure of Cu-Zr metallic glass

NASA Astrophysics Data System (ADS)

Li, Feng; Zhang, Huajian; Liu, Xiongjun; Dong, Yuecheng; Yu, Chunyan; Lu, Zhaoping

2018-02-01

The atomic structures of Cu52Zr48 and Cu45Zr48Al7 metallic glasses (MGs) have been studied by molecular dynamic simulations. The results reveal that the molar volume of the Cu45Zr48Al7 MG is smaller than that of the Cu52Zr48 MG, although the size of the Al atom is larger than that of the Cu atom, implying an enhanced atomic packing density achieved by introducing Al into the ternary MG. Bond shortening in unlike atomic pairs Zr-Al and Cu-Al is observed in the Cu45Zr48Al7 MG, which is attributed to strong interactions between Al and (Zr, Cu) atoms. Meanwhile, the atomic packing efficiency is enhanced by the minor addition of Al. Compared with the Cu52Zr48 binary MG, the potential energy of the ternary MG decreases and the glass transition temperature increases. Structural analyses indicate that more Cu- and Al-centered full icosahedral clusters emerge in the Cu45Zr48Al7 MG as some Cu atoms are substituted by Al. Furthermore, the addition of Al leads to more icosahedral medium-range orders in the ternary MG. The increase of full icosahedral clusters and the enhancement of the packing density are responsible for the improved glass-forming ability of Cu45Zr48Al7.

Surface Atomic Structure and Functionality of Metallic Nanoparticles: A Case Study of Au–Pd Nanoalloy Catalysts

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

Petkov, Valeri; Prasai, Binay; Shastri, Sarvjit

The surface atomic structure of metallic nanoparticles (NPs) plays a key role in shaping their physicochemical properties and response to external stimuli. Not surprisingly, current research increasingly focuses on exploiting its prime characteristics, including the amount, location, coordination, and electronic configuration of distinct surface atomic species, as tunable parameters for improving the functionality of metallic NPs in practical applications. The effort requires clear understanding of the extent to which changes in each of these characteristics would contribute to achieving the targeted functionality. This, in the first place, requires good knowledge of the actual surface of metallic NPs at atomic level.more » Through a case study on Au–Pd nanoalloy catalysts of industrial and environmental importance, we demonstrate that the surface atomic structure of metallic NPs can be determined in good detail by resonant high-energy X-ray diffraction (HE-XRD). Furthermore, using our experimental surface structure and CO oxidation activity data, we shed new light on the elusive origin of the remarkable catalytic synergy between surface Au and Pd atoms in the nanoalloys. In particular, we show that it arises from the formation of a specific “skin” on top of the nanoalloys that involves as many unlike, i.e., Au–Pd and Pd–Au, atomic pairs as possible given the overall chemical composition of the NPs. Moreover, unlike atoms from the “skin” interact strongly, including both changing their size and electronic structure in inverse proportions. That is, Au atoms shrink and acquire a partial positive charge of 5d-character whereas Pd atoms expand and become somewhat 4d-electron deficient. Accordingly, the reactivity of Au increases whereas Pd atoms become less reactive, as compared to atoms at the surface of pure Au and Pd NPs, respectively. Ultimately, this renders Au–Pd alloy NPs superb catalysts for CO oxidation reaction over a broad range of alloy compositions. Our findings are corroborated by DFT calculations based on a refined version of d-band center theory on the catalytic properties of late transition metals and alloys. Here, we discuss opportunities for improving the accuracy of current theory on surface-controlled properties of metallic NPs through augmenting the theory with surface structure data obtained by resonant XRD.« less

Surface Atomic Structure and Functionality of Metallic Nanoparticles: A Case Study of Au–Pd Nanoalloy Catalysts

DOE PAGES

Petkov, Valeri; Prasai, Binay; Shastri, Sarvjit; ...

2017-03-23

The surface atomic structure of metallic nanoparticles (NPs) plays a key role in shaping their physicochemical properties and response to external stimuli. Not surprisingly, current research increasingly focuses on exploiting its prime characteristics, including the amount, location, coordination, and electronic configuration of distinct surface atomic species, as tunable parameters for improving the functionality of metallic NPs in practical applications. The effort requires clear understanding of the extent to which changes in each of these characteristics would contribute to achieving the targeted functionality. This, in the first place, requires good knowledge of the actual surface of metallic NPs at atomic level.more » Through a case study on Au–Pd nanoalloy catalysts of industrial and environmental importance, we demonstrate that the surface atomic structure of metallic NPs can be determined in good detail by resonant high-energy X-ray diffraction (HE-XRD). Furthermore, using our experimental surface structure and CO oxidation activity data, we shed new light on the elusive origin of the remarkable catalytic synergy between surface Au and Pd atoms in the nanoalloys. In particular, we show that it arises from the formation of a specific “skin” on top of the nanoalloys that involves as many unlike, i.e., Au–Pd and Pd–Au, atomic pairs as possible given the overall chemical composition of the NPs. Moreover, unlike atoms from the “skin” interact strongly, including both changing their size and electronic structure in inverse proportions. That is, Au atoms shrink and acquire a partial positive charge of 5d-character whereas Pd atoms expand and become somewhat 4d-electron deficient. Accordingly, the reactivity of Au increases whereas Pd atoms become less reactive, as compared to atoms at the surface of pure Au and Pd NPs, respectively. Ultimately, this renders Au–Pd alloy NPs superb catalysts for CO oxidation reaction over a broad range of alloy compositions. Our findings are corroborated by DFT calculations based on a refined version of d-band center theory on the catalytic properties of late transition metals and alloys. Here, we discuss opportunities for improving the accuracy of current theory on surface-controlled properties of metallic NPs through augmenting the theory with surface structure data obtained by resonant XRD.« less

Comparative analysis of three-dimensional structures of homodimers of uridine phosphorylase from Salmonella typhimurium in the unligated state and in a complex with potassium ion

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

Lashkov, A. A.; Zhukhlistova, N. E.; Gabdulkhakov, A. G.

2009-03-15

The spatial organization of the homodimer of unligated uridine phosphorylase from Salmonella typhimurium (St UPh) was determined with high accuracy. The structure was refined at 1.80 A resolution to R{sub work} = 16.1% and R{sub free} = 20.0%. The rms deviations for the bond lengths, bond angles, and chiral angles are 0.006 A, 1.042{sup o}, and 0.071{sup o}, respectively. The coordinate error estimated by the Luzzati plot is 0.166 A. The coordinate error based on the maximum likelihood is 0.199 A. A comparative analysis of the spatial organization of the homodimer in two independently refined structures and the structure ofmore » the homodimer St UPh in the complex with a K{sup +} ion was performed. The substrate-binding sites in the homodimers StUPhs in the unligated state were found to act asynchronously. In the presence of a potassium ion, the three-dimensional structures of the subunits in the homodimer are virtually identical, which is apparently of importance for the synchronous action of both substrate-binding sites. The atomic coordinates of the refined structure of the homodimer and structure factors have been deposited in the Protein Data Bank (PDB ID code 3DPS).« less

Evaluating the quality of NMR structures by local density of protons.

PubMed

Ban, Yih-En Andrew; Rudolph, Johannes; Zhou, Pei; Edelsbrunner, Herbert

2006-03-01

Evaluating the quality of experimentally determined protein structural models is an essential step toward identifying potential errors and guiding further structural refinement. Herein, we report the use of proton local density as a sensitive measure to assess the quality of nuclear magnetic resonance (NMR) structures. Using 256 high-resolution crystal structures with protons added and optimized, we show that the local density of different proton types display distinct distributions. These distributions can be characterized by statistical moments and are used to establish local density Z-scores for evaluating both global and local packing for individual protons. Analysis of 546 crystal structures at various resolutions shows that the local density Z-scores increase as the structural resolution decreases and correlate well with the ClashScore (Word et al. J Mol Biol 1999;285(4):1711-1733) generated by all atom contact analysis. Local density Z-scores for NMR structures exhibit a significantly wider range of values than for X-ray structures and demonstrate a combination of potentially problematic inflation and compression. Water-refined NMR structures show improved packing quality. Our analysis of a high-quality structural ensemble of ubiquitin refined against order parameters shows proton density distributions that correlate nearly perfectly with our standards derived from crystal structures, further validating our approach. We present an automated analysis and visualization tool for proton packing to evaluate the quality of NMR structures. 2005 Wiley-Liss, Inc.

AMMOS2: a web server for protein-ligand-water complexes refinement via molecular mechanics.

PubMed

Labbé, Céline M; Pencheva, Tania; Jereva, Dessislava; Desvillechabrol, Dimitri; Becot, Jérôme; Villoutreix, Bruno O; Pajeva, Ilza; Miteva, Maria A

2017-07-03

AMMOS2 is an interactive web server for efficient computational refinement of protein-small organic molecule complexes. The AMMOS2 protocol employs atomic-level energy minimization of a large number of experimental or modeled protein-ligand complexes. The web server is based on the previously developed standalone software AMMOS (Automatic Molecular Mechanics Optimization for in silico Screening). AMMOS utilizes the physics-based force field AMMP sp4 and performs optimization of protein-ligand interactions at five levels of flexibility of the protein receptor. The new version 2 of AMMOS implemented in the AMMOS2 web server allows the users to include explicit water molecules and individual metal ions in the protein-ligand complexes during minimization. The web server provides comprehensive analysis of computed energies and interactive visualization of refined protein-ligand complexes. The ligands are ranked by the minimized binding energies allowing the users to perform additional analysis for drug discovery or chemical biology projects. The web server has been extensively tested on 21 diverse protein-ligand complexes. AMMOS2 minimization shows consistent improvement over the initial complex structures in terms of minimized protein-ligand binding energies and water positions optimization. The AMMOS2 web server is freely available without any registration requirement at the URL: http://drugmod.rpbs.univ-paris-diderot.fr/ammosHome.php. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

AMMOS2: a web server for protein–ligand–water complexes refinement via molecular mechanics

PubMed Central

Labbé, Céline M.; Pencheva, Tania; Jereva, Dessislava; Desvillechabrol, Dimitri; Becot, Jérôme; Villoutreix, Bruno O.; Pajeva, Ilza

2017-01-01

Abstract AMMOS2 is an interactive web server for efficient computational refinement of protein–small organic molecule complexes. The AMMOS2 protocol employs atomic-level energy minimization of a large number of experimental or modeled protein–ligand complexes. The web server is based on the previously developed standalone software AMMOS (Automatic Molecular Mechanics Optimization for in silico Screening). AMMOS utilizes the physics-based force field AMMP sp4 and performs optimization of protein–ligand interactions at five levels of flexibility of the protein receptor. The new version 2 of AMMOS implemented in the AMMOS2 web server allows the users to include explicit water molecules and individual metal ions in the protein–ligand complexes during minimization. The web server provides comprehensive analysis of computed energies and interactive visualization of refined protein–ligand complexes. The ligands are ranked by the minimized binding energies allowing the users to perform additional analysis for drug discovery or chemical biology projects. The web server has been extensively tested on 21 diverse protein–ligand complexes. AMMOS2 minimization shows consistent improvement over the initial complex structures in terms of minimized protein–ligand binding energies and water positions optimization. The AMMOS2 web server is freely available without any registration requirement at the URL: http://drugmod.rpbs.univ-paris-diderot.fr/ammosHome.php. PMID:28486703

Tropospheric Delay from VLBI and GNSS Measurements

NASA Astrophysics Data System (ADS)

Gubanov, V. S.

2018-02-01

Using an updated version of the QUASAR software package developed at the Institute of Applied Astronomy of the Russian Academy of Sciences, we have processed the VLBI observations within the international CONT14 program (May 6-20, 2014), in which a global network of 17 stations was involved (a total of 250 000 observations). The package update concerned the optimization of data structure and the refinement of stochastic models for the random variations in wet tropospheric delay and atomic clock difference. The main goal of this paper is to compare the VLBI determinations of the tropospheric delay with its independent determinations using global navigation satellite systems (GNSS). We show that both these determinations agree well between themselves only in the case of a global analysis of the VLBI observations, where the VLBI station coordinates are also refined, along with the tropospheric delay and the clock synchronization and Earth orientation parameters. If, alternatively, the station coordinates are insufficiently accurate and are not refined from VLBI observations, then it is appropriate not to determine the tropospheric delay from these observations, but to take it from the publicly accessible independent GNSS data. However, this requires that the VLBI and GNSS techniques operate simultaneously at a common observing site. We have established the shortcomings of the universally accepted method of stabilizing the global solution associated with the absence of a criterion for choosing reference stations and radio sources. Two ways of their elimination are proposed: (i) introducing a coordinated list of weight factors for the errors in the coordinates of such stations and sources into the stabilization algorithm and (ii) adopting a coordinated list of stations and sources the refinement of whose coordinates is not required at all for a certain time.

Density functional of a two-dimensional gas of dipolar atoms: Thomas-Fermi-Dirac treatment

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

Fang, Bess; Englert, Berthold-Georg

We derive the density functional for the ground-state energy of a two-dimensional, spin-polarized gas of neutral fermionic atoms with magnetic-dipole interaction, in the Thomas-Fermi-Dirac approximation. For many atoms in a harmonic trap, we give analytical solutions for the single-particle spatial density and the ground-state energy, in dependence on the interaction strength, and we discuss the weak-interaction limit that is relevant for experiments. We then lift the restriction of full spin polarization and account for a time-independent inhomogeneous external magnetic field. The field strength necessary to ensure full spin polarization is derived.

Chemical and structural characterization of boron carbide powders and ceramics

NASA Astrophysics Data System (ADS)

Kuwelkar, Kanak Anant

Boron carbide is the material of choice for lightweight armor applications due to its extreme hardness, high Young's modulus and low specific weight. The homogeneity range in boron carbide extends from 9 to 20 at% carbon with the solubility limits not uniquely defined in literature. Over the homogeneity range, the exact lattice positions of boron and carbon atoms have not been unambiguously established, and this topic has been the consideration of significant debate over the last 60 years. The atomic configuration and positions of the boron and carbon atoms play a key role in the crystal structure of the boron carbide phases. Depending on the atomic structure, boron carbide exhibits different mechanical properties which may alter its ballistic performance under extreme dynamic conditions. This work focusses on refinement and development of analytical and chemical methods for an accurate determination of the boron carbide stoichiometry. These methods were then utilized to link structural changes of boron carbide across the solubility range to variations in mechanical properties. After an extensive assessment of the currently employed characterization techniques, it was discerned that the largest source of uncertainty in the determination of the boron carbide stoichiometry was found to arise from the method utilized to evaluate the free carbon concentration. To this end, a modified spiking technique was introduced for free carbon determination where curve fitting techniques were employed to model the asymmetry of the 002 free carbon diffraction peak based on the amorphous, disordered and graphitic nature of carbon. A relationship was then established between the relative intensities of the carbon and boron carbide peaks to the percentage of added carbon and the free-carbon content was obtained by extrapolation. Samples with varying chemistry and high purity were synthesized across the solubility range by hot pressing mixtures of amorphous boron and boron carbide. Vibrational mode frequencies and lattice parameter measurements from Rietveld refinement were correlated to the respective B:C ratios calculated using the developed characterization techniques. An expansion of the unit cell and change in slope in the lattice parameter-stoichiometry relationship were observed at more boron rich stoichiometries. These observations were justified through the proposal of a simplified structural model considering preferential substitution of boron atoms for carbon atoms in the icosahedra from 20 at% to 13.3 at% carbon, followed by formation of B-B bonds from 13.3 at % C to 9 at% C. Hardness measurements uncovered decreased hardness values in boron rich boron carbide which was attributed to the formation of weaker unit cells. Load induced amorphization was also detected in all the indented materials. Finally, experimental observations have shown that failure in boron carbide may be governed by a mechanism other than amorphization and synthesizing boron carbide with a modified microstructure at stoichiometries close to B4C may be the way forward to attain improved ballistic performance.

Zinc-blende MnN bilayer formation on the GaN(111) surface

NASA Astrophysics Data System (ADS)

Gutierrez-Ojeda, S. J.; Guerrero-Sánchez, J.; Garcia-Diaz, R.; Ramirez-Torres, A.; Takeuchi, Noboru; H. Cocoletzi, Gregorio

2017-07-01

Atomic layers of manganese nitride, deposited on the cubic gallium nitride (111) surface, are investigated using spin polarized periodic density functional theory calculations. The adsorption of a manganese atom has been evaluated at different high symmetry sites. Incorporation into the GaN substrate by replacing gallium atoms drives the formation of a site in which the displaced Ga atom forms bonds with Ga atoms at the surface. This energetically favorable configuration shows a ferromagnetic alignment. Surface formation energy calculations demonstrate that when a full Mn ML is incorporated into the GaN structure, a Ga ML on top of a MnN bilayer may be formed for very Ga-rich conditions. On the other hand, when a full Mn ML is deposited on top of the nitrogen terminated surface, an epitaxial MnN bilayer is formed with antiferromagnetic characteristics. Density of states and partial density of states are reported to show the antiferromagnetic alignment in both structures. This behavior is mainly induced by the Mn-d orbitals.

Marine Controlled-Source Electromagnetic 2D Inversion for synthetic models.

NASA Astrophysics Data System (ADS)

Liu, Y.; Li, Y.

2016-12-01

We present a 2D inverse algorithm for frequency domain marine controlled-source electromagnetic (CSEM) data, which is based on the regularized Gauss-Newton approach. As a forward solver, our parallel adaptive finite element forward modeling program is employed. It is a self-adaptive, goal-oriented grid refinement algorithm in which a finite element analysis is performed on a sequence of refined meshes. The mesh refinement process is guided by a dual error estimate weighting to bias refinement towards elements that affect the solution at the EM receiver locations. With the use of the direct solver (MUMPS), we can effectively compute the electromagnetic fields for multi-sources and parametric sensitivities. We also implement the parallel data domain decomposition approach of Key and Ovall (2011), with the goal of being able to compute accurate responses in parallel for complicated models and a full suite of data parameters typical of offshore CSEM surveys. All minimizations are carried out by using the Gauss-Newton algorithm and model perturbations at each iteration step are obtained by using the Inexact Conjugate Gradient iteration method. Synthetic test inversions are presented.

Remote preparation of an atomic quantum memory.

PubMed

Rosenfeld, Wenjamin; Berner, Stefan; Volz, Jürgen; Weber, Markus; Weinfurter, Harald

2007-02-02

Storage and distribution of quantum information are key elements of quantum information processing and future quantum communication networks. Here, using atom-photon entanglement as the main physical resource, we experimentally demonstrate the preparation of a distant atomic quantum memory. Applying a quantum teleportation protocol on a locally prepared state of a photonic qubit, we realized this so-called remote state preparation on a single, optically trapped 87Rb atom. We evaluated the performance of this scheme by the full tomography of the prepared atomic state, reaching an average fidelity of 82%.

New Insight into the Local Structure of Hydrous Ferric Arsenate Using Full-Potential Multiple Scattering Analysis, Density Functional Theory Calculations, and Vibrational Spectroscopy.

PubMed

Wang, Shaofeng; Ma, Xu; Zhang, Guoqing; Jia, Yongfeng; Hatada, Keisuke

2016-11-15

Hydrous ferric arsenate (HFA) is an important arsenic-bearing precipitate in the mining-impacted environment and hydrometallurgical tailings. However, there is no agreement on its local atomic structure. The local structure of HFA was reprobed by employing a full-potential multiple scattering (FPMS) analysis, density functional theory (DFT) calculations, and vibrational spectroscopy. The FPMS simulations indicated that the coordination number of the As-Fe, Fe-As, or both in HFA was approximately two. The DFT calculations constructed a structure of HFA with the formula of Fe(HAsO 4 ) x (H 2 AsO 4 ) 1-x (OH) y ·zH 2 O. The presence of protonated arsenate in HFA was also evidenced by vibrational spectroscopy. The As and Fe K-edge X-ray absorption near-edge structure spectra of HFA were accurately reproduced by FPMS simulations using the chain structure, which was also a reasonable model for extended X-Ray absorption fine structure fitting. The FPMS refinements indicated that the interatomic Fe-Fe distance was approximately 5.2 Å, consistent with that obtained by Mikutta et al. (Environ. Sci. Technol. 2013, 47 (7), 3122-3131) using wavelet analysis. All of the results suggested that HFA was more likely to occur as a chain with AsO 4 tetrahedra and FeO 6 octahedra connecting alternately in an isolated bidentate-type fashion. This finding is of significance for understanding the fate of arsenic and the formation of ferric arsenate minerals in an acidic environment.

