Redetermination of dicerium(III) tris-(sulfate) tetra-hydrate.

PubMed

Xu, Xin

2007-12-06

Ce(2)(SO(4))(3)(H(2)O)(4) was obtained hydro-thermally from an aqueous solution of cerium(III) oxide, trimethyl-amine and sulfuric acid. The precision of the structure determination has been significantly improved compared with the previous result [Dereigne (1972 ▶). Bull. Soc. Fr. Mineral. Cristallogr.95, 269-280]. The coordination about the two Ce atoms is achieved by seven and six bridging O atoms from sulfate anions. Each S atom makes four S-O-Ce linkages through bridging O atoms. The coordination sphere of each Ce is completed by two water molecules, which act as terminal ligands.

Unraveling protein catalysis through neutron diffraction

NASA Astrophysics Data System (ADS)

Myles, Dean

Neutron scattering and diffraction are exquisitely sensitive to the location, concentration and dynamics of hydrogen atoms in materials and provide a powerful tool for the characterization of structure-function and interfacial relationships in biological systems. Modern neutron scattering facilities offer access to a sophisticated, non-destructive suite of instruments for biophysical characterization that provide spatial and dynamic information spanning from Angstroms to microns and from picoseconds to microseconds, respectively. Applications range from atomic-resolution analysis of individual hydrogen atoms in enzymes, through to multi-scale analysis of hierarchical structures and assemblies in biological complexes, membranes and in living cells. Here we describe how the precise location of protein and water hydrogen atoms using neutron diffraction provides a more complete description of the atomic and electronic structures of proteins, enabling key questions concerning enzyme reaction mechanisms, molecular recognition and binding and protein-water interactions to be addressed. Current work is focused on understanding how molecular structure and dynamics control function in photosynthetic, cell signaling and DNA repair proteins. We will highlight recent studies that provide detailed understanding of the physiochemical mechanisms through which proteins recognize ligands and catalyze reactions, and help to define and understand the key principles involved.

Identification of light elements in silicon nitride by aberration-corrected scanning transmission electron microscopy.

PubMed

Idrobo, Juan C; Walkosz, Weronika; Klie, Robert F; Oğüt, Serdar

2012-12-01

In silicon nitride structural ceramics, the overall mechanical and thermal properties are controlled by the atomic and electronic structures at the interface between the ceramic grains and the amorphous intergranular films (IGFs) formed by various sintering additives. In the last ten years the atomic arrangements of heavy elements (rare-earths) at the Si(3)N(4)/IGF interfaces have been resolved. However, the atomic position of light elements, without which it is not possible to obtain a complete description of the interfaces, has been lacking. This review article details the authors' efforts to identify the atomic arrangement of light elements such as nitrogen and oxygen at the Si(3)N(4)/SiO(2) interface and in bulk Si(3)N(4) using aberration-corrected scanning transmission electron microscopy. Published by Elsevier B.V.

Revealing the planar chemistry of two-dimensional heterostructures at the atomic level.

PubMed

Chou, Harry; Ismach, Ariel; Ghosh, Rudresh; Ruoff, Rodney S; Dolocan, Andrei

2015-06-23

Two-dimensional (2D) atomic crystals and their heterostructures are an intense area of study owing to their unique properties that result from structural planar confinement. Intrinsically, the performance of a planar vertical device is linked to the quality of its 2D components and their interfaces, therefore requiring characterization tools that can reveal both its planar chemistry and morphology. Here, we propose a characterization methodology combining (micro-) Raman spectroscopy, atomic force microscopy and time-of-flight secondary ion mass spectrometry to provide structural information, morphology and planar chemical composition at virtually the atomic level, aimed specifically at studying 2D vertical heterostructures. As an example system, a graphene-on-h-BN heterostructure is analysed to reveal, with an unprecedented level of detail, the subtle chemistry and interactions within its layer structure that can be assigned to specific fabrication steps. Such detailed chemical information is of crucial importance for the complete integration of 2D heterostructures into functional devices.

Atomic Decay Data for Modeling K Lines of Iron Peak and Light Odd-Z Elements*

NASA Technical Reports Server (NTRS)

Palmeri, P.; Quinet, P.; Mendoza, C.; Bautista, M. A.; Garcia, J.; Witthoeft, M. C.; Kallman, T. R.

2012-01-01

Complete data sets of level energies, transition wavelengths, A-values, radiative and Auger widths and fluorescence yields for K-vacancy levels of the F, Na, P, Cl, K, Sc, Ti, V, Cr, Mn, Co, Cu and Zn isonuclear sequences have been computed by a Hartree-Fock method that includes relativistic corrections as implemented in Cowan's atomic structure computer suite. The atomic parameters for more than 3 million fine-structure K lines have been determined. Ions with electron number N greater than 9 are treated for the first time, and detailed comparisons with available measurements and theoretical data for ions with N less than or equal to 9 are carried out in order to estimate reliable accuracy ratings.

Causes of High-temperature Superconductivity in the Hydrogen Sulfide Electron-phonon System

NASA Astrophysics Data System (ADS)

Degtyarenko, N. N.; Mazur, E. A.

The electron and phonon spectra, as well as the density of electron and phonon states of the stable orthorhombic structure of hydrogen sulfide (SH2) at pressures 100-180 GPa have been calculated. It is found that the set of parallel planes of hydrogen atoms is formed at pressure ∼175 GPa as a result of structural changes in the unit cell of the crystal under pressure. There should be complete concentration of hydrogen atoms in these planes. As a result the electron properties of the system acquire a quasi-two-dimensional character. The features of in phase and antiphase oscillations of hydrogen atoms in these planes leading to two narrow high-energy peaks in the phonon density of states are investigated.

Reasons for high-temperature superconductivity in the electron-phonon system of hydrogen sulfide

NASA Astrophysics Data System (ADS)

Degtyarenko, N. N.; Mazur, E. A.

2015-08-01

We have calculated the electron and phonon spectra, as well as the densities of the electron and phonon states, of the stable orthorhombic structure of hydrogen sulfide SH2 in the pressure interval 100-180 GPa. It is found that at a pressure of 175 GPa, a set of parallel planes of hydrogen atoms is formed due to a structural modification of the unit cell under pressure with complete accumulation of all hydrogen atoms in these planes. As a result, the electronic properties of the system become quasi-two-dimensional. We have also analyzed the collective synphase and antiphase vibrations of hydrogen atoms in these planes, leading to the occurrence of two high-energy peaks in the phonon density of states.

Redetermination of dicerium(III) tris­(sulfate) tetra­hydrate

PubMed Central

Xu, Xin

2008-01-01

Ce2(SO4)3(H2O)4 was obtained hydro­thermally from an aqueous solution of cerium(III) oxide, trimethyl­amine and sulfuric acid. The precision of the structure determination has been significantly improved compared with the previous result [Dereigne (1972 ▶). Bull. Soc. Fr. Mineral. Cristallogr. 95, 269–280]. The coordination about the two Ce atoms is achieved by seven and six bridging O atoms from sulfate anions. Each S atom makes four S—O—Ce linkages through bridging O atoms. The coordination sphere of each Ce is completed by two water molecules, which act as terminal ligands. PMID:21200451

Microgravity

NASA Image and Video Library

2004-04-15

A semiconductor's usefulness is determined by how atoms are ordered within the crystal's underlying three-dimensional structure. While this mercury telluride and cadmium telluride alloy sample mixes completely in Earth -based laboratories, convective flows prevent them from mixing uniformly.

Longitudinal structure in atomic oxygen concentrations observed with WINDII on UARS. [Wind Imaging Interferometer

NASA Technical Reports Server (NTRS)

Shepherd, G. G.; Thuillier, G.; Solheim, B. H.; Chandra, S.; Cogger, L. L.; Duboin, M. L.; Evans, W. F. J.; Gattinger, R. L.; Gault, W. A.; Herse, M.

1993-01-01

WINDII, the Wind Imaging Interferometer on the Upper Atmosphere Research Satellite, began atmospheric observations on September 28, 1991 and since then has been collecting data on winds, temperatures and emissions rates from atomic, molecular and ionized oxygen species, as well as hydroxyl. The validation of winds and temperatures is not yet complete, and scientific interpretation has barely begun, but the dominant characteristic of these data so far is the remarkable structure in the emission rate from the excited species produced by the recombination of atomic oxygen. The latitudinal and temporal variability has been noted before by many others. In this preliminary report on WINDII results we draw attention to the dramatic longitudinal variations of planetary wave character in atomic oxygen concentration, as reflected in the OI 557.7 nm emission, and to similar variations seen in the Meine1 hydroxyl band emission.

Ground-state hyperfine splitting for Rb, Cs, Fr, Ba+, and Ra+

NASA Astrophysics Data System (ADS)

Ginges, J. S. M.; Volotka, A. V.; Fritzsche, S.

2017-12-01

We have systematically investigated the ground-state hyperfine structure for alkali-metal atoms 87Rb,133Cs, and 211Fr and alkali-metal-like ions +135Ba and +225Ra, which are of particular interest for parity violation studies. The quantum electrodynamic one-loop radiative corrections have been rigorously evaluated within an extended Furry picture employing core-Hartree and Kohn-Sham atomic potentials. Moreover, the effect of the nuclear magnetization distribution on the hyperfine structure intervals has been studied in detail and its uncertainty has been estimated. Finally, the theoretical description of the hyperfine structure has been completed with full many-body calculations performed in the all-orders correlation potential method.

Structural and electronic properties of isovalent boron atoms in GaAs

NASA Astrophysics Data System (ADS)

Krammel, C. M.; Nattermann, L.; Sterzer, E.; Volz, K.; Koenraad, P. M.

2018-04-01

Boron containing GaAs, which is grown by metal organic vapour phase epitaxy, is studied at the atomic level by cross-sectional scanning tunneling microscopy (X-STM) and spectroscopy (STS). In topographic X-STM images, three classes of B related features are identified, which are attributed to individual B atoms on substitutional Ga sites down to the second layer below the natural {110} cleavage planes. The X-STM contrast of B atoms below the surface reflects primarily the structural modification of the GaAs matrix by the small B atoms. However, B atoms in the cleavage plane have in contrast to conventional isovalent impurities, such as Al and In, a strong influence on the local electronic structure similar to donors or acceptors. STS measurements show that B in the GaAs {110} surfaces gives rise to a localized state short below the conduction band (CB) edge while in bulk GaAs, the B impurity state is resonant with the CB. The analysis of BxGa1-xAs/GaAs quantum wells reveals a good crystal quality and shows that the incorporation of B atoms in GaAs can be controlled along the [001] growth direction at the atomic level. Surprisingly, the formation of the first and fourth nearest neighbor B pairs, which are oriented along the <110 > directions, is strongly suppressed at a B concentration of 1% while the third nearest neighbor B pairs are found more than twice as often than expected for a completely spatially random pattern.

Sparse Representation for Infrared Dim Target Detection via a Discriminative Over-Complete Dictionary Learned Online

PubMed Central

Li, Zheng-Zhou; Chen, Jing; Hou, Qian; Fu, Hong-Xia; Dai, Zhen; Jin, Gang; Li, Ru-Zhang; Liu, Chang-Ju

2014-01-01

It is difficult for structural over-complete dictionaries such as the Gabor function and discriminative over-complete dictionary, which are learned offline and classified manually, to represent natural images with the goal of ideal sparseness and to enhance the difference between background clutter and target signals. This paper proposes an infrared dim target detection approach based on sparse representation on a discriminative over-complete dictionary. An adaptive morphological over-complete dictionary is trained and constructed online according to the content of infrared image by K-singular value decomposition (K-SVD) algorithm. Then the adaptive morphological over-complete dictionary is divided automatically into a target over-complete dictionary describing target signals, and a background over-complete dictionary embedding background by the criteria that the atoms in the target over-complete dictionary could be decomposed more sparsely based on a Gaussian over-complete dictionary than the one in the background over-complete dictionary. This discriminative over-complete dictionary can not only capture significant features of background clutter and dim targets better than a structural over-complete dictionary, but also strengthens the sparse feature difference between background and target more efficiently than a discriminative over-complete dictionary learned offline and classified manually. The target and background clutter can be sparsely decomposed over their corresponding over-complete dictionaries, yet couldn't be sparsely decomposed based on their opposite over-complete dictionary, so their residuals after reconstruction by the prescribed number of target and background atoms differ very visibly. Some experiments are included and the results show that this proposed approach could not only improve the sparsity more efficiently, but also enhance the performance of small target detection more effectively. PMID:24871988

Sparse representation for infrared Dim target detection via a discriminative over-complete dictionary learned online.

PubMed

Li, Zheng-Zhou; Chen, Jing; Hou, Qian; Fu, Hong-Xia; Dai, Zhen; Jin, Gang; Li, Ru-Zhang; Liu, Chang-Ju

2014-05-27

It is difficult for structural over-complete dictionaries such as the Gabor function and discriminative over-complete dictionary, which are learned offline and classified manually, to represent natural images with the goal of ideal sparseness and to enhance the difference between background clutter and target signals. This paper proposes an infrared dim target detection approach based on sparse representation on a discriminative over-complete dictionary. An adaptive morphological over-complete dictionary is trained and constructed online according to the content of infrared image by K-singular value decomposition (K-SVD) algorithm. Then the adaptive morphological over-complete dictionary is divided automatically into a target over-complete dictionary describing target signals, and a background over-complete dictionary embedding background by the criteria that the atoms in the target over-complete dictionary could be decomposed more sparsely based on a Gaussian over-complete dictionary than the one in the background over-complete dictionary. This discriminative over-complete dictionary can not only capture significant features of background clutter and dim targets better than a structural over-complete dictionary, but also strengthens the sparse feature difference between background and target more efficiently than a discriminative over-complete dictionary learned offline and classified manually. The target and background clutter can be sparsely decomposed over their corresponding over-complete dictionaries, yet couldn't be sparsely decomposed based on their opposite over-complete dictionary, so their residuals after reconstruction by the prescribed number of target and background atoms differ very visibly. Some experiments are included and the results show that this proposed approach could not only improve the sparsity more efficiently, but also enhance the performance of small target detection more effectively.

Elementary defects in graphane

NASA Astrophysics Data System (ADS)

Podlivaev, A. I.; Openov, L. A.

2017-07-01

The main zero-dimensional defects in graphane, a completely hydrogenated single-layer graphene, having the chair-type conformation have been numerically simulated. The hydrogen and carbon-hydrogen vacancies, Stone-Wales defect, and "transmutation defect" resulting from the simultaneous hoppings of two hydrogen atoms between the neighboring carbon atoms have been considered. The energies of formations of these defects have been calculated and their effect on the electronic structure, phonon spectra, and Young modulus has been studied.

Software Package Completed for Alloy Design at the Atomic Level

NASA Technical Reports Server (NTRS)

Bozzolo, Guillermo H.; Noebe, Ronald D.; Abel, Phillip B.; Good, Brian S.

2001-01-01

As a result of a multidisciplinary effort involving solid-state physics, quantum mechanics, and materials and surface science, the first version of a software package dedicated to the atomistic analysis of multicomponent systems was recently completed. Based on the BFS (Bozzolo, Ferrante, and Smith) method for the calculation of alloy and surface energetics, this package includes modules devoted to the analysis of many essential features that characterize any given alloy or surface system, including (1) surface structure analysis, (2) surface segregation, (3) surface alloying, (4) bulk crystalline material properties and atomic defect structures, and (5) thermal processes that allow us to perform phase diagram calculations. All the modules of this Alloy Design Workbench 1.0 (ADW 1.0) are designed to run in PC and workstation environments, and their operation and performance are substantially linked to the needs of the user and the specific application.

Atomtronics: Realizing the behavior of electronic components in ultracold atomic systems

NASA Astrophysics Data System (ADS)

Pepino, Ron

2007-06-01

Atomtronics focuses on creating an analogy of electronic devices and circuits with ultracold atoms. Such an analogy can come from the highly tunable band structure of ultracold neutral atoms trapped in optical lattices. Solely by tuning the parameters of the optical lattice, we demonstrate that conditions can be created that cause atoms in lattices to exhibit the same behavior as electrons moving through solid state media. We present our model and show how the atomtronic diode, field effect transistor, and bipolar junction transistor can all be realized. Our analogs of these fundamental components exhibit precisely-controlled atomic signal amplification, trimming, and switching (on/off) characteristics. In addition, the evolution of dynamics of the superfluid atomic currents within these systems is completely reversible. This implies a possible use of atomtronic systems in the development of quantum computational devices.

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.

Modification in structure, phase transition, and magnetic property of metallic gallium driven by atom-molecule interactions.

PubMed

Song, Le Xin; Chen, Jie; Zhu, Lin Hong; Xia, Juan; Yang, Jun

2011-09-05

The present work supports a novel paradigm in which the surface structure and stacking behavior of metallic gallium (Ga) were significantly influenced by the preparation process in the presence of organic small molecules (ethanol, acetone, dichloromethane, and diethyl ether). The extent of the effect strongly depends on the polarity of the molecules. Especially, a series of new atom-molecule aggregates consisting of metallic Ga and macrocyclic hosts (cyclodextrins, CDs) were prepared and characterized by various techniques. A comprehensive comparative analysis between free metallic Ga and the Ga samples obtained provides important and at present rare information on the modification in structure, phase transition, and magnetic property of Ga driven by atom-molecule interactions. First, there is a notable difference in microstructure and electronic structure between the different types of Ga samples. Second, differential scanning calorimetry analysis gives us a complete picture (such as the occurrence of a series of metastable phases of Ga in the presence of CDs) that has allowed us to consider that Ga atoms were protected by the shielding effect provided by the cavities of CDs. Third, the metallic Ga distributed in the aggregates exhibits very interesting magnetic property compared to free metallic Ga, such as the uniform zero-field-cooled and field-cooled magnetization processes, the enhanced responses in magnetization to temperature and applied field, and the fundamental change in shape of magnetic hysteresis loops. These significant changes in structural transformation and physical property of Ga provide a novel insight into the understanding of atom-molecule interactions between metallic atoms and organic molecules.

Chemistry Notes.

ERIC Educational Resources Information Center

School Science Review, 1982

1982-01-01

Presents laboratory procedures, classroom materials/activities, and demonstrations, including: vapor pressure of liquid mixtures and Raoult's law; preparation/analysis of transition metal complexes of ethylammonium chloride; atomic structure display using a ZX81 (includes complete program listing); "pop-up" models of molecules and ions;…

Fe doped Magnetic Nanodiamonds made by Ion Implantation.

PubMed

Chen, ChienHsu; Cho, I C; Jian, Hui-Shan; Niu, H

2017-02-09

Here we present a simple physical method to prepare magnetic nanodiamonds (NDs) using high dose Fe ion-implantation. The Fe atoms are embedded into NDs through Fe ion-implantation and the crystal structure of NDs are recovered by thermal annealing. The results of TEM and Raman examinations indicated the crystal structure of the Fe implanted NDs is recovered completely. The SQUID-VSM measurement shows the Fe-NDs possess room temperature ferromagnetism. That means the Fe atoms are distributed inside the NDs without affecting NDs crystal structure, so the NDs can preserve the original physical and chemical properties of the NDs. In addition, the ion-implantation-introduced magnetic property might make the NDs to become suitable for variety of medical applications.

Fe doped Magnetic Nanodiamonds made by Ion Implantation

NASA Astrophysics Data System (ADS)

Chen, Chienhsu; Cho, I. C.; Jian, Hui-Shan; Niu, H.

2017-02-01

Here we present a simple physical method to prepare magnetic nanodiamonds (NDs) using high dose Fe ion-implantation. The Fe atoms are embedded into NDs through Fe ion-implantation and the crystal structure of NDs are recovered by thermal annealing. The results of TEM and Raman examinations indicated the crystal structure of the Fe implanted NDs is recovered completely. The SQUID-VSM measurement shows the Fe-NDs possess room temperature ferromagnetism. That means the Fe atoms are distributed inside the NDs without affecting NDs crystal structure, so the NDs can preserve the original physical and chemical properties of the NDs. In addition, the ion-implantation-introduced magnetic property might make the NDs to become suitable for variety of medical applications.

Neutron Nucleic Acid Crystallography.

PubMed

Chatake, Toshiyuki

2016-01-01

The hydration shells surrounding nucleic acids and hydrogen-bonding networks involving water molecules and nucleic acids are essential interactions for the structural stability and function of nucleic acids. Water molecules in the hydration shells influence various conformations of DNA and RNA by specific hydrogen-bonding networks, which often contribute to the chemical reactivity and molecular recognition of nucleic acids. However, X-ray crystallography could not provide a complete description of structural information with respect to hydrogen bonds. Indeed, X-ray crystallography is a powerful tool for determining the locations of water molecules, i.e., the location of the oxygen atom of H2O; however, it is very difficult to determine the orientation of the water molecules, i.e., the orientation of the two hydrogen atoms of H2O, because X-ray scattering from the hydrogen atom is very small.Neutron crystallography is a specialized tool for determining the positions of hydrogen atoms. Neutrons are not diffracted by electrons, but are diffracted by atomic nuclei; accordingly, neutron scattering lengths of hydrogen and its isotopes are comparable to those of non-hydrogen atoms. Therefore, neutron crystallography can determine both of the locations and orientations of water molecules. This chapter describes the current status of neutron nucleic acid crystallographic research as well as the basic principles of neutron diffraction experiments performed on nucleic acid crystals: materials, crystallization, diffraction experiments, and structure determination.

Identification of Conserved Moieties in Metabolic Networks by Graph Theoretical Analysis of Atom Transition Networks

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

Haraldsdóttir, Hulda S.; Fleming, Ronan M. T.

Conserved moieties are groups of atoms that remain intact in all reactions of a metabolic network. Identification of conserved moieties gives insight into the structure and function of metabolic networks and facilitates metabolic modelling. All moiety conservation relations can be represented as nonnegative integer vectors in the left null space of the stoichiometric matrix corresponding to a biochemical network. Algorithms exist to compute such vectors based only on reaction stoichiometry but their computational complexity has limited their application to relatively small metabolic networks. Moreover, the vectors returned by existing algorithms do not, in general, represent conservation of a specific moietymore » with a defined atomic structure. Here, we show that identification of conserved moieties requires data on reaction atom mappings in addition to stoichiometry. We present a novel method to identify conserved moieties in metabolic networks by graph theoretical analysis of their underlying atom transition networks. Our method returns the exact group of atoms belonging to each conserved moiety as well as the corresponding vector in the left null space of the stoichiometric matrix. It can be implemented as a pipeline of polynomial time algorithms. Our implementation completes in under five minutes on a metabolic network with more than 4,000 mass balanced reactions. The scalability of the method enables extension of existing applications for moiety conservation relations to genome-scale metabolic networks. Finally, we also give examples of new applications made possible by elucidating the atomic structure of conserved moieties.« less

Identification of Conserved Moieties in Metabolic Networks by Graph Theoretical Analysis of Atom Transition Networks

PubMed Central

Haraldsdóttir, Hulda S.; Fleming, Ronan M. T.

2016-01-01

Conserved moieties are groups of atoms that remain intact in all reactions of a metabolic network. Identification of conserved moieties gives insight into the structure and function of metabolic networks and facilitates metabolic modelling. All moiety conservation relations can be represented as nonnegative integer vectors in the left null space of the stoichiometric matrix corresponding to a biochemical network. Algorithms exist to compute such vectors based only on reaction stoichiometry but their computational complexity has limited their application to relatively small metabolic networks. Moreover, the vectors returned by existing algorithms do not, in general, represent conservation of a specific moiety with a defined atomic structure. Here, we show that identification of conserved moieties requires data on reaction atom mappings in addition to stoichiometry. We present a novel method to identify conserved moieties in metabolic networks by graph theoretical analysis of their underlying atom transition networks. Our method returns the exact group of atoms belonging to each conserved moiety as well as the corresponding vector in the left null space of the stoichiometric matrix. It can be implemented as a pipeline of polynomial time algorithms. Our implementation completes in under five minutes on a metabolic network with more than 4,000 mass balanced reactions. The scalability of the method enables extension of existing applications for moiety conservation relations to genome-scale metabolic networks. We also give examples of new applications made possible by elucidating the atomic structure of conserved moieties. PMID:27870845

Identification of Conserved Moieties in Metabolic Networks by Graph Theoretical Analysis of Atom Transition Networks

DOE PAGES

Haraldsdóttir, Hulda S.; Fleming, Ronan M. T.

2016-11-21

Conserved moieties are groups of atoms that remain intact in all reactions of a metabolic network. Identification of conserved moieties gives insight into the structure and function of metabolic networks and facilitates metabolic modelling. All moiety conservation relations can be represented as nonnegative integer vectors in the left null space of the stoichiometric matrix corresponding to a biochemical network. Algorithms exist to compute such vectors based only on reaction stoichiometry but their computational complexity has limited their application to relatively small metabolic networks. Moreover, the vectors returned by existing algorithms do not, in general, represent conservation of a specific moietymore » with a defined atomic structure. Here, we show that identification of conserved moieties requires data on reaction atom mappings in addition to stoichiometry. We present a novel method to identify conserved moieties in metabolic networks by graph theoretical analysis of their underlying atom transition networks. Our method returns the exact group of atoms belonging to each conserved moiety as well as the corresponding vector in the left null space of the stoichiometric matrix. It can be implemented as a pipeline of polynomial time algorithms. Our implementation completes in under five minutes on a metabolic network with more than 4,000 mass balanced reactions. The scalability of the method enables extension of existing applications for moiety conservation relations to genome-scale metabolic networks. Finally, we also give examples of new applications made possible by elucidating the atomic structure of conserved moieties.« less

Identification of Conserved Moieties in Metabolic Networks by Graph Theoretical Analysis of Atom Transition Networks.

PubMed

Haraldsdóttir, Hulda S; Fleming, Ronan M T

2016-11-01

Conserved moieties are groups of atoms that remain intact in all reactions of a metabolic network. Identification of conserved moieties gives insight into the structure and function of metabolic networks and facilitates metabolic modelling. All moiety conservation relations can be represented as nonnegative integer vectors in the left null space of the stoichiometric matrix corresponding to a biochemical network. Algorithms exist to compute such vectors based only on reaction stoichiometry but their computational complexity has limited their application to relatively small metabolic networks. Moreover, the vectors returned by existing algorithms do not, in general, represent conservation of a specific moiety with a defined atomic structure. Here, we show that identification of conserved moieties requires data on reaction atom mappings in addition to stoichiometry. We present a novel method to identify conserved moieties in metabolic networks by graph theoretical analysis of their underlying atom transition networks. Our method returns the exact group of atoms belonging to each conserved moiety as well as the corresponding vector in the left null space of the stoichiometric matrix. It can be implemented as a pipeline of polynomial time algorithms. Our implementation completes in under five minutes on a metabolic network with more than 4,000 mass balanced reactions. The scalability of the method enables extension of existing applications for moiety conservation relations to genome-scale metabolic networks. We also give examples of new applications made possible by elucidating the atomic structure of conserved moieties.