2-Amino­pyrimidin-1-ium 4-methyl­benzene­sulfonate

PubMed Central

Tabatabaee, Masoumeh; Noozari, Najmeh

2011-01-01

In the crystal structure of the title compound, C4H6N3 +·C7H7O3S−, inter­molecular N—H⋯O hydrogen bonds link the cations and anions into chains along [100]. Additional stabilization is provided by weak C—H⋯O hydrogen bonds. An inter­molecular π–π stacking inter­action with a centroid–centroid distance of 3.6957 (7) Å is also observed. The H atoms of the methyl group were refined as disordered over two sets of sites with equal occupancies PMID:21754830

Extended atmospheres of outer planet satellites and comets

NASA Technical Reports Server (NTRS)

Smyth, W. H.; Combi, M. R.

1985-01-01

Model analysis of the extended atmospheres of outer planet satellites and comets are discussed. Understanding the neutral hydrogen distribution in the Saturn system concentrated on assessing the spatial dependence of the lifetime of hydrogen atoms and on obtaining appropriately sorted Lyman ALPHA data from the Voyager 1 UVS instrument. Progress in the area of the extended cometary atmospheres included analysis of Pioneer Venus Layman alpha observations of Comet P/Encke with the fully refined hydrogen cloud model, development of the basic carbon and oxygen models, and planning for the Pioneer Venus UVS observations of Comets P/Giacobini-Zinner and P/Halley.

Effect of the Temperature of the Moderator on the Velocity Distribution of Neutrons with Numerical Calculations for H as Moderator

DOE R&D Accomplishments Database

Wigner, E. P.; Wilkins, J. E. Jr.

1944-09-14

In this paper we set up an integral equation governing the energy distribution of neutrons that are being slowed down uniformly throughout the entire space by a uniformly distributed moderator whose atoms are in motion with a Maxwellian distribution of velocities. The effects of chemical binding and crystal reflection are ignored. When the moderator is hydrogen, the integral equation is reduced to a differential equation and solved by numerical methods. In this manner we obtain a refinement of the dv/v{sup 2} law. (auth)

Gas atomization processing of tin and silicon modified LaNi 5 for nickel-metal hydride battery applications

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

Ting, Jason

1999-02-12

Numerous researchers have studied the relevant material properties of so-called AB 5 alloys for battery applications. These studies involved LaNi 5 substituted alloys which were prepared using conventional cast and crush alloying techniques. While valuable to the understanding of metal hydride effects, the previous work nearly ignored the potential for alternative direct powder production methods, like high pressure gas atomization (HPGA). Thus, there is a need to understand the relationship between gas atomization processes, powder particle solidification phases, and hydrogen absorption properties of ultra fine (< 25 μm) atomized powders with high surface area for enhanced battery performance. Concurrently, developmentmore » of a gas atomization nozzle that is more efficient than all current designs is needed to increase the yield of ultrafine AB 5 alloy powder for further processing advantage. Gas atomization processing of the AB 5 alloys was demonstrated to be effective in producing ultrafine spherical powders that were resilient to hydrogen cycling for the benefit of improving corrosion resistance in battery application. These ultrafine powders benefited from the rapid solidification process by having refined solute segregation in the microstructure of the gas atomized powders which enabled a rapid anneal treatment of the powders. The author has demonstrated the ability to produce high yields of ultrafine powder efficiently and cost effectively, using the new HPGA-III technology. Thus, the potential benefits of processing AB 5 alloys using the new HPGA technology could reduce manufacturing cost of nickel-metal hydride powder. In the near future, the manufacture of AB 5 alloy powders could become a continuous and rapid production process. The economic benefit of an improved AB 5 production process may thereby encourage the use of nickel-metal hydride rechargeable batteries in electrical vehicle applications in the foreseeable future.« less

Explore Full Range of QSO/AGN Properties

NASA Technical Reports Server (NTRS)

Oliversen, Ronald (Technical Monitor); Wilkes, Belinda

2005-01-01

The goal of the proposal is to perform ISO spectroscopic studies, including data analysis and modeling, of star formation regions using an ensemble of archival space-based data from the Infrared Space Observatory s Long Wavelength Spectrometer and Short Wavelength Spectrometer, but including as well some other spectroscopic databases. Four kinds of regions are considered in the studies: (1) disks around more evolved objects; (2) young, low or high mass pre-main sequence stars in star formation regions; (3) star formation in external, bright IR galaxies; and (4) the galactic center. One prime focus of the program is the OH lines in the far infrared. The program had the following goals: 1) Refine the data analysis of IS0 observations to obtain deeper and better SNR results on selected sources. The IS0 data itself underwent "pipeline 10" reductions in early 2001, and additional "hands-on data reduction packages" were supplied by the IS0 teams in 2001. The Fabry-Perot database is particularly sensitive to noise and slight calibration errors. 2) Model the atomic and molecular line shapes, in particular the OH lines, using revised monte- carlo techniques developed by the SWAS team at the Center for Astrophysics; 3) Attend scientific meetings and workshops; 4) Do E&PO activities related to infrared astrophysics and/or spectroscopy.

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

GeneSilico protein structure prediction meta-server.

PubMed

Kurowski, Michal A; Bujnicki, Janusz M

2003-07-01

Rigorous assessments of protein structure prediction have demonstrated that fold recognition methods can identify remote similarities between proteins when standard sequence search methods fail. It has been shown that the accuracy of predictions is improved when refined multiple sequence alignments are used instead of single sequences and if different methods are combined to generate a consensus model. There are several meta-servers available that integrate protein structure predictions performed by various methods, but they do not allow for submission of user-defined multiple sequence alignments and they seldom offer confidentiality of the results. We developed a novel WWW gateway for protein structure prediction, which combines the useful features of other meta-servers available, but with much greater flexibility of the input. The user may submit an amino acid sequence or a multiple sequence alignment to a set of methods for primary, secondary and tertiary structure prediction. Fold-recognition results (target-template alignments) are converted into full-atom 3D models and the quality of these models is uniformly assessed. A consensus between different FR methods is also inferred. The results are conveniently presented on-line on a single web page over a secure, password-protected connection. The GeneSilico protein structure prediction meta-server is freely available for academic users at http://genesilico.pl/meta.

GeneSilico protein structure prediction meta-server

PubMed Central

Kurowski, Michal A.; Bujnicki, Janusz M.

2003-01-01

Rigorous assessments of protein structure prediction have demonstrated that fold recognition methods can identify remote similarities between proteins when standard sequence search methods fail. It has been shown that the accuracy of predictions is improved when refined multiple sequence alignments are used instead of single sequences and if different methods are combined to generate a consensus model. There are several meta-servers available that integrate protein structure predictions performed by various methods, but they do not allow for submission of user-defined multiple sequence alignments and they seldom offer confidentiality of the results. We developed a novel WWW gateway for protein structure prediction, which combines the useful features of other meta-servers available, but with much greater flexibility of the input. The user may submit an amino acid sequence or a multiple sequence alignment to a set of methods for primary, secondary and tertiary structure prediction. Fold-recognition results (target-template alignments) are converted into full-atom 3D models and the quality of these models is uniformly assessed. A consensus between different FR methods is also inferred. The results are conveniently presented on-line on a single web page over a secure, password-protected connection. The GeneSilico protein structure prediction meta-server is freely available for academic users at http://genesilico.pl/meta. PMID:12824313

[Pb(H2O)]2+ and [Pb(OH)]+: four-component density functional theory calculations, correlated scalar relativistic constrained-space orbital variation energy decompositions, and topological analysis.

PubMed

Gourlaouen, Christophe; Piquemal, Jean-Philip; Parisel, Olivier

2006-05-07

Within the scope of studying the molecular implications of the Pb(2+) cation in environmental and polluting processes, this paper reports Hartree-Fock and density functional theory (B3LYP) four-component relativistic calculations using an all-electron basis set applied to [Pb(H(2)O)](2+) and [Pb(OH)](+), two complexes expected to be found in the terrestrial atmosphere. It is shown that full-relativistic calculations validate the use of scalar relativistic approaches within the framework of density functional theory. [Pb(H(2)O)](2+) is found C(2v) at any level of calculations whereas [Pb(OH)](+) can be found bent or linear depending of the computational methodology used. When C(s) is found the barrier to inversion through the C(infinityv) structure is very low, and can be overcome at high enough temperature, making the molecule floppy. In order to get a better understanding of the bonding occurring between the Pb(2+) cation and the H(2)O and OH(-) ligands, natural bond orbital and atoms-in-molecule calculations have been performed. These approaches are supplemented by a topological analysis of the electron localization function. Finally, the description of these complexes is refined using constrained-space orbital variation complexation energy decompositions.

Transmission Magnitude and Phase Control for Polarization-Preserving Reflectionless Metasurfaces

NASA Astrophysics Data System (ADS)

Kwon, Do-Hoon; Ptitcyn, Grigorii; Díaz-Rubio, Ana; Tretyakov, Sergei A.

2018-03-01

For transmissive applications of electromagnetic metasurfaces, an array of subwavelength Huygens' meta-atoms are typically used to eliminate reflection and achieve a high-transmission power efficiency together with a wide transmission phase coverage. We show that the underlying principle of low reflection and full control over transmission is asymmetric scattering into the specular reflection and transmission directions that results from a superposition of symmetric and antisymmetric scattering components, with Huygens' meta-atoms being one example configuration. Available for oblique illumination in TM polarization, a meta-atom configuration comprising normal and tangential electric polarizations is presented, which is capable of reflectionless, full-power transmission and a 2 π transmission phase coverage as well as full absorption. For lossy metasurfaces, we show that a complete phase coverage is still available for reflectionless designs for any value of absorptance. Numerical examples in the microwave and optical regimes are provided.

Crystallography of waxes - an electron diffraction study of refined and natural products

NASA Astrophysics Data System (ADS)

Dorset, Douglas L.

1997-02-01

The crystal structure of four waxes has been investigated by electron crystallography. Two of these waxes, including a refined petroleum product (Gulfwax) and a material from lignite (montan wax), form well ordered crystals and their structure could be solved quantitatively from the observed 0022-3727/30/3/018/img1 diffraction patterns. As also found previously for simpler binary n-paraffin solid solutions, the average structure resembles that of a pure paraffin (e.g. n-0022-3727/30/3/018/img2) but with a Gaussian distribution of atomic occupancies near the chain ends to account for the statistical distribution of chain lengths within a lamella. Two other waxes from living organisms, South African bee honeycomb and the leaves of the Brazilian carnauba palm, are much less ordered, even though they share the same methylene subcell packing of the most crystalline parts of the previous materials. It appears that these waxes cannot fully separate into distinct lamellae, perhaps due to the presence of very long `tie' molecules, and are therefore `frustrated' crystal structures.

Synthesis and characterization of Y2O3 nano-material: An experimental and theoretical study

NASA Astrophysics Data System (ADS)

Ahmad, Sheeraz; Faizan, Mohd; Ahmad, Shabbir; Ikram, Mohd

2018-04-01

We made an attempt to synthesize pure Y2O3 nanomaterial by using the sol-gel method followed by annealing at 600°C and 900°C. The synthesized Y2O3 nanoparticle was characterized by using XRD, FTIR, and UV-Vis spectroscopy. The structural refinement was performed using FULLPROF software by the Rietveld method. The refinement parameters such as lattice constant, atomic position, occupancy, R-factor and goodness of fit (χ2) were calculated. The nanoparticle has a single phase cubic structure with Ia -3 space group. The main absorption band in FTIR spectra centered at 560 cm-1 is attributed to Y-O vibration while the broadband at 3450 cm-1 arises due to O-H vibration. The band gap was obtained from the reflectance spectra using the K-M function F(R∞). The optimized structural parameters and UV-Vis spectrum were calculated using DFT and TD-DFT/B3LYP methods in bulk phase of Y2O3 and compared with experimental UV-Vis spectra in nanophase.

Refinement of atomic and magnetic structures using neutron diffraction for synthesized bulk and nano-nickel zinc gallate ferrite

NASA Astrophysics Data System (ADS)

Ata-Allah, S. S.; Balagurov, A. M.; Hashhash, A.; Bobrikov, I. A.; Hamdy, Sh.

2016-01-01

The parent NiFe2O4 and Zn/Ga substituted spinel ferrite powders have been prepared by solid state reaction technique. As a typical example, the Ni0.7Zn0.3Fe1.5Ga0.5O4 sample has been prepared by sol-gel auto combustion method with the nano-scale crystallites size. X-ray and Mössbauer studies were carried out for the prepared samples. Structure and microstructure properties were investigated using the time-of-flight HRFD instrument at the IBR-2 pulsed reactor, at a temperatures range 15-473 K. The Rietveld refinement of the neutron diffraction data revealed that all samples possess cubic symmetry corresponding to the space group Fd3m. Cations distribution show that Ni2+ is a complete inverse spinel ion, while Ga3+ equally distributed between the two A and B-sublattices. The level of microstrains in bulk samples was estimated as very small while the size of coherently scattered domains is quite large. For nano-structured sample the domain size is around 120 Å.

Structural simplicity as a restraint on the structure of amorphous silicon

NASA Astrophysics Data System (ADS)

Cliffe, Matthew J.; Bartók, Albert P.; Kerber, Rachel N.; Grey, Clare P.; Csányi, Gábor; Goodwin, Andrew L.

2017-06-01

Understanding the structural origins of the properties of amorphous materials remains one of the most important challenges in structural science. In this study, we demonstrate that local "structural simplicity", embodied by the degree to which atomic environments within a material are similar to each other, is a powerful concept for rationalizing the structure of amorphous silicon (a -Si) a canonical amorphous material. We show, by restraining a reverse Monte Carlo refinement against pair distribution function (PDF) data to be simpler, that the simplest model consistent with the PDF is a continuous random network (CRN). A further effect of producing a simple model of a -Si is the generation of a (pseudo)gap in the electronic density of states, suggesting that structural homogeneity drives electronic homogeneity. That this method produces models of a -Si that approach the state-of-the-art without the need for chemically specific restraints (beyond the assumption of homogeneity) suggests that simplicity-based refinement approaches may allow experiment-driven structural modeling techniques to be developed for the wide variety of amorphous semiconductors with strong local order.

Automated protein structure modeling in CASP9 by I-TASSER pipeline combined with QUARK-based ab initio folding and FG-MD-based structure refinement

PubMed Central

Xu, Dong; Zhang, Jian; Roy, Ambrish; Zhang, Yang

2011-01-01

I-TASSER is an automated pipeline for protein tertiary structure prediction using multiple threading alignments and iterative structure assembly simulations. In CASP9 experiments, two new algorithms, QUARK and FG-MD, were added to the I-TASSER pipeline for improving the structural modeling accuracy. QUARK is a de novo structure prediction algorithm used for structure modeling of proteins that lack detectable template structures. For distantly homologous targets, QUARK models are found useful as a reference structure for selecting good threading alignments and guiding the I-TASSER structure assembly simulations. FG-MD is an atomic-level structural refinement program that uses structural fragments collected from the PDB structures to guide molecular dynamics simulation and improve the local structure of predicted model, including hydrogen-bonding networks, torsion angles and steric clashes. Despite considerable progress in both the template-based and template-free structure modeling, significant improvements on protein target classification, domain parsing, model selection, and ab initio folding of beta-proteins are still needed to further improve the I-TASSER pipeline. PMID:22069036

Equations of state of anhydrous AlF3 and AlI3: Modeling of extreme condition halide chemistry

NASA Astrophysics Data System (ADS)

Stavrou, Elissaios; Zaug, Joseph M.; Bastea, Sorin; Crowhurst, Jonathan C.; Goncharov, Alexander F.; Radousky, Harry B.; Armstrong, Michael R.; Roberts, Sarah K.; Plaue, Jonathan W.

2015-06-01

Pressure dependent angle-dispersive x-ray powder diffraction measurements of alpha-phase aluminum trifluoride (α-AlF3) and separately, aluminum triiodide (AlI3) were conducted using a diamond-anvil cell. Results at 295 K extend to 50 GPa. The equations of state of AlF3 and AlI3 were determined through refinements of collected x-ray diffraction patterns. The respective bulk moduli and corresponding pressure derivatives are reported for multiple orders of the Birch-Murnaghan (B-M), finite-strain (F-f), and higher pressure finite-strain (G-g) EOS analysis models. Aluminum trifluoride exhibits an apparent isostructural phase transition at approximately 12 GPa. Aluminum triiodide also undergoes a second-order atomic rearrangement: applied stress transformed a monoclinically distorted face centered cubic (fcc) structure into a standard fcc structural arrangement of iodine atoms. Results from semi-empirical thermochemical computations of energetic materials formulated with fluorine containing reactants were obtained with the aim of predicting the yield of halogenated products.

cryoem-cloud-tools: A software platform to deploy and manage cryo-EM jobs in the cloud.

PubMed

Cianfrocco, Michael A; Lahiri, Indrajit; DiMaio, Frank; Leschziner, Andres E

2018-06-01

Access to streamlined computational resources remains a significant bottleneck for new users of cryo-electron microscopy (cryo-EM). To address this, we have developed tools that will submit cryo-EM analysis routines and atomic model building jobs directly to Amazon Web Services (AWS) from a local computer or laptop. These new software tools ("cryoem-cloud-tools") have incorporated optimal data movement, security, and cost-saving strategies, giving novice users access to complex cryo-EM data processing pipelines. Integrating these tools into the RELION processing pipeline and graphical user interface we determined a 2.2 Å structure of ß-galactosidase in ∼55 hours on AWS. We implemented a similar strategy to submit Rosetta atomic model building and refinement to AWS. These software tools dramatically reduce the barrier for entry of new users to cloud computing for cryo-EM and are freely available at cryoem-tools.cloud. Copyright © 2018. Published by Elsevier Inc.

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

NASA Astrophysics Data System (ADS)

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

2013-03-01

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

NASA Astrophysics Data System (ADS)

McHugh, K. M.; Key, J. F.

1994-06-01

Spray forming is a near- net- shape fabrication technology in which a spray of finely atomized liquid droplets is deposited onto a suitably shaped substrate or pattern to produce a coherent solid. The technology offers unique opportunities for simplifying materials processing, often while substantially improving product quality. Spray forming is applicable to a wide range of metals and nonmetals and offers property improvements resulting from rapid solidification (e.g., refined microstructures, extended solid solubilities, and reduced segregation). Economic benefits result from process simplification and the elimination of unit operations. Researchers at the Idaho National Engineering Laboratory (INEL) are developing spray forming technology for producing near- net- shape solids and coatings of a variety of metals, polymers, and composite materials using de Laval nozzles. This article briefly describes the atomization behavior of liquid metals in linear de Laval nozzles and illustrates the versatility of the process by summarizing results from two spray forming programs. In one program, low-carbon steel strip >0.75 mm thick was produced; in the other, polymer membranes ˜5 μm thick were spray formed.

Modeling Solar Wind Flow with the Multi-Scale Fluid-Kinetic Simulation Suite

DOE PAGES

Pogorelov, N.V.; Borovikov, S. N.; Bedford, M. C.; ...