Surface faceting and elemental diffusion behaviour at atomic scale for alloy nanoparticles during in situ annealing

PubMed Central

Chi, Miaofang; Wang, Chao; Lei, Yinkai; Wang, Guofeng; Li, Dongguo; More, Karren L.; Lupini, Andrew; Allard, Lawrence F.; Markovic, Nenad M.; Stamenkovic, Vojislav R.

2015-01-01

The catalytic performance of nanoparticles is primarily determined by the precise nature of the surface and near-surface atomic configurations, which can be tailored by post-synthesis annealing effectively and straightforwardly. Understanding the complete dynamic response of surface structure and chemistry to thermal treatments at the atomic scale is imperative for the rational design of catalyst nanoparticles. Here, by tracking the same individual Pt3Co nanoparticles during in situ annealing in a scanning transmission electron microscope, we directly discern five distinct stages of surface elemental rearrangements in Pt3Co nanoparticles at the atomic scale: initial random (alloy) elemental distribution; surface platinum-skin-layer formation; nucleation of structurally ordered domains; ordered framework development and, finally, initiation of amorphization. Furthermore, a comprehensive interplay among phase evolution, surface faceting and elemental inter-diffusion is revealed, and supported by atomistic simulations. This work may pave the way towards designing catalysts through post-synthesis annealing for optimized catalytic performance. PMID:26576477

Atomic disorder, phase transformation, and phase restoration in Co3Sn2

NASA Astrophysics Data System (ADS)

di, L. M.; Zhou, G. F.; Bakker, H.

1993-03-01

The behavior of the intermetallic compound Co3Sn2 upon ball milling was studied by x-ray diffraction, high-field-magnetization measurements, and subsequently by differential scanning calorimetry. It turns out that starting from the stoichiometric-ordered compound, mechanical attrition of Co3Sn2 generates atomic disorder in the early stage of milling. The nonequilibrium phase transformation from the low-temperature phase with orthorhombic structure to the high-temperature phase with a hexagonal structure was observed in the intermediate stage of milling. It was accompanied by the creation of increasing atomic disorder. After long milling periods, the phase transformation was completed and the atomic disordering became saturated. All the physical parameters measured in the present work remained constant during this period. The above outcome was confirmed by comparison with the high-temperature phase thermally induced by quenching. The good agreement of the results obtained by different techniques proves that the ball milling generates well-defined metastable states in Co3Sn2.

Surface faceting and elemental diffusion behaviour at atomic scale for alloy nanoparticles during in situ annealing

DOE PAGES

Chi, Miaofang; Wang, Chao; Lei, Yinkai; ...

2015-11-18

The catalytic performance of nanoparticles is primarily determined by the precise nature of the surface and near-surface atomic configurations, which can be tailored by post-synthesis annealing effectively and straightforwardly. Understanding the complete dynamic response of surface structure and chemistry to thermal treatments at the atomic scale is imperative for the rational design of catalyst nanoparticles. Here, by tracking the same individual Pt 3Co nanoparticles during in situ annealing in a scanning transmission electron microscope, we directly discern five distinct stages of surface elemental rearrangements in Pt 3Co nanoparticles at the atomic scale: initial random (alloy) elemental distribution; surface platinum-skin-layer formation;more » nucleation of structurally ordered domains; ordered framework development and, finally, initiation of amorphization. Furthermore, a comprehensive interplay among phase evolution, surface faceting and elemental inter-diffusion is revealed, and supported by atomistic simulations. In conlcusion, this work may pave the way towards designing catalysts through post-synthesis annealing for optimized catalytic performance.« less

Effect of elastic collisions and electronic excitation on lattice structure of NiTi bulk intermetallic compound irradiated with energetic ions

NASA Astrophysics Data System (ADS)

Ochi, M.; Kojima, H.; Hori, F.; Kaneno, Y.; Semboshi, S.; Saitoh, Y.; Okamoto, Y.; Ishikawa, N.; Iwase, A.

2018-07-01

NiTi bulk intermetallic compound with the B19‧ structure was irradiated with 1 MeV He, 5 MeV Al, 16 MeV Au and 200 MeV Xe ions, and the change in lattice structure near the surface by the ion bombardment was investigated by using the grazing incidence X-ray diffraction (GIXD) and the extended X-ray absorption fine structure (EXAFS). The lattice structure transformation by the irradiation strongly depends on ion species and/or energies. For the 1 MeV He irradiation, the lattice structure changed from B19‧ to the A2 structure, but did not show an amorphization even after the high fluence irradiation. For the 5 MeV Al irradiation, the samples are partially amorphized. For the 16 MeV Au irradiation, the lattice structure of the NiTi samples changed nearly completely from the B19‧ structure to the amorphous state via the A2 structure. The value of dpa (displacement per atom) which is needed for the amorphization is, however, much smaller than the case of the Al ion irradiation. For the 200 MeV Xe ion irradiation, the lattice structure completely changed to the A2 structure even by a small ion fluence. The dependence of the lattice structure transformation on elastic collisions (dpa), the spectrum of the primary knock-on (PKA) atoms and the density of energy deposited through electronic excitation was discussed.

Interfacial structure of two-dimensional epitaxial Er silicide on Si(111)

NASA Astrophysics Data System (ADS)

Tuilier, M. H.; Wetzel, P.; Pirri, C.; Bolmont, D.; Gewinner, G.

1994-07-01

Auger-electron diffraction (AED) and surface-extended x-ray-absorption fine structure (SEXAFS) have been used to obtain a complete description of the atomic structure of a two-dimensional epitaxial Er silicide layer on Si(111). AED reveals that a monolayer of Er is located underneath a buckled Si double layer. The relevant Er-Si interlayer spacings are determined by means of single scattering cluster simulations and a R-factor analysis to be 1.92+/-0.05 Å to the first and 2.70+/-0.05 Å to the second Si top layer. Er near-neighbor bond lengths and coordination numbers are obtained independently from polarization-dependent SEXAFS. The SEXAFS data, when combined with the Si top-layer geometry inferred from AED, permit the determination of the atomic positions at the silicide/Si(111) interface. The Er is found to reside in relaxed T4 sites of Si(111) with a single Er-Si distance of 3.09+/-0.04 Å to the first- and second-layer Si atoms of the substrate.

Comparative structural and electronic studies of hydrogen interaction with isolated versus ordered silicon nanoribbons grown on Ag(110)

NASA Astrophysics Data System (ADS)

Dávila, M. E.; Marele, A.; De Padova, P.; Montero, I.; Hennies, F.; Pietzsch, A.; Shariati, M. N.; Gómez-Rodríguez, J. M.; Le Lay, G.

2012-09-01

We have investigated the geometry and electronic structure of two different types of self-aligned silicon nanoribbons (SiNRs), forming either isolated SiNRs or a self-assembled 5 × 2/5 × 4 grating on an Ag(110) substrate, by scanning tunnelling microscopy and high resolution x-ray photoelectron spectroscopy. At room temperature we further adsorb on these SiNRs either atomic or molecular hydrogen. The hydrogen absorption process and hydrogenation mechanism are similar for isolated or 5 × 2/5 × 4 ordered SiNRs and are not site selective; the main difference arises from the fact that the isolated SiNRs are more easily attacked and destroyed faster. In fact, atomic hydrogen strongly interacts with any Si atoms, modifying their structural and electronic properties, while molecular hydrogen has first to dissociate. Hydrogen finally etches the Si nanoribbons and their complete removal from the Ag(110) surface could eventually be expected.

PubChem atom environments.

PubMed

Hähnke, Volker D; Bolton, Evan E; Bryant, Stephen H

2015-01-01

Atom environments and fragments find wide-spread use in chemical information and cheminformatics. They are the basis of prediction models, an integral part in similarity searching, and employed in structure search techniques. Most of these methods were developed and evaluated on the relatively small sets of chemical structures available at the time. An analysis of fragment distributions representative of most known chemical structures was published in the 1970s using the Chemical Abstracts Service data system. More recently, advances in automated synthesis of chemicals allow millions of chemicals to be synthesized by a single organization. In addition, open chemical databases are readily available containing tens of millions of chemical structures from a multitude of data sources, including chemical vendors, patents, and the scientific literature, making it possible for scientists to readily access most known chemical structures. With this availability of information, one can now address interesting questions, such as: what chemical fragments are known today? How do these fragments compare to earlier studies? How unique are chemical fragments found in chemical structures? For our analysis, after hydrogen suppression, atoms were characterized by atomic number, formal charge, implicit hydrogen count, explicit degree (number of neighbors), valence (bond order sum), and aromaticity. Bonds were differentiated as single, double, triple or aromatic bonds. Atom environments were created in a circular manner focused on a central atom with radii from 0 (atom types) up to 3 (representative of ECFP_6 fragments). In total, combining atom types and atom environments that include up to three spheres of nearest neighbors, our investigation identified 28,462,319 unique fragments in the 46 million structures found in the PubChem Compound database as of January 2013. We could identify several factors inflating the number of environments involving transition metals, with many seemingly due to erroneous interpretation of structures from patent data. Compared to fragmentation statistics published 40 years ago, the exponential growth in chemistry is mirrored in a nearly eightfold increase in the number of unique chemical fragments; however, this result is clearly an upper bound estimate as earlier studies employed structure sampling approaches and this study shows that a relatively high rate of atom fragments are found in only a single chemical structure (singletons). In addition, the percentage of singletons grows as the size of the chemical fragment is increased. The observed growth of the numbers of unique fragments over time suggests that many chemically possible connections of atom types to larger fragments have yet to be explored by chemists. A dramatic drop in the relative rate of increase of atom environments from smaller to larger fragments shows that larger fragments mainly consist of diverse combinations of a limited subset of smaller fragments. This is further supported by the observed concomitant increase of singleton atom environments. Combined, these findings suggest that there is considerable opportunity for chemists to combine known fragments to novel chemical compounds. The comparison of PubChem to an older study of known chemical structures shows noticeable differences. The changes suggest advances in synthetic capabilities of chemists to combine atoms in new patterns. Log-log plots of fragment incidence show small numbers of fragments are found in many structures and that large numbers of fragments are found in very few structures, with nearly half being novel using the methods in this work. The relative decrease in the count of new fragments as a function of size further suggests considerable opportunity for more novel chemicals exists. Lastly, the differences in atom environment diversity between PubChem Substance and Compound showcase the effect of PubChem standardization protocols, but also indicate that a normalization procedure for atom types, functional groups, and tautomeric/resonance forms based on atom environments is possible. The complete sets of atom types and atom environments are supplied as supporting information.

Novel Organotin(IV) Schiff Base Complexes with Histidine Derivatives: Synthesis, Characterization, and Biological Activity

PubMed Central

Garza-Ortiz, Ariadna; Camacho-Camacho, Carlos; Sainz-Espuñes, Teresita; Rojas-Oviedo, Irma; Gutiérrez-Lucas, Luis Raúl; Gutierrez Carrillo, Atilano; Vera Ramirez, Marco A.

2013-01-01

Five novel tin Schiff base complexes with histidine analogues (derived from the condensation reaction between L-histidine and 3,5-di-tert-butyl-2-hydroxybenzaldehyde) have been synthesized and characterized. Characterization has been completed by IR and high-resolution mass spectroscopy, 1D and 2D solution NMR (1H, 13C  and 119Sn), as well as solid state 119Sn NMR. The spectroscopic evidence shows two types of structures: a trigonal bipyramidal stereochemistry with the tin atom coordinated to five donating atoms (two oxygen atoms, one nitrogen atom, and two carbon atoms belonging to the alkyl moieties), where one molecule of ligand is coordinated in a three dentate fashion. The second structure is spectroscopically described as a tetrahedral tin complex with four donating atoms (one oxygen atom coordinated to the metal and three carbon atoms belonging to the alkyl or aryl substituents), with one molecule of ligand attached. The antimicrobial activity of the tin compounds has been tested against the growth of bacteria in vitro to assess their bactericidal properties. While pentacoordinated compounds 1, 2, and 3 are described as moderate effective to noneffective drugs against both Gram-positive and Gram-negative bacteria, tetracoordinated tin(IV) compounds 4 and 5 are considered as moderate effective and most effective compounds, respectively, against the methicillin-resistant Staphylococcus aureus strains (Gram-positive). PMID:23864839

NMR spectra of androstane analogs of brassinosteroids

NASA Astrophysics Data System (ADS)

Baranovskii, A. V.; Litvinovskaya, R. P.; Aver'kova, M. A.; Khripach, N. B.; Khripach, V. A.

2007-09-01

We have used two-dimensional NMR spectroscopy to make a complete assignment of signals from the nuclei of hydrogen and carbon atoms in the spectra of brassinosteroids in the androstane series. We have confirmed the stereochemistry of the chiral centers and the structure of the molecules. We have studied the effect of the configuration of the 2,3-diol groups in the A ring of the steroids on the chemical shift of adjacent atoms in the 13C and 1H NMR spectra.

In silico folding of a three helix protein and characterization of its free-energy landscape in an all-atom force field.

PubMed

Herges, T; Wenzel, W

2005-01-14

We report the reproducible first-principles folding of the 40 amino-acid, three-helix headpiece of the HIV accessory protein in a recently developed all-atom free-energy force field. Six of 20 simulations using an adapted basin-hopping method converged to better than 3 A backbone rms deviation to the experimental structure. Using over 60 000 low-energy conformations of this protein, we constructed a decoy tree that completely characterizes its folding funnel.

In Silico Folding of a Three Helix Protein and Characterization of Its Free-Energy Landscape in an All-Atom Force Field

NASA Astrophysics Data System (ADS)

Herges, T.; Wenzel, W.

2005-01-01

We report the reproducible first-principles folding of the 40 amino-acid, three-helix headpiece of the HIV accessory protein in a recently developed all-atom free-energy force field. Six of 20 simulations using an adapted basin-hopping method converged to better than 3Å backbone rms deviation to the experimental structure. Using over 60 000 low-energy conformations of this protein, we constructed a decoy tree that completely characterizes its folding funnel.

2D polymeric cadmium(II) complexes containing 1,3-imidazolidine-2-thione (Imt) ligand, [Cd(Imt)(H2O)2(SO4)]n and [Cd(Imt)2(N3)2]n

NASA Astrophysics Data System (ADS)

Mahmood, Rashid; Ahmad, Saeed; Fettouhi, Mohammed; Roisnel, Thierry; Gilani, Mazhar Amjad; Mehmood, Kashif; Murtaza, Ghulam; Isab, Anvarhusein A.

2018-03-01

The present study aims at preparing and carrying out the structural investigation of two polymeric cadmium(II) complexes of imidazolidine-2-thione (Imt) based on sulfate or azide ions, [Cd(Imt)(H2O)2(SO4)]n (1) and [Cd(Imt)2(N3)2]n (2). The structures of the complexes were determined by single crystal X-ray analysis. Both compounds, 1 and 2 crystallize in the form of 2D coordination polymers and the cadmium(II) ion is six-coordinate having a distorted octahedral geometry in each compound. In 1, the metal ion is bonded to one sulfur atom of Imt and five oxygen atoms with two from water and three of bridging sulfate ions. In 2, the cadmium coordination sphere is completed by two Imt molecules binding through the sulfur atoms and four nitrogen atoms of bridging azide ions. The crystal structures are stabilized by intra and intermolecular hydrogen bonding interactions. The complexes were also characterized by IR and NMR spectroscopy and the spectroscopic data is consistent with the binding of the ligands.

Formation of fivefold axes in the FCC-metal nanoclusters

NASA Astrophysics Data System (ADS)

Myasnichenko, Vladimir S.; Starostenkov, Mikhail D.

2012-11-01

Formation of atomistic structures of metallic Cu, Au, Ag clusters and bimetallic Cu-Au clusters was studied with the help of molecular dynamics using the many-body tight-binding interatomic potential. The simulation of the crystallization process of clusters with the number of atoms ranging from 300 to 1092 was carried out. The most stable configurations of atoms in the system, corresponding to the minimum of potential energy, was found during super-fast cooling from 1000 K. Atoms corresponding to fcc, hcp, and Ih phases were identified by the method of common neighbor analysis. Incomplete icosahedral core can be discovered at the intersection of one of the Ih axes with the surface of monometallic cluster. The decahedron-shaped structure of bimetallic Cu-Au cluster with seven completed icosahedral cores was obtained. The principles of the construction of small bimetallic clusters with icosahedral symmetry and increased fractal dimensionality were offered.

On the road to metallic nanoparticles by rational design: bridging the gap between atomic-level theoretical modeling and reality by total scattering experiments

NASA Astrophysics Data System (ADS)

Prasai, Binay; Wilson, A. R.; Wiley, B. J.; Ren, Y.; Petkov, Valeri

2015-10-01

The extent to which current theoretical modeling alone can reveal real-world metallic nanoparticles (NPs) at the atomic level was scrutinized and demonstrated to be insufficient and how it can be improved by using a pragmatic approach involving straightforward experiments is shown. In particular, 4 to 6 nm in size silica supported Au100-xPdx (x = 30, 46 and 58) explored for catalytic applications is characterized structurally by total scattering experiments including high-energy synchrotron X-ray diffraction (XRD) coupled to atomic pair distribution function (PDF) analysis. Atomic-level models for the NPs are built by molecular dynamics simulations based on the archetypal for current theoretical modeling Sutton-Chen (SC) method. Models are matched against independent experimental data and are demonstrated to be inaccurate unless their theoretical foundation, i.e. the SC method, is supplemented with basic yet crucial information on the length and strength of metal-to-metal bonds and, when necessary, structural disorder in the actual NPs studied. An atomic PDF-based approach for accessing such information and implementing it in theoretical modeling is put forward. For completeness, the approach is concisely demonstrated on 15 nm in size water-dispersed Au particles explored for bio-medical applications and 16 nm in size hexane-dispersed Fe48Pd52 particles explored for magnetic applications as well. It is argued that when ``tuned up'' against experiments relevant to metals and alloys confined to nanoscale dimensions, such as total scattering coupled to atomic PDF analysis, rather than by mere intuition and/or against data for the respective solids, atomic-level theoretical modeling can provide a sound understanding of the synthesis-structure-property relationships in real-world metallic NPs. Ultimately this can help advance nanoscience and technology a step closer to producing metallic NPs by rational design.The extent to which current theoretical modeling alone can reveal real-world metallic nanoparticles (NPs) at the atomic level was scrutinized and demonstrated to be insufficient and how it can be improved by using a pragmatic approach involving straightforward experiments is shown. In particular, 4 to 6 nm in size silica supported Au100-xPdx (x = 30, 46 and 58) explored for catalytic applications is characterized structurally by total scattering experiments including high-energy synchrotron X-ray diffraction (XRD) coupled to atomic pair distribution function (PDF) analysis. Atomic-level models for the NPs are built by molecular dynamics simulations based on the archetypal for current theoretical modeling Sutton-Chen (SC) method. Models are matched against independent experimental data and are demonstrated to be inaccurate unless their theoretical foundation, i.e. the SC method, is supplemented with basic yet crucial information on the length and strength of metal-to-metal bonds and, when necessary, structural disorder in the actual NPs studied. An atomic PDF-based approach for accessing such information and implementing it in theoretical modeling is put forward. For completeness, the approach is concisely demonstrated on 15 nm in size water-dispersed Au particles explored for bio-medical applications and 16 nm in size hexane-dispersed Fe48Pd52 particles explored for magnetic applications as well. It is argued that when ``tuned up'' against experiments relevant to metals and alloys confined to nanoscale dimensions, such as total scattering coupled to atomic PDF analysis, rather than by mere intuition and/or against data for the respective solids, atomic-level theoretical modeling can provide a sound understanding of the synthesis-structure-property relationships in real-world metallic NPs. Ultimately this can help advance nanoscience and technology a step closer to producing metallic NPs by rational design. Electronic supplementary information (ESI) available: XRD patterns, TEM and 3D structure modelling methodology. See DOI: 10.1039/c5nr04678e

Alkali metal and ammonium fluoro(trifluoroacetato)metallates M'[ M''3(μ3-F)(CF3COO)6(CF3COOH)3], where M' = Li, Na, K, NH4, Rb, or Cs and M'' = Ni or Co. Synthesis and crystal structures

NASA Astrophysics Data System (ADS)

Tereshchenko, D. S.; Morozov, I. V.; Boltalin, A. I.; Karpova, E. V.; Glazunova, T. Yu.; Troyanov, S. I.

2013-01-01

A series of fluoro(trifluoroacetato)metallates were synthesized by crystallization from solutions in trifluoroacetic acid containing nickel(II) or cobalt(II) nitrate hydrates and alkali metal or ammonium fluorides: Li[Ni3(μ3-F)(CF3COO)6(CF3COOH)3](CF3COOH)3 ( I), M'[Ni3(μ3-F)(CF3COO)6(CF3COOH)3] ( M' = Na ( II), NH4 ( IV), Rb ( V), and Cs ( VI)), NH4[Co3(μ3-F) (CF3COO)6(CF3COOH)3] ( III), and Cs[Ni3(μ3-F)(CF3COO)6(CF3COOH)3](CF3COOH)0.5 ( VII). The crystal structures of these compounds were determined by single-crystal X-ray diffraction. All structures contain triangular trinuclear complex anions [ M 3″(μ3-F)(CF3COO)6(CF3COOH)3]- ( M″ = Ni, Co) structurally similar to trinuclear 3d metal oxo carboxylate complexes. The three-coordinated F atom is located at the center of the triangle formed by Ni(II) or Co(II) atoms. The metal atoms are linked in pairs by six bridging trifluoroacetate groups located above and below the plane of the [ M″3 F] triangle. The oxygen atoms of the axial CF3COOH molecules complete the coordination environment of M″ atoms to an octahedron.

Filtrates and Residues: Ice Cream: Delicious Chemistry.

ERIC Educational Resources Information Center

Martino, James

1983-01-01

An experiment involving preparation of ice cream is conducted after students complete units on solutions, atomic structure, molecular architecture, and bonding. The laboratory gives practical illustration of relation of physical properties to bond type and solution theory developed. Materials needed, procedures used, and questions asked are…

Microgravity

NASA Image and Video Library

2004-04-15

A semiconductor's usefulness is determined by how atoms are ordered within the crystal's underlying three-dimensional structure. While this mercury telluride and cadmium telluride alloy sample mixes completely in Earth -based laboratories, convective flows prevent them from mixing uniformly. In space, the ingredients mix more homogenously, resulting in a superior product.

Compositional modulated atomic layer stacking and uniaxial magnetocrystalline anisotropy of CoPt alloy sputtered films with close-packed plane orientation

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

Saito, Shin, E-mail: ssaito@ecei.tohoku.ac.jp; Nozawa, Naoki; Hinata, Shintaro

An atomic layer stacking structure in hexagonal close packed (hcp) Co{sub 100−x}Pt{sub x} alloy films with c-plane sheet texture was directly observed by a high-angle annular dark-field imaging scanning transmission electron microscopy. The analysis of sequential and/or compositional atomic layer stacking structure and uniaxial magnetocrystalline anisotropy (K{sub u} = K{sub u1} + K{sub u2}) revealed that (1) integrated intensity of the superlattice diffraction takes the maximum at x = 20 at. % and shows broadening feature against x for the film fabricated under the substrate temperature (T{sub sub}) of 400 °C. (2) Compositional separation structure in atomic layers is formed for the films fabricated under T{sub sub} = 400 °C.more » A sequential alternative stacking of atomic layers with different compositions is hardly formed in the film with x = 50 at. %, whereas easily formed in the film with x = 20 at. %. This peculiar atomic layer stacking structure consists of in-plane-disordered Pt-rich and Pt-poor layers, which is completely different from the so-called atomic site ordered structure. (3) A face centered cubic atomic layer stacking as faults appeared in the host hcp atomic layer stacking exists in accompanies with irregularities for the periodicity of the compositional modulation atomic layers. (4) K{sub u1} takes the maximum of 1.4 × 10{sup 7 }erg/cm{sup 3} at around x = 20 at. %, whereas K{sub u2} takes the maximum of 0.7 × 10{sup 7 }erg/cm{sup 3} at around x = 40 at. %, which results in the maximum of 1.8 × 10{sup 7 }erg/cm{sup 3} of K{sub u} at x = 30 at. % and a shoulder in compositional dependence of K{sub u} in the range of x = 30–60 at. %. Not only compositional separation of atomic layers but also sequential alternative stacking of different compositional layers is quite important to improve essential uniaxial magnetocrystalline anisotropy.« less

Mechanical properties and structure evolution of single-crystalline silicon irradiated by 1 MeV Au+ and Cu+ ions

NASA Astrophysics Data System (ADS)

Liang, Wei; Zhu, Fei; Ling, Yunhan; Liu, Kezhao; Hu, Yin; Pan, Qifa; Chen, Limin; Zhang, Zhengjun

2018-05-01

Mechanical and structural evolutions of single-crystalline silicon irradiated by a series of doses 1 MeV Au+ ions and Cu+ ions are characterized by Surface laser-acoustic wave spectroscopy by (LA wave), Rutherford backscattering spectrometry and channeling (RBS/C) and transmission electron microscopy (TEM). The behavior of implanted Au+ and Cu+ ions was also simulated by using Stopping and range of ions in matter (SRIM) software package, respectively. It is demonstrated that LA wave and RBS could be applied for accurate evaluation of the TEM observed amorphous layer's thickness. The modified mechanical properties depend on the species and the dose of implantation. For 1 MeV Au+ ions, the threshold dose of completely amorphous is 5 × 1014 atoms/cm2, while the one for Cu+ ions is 5 × 1015 atoms/cm2. Upon completely amorphous, the young's modulus and layer density decreased significantly while saturated with the dose increasing sequentially.