2013-04-01

Multi-Scale Fluid-Kinetic Simulation Suite (MS-FLUKSS) is a package of numerical codes capable of performing adaptive mesh refinement simulations of complex plasma flows in the presence of discontinuities and charge exchange between ions and neutral atoms. The flow of the ionized component is described with the ideal MHD equations, while the transport of atoms is governed either by the Boltzmann equation or multiple Euler gas dynamics equations. We have enhanced the code with additional physical treatments for the transport of turbulence and acceleration of pickup ions in the interplanetary space and at the termination shock. In this article, we present themore » results of our numerical simulation of the solar wind (SW) interaction with the local interstellar medium (LISM) in different time-dependent and stationary formulations. Numerical results are compared with the Ulysses, Voyager, and OMNI observations. Finally, the SW boundary conditions are derived from in-situ spacecraft measurements and remote observations.« less

Experimental evidence and structural modeling of nonstoichiometric (010) surfaces coexisting in hydroxyapatite nano-crystals.

PubMed

Ospina, C A; Terra, J; Ramirez, A J; Farina, M; Ellis, D E; Rossi, A M

2012-01-01

High-resolution transmission electron microscopy (HRTEM) and ab initio quantum-mechanical calculations of electronic structure were combined to investigate the structure of the hydroxyapatite (HA) (010) surface, which plays an important role in HA interactions with biological media. HA was synthesized by in vitro precipitation at 37°C. HRTEM images revealed thin elongated rod nanoparticles with preferential growth along the [001] direction and terminations parallel to the (010) plane. The focal series reconstruction (FSR) technique was applied to develop an atomic-scale structural model of the high-resolution images. The HRTEM simulations identified the coexistence of two structurally distinct terminations for (010) surfaces: a rather flat Ca(II)-terminated surface and a zig-zag structure with open OH channels. Density functional theory (DFT) was applied in a periodic slab plane-wave pseudopotential approach to refine details of atomic coordination and bond lengths of Ca(I) and Ca(II) sites in hydrated HA (010) surfaces, starting from the HRTEM model. Copyright © 2011 Elsevier B.V. All rights reserved.

(Z)-3-Methyl-4-[1-(4-methyl­anilino)propyl­idene]-1-phenyl-1H-pyrazol-5(4H)-one

PubMed Central

Sharma, Naresh; Vyas, Komal M.; Jadeja, R. N.; Kant, Rajni; Gupta, Vivek K.

2013-01-01

In the title mol­ecule, C20H21N3O, the central pyrazole ring forms dihedral angles of 4.75 (9) and 49.11 (9)°, respectively, with the phenyl and methyl-substituted benzene rings. The dihedral angle between the phenyl and benzene rings is 51.76 (8)°. The amino group and carbonyl O atom are involved in an intra­molecular N—H⋯O hydrogen bond. In the crystal, π–π inter­actions are observed between benzene rings [centroid–centroid seperation = 3.892 (2) Å] and pyrazole rings [centroid–centroid seperation = 3.626 (2) Å], forming chains along [111]. The H atoms of the methyl group on the p-tolyl substituent were refined as disordered over two sets of sites in a 0.60 (4):0.40 (4) ratio. PMID:24109353

AAuAl (A = Ca, Sc, and Ti): Peierls Distortion, Atomic Coloring, and Structural Competition

DOE PAGES

Pham, Joyce; Miller, Gordon J.

2018-04-02

Using density functional theory, the crystal structure variation of AAuAl (A = Ca, Sc, and Ti) from orthorhombic Co 2Si-type to distorted hexagonal Fe 2P-type and then Ni 2In-type structures is shown to correlate with their electronic structures and valence electron counts, sizes of the active metals A, and site preferences for Au and Al atoms, which are arranged to maximize Au–Al nearest neighbor contacts. An evaluation of chemical pressure imposed by the varying A metals using total energy vs volume calculations indicates that larger unit cell volumes favor the orthorhombic structure, whereas smaller volumes favor the hexagonal structures. Themore » electronic origin of the Mg 2Ga-type crystal structure of ScAuAl, refined as a distorted Fe 2P-type supercell doubled along the c-axis, indicates a Peierls-type distortion mechanism of the Au chains along the c-axis.« less

Atomic Structure of a Cesium Aluminosilicate Geopolymer: A Pair Distribution Function Study

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

Bell, J.; Sarin, P; Provis, J

2008-01-01

The atomic pair distribution function (PDF) method was used to study the structure of cesium aluminosilicate geopolymer. The geopolymer was prepared by reacting metakaolin with cesium silicate solution followed by curing at 50C for 24 h in a sealed container. Heating of Cs-geopolymer above 1000C resulted in formation of crystalline pollucite (CsAlSi{sub 2}O{sub 6}). PDF refinement of the pollucite phase formed displayed an excellent fit over the 10-30 {angstrom} range when compared with a cubic pollucite model. A poorer fit was attained from 1-10 {angstrom} due to an additional amorphous phase present in the heated geopolymer. On the basis ofmore » PDF analysis, unheated Cs-geopolymer displayed structural ordering similar to pollucite up to a length scale of 9 {angstrom}, despite some differences. Our results suggest that hydrated Cs{sup +} ions were an integral part of the Cs-geopolymer structure and that most of the water present was not associated with Al-OH or Si-OH bonds.« less

An analytic model for accurate spring constant calibration of rectangular atomic force microscope cantilevers.

PubMed

Li, Rui; Ye, Hongfei; Zhang, Weisheng; Ma, Guojun; Su, Yewang

2015-10-29

Spring constant calibration of the atomic force microscope (AFM) cantilever is of fundamental importance for quantifying the force between the AFM cantilever tip and the sample. The calibration within the framework of thin plate theory undoubtedly has a higher accuracy and broader scope than that within the well-established beam theory. However, thin plate theory-based accurate analytic determination of the constant has been perceived as an extremely difficult issue. In this paper, we implement the thin plate theory-based analytic modeling for the static behavior of rectangular AFM cantilevers, which reveals that the three-dimensional effect and Poisson effect play important roles in accurate determination of the spring constants. A quantitative scaling law is found that the normalized spring constant depends only on the Poisson's ratio, normalized dimension and normalized load coordinate. Both the literature and our refined finite element model validate the present results. The developed model is expected to serve as the benchmark for accurate calibration of rectangular AFM cantilevers.

Cholesterol oxidase: ultrahigh-resolution crystal structure and multipolar atom model-based analysis.

PubMed

Zarychta, Bartosz; Lyubimov, Artem; Ahmed, Maqsood; Munshi, Parthapratim; Guillot, Benoît; Vrielink, Alice; Jelsch, Christian

2015-04-01

Examination of protein structure at the subatomic level is required to improve the understanding of enzymatic function. For this purpose, X-ray diffraction data have been collected at 100 K from cholesterol oxidase crystals using synchrotron radiation to an optical resolution of 0.94 Å. After refinement using the spherical atom model, nonmodelled bonding peaks were detected in the Fourier residual electron density on some of the individual bonds. Well defined bond density was observed in the peptide plane after averaging maps on the residues with the lowest thermal motion. The multipolar electron density of the protein-cofactor complex was modelled by transfer of the ELMAM2 charge-density database, and the topology of the intermolecular interactions between the protein and the flavin adenine dinucleotide (FAD) cofactor was subsequently investigated. Taking advantage of the high resolution of the structure, the stereochemistry of main-chain bond lengths and of C=O···H-N hydrogen bonds was analyzed with respect to the different secondary-structure elements.

Nucleosynthesis: Stellar and Solar Abundances and Atomic Data

NASA Technical Reports Server (NTRS)

Cowan, John J.; Lawler, James E.; Sneden, Christopher; DenHartog, E. A.; Collier, Jason; Dodge, Homer L.

2006-01-01

Abundance observations indicate the presence of often surprisingly large amounts of neutron capture (i.e., s- and r-process) elements in old Galactic halo and globular cluster stars. These observations provide insight into the nature of the earliest generations of stars in the Galaxy the progenitors of the halo stars responsible for neutron-capture synthesis. Comparisons of abundance trends can be used to understand the chemical evolution of the Galaxy and the nature of heavy element nucleosynthesis. In addition age determinations, based upon long-lived radioactive nuclei abundances, can now be obtained. These stellar abundance determinations depend critically upon atomic data. Improved laboratory transition probabilities have been recently obtained for a number of elements. These new gf values have been used to greatly refine the abundances of neutron-capture elemental abundances in the solar photosphere and in very metal-poor Galactic halo stars. The newly determined stellar abundances are surprisingly consistent with a (relative) Solar System r-process pattern, and are also consistent with abundance predictions expected from such neutron-capture nucleosynthesis.

AAuAl (A = Ca, Sc, and Ti): Peierls Distortion, Atomic Coloring, and Structural Competition

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

Pham, Joyce; Miller, Gordon J.

Using density functional theory, the crystal structure variation of AAuAl (A = Ca, Sc, and Ti) from orthorhombic Co 2Si-type to distorted hexagonal Fe 2P-type and then Ni 2In-type structures is shown to correlate with their electronic structures and valence electron counts, sizes of the active metals A, and site preferences for Au and Al atoms, which are arranged to maximize Au–Al nearest neighbor contacts. An evaluation of chemical pressure imposed by the varying A metals using total energy vs volume calculations indicates that larger unit cell volumes favor the orthorhombic structure, whereas smaller volumes favor the hexagonal structures. Themore » electronic origin of the Mg 2Ga-type crystal structure of ScAuAl, refined as a distorted Fe 2P-type supercell doubled along the c-axis, indicates a Peierls-type distortion mechanism of the Au chains along the c-axis.« less

Photon-photon entanglement with a single trapped atom.

PubMed

Weber, B; Specht, H P; Müller, T; Bochmann, J; Mücke, M; Moehring, D L; Rempe, G

2009-01-23

An experiment is performed where a single rubidium atom trapped within a high-finesse optical cavity emits two independently triggered entangled photons. The entanglement is mediated by the atom and is characterized both by a Bell inequality violation of S=2.5, as well as full quantum-state tomography, resulting in a fidelity exceeding F=90%. The combination of cavity-QED and trapped atom techniques makes our protocol inherently deterministic--an essential step for the generation of scalable entanglement between the nodes of a distributed quantum network.

Characterization and limits of a cold-atom Sagnac interferometer

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

Gauguet, A.; Canuel, B.; Leveque, T.

2009-12-15

We present the full evaluation of a cold-atom gyroscope based on atom interferometry. We have performed extensive studies to determine the systematic errors, scale factor and sensitivity. We demonstrate that the acceleration noise can be efficiently removed from the rotation signal, allowing us to reach the fundamental limit of the quantum projection noise for short term measurements. The technical limits to the long term sensitivity and accuracy have been identified, clearing the way for the next generation of ultrasensitive atom gyroscopes.

Observation of entanglement of a single photon with a trapped atom.

PubMed

Volz, Jürgen; Weber, Markus; Schlenk, Daniel; Rosenfeld, Wenjamin; Vrana, Johannes; Saucke, Karen; Kurtsiefer, Christian; Weinfurter, Harald

2006-01-27

We report the observation of entanglement between a single trapped atom and a single photon at a wavelength suitable for low-loss communication over large distances, thereby achieving a crucial step towards long range quantum networks. To verify the entanglement, we introduce a single atom state analysis. This technique is used for full state tomography of the atom-photon qubit pair. The detection efficiency and the entanglement fidelity are high enough to allow in a next step the generation of entangled atoms at large distances, ready for a final loophole-free Bell experiment.

Neutron Diffraction Study Oxygen Dissolution Alpha(sub 2)-Ti3Al

NASA Technical Reports Server (NTRS)

Jones, Camille Y.; Luecke, William E.; Copland, Evan

2005-01-01

Rietveld refinements of neutron powder diffraction data on alpha(sub 2)-Ti3Al have been performed to determine the crystal structure as a function of interstitial oxygen (O) concentration for three alloys with a Ti/Al ratio of approximately equal to 2.34 and O concentrations of 0.25%, 3.99% and 7.71%. The structures of the allows are hexagonal in space group P6(sub 3)/mmc where Ti and Al atoms populate unique sites with excess Al at the Ti site and O atoms occupy octahedral interstitial sites surrounded by six Ti sites. The length of the c-axis was found to increase linearly as the O occupancy of the interstitial sites increased; this lattice lengthening effect was much less pronounced along the alpha axis. Correspondingly, the increases in the lengths of Ti-Al and Ti-Ti bonds with a major component of their direction parallel to the c-axis were roughly an order of magnitude greater than the increases in the lengths of Ti-al and Ti-Ti bonds more closely aligned with the alpha-axis. Densities calculated form the lattice parameters and occupancy factors fall in the range (4.118 plus or minus 0.004) grams per cubic centimeter to (4.194 plus or minus 0.004) grams per cubic centimeter, and exhibit a nearly linear increase with oxygen concentration. Measured densities of (4.113 plus or minus 0.001) grams per cubic centimeter, (4.146 plus or minus 0.009) grams per cubic centimeter, and (4.191 plus or minus 0.002) grams per cubic centimeter for these alloys agree with the results of the refinements.

Catalysis of GTP Hydrolysis by Small GTPases at Atomic Detail by Integration of X-ray Crystallography, Experimental, and Theoretical IR Spectroscopy*

PubMed Central

Rudack, Till; Jenrich, Sarah; Brucker, Sven; Vetter, Ingrid R.; Gerwert, Klaus; Kötting, Carsten

2015-01-01

Small GTPases regulate key processes in cells. Malfunction of their GTPase reaction by mutations is involved in severe diseases. Here, we compare the GTPase reaction of the slower hydrolyzing GTPase Ran with Ras. By combination of time-resolved FTIR difference spectroscopy and QM/MM simulations we elucidate that the Mg2+ coordination by the phosphate groups, which varies largely among the x-ray structures, is the same for Ran and Ras. A new x-ray structure of a Ran·RanBD1 complex with improved resolution confirmed this finding and revealed a general problem with the refinement of Mg2+ in GTPases. The Mg2+ coordination is not responsible for the much slower GTPase reaction of Ran. Instead, the location of the Tyr-39 side chain of Ran between the γ-phosphate and Gln-69 prevents the optimal positioning of the attacking water molecule by the Gln-69 relative to the γ-phosphate. This is confirmed in the RanY39A·RanBD1 crystal structure. The QM/MM simulations provide IR spectra of the catalytic center, which agree very nicely with the experimental ones. The combination of both methods can correlate spectra with structure at atomic detail. For example the FTIR difference spectra of RasA18T and RanT25A mutants show that spectral differences are mainly due to the hydrogen bond of Thr-25 to the α-phosphate in Ran. By integration of x-ray structure analysis, experimental, and theoretical IR spectroscopy the catalytic center of the x-ray structural models are further refined to sub-Å resolution, allowing an improved understanding of catalysis. PMID:26272610

Catalysis of GTP hydrolysis by small GTPases at atomic detail by integration of X-ray crystallography, experimental, and theoretical IR spectroscopy.

PubMed

Rudack, Till; Jenrich, Sarah; Brucker, Sven; Vetter, Ingrid R; Gerwert, Klaus; Kötting, Carsten

2015-10-02

Small GTPases regulate key processes in cells. Malfunction of their GTPase reaction by mutations is involved in severe diseases. Here, we compare the GTPase reaction of the slower hydrolyzing GTPase Ran with Ras. By combination of time-resolved FTIR difference spectroscopy and QM/MM simulations we elucidate that the Mg(2+) coordination by the phosphate groups, which varies largely among the x-ray structures, is the same for Ran and Ras. A new x-ray structure of a Ran·RanBD1 complex with improved resolution confirmed this finding and revealed a general problem with the refinement of Mg(2+) in GTPases. The Mg(2+) coordination is not responsible for the much slower GTPase reaction of Ran. Instead, the location of the Tyr-39 side chain of Ran between the γ-phosphate and Gln-69 prevents the optimal positioning of the attacking water molecule by the Gln-69 relative to the γ-phosphate. This is confirmed in the RanY39A·RanBD1 crystal structure. The QM/MM simulations provide IR spectra of the catalytic center, which agree very nicely with the experimental ones. The combination of both methods can correlate spectra with structure at atomic detail. For example the FTIR difference spectra of RasA18T and RanT25A mutants show that spectral differences are mainly due to the hydrogen bond of Thr-25 to the α-phosphate in Ran. By integration of x-ray structure analysis, experimental, and theoretical IR spectroscopy the catalytic center of the x-ray structural models are further refined to sub-Å resolution, allowing an improved understanding of catalysis. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.

A refined model of claudin-15 tight junction paracellular architecture by molecular dynamics simulations

PubMed Central

Alberini, Giulio; Benfenati, Fabio

2017-01-01

Tight-junctions between epithelial cells of biological barriers are specialized molecular structures that regulate the flux of solutes across the barrier, parallel to cell walls. The tight-junction backbone is made of strands of transmembrane proteins from the claudin family, but the molecular mechanism of its function is still not completely understood. Recently, the crystal structure of a mammalian claudin-15 was reported, displaying for the first time the detailed features of transmembrane and extracellular domains. Successively, a structural model of claudin-15-based paracellular channels has been proposed, suggesting a putative assembly that illustrates how claudins associate in the same cell (via cis interactions) and across adjacent cells (via trans interactions). Although very promising, the model offers only a static conformation, with residues missing in the most important extracellular regions and potential steric clashes. Here we present detailed atomic models of paracellular single and double pore architectures, obtained from the putative assembly and refined via structural modeling and all-atom molecular dynamics simulations in double membrane bilayer and water environment. Our results show an overall stable configuration of the complex with a fluctuating pore size. Extracellular residue loops in trans interaction are able to form stable contacts and regulate the size of the pore, which displays a stationary radius of 2.5–3.0 Å at the narrowest region. The side-by-side interactions of the cis configuration are preserved via stable hydrogen bonds, already predicted by cysteine crosslinking experiments. Overall, this work introduces an improved version of the claudin-15-based paracellular channel model that strengthens its validity and that can be used in further computational studies to understand the structural features of tight-junctions regulation. PMID:28863193

A Matlab-based finite-difference solver for the Poisson problem with mixed Dirichlet-Neumann boundary conditions

NASA Astrophysics Data System (ADS)

Reimer, Ashton S.; Cheviakov, Alexei F.

2013-03-01

A Matlab-based finite-difference numerical solver for the Poisson equation for a rectangle and a disk in two dimensions, and a spherical domain in three dimensions, is presented. The solver is optimized for handling an arbitrary combination of Dirichlet and Neumann boundary conditions, and allows for full user control of mesh refinement. The solver routines utilize effective and parallelized sparse vector and matrix operations. Computations exhibit high speeds, numerical stability with respect to mesh size and mesh refinement, and acceptable error values even on desktop computers. Catalogue identifier: AENQ_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AENQ_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: GNU General Public License v3.0 No. of lines in distributed program, including test data, etc.: 102793 No. of bytes in distributed program, including test data, etc.: 369378 Distribution format: tar.gz Programming language: Matlab 2010a. Computer: PC, Macintosh. Operating system: Windows, OSX, Linux. RAM: 8 GB (8, 589, 934, 592 bytes) Classification: 4.3. Nature of problem: To solve the Poisson problem in a standard domain with “patchy surface”-type (strongly heterogeneous) Neumann/Dirichlet boundary conditions. Solution method: Finite difference with mesh refinement. Restrictions: Spherical domain in 3D; rectangular domain or a disk in 2D. Unusual features: Choice between mldivide/iterative solver for the solution of large system of linear algebraic equations that arise. Full user control of Neumann/Dirichlet boundary conditions and mesh refinement. Running time: Depending on the number of points taken and the geometry of the domain, the routine may take from less than a second to several hours to execute.

Crystal structure and electrochemical properties of [Ni(bztmpen)(CH3CN)](BF4)2 {bztmpen is N-benzyl-N,N',N'-tris-[(6-methyl-pyridin-2-yl)meth-yl]ethane-1,2-di-amine}.