Crystal structure of bis­[cis-(1,4,8,11-tetra­aza­cyclo­tetra­deca­ne-κ4 N)bis(thio­cyanato-κN)chrom­ium(III)] dichromate monohydrate from synchrotron X-ray diffraction data

PubMed Central

Moon, Dohyun; Takase, Masahiro; Akitsu, Takashiro; Choi, Jong-Ha

2017-01-01

The structure of the complex salt, cis-[Cr(NCS)2(cyclam)]2[Cr2O7]·H2O (cyclam = 1,4,8,11-tetra­aza­cyclo­tetra­decane, C10H24N4), has been determined from synchrotron data. The asymmetric unit comprises of one [Cr(NCS)2(cyclam)]+ cation, one half of a Cr2O7 2− anion (completed by inversion symmetry) and one half of a water mol­ecule (completed by twofold rotation symmetry). The CrIII ion is coordinated by the four cyclam N atoms and by two N atoms of cis-arranged thio­cyanate anions, displaying a distorted octa­hedral coordination sphere. The Cr—N(cyclam) bond lengths are in the range 2.080 (2) to 2.097 (2) Å while the average Cr—N(NCS) bond length is 1.985 (4) Å. The macrocyclic cyclam moiety adopts the cis-V conformation. The bridging O atom of the dichromate anion is disordered around an inversion centre, leading to a bending of the Cr—O—Cr bridging angle [157.7 (3)°]; the anion has a staggered conformation. The crystal structure is stabilized by inter­molecular hydrogen bonds involving the cyclam N—H groups and water O—H groups as donor groups, and the O atoms of the Cr2O7 2− anion and water mol­ecules as acceptor groups, giving rise to a three-dimensional network. PMID:28083140

Reading PDB: perception of molecules from 3D atomic coordinates.

PubMed

Urbaczek, Sascha; Kolodzik, Adrian; Groth, Inken; Heuser, Stefan; Rarey, Matthias

2013-01-28

The analysis of small molecule crystal structures is a common way to gather valuable information for drug development. The necessary structural data is usually provided in specific file formats containing only element identities and three-dimensional atomic coordinates as reliable chemical information. Consequently, the automated perception of molecular structures from atomic coordinates has become a standard task in cheminformatics. The molecules generated by such methods must be both chemically valid and reasonable to provide a reliable basis for subsequent calculations. This can be a difficult task since the provided coordinates may deviate from ideal molecular geometries due to experimental uncertainties or low resolution. Additionally, the quality of the input data often differs significantly thus making it difficult to distinguish between actual structural features and mere geometric distortions. We present a method for the generation of molecular structures from atomic coordinates based on the recently published NAOMI model. By making use of this consistent chemical description, our method is able to generate reliable results even with input data of low quality. Molecules from 363 Protein Data Bank (PDB) entries could be perceived with a success rate of 98%, a result which could not be achieved with previously described methods. The robustness of our approach has been assessed by processing all small molecules from the PDB and comparing them to reference structures. The complete data set can be processed in less than 3 min, thus showing that our approach is suitable for large scale applications.

Synthesis and crystal structure of catena-bis(nicotinamide)aqua({mu}-phthalato)copper(II) hemihydrate

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

Sadikov, G. G., E-mail: sadgg@igic.ras.ru; Koksharova, T. V.; Antsyshkina, A. S.

2008-07-15

The copper(II) phthalate complex with nicotinamide [CuL{sub 2}({mu}-Pht)(H{sub 2}O)] . 0.5H{sub 2}O(I) (where L is nicotinamide and Pht{sup 2-} is an anion of phthalic acid) is synthesized and investigated using IR spectroscopy and X-ray diffraction. The crystals of compound I are monoclinic, a = 13.368(2) A, b = 7.891(3) A, c = 20.480(2) A, {beta} = 108.69(2){sup o}, Z = 4, and space group P2{sub 1}/c. The structural units of crystal I are linear chains formed by bridging phthalate anions and crystallization water molecules. The copper atom is coordinated by two pyridine nitrogen atoms of two nicotinamide ligands (Cu-N, 2.001more » and 2.045 A), two oxygen atoms of different phthalate anions (Cu-O, 1.964 and 2.235 A), and the oxygen atom of the H{sub 2} O molecule (Cu-O, 2.014 A). The coordination polyhedron of the copper atom is completed to an elongated (4 + 1 + 1) tetragonal bipyramid by the second (chelating) oxygen atom of the carboxyl group (Cu-O, 2.587 A), which is one of the anions of phthalic acid. The linear polymer molecules are joined into complex macromolecular dimers with the closest internal contacts of the specific type. The macromolecular dimers are the main supramolecular ensembles of the crystal structure.« less

Two novel mixed-ligand complexes containing organosulfonate ligands.

PubMed

Li, Mingtian; Huang, Jun; Zhou, Xuan; Fang, Hua; Ding, Liyun

2008-07-01

The structures reported herein, viz. bis(4-aminonaphthalene-1-sulfonato-kappaO)bis(4,5-diazafluoren-9-one-kappa(2)N,N')copper(II), [Cu(C(10)H(8)NO(3)S)(2)(C(11)H(6)N(2)O)(2)], (I), and poly[[[diaquacadmium(II)]-bis(mu-4-aminonaphthalene-1-sulfonato)-kappa(2)O:N;kappa(2)N:O] dihydrate], {[Cd(C(10)H(8)NO(3)S)(2)(H(2)O)(2)].2H(2)O}(n), (II), are rare examples of sulfonate-containing complexes where the anion does not fulfill a passive charge-balancing role, but takes an active part in coordination as a monodentate and/or bridging ligand. Monomeric complex (I) possesses a crystallographic inversion center at the Cu(II) atom, and the asymmetric unit contains one-half of a Cu atom, one complete 4-aminonaphthalene-1-sulfonate (ans) ligand and one 4,5-diazafluoren-9-one (DAFO) ligand. The Cu(II) atom has an elongated distorted octahedral coordination geometry formed by two O atoms from two monodentate ans ligands and by four N atoms from two DAFO molecules. Complex (II) is polymeric and its crystal structure is built up by one-dimensional chains and solvent water molecules. Here also the cation (a Cd(II) atom) lies on a crystallographic inversion center and adopts a slightly distorted octahedral geometry. Each ans anion serves as a bridging ligand linking two Cd(II) atoms into one-dimensional infinite chains along the [010] direction, with each Cd(II) center coordinated by four ans ligands via O and N atoms and by two aqua ligands. In both structures, there are significant pi-pi stacking interactions between adjacent ligands and hydrogen bonds contribute to the formation of two- and three-dimensional networks.

Computational redesign of a protein-protein interface for high affinity and binding specificity using modular architecture and naturally occurring template fragments.

PubMed

Potapov, V; Reichmann, D; Abramovich, R; Filchtinski, D; Zohar, N; Ben Halevy, D; Edelman, M; Sobolev, V; Schreiber, G

2008-12-05

A new method is presented for the redesign of protein-protein interfaces, resulting in specificity of the designed pair while maintaining high affinity. The design is based on modular interface architecture and was carried out on the interaction between TEM1 beta-lactamase and its inhibitor protein, beta-lactamase inhibitor protein. The interface between these two proteins is composed of several mostly independent modules. We previously showed that it is possible to delete a complete module without affecting the overall structure of the interface. Here, we replace a complete module with structure fragments taken from nonrelated proteins. Nature-optimized fragments were chosen from 10(7) starting templates found in the Protein Data Bank. A procedure was then developed to identify sets of interacting template residues with a backbone arrangement mimicking the original module. This generated a final list of 361 putative replacement modules that were ranked using a novel scoring function based on grouped atom-atom contact surface areas. The top-ranked designed complex exhibited an affinity of at least the wild-type level and a mode of binding that was remarkably specific despite the absence of negative design in the procedure. In retrospect, the combined application of three factors led to the success of the design approach: utilizing the modular construction of the interface, capitalizing on native rather than artificial templates, and ranking with an accurate atom-atom contact surface scoring function.

Electronic components embedded in a single graphene nanoribbon.

PubMed

Jacobse, P H; Kimouche, A; Gebraad, T; Ervasti, M M; Thijssen, J M; Liljeroth, P; Swart, I

2017-07-25

The use of graphene in electronic devices requires a band gap, which can be achieved by creating nanostructures such as graphene nanoribbons. A wide variety of atomically precise graphene nanoribbons can be prepared through on-surface synthesis, bringing the concept of graphene nanoribbon electronics closer to reality. For future applications it is beneficial to integrate contacts and more functionality directly into single ribbons by using heterostructures. Here, we use the on-surface synthesis approach to fabricate a metal-semiconductor junction and a tunnel barrier in a single graphene nanoribbon consisting of 5- and 7-atom wide segments. We characterize the atomic scale geometry and electronic structure by combined atomic force microscopy, scanning tunneling microscopy, and conductance measurements complemented by density functional theory and transport calculations. These junctions are relevant for developing contacts in all-graphene nanoribbon devices and creating diodes and transistors, and act as a first step toward complete electronic devices built into a single graphene nanoribbon.Adding functional electronic components to graphene nanoribbons requires precise control over their atomic structure. Here, the authors use a bottom-up approach to build a metal-semiconductor junction and a tunnel barrier directly into a single graphene nanoribbon, an exciting development for graphene-based electronic devices.

Ab initio solution of macromolecular crystal structures without direct methods.

PubMed

McCoy, Airlie J; Oeffner, Robert D; Wrobel, Antoni G; Ojala, Juha R M; Tryggvason, Karl; Lohkamp, Bernhard; Read, Randy J

2017-04-04

The majority of macromolecular crystal structures are determined using the method of molecular replacement, in which known related structures are rotated and translated to provide an initial atomic model for the new structure. A theoretical understanding of the signal-to-noise ratio in likelihood-based molecular replacement searches has been developed to account for the influence of model quality and completeness, as well as the resolution of the diffraction data. Here we show that, contrary to current belief, molecular replacement need not be restricted to the use of models comprising a substantial fraction of the unknown structure. Instead, likelihood-based methods allow a continuum of applications depending predictably on the quality of the model and the resolution of the data. Unexpectedly, our understanding of the signal-to-noise ratio in molecular replacement leads to the finding that, with data to sufficiently high resolution, fragments as small as single atoms of elements usually found in proteins can yield ab initio solutions of macromolecular structures, including some that elude traditional direct methods.

UTa{sub 2}O(S{sub 2}){sub 3}Cl{sub 6}: A ribbon structure containing a heterobimetallic 5d-5f M{sub 3} cluster

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

Wells, Daniel M.; Chan, George H.; Ellis, Donald E.

2010-02-15

A new solid-state compound containing a heterobimetallic cluster of U and Ta, UTa{sub 2}O(S{sub 2}){sub 3}Cl{sub 6}, has been synthesized and its structure has been characterized by single-crystal X-ray diffraction methods. UTa{sub 2}O(S{sub 2}){sub 3}Cl{sub 6} was synthesized from UCl{sub 4} and Ta{sub 1.2}S{sub 2} at 883 K. The O is believed to have originated in the Ta{sub 1.2}S{sub 2} reactant. The compound crystallizes in the space group P1-bar of the triclinic system. The structure comprises a UTa{sub 2} unit bridged by mu{sub 2}-S{sub 2} and mu{sub 3}-O groups. Each Ta atom bonds to two mu{sub 2}-S{sub 2}, the mu{submore » 3}-O, and two terminal Cl atoms. Each U atom bonds to two mu{sub 2}-S{sub 2}, the mu{sub 3}-O, and four Cl atoms. The Cl atoms bridge in pairs to neighboring U atoms to form a ribbon structure. The bond distances are normal and are consistent with formal oxidation states of +IV/+V/-II/-I/-I for U/Ta/O/S/Cl, respectively. The optical absorbance spectrum displays characteristic transition peaks near the absorption edge. Density functional theory was used to assign these peaks to transitions between S{sup 1-} valence-band states and empty U 5f-6d hybrid bands. Density-of-states analysis shows overlap between Ta 5d and U bands, consistent with metal-metal interactions. - The UTa2O(S2)3Cl6 cluster with completed coordination sphere around uranium« less

The Materials Chemistry of Atomic Oxygen with Applications to Anisotropic Etching of Submicron Structures in Microelectronics and the Surface Chemistry Engineering of Porous Solids

NASA Technical Reports Server (NTRS)

Koontz, Steve L.; Leger, Lubert J.; Wu, Corina; Cross, Jon B.; Jurgensen, Charles W.

1994-01-01

Neutral atomic oxygen is the most abundant component of the ionospheric plasma in the low Earth orbit environment (LEO; 200 to 700 kilometers altitude) and can produce significant degradation of some spacecraft materials. In order to produce a more complete understanding of the materials chemistry of atomic oxygen, the chemistry and physics of O-atom interactions with materials were determined in three radically different environments: (1) The Space Shuttle cargo bay in low Earth orbit (the EOIM-3 space flight experiment), (2) a high-velocity neutral atom beam system (HVAB) at Los Alamos National Laboratory (LANL), and (3) a microwave-plasma flowing-discharge system at JSC. The Space Shuttle and the high velocity atom beam systems produce atom-surface collision energies ranging from 0.1 to 7 eV (hyperthermal atoms) under high-vacuum conditions, while the flowing discharge system produces a 0.065 eV surface collision energy at a total pressure of 2 Torr. Data obtained in the three different O-atom environments referred to above show that the rate of O-atom reaction with polymeric materials is strongly dependent on atom kinetic energy, obeying a reactive scattering law which suggests that atom kinetic energy is directly available for overcoming activation barriers in the reaction. General relationships between polymer reactivity with O atoms and polymer composition and molecular structure have been determined. In addition, vacuum ultraviolet photochemical effects have been shown to dominate the reaction of O atoms with fluorocarbon polymers. Finally, studies of the materials chemistry of O atoms have produced results which may be of interest to technologists outside the aerospace industry. Atomic oxygen 'spin-off' or 'dual use' technologies in the areas of anisotropic etching in microelectronic materials and device processing, as well as surface chemistry engineering of porous solid materials are described.

Complete Al-SI Order in Scapolite Me[subscript 37.5], Ideally Ca[subscript 3]Na[subscript 5][Al[subscript 8]Si[subscript 16]O[subscript 48

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

Antao, Sytle M.; Hassan, Ishmael; West Indies)

2011-09-06

The structure of an intermediate scapolite (Me{sub 36.6}) from Lake Clear, Ontario, was obtained using synchrotron high-resolution powder X-ray diffraction (HRPXRD) data and Rietveld structure refinement in space group P4{sub 2}/n. The chemical formula obtained by electron microprobe is Na{sub 2.19}Ca{sub 1.35}K{sub 0.16}[Al{sub 3.95}Si{sub 8.05}O{sub 24}]Cl{sub 0.55}(CO{sub 3}){sub 0.41}(SO{sub 4}){sub 0.04}, equivalent to Me{sub 36.6}. The unit-cell parameters are a 12.07899(1), c 7.583467(9) {angstrom}, and V 1106.443(2) {angstrom}{sup 3}. The average distances are = 1.617(1) {angstrom}, = 1.744(1) {angstrom}, and = 1.601(1) {angstrom}. Therefore, the T1 and T3 sites contain only Si atoms, and the T2 sitemore » contains only Al atoms, so the Al and Si atoms are completely ordered. Complete Al-Si order was predicted for Me{sub 37.5}, ideally Ca{sub 3}Na{sub 5}[Al{sub 8}Si{sub 16}O{sub 48}]Cl(CO{sub 3}), and is confirmed in this study. Antiphase domain boundaries (APBs) in scapolite cannot arise from Al-Si order because the average distances indicate complete Al-Si order in Me{sub 36.6}. If APBs were to arise from Al-Si order, switching of the T sites across the APBs will occur, and complete Al-Si order cannot be observed. Therefore, Al-Si order, which is present to various extents across the scapolite series, can be ruled out as the cause for the APBs. Order involving Cl and CO{sub 3} is the cause for the APBs in scapolite.« 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.

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

Protein Folding and Structure Prediction from the Ground Up: The Atomistic Associative Memory, Water Mediated, Structure and Energy Model.

PubMed

Chen, Mingchen; Lin, Xingcheng; Zheng, Weihua; Onuchic, José N; Wolynes, Peter G

2016-08-25

The associative memory, water mediated, structure and energy model (AWSEM) is a coarse-grained force field with transferable tertiary interactions that incorporates local in sequence energetic biases using bioinformatically derived structural information about peptide fragments with locally similar sequences that we call memories. The memory information from the protein data bank (PDB) database guides proper protein folding. The structural information about available sequences in the database varies in quality and can sometimes lead to frustrated free energy landscapes locally. One way out of this difficulty is to construct the input fragment memory information from all-atom simulations of portions of the complete polypeptide chain. In this paper, we investigate this approach first put forward by Kwac and Wolynes in a more complete way by studying the structure prediction capabilities of this approach for six α-helical proteins. This scheme which we call the atomistic associative memory, water mediated, structure and energy model (AAWSEM) amounts to an ab initio protein structure prediction method that starts from the ground up without using bioinformatic input. The free energy profiles from AAWSEM show that atomistic fragment memories are sufficient to guide the correct folding when tertiary forces are included. AAWSEM combines the efficiency of coarse-grained simulations on the full protein level with the local structural accuracy achievable from all-atom simulations of only parts of a large protein. The results suggest that a hybrid use of atomistic fragment memory and database memory in structural predictions may well be optimal for many practical applications.

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.

Three Distinct Deformation Behaviors of Cementite Lamellae in a Cold-Drawn Pearlitic Wire

NASA Astrophysics Data System (ADS)

Xin, Tuo; Liu, Guiju; Liang, Wenshuang; Cai, Rongsheng; Feng, Honglei; Li, Chen; Li, Jian; Wang, Yiqian

2018-03-01

High-resolution transmission electron microscopy is used to investigate the deformation behaviors of cementite lamellae in the heavily cold-drawn piano wires. Three distinct morphologies of cementite are observed, namely, complete lamella, partly-broken lamella and nearly-disappeared lamella. For the complete cementite lamella, it remains a single-crystalline structure. For the partly-broken cementite lamella, polycrystalline structure and neck-down region appear to release the residual strain. The lattice expansion of ferrite takes place in two perpendicular directions indicating that the carbon atoms dissolve from cementite into ferrite lattices. An orientation relationship is found between ferrite and cementite phases in the cold-drawn pearlitic wire.

Gold deposited on a Ge(0 0 1) surface: DFT calculations

NASA Astrophysics Data System (ADS)

Tsay, Shiow-Fon

2016-11-01

The atomic geometry, stability and electronic properties of self-organized Au induced nanowires on a Ge(0 0 1) surface are investigated based on the density-functional theory in the generalized gradient approximation and the stoichiometry of Au. According to the formation energy and the simulated STM image, the Ge atoms substituted by the Au atoms have been confirmed as occurring at a Au coverage lower than 0.25 Ml. The STM image with single and double dimer vacancies looks like the Au atoms have penetrated the subsurface. The energetically favorable dimer-row arrayed structures at 0.50 Ml and 0.75 Ml Au coverages have a 4  ×  1, 4  ×  2 or c(8  ×  2) transition symmetry, which comprise a flat Au-Au homodimer row and an alternating various buckling phase Ge-Ge or Au-Ge dimer row. The c(8  ×  2) zigzag-shaped protruding chains of shallow-groove STM images are highly consistent with the observations, but a long-range order dimer-row arrayed structure formation requires sufficient mobile energy to complete mass transport of the substituted Ge atoms in order to avoid the re-adsorption of these atoms; otherwise a deep-groove structure reconstruction is sequentially formed. A quasi-1D electron-like energy trough aligns in the direction perpendicular to the nanowire of the dimer-row arrayed structure in the c(8  ×  2) phase on a 0.75 Ml Au/Ge(0 0 1) surface, which is contributed by the Au-Ge dimer rows and the subsurface Ge atoms below them. The bottom energy of the energy trough is consistent with angle-resolved photo-emission spectroscopy studies (Schäfer et al 2008 Phys. Rev. Lett. 101 236802, Meyer et al 2011 Phys. Rev. B 83 121411(R)).

Atomic structure of the vimentin central α-helical domain and its implications for intermediate filament assembly.

PubMed

Chernyatina, Anastasia A; Nicolet, Stefan; Aebi, Ueli; Herrmann, Harald; Strelkov, Sergei V

2012-08-21

Together with actin filaments and microtubules, intermediate filaments (IFs) are the basic cytoskeletal components of metazoan cells. Over 80 human diseases have been linked to mutations in various IF proteins to date. However, the filament structure is far from being resolved at the atomic level, which hampers rational understanding of IF pathologies. The elementary building block of all IF proteins is a dimer consisting of an α-helical coiled-coil (CC) "rod" domain flanked by the flexible head and tail domains. Here we present three crystal structures of overlapping human vimentin fragments that comprise the first half of its rod domain. Given the previously solved fragments, a nearly complete atomic structure of the vimentin rod has become available. It consists of three α-helical segments (coils 1A, 1B, and 2) interconnected by linkers (L1 and L12). Most of the CC structure has a left-handed twist with heptad repeats, but both coil 1B and coil 2 also exhibit untwisted, parallel stretches with hendecad repeats. In the crystal structure, linker L1 was found to be α-helical without being involved in the CC formation. The available data allow us to construct an atomic model of the antiparallel tetramer representing the second level of vimentin assembly. Although the presence of the nonhelical head domains is essential for proper tetramer stabilization, the precise alignment of the dimers forming the tetramer appears to depend on the complementarity of their surface charge distribution patterns, while the structural plasticity of linker L1 and coil 1A plays a role in the subsequent IF assembly process.

Calculation of the electron structure of vacancies and their compensated states in III-VI semiconductors

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

Mehrabova, M. A., E-mail: Mehrabova@mail.ru; Madatov, R. S.

2011-08-15

The Green's functions theory and the bond-orbital model are used as a basis for calculations of the electron structure of local defects-specifically, vacancies and their compensated states in III-VI semiconductors. The energy levels in the band gap are established, and the changes induced in the electron densities in the GaS, GaSe, and InSe semiconductors by anion and cation vacancies and their compensated states are calculated. It is established that, if a vacancy is compensated by an atom of an element from the same subgroup with the same tetrahedral coordination and if the ionic radius of the compensating atom is smallermore » than that of the substituted atom, the local levels formed by the vacancy completely disappear. It is shown that this mechanism of compensation of vacancies provides a means not only for recovering the parameters of the crystal, but for improving the characteristics of the crystal as well.« less

Phenylethynyl-butyltellurium inhibits the sulfhydryl enzyme Na+, K+ -ATPase: an effect dependent on the tellurium atom.

PubMed

Quines, Caroline B; Rosa, Suzan G; Neto, José S S; Zeni, Gilson; Nogueira, Cristina W

2013-11-01

Organotellurium compounds are known for their toxicological effects. These effects may be associated with the chemical structure of these compounds and the oxidation state of the tellurium atom. In this context, 2-phenylethynyl-butyltellurium (PEBT) inhibits the activity of the sulfhydryl enzyme, δ-aminolevulinate dehydratase. The present study investigated on the importance of the tellurium atom in the PEBT ability to oxidize mono- and dithiols of low molecular weight and sulfhydryl enzymes in vitro. PEBT, at high micromolar concentrations, oxidized dithiothreitol (DTT) and inhibited cerebral Na(+), K(+)-ATPase activity, but did not alter the lactate dehydrogenase activity. The inhibition of cerebral Na(+), K(+)-ATPase activity was completely restored by DTT. By contrast, 2-phenylethynyl-butyl, a molecule without the tellurium atom, neither oxidized DTT nor altered the Na(+), K(+)-ATPase activity. In conclusion, the tellurium atom of PEBT is crucial for the catalytic oxidation of sulfhydryl groups from thiols of low molecular weight and from Na(+), K(+)-ATPase.

Heterogeneity in homogeneous nucleation from billion-atom molecular dynamics simulation of solidification of pure metal.

PubMed

Shibuta, Yasushi; Sakane, Shinji; Miyoshi, Eisuke; Okita, Shin; Takaki, Tomohiro; Ohno, Munekazu

2017-04-05

Can completely homogeneous nucleation occur? Large scale molecular dynamics simulations performed on a graphics-processing-unit rich supercomputer can shed light on this long-standing issue. Here, a billion-atom molecular dynamics simulation of homogeneous nucleation from an undercooled iron melt reveals that some satellite-like small grains surrounding previously formed large grains exist in the middle of the nucleation process, which are not distributed uniformly. At the same time, grains with a twin boundary are formed by heterogeneous nucleation from the surface of the previously formed grains. The local heterogeneity in the distribution of grains is caused by the local accumulation of the icosahedral structure in the undercooled melt near the previously formed grains. This insight is mainly attributable to the multi-graphics processing unit parallel computation combined with the rapid progress in high-performance computational environments.Nucleation is a fundamental physical process, however it is a long-standing issue whether completely homogeneous nucleation can occur. Here the authors reveal, via a billion-atom molecular dynamics simulation, that local heterogeneity exists during homogeneous nucleation in an undercooled iron melt.

Background of the completed research; relevances to solar physics

NASA Technical Reports Server (NTRS)

Sellin, I. A.

1973-01-01

Research activities reported consider the atomic structures of highly stripped heavy ions and their modes of formation and destruction in collisions. The lifetime of the metastable 2 3p1 state of the two electron ion F-7(+) was determined by measuring the radiative decay of an excited helium-like fluorine beam, Metastable state quenching measurements were performed on a helium-like ion to obtain the 1 1S0 to 2 3p2 transition probability. Exponential exchange state dependence of X-ray production cross sections was studied in heavy target atoms during collisions with light charged particles.

Building chemistry one atom at a time: An investigation of the effects of two curricula in students' understanding of covalent bonding and atomic size

NASA Astrophysics Data System (ADS)

Bull, Barbara Jeanne

Chemists have to rely on models to aid in the explanation of phenomena they experience. Instruction of atomic theory has been used as the introduction and primary model for many concepts in chemistry. Therefore, it is important for students to have a robust understanding of the different atomic models, their relationships and their limitations. Previous research has shown that students have alternative conceptions concerning their interpretation of atomic models, but there is less exploration into how students apply their understanding of atomic structure to other chemical concepts. Therefore, this research concentrated on the development of three Model Eliciting Activities to investigate the most fundamental topic of the atom and how students applied their atomic model to covalent bonding and atomic size. Along with the investigation into students' use of their atomic models, a comparison was included between a traditional chemistry curriculum using an Atoms First approach and Chemistry, Life, the Universe and Everything (CLUE), a NSF-funded general chemistry curriculum. Treatment and Control groups were employed to determine the effectiveness of the curricula in conveying the relationship between atoms, covalent bonds and atomic size. The CLUE students developed a Cloud representation on the Atomic Model Eliciting Activity and maintained this depiction through the Covalent Bonding Model Eliciting Activity. The traditional students more often illustrated the atom using a Bohr representation and continued to apply the same model to their portrayal of covalent bonding. During the analysis of the Atomic Size Model Eliciting Activity, students had difficulty fully supporting their explanation of the atomic size trend. Utilizing the beSocratic platform, an activity was designed to aid students' construction of explanations using Toulmin's Argumentation Pattern. In order to study the effectiveness of the activity, the students were asked questions relating to a four-week long investigation into the identity of an inorganic salt during their laboratory class. Students who completed the activity exhibited an improvement in their explanation of the identity of their salt's cation. After completing the activity, another question was posed about the identity of their anion. Both groups saw a decrease in the percentage of students who included reasoning in their answer; however, the activity group maintained a significantly higher percentage of responses with a reasoning than the control group.