PubMed

Chen, Lin; Ren, Gan; Guo, Yakun; Sang, Ge

2017-06-01

The mononuclear nickel title complex (acetonitrile-κ N ){ N -benzyl- N , N ', N '-tris-[(6-methyl-pyridin-2-yl)meth-yl]ethane-1,2-di-amine}-nickel(II) bis-(tetra-fluor-ido-borate), [Ni(C 30 H 35 N 5 )(CH 3 CN)](BF 4 ) 2 , was prepared from the reaction of Ni(BF 4 ) 2 ·6H 2 O with N -benzyl- N , N ', N '-tris-[(6-methyl-pyridin-2-yl)meth-yl]ethane-1,2-di-amine ( bztmpen ) in aceto-nitrile at room temperature. With an open site occupied by the aceto-nitrile mol-ecule, the nickel(II) atom is chelated by five N-atom sites from the ligand and one N atom from the ligand, showing an overall octa-hedral coordination environment. Compared with analogues where the 6-methyl substituent is absent, the bond length around the Ni 2+ cation are evidently longer. Upon reductive dissociation of the acetro-nitrile mol-ecule, the title complex has an open site for a catalytic reaction. The title complex has two redox couples at -1.50 and -1.80 V ( versus F c +/0 ) based on nickel. The F atoms of the two BF 4 - counter-anions are split into two groups and the occupancy ratios refined to 0.611 (18):0.389 (18) and 0.71 (2):0.29 (2).

Non-LTE effects in Al I lines

NASA Astrophysics Data System (ADS)

Menzhevitski, V. S.; Shimansky, V. V.; Shimanskaya, N. N.

2012-07-01

We present the theoretical analysis of the Al I line formation in the spectra of late-type stars ignoring the assumption of local thermodynamic equilibrium (LTE). The calculations were based on the 39-level aluminum atom model for one-dimensional hydrostatic stellar atmosphere models with the parameters: T eff from 4000 to 9000 K, log g = 0.0-4.5, and metallicity [ A] = 0.0;-1.0;-2.0;-3.0;-4.0. The aluminum atom model and the method of calculations were tested by the study of line profiles in the solar spectrum. We refined the oscillator strengths and Van-der-Vaals broadening constants C 6 of the investigated transitions. We conclude that the Al I atom is in the overionization state: the 3 p level is underpopulated in the line formation region. This leads to the line weakening, as compared with the LTE results. The overionization effect becomes more pronounced with increasing temperature and decreasing metallicity. We show that the use of various atomic data (ionization cross-sections) for the low levels of Al I does not change the behavior of non-LTE deviations, whereas the value of these deviations varies essentially. For nine selected Al I lines we calculated the grids of theoretical non-LTE corrections (Δ X NLTE = log ɛ NLTE - log ɛ LTE) to the Al abundances determinedwith the LTE assumption. The non-LTE corrections are positive and significant for the stars with temperatures T eff > 6000 K. These corrections weakly depend on log g, and increase with declining stellar metallicity.

Reaction Kinetics of Hydrogen Atom Abstraction from C4-C6 Alkenes by the Hydrogen Atom and Methyl Radical.

PubMed

Wang, Quan-De; Liu, Zi-Wu

2018-06-14

Alkenes are important ingredients of realistic fuels and are also critical intermediates during the combustion of a series of other fuels including alkanes, cycloalkanes, and biofuels. To provide insights into the combustion behavior of alkenes, detailed quantum chemical studies for crucial reactions are desired. Hydrogen abstractions of alkenes play a very important role in determining the reactivity of fuel molecules. This work is motivated by previous experimental and modeling evidence that current literature rate coefficients for the abstraction reactions of alkenes are still in need of refinement and/or redetermination. In light of this, this work reports a theoretical and kinetic study of hydrogen atom abstraction reactions from C4-C6 alkenes by the hydrogen (H) atom and methyl (CH 3 ) radical. A series of C4-C6 alkene molecules with enough structural diversity are taken into consideration. Geometry and vibrational properties are determined at the B3LYP/6-31G(2df,p) level implemented in the Gaussian-4 (G4) composite method. The G4 level of theory is used to calculate the electronic single point energies for all species to determine the energy barriers. Conventional transition state theory with Eckart tunneling corrections is used to determine the high-pressure-limit rate constants for 47 elementary reaction rate coefficients. To faciliate their applications in kinetic modeling, the obtained rate constants are given in the Arrhenius expression and rate coefficients for typical reaction classes are recommended. The overall rate coefficients for the reaction of H atom and CH 3 radical with all the studied alkenes are also compared. Branching ratios of these reaction channels for certain alkenes have also been analyzed.

Boroxol rings from diffraction data on vitreous boron trioxide.

PubMed

Soper, Alan K

2011-09-14

There has been a considerable debate about the nature of the short range atomic order in vitreous B(2)O(3). Some authorities state that it is not possible to build a model of glassy boron oxide of the correct density containing a large number of six-membered rings which also fits experimental diffraction data, but recent computer simulations appear to overrule that view. To discover which view is correct I use empirical potential structure refinement (EPSR) on existing neutron and x-ray diffraction data to build two models of vitreous B(2)O(3). One of these consists only of single boron and oxygen atoms arranged in a network to reproduce the diffraction data as closely as possible. This model has less than 10% of boron atoms in boroxol rings. The second model is made up of an equimolar mixture of B(3)O(3) hexagonal ring 'molecules' and BO(3) triangular molecules, with no free boron or oxygen atoms. This second model therefore has 75% of the boron atoms in boroxol rings. It is found that both models give closely similar diffraction patterns, suggesting that the diffraction data in this case are not sensitive to the number of boroxol rings present in the structure. This reinforces recent Raman, ab initio, and NMR claims that the percentage of boroxol rings in this material may be as high as 75%. The findings of this study probably explain why some interpretations based on different simulation techniques only find a small fraction of boroxol rings. The results also highlight the power of EPSR for the extraction of accurate atomistic representations of amorphous structures, provided adequate additional, non-scattering data (such as Raman and NMR in this case) are available.

(But­oxy­methyl­idene)di­methyl­aza­nium tetra­phenyl­borate aceto­nitrile monosolvate

PubMed Central

Tiritiris, Ioannis; Saur, Stefan; Kantlehner, Willi

2014-01-01

In the title solvated salt, C7H16NO+·C24H20B−·C2H3N, the C—N bond lengths in the cation are 1.2831 (19), 1.467 (2) and 1.465 (2) Å, indicating double- and single-bond character, respectively. The C—O bond length of 1.2950 (18) Å shows a double-bond character, pointing towards charge delocalization within the NCO plane of the iminium ion. The two C atoms of the n-butyl group are disordered over the two sites, with refined occupancy ratios of 0.890 (5):0.110 (5) and 0.888 (4):0.112 (4). In the crystal, C—H⋯π inter­actions occur between the methine H atom, H atoms of the –N(CH3)2 and –CH2 groups of the cation, and two of the phenyl rings of the tetra­phenyl­borate anion. The latter inter­action forms an aromatic pocket in which the cation is embedded. Thus, a two-dimensional pattern is created in the ac plane. PMID:24826158

Crystal structure and chemical bonding of the high-temperature phase of AgN3.

PubMed

Schmidt, Carsten L; Dinnebier, Robert; Wedig, Ulrich; Jansen, Martin

2007-02-05

The crystal structure of silver azide (AgN3) in its high-temperature (HT) modification was determined from X-ray powder diffraction data, recorded at T = 170 degrees C and was further refined by the Rietveld method. The structure is monoclinic (P21/c (No. 14), a = 6.0756(2) A, b = 6.1663(2) A, c = 6.5729(2) A, beta = 114.19(0) degrees, V = 224.62(14) A3, Z = 4) and consists of two-dimensional Ag and N containing layers in which the silver atoms are coordinated by four nitrogen atoms exhibiting a distorted square coordination environment. These sheets are linked together by weaker perpendicular Ag-N contacts, thus forming a 4 + 2 coordination geometry around the silver atoms. The phase transition has been characterized by DTA, DSC, and measurement of the density, as well as of the ionic conductivity. Both, the room-temperature and the HT phase are electrically insulating. This fact is getting support by DFT band structure calculations within the generalized gradient approximation, using the PBE functional. On the basis of the DFT band structure, the bonding characteristics of both phases are essentially the same. Finally, the implication of the existence of a low-symmetry HT-phase in a crystalline explosive concerning decomposition mechanisms is discussed.

Periodic cation segregation in Cs0.44[Nb2.54W2.46O14] quantified by high-resolution scanning transmission electron microscopy.

PubMed

Heidelmann, Markus; Barthel, Juri; Cox, Gerhard; Weirich, Thomas E

2014-10-01

The atomic structure of Cs0.44[Nb2.54W2.46O14] closely resembles the structure of the most active catalyst for the synthesis of acrylic acid, the M1 phase of Mo10V2(4+)Nb2TeO42-x. Consistently with observations made for the latter compound, the high-angle electron scattering signal recorded by scanning transmission electron microscopy shows a significant intensity variation, which repeats periodically with the projected crystallographic unit cell. The occupation factors for the individual mixed Nb/W atomic columns are extracted from the observed intensity variations. For this purpose, experimental images and simulated images are compared on an identical intensity scale, which enables a quantification of the cation distribution. According to our analysis specific sites possess low tungsten concentrations of 25%, whereas other sites have tungsten concentrations above 70%. These findings allow us to refine the existing structure model of the target compound, which has until now described a uniform distribution of the niobium and tungsten atoms in the unit cell, showing that the similarity between Cs0.44[Nb2.54W2.46O14] and the related catalytic compounds also extends to the level of the cation segregation.

A novel perovskite-like Ta-bronze KTa1+zO3: preparation, stoichiometry, conductivity and crystal structure studies.

PubMed

Arakcheeva, A; Chapuis, G; Grinevitch, V; Shamray, V

2001-04-01

A new cubic Ta-bronze (1) KTa(1+z)(+(5-delta))O(3) [z approximately 0.107 (3)] was obtained on a cathode by molten salt electrolysis of the system K(2)TaOF(5)-K(3)TaO(2)F(4)-(KF + NaF + LiF)(eutectic). Black, metallic cubic crystals of (1) are formed together with tetragonal beta-Ta. The perovskite-like crystal structure of (1) [a = 4.005 (1) A, space group Pm3m] was refined with anharmonic displacement parameters for Ta and K atoms and anisotropic displacement parameters for a split O-atom position [KM4CCD diffractometer; lambda(Mo Kalpha); 3320 measured reflections with I > 3sigma(I); R = 0.0095, wR = 0.0065, Deltarho(min) = -0.91 e A(-3), Deltarho(max) = 0.65 e A(-3)]. Defects in the O and K atomic positions were found. (1) is a semiconductor in the temperature range 4-300 K, whereas the well studied and closely related colourless transparent crystals KTa(+5)O(3) (2) are dielectric. Differences in the properties of (1) and (2) are assumed to be connected with the existence of Ta dumb-bells statistically distributed into the KTaO(3) matrix.

Unique coordination of pyrazine in T[Ni(CN){sub 4}].2pyz with T=Mn, Zn, Cd

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

Lemus-Santana, A.A.; Rodriguez-Hernandez, J.; Castillo, L.F. del, E-mail: lfelipe@servidor.unam.m

2009-04-15

The materials under study, T[Ni(CN){sub 4}].2pyz with T=Mn, Zn, Cd, were prepared by separation of T[Ni(CN){sub 4}] layers in citrate aqueous solution to allow the intercalation of the pyrazine molecules. The obtained solids were characterized from chemical analyses, X-ray diffraction, infrared, Raman, thermogravimetry, UV-Vis, magnetic and adsorption data. Their crystal structure was solved from ab initio using direct methods and then refined by the Rietveld method. A unique coordination for pyrazine to metal centers at neighboring layers was observed. The pyrazine molecule is found forming a bridge between Ni and T atoms, quite different from the proposed structures for T=Fe,more » Ni where it remains coordinated to two T atoms to form a vertical pillar between neighboring layers. The coordination of pyrazine to both Ni and T atoms minimizes the material free volume and leads to form a hydrophobic framework. On heating the solids remain stable up to 140 deg. C. No CO{sub 2} and H{sub 2} adsorption was observed in the small free spaces of their frameworks. - Graphical abstract: Framework for T[Ni(CN){sub 4}].2pyz with T=Mn, Zn, Cd.« less

Low-temperature x-ray crystal structure analysis of the cage-structured compounds M Be13 (M =La,Sm, and U)

NASA Astrophysics Data System (ADS)

Hidaka, Hiroyuki; Nagata, Ryoma; Tabata, Chihiro; Shimizu, Yusei; Miura, Naoyuki; Yanagisawa, Tatsuya; Amitsuka, Hiroshi

2018-05-01

The beryllides M Be13 (M = rare earths and actinides) crystallize in a NaZn13-type cubic structure, which can be categorized as a cage-structured compound. In this study, powder x-ray diffraction measurements have been performed on LaBe13,SmBe13, and UBe13 in the temperature range between 7 and 300 K in order to investigate their crystallographic characteristics systematically. They keep the NaZn13-type cubic structure down to the lowest temperature. We estimated their Debye temperature to be 600-750 K from analyses of the temperature dependence of a lattice parameter, being in good agreement with the values reported previously. Rietveld refinements on the obtained powder patterns revealed that the M atom in the 8 a site is located in an almost ideal snub cube formed by 24 BeII atoms in the 96 i site, whose caged structure is unchanged even at the low temperatures. In addition, it is argued from the temperature variation of an isotropic mean-square displacement parameter that the M Be13 compounds commonly have a low-energy phonon mode, which can be described by a model assuming an Einstein oscillation of the M atom with a characteristic temperature of ˜160 K.

Quantitative ROESY analysis of computational models: structural studies of citalopram and β-cyclodextrin complexes by (1) H-NMR and computational methods.

PubMed

Ali, Syed Mashhood; Shamim, Shazia

2015-07-01

Complexation of racemic citalopram with β-cyclodextrin (β-CD) in aqueous medium was investigated to determine atom-accurate structure of the inclusion complexes. (1) H-NMR chemical shift change data of β-CD cavity protons in the presence of citalopram confirmed the formation of 1 : 1 inclusion complexes. ROESY spectrum confirmed the presence of aromatic ring in the β-CD cavity but whether one of the two or both rings was not clear. Molecular mechanics and molecular dynamic calculations showed the entry of fluoro-ring from wider side of β-CD cavity as the most favored mode of inclusion. Minimum energy computational models were analyzed for their accuracy in atomic coordinates by comparison of calculated and experimental intermolecular ROESY peak intensities, which were not found in agreement. Several least energy computational models were refined and analyzed till calculated and experimental intensities were compatible. The results demonstrate that computational models of CD complexes need to be analyzed for atom-accuracy and quantitative ROESY analysis is a promising method. Moreover, the study also validates that the quantitative use of ROESY is feasible even with longer mixing times if peak intensity ratios instead of absolute intensities are used. Copyright © 2015 John Wiley & Sons, Ltd.

SU-E-J-128: Two-Stage Atlas Selection in Multi-Atlas-Based Image Segmentation

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

Zhao, T; Ruan, D

2015-06-15

Purpose: In the new era of big data, multi-atlas-based image segmentation is challenged by heterogeneous atlas quality and high computation burden from extensive atlas collection, demanding efficient identification of the most relevant atlases. This study aims to develop a two-stage atlas selection scheme to achieve computational economy with performance guarantee. Methods: We develop a low-cost fusion set selection scheme by introducing a preliminary selection to trim full atlas collection into an augmented subset, alleviating the need for extensive full-fledged registrations. More specifically, fusion set selection is performed in two successive steps: preliminary selection and refinement. An augmented subset is firstmore » roughly selected from the whole atlas collection with a simple registration scheme and the corresponding preliminary relevance metric; the augmented subset is further refined into the desired fusion set size, using full-fledged registration and the associated relevance metric. The main novelty of this work is the introduction of an inference model to relate the preliminary and refined relevance metrics, based on which the augmented subset size is rigorously derived to ensure the desired atlases survive the preliminary selection with high probability. Results: The performance and complexity of the proposed two-stage atlas selection method were assessed using a collection of 30 prostate MR images. It achieved comparable segmentation accuracy as the conventional one-stage method with full-fledged registration, but significantly reduced computation time to 1/3 (from 30.82 to 11.04 min per segmentation). Compared with alternative one-stage cost-saving approach, the proposed scheme yielded superior performance with mean and medium DSC of (0.83, 0.85) compared to (0.74, 0.78). Conclusion: This work has developed a model-guided two-stage atlas selection scheme to achieve significant cost reduction while guaranteeing high segmentation accuracy. The benefit in both complexity and performance is expected to be most pronounced with large-scale heterogeneous data.« less

Crystal structure of hydrocortisone acetate, C23H32O6

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

Kaduk, James A.; Gindhart, Amy M.; Blanton, Thomas N.

The crystal structure of hydrocortisone acetate has been solved and refined using synchrotron X-ray powder diffraction data, and optimized using density functional techniques. Hydrocortisone acetate crystallizes in space groupP2 1(#4) witha= 8.85173(3) Å,b= 13.53859(3) Å,c= 8.86980(4) Å,β= 101.5438(3)°,V= 1041.455(6) Å 3, andZ= 2. Both hydroxyl groups form hydrogen bonds to the ketone oxygen atom on the steroid ring system, resulting in a three-dimensional hydrogen bond network. The powder pattern has been submitted to ICDD for inclusion in the Powder Diffraction File™.

Integration of neutron time-of-flight single-crystal Bragg peaks in reciprocal space

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

Schultz, Arthur J; Joergensen, Mads; Wang, Xiaoping

2014-01-01

The intensity of single crystal Bragg peaks obtained by mapping neutron time-of-flight event data into reciprocal space and integrating in various ways are compared. These include spherical integration with a fixed radius, ellipsoid fitting and integrating of the peak intensity and one-dimensional peak profile fitting. In comparison to intensities obtained by integrating in real detector histogram space, the data integrated in reciprocal space results in better agreement factors and more accurate atomic parameters. Furthermore, structure refinement using integrated intensities from one-dimensional profile fitting is demonstrated to be more accurate than simple peak-minus-background integration.

Solving local structure around dopants in metal nanoparticles with ab initio modeling of X-ray absorption near edge structure

DOE PAGES

Timoshenko, J.; Shivhare, A.; Scott, R. W.; ...

2016-06-30

We adopted ab-initio X-ray Absorption Near Edge Structure (XANES) modelling for structural refinement of local environments around metal impurities in a large variety of materials. Our method enables both direct modelling, where the candidate structures are known, and the inverse modelling, where the unknown structural motifs are deciphered from the experimental spectra. We present also estimates of systematic errors, and their influence on the stability and accuracy of the obtained results. We illustrate our approach by following the evolution of local environment of palladium atoms in palladium-doped gold thiolate clusters upon chemical and thermal treatments.

Synthesis of LiNiO2 cathode materials with homogeneous Al doping at the atomic level

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

Liu, Zengcai; Zhen, Honghe; Kim, Yoongu

2011-01-01

Aluminum doped LiNiO2 cathode materials are synthesized by using Raney nickel as the starting material. The structure and composition are characterized by X-ray diffraction (XRD) and scanning electron microscopy (SEM) coupled with elemental mapping. The lithium deficiency is analyzed by Rieveld refinement. The initial capacity and retention of capacity are correlated to the lithium deficiency of the resulting cathode material. Using strong oxidant of Li2O2 in the synthesis results in materials with improved electrochemical cyclability. The improvement is related to the diminishing of lithium deficiency in strong oxidizing synthesis conditions.

Sharp chemical interface in epitaxial Fe{sub 3}O{sub 4} thin films

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

Gálvez, S.; Rubio-Zuazo, J., E-mail: rubio@esrf.fr; Salas-Colera, E.

Chemically sharp interface was obtained on single phase single oriented Fe{sub 3}O{sub 4} (001) thin film (7 nm) grown on NiO (001) substrate using oxygen assisted molecular beam epitaxy. Refinement of the atomic structure, stoichiometry, and oxygen vacancies were determined by soft and hard x-ray photoelectron spectroscopy, low energy electron diffraction and synchrotron based X-ray reflectivity, and X-ray diffraction. Our results demonstrate an epitaxial growth of the magnetite layer, perfect iron stoichiometry, absence of oxygen vacancies, and the existence of an intermixing free interface. Consistent magnetic and electrical characterizations are also shown.

Tin-Platinum catalysts interactions on titania and silica

NASA Astrophysics Data System (ADS)

Nava, N.; Del Angel, P.; Salmones, J.; Baggio-Saitovitch, E.; Santiago, P.

2007-09-01

Pt-Sn was supported on titania and silica, and the resulting interactions between the components in prepared samples and the resulting interactions between the components before and after treatment with hydrogen were characterized by Mössbauer spectroscopy, X-ray diffraction, Rietveld refinement, high-resolution transmission electron microscopy (HRTEM) and catalytic tests data. Results show the presence of Pt and SnO 2 after calcinations, and Pt 3Sn, PtSn and PtSn 3 after reduction. Rietveld analysis shows that some Ti 4+ are replaced by Sn 4+ atoms in the titania structure. Finally, HRTEM and the practically absence of activity observed confirms that metallic platinum is encapsulated.

Synthesis-atomic structure-properties relationships in metallic nanoparticles by total scattering experiments and 3D computer simulations: case of Pt-Ru nanoalloy catalysts

NASA Astrophysics Data System (ADS)

Prasai, Binay; Ren, Yang; Shan, Shiyao; Zhao, Yinguang; Cronk, Hannah; Luo, Jin; Zhong, Chuan-Jian; Petkov, Valeri

2015-04-01

An approach to determining the 3D atomic structure of metallic nanoparticles (NPs) in fine detail and using the unique knowledge obtained for rationalizing their synthesis and properties targeted for optimization is described and exemplified on Pt-Ru alloy NPs of importance to the development of devices for clean energy conversion such as fuel cells. In particular, PtxRu100-x alloy NPs, where x = 31, 49 and 75, are synthesized by wet chemistry and activated catalytically by a post-synthesis treatment involving heating under controlled N2-H2 atmosphere. So-activated NPs are evaluated as catalysts for gas-phase CO oxidation and ethanol electro-oxidation reactions taking place in fuel cells. Both as-synthesized and activated NPs are characterized structurally by total scattering experiments involving high-energy synchrotron X-ray diffraction coupled to atomic pair distribution functions (PDFs) analysis. 3D structure models both for as-synthesized and activated NPs are built by molecular dynamics simulations based on the archetypal for current theoretical modelling Sutton-Chen method. Models are refined against the experimental PDF data by reverse Monte Carlo simulations and analysed in terms of prime structural characteristics such as metal-to-metal bond lengths, bond angles and first coordination numbers for Pt and Ru atoms. Analysis indicates that, though of a similar type, the atomic structure of as-synthesized and respective activated NPs differ in several details of importance to NP catalytic properties. Structural characteristics of activated NPs and data for their catalytic activity are compared side by side and strong evidence found that electronic effects, indicated by significant changes in Pt-Pt and Ru-Ru metal bond lengths at NP surface, and practically unrecognized so far atomic ensemble effects, indicated by distinct stacking of atomic layers near NP surface and prevalence of particular configurations of Pt and Ru atoms in these layers, contribute to the observed enhancement of the catalytic activity of PtxRu100-x alloy NPs at x ~ 50. Implications of so-established relationships between the atomic structure and catalytic activity of Pt-Ru alloy NPs on efforts aimed at improving further the latter by tuning-up the former are discussed and the usefulness of detailed NP structure studies to advancing science and technology of metallic NPs - exemplified.An approach to determining the 3D atomic structure of metallic nanoparticles (NPs) in fine detail and using the unique knowledge obtained for rationalizing their synthesis and properties targeted for optimization is described and exemplified on Pt-Ru alloy NPs of importance to the development of devices for clean energy conversion such as fuel cells. In particular, PtxRu100-x alloy NPs, where x = 31, 49 and 75, are synthesized by wet chemistry and activated catalytically by a post-synthesis treatment involving heating under controlled N2-H2 atmosphere. So-activated NPs are evaluated as catalysts for gas-phase CO oxidation and ethanol electro-oxidation reactions taking place in fuel cells. Both as-synthesized and activated NPs are characterized structurally by total scattering experiments involving high-energy synchrotron X-ray diffraction coupled to atomic pair distribution functions (PDFs) analysis. 3D structure models both for as-synthesized and activated NPs are built by molecular dynamics simulations based on the archetypal for current theoretical modelling Sutton-Chen method. Models are refined against the experimental PDF data by reverse Monte Carlo simulations and analysed in terms of prime structural characteristics such as metal-to-metal bond lengths, bond angles and first coordination numbers for Pt and Ru atoms. Analysis indicates that, though of a similar type, the atomic structure of as-synthesized and respective activated NPs differ in several details of importance to NP catalytic properties. Structural characteristics of activated NPs and data for their catalytic activity are compared side by side and strong evidence found that electronic effects, indicated by significant changes in Pt-Pt and Ru-Ru metal bond lengths at NP surface, and practically unrecognized so far atomic ensemble effects, indicated by distinct stacking of atomic layers near NP surface and prevalence of particular configurations of Pt and Ru atoms in these layers, contribute to the observed enhancement of the catalytic activity of PtxRu100-x alloy NPs at x ~ 50. Implications of so-established relationships between the atomic structure and catalytic activity of Pt-Ru alloy NPs on efforts aimed at improving further the latter by tuning-up the former are discussed and the usefulness of detailed NP structure studies to advancing science and technology of metallic NPs - exemplified. Electronic supplementary information (ESI) available: XRD patterns, TEM and 3D structure modelling methodology. See DOI: 10.1039/c5nr00800j

Ultra-precise single-ion atomic mass measurements on deuterium and helium-3

NASA Astrophysics Data System (ADS)

Zafonte, S. L.; Van Dyck, R. S., Jr.

2015-04-01

The former University of Washington Penning Trap Mass Spectrometer (UW-PTMS), now located at the Max Planck Institute for Nuclear Physics in Heidelberg, Germany, was used in the decade before the move to determine new values for the deuteron atomic mass, M (2H+) = 2.013 553 212 745(40) u, and the deuterium atomic mass, M (2H) = 2.014 101 778 052(40) u, both of which are now more than an order-of-magnitude more accurate than the previous best 1994-MIT measurements of these quantities. The new value for the deuteron’s mass can then be used with the accepted 2010-CODATA proton mass and the most recent 1999-measurement of the 2.2 MeV gamma-ray binding energy of the deuteron to refine the neutron’s mass to mn = 1.008 664 916 018(435) u which has about half the uncertainty relative to the value computed using that previous 1994-MIT deuterium measurement. As a result, further improvements of mn must now come from a more accurate determination of the wavelength of this gamma ray. In this same period of time, this spectrometer has also been used to determine new values for the helion atomic mass, M (3He2+) = 3.014 932 246 668(43) u, and the neutral helium-3 atomic mass, M (3He) = 3.016 029 321 675(43) u, which are both about 60 times more accurate than the 2006-SMILETRAP measurements, but disagree with the 4.4-times less-accurate 2015-Florida-State measurements by 0.76 nu. It is expected that these helium-3 results will be used in the future 3H/3He mass ratio (to be determined by the Heidelberg, Germany version of the old UW-PTMS) in order to generate a more accurate value for the tritium atomic mass.

Knowledge Extraction from Atomically Resolved Images.

PubMed

Vlcek, Lukas; Maksov, Artem; Pan, Minghu; Vasudevan, Rama K; Kalinin, Sergei V

2017-10-24

Tremendous strides in experimental capabilities of scanning transmission electron microscopy and scanning tunneling microscopy (STM) over the past 30 years made atomically resolved imaging routine. However, consistent integration and use of atomically resolved data with generative models is unavailable, so information on local thermodynamics and other microscopic driving forces encoded in the observed atomic configurations remains hidden. Here, we present a framework based on statistical distance minimization to consistently utilize the information available from atomic configurations obtained from an atomically resolved image and extract meaningful physical interaction parameters. We illustrate the applicability of the framework on an STM image of a FeSe x Te 1-x superconductor, with the segregation of the chalcogen atoms investigated using a nonideal interacting solid solution model. This universal method makes full use of the microscopic degrees of freedom sampled in an atomically resolved image and can be extended via Bayesian inference toward unbiased model selection with uncertainty quantification.

Review of footnotes and annotations to the 1949–2013 tables of standard atomic weights and tables of isotopic compositions of the elements (IUPAC Technical Report)

DOE PAGES

Coplen, Tyler B.; Holden, Norman E.

2016-01-01

Abstract The Commission on Isotopic Abundances and Atomic Weights uses annotations given in footnotes that are an integral part of the Tables of Standard Atomic Weights to alert users to the possibilities of quite extraordinary occurrences, as well as sources with abnormal atomic-weight values outside an otherwise acceptable range. The basic need for footnotes to the Standard Atomic Weights Table and equivalent annotations to the Table of Isotopic Compositions of the Elements arises from the necessity to provide users with information that is relevant to one or more elements, but that cannot be provided using numerical data in columns. Anymore » desire to increase additional information conveyed by annotations to these Tables is tempered by the need to preserve a compact format and a style that can alert users, who would not be inclined to consult either the last full element-by-element review or the full text of a current Standard Atomic Weights of the Elements report. Since 1989, the footnotes of the Tables of Standard Atomic Weights and the annotations in column 5 of the Table of Isotopic Compositions of the Elements have been harmonized by use of three lowercase footnotes, “g”, “m”, and “r”, that signify geologically exceptionally specimens (“g”), modified isotopic compositions in material subjected to undisclosed or inadvertent isotopic fractionation (“m”), and the range in isotopic composition of normal terrestrial material prevents more precise atomic-weight value being given (“r”). As some elements are assigned intervals for their standard atomic-weight values (applies to 12 elements since 2009), footnotes “g” and “r” are no longer needed for these elements.« less

Review of footnotes and annotations to the 1949–2013 tables of standard atomic weights and tables of isotopic compositions of the elements (IUPAC Technical Report)

USGS Publications Warehouse

Coplen, Tyler B.; Holden, Norman E.

2016-01-01

The Commission on Isotopic Abundances and Atomic Weights uses annotations given in footnotes that are an integral part of the Tables of Standard Atomic Weights to alert users to the possibilities of quite extraordinary occurrences, as well as sources with abnormal atomic-weight values outside an otherwise acceptable range. The basic need for footnotes to the Standard Atomic Weights Table and equivalent annotations to the Table of Isotopic Compositions of the Elements arises from the necessity to provide users with information that is relevant to one or more elements, but that cannot be provided using numerical data in columns. Any desire to increase additional information conveyed by annotations to these Tables is tempered by the need to preserve a compact format and a style that can alert users, who would not be inclined to consult either the last full element-by-element review or the full text of a current Standard Atomic Weights of the Elements report. Since 1989, the footnotes of the Tables of Standard Atomic Weights and the annotations in column 5 of the Table of Isotopic Compositions of the Elements have been harmonized by use of three lowercase footnotes, “g”, “m”, and “r”, that signify geologically exceptionally specimens (“g”), modified isotopic compositions in material subjected to undisclosed or inadvertent isotopic fractionation (“m”), and the range in isotopic composition of normal terrestrial material prevents more precise atomic-weight value being given (“r”). As some elements are assigned intervals for their standard atomic-weight values (applies to 12 elements since 2009), footnotes “g” and “r” are no longer needed for these elements.

Single-Slit Diffraction Pattern of a Thermal Atomic Potassium Beam

ERIC Educational Resources Information Center

Leavitt, John A.; Bills, Francis A.

1969-01-01

The diffraction of a full thermal atomic potassium beam by a single slit was observed. Four experimental diffraction patterns were compared with that predicted by de Brogtie's hypothesis and simple scalar Fresnel diffraction theory. Possible reasons for the differences were discussed. (LC)

Anisotropic Interactions between Cold Rydberg Atoms

DTIC Science & Technology

2015-09-28

AFRL-AFOSR-CL-TR-2015-0002 Anisotropic interactions between cold Rydberg atoms Luis Marcassa INSTITUTO DE FISICA DE SAO CARLOS Final Report 09/28...problem with the report +551633739806 Organization / Institution name Instituto de Fisica de Sao Carlos Grant/Contract Title The full title of the

Lattice model for amyloid peptides: OPEP force field parametrization and applications to the nucleus size of Alzheimer’s peptides

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

Tran, Thanh Thuy; Nguyen, Phuong H., E-mail: phuong.nguyen@ibpc.fr; Derreumaux, Philippe, E-mail: philippe.derreumaux@ibpc.fr

Coarse-grained protein lattice models approximate atomistic details and keep the essential interactions. They are, therefore, suitable for capturing generic features of protein folding and amyloid formation at low computational cost. As our aim is to study the critical nucleus sizes of two experimentally well-characterized peptide fragments Aβ{sub 16−22} and Aβ{sub 37−42} of the full length Aβ{sub 1−42} Alzheimer’s peptide, it is important that simulations with the lattice model reproduce all-atom simulations. In this study, we present a comprehensive force field parameterization based on the OPEP (Optimized Potential for Efficient protein structure Prediction) force field for an on-lattice protein model, whichmore » incorporates explicitly the formation of hydrogen bonds and directions of side-chains. Our bottom-up approach starts with the determination of the best lattice force parameters for the Aβ{sub 16−22} dimer by fitting its equilibrium parallel and anti-parallel β-sheet populations to all-atom simulation results. Surprisingly, the calibrated force field is transferable to the trimer of Aβ{sub 16−22} and the dimer and trimer of Aβ{sub 37−42}. Encouraged by this finding, we characterized the free energy landscapes of the two decamers. The dominant structure of the Aβ{sub 16−22} decamer matches the microcrystal structure. Pushing the simulations for aggregates between 4-mer and 12-mer suggests a nucleus size for fibril formation of 10 chains. In contrast, the Aβ{sub 37−42} decamer is largely disordered with mixed by parallel and antiparallel chains, suggesting that the nucleus size is >10 peptides. Our refined force field coupled to this on-lattice model should provide useful insights into the critical nucleation number associated with neurodegenerative diseases.« less

Improving consensus structure by eliminating averaging artifacts

PubMed Central

KC, Dukka B

2009-01-01

Background Common structural biology methods (i.e., NMR and molecular dynamics) often produce ensembles of molecular structures. Consequently, averaging of 3D coordinates of molecular structures (proteins and RNA) is a frequent approach to obtain a consensus structure that is representative of the ensemble. However, when the structures are averaged, artifacts can result in unrealistic local geometries, including unphysical bond lengths and angles. Results Herein, we describe a method to derive representative structures while limiting the number of artifacts. Our approach is based on a Monte Carlo simulation technique that drives a starting structure (an extended or a 'close-by' structure) towards the 'averaged structure' using a harmonic pseudo energy function. To assess the performance of the algorithm, we applied our approach to Cα models of 1364 proteins generated by the TASSER structure prediction algorithm. The average RMSD of the refined model from the native structure for the set becomes worse by a mere 0.08 Å compared to the average RMSD of the averaged structures from the native structure (3.28 Å for refined structures and 3.36 A for the averaged structures). However, the percentage of atoms involved in clashes is greatly reduced (from 63% to 1%); in fact, the majority of the refined proteins had zero clashes. Moreover, a small number (38) of refined structures resulted in lower RMSD to the native protein versus the averaged structure. Finally, compared to PULCHRA [1], our approach produces representative structure of similar RMSD quality, but with much fewer clashes. Conclusion The benchmarking results demonstrate that our approach for removing averaging artifacts can be very beneficial for the structural biology community. Furthermore, the same approach can be applied to almost any problem where averaging of 3D coordinates is performed. Namely, structure averaging is also commonly performed in RNA secondary prediction [2], which could also benefit from our approach. PMID:19267905

Structure determination of two modulated gamma-brass structures in the Zn-Pd System through a (3 + 1)-dimensional space description.

PubMed

Gourdon, Olivier; Izaola, Zunbeltz; Elcoro, Luis; Petricek, Vaclav; Miller, Gordon J

2009-10-19

The structure determination of two composite compounds in the Zn-Pd system with close relationships to the cubic gamma-brass structure Zn(11-delta)Pd(2+delta) is reported. Their structures have been solved from single crystal X-ray diffraction data within a (3 + 1)-dimensional [(3 + 1)D] formalism. Zn(75.7(7))Pd(24.3) and Zn(78.8(7))Pd(21.2) crystallize with orthorhombic symmetry, superspace group Xmmm(00gamma)0s0 (X = [(1/2,1/2,0,0); (0,1/2,1/2,1/2); (1/2,0,1/2,1/2)]), with the following lattice parameters, respectively: a(s) = 12.929(3) A, b(s) = 9.112(4) A, c(s) = 2.5631(7) A, q = 8/13 c* and V(s) = 302.1(3) A(3) and a(s) = 12.909(3) A, b(s) = 9.115(3) A, c(s) = 2.6052(6) A, q = 11/18 c* and V(s) = 306.4(2) A(3). Their structures may be considered as commensurate because they can be refined in the conventional 3D space groups (Cmce and Cmcm, respectively) using supercells, but they also refined within the (3 + 1)D formalism to residual factors R = 3.14% for 139 parameters and 1184 independent reflections for Zn(75.7(7))Pd(24.3) and R = 3.16% for 175 parameters and 1804 independent reflections for Zn(78.8(7))Pd(21.2). The use of the (3 + 1)D formalism improves the results of the refinement and leads to a better understanding of the complexity of the atomic arrangement through the various modulations (occupation waves and displacive waves). Our refinements emphasize a unique Pd/Zn occupancy modulation at the center of distorted icosahedra, a modulation which correlates with the distortion of these polyhedra.

Topological quantum computation of the Dold-Thom functor

NASA Astrophysics Data System (ADS)

Ospina, Juan

2014-05-01

A possible topological quantum computation of the Dold-Thom functor is presented. The method that will be used is the following: a) Certain 1+1-topological quantum field theories valued in symmetric bimonoidal categories are converted into stable homotopical data, using a machinery recently introduced by Elmendorf and Mandell; b) we exploit, in this framework, two recent results (independent of each other) on refinements of Khovanov homology: our refinement into a module over the connective k-theory spectrum and a stronger result by Lipshitz and Sarkar refining Khovanov homology into a stable homotopy type; c) starting from the Khovanov homotopy the Dold-Thom functor is constructed; d) the full construction is formulated as a topological quantum algorithm. It is conjectured that the Jones polynomial can be described as the analytical index of certain Dirac operator defined in the context of the Khovanov homotopy using the Dold-Thom functor. As a line for future research is interesting to study the corresponding supersymmetric model for which the Khovanov-Dirac operator plays the role of a supercharge.

Air-atomizing splash-cone fuel nozzle reduces pollutant emissions from turbojet engines

NASA Technical Reports Server (NTRS)

Ingebo, R. D.; Norgren, C. T.

1973-01-01

Advantages of fuel nozzle over conventional pressure-atomizing fuel nozzles: simplicity of construction, ability to distribute fuel-air mixture uniformly across full height of combustor without using auxiliary air supply, reliability when using contaminated fuels, and durability of nozzle at high operating temperatures.

A measurement of the angular distribution of 5 eV atomic oxygen scattered off a solid surface in earth orbit

NASA Technical Reports Server (NTRS)

Gregory, John C.; Peters, Palmer N.

1986-01-01

The angular distribution of 5 eV atomic oxygen scattered off a polished vitreous carbon surface was measured on a recent Space Shuttle flight. The experimental apparatus was of novel design, completely passive, and used thin silver films as the recording device for oxygen atoms. Most of the incident oxygen was contained in the reflected beam and remained in an active form and probably still atoms. Allowance was made for 12 percent loss of incident atoms which are converted to CO at the carbon surface. The scattered distribution which is wide lobular, peaking 15 deg in the forward direction, shows almost but not quite full accommodation.