Reasons for high-temperature superconductivity in the electron–phonon system of hydrogen sulfide

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

Degtyarenko, N. N.; Mazur, E. A., E-mail: eugen-masur@mail.ru

We have calculated the electron and phonon spectra, as well as the densities of the electron and phonon states, of the stable orthorhombic structure of hydrogen sulfide SH{sub 2} in the pressure interval 100–180 GPa. It is found that at a pressure of 175 GPa, a set of parallel planes of hydrogen atoms is formed due to a structural modification of the unit cell under pressure with complete accumulation of all hydrogen atoms in these planes. As a result, the electronic properties of the system become quasi-two-dimensional. We have also analyzed the collective synphase and antiphase vibrations of hydrogen atomsmore » in these planes, leading to the occurrence of two high-energy peaks in the phonon density of states.« less

Roles of water in protein structure and function studied by molecular liquid theory.

PubMed

Imai, Takashi

2009-01-01

The roles of water in the structure and function of proteins have not been completely elucidated. Although molecular simulation has been widely used for the investigation of protein structure and function, it is not always useful for elucidating the roles of water because the effect of water ranges from atomic to thermodynamic level. The three-dimensional reference interaction site model (3D-RISM) theory, which is a statistical-mechanical theory of molecular liquids, can yield the solvation structure at the atomic level and calculate the thermodynamic quantities from the intermolecular potentials. In the last few years, the author and coworkers have succeeded in applying the 3D-RISM theory to protein aqueous solution systems and demonstrated that the theory is useful for investigating the roles of water. This article reviews some of the recent applications and findings, which are concerned with molecular recognition by protein, protein folding, and the partial molar volume of protein which is related to the pressure effect on protein.

DelPhi Web Server: A comprehensive online suite for electrostatic calculations of biological macromolecules and their complexes

PubMed Central

Sarkar, Subhra; Witham, Shawn; Zhang, Jie; Zhenirovskyy, Maxim; Rocchia, Walter; Alexov, Emil

2011-01-01

Here we report a web server, the DelPhi web server, which utilizes DelPhi program to calculate electrostatic energies and the corresponding electrostatic potential and ionic distributions, and dielectric map. The server provides extra services to fix structural defects, as missing atoms in the structural file and allows for generation of missing hydrogen atoms. The hydrogen placement and the corresponding DelPhi calculations can be done with user selected force field parameters being either Charmm22, Amber98 or OPLS. Upon completion of the calculations, the user is given option to download fixed and protonated structural file, together with the parameter and Delphi output files for further analysis. Utilizing Jmol viewer, the user can see the corresponding structural file, to manipulate it and to change the presentation. In addition, if the potential map is requested to be calculated, the potential can be mapped onto the molecule surface. The DelPhi web server is available from http://compbio.clemson.edu/delphi_webserver. PMID:24683424

Energetics and solvation structure of a dihalogen dopant (I2) in (4)He clusters.

PubMed

Pérez de Tudela, Ricardo; Barragán, Patricia; Valdés, Álvaro; Prosmiti, Rita

2014-08-21

The energetics and structure of small HeNI2 clusters are analyzed as the size of the system changes, with N up to 38. The full interaction between the I2 molecule and the He atoms is based on analytical ab initio He-I2 potentials plus the He-He interaction, obtained from first-principle calculations. The most stable structures, as a function of the number of solvent He atoms, are obtained by employing an evolutionary algorithm and compared with CCSD(T) and MP2 ab initio computations. Further, the classical description is completed by explicitly including thermal corrections and quantum features, such as zero-point-energy values and spatial delocalization. From quantum PIMC calculations, the binding energies and radial/angular probability density distributions of the thermal equilibrium state for selected-size clusters are computed at a low temperature. The sequential formation of regular shell structures is analyzed and discussed for both classical and quantum treatments.

Growth and interfacial structure of methylammonium lead iodide thin films on Au(111)

NASA Astrophysics Data System (ADS)

She, Limin; Liu, Meizhuang; Li, Xiaoli; Cai, Zeying; Zhong, Dingyong

2017-02-01

Due to the promising optoelectronic properties, organic-inorganic hybrid perovskites have been intensively studied as the active layers in perovskite solar cells. However, the structural information about their interface, one of the key factors determining device performances, is so far very rare. Herein, we report on the growth of CH3NH3PbI3 (MAPbI3, MA=CH3NH3) thin films by means of vapor deposition under ultrahigh vacuum. The surface morphology and interfacial structure have been investigated by scanning tunneling microscopy. At the initial growth stage, a complicated transient phase consisting of three atomic layers, i.e., iodine, MA-PbI4 and MA-I, was formed on the Au(111) substrate. With the coverage increasing, atomically smooth MAPbI3 films with orthorhombic structure have been obtained after annealing to 373 K. The films followed a self-organized twofold-layer by twofold-layer growth mode with the formation of complete PbI6 octahedrons and the exposure of MA-I terminated (001) surface.

Writing Electron Dot Structures: Abstract of Issue 9905M

NASA Astrophysics Data System (ADS)

Magnell, Kenneth R.

1999-10-01

Writing Electron Dot Structures is a computer program for Mac OS that provides drill with feedback for students learning to write electron dot structures. While designed for students in the first year of college general chemistry it may also be used by high school chemistry students. A systematic method similar to that found in many general chemistry texts is employed:

1. determine the number of valence shell electrons,
2. select the central atom,
3. construct a skeleton,
4. add electrons to complete octets,
5. examine the structure for resonance forms.

Role of Protein Flexibility in Ion Permeation: A Case Study in Gramicidin A

PubMed Central

Baştuğ, Turgut; Gray-Weale, Angus; Patra, Swarna M.; Kuyucak, Serdar

2006-01-01

Proteins have a flexible structure, and their atoms exhibit considerable fluctuations under normal operating conditions. However, apart from some enzyme reactions involving ligand binding, our understanding of the role of flexibility in protein function remains mostly incomplete. Here we investigate this question in the realm of membrane proteins that form ion channels. Specifically, we consider ion permeation in the gramicidin A channel, and study how the energetics of ion conduction changes as the channel structure is progressively changed from completely flexible to a fixed one. For each channel structure, the potential of mean force for a permeating potassium ion is determined from molecular dynamics (MD) simulations. Using the same molecular dynamics data for completely flexible gramicidin A, we also calculate the average densities and fluctuations of the peptide atoms and investigate the correlations between these fluctuations and the motion of a permeating ion. Our results show conclusively that peptide flexibility plays an important role in ion permeation in the gramicidin A channel, thus providing another reason—besides the well-known problem with the description of single file pore water—why this channel cannot be modeled using continuum electrostatics with a fixed structure. The new method developed here for studying the role of protein flexibility on its function clarifies the contributions of the fluctuations to energy and entropy, and places limits on the level of detail required in a coarse-grained model. PMID:16415054

Formation of atomically ordered and chemically selective Si-O-Ti monolayer on Si0.5Ge0.5(110) for a MIS structure via H2O2(g) functionalization.

PubMed

Park, Sang Wook; Choi, Jong Youn; Siddiqui, Shariq; Sahu, Bhagawan; Galatage, Rohit; Yoshida, Naomi; Kachian, Jessica; Kummel, Andrew C

2017-02-07

Si 0.5 Ge 0.5 (110) surfaces were passivated and functionalized using atomic H, hydrogen peroxide (H 2 O 2 ), and either tetrakis(dimethylamino)titanium (TDMAT) or titanium tetrachloride (TiCl 4 ) and studied in situ with multiple spectroscopic techniques. To passivate the dangling bonds, atomic H and H 2 O 2 (g) were utilized and scanning tunneling spectroscopy (STS) demonstrated unpinning of the surface Fermi level. The H 2 O 2 (g) could also be used to functionalize the surface for metal atomic layer deposition. After subsequent TDMAT or TiCl 4 dosing followed by a post-deposition annealing, scanning tunneling microscopy demonstrated that a thermally stable and well-ordered monolayer of TiO x was deposited on Si 0.5 Ge 0.5 (110), and X-ray photoelectron spectroscopy verified that the interfaces only contained Si-O-Ti bonds and a complete absence of GeO x . STS measurements confirmed a TiO x monolayer without mid-gap and conduction band edge states, which should be an ideal ultrathin insulating layer in a metal-insulator-semiconductor structure. Regardless of the Ti precursors, the final Ti density and electronic structure were identical since the Ti bonding is limited by the high coordination of Ti to O.

Nanosized (mu12-Pt)Pd164-xPtx(CO)72(PPh3)20 (x approximately 7) containing Pt-centered four-shell 165-atom Pd-Pt core with unprecedented intershell bridging carbonyl ligands: comparative analysis of icosahedral shell-growth patterns with geometrically related Pd145(CO)x(PEt3)30 (x approximately 60) containing capped three-shell Pd145 core.

PubMed

Mednikov, Evgueni G; Jewell, Matthew C; Dahl, Lawrence F

2007-09-19

Presented herein are the preparation and crystallographic/microanalytical/magnetic/spectroscopic characterization of the Pt-centered four-shell 165-atom Pd-Pt cluster, (mu(12)-Pt)Pd(164-x)Pt(x)(CO)(72)(PPh(3))(20) (x approximately 7), 1, that replaces the geometrically related capped three-shell icosahedral Pd(145) cluster, Pd(145)(CO)(x)(PEt(3))(30) (x approximately 60), 2, as the largest crystallographically determined discrete transition metal cluster with direct metal-metal bonding. A detailed comparison of their shell-growth patterns gives rise to important stereochemical implications concerning completely unexpected structural dissimilarities as well as similarities and provides new insight concerning possible synthetic approaches for generation of multi-shell metal clusters. 1 was reproducibly prepared in small yields (<10%) from the reaction of Pd(10)(CO)(12)(PPh(3))(6) with Pt(CO)(2)(PPh(3))(2). Its 165-atom metal-core geometry and 20 PPh(3) and 72 CO ligands were established from a low-temperature (100 K) CCD X-ray diffraction study. The well-determined crystal structure is attributed largely to 1 possessing cubic T(h) (2/m3) site symmetry, which is the highest crystallographic subgroup of the noncrystallographic pseudo-icosahedral I(h) (2/m35) symmetry. The "full" four-shell Pd-Pt anatomy of 1 consists of: (a) shell 1 with the centered (mu(12)-Pt) atom encapsulated by the 12-atom icosahedral Pt(x)Pd(12-x) cage, x = 1.2(3); (b) shell 2 with the 42-atom nu(2) icosahedral Pt(x)Pd(42-x) cage, x = 3.5(5); (c) shell 3 with the anti-Mackay 60-atom semi-regular rhombicosidodecahedral Pt(x)Pd(60-x) cage, x = 2.2(6); (d) shell 4 with the 50-atom nu(2) pentagonal dodecahedral Pd(50) cage. The total number of crystallographically estimated Pt atoms, 8 +/- 3, which was obtained from least-squares (Pt(x)/Pd(1-x))-occupancy analysis of the X-ray data that conclusively revealed the central atom to be pure Pt (occupancy factor, x = 1.00(3)), is fortuitously in agreement with that of 7.6(7) found from an X-ray Pt/Pd microanalysis (WDS spectrometer) on three crystals of 1. Our utilization of this site-occupancy (Pt(x)Pd(1-x))-analysis for shells 1-3 originated from the microanalytical results; otherwise, the presumed metal-core composition would have been (mu(12)-Pt)Pd(164). [Alternatively, the (mu(12)-Pt)M(164) core-geometry of 1 may be viewed as a pseudo-Ih Pt-centered six-shell successive nu(1) polyhedral system, each with radially equivalent vertex atoms: Pt@M(12)(icosahedron)@M(30)(icosidodecahedron)@M(12)(icosahedron)@M(60)(rhombicosidodecahedron)@M(30)(icosidodecahedron)@M(20)(pentagonal dodecahedron)]. Completely surprising structural dissimilarities between 1 and 2 are: (1) to date 1 is only reproducibly isolated as a heterometallic Pd-Pt cluster with a central Pt instead of Pd atom; (2) the 50 atoms comprising the outer fourth nu(2) pentagonal dodecahedral shell in 1 are less than the 60 atoms of the inner third shell in 1, in contradistinction to shell-by-shell growth processes in all other known shell-based structures; (3) the 10 fewer PR3 ligands in 1 necessitate larger bulky PPh(3) ligands to protect the Pd-Pt core-geometry; (4) the 72 CO ligands consist of six bridging COs within each of the 12 pentagons in shell 4 that are coordinated to intershell metal atoms. SQUID magnetometry measurements showed a single-crystal sample of 1 to be diamagnetic over the entire temperature range of 10-300 K.

Nanothermodynamics of iron clusters: Small clusters, icosahedral and fcc-cuboctahedral structures

NASA Astrophysics Data System (ADS)

Angelié, C.; Soudan, J.-M.

2017-05-01

The study of the thermodynamics and structures of iron clusters has been carried on, focusing on small clusters and initial icosahedral and fcc-cuboctahedral structures. Two combined tools are used. First, energy intervals are explored by the Monte Carlo algorithm, called σ-mapping, detailed in the work of Soudan et al. [J. Chem. Phys. 135, 144109 (2011), Paper I]. In its flat histogram version, it provides the classical density of states, gp(Ep), in terms of the potential energy of the system. Second, the iron system is described by a potential which is called "corrected EAM" (cEAM), explained in the work of Basire et al. [J. Chem. Phys. 141, 104304 (2014), Paper II]. Small clusters from 3 to 12 atoms in their ground state have been compared first with published Density Functional Theory (DFT) calculations, giving a complete agreement of geometries. The series of 13, 55, 147, and 309 atom icosahedrons is shown to be the most stable form for the cEAM potential. However, the 147 atom cluster has a special behaviour, since decreasing the energy from the liquid zone leads to the irreversible trapping of the cluster in a reproducible amorphous state, 7.38 eV higher in energy than the icosahedron. This behaviour is not observed at the higher size of 309 atoms. The heat capacity of the 55, 147, and 309 atom clusters revealed a pronounced peak in the solid zone, related to a solid-solid transition, prior to the melting peak. The corresponding series of 13, 55, and 147 atom cuboctahedrons has been compared, underscoring the unstability towards the icosahedral structure. This unstability occurs clearly in several steps for the 147 atom cluster, with a sudden transformation at a transition state. This illustrates the concerted icosahedron-cuboctahedron transformation of Buckminster Fuller-Mackay, which is calculated for the cEAM potential. Two other clusters of initial fcc structures with 24 and 38 atoms have been studied, as well as a 302 atom cluster. Each one relaxes towards a more stable structure without regularity. The 38 atom cluster exhibits a nearly glassy relaxation, through a cascade of six metastable states of long life. This behaviour, as that of the 147 atom cluster towards the amorphous state, shows that difficulties to reach ergodicity in the lower half of the solid zone are related to particular features of the potential energy landscape, and not necessarily to a too large size of the system. Comparisons of the cEAM iron system with published results about Lennard-Jones systems and DFT calculations are made. The results of the previous clusters have been combined with that of Paper II to plot the cohesive energy Ec and the melting temperature Tm in terms of the cluster atom number Nat. The Nat -1 /3 linear dependence of the melting temperature (Pawlow law) is observed again for Nat > 150. In contrast, for Nat < 150, the curve diverges strongly from the Pawlow law, giving it an overall V-shape, with a linear increase of Tm when Nat goes from 55 to 13 atoms. Surprisingly, the 38 atom cluster is anomalously below the overall curve.

The Complete Heavy-Atom Structure of a Cp-Ftmw Chiral Tag Precursor, Verbenone

NASA Astrophysics Data System (ADS)

Marshall, Frank E.; West, Channing; Sedo, Galen; Pate, Brooks; Grubbs, G. S., II

2017-06-01

The microwave spectrum of the chiral molecule verbenone has been recorded from 2-18 GHz using two CP-FTMW spectrometers. 2-8 GHz data has been acquired on a 2-8 GHz CP-FTMW located at the University of Virginia and 8-18 data has been acquired on a 6-18 GHz spectrometer located at Missouri S&T. From the experiments the authors were able to assign and fit isotopologues corresponding to each heavy atom position (either ^{13}C or ^{18}O), providing for the heavy-atom structure. Previous studies by Evans and coworkers have been added to these measurements in a global fit of the parent species. The measurement and assignment of these transitions provide preliminary information needed for enatiomeric excess experiments using CP-FTMW van der Waals-type chiral tagging processes already being performed at UVa. Details of the experiment, fits, and structure will be discussed. C. J. Evans, S. M. Allpress, P. D. Godfrey, D. McNaughton, 67th International Symposium on Molecular Spectroscopy, 2012, RH13 S. M. Allpress, Spectroscopic and Computational Chemistry Studies on Terpene Related Compounds, University of Leicester, 2015, Chapter 6: Microwave Spectroscopy of Verbenone

Perforated hollow-core optical waveguides for on-chip atomic spectroscopy and gas sensing

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

Giraud-Carrier, M., E-mail: mgeecee@byu.edu; Hill, C.; Decker, T.

2016-03-28

A hollow-core waveguide structure for on-chip atomic spectroscopy is presented. The devices are based on Anti-Resonant Reflecting Optical Waveguides and may be used for a wide variety of applications which rely on the interaction of light with gases and vapors. The designs presented here feature short delivery paths of the atomic vapor into the hollow waveguide. They also have excellent environmental stability by incorporating buried solid-core waveguides to deliver light to the hollow cores. Completed chips were packaged with an Rb source and the F = 3 ≥ F′ = 2, 3, 4 transitions of the D2 line in {sup 85}Rb were monitored formore » optical absorption. Maximum absorption peak depths of 9% were measured.« less

Nondestructive imaging of atomically thin nanostructures buried in silicon

PubMed Central

Gramse, Georg; Kölker, Alexander; Lim, Tingbin; Stock, Taylor J. Z.; Solanki, Hari; Schofield, Steven R.; Brinciotti, Enrico; Aeppli, Gabriel; Kienberger, Ferry; Curson, Neil J.

2017-01-01

It is now possible to create atomically thin regions of dopant atoms in silicon patterned with lateral dimensions ranging from the atomic scale (angstroms) to micrometers. These structures are building blocks of quantum devices for physics research and they are likely also to serve as key components of devices for next-generation classical and quantum information processing. Until now, the characteristics of buried dopant nanostructures could only be inferred from destructive techniques and/or the performance of the final electronic device; this severely limits engineering and manufacture of real-world devices based on atomic-scale lithography. Here, we use scanning microwave microscopy (SMM) to image and electronically characterize three-dimensional phosphorus nanostructures fabricated via scanning tunneling microscope–based lithography. The SMM measurements, which are completely nondestructive and sensitive to as few as 1900 to 4200 densely packed P atoms 4 to 15 nm below a silicon surface, yield electrical and geometric properties in agreement with those obtained from electrical transport and secondary ion mass spectroscopy for unpatterned phosphorus δ layers containing ~1013 P atoms. The imaging resolution was 37 ± 1 nm in lateral and 4 ± 1 nm in vertical directions, both values depending on SMM tip size and depth of dopant layers. In addition, finite element modeling indicates that resolution can be substantially improved using further optimized tips and microwave gradient detection. Our results on three-dimensional dopant structures reveal reduced carrier mobility for shallow dopant layers and suggest that SMM could aid the development of fabrication processes for surface code quantum computers. PMID:28782006

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

Hegde, Raghurama P.; Fedorov, Alexander A.; Sauder, J. Michael

Single-wavelength anomalous dispersion (SAD) utilizing anomalous signal from native S atoms, or other atoms withZ≤ 20, generally requires highly redundant data collected using relatively long-wavelength X-rays. Here, the results from two proteins are presented where the anomalous signal from serendipitously acquired surface-bound Ca atoms with an anomalous data multiplicity of around 10 was utilized to drivede novostructure determination. In both cases, the Ca atoms were acquired from the crystallization solution, and the data-collection strategy was not optimized to exploit the anomalous signal from these scatterers. The X-ray data were collected at 0.98 Å wavelength in one case and at 1.74more » Å in the other (the wavelength was optimized for sulfur, but the anomalous signal from calcium was exploited for structure solution). Similarly, using a test case, it is shown that data collected at ~1.0 Å wavelength, where thef'' value for sulfur is 0.28 e, are sufficient for structure determination using intrinsic S atoms from a strongly diffracting crystal. Interestingly, it was also observed thatSHELXDwas capable of generating a substructure solution from high-exposure data with a completeness of 70% for low-resolution reflections extending to 3.5 Å resolution with relatively low anomalous multiplicity. Considering the fact that many crystallization conditions contain anomalous scatterers such as Cl, Ca, Mnetc., checking for the presence of fortuitous anomalous signal in data from well diffracting crystals could prove useful in either determining the structurede novoor in accurately assigning surface-bound atoms.« less

Crystal structure of paddle-wheel sandwich-type [Cu2{(CH3)2CO}{μ-Fe(η5-C5H4C N)2}3](BF4)2·(CH3)2CO

PubMed Central

Strehler, Frank; Korb, Marcus; Lang, Heinrich

2015-01-01

The mol­ecular structure of (acetone-κO)tris­(μ-ferrocene-1,1′-dicarbo­nitrile-κ2 N:N′)dicopper(I) bis­(tetra­fluorido­borate) acetone monosolvate, [Cu2Fe3(C6H4N)6(C3H6O)](BF4)2·C3H6O, consists of two CuI ions bridged by a ferrocene-1,1′-dicarbo­nitrile moiety in a paddle-wheel-architectured sandwich complex with two BF4 − units as counter-ions. One of the latter is equally disordered over two sets of sites. The two CuI ions are complexed in a trigonal–planar manner by three nitrile N-donor atoms. Further inter­actions by the O atom of an acetone mol­ecule to one of the CuI atoms and a weak η2,π-inter­action of two atoms of a cyclo­penta­dienyl ring to the other CuI atom complete a distorted trigonal–pyramidal environment for each of the metal ions. A further acetone mol­ecule is also present as a solvent mol­ecule. The crystal packing is consolidated by several π–π inter­actions. PMID:25878831

AtomPy: an open atomic-data curation environment

NASA Astrophysics Data System (ADS)

Bautista, Manuel; Mendoza, Claudio; Boswell, Josiah S; Ajoku, Chukwuemeka

2014-06-01

We present a cloud-computing environment for atomic data curation, networking among atomic data providers and users, teaching-and-learning, and interfacing with spectral modeling software. The system is based on Google-Drive Sheets, Pandas (Python Data Analysis Library) DataFrames, and IPython Notebooks for open community-driven curation of atomic data for scientific and technological applications. The atomic model for each ionic species is contained in a multi-sheet Google-Drive workbook, where the atomic parameters from all known public sources are progressively stored. Metadata (provenance, community discussion, etc.) accompanying every entry in the database are stored through Notebooks. Education tools on the physics of atomic processes as well as their relevance to plasma and spectral modeling are based on IPython Notebooks that integrate written material, images, videos, and active computer-tool workflows. Data processing workflows and collaborative software developments are encouraged and managed through the GitHub social network. Relevant issues this platform intends to address are: (i) data quality by allowing open access to both data producers and users in order to attain completeness, accuracy, consistency, provenance and currentness; (ii) comparisons of different datasets to facilitate accuracy assessment; (iii) downloading to local data structures (i.e. Pandas DataFrames) for further manipulation and analysis by prospective users; and (iv) data preservation by avoiding the discard of outdated sets.

On the road to metallic nanoparticles by rational design: bridging the gap between atomic-level theoretical modeling and reality by total scattering experiments.

PubMed

Prasai, Binay; Wilson, A R; Wiley, B J; Ren, Y; Petkov, Valeri

2015-11-14

The extent to which current theoretical modeling alone can reveal real-world metallic nanoparticles (NPs) at the atomic level was scrutinized and demonstrated to be insufficient and how it can be improved by using a pragmatic approach involving straightforward experiments is shown. In particular, 4 to 6 nm in size silica supported Au(100-x)Pd(x) (x = 30, 46 and 58) explored for catalytic applications is characterized structurally by total scattering experiments including high-energy synchrotron X-ray diffraction (XRD) coupled to atomic pair distribution function (PDF) analysis. Atomic-level models for the NPs are built by molecular dynamics simulations based on the archetypal for current theoretical modeling Sutton-Chen (SC) method. Models are matched against independent experimental data and are demonstrated to be inaccurate unless their theoretical foundation, i.e. the SC method, is supplemented with basic yet crucial information on the length and strength of metal-to-metal bonds and, when necessary, structural disorder in the actual NPs studied. An atomic PDF-based approach for accessing such information and implementing it in theoretical modeling is put forward. For completeness, the approach is concisely demonstrated on 15 nm in size water-dispersed Au particles explored for bio-medical applications and 16 nm in size hexane-dispersed Fe48Pd52 particles explored for magnetic applications as well. It is argued that when "tuned up" against experiments relevant to metals and alloys confined to nanoscale dimensions, such as total scattering coupled to atomic PDF analysis, rather than by mere intuition and/or against data for the respective solids, atomic-level theoretical modeling can provide a sound understanding of the synthesis-structure-property relationships in real-world metallic NPs. Ultimately this can help advance nanoscience and technology a step closer to producing metallic NPs by rational design.

Final Technical Report of Project DE-FG02-96ER14647

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

Lundeen, Stephen R.

This is the final technical report of work completed under DOE support over the period Sept. 1, 1996 until May 31, 2015. The title of the project was "Ion/Excited Atom Collision Studies with a Rydberg Target and a CO2 Laser" from 9/1/96 to 10/31/06, and "Properties of Actinide Ions from Measurements of Rydberg Ion Fine Structure" from 11/1/06 until 5/31/15. The primary technical results were a detailed experimental study of resonant charge transfer between Rydberg atoms and highly-charged ions, and unique measurements of many properties of multiply-charged Thorium ions.