On-chip quantum tomography of mechanical nanoscale oscillators with guided Rydberg atoms

NASA Astrophysics Data System (ADS)

Sanz-Mora, A.; Wüster, S.; Rost, J.-M.

2017-07-01

Nanomechanical oscillators as well as Rydberg-atomic waveguides hosted on microfabricated chip surfaces hold promise to become pillars of future quantum technologies. In a hybrid platform with both, we show that beams of Rydberg atoms in waveguides can quantum coherently interrogate and manipulate nanomechanical elements, allowing full quantum state tomography. Central to the tomography are quantum nondemolition measurements using the Rydberg atoms as probes. Quantum coherent displacement of the oscillator is also made possible by driving the atoms with external fields while they interact with the oscillator. We numerically demonstrate the feasibility of this fully integrated on-chip control and read-out suite for quantum nanomechanics, taking into account noise and error sources.

Poly[[tetra-μ-cyanido-κ8 C:N-dodeca-cyanido-κ12 C-tris­(N,N-di­methyl­formamide-κO)tris­(methanol-κO)tris­(3,4,7,8-tetra­methyl-1,10-phenanthroline-κ2 N,N′)trimanganese(II)ditungstate(V)] dihydrate

PubMed Central

Yang, Fei-Lin; Yang, Dan

2014-01-01

The asymmetric unit of the title compound, {[Mn3{W(CN)8}2(C16H16N2)3(C3H7NO)3(CH3OH)3]·2H2O}n, consists of three [Mn(N,N-di­methyl­formamide)(methanol)(3,4,7,8-tetra­methyl-1,10-phenanthroline)]2+ cations, two [W(CN)8]3− anions and two water mol­ecules. Each water mol­ecule is disordered over three sets of sites, with a refined occupancy ratio of 0.310 (9):0.275 (9):0.415 (9) for one mol­ecule and 0.335 (9):0.288 (9):0.377 (9) for the other mol­ecule. The MnII atoms exhibit a distorted octa­hedral geometry, while the WV atoms adopt a distorted square-anti­prismatic geometry. The MnII and WV atoms are linked alternatively through cyanide groups, forming a tetra­nuclear 12-atom rhombic metallacycle. Adjacent metallacycles are further connected by μ2-bridging cyanide anions, generating a 3,2-chain structure running parallel to [101]. Inter­chain π–π inter­actions are observed [centroid–centroid distances = 3.763 (3) and 3.620 (2) Å]. PMID:24860305

Integrated description of protein dynamics from room-temperature X-ray crystallography and NMR

PubMed Central

Fenwick, R. Bryn; van den Bedem, Henry; Fraser, James S.; Wright, Peter E.

2014-01-01

Detailed descriptions of atomic coordinates and motions are required for an understanding of protein dynamics and their relation to molecular recognition, catalytic function, and allostery. Historically, NMR relaxation measurements have played a dominant role in the determination of the amplitudes and timescales (picosecond–nanosecond) of bond vector fluctuations, whereas high-resolution X-ray diffraction experiments can reveal the presence of and provide atomic coordinates for multiple, weakly populated substates in the protein conformational ensemble. Here we report a hybrid NMR and X-ray crystallography analysis that provides a more complete dynamic picture and a more quantitative description of the timescale and amplitude of fluctuations in atomic coordinates than is obtainable from the individual methods alone. Order parameters (S2) were calculated from single-conformer and multiconformer models fitted to room temperature and cryogenic X-ray diffraction data for dihydrofolate reductase. Backbone and side-chain order parameters derived from NMR relaxation experiments are in excellent agreement with those calculated from the room-temperature single-conformer and multiconformer models, showing that the picosecond timescale motions observed in solution occur also in the crystalline state. These motions are quenched in the crystal at cryogenic temperatures. The combination of NMR and X-ray crystallography in iterative refinement promises to provide an atomic resolution description of the alternate conformational substates that are sampled through picosecond to nanosecond timescale fluctuations of the protein structure. The method also provides insights into the structural heterogeneity of nonmethyl side chains, aromatic residues, and ligands, which are less commonly analyzed by NMR relaxation measurements. PMID:24474795

ZVI-CLAY SOIL MIXING TREATS DNAPL SOURCE AREA AT 35-FOOT DEPTH

EPA Science Inventory

The DuPont Company and Colorado State University (CSU) are collaborating in development and refinement of a technology that involves in-situ admixing of contaminated soil, granular zero valent iron (ZVI), and clay using conventional soil mixing equipment. A full-scale application...

Refined ambient PM2.5 exposure surrogates and the risk of myocardial infarction

EPA Science Inventory

Using a case-crossover study design and conditional logistic regression, we compared the relative odds of transmural (full-wall) myocardial infarction (MI) calculated using exposure surrogates that account for human activity patterns and the indoor transport of ambient PM_2....

Engineering quantum hyperentangled states in atomic systems

NASA Astrophysics Data System (ADS)

Nawaz, Mehwish; -Islam, Rameez-ul; Abbas, Tasawar; Ikram, Manzoor

2017-11-01

Hyperentangled states have boosted many quantum informatics tasks tremendously due to their high information content per quantum entity. Until now, however, the engineering and manipulation of such states were limited to photonic systems only. In present article, we propose generating atomic hyperentanglement involving atomic internal states as well as atomic external momenta states. Hypersuperposition, hyperentangled cluster, Bell and Greenberger-Horne-Zeilinger states are engineered deterministically through resonant and off-resonant Bragg diffraction of neutral two-level atoms. Based on the characteristic parameters of the atomic Bragg diffraction, such as comparatively large interaction times and spatially well-separated outputs, such decoherence resistant states are expected to exhibit good overall fidelities and offer the evident benefits of full controllability, along with extremely high detection efficiency, over the counterpart photonic states comprised entirely of flying qubits.

Matterwave interferometric velocimetry of cold Rb atoms

NASA Astrophysics Data System (ADS)

Carey, Max; Belal, Mohammad; Himsworth, Matthew; Bateman, James; Freegarde, Tim

2018-03-01

We consider the matterwave interferometric measurement of atomic velocities, which forms a building block for all matterwave inertial measurements. A theoretical analysis, addressing both the laboratory and atomic frames and accounting for residual Doppler sensitivity in the beamsplitter and recombiner pulses, is followed by an experimental demonstration, with measurements of the velocity distribution within a 20 ?K cloud of rubidium atoms. Our experiments use Raman transitions between the long-lived ground hyperfine states, and allow quadrature measurements that yield the full complex interferometer signal and hence discriminate between positive and negative velocities. The technique is most suitable for measurement of colder samples.

Matterwave interferometric velocimetry of cold Rb atoms

NASA Astrophysics Data System (ADS)

Carey, Max; Belal, Mohammad; Himsworth, Matthew; Bateman, James; Freegarde, Tim

2018-02-01

We consider the matterwave interferometric measurement of atomic velocities, which forms a building block for all matterwave inertial measurements. A theoretical analysis, addressing both the laboratory and atomic frames and accounting for residual Doppler sensitivity in the beamsplitter and recombiner pulses, is followed by an experimental demonstration, with measurements of the velocity distribution within a 20 $\\mu$K cloud of rubidium atoms. Our experiments use Raman transitions between the long-lived ground hyperfine states, and allow quadrature measurements that yield the full complex interferometer signal and hence discriminate between positive and negative velocities. The technique is most suitable for measurement of colder samples.

FRankenstein becomes a cyborg: the automatic recombination and realignment of fold recognition models in CASP6.

PubMed

Kosinski, Jan; Gajda, Michal J; Cymerman, Iwona A; Kurowski, Michal A; Pawlowski, Marcin; Boniecki, Michal; Obarska, Agnieszka; Papaj, Grzegorz; Sroczynska-Obuchowicz, Paulina; Tkaczuk, Karolina L; Sniezynska, Paulina; Sasin, Joanna M; Augustyn, Anna; Bujnicki, Janusz M; Feder, Marcin

2005-01-01

In the course of CASP6, we generated models for all targets using a new version of the "FRankenstein's monster approach." Previously (in CASP5) we were able to build many very accurate full-atom models by selection and recombination of well-folded fragments obtained from crude fold recognition (FR) results, followed by optimization of the sequence-structure fit and assessment of alternative alignments on the structural level. This procedure was however very arduous, as most of the steps required extensive visual and manual input from the human modeler. Now, we have automated the most tedious steps, such as superposition of alternative models, extraction of best-scoring fragments, and construction of a hybrid "monster" structure, as well as generation of alternative alignments in the regions that remain poorly scored in the refined hybrid model. We have also included the ROSETTA method to construct those parts of the target for which no reasonable structures were generated by FR methods (such as long insertions and terminal extensions). The analysis of successes and failures of the current version of the FRankenstein approach in modeling of CASP6 targets reveals that the considerably streamlined and automated method performs almost as well as the initial, mostly manual version, which suggests that it may be a useful tool for accurate protein structure prediction even in the hands of nonexperts. 2005 Wiley-Liss, Inc.

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

PubMed

Gaudin; Petricek; Boucher; Taulelle; Evain

2000-12-01

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

The molecular structure of the isopoly complex ion, decavanadate (V10O286-)

USGS Publications Warehouse

Evans, H.T.

1966-01-01

The structure of the decavanadate ion V10O286- has been found by a determination of the crystal structure of K2Zn2V10O28?? 16H2O. The soluble, orange crystals are triclinic with space group P1 and have a unit cell with a = 10.778 A, b = 11.146 A, c = 8.774 A, ?? = 104?? 57???, ?? = 109?? 3???', and ?? = 65?? 0??? (Z = 1). The structure was solved from a three-dimensional Patterson map based on 5143 Weissenberg-film data. The full-matrix, least-squares refinement gave R = 0.094 and ?? for V-O bond lengths of 0.008 A. The unit cell contains one V10O286- unit, two Zn(H2O)62+ groups, two K+ ions, and four additional water molecules. The decavanadate ion is an isolated group of ten condensed VO6 octahedra, six in a rectangular 2 x 3 array sharing edges, and four more, two fitted in above and two below by sharing sloping edges. The structure, which is based on a sodium-chloride-like arrangement of V and O atoms, has a close relationship to other isopoly complex molybdates, niobates, and tantalates. Strong distortions in the VO6 octahedra are analogous to square-pyramid and other special coordination features known in other vanadate structures.

A Game-Theoretic Approach to Branching Time Abstract-Check-Refine Process

NASA Technical Reports Server (NTRS)

Wang, Yi; Tamai, Tetsuo

2009-01-01

Since the complexity of software systems continues to grow, most engineers face two serious problems: the state space explosion problem and the problem of how to debug systems. In this paper, we propose a game-theoretic approach to full branching time model checking on three-valued semantics. The three-valued models and logics provide successful abstraction that overcomes the state space explosion problem. The game style model checking that generates counter-examples can guide refinement or identify validated formulas, which solves the system debugging problem. Furthermore, output of our game style method will give significant information to engineers in detecting where errors have occurred and what the causes of the errors are.

Additional Improvements to the NASA Lewis Ice Accretion Code LEWICE

NASA Technical Reports Server (NTRS)

Wright, William B.; Bidwell, Colin S.

1995-01-01

Due to the feedback of the user community, three major features have been added to the NASA Lewis ice accretion code LEWICE. These features include: first, further improvements to the numerics of the code so that more time steps can be run and so that the code is more stable; second, inclusion and refinement of the roughness prediction model described in an earlier paper; third, inclusion of multi-element trajectory and ice accretion capabilities to LEWICE. This paper will describe each of these advancements in full and make comparisons with the experimental data available. Further refinement of these features and inclusion of additional features will be performed as more feedback is received.

Refinement, Validation and Benchmarking of a Model for E-Government Service Quality

NASA Astrophysics Data System (ADS)

Magoutas, Babis; Mentzas, Gregoris

This paper presents the refinement and validation of a model for Quality of e-Government Services (QeGS). We built upon our previous work where a conceptualized model was identified and put focus on the confirmatory phase of the model development process, in order to come up with a valid and reliable QeGS model. The validated model, which was benchmarked with very positive results with similar models found in the literature, can be used for measuring the QeGS in a reliable and valid manner. This will form the basis for a continuous quality improvement process, unleashing the full potential of e-government services for both citizens and public administrations.

Nuclear charge radii: density functional theory meets Bayesian neural networks

NASA Astrophysics Data System (ADS)

Utama, R.; Chen, Wei-Chia; Piekarewicz, J.

2016-11-01

The distribution of electric charge in atomic nuclei is fundamental to our understanding of the complex nuclear dynamics and a quintessential observable to validate nuclear structure models. The aim of this study is to explore a novel approach that combines sophisticated models of nuclear structure with Bayesian neural networks (BNN) to generate predictions for the charge radii of thousands of nuclei throughout the nuclear chart. A class of relativistic energy density functionals is used to provide robust predictions for nuclear charge radii. In turn, these predictions are refined through Bayesian learning for a neural network that is trained using residuals between theoretical predictions and the experimental data. Although predictions obtained with density functional theory provide a fairly good description of experiment, our results show significant improvement (better than 40%) after BNN refinement. Moreover, these improved results for nuclear charge radii are supplemented with theoretical error bars. We have successfully demonstrated the ability of the BNN approach to significantly increase the accuracy of nuclear models in the predictions of nuclear charge radii. However, as many before us, we failed to uncover the underlying physics behind the intriguing behavior of charge radii along the calcium isotopic chain.

Model-Based Reasoning in Upper-division Lab Courses

NASA Astrophysics Data System (ADS)

Lewandowski, Heather

2015-05-01

Modeling, which includes developing, testing, and refining models, is a central activity in physics. Well-known examples from AMO physics include everything from the Bohr model of the hydrogen atom to the Bose-Hubbard model of interacting bosons in a lattice. Modeling, while typically considered a theoretical activity, is most fully represented in the laboratory where measurements of real phenomena intersect with theoretical models, leading to refinement of models and experimental apparatus. However, experimental physicists use models in complex ways and the process is often not made explicit in physics laboratory courses. We have developed a framework to describe the modeling process in physics laboratory activities. The framework attempts to abstract and simplify the complex modeling process undertaken by expert experimentalists. The framework can be applied to understand typical processes such the modeling of the measurement tools, modeling ``black boxes,'' and signal processing. We demonstrate that the framework captures several important features of model-based reasoning in a way that can reveal common student difficulties in the lab and guide the development of curricula that emphasize modeling in the laboratory. We also use the framework to examine troubleshooting in the lab and guide students to effective methods and strategies.

Crystal structure of low-symmetry rondorfite

NASA Astrophysics Data System (ADS)

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

2008-03-01

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

Quantum group spin nets: Refinement limit and relation to spin foams

NASA Astrophysics Data System (ADS)

Dittrich, Bianca; Martin-Benito, Mercedes; Steinhaus, Sebastian

2014-07-01

So far spin foam models are hardly understood beyond a few of their basic building blocks. To make progress on this question, we define analogue spin foam models, so-called "spin nets," for quantum groups SU(2)k and examine their effective continuum dynamics via tensor network renormalization. In the refinement limit of this coarse-graining procedure, we find a vast nontrivial fixed-point structure beyond the degenerate and the BF phase. In comparison to previous work, we use fixed-point intertwiners, inspired by Reisenberger's construction principle [M. P. Reisenberger, J. Math. Phys. (N.Y.) 40, 2046 (1999)] and the recent work [B. Dittrich and W. Kaminski, arXiv:1311.1798], as the initial parametrization. In this new parametrization fine-tuning is not required in order to flow to these new fixed points. Encouragingly, each fixed point has an associated extended phase, which allows for the study of phase transitions in the future. Finally we also present an interpretation of spin nets in terms of melonic spin foams. The coarse-graining flow of spin nets can thus be interpreted as describing the effective coupling between two spin foam vertices or space time atoms.

Low temperature structures of dCpG-proflavine. Conformational and hydration effects.

PubMed Central

Schneider, B; Ginell, S L; Berman, H M

1992-01-01

The structure of the complex of dCpG with proflavine was determined using x-ray data taken at -130 degrees C (low temperature) and at -2 degrees C (cold temperature) and compared with the structure of the complex determined previously at room temperature (Shieh, H. S., H. M. Berman, M. Dabrow, and S. Neidle. 1980. Nucleic Acids Res. 8:85-97). Low temperature was refined with 5,125 reflections between 8.0 and 0.93 A, Anisotropically modeled temperature factors were used for DNA/drug atoms and isotropic ones for water oxygens to R factor of 12.2% in P2(1)2(1)2; a = 32.853, b = 21.760, c = 13.296 A. Cold temperature was refined isotropically with 2,846 reflections 8.0-0.89 A to R = 15.1% in P2(1)2(1)2; a = 32.867, b = 22.356, c = 13.461 A. Both structures are very similar to the room temperature one, though some important differences were observed: one guanine sugar moiety is disordered and additional water molecules have been located that give rise to infinite polyhedral hydration networks. Images FIGURE 2 PMID:1489914

Low temperature structures of dCpG-proflavine.

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

Schneider, B.; Ginell, S. L.; Berman, H. M.

1992-12-01

The structure of the complex of dCpG with proflavine was determined using x-ray data taken at -130 degrees C (low temperature) and at -2 degrees C (cold temperature) and compared with the structure of the complex determined previously at room temperature (Shieh, H. S., H. M. Berman, M. Dabrow, and S. Neidle. 1980. Nucleic Acids Res. 8:85-97). Low temperature was refined with 5,125 reflections between 8.0 and 0.93 A, Anisotropically modeled temperature factors were used for DNA/drug atoms and isotropic ones for water oxygens to R factor of 12.2% in P2(1)2(1)2; a = 32.853, b = 21.760, c = 13.296more » A. Cold temperature was refined isotropically with 2,846 reflections 8.0-0.89 A to R = 15.1% in P2(1)2(1)2; a = 32.867, b = 22.356, c = 13.461 A. Both structures are very similar to the room temperature one, though some important differences were observed: one guanine sugar moiety is disordered and additional water molecules have been located that give rise to infinite polyhedral hydration networks.« less

Volta phase plate data collection facilitates image processing and cryo-EM structure determination.

PubMed

von Loeffelholz, Ottilie; Papai, Gabor; Danev, Radostin; Myasnikov, Alexander G; Natchiar, S Kundhavai; Hazemann, Isabelle; Ménétret, Jean-François; Klaholz, Bruno P

2018-06-01

A current bottleneck in structure determination of macromolecular complexes by cryo electron microscopy (cryo-EM) is the large amount of data needed to obtain high-resolution 3D reconstructions, including through sorting into different conformations and compositions with advanced image processing. Additionally, it may be difficult to visualize small ligands that bind in sub-stoichiometric levels. Volta phase plates (VPP) introduce a phase shift in the contrast transfer and drastically increase the contrast of the recorded low-dose cryo-EM images while preserving high frequency information. Here we present a comparative study to address the behavior of different data sets during image processing and quantify important parameters during structure refinement. The automated data collection was done from the same human ribosome sample either as a conventional defocus range dataset or with a Volta phase plate close to focus (cfVPP) or with a small defocus (dfVPP). The analysis of image processing parameters shows that dfVPP data behave more robustly during cryo-EM structure refinement because particle alignments, Euler angle assignments and 2D & 3D classifications behave more stably and converge faster. In particular, less particle images are required to reach the same resolution in the 3D reconstructions. Finally, we find that defocus range data collection is also applicable to VPP. This study shows that data processing and cryo-EM map interpretation, including atomic model refinement, are facilitated significantly by performing VPP cryo-EM, which will have an important impact on structural biology. Copyright © 2018 Elsevier Inc. All rights reserved.