Geometries and properties of bimetallic phosphido-bridged complex Cp(CO) 2W(μ-PPh 2)W(CO) 5 and Cp(CO) 3W(μ-PPh 2)W(CO) 5

NASA Astrophysics Data System (ADS)

Wang, Fang; Yang, Hongmei; Yang, Zuoyin; Zhang, Jingchang; Cao, Weiliang

2007-01-01

Complete geometry optimizations were carried out by HF and DFT methods to study the molecular structure of binuclear transition-metal compounds (Cp(CO) 3W(μ-PPh 2)W(CO) 5) (I) and (Cp(CO) 2W(μ-PPh 2)W(CO) 5) (II). A comparison of the experimental data and calculated structural parameters demonstrates that the most accurate geometry parameters are predicted by the MPW1PW91/LANL2DZ among the three DFT methods. Topological properties of molecular charge distributions were analyzed with the theory of atoms in molecules. (3, -1) critical points, namely bond critical point, were found between the two tungsten atoms, and between W1 and C10 in complex II, which confirms the existence of the metal-metal bond and a semi-bridging CO between the two tungsten atoms. The result provided a theoretical guidance of detailed study on the binuclear phosphido-bridged complex containing transition metal-metal bond, which could be useful in the further study of the heterobimetallic phosphido-bridged complexes.

Protein-protein interaction specificity is captured by contact preferences and interface composition.

PubMed

Nadalin, Francesca; Carbone, Alessandra

2018-02-01

Large-scale computational docking will be increasingly used in future years to discriminate protein-protein interactions at the residue resolution. Complete cross-docking experiments make in silico reconstruction of protein-protein interaction networks a feasible goal. They ask for efficient and accurate screening of the millions structural conformations issued by the calculations. We propose CIPS (Combined Interface Propensity for decoy Scoring), a new pair potential combining interface composition with residue-residue contact preference. CIPS outperforms several other methods on screening docking solutions obtained either with all-atom or with coarse-grain rigid docking. Further testing on 28 CAPRI targets corroborates CIPS predictive power over existing methods. By combining CIPS with atomic potentials, discrimination of correct conformations in all-atom structures reaches optimal accuracy. The drastic reduction of candidate solutions produced by thousands of proteins docked against each other makes large-scale docking accessible to analysis. CIPS source code is freely available at http://www.lcqb.upmc.fr/CIPS. alessandra.carbone@lip6.fr. Supplementary data are available at Bioinformatics online. © The Author(s) 2017. Published by Oxford University Press.

Crystal structure of bis-[μ-(4-meth-oxy-phen-yl)methane-thiol-ato-κ(2) S:S]bis-[chlorido-(η(6)-1-isopropyl-4-methyl-benzene)-ruthenium(II)] chloro-form disolvate.

PubMed

Stíbal, David; Süss-Fink, Georg; Therrien, Bruno

2015-10-01

The mol-ecular structure of the title complex, [Ru2(C8H9OS)2Cl2(C10H14)2]·2CHCl3 or (p-MeC6H4Pr (i) )2Ru2(SCH2-p-C6H5-OCH3)2Cl2·2CHCl3, shows inversion symmetry. The two symmetry-related Ru(II) atoms are bridged by two 4-meth-oxy-α-toluene-thiol-ato [(4-meth-oxy-phen-yl)methane-thiol-ato] units. One chlorido ligand and the p-cymene ligand complete the typical piano-stool coordination environment of the Ru(II) atom. In the crystal, the CH moiety of the chloro-form mol-ecule inter-acts with the chlorido ligand of the dinuclear complex, while one Cl atom of the solvent inter-acts more weakly with the methyl group of the bridging 4-meth-oxy-α-toluene-thiol-ato unit. This assembly leads to the formation of supra-molecular chains extending parallel to [021].

NLTE atomic kinetics modeling in ICF target simulations

NASA Astrophysics Data System (ADS)

Patel, Mehul V.; Mauche, Christopher W.; Scott, Howard A.; Jones, Ogden S.; Shields, Benjamin T.

2017-10-01

Radiation hydrodynamics (HYDRA) simulations using recently developed 1D spherical and 2D cylindrical hohlraum models have enabled a reassessment of the accuracy of energetics modeling across a range of NIF target configurations. Higher-resolution hohlraum calculations generally find that the X-ray drive discrepancies are greater than previously reported. We identify important physics sensitivities in the modeling of the NLTE wall plasma and highlight sensitivity variations between different hohlraum configurations (e.g. hohlraum gas fill). Additionally, 1D capsule only simulations show the importance of applying a similar level of rigor to NLTE capsule ablator modeling. Taken together, these results show how improved target performance predictions can be achieved by performing inline atomic kinetics using more complete models for the underlying atomic structure and transitions. Prepared by LLNL under Contract DE-AC52-07NA27344.

The coordination structure of the extracted copper(II) complex with a synergistic mixture containing dinonylnaphthalene sulfonic acid and n-hexyl 3-pyridinecarboxylate ester

NASA Astrophysics Data System (ADS)

Zhu, Shan; Hu, Huiping; Hu, Jiugang; Li, Jiyuan; Hu, Fang; Wang, Yongxi

2017-09-01

In continuation of our interest in the coordination structure of the nickel(II) complex with dinonylnaphthalene sulfonic acid (HDNNS) and 2-ethylhexyl 4-pyridinecarboxylate ester (4PC), it was observed that the coordination sphere was completed by the coordination of two N atoms of pyridine rings in ligands 4PC and four water molecules while no direct interaction between Ni(II) and deprotonated HDNNS was observed. To investigate whether the coordination structure of nickel(II) with the synergistic mixture containing HDNNS and 4PC predominates or not in the copper(II) complex with the synergistic mixtures containing HDNNS and pyridinecarboxylate esters, a copper(II) synergist complex with n-hexyl 3-pyridinecarboxylate ester (L) and naphthalene-2-sulfonic acid (HNS, the short chain analogue of HDNNS), was prepared and studied by X-ray single crystal diffraction, elemental analyses and thermo gravimetric analysis (TGA), respectively. It was shown that the composition of the copper(II) synergist complex was [Cu(H2O)2(L)2(NS)2] and formed a trans-form distorted octahedral coordination structure. Two oxygen atoms of the two coordinated water molecules and two N atoms of the pyridine rings in the ligands L defined the basal plane while two O atoms from two sulfonate anions of the deprotonated HNS ligands occupied the apical positions by direct coordination with Cu(II), which was distinguished from the coordination structure of the nickel(II) synergist complex as reported in our previous work. In the crystal lattice, neighboring molecules [Cu(H2O)2L2(NS)2] were linked through the intermolecular hydrogen bonds between the hydrogen atoms of the coordinated water molecules and the oxygen atoms of the sulfonate anions in the copper(II) synergist complex to form a 2D plane. In order to bridge the gap between the solid state structure of the copper(II) synergist complex and the solution structure of the extracted copper(II) complex with the actual synergistic mixture containing L and HDNNS in the non-polar organic phase, the structures of the two copper(II) complexes were further investigated by Fourier transform infrared spectroscopy (FT-IR) and electrospray ionization mass spectrometry (ESI-MS), and the results indicated that the extracted copper(II) complex in the non-polar organic phase might possess a similar coordination structure as the copper(II) synergist complex.

A Complete NMR Spectral Assignment of the Lipid-free Mouse Apolipoprotein A-I (ApoAI) C-terminal Truncation Mutant, ApoAI(1-216)

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

Yang, Yunhuang; Hoyt, David W.; Wang, Jianjun

2007-07-28

Apolipoprotein A-I (apoAI) is the major protein component of the high-density lipoprotein (HDL) that has been a hot subject of interests because of its anti-atherogenic properties. Upon lipid-binding, apoAI undergoes conformational changes from lipid-free to several different HDL-associated states (1). These different conformational states regulate HDL formation, maturation and transportation. Recent crystal structure of lipid-free human apoAI represents a major progress of structural study of lipid-free apoAI (2). However, no structural is available for lipid-free mouse apoAI (240-residues). Since mouse HDL is homogenous with only HDL2-like size, whereas human HDL is heterogeneous, containing HDL2/HDL3 as its main species, a structuralmore » comparison between human and mouse apoAI may allow us to identify structure basis of HDL size distribution difference between human and mouse. We carried out an NMR structure determination of lipid-free mouse apoAI (1-216) and completely assigned backbone atoms (except backbone amide proton and nitrogen atoms for residues D1, N48, W107, K108, K132, E135, F147, R148, M169 and K203). Secondary structure prediction using backbone NMR parameters indicates that lipid-free mouse apoAI consists of a four helical segments in the N-terminal domain, residues 1-180. In addition, two short helices are also observed between residues 190-195 and 210-215. The helix locations are significantly different from those in the crystal structure of human apoAI, suggesting that mouse apoAI may have a different conformational adaptation upon lipid-binding. BMRB deposit with accession number: 15091.« less

Accuracy of Lagrange-sinc functions as a basis set for electronic structure calculations of atoms and molecules

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

Choi, Sunghwan; Hong, Kwangwoo; Kim, Jaewook

2015-03-07

We developed a self-consistent field program based on Kohn-Sham density functional theory using Lagrange-sinc functions as a basis set and examined its numerical accuracy for atoms and molecules through comparison with the results of Gaussian basis sets. The result of the Kohn-Sham inversion formula from the Lagrange-sinc basis set manifests that the pseudopotential method is essential for cost-effective calculations. The Lagrange-sinc basis set shows faster convergence of the kinetic and correlation energies of benzene as its size increases than the finite difference method does, though both share the same uniform grid. Using a scaling factor smaller than or equal tomore » 0.226 bohr and pseudopotentials with nonlinear core correction, its accuracy for the atomization energies of the G2-1 set is comparable to all-electron complete basis set limits (mean absolute deviation ≤1 kcal/mol). The same basis set also shows small mean absolute deviations in the ionization energies, electron affinities, and static polarizabilities of atoms in the G2-1 set. In particular, the Lagrange-sinc basis set shows high accuracy with rapid convergence in describing density or orbital changes by an external electric field. Moreover, the Lagrange-sinc basis set can readily improve its accuracy toward a complete basis set limit by simply decreasing the scaling factor regardless of systems.« less

Crystal structure and Hirshfeld surface analysis of aqua-bis-(nicotinamide-κN)bis-(4-sulfamoylbenzoato-κO1)copper(II).

PubMed

Hökelek, Tuncer; Yavuz, Vijdan; Dal, Hakan; Necefoğlu, Hacali

2018-01-01

In the crystal of the title complex, [Cu(C 7 H 6 NO 4 S) 2 (C 6 H 6 N 2 O) 2 (H 2 O)], the Cu II cation and the O atom of the coordinated water mol-ecule reside on a twofold rotation axis. The Cu II ion is coordinated by two carboxyl-ate O atoms of the two symmetry-related 4-sulfamoylbenzoate (SB) anions and by two N atoms of the two symmetry-related nicotinamide (NA) mol-ecules at distances of 1.978 (2) and 2.025 (3) Å, respectively, forming a slightly distorted square-planar arrangement. The distorted square-pyramidal coordination environment is completed by the water O atom in the axial position at a distance of 2.147 (4) Å. In the crystal, the mol-ecules are linked via O-H⋯O and N-H⋯O hydrogen bonds with R 2 2 (8) and R 2 2 (18) ring motifs, forming a three-dimensional architecture. The Hirshfeld surface analysis of the crystal structure indicates that the most important contributions for the crystal packing are from H⋯O/O⋯H (42.2%), H⋯H (25.7%) and H⋯C/C⋯H (20.0%) inter-actions.

Laboratory studies in ultraviolet solar physics

NASA Technical Reports Server (NTRS)

Parkinson, W. H.; Kohl, J. L.; Gardner, L. D.; Raymond, J. C.; Smith, P. L.

1991-01-01

The research activity comprised the measurement of basic atomic processes and parameters which relate directly to the interpretation of solar ultraviolet observations and to the development of comprehensive models of the component structures of the solar atmosphere. The research was specifically directed towards providing the relevant atomic data needed to perform and to improve solar diagnostic techniques which probe active and quiet portions of the solar chromosphere, the transition zone, the inner corona, and the solar wind acceleration regions of the extended corona. The accuracy with which the physical conditions in these structures can be determined depends directly on the accuracy and completeness of the atomic and molecular data. These laboratory data are used to support the analysis programs of past and current solar observations (e.g., the Orbiting solar Observatories, the Solar Maximum Mission, the Skylab Apollo Telescope Mount, and the Naval Research Laboratory's rocket-borne High Resolution Telescope and Spectrograph). In addition, we attempted to anticipate the needs of future space-borne solar studies such as from the joint ESA/NASA Solar and Heliospheric Observatory (SOHO) spacecraft. Our laboratory activities stressed two categories of study: (1) the measurement of absolute rate coefficients for dielectronic recombination and electron impact excitation; and (2) the measurement of atomic transition probabilities for solar density diagnostics. A brief summary of the research activity is provided.

The Calculation Study of Electronic Properties of Doped RE (Eu, Er and Tm)-GaN using Density Functional Theory

NASA Astrophysics Data System (ADS)

Zaharo, Aflah; Purqon, Acep

2017-07-01

The calculation of the structure and electronic properties of Rare Earth (RE) at the wurtzite Gallium Nitride (GaN) based on DFT has completed. GGA approximation used for exchange correlation and Ultra soft pseudo potential too. The stability structure of GaN is seen that difference lattice parameter 11% lower than another calculation and experiment result. It is shown the stability structure GaN have direct band gap energy on Gamma point hexagonal lattice Brillouin zone. The width Eg is 2.6 eV. When one atom Ga is substituted with one atom RE, the bond length is change 12 % longest. An in good agreement with theoretical doping RE concentration increases, the edge of energy level shifted towards to make the band gap narrow which is allow the optical transitions and help to improve the optical performance of GaN. The RE doped GaN is potentially applicable for various color of LED with lower energy consumption and potentially energy saving application

A Near-Atomic Structure of the Dark Apoptosome Provides Insight into Assembly and Activation.

PubMed

Cheng, Tat Cheung; Akey, Ildikó V; Yuan, Shujun; Yu, Zhiheng; Ludtke, Steven J; Akey, Christopher W

2017-01-03

In Drosophila, the Apaf-1-related killer (Dark) forms an apoptosome that activates procaspases. To investigate function, we have determined a near-atomic structure of Dark double rings using cryo-electron microscopy. We then built a nearly complete model of the apoptosome that includes 7- and 8-blade β-propellers. We find that the preference for dATP during Dark assembly may be governed by Ser325, which is in close proximity to the 2' carbon of the deoxyribose ring. Interestingly, β-propellers in V-shaped domains of the Dark apoptosome are more widely separated, relative to these features in the Apaf-1 apoptosome. This wider spacing may be responsible for the lack of cytochrome c binding to β-propellers in the Dark apoptosome. Our structure also highlights the roles of two loss-of-function mutations that may block Dark assembly. Finally, the improved model provides a framework to understand apical procaspase activation in the intrinsic cell death pathway. Copyright © 2016 Elsevier Ltd. All rights reserved.

Intrinsic retrieval efficiency for quantum memories: A three-dimensional theory of light interaction with an atomic ensemble

NASA Astrophysics Data System (ADS)

Gujarati, Tanvi P.; Wu, Yukai; Duan, Luming

2018-03-01

Duan-Lukin-Cirac-Zoller quantum repeater protocol, which was proposed to realize long distance quantum communication, requires usage of quantum memories. Atomic ensembles interacting with optical beams based on off-resonant Raman scattering serve as convenient on-demand quantum memories. Here, a complete free space, three-dimensional theory of the associated read and write process for this quantum memory is worked out with the aim of understanding intrinsic retrieval efficiency. We develop a formalism to calculate the transverse mode structure for the signal and the idler photons and use the formalism to study the intrinsic retrieval efficiency under various configurations. The effects of atomic density fluctuations and atomic motion are incorporated by numerically simulating this system for a range of realistic experimental parameters. We obtain results that describe the variation in the intrinsic retrieval efficiency as a function of the memory storage time for skewed beam configuration at a finite temperature, which provides valuable information for optimization of the retrieval efficiency in experiments.

Octa-akis(4-amino-pyridine)-1κN,2κN-aqua-2κO-μ-carbonato-1:2κO,O':O''-dinickel(II) dichloride penta-hydrate.

PubMed

Fun, Hoong-Kun; Sinthiya, A; Jebas, Samuel Robinson; Ravindran Durai Nayagam, B; Alfred Cecil Raj, S

2008-10-18

In the title compound, [Ni(2)(CO(3))(C(5)H(6)N(2))(8)(H(2)O)]Cl(2)·5H(2)O, one of the the Ni(II) ions is six-coordinated in a distorted octa-hedral geometry, with the equatorial plane defined by four pyridine N atoms from four amino-pyridine ligands, the axial positions being occupied by one water O and a carbonate O atom. The other Ni(II) ion is also six-coordinated, by four other pyridine N atoms from four other amino-pyridine ligands and two carbonate O atoms to complete a distorted octa-hedral geometry. In the crystal structure, mol-ecules are linked into an infinite three-dimensional network by O-H⋯O, N-H⋯Cl, N-H⋯O, O-H⋯N, C-H⋯O, C-H⋯N and C/N-H⋯π inter-actions involving the pyridine rings.

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).

Magnetic properties of Mg12O12 nanocage doped with transition metal atoms (Mn, Fe, Co and Ni): DFT study

NASA Astrophysics Data System (ADS)

Javan, Masoud Bezi

2015-07-01

Binding energy of the Mg12O12 nanocage doped with transition metals (TM=Mn, Fe, Co and Ni) in endohedrally, exohedrally and substitutionally forms were studied using density functional theory with the generalized gradient approximation exchange-correlation functional along 6 different paths inside and outside of the Mg12O12 nanocage. The most stable structures were determined with full geometry optimization near the minimum of the binding energy curves of all the examined paths inside and outside of the Mg12O12 nanocage. The results reveal that for all stable structures, the Ni atom has a larger binding energy than the other TM atoms. It is also found that for all complexes additional peaks contributed by TM-3d, 4s and 4p states appear in the highest occupied molecular orbital (HOMO) and the lowest unoccupied molecular orbital (LUMO) gap of the host MgO cluster. The mid-gap states are mainly due to the hybridization between TM-3d, 4s and 4p orbitals and the cage π orbitals. The magnetic moment of the endohedrally doped TM atoms in the Mg12O12 are preserved to some extent due to the interaction between the TM and Mg12O12 nanocage, in contrast to the completely quenched magnetic moment of the Fe and Ni atoms in the Mg11(TM)O12 complexes. Furthermore, charge population analysis shows that charge transfer occurs from TM atom to the cage for endohedrally and substitutionally doping.

Building proteins from C alpha coordinates using the dihedral probability grid Monte Carlo method.

PubMed Central

Mathiowetz, A. M.; Goddard, W. A.

1995-01-01

Dihedral probability grid Monte Carlo (DPG-MC) is a general-purpose method of conformational sampling that can be applied to many problems in peptide and protein modeling. Here we present the DPG-MC method and apply it to predicting complete protein structures from C alpha coordinates. This is useful in such endeavors as homology modeling, protein structure prediction from lattice simulations, or fitting protein structures to X-ray crystallographic data. It also serves as an example of how DPG-MC can be applied to systems with geometric constraints. The conformational propensities for individual residues are used to guide conformational searches as the protein is built from the amino-terminus to the carboxyl-terminus. Results for a number of proteins show that both the backbone and side chain can be accurately modeled using DPG-MC. Backbone atoms are generally predicted with RMS errors of about 0.5 A (compared to X-ray crystal structure coordinates) and all atoms are predicted to an RMS error of 1.7 A or better. PMID:7549885

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

Structure-conserving spontaneous transformations between nanoparticles

NASA Astrophysics Data System (ADS)

Krishnadas, K. R.; Baksi, Ananya; Ghosh, Atanu; Natarajan, Ganapati; Pradeep, Thalappil

2016-11-01

Ambient, structure- and topology-preserving chemical reactions between two archetypal nanoparticles, Ag25(SR)18 and Au25(SR)18, are presented. Despite their geometric robustness and electronic stability, reactions between them in solution produce alloys, AgmAun(SR)18 (m+n=25), keeping their M25(SR)18 composition, structure and topology intact. We demonstrate that a mixture of Ag25(SR)18 and Au25(SR)18 can be transformed to any arbitrary alloy composition, AgmAun(SR)18 (n=1-24), merely by controlling the reactant compositions. We capture one of the earliest events of the process, namely the formation of the dianionic adduct, (Ag25Au25(SR)36)2-, by electrospray ionization mass spectrometry. Molecular docking simulations and density functional theory (DFT) calculations also suggest that metal atom exchanges occur through the formation of an adduct between the two clusters. DFT calculations further confirm that metal atom exchanges are thermodynamically feasible. Such isomorphous transformations between nanoparticles imply that microscopic pieces of matter can be transformed completely to chemically different entities, preserving their structures, at least in the nanometric regime.

A complete assignment of the vibrational spectra of 2-furoic acid based on the structures of the more stable monomer and dimer

NASA Astrophysics Data System (ADS)

Ghalla, Houcine; Issaoui, Noureddine; Castillo, María Victoria; Brandán, Silvia Antonia; Flakus, Henryk T.

2014-03-01

The structural and vibrational properties of cyclic dimer of 2-furoic acid (2FA) were predicted by combining the available experimental infrared and Raman spectra in the solid phase and ab initio calculations based on density functional theory (DFT) with Pople's basis sets. The calculations show that there are two cyclic dimers for the title molecule that have been theoretically determined in the gas phase, and that only one of them, cis conformer, is present in the solid phase. The complete assignment of the 66 normal vibrational modes for the cis cyclic dimer was performed using the Pulay's Scaled Quantum Mechanics Force Field (SQMFF) methodology. Four strong bands in the infrared spectrum at 1583, 1427, 1126 and 887 cm-1 and the group of bands in the Raman spectrum at 1464, 1452, 1147, 1030, 885, 873, 848, 715 and 590 cm-1 are characteristic of the dimeric form of 2FA in the solid phase. In this work, the calculated structural and vibrational properties of both dimeric species were analyzed and compared between them. In addition, three types of atomic charges, bond orders, possible charge transfer, topological properties of the furan rings, Natural Bond Orbital (NBO) and Atoms in Molecules (AIM) theory calculations were employed to study the stabilities and intermolecular interactions of the both dimers of 2FA.

Capping Ligand Vortices as “Atomic Orbitals” in Nanocrystal Self-Assembly

DOE PAGES

Waltmann, Curt; Horst, Nathan; Travesset, Alex

2017-10-27

In this work, we present a detailed analysis of the interaction between two nanocrystals capped with ligands consisting of hydrocarbon chains by united atom molecular dynamics simulations. We show that the bonding of two nanocrystals is characterized by ligand textures in the form of vortices. These results are generalized to nanocrystals of different types (differing core and ligand sizes) where the structure of the vortices depends on the softness asymmetry. We provide rigorous calculations for the binding free energy, show that these energies are independent of the chemical composition of the cores, and derive analytical formulas for the equilibrium separation.more » We discuss the implications of our results for the self-assembly of single-component and binary nanoparticle superlattices. Overall, our results show that the structure of the ligands completely determines the bonding of nanocrystals, fully supporting the predictions of the recently proposed Orbifold topological model.« less

Capping Ligand Vortices as "Atomic Orbitals" in Nanocrystal Self-Assembly.

PubMed

Waltmann, Curt; Horst, Nathan; Travesset, Alex

2017-11-28

We present a detailed analysis of the interaction between two nanocrystals capped with ligands consisting of hydrocarbon chains by united atom molecular dynamics simulations. We show that the bonding of two nanocrystals is characterized by ligand textures in the form of vortices. These results are generalized to nanocrystals of different types (differing core and ligand sizes) where the structure of the vortices depends on the softness asymmetry. We provide rigorous calculations for the binding free energy, show that these energies are independent of the chemical composition of the cores, and derive analytical formulas for the equilibrium separation. We discuss the implications of our results for the self-assembly of single-component and binary nanoparticle superlattices. Overall, our results show that the structure of the ligands completely determines the bonding of nanocrystals, fully supporting the predictions of the recently proposed Orbifold topological model.

QSAR for cholinesterase inhibition by organophosphorus esters and CNDO/2 calculations for organophosphorus ester hydrolysis. [quantitative structure-activity relationship, complete neglect of differential overlap

NASA Technical Reports Server (NTRS)

Johnson, H.; Kenley, R. A.; Rynard, C.; Golub, M. A.

1985-01-01

Quantitative structure-activity relationships were derived for acetyl- and butyrylcholinesterase inhibition by various organophosphorus esters. Bimolecular inhibition rate constants correlate well with hydrophobic substituent constants, and with the presence or absence of cationic groups on the inhibitor, but not with steric substituent constants. CNDO/2 calculations were performed on a separate set of organophosphorus esters, RR-primeP(O)X, where R and R-prime are alkyl and/or alkoxy groups and X is fluorine, chlorine or a phenoxy group. For each subset with the same X, the CNDO-derived net atomic charge at the central phosphorus atom in the ester correlates well with the alkaline hydrolysis rate constant. For the whole set of esters with different X, two equations were derived that relate either charge and leaving group steric bulk, or orbital energy and bond order to the hydrolysis rate constant.

Crystal structure of bis-(μ-3-nitro-benzoato)-κ3O,O':O;κ3O:O,O'-bis-[bis-(3-cyano-pyridine-κN1)(3-nitro-benzoato-κ2O,O')cadmium].

PubMed

Hökelek, Tuncer; Akduran, Nurcan; Özen, Azer; Uğurlu, Güventürk; Necefoğlu, Hacali

2017-03-01

The asymmetric unit of the title compound, [Cd 2 (C 7 H 4 NO 4 ) 4 (C 6 H 4 N 2 ) 4 ], contains one Cd II atom, two 3-nitro-benzoate (NB) anions and two 3-cyano-pyridine (CPy) ligands. The two CPy ligands act as monodentate N(pyridine)-bonding ligands, while the two NB anions act as bidentate ligands through the carboxyl-ate O atoms. The centrosymmetric dinuclear complex is generated by application of inversion symmetry, whereby the Cd II atoms are bridged by the carboxyl-ate O atoms of two symmetry-related NB anions, thus completing the distorted N 2 O 5 penta-gonal-bipyramidal coordination sphere of each Cd II atom. The benzene and pyridine rings are oriented at dihedral angles of 10.02 (7) and 5.76 (9)°, respectively. In the crystal, C-H⋯N hydrogen bonds link the mol-ecules, enclosing R 2 2 (26) ring motifs, in which they are further linked via C-H⋯O hydrogen bonds, resulting in a three-dimensional network. In addition, π-π stacking inter-actions between parallel benzene rings and between parallel pyridine rings of adjacent mol-ecules [shortest centroid-to-centroid distances = 3.885 (1) and 3.712 (1) Å, respectively], as well as a weak C-H⋯π inter-action, may further stabilize the crystal structure.

Method for large-scale fabrication of atomic-scale structures on material surfaces using surface vacancies

DOEpatents

Lim, Chong Wee; Ohmori, Kenji; Petrov, Ivan Georgiev; Greene, Joseph E.

2004-07-13

A method for forming atomic-scale structures on a surface of a substrate on a large-scale includes creating a predetermined amount of surface vacancies on the surface of the substrate by removing an amount of atoms on the surface of the material corresponding to the predetermined amount of the surface vacancies. Once the surface vacancies have been created, atoms of a desired structure material are deposited on the surface of the substrate to enable the surface vacancies and the atoms of the structure material to interact. The interaction causes the atoms of the structure material to form the atomic-scale structures.

An atomic model of the tropomyosin cable on F-actin.

PubMed

Orzechowski, Marek; Li, Xiaochuan Edward; Fischer, Stefan; Lehman, William

2014-08-05

Tropomyosin regulates a wide variety of actin filament functions and is best known for the role that it plays together with troponin in controlling muscle activity. For effective performance on actin filaments, adjacent 42-nm-long tropomyosin molecules are joined together by a 9- to 10-residue head-to-tail overlapping domain to form a continuous cable that wraps around the F-actin helix. Yet, despite the apparent simplicity of tropomyosin's coiled-coil structure and its well-known periodic association with successive actin subunits along F-actin, the structure of the tropomyosin cable on actin is uncertain. This is because the conformation of the overlap region that joins neighboring molecules is poorly understood, thus leaving a significant gap in our understanding of thin-filament structure and regulation. However, recent molecular-dynamics simulations of overlap segments defined their overall shape and provided unique and sufficient cues to model the whole actin-tropomyosin filament assembly in atomic detail. In this study, we show that these MD structures merge seamlessly onto the ends of tropomyosin coiled-coils. Adjacent tropomyosin molecules can then be joined together to provide a comprehensive model of the tropomyosin cable running continuously on F-actin. The resulting complete model presented here describes for the first time (to our knowledge) an atomic-level structure of αα-striated muscle tropomyosin bound to an actin filament that includes the critical overlap domain. Thus, the model provides a structural correlate to evaluate thin-filament mechanics, self-assembly mechanisms, and the effect of disease-causing mutations. Copyright © 2014 Biophysical Society. Published by Elsevier Inc. All rights reserved.

DECOMP: a PDB decomposition tool on the web.

PubMed

Ordog, Rafael; Szabadka, Zoltán; Grolmusz, Vince

2009-07-27

The protein databank (PDB) contains high quality structural data for computational structural biology investigations. We have earlier described a fast tool (the decomp_pdb tool) for identifying and marking missing atoms and residues in PDB files. The tool also automatically decomposes PDB entries into separate files describing ligands and polypeptide chains. Here, we describe a web interface named DECOMP for the tool. Our program correctly identifies multi-monomer ligands, and the server also offers the preprocessed ligand-protein decomposition of the complete PDB for downloading (up to size: 5GB) AVAILABILITY: http://decomp.pitgroup.org.

Efecto de la difusión y la velocidad en la ionización del átomo de Carbono

NASA Astrophysics Data System (ADS)

Rovira, M. G.; Fontenla, J. M.

The equations of statistical equilibrium for all ionization states of the atom are solved. The effects of diffusion and center of mass velocity are included. In order to estimate the modifications of the ionization curves, they were applied to the Carbon atom. To solve these equations, solar prominences' models obtained in a previous paper were adopted. They were extended to reach a temperature of 1.5 × 106 K and the complete model of the prominence was calculated. Ionization curves for different values of velocity, diffusion and medium models were obtained. The different models represent structures with different densities. Considerable modifications due to these effects are found.

Footprints of electron correlation in strong-field double ionization of Kr close to the sequential-ionization regime

NASA Astrophysics Data System (ADS)

Li, Xiaokai; Wang, Chuncheng; Yuan, Zongqiang; Ye, Difa; Ma, Pan; Hu, Wenhui; Luo, Sizuo; Fu, Libin; Ding, Dajun

2017-09-01

By combining kinematically complete measurements and a semiclassical Monte Carlo simulation we study the correlated-electron dynamics in the strong-field double ionization of Kr. Interestingly, we find that, as we step into the sequential-ionization regime, there are still signatures of correlation in the two-electron joint momentum spectrum and, more intriguingly, the scaling law of the high-energy tail is completely different from early predictions on the low-Z atom (He). These experimental observations are well reproduced by our generalized semiclassical model adapting a Green-Sellin-Zachor potential. It is revealed that the competition between the screening effect of inner-shell electrons and the Coulomb focusing of nuclei leads to a non-inverse-square central force, which twists the returned electron trajectory at the vicinity of the parent core and thus significantly increases the probability of hard recollisions between two electrons. Our results might have promising applications ranging from accurately retrieving atomic structures to simulating celestial phenomena in the laboratory.

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

Ternary complexes of Zn(II) and Cu(II) with 1-((2-hydroxynaphthalen-1-yl)methylene)-4-phenylthiosemicarbazide in the presence of heterocyclic bases as auxiliary ligands: Synthesis, spectroscopic and structural characterization and antibacterial activity

NASA Astrophysics Data System (ADS)

Azarkish, Mohammad; Akbari, Alireza; Sedaghat, Tahereh; Simpson, Jim

2018-03-01

The new ternary complexes, ZnLL‧ [L = 1-((2-hydroxynaphthalen-1-yl)methylene)-4-phenylthiosemicarbazide and L‧ = imidazole (1), 2, 2‧-bipyridine (2) and 2-methyimidazole (3)], Zn2L2L‧ [L‧ = 4, 4‧-bipy (4)] and CuLL‧ [L‧ = 2, 2‧-bipy (5)] have been synthesized by the reaction of a metal(II) acetate salt with the thiosemicarbazone and in presence of heterocyclic bases as auxiliary ligands. The synthesized compounds were investigated by elemental analysis and IR, 1H NMR, and 13C NMR spectroscopy and complex 5 was structurally characterized by X-ray crystallography. The results indicate the thiosemicarbazone doubly deprotonated and coordinates to metal through the thiolate sulfur, imine nitrogen and phenolic oxygen atoms. The nitrogen atom(s) of the auxiliary ligand complete the coordination sphere. Complex 4 is binuclear with 4, 4‧-bipy acting as a bridging ligand. The structure of 5 is a distorted square pyramid with one of the bipyridine nitrogen atoms in the apical position. This compound creates an inversion dimer in solid state by intermolecular hydrogen bonds of Nsbnd H⋯S type. The in vitro antibacterial activity of the synthesized compounds were evaluated against Gram-positive (B. subtilis and S. aureus) and Gram-negative (P. aeruginosa) bacteria and is compared to that of standard antibacterial drugs. All complexes exhibit good inhibitory effects and are significantly more effective than the parent ligand.

Coupled molecular and cantilever dynamics model for frequency-modulated atomic force microscopy.

PubMed

Klocke, Michael; Wolf, Dietrich E

2016-01-01

A molecular dynamics model is presented, which adds harmonic potentials to the atomic interactions to mimic the elastic properties of an AFM cantilever. It gives new insight into the correlation between the experimentally monitored frequency shift and cantilever damping due to the interaction between tip atoms and scanned surface. Applying the model to ionic crystals with rock salt structure two damping mechanisms are investigated, which occur separately or simultaneously depending on the tip position. These mechanisms are adhesion hysteresis on the one hand and lateral excitations of the cantilever on the other. We find that the short range Lennard-Jones part of the atomic interaction alone is sufficient for changing the predominant mechanism. When the long range ionic interaction is switched off, the two damping mechanisms occur with a completely different pattern, which is explained by the energy landscape for the apex atom of the tip. In this case the adhesion hysteresis is always associated with a distinct lateral displacement of the tip. It is shown how this may lead to a systematic shift between the periodic patterns obtained from the frequency and from the damping signal, respectively.

Modeling the Oxygen K Absorption in the Interstellar Medium: An XMM-Newton View of Sco X-1

NASA Technical Reports Server (NTRS)

Garcia, J.; Ramirez, J. M.; Kallman, T. R.; Witthoeft, M.; Bautista, M. A.; Mendoza, C.; Palmeri, P.; Quinet, P.

2011-01-01

We investigate the absorption structure of the oxygen in the interstellar medium by analyzing XMM-Newton observations of the low mass X-ray binary Sco X-1. We use simple models based on the O I atomic cross section from different sources to fit the data and evaluate the impact of the atomic data in the interpretation of astrophysical observations. We show that relatively small differences in the atomic calculations can yield spurious results. We also show that the most complete and accurate set of atomic cross sections successfully reproduce the observed data in the 21 - 24.5 Angstrom wavelength region of the spectrum. Our fits indicate that the absorption is mainly due to neutral gas with an ionization parameter of Epsilon = 10(exp -4) erg/sq cm, and an oxygen column density of N(sub O) approx. = 8-10 x 10(exp 17)/sq cm. Our models are able to reproduce both the K edge and the K(alpha) absorption line from O I, which are the two main features in this region. We find no conclusive evidence for absorption by other than atomic oxygen.

Formation of Surface and Quantum-Well States in Ultra Thin Pt Films on the Au(111) Surface

PubMed Central

Silkin, Igor V.; Koroteev, Yury M.; Echenique, Pedro M.; Chulkov, Evgueni V.

2017-01-01

The electronic structure of the Pt/Au(111) heterostructures with a number of Pt monolayers n ranging from one to three is studied in the density-functional-theory framework. The calculations demonstrate that the deposition of the Pt atomic thin films on gold substrate results in strong modifications of the electronic structure at the surface. In particular, the Au(111) s-p-type Shockley surface state becomes completely unoccupied at deposition of any number of Pt monolayers. The Pt adlayer generates numerous quantum-well states in various energy gaps of Au(111) with strong spatial confinement at the surface. As a result, strong enhancement in the local density of state at the surface Pt atomic layer in comparison with clean Pt surface is obtained. The excess in the density of states has maximal magnitude in the case of one monolayer Pt adlayer and gradually reduces with increasing number of Pt atomic layers. The spin–orbit coupling produces strong modification of the energy dispersion of the electronic states generated by the Pt adlayer and gives rise to certain quantum states with a characteristic Dirac-cone shape. PMID:29232833

Crystal structure of [NaZn(BTC)(H2O)4]·1.5H2O (BTC = benzene-1,3,5-tri-carb-oxy-l-ate): a heterometallic coordination compound.

PubMed

Ni, Min; Li, Quanle; Chen, Hao; Li, Shengqing

2015-07-01

The title coordination polymer, poly[[μ-aqua-tri-aqua-(μ3-benzene-1,3,5-tri-carboxyl-ato)sodiumzinc] sesquihydrate], {[NaZn(C9H3O6)(H2O)4]·1.5H2O} n , was obtained in ionic liquid microemulsion at room temperture by the reaction of benzene-1,3,5-tri-carb-oxy-lic acid (H3BTC) with Zn(NO3)2·6H2O in the presence of NaOH. The asymmetric unit comprises two Na(+) ions (each located on an inversion centre), one Zn(2+) ion, one BTC ligand, four coordinating water mol-ecules and two solvent water molecules, one of which is disordered about an inversion centre and shows half-occupation. The Zn(2+) cation is five-coordinated by two carboxyl-ate O atoms from two different BTC ligands and three coordinating H2O mol-ecules; the Zn-O bond lengths are in the range 1.975 (2)-2.058 (3) Å. The Na(+) cations are six-coordinated but have different arrangements of the ligands: one is bound to two carboxyl-ate O atoms of two BTC ligands and four O atoms from four coordinating H2O mol-ecules while the other is bound by four carboxyl-ate O atoms from four BTC linkers and two O atoms of coordinating H2O mol-ecules. The completely deprotonated BTC ligand acts as a bridging ligand binding the Zn(2+) atom and Na(+) ions, forming a layered structure extending parallel to (100). An intricate network of O-H⋯O hydrogen bonds is present within and between the layers.

Thermodynamic properties of arsenic compounds and the heat of formation of the As atom from high level electronic structure calculations.

PubMed

Feller, David; Vasiliu, Monica; Grant, Daniel J; Dixon, David A

2011-12-29

Structures, vibrational frequencies, atomization energies at 0 K, and heats of formation at 0 and 298 K are predicted for the compounds As(2), AsH, AsH(2), AsH(3), AsF, AsF(2), and AsF(3) from frozen core coupled cluster theory calculations performed with large correlation consistent basis sets, up through augmented sextuple zeta quality. The coupled cluster calculations involved up through quadruple excitations. For As(2) and the hydrides, it was also possible to examine the impact of full configuration interaction on some of the properties. In addition, adjustments were incorporated to account for extrapolation to the frozen core complete basis set limit, core/valence correlation, scalar relativistic effects, the diagonal Born-Oppenheimer correction, and atomic spin orbit corrections. Based on our best theoretical D(0)(As(2)) and the experimental heat of formation of As(2), we propose a revised 0 K arsenic atomic heat of formation of 68.86 ± 0.8 kcal/mol. While generally good agreement was found between theory and experiment, the heat of formation of AsF(3) was an exception. Our best estimate is more than 7 kcal/mol more negative than the single available experimental value, which argues for a re-examination of that measurement. © 2011 American Chemical Society

Crystal structure and Hirshfeld surface analysis of aqua­bis­(nicotinamide-κN)bis­(4-sulfamoylbenzoato-κO 1)copper(II)

PubMed Central

Hökelek, Tuncer; Yavuz, Vijdan; Dal, Hakan; Necefoğlu, Hacali

2018-01-01

In the crystal of the title complex, [Cu(C7H6NO4S)2(C6H6N2O)2(H2O)], the CuII cation and the O atom of the coordinated water mol­ecule reside on a twofold rotation axis. The CuII ion is coordinated by two carboxyl­ate O atoms of the two symmetry-related 4-sulfamoylbenzoate (SB) anions and by two N atoms of the two symmetry-related nicotinamide (NA) mol­ecules at distances of 1.978 (2) and 2.025 (3) Å, respectively, forming a slightly distorted square-planar arrangement. The distorted square-pyramidal coordination environment is completed by the water O atom in the axial position at a distance of 2.147 (4) Å. In the crystal, the mol­ecules are linked via O—H⋯O and N—H⋯O hydrogen bonds with R 2 2(8) and R 2 2(18) ring motifs, forming a three-dimensional architecture. The Hirshfeld surface analysis of the crystal structure indicates that the most important contributions for the crystal packing are from H⋯O/O⋯H (42.2%), H⋯H (25.7%) and H⋯C/C⋯H (20.0%) inter­actions. PMID:29416889

Coherent and radiative couplings through two-dimensional structured environments

NASA Astrophysics Data System (ADS)

Galve, F.; Zambrini, R.

2018-03-01

We study coherent and radiative interactions induced among two or more quantum units by coupling them to two-dimensional (2D) lattices acting as structured environments. This model can be representative of atoms trapped near photonic crystal slabs, trapped ions in Coulomb crystals, or to surface acoustic waves on piezoelectric materials, cold atoms on state-dependent optical lattices, or even circuit QED architectures, to name a few. We compare coherent and radiative contributions for the isotropic and directional regimes of emission into the lattice, for infinite and finite lattices, highlighting their differences and existing pitfalls, e.g., related to long-time or large-lattice limits. We relate the phenomenon of directionality of emission with linear-shaped isofrequency manifolds in the dispersion relation, showing a simple way to disrupt it. For finite lattices, we study further details such as the scaling of resonant number of lattice modes for the isotropic and directional regimes, and relate this behavior with known van Hove singularities in the infinite lattice limit. Furthermore, we export the understanding of emission dynamics with the decay of entanglement for two quantum, atomic or bosonic, units coupled to the 2D lattice. We analyze in some detail completely subradiant configurations of more than two atoms, which can occur in the finite lattice scenario, in contrast with the infinite lattice case. Finally, we demonstrate that induced coherent interactions for dark states are zero for the finite lattice.

Inhibition of dog and human gastric lipases by enantiomeric phosphonate inhibitors: a structure-activity study.

PubMed

Miled, Nabil; Roussel, Alain; Bussetta, Cécile; Berti-Dupuis, Liliane; Rivière, Mireille; Buono, Gérard; Verger, Robert; Cambillau, Christian; Canaan, Stéphane

2003-10-14

The crystal structures of gastric lipases in the apo form [Roussel, A., et al. (1999) J. Biol. Chem. 274, 16995-17002] or in complex with the (R(P))-undecyl butyl phosphonate [C(11)Y(4)(+)] [Roussel, A., et al. (2002) J. Biol. Chem. 277, 2266-2274] have improved our understanding of the structure-activity relationships of acid lipases. In this report, we have performed a kinetic study with dog and human gastric lipases (DGL and HGL, respectively) using several phosphonate inhibitors by varying the absolute configuration of the phosphorus atom and the chain length of the alkyl/alkoxy substituents. Using the two previously determined structures and that of a new crystal structure obtained with the other (S(P))-phosphonate enantiomer [C(11)Y(4)(-)], we constructed models of phosphonate inhibitors fitting into the active site crevices of DGL and HGL. All inhibitors with a chain length of fewer than 12 carbon atoms were found to be completely buried in the catalytic crevice, whereas longer alkyl/alkoxy chains were found to point out of the cavity. The main stereospecific determinant explaining the stronger inhibition of the S(P) enantiomers is the presence of a hydrogen bond involving the catalytic histidine as found in the DGL-C(11)Y(4)(-) complex. On the basis of these results, we have built a model of the first tetrahedral intermediate corresponding to the tristearoyl-lipase complex. The triglyceride molecule completely fills the active site crevice of DGL, in contrast with what is observed with other lipases such as pancreatic lipases which have a shallower and narrower active site. For substrate hydrolysis, the supply of water molecules to the active site might be achieved through a lateral channel identified in the protein core.

An epistemology on the nature of polymers.

PubMed

Laridjani, Mortéza; Leboucher, Pierre

2014-01-01

Liquids have neither a periodic structure nor the completely random character of gases therefore the detailed study of their x-ray scattering diagram encounters many difficulties. The idea of periodic regularity in molecules of liquid polymers has been an attractive proposition for the simple interpretation of liquid polymer x-ray diagrams. The categorisation of polymer substances as being between a crystal phase with a perfect order and an amorphous disordered state is an over simplification of the complex reality. For obtaining structural information, during the early stages of the application of x-ray diffraction, a near crystalline model of the molecular arrangements in liquids was utilised. However, the results from these investigations led to just an approximation of the crystalline state. Our studies have analysed the real image of Fourier space of liquid polymers, for the first time, using anomalous diffractometry. The findings show the precise atomic structure of liquid polymers when transformed, by cooling, to solid polymers. We demonstrate that there is an intermediate ordered structure, characterised by the real full image of Fourier space. This prominent state of matter, an intermediate ordered structure, is defined by a regular unit cell with a five-fold symmetry. These structural atomic studies contribute to a more detailed understanding of the properties of polymers than the traditional studies of the degree of crystallinity.

An Epistemology on the Nature of Polymers

PubMed Central

Laridjani, Mortéza; Leboucher, Pierre

2014-01-01

Liquids have neither a periodic structure nor the completely random character of gases therefore the detailed study of their x-ray scattering diagram encounters many difficulties. The idea of periodic regularity in molecules of liquid polymers has been an attractive proposition for the simple interpretation of liquid polymer x-ray diagrams. The categorisation of polymer substances as being between a crystal phase with a perfect order and an amorphous disordered state is an over simplification of the complex reality. For obtaining structural information, during the early stages of the application of x-ray diffraction, a near crystalline model of the molecular arrangements in liquids was utilised. However, the results from these investigations led to just an approximation of the crystalline state. Our studies have analysed the real image of Fourier space of liquid polymers, for the first time, using anomalous diffractometry. The findings show the precise atomic structure of liquid polymers when transformed, by cooling, to solid polymers. We demonstrate that there is an intermediate ordered structure, characterised by the real full image of Fourier space. This prominent state of matter, an intermediate ordered structure, is defined by a regular unit cell with a five-fold symmetry. These structural atomic studies contribute to a more detailed understanding of the properties of polymers than the traditional studies of the degree of crystallinity. PMID:25329440

Silicon impacts on structure, stability and aromaticity of C20-nSin heterofullerenes (n = 1-10): A density functional perspective

NASA Astrophysics Data System (ADS)

Koohi, M.; Soleimani Amiri, S.; Shariati, M.

2017-01-01

Density functional theory (DFT) calculations are applied to compare and contrast silicon atom substitution doped C20-nSin heterofullerene analogous with n = 1-10, at B3LYP/AUG-cc-pVTZ. Vibrational frequency analysis confirms that all studied systems are true minima. Isolating the dopants is an applicable strategy for obtaining highly doped stable heterofullerenes, since it avoids weak silicon―silicon single bonds. Comparing and contrasting the optimized geometries shows that except C11Si9 and C10Si10 species (with deformed cages of segregated analogous), all eight fullerenic cages are the complete isolated-pentagon analogous. Hence, the dopants must be completely isolated from each other by means of strong Cdbnd C double bonds. Isolable or extractable fullerene isomers must be not only thermodynamically but also stable against electronic excitations. We then predicted that these isomers must have not only relatively large heats of atomization per carbon as a criterion of thermodynamic stability but also relatively large HOMO-LUMO energy separation against electronic excitations. The calculated the highest binding energy (6.52 eV/atom), heat of atomization per carbon (3193.2 kcal mol-1), band gap (2.86 eV) and nucleus independent chemical shift at the cage center (-50.00 ppm) for C18Si2 reveals it as the most stable heterofullerene. It has Ci symmetry and contains two silicon atoms in equatorial. High charge transfer on the surfaces of our scrutinized heterofullerenes provokes further investigations on their possible application for hydrogen storage. We hope that the present study will stimulate new experiments.

Related Structure Characters and Stability of Structural Defects in a Metallic Glass

PubMed Central

Niu, Xiaofeng; Feng, Shidong; Pan, Shaopeng

2018-01-01

Structural defects were investigated by a recently proposed structural parameter, quasi-nearest atom (QNA), in a modeled Zr50Cu50 metallic glass through molecular dynamics simulations. More QNAs around an atom usually means that more defects are located near the atom. Structural analysis reveals that the spatial distribution of the numbers of QNAs displays to be clearly heterogeneous. Furthermore, QNA is closely correlated with cluster connections, especially four-atom cluster connections. Atoms with larger coordination numbers usually have less QNAs. When two atoms have the same coordination number, the atom with larger five-fold symmetry has less QNAs. The number of QNAs around an atom changes rather frequently and the change of QNAs might be correlated with the fast relaxation metallic glasses. PMID:29565298

Diagnosing Students’ conception on atomic structure using open ended questions

NASA Astrophysics Data System (ADS)

Fitriza, Z.; Gazali, F.

2018-05-01

This study aims to diagnose students’ conception on atomic structure concepts using open ended questions. For this reason, a 7 items of assay test was administered to 135 senior high school students from different schools in West Sumatera. The data were collected using a an open ended test which is covering the concept used in the topic Atomic Structure. The open ended test of students’ conceptual was developed to identify the alternative conceptions that student might have regarding the concepts in Atomic Structure, to measure the level of students’ conceptions, and the way of students’ thinking concerning the concepts. The results showed that students find difficulties about some concepts of Atomic structure such as atom, atomic model, electron configuration, period and group.The result of this study illuminated the concepts to be underlined in developing teaching and learning approach concerning the topic of Atomic Structure.

The cytotoxicity of organobismuth compounds with certain molecular structures can be diminished by replacing the bismuth atom with an antimony atom in the molecules.

PubMed

Kohri, Kumiko; Yoshida, Eiko; Yasuike, Shuji; Fujie, Tomoya; Yamamoto, Chika; Kaji, Toshiyuki

2015-06-01

Organic-inorganic hybrid molecules, which are composed of an organic structure and metal(s), are indispensable for synthetic chemical reactions; however, their toxicity has been incompletely understood. In the present study, we discovered two cytotoxic organobismuth compounds whose cytotoxicity diminished upon replacement of the intramolecular bismuth atom with an antimony atom. The intracellular accumulation of the organobismuth compounds was much higher than that of the organoantimony compounds with the corresponding organic structures. We also showed that both the organic structure and bismuth atom are required for certain organobismuth compounds to exert their cytotoxic effect, suggesting that the cytotoxicity of such a compound is a result of an interaction between the organic structure and the bismuth atom. The present data suggest that organobismuth compounds with certain molecular structures exhibit cytotoxicity via an interaction between the molecular structure and the bismuth atom, and this cytotoxicity can be diminished by replacing the bismuth atom with an antimony atom, resulting in lower intracellular accumulation.

Evaluation of Oxygen Interactions with Materials 3: Mission and induced environments

NASA Technical Reports Server (NTRS)

Koontz, Steven L.; Leger, Lubert J.; Rickman, Steven L.; Hakes, Charles L.; Bui, David T.; Hunton, Donald; Cross, Jon B.

1995-01-01

The Evaluation of Oxygen Interactions with Materials 3 (EOIM-3) flight experiment was developed to obtain benchmark atomic oxygen/material reactivity data. The experiment was conducted during Space Shuttle mission 46 (STS-46), which flew July 31 to August 7, 1992. Quantitative interpretation of the materials reactivity measurements requires a complete and accurate definition of the space environment exposure, including the thermal history of the payload, the solar ultraviolet exposure, the atomic oxygen fluence, and any spacecraft outgassing contamination effects. The thermal history of the payload was measured using twelve thermocouple sensors placed behind selected samples and on the EOIM-3 payload structure. The solar ultraviolet exposure history of the EOIM-3 payload was determined by analysis of the as-flown orbit and vehicle attitude combined with daily average solar ultraviolet and vacuum ultraviolet (UV/VUV) fluxes. The atomic oxygen fluence was assessed in three different ways. First, the O-atom fluence was calculated using a program that incorporates the MSIS-86 atmospheric model, the as-flown Space Shuttle trajectory, and solar activity parameters. Second, the oxygen atom fluence was estimated directly from Kapton film erosion. Third, ambient oxygen atom measurements were made using the quadrupole mass spectrometer on the EOIM-3 payload. Our best estimate of the oxygen atom fluence as of this writing is 2.3 +/- 0.3 x 10(exp 20) atoms/sq cm. Finally, results of post-flight X-ray photoelectron spectroscopy (XPS) surface analyses of selected samples indicate low levels of contamination on the payload surface.