NMR data-driven structure determination using NMR-I-TASSER in the CASD-NMR experiment

PubMed Central

Jang, Richard; Wang, Yan

2015-01-01

NMR-I-TASSER, an adaption of the I-TASSER algorithm combining NMR data for protein structure determination, recently joined the second round of the CASD-NMR experiment. Unlike many molecular dynamics-based methods, NMR-I-TASSER takes a molecular replacement-like approach to the problem by first threading the target through the PDB to identify structural templates which are then used for iterative NOE assignments and fragment structure assembly refinements. The employment of multiple templates allows NMR-I-TASSER to sample different topologies while convergence to a single structure is not required. Retroactive and blind tests of the CASD-NMR targets from Rounds 1 and 2 demonstrate that even without using NOE peak lists I-TASSER can generate correct structure topology with 15 of 20 targets having a TM-score above 0.5. With the addition of NOE-based distance restraints, NMR-I-TASSER significantly improved the I-TASSER models with all models having the TM-score above 0.5. The average RMSD was reduced from 5.29 to 2.14 Å in Round 1 and 3.18 to 1.71 Å in Round 2. There is no obvious difference in the modeling results with using raw and refined peak lists, indicating robustness of the pipeline to the NOE assignment errors. Overall, despite the low-resolution modeling the current NMR-I-TASSER pipeline provides a coarse-grained structure folding approach complementary to traditional molecular dynamics simulations, which can produce fast near-native frameworks for atomic-level structural refinement. PMID:25737244

Refining the threshold of toxicological concern (TTC) for risk prioritization of trace chemicals in food.

PubMed

Felter, Susan; Lane, Richard W; Latulippe, Marie E; Llewellyn, G Craig; Olin, Stephen S; Scimeca, Joseph A; Trautman, Thomas D

2009-09-01

Due to ever-improving analytical capabilities, very low levels of unexpected chemicals can now be detected in foods. Although these may be toxicologically insignificant, such incidents often garner significant attention. The threshold of toxicological concern (TTC) methodology provides a scientifically defensible, transparent approach for putting low-level exposures in the context of potential risk, as a tool to facilitate prioritization of responses, including potential mitigation. The TTC method supports the establishment of tiered, health-protective exposure limits for chemicals lacking a full toxicity database, based on evaluation of the known toxicity of chemicals which share similar structural characteristics. The approach supports the view that prudent actions towards public health protection are based on evaluation of safety as opposed to detection chemistry. This paper builds on the existing TTC literature and recommends refinements that address two key areas. The first describes the inclusion of genotoxicity data as a way to refine the TTC limit for chemicals that have structural alerts for genotoxicity. The second area addresses duration of exposure. Whereas the existing TTC exposure limits assume a lifetime of exposure, human exposure to unintended chemicals in food is often only for a limited time. Recommendations are made to refine the approach for less-than-lifetime exposures.

Constrained-transport Magnetohydrodynamics with Adaptive Mesh Refinement in CHARM

NASA Astrophysics Data System (ADS)

Miniati, Francesco; Martin, Daniel F.

2011-07-01

We present the implementation of a three-dimensional, second-order accurate Godunov-type algorithm for magnetohydrodynamics (MHD) in the adaptive-mesh-refinement (AMR) cosmological code CHARM. The algorithm is based on the full 12-solve spatially unsplit corner-transport-upwind (CTU) scheme. The fluid quantities are cell-centered and are updated using the piecewise-parabolic method (PPM), while the magnetic field variables are face-centered and are evolved through application of the Stokes theorem on cell edges via a constrained-transport (CT) method. The so-called multidimensional MHD source terms required in the predictor step for high-order accuracy are applied in a simplified form which reduces their complexity in three dimensions without loss of accuracy or robustness. The algorithm is implemented on an AMR framework which requires specific synchronization steps across refinement levels. These include face-centered restriction and prolongation operations and a reflux-curl operation, which maintains a solenoidal magnetic field across refinement boundaries. The code is tested against a large suite of test problems, including convergence tests in smooth flows, shock-tube tests, classical two- and three-dimensional MHD tests, a three-dimensional shock-cloud interaction problem, and the formation of a cluster of galaxies in a fully cosmological context. The magnetic field divergence is shown to remain negligible throughout.

Interplay of I-TASSER and QUARK for template-based and ab initio protein structure prediction in CASP10

PubMed Central

Zhang, Yang

2014-01-01

We develop and test a new pipeline in CASP10 to predict protein structures based on an interplay of I-TASSER and QUARK for both free-modeling (FM) and template-based modeling (TBM) targets. The most noteworthy observation is that sorting through the threading template pool using the QUARK-based ab initio models as probes allows the detection of distant-homology templates which might be ignored by the traditional sequence profile-based threading alignment algorithms. Further template assembly refinement by I-TASSER resulted in successful folding of two medium-sized FM targets with >150 residues. For TBM, the multiple threading alignments from LOMETS are, for the first time, incorporated into the ab initio QUARK simulations, which were further refined by I-TASSER assembly refinement. Compared with the traditional threading assembly refinement procedures, the inclusion of the threading-constrained ab initio folding models can consistently improve the quality of the full-length models as assessed by the GDT-HA and hydrogen-bonding scores. Despite the success, significant challenges still exist in domain boundary prediction and consistent folding of medium-size proteins (especially beta-proteins) for nonhomologous targets. Further developments of sensitive fold-recognition and ab initio folding methods are critical for solving these problems. PMID:23760925

Interplay of I-TASSER and QUARK for template-based and ab initio protein structure prediction in CASP10.

PubMed

Zhang, Yang

2014-02-01

We develop and test a new pipeline in CASP10 to predict protein structures based on an interplay of I-TASSER and QUARK for both free-modeling (FM) and template-based modeling (TBM) targets. The most noteworthy observation is that sorting through the threading template pool using the QUARK-based ab initio models as probes allows the detection of distant-homology templates which might be ignored by the traditional sequence profile-based threading alignment algorithms. Further template assembly refinement by I-TASSER resulted in successful folding of two medium-sized FM targets with >150 residues. For TBM, the multiple threading alignments from LOMETS are, for the first time, incorporated into the ab initio QUARK simulations, which were further refined by I-TASSER assembly refinement. Compared with the traditional threading assembly refinement procedures, the inclusion of the threading-constrained ab initio folding models can consistently improve the quality of the full-length models as assessed by the GDT-HA and hydrogen-bonding scores. Despite the success, significant challenges still exist in domain boundary prediction and consistent folding of medium-size proteins (especially beta-proteins) for nonhomologous targets. Further developments of sensitive fold-recognition and ab initio folding methods are critical for solving these problems. Copyright © 2013 Wiley Periodicals, Inc.

The state of animal welfare in the context of refinement.

PubMed

Zurlo, Joanne; Hutchinson, Eric

2014-01-01

The ultimate goal of the Three Rs is the full replacement of animals used in biomedical research and testing. However, replacement is unlikely to occur in the near future; therefore the scientific community as a whole must continue to devote considerable effort to ensure optimal animal welfare for the benefit of the science and the animals, i.e., the R of refinement. Laws governing the care and use of laboratory animals have recently been revised in Europe and the US and these place greater emphasis on promoting the well-being of the animals in addition to minimizing pain and distress. Social housing for social species is now the default condition, which can present a challenge in certain experimental settings and for certain species. The practice of positive reinforcement training of laboratory animals, particularly non-human primates, is gathering momentum but is not yet universally employed. Enhanced consideration of refinement extends to rodents, particularly mice, whose use is still increasing as more genetically modified models are generated. The wastage of extraneous mice and the method of their euthanasia are refinement issues that still need to be addressed. An international, concerted effort into defining the needs of laboratory animals is still necessary to improve the quality of the animal models used as well as their welfare.

On spinodal decomposition in alnico - A transmission electron microscopy and atom probe tomography study

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

Zhou, Lin; Guo, Wei; Poplawsky, J. D.

Here, alnico is a prime example of a finely tuned nanostructure whose magnetic properties are intimately connected to magnetic annealing (MA) during spinodal transformation and subsequent lower temperature annealing (draw) cycles. Using a combination of transmission electron microscopy and atom probe tomography, we show how these critical processing steps affect the local composition and nanostructure evolution with impact on magnetic properties. The nearly 2-fold increase of intrinsic coercivity (H ci) during the draw cycle is not adequately explained by chemical refinement of the spinodal phases. Instead, increased Fe-Co phase (α 1) isolation, development of Cu-rich spheres/rods/blades and additional α 1more » rod precipitation that occurs during the MA and draw, likely play a key role in Hci enhancement. Chemical ordering of the Al-Ni-phase (α 2) and formation of Ni-rich (α 3) may also contribute. Unraveling of the subtle effect of these nano-scaled features is crucial to understanding on how to improve shape anisotropy in alnico magnets.« less

Incommensurate structure of a lillianite-type samarium chromium sulfide Sm{sub 2/3}Cr{sub 2}S{sub 4}

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

Lafond, A.; Cario, L.; Meerschaut, A.

1996-12-01

The structure of Sm{sub 2/3}Cr{sub 2}S{sub 4} has been solved from single-crystal X-ray diffraction data. This compound presents a 3 X a superstructure along a and an incommensurate superstructure along b close to 3 x b. The basic structure is described in the space group Pmnb with a = 3.5030(3) {Angstrom}, b = 10.9199(8) {Angstrom}, c = 12.7987(8) {Angstrom}, Z = 4, R = 0.046 for 916 observed reflections. The modulated structure refinement, taking into account the two superstructures, was carried out in a (3 + 2)D superspace group and leads to R = 0.063 for 1706 reflections. This structuremore » consists of staggered double columns of [CrS{sub 6}] octahedra connected by samarium atoms in a trigonal prismatic bicapped environment. This structure is reminiscent of that found in the lillianite mineral family. The statistical occupancy of samarium atoms (1/3), in agreement with the charge equilibrium (Sm{sup 3+}, Cr{sup 3+}, S{sup 2-}), is related to the superstructure.« less

On spinodal decomposition in alnico - A transmission electron microscopy and atom probe tomography study

DOE PAGES

Zhou, Lin; Guo, Wei; Poplawsky, J. D.; ...

2018-04-26

Here, alnico is a prime example of a finely tuned nanostructure whose magnetic properties are intimately connected to magnetic annealing (MA) during spinodal transformation and subsequent lower temperature annealing (draw) cycles. Using a combination of transmission electron microscopy and atom probe tomography, we show how these critical processing steps affect the local composition and nanostructure evolution with impact on magnetic properties. The nearly 2-fold increase of intrinsic coercivity (H ci) during the draw cycle is not adequately explained by chemical refinement of the spinodal phases. Instead, increased Fe-Co phase (α 1) isolation, development of Cu-rich spheres/rods/blades and additional α 1more » rod precipitation that occurs during the MA and draw, likely play a key role in Hci enhancement. Chemical ordering of the Al-Ni-phase (α 2) and formation of Ni-rich (α 3) may also contribute. Unraveling of the subtle effect of these nano-scaled features is crucial to understanding on how to improve shape anisotropy in alnico magnets.« less

Equations of state of anhydrous AlF 3 and AlI 3 : Modeling of extreme condition halide chemistry

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

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

Pressure dependent angle-dispersive x-ray powder diffraction measurements of alpha-phase aluminum trifluoride (α-AlF 3) and separately, aluminum triiodide (AlI 3) were conducted using a diamond-anvil cell. Results at 295 K extend to 50 GPa. The equations of state of AlF 3 and AlI 3 were determined through refinements of collected x-ray diffraction patterns. The respective bulk moduli and corresponding pressure derivatives are reported for multiple orders of the Birch-Murnaghan (B-M), finite-strain (F-f), and higher pressure finite-strain (G-g) EOS analysis models. Aluminum trifluoride exhibits an apparent isostructural phase transition at approximately 12 GPa. Aluminum triiodide also undergoes a second-order atomic rearrangement: appliedmore » stress transformed a monoclinically distorted face centered cubic (fcc) structure into a standard fcc structural arrangement of iodine atoms. In conclusion, results from semi-empirical thermochemical computations of energetic materials formulated with fluorine containing reactants were obtained with the aim of predicting the yield of halogenated products.« less

Equations of state of anhydrous AlF{sub 3} and AlI{sub 3}: Modeling of extreme condition halide chemistry

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

Stavrou, Elissaios, E-mail: stavrou1@llnl.gov; Lawrence Livermore National Laboratory, Physical and Life Sciences Directorate, P.O. Box 808 L-350, Livermore, California 94550; Zaug, Joseph M., E-mail: zaug1@llnl.gov

Pressure dependent angle-dispersive x-ray powder diffraction measurements of alpha-phase aluminum trifluoride (α-AlF{sub 3}) and separately, aluminum triiodide (AlI{sub 3}) were conducted using a diamond-anvil cell. Results at 295 K extend to 50 GPa. The equations of state of AlF{sub 3} and AlI{sub 3} were determined through refinements of collected x-ray diffraction patterns. The respective bulk moduli and corresponding pressure derivatives are reported for multiple orders of the Birch-Murnaghan (B-M), finite-strain (F-f), and higher pressure finite-strain (G-g) EOS analysis models. Aluminum trifluoride exhibits an apparent isostructural phase transition at approximately 12 GPa. Aluminum triiodide also undergoes a second-order atomic rearrangement: appliedmore » stress transformed a monoclinically distorted face centered cubic (fcc) structure into a standard fcc structural arrangement of iodine atoms. Results from semi-empirical thermochemical computations of energetic materials formulated with fluorine containing reactants were obtained with the aim of predicting the yield of halogenated products.« less

Atomic resolution (0.97 Å) structure of the triple mutant (K53,56,121M) of bovine pancreatic phospholipase A2

PubMed Central

Sekar, K.; Rajakannan, V.; Gayathri, D.; Velmurugan, D.; Poi, M.-J.; Dauter, M.; Dauter, Z.; Tsai, M.-D.

2005-01-01

The enzyme phospholipase A2 catalyzes the hydrolysis of the sn-2 acyl chain of phospholipids, forming fatty acids and lysophospholipids. The crystal structure of a triple mutant (K53,56,121M) of bovine pancreatic phospholipase A2 in which the lysine residues at positions 53, 56 and 121 are replaced recombinantly by methionines has been determined at atomic resolution (0.97 Å). The crystal is monoclinic (space group P2), with unit-cell parameters a = 36.934, b = 23.863, c = 65.931 Å, β = 101.47°. The structure was solved by molecular replacement and has been refined to a final R factor of 10.6% (R free = 13.4%) using 63 926 unique reflections. The final protein model consists of 123 amino-acid residues, two calcium ions, one chloride ion, 243 water molecules and six 2-methyl-2,4-pentanediol molecules. The surface-loop residues 60–70 are ordered and have clear electron density. PMID:16508077

Outer satellite atmospheres: Their nature and planetary interactions

NASA Technical Reports Server (NTRS)

Smyth, W. H.

1981-01-01

Modeling capabilities and initial model calculations are reported for the peculiar directional features of the Io sodium cloud discovered by Pilcher and the extended atomic oxygen atmosphere of Io discovered by Brown. Model results explaining the directional feature by a localized emission from the satellite are encouraging, but as yet, inconclusive; whereas for the oxygen cloud, an escape rate of 1 to 2 x 10 to the 27th power atoms/sec or higher from Io is suggested. Preliminary modeling efforts were also initiated for the extended hydrogen ring-atmosphere of Saturn detected by the Voyager spacecraft and for possible extended atmospheres of some of the smaller satellites located in the E-ring. Continuing research efforts reported for the Io sodium cloud include further refinement in the modeling of the east-west asymmetry data, the asymmetric line profile shape, and the intersection of the cloud with the Io plasma torus. In addition, the completed pre-Voyager modeling of Titan's hydrogen torus is included and the near completed model development for the extended atmosphere of comets is discussed.

Revolving scanning transmission electron microscopy: correcting sample drift distortion without prior knowledge.

PubMed

Sang, Xiahan; LeBeau, James M

2014-03-01

We report the development of revolving scanning transmission electron microscopy--RevSTEM--a technique that enables characterization and removal of sample drift distortion from atomic resolution images without the need for a priori crystal structure information. To measure and correct the distortion, we acquire an image series while rotating the scan coordinate system between successive frames. Through theory and experiment, we show that the revolving image series captures the information necessary to analyze sample drift rate and direction. At atomic resolution, we quantify the image distortion using the projective standard deviation, a rapid, real-space method to directly measure lattice vector angles. By fitting these angles to a physical model, we show that the refined drift parameters provide the input needed to correct distortion across the series. We demonstrate that RevSTEM simultaneously removes the need for a priori structure information to correct distortion, leads to a dramatically improved signal-to-noise ratio, and enables picometer precision and accuracy regardless of drift rate. Copyright © 2013 Elsevier B.V. All rights reserved.

Temperature Dependence of the Structural Parameters in the Transformation of Aragonite to Calcite, as Determined from In Situ Synchrotron Powder X-ray-Diffratction Data

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

Antao, Sytle M.; Hassan, Ishmael; West Indies)

The temperature dependency of the crystal structure and the polymorphic transition of CaCO{sub 3} from aragonite to calcite were studied using Rietveld structure refinement and high-temperature in situ synchrotron powder X-ray-diffraction data at ambient pressure, P. The orthorhombic metastable aragonite at room P, space group Pmcn, transforms to trigonal calcite, space group R{bar 3}c, at about T{sub c} = 468 C. This transformation occurs rapidly; it starts at about 420 C and is completed by 500 C, an 80 C interval that took about 10 minutes using a heating rate of 8 C/min. Structurally, from aragonite to calcite, the distributionmore » of the Ca atom changes from approximately hexagonal to cubic close-packing. A 5.76% discontinuous increase in volume accompanies the reconstructive first-order transition. Besides the change in coordination of the Ca atom from nine to six from aragonite to calcite, the CO{sub 3} groups change by a 30{sup o} rotation across the transition.« less

PaLaCe: A Coarse-Grain Protein Model for Studying Mechanical Properties.

PubMed

Pasi, Marco; Lavery, Richard; Ceres, Nicoletta

2013-01-08

We present a coarse-grain protein model PaLaCe (Pasi-Lavery-Ceres) that has been developed principally to allow fast computational studies of protein mechanics and to clarify the links between mechanics and function. PaLaCe uses a two-tier protein representation with one to three pseudoatoms representing each amino acid for the main nonbonded interactions, combined with atomic-scale peptide groups and some side chain atoms to allow the explicit representation of backbone hydrogen bonds and to simplify the treatment of bonded interactions. The PaLaCe force field is composed of physics-based terms, parametrized using Boltzmann inversion of conformational probability distributions derived from a protein structure data set, and iteratively refined to reproduce the experimental distributions. PaLaCe has been implemented in the MMTK simulation package and can be used for energy minimization, normal mode calculations, and molecular or stochastic dynamics. We present simulations with PaLaCe that test its ability to maintain stable structures for folded proteins, reproduce their dynamic fluctuations, and correctly model large-scale, force-induced conformational changes.