Ethene adsorption and dehydrogenation on clean and oxygen precovered Ni(111) studied by high resolution x-ray photoelectron spectroscopy

NASA Astrophysics Data System (ADS)

Lorenz, M. P. A.; Fuhrmann, T.; Streber, R.; Bayer, A.; Bebensee, F.; Gotterbarm, K.; Kinne, M.; Tränkenschuh, B.; Zhu, J. F.; Papp, C.; Denecke, R.; Steinrück, H.-P.

2010-07-01

The adsorption and thermal evolution of ethene (ethylene) on clean and oxygen precovered Ni(111) was investigated with high resolution x-ray photoelectron spectroscopy using synchrotron radiation at BESSY II. The high resolution spectra allow to unequivocally identify the local environment of individual carbon atoms. Upon adsorption at 110 K, ethene adsorbs in a geometry, where the two carbon atoms within the intact ethene molecule occupy nonequivalent sites, most likely hollow and on top; this new result unambiguously solves an old puzzle concerning the adsorption geometry of ethene on Ni(111). On the oxygen precovered surface a different adsorption geometry is found with both carbon atoms occupying equivalent hollow sites. Upon heating ethene on the clean surface, we can confirm the dehydrogenation to ethine (acetylene), which adsorbs in a geometry, where both carbon atoms occupy equivalent sites. On the oxygen precovered surface dehydrogenation of ethene is completely suppressed. For the identification of the adsorbed species and the quantitative analysis the vibrational fine structure of the x-ray photoelectron spectra was analyzed in detail.

Octa­akis(4-amino­pyridine)-1κ4 N 1,2κ4 N 1-aqua-2κO-μ-carbonato-1:2κ3 O,O′:O′′-dinickel(II) dichloride penta­hydrate

PubMed Central

Fun, Hoong-Kun; Sinthiya, A; Jebas, Samuel Robinson; Ravindran Durai Nayagam, B.; Alfred Cecil Raj, S.

2008-01-01

In the title compound, [Ni2(CO3)(C5H6N2)8(H2O)]Cl2·5H2O, one of the the NiII ions is six-coordinated in a distorted octa­hedral geometry, with the equatorial plane defined by four pyridine N atoms from four amino­pyridine ligands, the axial positions being occupied by one water O and a carbonate O atom. The other NiII ion is also six-coordinated, by four other pyridine N atoms from four other amino­pyridine ligands and two carbonate O atoms to complete a distorted octa­hedral geometry. In the crystal structure, mol­ecules are linked into an infinite three-dimensional network by O—H⋯O, N—H⋯Cl, N—H⋯O, O—H⋯N, C—H⋯O, C—H⋯N and C/N—H⋯π inter­actions involving the pyridine rings. PMID:21580879

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.

A complete assignment of the vibrational spectra of 2-furoic acid based on the structures of the more stable monomer and dimer.

PubMed

Ghalla, Houcine; Issaoui, Noureddine; Castillo, María Victoria; Brandán, Silvia Antonia; Flakus, Henryk T

2014-01-01

The structural and vibrational properties of cyclic dimer of 2-furoic acid (2FA) were predicted by combining the available experimental infrared and Raman spectra in the solid phase and ab initio calculations based on density functional theory (DFT) with Pople's basis sets. The calculations show that there are two cyclic dimers for the title molecule that have been theoretically determined in the gas phase, and that only one of them, cis conformer, is present in the solid phase. The complete assignment of the 66 normal vibrational modes for the cis cyclic dimer was performed using the Pulay's Scaled Quantum Mechanics Force Field (SQMFF) methodology. Four strong bands in the infrared spectrum at 1583, 1427, 1126 and 887 cm(-1) and the group of bands in the Raman spectrum at 1464, 1452, 1147, 1030, 885, 873, 848, 715 and 590 cm(-1) are characteristic of the dimeric form of 2FA in the solid phase. In this work, the calculated structural and vibrational properties of both dimeric species were analyzed and compared between them. In addition, three types of atomic charges, bond orders, possible charge transfer, topological properties of the furan rings, Natural Bond Orbital (NBO) and Atoms in Molecules (AIM) theory calculations were employed to study the stabilities and intermolecular interactions of the both dimers of 2FA. Copyright © 2013 Elsevier B.V. All rights reserved.

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

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

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

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

AFLOW-SYM: platform for the complete, automatic and self-consistent symmetry analysis of crystals.

PubMed

Hicks, David; Oses, Corey; Gossett, Eric; Gomez, Geena; Taylor, Richard H; Toher, Cormac; Mehl, Michael J; Levy, Ohad; Curtarolo, Stefano

2018-05-01

Determination of the symmetry profile of structures is a persistent challenge in materials science. Results often vary amongst standard packages, hindering autonomous materials development by requiring continuous user attention and educated guesses. This article presents a robust procedure for evaluating the complete suite of symmetry properties, featuring various representations for the point, factor and space groups, site symmetries and Wyckoff positions. The protocol determines a system-specific mapping tolerance that yields symmetry operations entirely commensurate with fundamental crystallographic principles. The self-consistent tolerance characterizes the effective spatial resolution of the reported atomic positions. The approach is compared with the most used programs and is successfully validated against the space-group information provided for over 54 000 entries in the Inorganic Crystal Structure Database (ICSD). Subsequently, a complete symmetry analysis is applied to all 1.7+ million entries of the AFLOW data repository. The AFLOW-SYM package has been implemented in, and made available for, public use through the automated ab initio framework AFLOW.

On the clathrate form of elemental silicon, Si 136: preparation and characterisation of Na xSi 136 ( x→0)

NASA Astrophysics Data System (ADS)

Ammar, Abdelaziz; Cros, Christian; Pouchard, Michel; Jaussaud, Nicolas; Bassat, Jean-Marc; Villeneuve, Gérard; Duttine, Mathieu; Ménétrier, Michel; Reny, Edouard

2004-05-01

The clathrate form of silicon, Si 136 (otherwise known as Si 34), having a residual sodium content as low as 35 ppm (i.e., x˜0.0058 in Na xSi 136), has been prepared by thermal decomposition of NaSi under high vacuum, followed by several other treatments under vacuum, and completed by repeated reactions with iodine. The residual amount of sodium has been determined by a combination of analytic and spectroscopic methods involving XRD, electron probe microanalysis, atomic absorption, NMR and EPR. This latter technique proved to be very appropriate to the characterisation of very diluted sodium atoms in such clathrate structure and to the quantitative determination of its residual concentration.

Measurement of complete and continuous Wigner functions for discrete atomic systems

NASA Astrophysics Data System (ADS)

Tian, Yali; Wang, Zhihui; Zhang, Pengfei; Li, Gang; Li, Jie; Zhang, Tiancai

2018-01-01

We measure complete and continuous Wigner functions of a two-level cesium atom in both a nearly pure state and highly mixed states. We apply the method [T. Tilma et al., Phys. Rev. Lett. 117, 180401 (2016), 10.1103/PhysRevLett.117.180401] of strictly constructing continuous Wigner functions for qubit or spin systems. We find that the Wigner function of all pure states of a qubit has negative regions and the negativity completely vanishes when the purity of an arbitrary mixed state is less than 2/3 . We experimentally demonstrate these findings using a single cesium atom confined in an optical dipole trap, which undergoes a nearly pure dephasing process. Our method can be applied straightforwardly to multi-atom systems for measuring the Wigner function of their collective spin state.

Physico-chemical study of some areas of fundamental significance to biophysics. Annual report, 1975--1976. [Chemistry Dept. , Louisiana State University, Baton Rouge

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

McGlynn, S.P.

1976-05-15

Lists of titles published, symposia attended, laboratory guests, departing personnel, and equipment purchased are presented in the first part of this report. It is to be emphasized that completed work already published is mentioned only by title. Reports are provided for research recently completed or in progress in the following areas: Rydberg spectroscopy, intermediate-coupling model for linear molecules, atomic correlation lines, electronic structure of dicarbonyl compounds, absorption and emission characteristics of highly polar aromatics, valence-bond description of metal--anion interaction, and matrix elements of mono-excited Slater determinants constructed from axial spin-orbitals. (RWR)

A predictive structural model for bulk metallic glasses

PubMed Central

Laws, K. J.; Miracle, D. B.; Ferry, M.

2015-01-01

Great progress has been made in understanding the atomic structure of metallic glasses, but there is still no clear connection between atomic structure and glass-forming ability. Here we give new insights into perhaps the most important question in the field of amorphous metals: how can glass-forming ability be predicted from atomic structure? We give a new approach to modelling metallic glass atomic structures by solving three long-standing problems: we discover a new family of structural defects that discourage glass formation; we impose efficient local packing around all atoms simultaneously; and we enforce structural self-consistency. Fewer than a dozen binary structures satisfy these constraints, but extra degrees of freedom in structures with three or more different atom sizes significantly expand the number of relatively stable, ‘bulk' metallic glasses. The present work gives a new approach towards achieving the long-sought goal of a predictive capability for bulk metallic glasses. PMID:26370667

Cation-Poor Complex Metallic Alloys in Ba(Eu)-Au-Al(Ga) Systems: Identifying the Keys that Control Structural Arrangements and Atom Distributions at the Atomic Level.

PubMed

Smetana, Volodymyr; Steinberg, Simon; Mudryk, Yaroslav; Pecharsky, Vitalij; Miller, Gordon J; Mudring, Anja-Verena

2015-11-02

Four complex intermetallic compounds BaAu(6±x)Ga(6±y) (x = 1, y = 0.9) (I), BaAu(6±x)Al(6±y) (x = 0.9, y = 0.6) (II), EuAu6.2Ga5.8 (III), and EuAu6.1Al5.9 (IV) have been synthesized, and their structures and homogeneity ranges have been determined by single crystal and powder X-ray diffraction. Whereas I and II originate from the NaZn13-type structure (cF104-112, Fm3̅c), III (tP52, P4/nbm) is derived from the tetragonal Ce2Ni17Si9-type, and IV (oP104, Pbcm) crystallizes in a new orthorhombic structure type. Both I and II feature formally anionic networks with completely mixed site occupation by Au and triel (Tr = Al, Ga) atoms, while a successive decrease of local symmetry from the parental structures of I and II to III and, ultimately, to IV correlates with increasing separation of Au and Tr on individual crystallographic sites. Density functional theory-based calculations were employed to determine the crystallographic site preferences of Au and the respective triel element to elucidate reasons for the atom distribution ("coloring scheme"). Chemical bonding analyses for two different "EuAu6Tr6" models reveal maximization of the number of heteroatomic Au-Tr bonds as the driving force for atom organization. The Fermi levels fall in broad pseudogaps for both models allowing some electronic flexibility. Spin-polarized band structure calculations on the "EuAu6Tr6" models hint to singlet ground states for europium and long-range magnetic coupling for both EuAu6.2Ga5.8 (III) and EuAu6.1Al5.9 (IV). This is substantiated by experimental evidence because both compounds show nearly identical magnetic behavior with ferromagnetic transitions at TC = 6 K and net magnetic moments of 7.35 μB/f.u. at 2 K. The effective moments of 8.3 μB/f.u., determined from Curie-Weiss fits, point to divalent oxidation states for europium in both III and IV.

Cation-poor complex metallic alloys in Ba(Eu)–Au–Al(Ga) systems: Identifying the keys that control structural arrangements and atom distributions at the atomic level

DOE PAGES

Smetana, Volodymyr; Steinberg, Simon; Mudryk, Yaroslav; ...

2015-10-19

Four complex intermetallic compounds BaAu 6±xGa 6±y (x = 1, y = 0.9) (I), BaAu 6±xAl 6±y (x = 0.9, y = 0.6) (II), EuAu 6.2Ga 5.8 (III), and EuAu 6.1Al 5.9 (IV) have been synthesized, and their structures and homogeneity ranges have been determined by single crystal and powder X-ray diffraction. Whereas I and II originate from the NaZn 13-type structure (cF104–112, Fm3C), III (tP52, P4/nbm) is derived from the tetragonal Ce 2Ni 17Si 9-type, and IV (oP104, Pbcm) crystallizes in a new orthorhombic structure type. Both I and II feature formally anionic networks with completely mixed site occupationmore » by Au and triel (Tr = Al, Ga) atoms, while a successive decrease of local symmetry from the parental structures of I and II to III and, ultimately, to IV correlates with increasing separation of Au and Tr on individual crystallographic sites. Density functional theory-based calculations were employed to determine the crystallographic site preferences of Au and the respective triel element to elucidate reasons for the atom distribution (“coloring scheme”). Chemical bonding analyses for two different “EuAu 6Tr 6” models reveal maximization of the number of heteroatomic Au–Tr bonds as the driving force for atom organization. The Fermi levels fall in broad pseudogaps for both models allowing some electronic flexibility. Spin-polarized band structure calculations on the “EuAu 6Tr 6” models hint to singlet ground states for europium and long-range magnetic coupling for both EuAu 6.2Ga 5.8 (III) and EuAu 6.1Al 5.9 (IV). This is substantiated by experimental evidence because both compounds show nearly identical magnetic behavior with ferromagnetic transitions at T C = 6 K and net magnetic moments of 7.35 μB/f.u. at 2 K. As a result, the effective moments of 8.3 μB/f.u., determined from Curie–Weiss fits, point to divalent oxidation states for europium in both III and IV.« less

Spontaneous resolution of binary copper(II) complexes with racemic dipeptides: crystal structures of glycyl-L-alpha-amino-n-butyrato copper(II) monohydrate, glycyl-D-valinato copper(II) hemihydrate, and glycyl-L-valinato copper(II) hemihydrate.

PubMed

Inomata, Yoshie; Yamaguchi, Takeshi; Tomita, Airi; Yamada, Dai; Howell, F Scott

2005-08-01

Copper(II) complexes with glycyl-DL-alpha-amino-n-butyric acid (H2gly-DL-but), glycyl-DL-valine (H2gly-DL-val), glycyl-DL-norleucine (H2gly-DL-norleu), glycyl-DL-threonine (H2gly-DL-thr), glycyl-DL-serine (H2gly-DL-ser), glycyl-DL-phenylalanine (H2gly-DL-phe), and glycyl-L-valine (H2gly-L-val), have been prepared and characterized by IR, powder diffuse reflection, CD and ORD spectra, and magnetic susceptibility measurements, and by single-crystal X-ray diffraction. The crystal structures of the copper complex with H2gly-DL-but, the copper complex with H2gly-DL-val, and [Cu(gly-L-val)]n.0.5nH2O have been determined by a single-crystal X-ray diffraction method. As for the structure of the copper complex with H2gly-DL-but, the configuration around the asymmetric carbon atom is similar to that of [Cu(gly-L-val)]n.0.5nH2O. Therefore it is concluded that the copper complex with H2gly-DL-but is [Cu(gly-L-but)]n.nH2O. On the contrary, as for the structure of the copper complex with H2gly-DL-val, the configuration around the asymmetric carbon atom is different from that of [Cu(gly-L-val)]n.0.5nH2O. Therefore it is concluded that the copper complex with H2gly-dl-val is [Cu(gly-D-val)]n.0.5nH2O. So during the crystallization of the copper(II) complexes with H2gly-DL-but and H2gly-DL-val, spontaneous resolution has been observed; the four complexes have separated as [Cu(gly-D-but)]n.nH2O, [Cu(gly-L-but)]n.nH2O, [Cu(gly-D-val)]n.0.5nH2O, and [Cu(gly-L-val)]n.0.5nH2O, respectively. [Cu(gly-L-but)]n.nH2O is orthorhombic with the space group P2(1)2(1)2(1). [Cu(gly-D-val)]n.0.5nH2O and [Cu(gly-L-val)]n.0.5nH2O are monoclinic with the space group C2. In these complexes, the copper atom is in a square-pyramidal geometry, ligated by a peptide nitrogen atom, an amino nitrogen atom, a carboxyl oxygen atom, and a carboxyl oxygen atom and a peptide oxygen atom from neighboring molecules. So these complexes consist of a two-dimensional polymer chain bridged by a carboxyl oxygen atom and a peptide oxygen atom from neighboring molecules. The axial oxygen atom is located above the basal plane and the side chain of an amino acid is located below it. These polymer chains consist of only one or the other type of optical isomers; no racemic dipeptides are found. Therefore, spontaneous resolution has been observed in the crystallization of copper(II) complexes with H2gly-DL-but and H2gly-DL-val. The crystal structure of [Cu(gly-D-val)]n.0.5nH2O agrees almost completely with that of [Cu(gly-L-val)]n.0.5nH2O, except for the configuration around the asymmetric carbon atom.

Holographic Reconstruction of Photoelectron Diffraction and Its Circular Dichroism for Local Structure Probing

NASA Astrophysics Data System (ADS)

Matsui, Fumihiko; Matsushita, Tomohiro; Daimon, Hiroshi

2018-06-01

The local atomic structure around a specific element atom can be recorded as a photoelectron diffraction pattern. Forward focusing peaks and diffraction rings around them indicate the directions and distances from the photoelectron emitting atom to the surrounding atoms. The state-of-the-art holography reconstruction algorithm enables us to image the local atomic arrangement around the excited atom in a real space. By using circularly polarized light as an excitation source, the angular momentum transfer from the light to the photoelectron induces parallax shifts in these diffraction patterns. As a result, stereographic images of atomic arrangements are obtained. These diffraction patterns can be used as atomic-site-resolved probes for local electronic structure investigation in combination with spectroscopy techniques. Direct three-dimensional atomic structure visualization and site-specific electronic property analysis methods are reviewed. Furthermore, circular dichroism was also found in valence photoelectron and Auger electron diffraction patterns. The investigation of these new phenomena provides hints for the development of new techniques for local structure probing.

Microwave spectrum and structure of bicyclo /1.1.1/ pentanone and comparison with several theoretical structures

NASA Technical Reports Server (NTRS)

Mcrae, Glenn A.; Cohen, Edward A.; Sponsler, Michael B.; Dougherty, Dennis A.

1986-01-01

The microwave spectra of five isotopic species of bicyclo (1.1.1) pentanone have been investigated. The rotational constants along with various centrifugal distortion constants for each species have been determined. From the rotational constants, a complete r(s) structure has been determined for the heavy atoms. Analysis of Stark effect measurements has shown the dipole moment to be along the a principal inertial axis with a magnitude of 3.164 (5) D. These results are compared with those obtained by four current theoretical methods: molecular mechanics (MM2), MNDO, and Hartree-Fock ab initio theory with STO-3G and 3-21G basis sets.

The GSAM software: A global search algorithm of minima exploration for the investigation of low lying isomers of clusters

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

Marchal, Rémi; Carbonnière, Philippe; Pouchan, Claude

2015-01-22

The study of atomic clusters has become an increasingly active area of research in the recent years because of the fundamental interest in studying a completely new area that can bridge the gap between atomic and solid state physics. Due to their specific properties, such compounds are of great interest in the field of nanotechnology [1,2]. Here, we would present our GSAM algorithm based on a DFT exploration of the PES to find the low lying isomers of such compounds. This algorithm includes the generation of an intial set of structure from which the most relevant are selected. Moreover, anmore » optimization process, called raking optimization, able to discard step by step all the non physically reasonnable configurations have been implemented to reduce the computational cost of this algorithm. Structural properties of Ga{sub n}Asm clusters will be presented as an illustration of the method.« less

Proposed software system for atomic-structure calculation

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

Fischer, C.F.

1981-07-01

Atomic structure calculations are understood well enough that, at a routine level, an atomic structure software package can be developed. At the Atomic Physics Conference in Riga, 1978 L.V. Chernysheva and M.Y. Amusia of Leningrad University, presented a paper on Software for Atomic Calculations. Their system, called ATOM is based on the Hartree-Fock approximation and correlation is included within the framework of RPAE. Energy level calculations, transition probabilities, photo-ionization cross-sections, electron scattering cross-sections are some of the physical properties that can be evaluated by their system. The MCHF method, together with CI techniques and the Breit-Pauli approximation also provides amore » sound theoretical basis for atomic structure calculations.« less

A First Principles Study of H2 Adsorption on LaNiO3(001) Surfaces

PubMed Central

Pan, Changchang; Chen, Yuhong; Wu, Na; Zhang, Meiling; Yuan, Lihua; Zhang, Cairong

2017-01-01

The adsorption of H2 on LaNiO3 was investigated using density functional theory (DFT) calculations. The adsorption sites, adsorption energy, and electronic structure of LaNiO3(001)/H2 systems were calculated and indicated through the calculated surface energy that the (001) surface was the most stable surface. By looking at optimized structure, adsorption energy and dissociation energy, we found that there were three types of adsorption on the surface. First, H2 molecules completely dissociate and then tend to bind with the O atoms, forming two –OH bonds. Second, H2 molecules partially dissociate with the H atoms bonding to the same O atom to form one H2O molecule. These two types are chemical adsorption modes; however, the physical adsorption of H2 molecules can also occur. When analyzing the electron structure of the H2O molecule formed by the partial dissociation of the H2 molecule and the surface O atom, we found that the interaction between H2O and the (001) surface was weaker, thus, H2O was easier to separate from the surface to create an O vacancy. On the (001) surface, a supercell was constructed to accurately study the most stable adsorption site. The results from analyses of the charge population; electron localization function; and density of the states indicated that the dissociated H and O atoms form a typical covalent bond and that the interaction between the H2 molecule and surface is mainly due to the overlap-hybridization among the H 1s, O 2s, and O 2p states. Therefore, the conductivity of LaNiO3(001)/H2 is stronger after adsorption and furthermore, the conductivity of the LaNiO3 surface is better than that of the LaFeO3 surface. PMID:28772396

Ion energy/momentum effects during ion assisted growth of niobium nitride films

NASA Astrophysics Data System (ADS)

Klingenberg, Melissa L.

The research described herein was performed to better understand and discern ion energy vs. ion momentum effects during ion beam assisted (IBAD) film growth and their effects on residual stress, crystalline structure, morphology, and composition, which influence film tribological properties. NbxN y was chosen for this research because it is a refractory material that can possess a large number of crystalline structures, and it has been found to have good tribological properties. To separate the effects of momentum transfer per arriving atom (p/a), which considers bombarding species mass, energy, and ion-to-atom transport ratio, from those of energy deposition per arriving atom (E/a), a mass independent parameter, different inert ion beams (krypton, argon, and neon) were used to create a matrix of coatings formed using similar energy deposition, but different momentum transfer and vice versa. Deposition was conducted in a research-scale IBAD system using electron beam evaporation, a radio frequency ion source, and a neutral nitrogen gas backfill. Films were characterized using x-ray diffraction, atomic force microscopy, Rutherford backscattering spectrometry, and residual stress analysis. Direct and quantifiable effects of bombardment were observed; however, energy deposition and momentum transfer effects could not be completely separated, confirming that thin film processes are complex. Complexities arose from ion-specific interactions (ion size, recoil energy, per cent reflected neutrals, Penning ionization, etc.) and chemistry effects that are not considered by the simple models. Overall, it can be stated that bombardment promoted nitride formation, nanocrystallinity, and compressive stress formation; influenced morphology (which influenced post-deposition oxygen uptake) and stress evolution; increased lattice parameter; modified crystalline phase and texture; and led to inert gas incorporation. High stress levels correlated strongly with material disorder and closed-structured morphologies.

Polarizability of Rydberg atoms and the dominant long-range interactions

NASA Astrophysics Data System (ADS)

Hahn, Yukap

2000-10-01

The dominant long-range interaction of an alkali-metal atom with charged particles at low energies is given for large separation R by the dispersive potential W~=-αd/R4 in terms of the dipole polarizability αd. For atoms prepared initially in Rydberg states of quantum numbers (n, l), the potential assumes a more complicated form due to the complete or near degeneracy of the n manifold. Contributions to the polarizability are treated in two parts, (a) one for the nondegenerate states and (b) the other for the degenerate or near degenerate cases. It is shown that α~(b)d for case (b) is in general R dependent, and in the limit of complete degeneracy, diverges as R2. That is, for a small energy gap Δ between a pair of nearly degenerate states which are dipole coupled, the dispersion potential W(b)~=D/R2 for RRx, where D is the dipole moment, Rx=[2\\|D/Δ\\|]1/2, and α(b)d~=D2/Δ. They may also compete with a 1/R3 potential for Rydberg atoms with l>0. The total αd can be very large in magnitude for small Δ and even assume negative values, but the corresponding Rx also increases as Δ decreases. The validity region in R of the R-4 behavior of the potential recedes to larger R as the polarizability grows. A general formula for αd is given, taking into account the effects of fine-structure splitting, the Lamb shift, and quantum defects.

Smallest Nanoelectronic with Atomic Devices with Precise Structures

NASA Technical Reports Server (NTRS)

Yamada, Toshishige

2000-01-01

Since its invention in 1948, the transistor has revolutionized our everyday life - transistor radios and TV's appeared in the early 1960s, personal computers came into widespread use in the mid-1980s, and cellular phones, laptops, and palm-sized organizers dominated the 1990s. The electronics revolution is based upon transistor miniaturization; smaller transistors are faster, and denser circuitry has more functionality. Transistors in current generation chips are 0.25 micron or 250 nanometers in size, and the electronics industry has completed development of 0.18 micron transistors which will enter production within the next few years. Industry researchers are now working to reduce transistor size down to 0.13 micron - a thousandth of the width of a human hair. However, studies indicate that the miniaturization of silicon transistors will soon reach its limit. For further progress in microelectronics, scientists have turned to nanotechnology to advance the science. Rather than continuing to miniaturize transistors to a point where they become unreliable, nanotechnology offers the new approach of building devices on the atomic scale [see sidebar]. One vision for the next generation of miniature electronics is atomic chain electronics, where devices are composed of atoms aligned on top of a substrate surface in a regular pattern. The Atomic Chain Electronics Project (ACEP) - part of the Semiconductor Device Modeling and Nanotechnology group, Integrated Product Team at the NAS Facility has been developing the theory of understanding atomic chain devices, and the author's patent for atomic chain electronics is now pending.