Equations of state of anhydrous AlF 3 and AlI 3 : Modeling of extreme condition halide chemistry

DOE PAGES

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

2015-06-04

Pressure dependent angle-dispersive x-ray powder diffraction measurements of alpha-phase aluminum trifluoride (α-AlF 3) and separately, aluminum triiodide (AlI 3) were conducted using a diamond-anvil cell. Results at 295 K extend to 50 GPa. The equations of state of AlF 3 and AlI 3 were determined through refinements of collected x-ray diffraction patterns. The respective bulk moduli and corresponding pressure derivatives are reported for multiple orders of the Birch-Murnaghan (B-M), finite-strain (F-f), and higher pressure finite-strain (G-g) EOS analysis models. Aluminum trifluoride exhibits an apparent isostructural phase transition at approximately 12 GPa. Aluminum triiodide also undergoes a second-order atomic rearrangement: appliedmore » stress transformed a monoclinically distorted face centered cubic (fcc) structure into a standard fcc structural arrangement of iodine atoms. In conclusion, results from semi-empirical thermochemical computations of energetic materials formulated with fluorine containing reactants were obtained with the aim of predicting the yield of halogenated products.« less

Estimating the Octanol/Water Partition Coefficient for Aliphatic Organic Compounds Using Semi-Empirical Electrotopological Index

PubMed Central

Souza, Erica Silva; Zaramello, Laize; Kuhnen, Carlos Alberto; Junkes, Berenice da Silva; Yunes, Rosendo Augusto; Heinzen, Vilma Edite Fonseca

2011-01-01

A new possibility for estimating the octanol/water coefficient (log P) was investigated using only one descriptor, the semi-empirical electrotopological index (ISET). The predictability of four octanol/water partition coefficient (log P) calculation models was compared using a set of 131 aliphatic organic compounds from five different classes. Log P values were calculated employing atomic-contribution methods, as in the Ghose/Crippen approach and its later refinement, AlogP; using fragmental methods through the ClogP method; and employing an approach considering the whole molecule using topological indices with the MlogP method. The efficiency and the applicability of the ISET in terms of calculating log P were demonstrated through good statistical quality (r > 0.99; s < 0.18), high internal stability and good predictive ability for an external group of compounds in the same order as the widely used models based on the fragmental method, ClogP, and the atomic contribution method, AlogP, which are among the most used methods of predicting log P. PMID:22072945

Estimating the octanol/water partition coefficient for aliphatic organic compounds using semi-empirical electrotopological index.

PubMed

Souza, Erica Silva; Zaramello, Laize; Kuhnen, Carlos Alberto; Junkes, Berenice da Silva; Yunes, Rosendo Augusto; Heinzen, Vilma Edite Fonseca

2011-01-01

A new possibility for estimating the octanol/water coefficient (log P) was investigated using only one descriptor, the semi-empirical electrotopological index (I(SET)). The predictability of four octanol/water partition coefficient (log P) calculation models was compared using a set of 131 aliphatic organic compounds from five different classes. Log P values were calculated employing atomic-contribution methods, as in the Ghose/Crippen approach and its later refinement, AlogP; using fragmental methods through the ClogP method; and employing an approach considering the whole molecule using topological indices with the MlogP method. The efficiency and the applicability of the I(SET) in terms of calculating log P were demonstrated through good statistical quality (r > 0.99; s < 0.18), high internal stability and good predictive ability for an external group of compounds in the same order as the widely used models based on the fragmental method, ClogP, and the atomic contribution method, AlogP, which are among the most used methods of predicting log P.

The crystal structures of potassium and cesium trivanadates

USGS Publications Warehouse

Evans, H.T.; Block, S.

1966-01-01

Potassium and cesium trivanadates are monoclinic and isomorphous, space group P21/m, with the following dimensions (Z = 2): KV3O8, a = 7.640 A, b = 8.380 A, c = 4.979 A, ??= 96?? 57???; CsV3O8, a = 8.176 A, b = 8.519 A, c = 4.988 A, ?? = 95?? 32???. The crystal structure of KV3O8 has been determined from hk0, 0kl, and h0l Weissenberg data with an R factor of 0.15. The structure of CsV3O8 has been refined with 1273 hkl Weissenberg data to an R factor of 0.089. The structures consist of corrugated sheets based on a linkage of distorted VO6, octahedra. Two of the vanadium atoms lie in double, square-pyramid groups V2O8, which are linked through opposite basal corners into chains along the b axis. The chains are joined laterally along the c axis into sheets by the third vanadium atom in VO groups, also forming part of a square-pyramid coordination. Various aspects of these structures are compared with other known oxovanadate structures.

Mustard Gas: Its Pre-World War I History

NASA Astrophysics Data System (ADS)

Duchovic, Ronald J.; Vilensky, Joel A.

2007-06-01

Mustard gas is perhaps the best-known chemical warfare agent and is commonly associated with World War I, both in its first use in warfare and its first synthesis. Although the former is correct, the latter is not. We review here the history of the repeated synthesis of mustard gas by 19th century European chemists. The techniques developed by these chemists were the ones relied upon by both the Central Powers and the Allies to manufacture this agent during World War I. Further, a historical review of mustard gas synthesis highlights the increasing sophistication of the chemical sciences. In particular, during the latter half of the 19th century, the concepts of atomic mass, chemical periodicity, and chemical structure underwent a rapid development that culminated in the application of quantum mechanics to chemistry in the 20th century. A comparison is made of the molecular formula for mustard gas from the 19th century with that of the 21st century, demonstrating that the concept of atomic mass has undergone significant refinement over this period of time.

Implementation of an Undergraduate Nutritional Support Clerkship.

ERIC Educational Resources Information Center

Stennett, Douglass J.; And Others

1983-01-01

A 10-week, full-time elective nutritional support clerkship designed for fifth-year pharmacy students is described. The course refines the student's communication skills and develops the student's ability to properly prepare and adjust a nutritional therapy plan. A weekly student activity plan and student evaluation form are appended. (MSE)

On-the-Spot Assessments

ERIC Educational Resources Information Center

Diezmann, Carmel

2008-01-01

Diezmann presents a series of classroom number-sense activities that encourage young students to use and refine their estimation, prediction, and observation skills. The activities explore the relationships between the number of objects in an opaque container and (1) its fullness and (2) the size of the objects in the container. Informal,…

An accurate full-dimensional potential energy surface for H-Au(111): Importance of nonadiabatic electronic excitation in energy transfer and adsorption.

PubMed

Janke, Svenja M; Auerbach, Daniel J; Wodtke, Alec M; Kandratsenka, Alexander

2015-09-28

We have constructed a potential energy surface (PES) for H-atoms interacting with fcc Au(111) based on fitting the analytic form of the energy from Effective Medium Theory (EMT) to ab initio energy values calculated with density functional theory. The fit used input from configurations of the H-Au system with Au atoms at their lattice positions as well as configurations with the Au atoms displaced from their lattice positions. It reproduces the energy, in full dimension, not only for the configurations used as input but also for a large number of additional configurations derived from ab initio molecular dynamics (AIMD) trajectories at finite temperature. Adiabatic molecular dynamics simulations on this PES reproduce the energy loss behavior of AIMD. EMT also provides expressions for the embedding electron density, which enabled us to develop a self-consistent approach to simulate nonadiabatic electron-hole pair excitation and their effect on the motion of the incident H-atoms. For H atoms with an energy of 2.7 eV colliding with Au, electron-hole pair excitation is by far the most important energy loss pathway, giving an average energy loss ≈3 times that of the adiabatic case. This increased energy loss enhances the probability of the H-atom remaining on or in the Au slab by a factor of 2. The most likely outcome for H-atoms that are not scattered also depends prodigiously on the energy transfer mechanism; for the nonadiabatic case, more than 50% of the H-atoms which do not scatter are adsorbed on the surface, while for the adiabatic case more than 50% pass entirely through the 4 layer simulation slab.

On the crystal structure of Cr2N precipitates in high-nitrogen austenitic stainless steel. III. Neutron diffraction study on the ordered Cr2N superstructure.

PubMed

Lee, Tae-Ho; Kim, Sung-Joon; Shin, Eunjoo; Takaki, Setsuo

2006-12-01

The ordered structure of Cr(2)N precipitates in high-nitrogen austenitic steel was investigated utilizing high-resolution neutron powder diffractometry (HRPD). On the basis of the Rietveld refinement of neutron diffraction patterns, the ordered Cr2N superstructure was confirmed to be trigonal (space group P31m), with lattice parameters a=4.800 (4) and c=4.472 (5) A, as suggested in previous transmission electron microscopy studies [Lee, Oh, Han, Lee, Kim & Takaki (2005). Acta Cryst. B61, 137-144; Lee, Kim & Takaki (2006). Acta Cryst. B62, 190-196]. The occupancies of the N atoms in four crystallographic sites [1(a), 1(b), 2(d) and 2(c) Wyckoff sites] were determined to be 1.00 (5), 0.0, 0.74 (9) and 0.12 (3), respectively, reflecting a partial disordering of N atoms along the c axis. The position of the metal atom was specified to be x=0.346 (8) and z=0.244 (6), corresponding to a deviation from the ideal position (x=0.333 and z=0.250). This deviation caused the ((1/3 1/3)(0))-type superlattice reflection to appear. A comparison between the ideal and measured crystal structures of Cr2N was performed using a computer simulation of selected-area diffraction patterns.

Systematic measurements of opacity dependence on temperature, density, and atomic number at stellar interior conditions

NASA Astrophysics Data System (ADS)

Nagayama, Taisuke

2017-10-01

Model predictions for iron opacity are notably different from measurements performed at matter conditions similar to the boundary between the solar radiation and convection zones. The calculated iron opacities have narrower spectral lines, weaker quasi-continuum at short wavelength, and deeper opacity windows than the measurements. If correct, these measurements help resolve a decade old problem in solar physics. A key question is therefore: What is responsible for the model-data discrepancy? The answer is complex because the experiments are challenging and opacity theories depend on multiple entangled physical processes such as the influence of completeness and accuracy of atomic states, line broadening, contributions from myriad transitions from excited states, and multi-photon absorption processes. To help determine the cause of this discrepancy, a systematic study of opacity variation with temperature, density, and atomic number is underway. Measurements of chromium, iron, and nickel opacities have been performed at two different temperatures and densities. The collection of measured opacities provides constraints on hypotheses to explain the discrepancy. We will discuss implications of measured opacities, experimental errors, and possible opacity model refinements. Sandia National Laboratories is a multi-mission laboratory managed and operated by National Technology and Engineering Solutions of Sandia, LLC., a wholly owned subsidiary of Honeywell International, Inc., for the U.S. Department of Energy's National Nuclear Security Administration under contract DE-NA0003525.

Tris(N-{bis­[meth­yl(phen­yl)amino]­phosphor­yl}benzene­sulfonamidato-κ2 O,O′)(1,10-phenanthroline-κ2 N,N′)lanthanum(III)

PubMed Central

Prytula-Kurkunova, Angelina Yu.; Trush, Victor A.; Dyakonenko, Viktoriya V.; Sliva, Tetyana Yu.; Amirkhanov, Vladimir M.

2017-01-01

The asymmetric unit of [La(C20H21N3O3PS)3(C12H8N2)] is created by one LaIII ion, three deprotonated N-{bis­[meth­yl(phen­yl)amino]­phosphor­yl}benzene­sulfonamidate (L −) ligands and one 1,10-phenanthroline (Phen) mol­ecule. Each LaIII ion is eight-coordinated (6O+2N) by three phosphoryl O atoms, three sulfonyl O atoms of three L − ligands and two N atoms of the chelating Phen ligand, leading to the formation of six- and five-membered metallacycles, respectively. The lanthanum coordination polyhedron has a bicapped trigonal–prismatic geometry. ‘Sandwich-like’ intra­molecular π–π stacking inter­actions are observed between the 1,10-phenanthroline ligand and two benzene rings of two different L − ligands. The phenyl rings of L − that are not involved in the stacking inter­actions show minor positional disorder. Mol­ecules form layers parallel to the (010) plane due to weak C—H⋯O inter­molecular hydrogen bonds. Unidentified highly disordered solvate mol­ecules that occupy ca 400 Å3 large voids have been omitted from the refinement model. PMID:28775887

Plasticity of Cl-Te-Cl Fragments. Synthesis, Single-Crystal X-ray, and NBO Study of (1-Thia-2-tellura-1-phenyl-4-chloro)cyclopentane 2,2,2-Trichloride.

PubMed

Sundberg, Markku R.; Laitalainen, Tarja; Bergman, Jan; Uggla, Rolf; Matikainen, Jorma; Kaltia, Seppo

1998-06-01

Tellurium tetrachloride and allylphenyl sulfide react to form (1-thia-2-tellura-1-phenyl-4-chloro)cyclopentane 2,2,2-trichloride. The crystal and molecular structure were determined by single-crystal X-ray techniques. The crystals belong to the monoclinic system, space group P2(1)/c (No. 14) with a = 6.020(3) Å, b = 11.46(1) Å, c = 20.156(2) Å, beta = 97.53(2) degrees, V = 1379(1) Å(3), and Z = 4. The structure was refined to the final R value of 0.036. The coordination around Te(IV) is distorted psi octahedral with three Cl atoms in the equatorial positions. The axial Te(1)-C(1) bond opposite to the lone pair of electrons at the Te(IV) atom completes the coordination polyhedron. The intramolecular Te-S distance is 2.903(3) Å. Symmetric and asymmetric deformation modes were established to describe the plasticity of the Cl-Te-Cl fragments extracted from the Cambridge Structural Database. The hypervalency of Te(IV) manifests itself as plasticity in the equatorial plane of the coordination sphere. The NBO calculations show that all of the equatorial Te-Cl bonds are highly polarized and the electrons reside mainly on the Cl atoms.

The Molecular Structure of a Phosphatidylserine Bilayer Determined by Scattering and Molecular Dynamics Simulations

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

Pan, Jianjun; Cheng, Xiaolin; Monticelli, Luca

2014-01-01

Phosphatidylserine (PS) lipids play essential roles in biological processes, including enzyme activation and apoptosis. We report on the molecular structure and atomic scale interactions of a fluid bilayer composed of 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphatidylserine (POPS). A scattering density profile model, aided by molecular dynamics (MD) simulations, was developed to jointly refine different contrast small-angle neutron and X-ray scattering data, which yielded a lipid area of 62.7 A2 at 25 C. MD simulations with POPS lipid area constrained at different values were also performed using all-atom and aliphatic united-atom models. The optimal simulated bilayer was obtained using a model-free comparison approach. Examination of themore » simulated bilayer, which agrees best with the experimental scattering data, reveals a preferential interaction between Na+ ions and the terminal serine and phosphate moieties. Long-range inter-lipid interactions were identified, primarily between the positively charged ammonium, and the negatively charged carboxylic and phosphate oxygens. The area compressibility modulus KA of the POPS bilayer was derived by quantifying lipid area as a function of surface tension from area-constrained MD simulations. It was found that POPS bilayers possess a much larger KA than that of neutral phosphatidylcholine lipid bilayers. We propose that the unique molecular features of POPS bilayers may play an important role in certain physiological functions.« less

Three-dimensional rearrangement of single atoms using actively controlled optical microtraps.

PubMed

Lee, Woojun; Kim, Hyosub; Ahn, Jaewook

2016-05-02

We propose and demonstrate three-dimensional rearrangements of single atoms. In experiments performed with single ⁸⁷Rb atoms in optical microtraps actively controlled by a spatial light modulator, we demonstrate various dynamic rearrangements of up to N = 9 atoms including rotation, 2D vacancy filling, guiding, compactification, and 3D shuffling. With the capability of a phase-only Fourier mask to generate arbitrary shapes of the holographic microtraps, it was possible to place single atoms at arbitrary geometries of a few μm size and even continuously reconfigure them by conveying each atom. For this purpose, we loaded a series of computer-generated phase masks in the full frame rate of 60 Hz of the spatial light modulator, so the animation of phase mask transformed the holographic microtraps in real time, driving each atom along the assigned trajectory. Possible applications of this method of transformation of single atoms include preparation of scalable quantum platforms for quantum computation, quantum simulation, and quantum many-body physics.

Permutation invariant polynomial neural network approach to fitting potential energy surfaces. II. Four-atom systems

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

Li, Jun; Jiang, Bin; Guo, Hua, E-mail: hguo@unm.edu

2013-11-28

A rigorous, general, and simple method to fit global and permutation invariant potential energy surfaces (PESs) using neural networks (NNs) is discussed. This so-called permutation invariant polynomial neural network (PIP-NN) method imposes permutation symmetry by using in its input a set of symmetry functions based on PIPs. For systems with more than three atoms, it is shown that the number of symmetry functions in the input vector needs to be larger than the number of internal coordinates in order to include both the primary and secondary invariant polynomials. This PIP-NN method is successfully demonstrated in three atom-triatomic reactive systems, resultingmore » in full-dimensional global PESs with average errors on the order of meV. These PESs are used in full-dimensional quantum dynamical calculations.« less

Electron density distribution and disordered crystal structure of 15R-SiAlON, SiAl{sub 4}O{sub 2}N{sub 4}

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

Banno, Hiroki; Hanai, Takaaki; Asaka, Toru

2014-03-15

The crystal structure of SiAl{sub 4}O{sub 2}N{sub 4} was characterized by laboratory X-ray powder diffraction (CuKα{sub 1}). The title compound is trigonal with space group R3-bar m. The hexagonal unit-cell dimensions (Z=3) are a=0.301332(3) nm, c=4.18616(4) nm and V=0.3291825(5) nm{sup 3}. The initial structural model was successfully derived by the charge-flipping method and further refined by the Rietveld method. The final structural model showed the positional disordering of one of the three (Si,Al) sites. The maximum-entropy method-based pattern fitting (MPF) method was used to confirm the validity of the split-atom model, in which conventional structure bias caused by assuming intensitymore » partitioning was minimized. The reliability indices calculated from the MPF were R{sub wp}=5.05%, S (=R{sub wp}/R{sub e})=1.21, R{sub p}=3.77%, R{sub B}=1.29% and R{sub F}=1.01%. The disordered crystal structure was successfully described by overlapping three types of domains with ordered atom arrangements. The distribution of atomic positions in one of the three types of domains can be achieved in the space group R3-bar m. The atom arrangements in the other two types of domains are noncentrosymmetrical with the space group R3m. These two structural configurations are related by the pseudo-symmetry inversion. -- Graphical abstract: A bird's eye view of electron densities up to 75.3% (0.133 nm{sup −3}) of the maximum on the plane parallel to (110) with the corresponding atomic arrangements of SiAl{sub 4}O{sub 2}N{sub 4}. Highlights: • Crystal structure of SiAl{sub 4}O{sub 2}N{sub 4} is determined by laboratory X-ray powder diffraction. • The atom arrangements are represented by the split-atom model. • The maximum-entropy method-based pattern fitting method is used to confirm the validity of the model. • The disordered structure is described by overlapping three types of domains with ordered atom arrangements.« less

Local and average structures of BaTiO 3-Bi(Zn 1/2Ti 1/2)O 3

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

Usher, Tedi-Marie; Iamsasri, Thanakorn; Forrester, Jennifer S.

The complex crystallographic structures of (1-x)BaTiO 3-xBi(Zn 1/2Ti 1/2)O 3 (BT-xBZT) are examined using high resolution synchrotron X-ray diffraction, neutron diffraction, and neutron pair distribution function (PDF) analyses. The short-range structures are characterized from the PDFs, and a combined analysis of the X-ray and neutron diffraction patterns is used to determine the long-range structures. Our results demonstrate that the structure appears different when averaged over different length scales. In all compositions, the local structures determined from the PDFs show local tetragonal distortions (i.e., c/a > 1). But, a box-car fitting analysis of the PDFs reveals variations at different length scales.more » For 0.80BT-0.20BZT and 0.90BT-0.10BZT, the tetragonal distortions decrease at longer atom-atom distances (e.g., 30 vs. 5 ). When the longest distances are evaluated (r > 40 ), the lattice parameters approach cubic. Neutron and X-ray diffraction yield further information about the long-range structure. Compositions 0.80BT-0.20BZT and 0.90BT-0.10BZT appear cubic by Bragg diffraction (no peak splitting), consistent with the PDFs at long distances. However, these patterns cannot be adequately fit using a cubic lattice model; modeling their structures with the P4mm space group allows for a better fit to the patterns because the space group allows for c-axis atomic displacements that occur at the local scale. Furthermore, for the compositions 0.92BT-0.08BZT and 0.94BT-0.06BZT, strong tetragonal distortions are observed at the local scale and a less-distorted tetragonal structure is observed at longer length scales. In Rietveld refinements, the latter is modeled using a tetragonal phase. Since the peak overlap in these two-phase compositions limits the ability to model the local-scale structures as tetragonal, it is approximated in the refinements as a cubic phase. These results demonstrate that alloying BT with BZT results in increased disorder and disrupts the long-range ferroelectric symmetry present in BT, while the large tetragonal distortion present in BZT persists at the local scale.« less