Crystal Structure and Magnetic Properties of New Cubic Quaternary Compounds RT2Sn2Zn18 (R = La, Ce, Pr, and Nd, and T = Co and Fe)

NASA Astrophysics Data System (ADS)

Isikawa, Yosikazu; Mizushima, Toshio; Ejiri, Jun-ichi; Kitayama, Shiori; Kumagai, Keigou; Kuwai, Tomohiko; Bordet, Pierre; Lejay, Pascal

2015-07-01

The new cubic quaternary intermetallic compounds RT2Sn2Zn18 (R = La, Ce, Pr, and Nd, and T = Co and Fe) were synthesized by the mixture-metal flux method using Zn and Sn. The crystal structure was investigated by powder X-ray diffraction and with a four-circle X-ray diffractometer using single crystals. The space group of the compounds is Fdbar{3}m (No. 227). The rare-earth atom is at the cubic site which is the center of a cage composed of Zn and Sn atoms. The crystal structure is the same as the CeCr2Al20-type crystal structure except the atoms at the 16c site, i.e., the Zn atoms at the 16c site are completely replaced by Sn atoms, indicating that the compounds are crystallographically new ordered quaternary compounds. The lattice parameter a and the physical properties of the magnetic susceptibility χ, the magnetization M, and the specific heat C of these cubic caged compounds were investigated. LaCo2Sn2Zn18 and LaFe2Sn2Zn18 are enhanced Pauli paramagnets that originate from the Co and Fe itinerant 3d electrons. CeCo2Sn2Zn18 and CeFe2Sn2Zn18 are also enhanced Pauli paramagnets that originate from both the 3d electrons and Ce 4f electrons. PrCo2Sn2Zn18 and PrFe2Sn2Zn18 are nonmagnetic materials with huge values of C divided by temperature, which indicates that the ground state of Pr ions is a non-Kramers' doublet. NdCo2Sn2Zn18 and NdFe2Sn2Zn18 are magnetic materials with the Néel temperatures of 1.0 and 3.8 K, respectively. All eight compounds have large magnetic moments of Co/Fe in the paramagnetic temperature region, and thus their magnetic moments are inferred to be magnetically frustrating owing to the pyrochlore lattice in the low-temperature region.

Two-dimensional nanowires on homoepitaxial interfaces: Atomic-scale mechanism of breakdown and disintegration

NASA Astrophysics Data System (ADS)

Michailov, Michail; Ranguelov, Bogdan

2018-03-01

We present a model for hole-mediated spontaneous breakdown of ahomoepitaxial two-dimensional (2D) flat nanowire based exclusively on random, thermally-activated motion of atoms. The model suggests a consecutive three-step mechanism driving the rupture and complete disintegration of the nanowire on a crystalline surface. The breakdown scenario includes: (i) local narrowing of a part of the stripe to a monatomic chain, (ii) formation of a recoverable single vacancy or a 2D vacancy cluster that causes temporary nanowire rupture, (iii) formation of a non-recoverable 2D hole leading to permanent nanowire breakdown. These successive events in the temporal evolution of the nanowire morphology bring the nanowire stripe into an irreversible unstable state, leading to a dramatic change in its peculiar physical properties and conductivity. The atomistic simulations also reveal a strong increase of the nanowire lifetime with an enlargement of its width and open up a way for a fine atomic-scale control of the nanowire lifetime and structural, morphological and thermodynamic stability.

Tunable Spin-orbit Coupling and Quantum Phase Transition in a Trapped Bose-Einstein Condensate

PubMed Central

Zhang, Yongping; Chen, Gang; Zhang, Chuanwei

2013-01-01

Spin-orbit coupling (SOC), the intrinsic interaction between a particle spin and its motion, is responsible for various important phenomena, ranging from atomic fine structure to topological condensed matter physics. The recent experimental breakthrough on the realization of SOC for ultra-cold atoms provides a completely new platform for exploring spin-orbit coupled superfluid physics. However, the SOC strength in the experiment is not tunable. In this report, we propose a scheme for tuning the SOC strength through a fast and coherent modulation of the laser intensities. We show that the many-body interaction between atoms, together with the tunable SOC, can drive a quantum phase transition (QPT) from spin-balanced to spin-polarized ground states in a harmonic trapped Bose-Einstein condensate (BEC), which resembles the long-sought Dicke QPT. We characterize the QPT using the periods of collective oscillations of the BEC, which show pronounced peaks and damping around the quantum critical point. PMID:23727689

Hexagonal OsB 2 reduction upon heating in H 2 containing environment

DOE PAGES

Xie, Zhilin; Blair, Richard G.; Orlovskaya, Nina; ...

2014-10-23

The stability of hexagonal ReB 2 type OsB 2 powder upon heating under reforming gas was investigated. Pure Os metal particles were detected by powder X-ray diffraction starting at 375⁰ C and complete transformation of OsB 2 to metallic Os was observed at 725⁰ C. The mechanisms of precipitation of metallic Os is proposed and changes in the lattice parameters of OsB 2 upon heating are analysed in terms of the presence of oxygen or water vapour in the heating chamber. Previous studies suggested that Os atoms possess (0) valence, while B atoms possess both (+3) and ( 3) valencesmore » in the alternating boron/osmium sheet structure of hexagonal (P63/mmc, No. 194) OsB 2; if controllable method for Os removal from the lattice could be found, the opportunity would arise to form two-dimensional (2D) layers consisting of pure B atoms.« less

Precision muon physics

NASA Astrophysics Data System (ADS)

Gorringe, T. P.; Hertzog, D. W.

2015-09-01

The muon is playing a unique role in sub-atomic physics. Studies of muon decay both determine the overall strength and establish the chiral structure of weak interactions, as well as setting extraordinary limits on charged-lepton-flavor-violating processes. Measurements of the muon's anomalous magnetic moment offer singular sensitivity to the completeness of the standard model and the predictions of many speculative theories. Spectroscopy of muonium and muonic atoms gives unmatched determinations of fundamental quantities including the magnetic moment ratio μμ /μp, lepton mass ratio mμ /me, and proton charge radius rp. Also, muon capture experiments are exploring elusive features of weak interactions involving nucleons and nuclei. We will review the experimental landscape of contemporary high-precision and high-sensitivity experiments with muons. One focus is the novel methods and ingenious techniques that achieve such precision and sensitivity in recent, present, and planned experiments. Another focus is the uncommonly broad and topical range of questions in atomic, nuclear and particle physics that such experiments explore.

Eigenstates and dynamics of Hooke's atom: Exact results and path integral simulations

NASA Astrophysics Data System (ADS)

Gholizadehkalkhoran, Hossein; Ruokosenmäki, Ilkka; Rantala, Tapio T.

2018-05-01

The system of two interacting electrons in one-dimensional harmonic potential or Hooke's atom is considered, again. On one hand, it appears as a model for quantum dots in a strong confinement regime, and on the other hand, it provides us with a hard test bench for new methods with the "space splitting" arising from the one-dimensional Coulomb potential. Here, we complete the numerous previous studies of the ground state of Hooke's atom by including the excited states and dynamics, not considered earlier. With the perturbation theory, we reach essentially exact eigenstate energies and wave functions for the strong confinement regime as novel results. We also consider external perturbation induced quantum dynamics in a simple separable case. Finally, we test our novel numerical approach based on real-time path integrals (RTPIs) in reproducing the above. The RTPI turns out to be a straightforward approach with exact account of electronic correlations for solving the eigenstates and dynamics without the conventional restrictions of electronic structure methods.

catena-Poly[[bis­(4-carboxy­cyclo­hexane­carboxyl­ato-κ2 O 1,O 1′)cadmium(II)]-μ-1,4-bis­(imidazol-1-ylmeth­yl)benzene-κ2 N 3:N 3′

PubMed Central

Li, Bing-Bing; Xiao, Bo

2009-01-01

In the title coordination polymer, [Cd(C8H11O4)2(C14H14N4)]n, the Cd atom (site symmetry 2) is six-coordin­ated by two O,O′-bidentate 4-carboxy­cyclo­hexa­necarboxyl­ate (Hchdc) ligands and two N atoms from two different 1,4-bis­(imidazol-1-ylmeth­yl)benzene (1,4-bix) mol­ecules in a very distorted cis-CdN2O4 octa­hedral environment. The 1,4-bix mol­ecules act as bridging ligands that bind two CdII atoms, thus forming an infinite chain propagating in [100], which is decorated by the Hchdc anions. The structure is completed by O—H⋯O hydrogen bonds, which link the chains together. PMID:21582692

Spin-orbit coupling manipulating composite topological spin textures in atomic-molecular Bose-Einstein condensates

NASA Astrophysics Data System (ADS)

Liu, Chao-Fei; Juzeliūnas, Gediminas; Liu, W. M.

2017-02-01

Atomic-molecular Bose-Einstein condensates (BECs) offer brand new opportunities to revolutionize quantum gases and probe the variation of fundamental constants with unprecedented sensitivity. The recent realization of spin-orbit coupling (SOC) in BECs provides a new platform for exploring completely new phenomena unrealizable elsewhere. In this study, we find a way of creating a Rashba-Dresselhaus SOC in atomic-molecular BECs by combining the spin-dependent photoassociation and Raman coupling, which can control the formation and distribution of a different type of topological excitation—carbon-dioxide-like skyrmion. This skyrmion is formed by two half-skyrmions of molecular BECs coupling with one skyrmion of atomic BECs, where the two half-skyrmions locate at both sides of one skyrmion. Carbon-dioxide-like skyrmion can be detected by measuring the vortices structures using the time-of-flight absorption imaging technique in real experiments. Furthermore, we find that SOC can effectively change the occurrence of the Chern number in k space, which causes the creation of topological spin textures from some separated carbon-dioxide-like monomers each with topological charge -2 to a polymer chain of the skyrmions. This work helps in creating dual SOC atomic-molecular BECs and opens avenues to manipulate topological excitations.

Crystal Structure of Faradaurate-279: Au279(SPh-tBu)84 Plasmonic Nanocrystal Molecules.

PubMed

Sakthivel, Naga Arjun; Theivendran, Shevanuja; Ganeshraj, Vigneshraja; Oliver, Allen G; Dass, Amala

2017-11-01

We report the discovery of an unprecedentedly large, 2.2 nm diameter, thiolate protected gold nanocrystal characterized by single crystal X-ray crystallography (sc-XRD), Au 279 (SPh-tBu) 84 named Faradaurate-279 (F-279) in honor of Michael Faraday's (1857) pioneering work on nanoparticles. F-279 nanocrystal has a core-shell structure containing a truncated octahedral core with bulk face-centered cubic-like arrangement, yet a nanomolecule with a precise number of metal atoms and thiolate ligands. The Au 279 S 84 geometry was established from a low-temperature 120 K sc-XRD study at 0.90 Å resolution. The atom counts in core-shell structure of Au 279 follows the mathematical formula for magic number shells: Au@Au 12 @Au 42 @Au 92 @Au 54 , which is further protected by a final shell of Au 48 . Au 249 core is protected by three types of staple motifs, namely: 30 bridging, 18 monomeric, and 6 dimeric staple motifs. Despite the presence of such diverse staple motifs, Au 279 S 84 structure has a chiral pseudo-D 3 symmetry. The core-shell structure can be viewed as nested, concentric polyhedra, containing a total of five forms of Archimedean solids. A comparison between the Au 279 and Au 309 cuboctahedral superatom model in shell-wise growth is illustrated. F-279 can be synthesized and isolated in high purity in milligram quantities using size exclusion chromatography, as evidenced by mass spectrometry. Electrospray ionization-mass spectrometry independently verifies the X-ray diffraction study based heavy atoms formula, Au 279 S 84 , and establishes the molecular formula with the complete ligands, namely, Au 279 (SPh-tBu) 84 . It is also the smallest gold nanocrystal to exhibit metallic behavior, with a surface plasmon resonance band around 510 nm.

Complex vibrations in arsenide skutterudites and oxyskutterudites

NASA Astrophysics Data System (ADS)

Bridges, F.; Car, B.; Sutton, L.; Hoffman-Stapleton, M.; Keiber, T.; Baumbach, R. E.; Maple, M. B.; Henkie, Z.; Wawryk, R.

2015-01-01

The local structure of two skutterudite families—Ce M4As12 (M =Fe , Ru, Os) and L n Cu3Ru4O12 (L n =La , Pr, and Nd)—have been studied using the extended x-ray absorption fine structure (EXAFS) technique with a focus on the lattice vibrations about the rare-earth "rattler atoms" and the extent to which these vibrations can be considered local modes, with the rattler vibrating inside a nearly rigid cage. X-ray absorption data at all the metal edges were collected over a temperature range of 4 to 300 K and analyzed using standard procedures. The pair distances from EXAFS results agree quite well with the average structure obtained from diffraction. The cage structure is formed by the M and As atoms in Ce M4As12 and by Cu, O, and Ru atoms in L n Cu3Ru4O12 . Although some of the bonds within the cage are quite stiff (correlated Debye temperatures, θcD, are ˜500 K for Ce M4As12 and above 800 K for L n Cu3Ru4O12 ), we show that the structure is not completely rigid. For the rattler atom the nearest-neighbor pairs have a relatively low Einstein temperature, θE:˜100 - 120 K for Ce-As and ˜130 K for L n -O . Surprisingly, the behaviors of the second-neighbor pairs are quite different: for Ce M4As12 the second-neighbor pairs (Ce -M ) have a weaker bond while for L n Cu3Ru4O12 the L n -Ru second-neighbor pair has a stiffer effective spring constant than the first-neighbor pair. In addition, we show that the As4 or CuO4 rings are relatively rigid units and that their vibrations are anisotropic within these cubic structures, with stiff restoring forces perpendicular to the rings and much weaker restoring forces in directions parallel to the rings. Consequently vibrations of the rings may also act as "rattlers" and help suppress thermal conductivity. In general neither the rigid-cage approximation nor the simple reduced-mass approximation are sufficient for describing rattler behavior.

Dopant distributions in n-MOSFET structure observed by atom probe tomography.

PubMed

Inoue, K; Yano, F; Nishida, A; Takamizawa, H; Tsunomura, T; Nagai, Y; Hasegawa, M

2009-11-01

The dopant distributions in an n-type metal-oxide-semiconductor field effect transistor (MOSFET) structure were analyzed by atom probe tomography. The dopant distributions of As, P, and B atoms in a MOSFET structure (gate, gate oxide, channel, source/drain extension, and halo) were obtained. P atoms were segregated at the interface between the poly-Si gate and the gate oxide, and on the grain boundaries of the poly-Si gate, which had an elongated grain structure along the gate height direction. The concentration of B atoms was enriched near the edge of the source/drain extension where the As atoms were implanted.

First-principles study of structure, electronic properties and stability of tungsten adsorption on TiC(111) surface with disordered vacancies

NASA Astrophysics Data System (ADS)

Ilyasov, Victor V.; Pham, Khang D.; Zhdanova, Tatiana P.; Phuc, Huynh V.; Hieu, Nguyen N.; Nguyen, Chuong V.

2017-12-01

In this paper, we systematically investigate the atomic structure, electronic and thermodynamic properties of adsorbed W atoms on the polar Ti-terminated TixCy (111) surface with different configurations of adsorptions using first principle calculations. The bond length, adsorption energy, and formation energy for different reconstructions of the atomic structure of the W/TixCy (111) systems were established. The effect of the tungsten coverage on the electronic structure and the adsorption mechanism of tungsten atom on the TixCy (111) are also investigated. We also suggest the possible mechanisms of W nucleation on the TixCy (111) surface. The effective charges on W atoms and nearest-neighbor atoms in the examined reconstructions were identified. Additionally, we have established the charge transfer from titanium atom to tungsten and carbon atoms which determine by the reconstruction of the local atomic and electronic structures. Our calculations showed that the charge transfer correlates with the electronegativity of tungsten and nearest-neighbor atoms. We also determined the effective charge per atom of titanium, carbon atoms, and neighboring adsorbed tungsten atom in different binding configurations. We found that, with reduction of the lattice symmetry associated with titanium and carbon vacancies, the adsorption energy increases by 1.2 times in the binding site A of W/TixCy systems.

Predicting RNA folding thermodynamics with a reduced chain representation model

PubMed Central

CAO, SONG; CHEN, SHI-JIE

2005-01-01

Based on the virtual bond representation for the nucleotide backbone, we develop a reduced conformational model for RNA. We use the experimentally measured atomic coordinates to model the helices and use the self-avoiding walks in a diamond lattice to model the loop conformations. The atomic coordinates of the helices and the lattice representation for the loops are matched at the loop–helix junction, where steric viability is accounted for. Unlike the previous simplified lattice-based models, the present virtual bond model can account for the atomic details of realistic three-dimensional RNA structures. Based on the model, we develop a statistical mechanical theory for RNA folding energy landscapes and folding thermodynamics. Tests against experiments show that the theory can give much more improved predictions for the native structures, the thermal denaturation curves, and the equilibrium folding/unfolding pathways than the previous models. The application of the model to the P5abc region of Tetrahymena group I ribozyme reveals the misfolded intermediates as well as the native-like intermediates in the equilibrium folding process. Moreover, based on the free energy landscape analysis for each and every loop mutation, the model predicts five lethal mutations that can completely alter the free energy landscape and the folding stability of the molecule. PMID:16251382

Direct Experimental Evidence for Differing Reactivity Alterations of Minerals following Irradiation: The Case of Calcite and Quartz

NASA Astrophysics Data System (ADS)

Pignatelli, Isabella; Kumar, Aditya; Field, Kevin G.; Wang, Bu; Yu, Yingtian; Le Pape, Yann; Bauchy, Mathieu; Sant, Gaurav

2016-01-01

Concrete, used in the construction of nuclear power plants (NPPs), may be exposed to radiation emanating from the reactor core. Until recently, concrete has been assumed immune to radiation exposure. Direct evidence acquired on Ar+-ion irradiated calcite and quartz indicates, on the contrary, that, such minerals, which constitute aggregates in concrete, may be significantly altered by irradiation. More specifically, while quartz undergoes disordering of its atomic structure resulting in a near complete lack of periodicity, calcite only experiences random rotations, and distortions of its carbonate groups. As a result, irradiated quartz shows a reduction in density of around 15%, and an increase in chemical reactivity, described by its dissolution rate, similar to a glassy silica. Calcite however, shows little change in dissolution rate - although its density noted to reduce by ≈9%. These differences are correlated with the nature of bonds in these minerals, i.e., being dominantly ionic or covalent, and the rigidity of the mineral’s atomic network that is characterized by the number of topological constraints (nc) that are imposed on the atoms in the network. The outcomes have major implications on the durability of concrete structural elements formed with calcite or quartz bearing aggregates in nuclear power plants.

Direct Experimental Evidence for Differing Reactivity Alterations of Minerals following Irradiation: The Case of Calcite and Quartz

PubMed Central

Pignatelli, Isabella; Kumar, Aditya; Field, Kevin G.; Wang, Bu; Yu, Yingtian; Le Pape, Yann; Bauchy, Mathieu; Sant, Gaurav

2016-01-01

Concrete, used in the construction of nuclear power plants (NPPs), may be exposed to radiation emanating from the reactor core. Until recently, concrete has been assumed immune to radiation exposure. Direct evidence acquired on Ar+-ion irradiated calcite and quartz indicates, on the contrary, that, such minerals, which constitute aggregates in concrete, may be significantly altered by irradiation. More specifically, while quartz undergoes disordering of its atomic structure resulting in a near complete lack of periodicity, calcite only experiences random rotations, and distortions of its carbonate groups. As a result, irradiated quartz shows a reduction in density of around 15%, and an increase in chemical reactivity, described by its dissolution rate, similar to a glassy silica. Calcite however, shows little change in dissolution rate - although its density noted to reduce by ≈9%. These differences are correlated with the nature of bonds in these minerals, i.e., being dominantly ionic or covalent, and the rigidity of the mineral’s atomic network that is characterized by the number of topological constraints (nc) that are imposed on the atoms in the network. The outcomes have major implications on the durability of concrete structural elements formed with calcite or quartz bearing aggregates in nuclear power plants. PMID:26822012

In situ chemical analyses of extraterrestrial bodies

NASA Technical Reports Server (NTRS)

Economou, Thanasis E.; Turkevich, Anthony L.

1988-01-01

One of the most important tasks on any sample return mission will have to be a quick sample characterization in order to guarantee a variety of collected samples. An alpha particle instrument with alpha, proton and X-ray modes can provide a quick and almost complete chemical analysis of Mars samples. This instrument is based on three interactions of the alpha particles from a radioactive source with matter: elastic scattering of the alpha particles by nuclei (alpha mode), (alpha,p) nuclear reaction with some light elements (proton mode), and excitation of the atomic structure of atoms by alpha particles, leading to emission of characteristic X-rays of the lunar surface at three sites during the Surveyor mission of 1967 to 1968. Since then the instrument has been improved and miniaturized substantially. As shown in the past, the alpha particle instrument can operate under Martian conditions without any degradation in the performance. The alpha and proton modes can provide vital information about the light elements, while the X-ray mode with its ambient temperature X-ray detector will be useful for the heavier elements. The excitation of the atomic structure is provided by the same alpha radioactive source that is used by alpha and proton modes or by an auxiliary X-ray source that is selected to enhance the sensitivity to some important geochemical elements.

Direct experimental evidence for differing reactivity alterations of minerals following irradiation. The case of calcite and quartz

DOE PAGES

Pignatelli, Isabella; Kumar, Aditya; Field, Kevin G.; ...

2016-01-29

Concrete, used in the construction of nuclear power plants (NPPs), may be exposed to radiation emanating from the reactor core. Until recently, concrete has been assumed immune to radiation exposure. Direct evidence acquired on Ar+ -ion irradiated calcite and quartz indicates, on the contrary, that, such minerals, which constitute aggregates in concrete, may be significantly altered by irradiation. More specifically, while quartz undergoes disordering of its atomic structure resulting in a near complete lack of periodicity, calcite only experiences random rotations, and distortions of its carbonate groups. As a result, irradiated quartz shows a reduction in density of around 15%,more » and an increase in chemical reactivity, described by its dissolution rate, similar to a glassy silica. However, calcite shows little change in dissolution rate - although its density noted to reduce by 9%. These differences are correlated with the nature of bonds in these minerals, i.e., being dominantly ionic or covalent, and the rigidity of the mineral's atomic network that is characterized by the number of topological constraints (nc) that are imposed on the atoms in the network. Our outcomes have major implications on the durability of concrete structural elements formed with calcitic or quartzitic aggregates in nuclear power plants.« less

An intrinsic representation of atomic structure: From clusters to periodic systems

NASA Astrophysics Data System (ADS)

Li, Xiao-Tian; Xu, Shao-Gang; Yang, Xiao-Bao; Zhao, Yu-Jun

2017-10-01

We have improved our distance matrix and eigen-subspace projection function (EPF) [X.-T. Li et al., J. Chem. Phys. 146, 154108 (2017)] to describe the atomic structure for periodic systems. Depicting the local structure of an atom, the EPF turns out to be invariant with respect to the choices of the unit cell and coordinate frame, leading to an intrinsic representation of the crystal with a set of EPFs of the nontrivial atoms. The difference of EPFs reveals the difference of atoms in local structure, while the accumulated difference between two sets of EPFs can be taken as the distance between configurations. Exemplified with the cases of carbon allotropes and boron sheets, our EPF approach shows exceptional rationality and efficiency to distinguish the atomic structures, which is crucial in structure recognition, comparison, and analysis.

An intrinsic representation of atomic structure: From clusters to periodic systems.

PubMed

Li, Xiao-Tian; Xu, Shao-Gang; Yang, Xiao-Bao; Zhao, Yu-Jun

2017-10-14

We have improved our distance matrix and eigen-subspace projection function (EPF) [X.-T. Li et al., J. Chem. Phys. 146, 154108 (2017)] to describe the atomic structure for periodic systems. Depicting the local structure of an atom, the EPF turns out to be invariant with respect to the choices of the unit cell and coordinate frame, leading to an intrinsic representation of the crystal with a set of EPFs of the nontrivial atoms. The difference of EPFs reveals the difference of atoms in local structure, while the accumulated difference between two sets of EPFs can be taken as the distance between configurations. Exemplified with the cases of carbon allotropes and boron sheets, our EPF approach shows exceptional rationality and efficiency to distinguish the atomic structures, which is crucial in structure recognition, comparison, and analysis.

Theoretical predictions of a bucky-diamond SiC cluster.

PubMed

Yu, Ming; Jayanthi, C S; Wu, S Y

2012-06-15

A study of structural relaxations of Si(n)C(m) clusters corresponding to different compositions, different relative arrangements of Si/C atoms, and different types of initial structure, reveals that the Si(n)C(m) bucky-diamond structure can be obtained for an initial network structure constructed from a truncated bulk 3C-SiC for a magic composition corresponding to n = 68 and m = 79. This study was performed using a semi-empirical Hamiltonian (SCED-LCAO) since it allowed an extensive search of different types of initial structures. However, the bucky-diamond structure predicted by this method was also confirmed by a more accurate density functional theory (DFT) based method. The bucky-diamond structure exhibited by a SiC-based system represents an interesting paradigm where a Si atom can form three-coordinated as well as four-coordinated networks with carbon atoms and vice versa and with both types of network co-existing in the same structure. Specifically, the bucky-diamond structure of the Si(68)C(79) cluster consists of a 35-atom diamond-like inner core (four-atom coordinations) suspended inside a 112-atom fullerene-like shell (three-atom coordinations).

Angiogenesis Research to Improve Therapies for Vascular Leak Syndromes, Intra-Abdominal Adhesions, and Arterial Injuries

DTIC Science & Technology

2006-02-01

production Endostatin protein was initially purified from the urine of tumor-bearing mice, providing a few micrograms for analysis of amino acid...whereas the wild-type bound 10 atoms of Zn per endostatin molecule. This finding is problematic because, in our crystal structure analysis of endostatin...complete prevention of pulmonary metas - tases. Lowest inhibition of tumor growth was ¨40–45% (Table 2B). In transgenic mice overexpressing endostatin, a

Trialkylphosphine-stabilized copper(I) gallium(III) phenylchalcogenolate complexes: crystal structures and generation of ternary semiconductors by thermolysis.

PubMed

Kluge, Oliver; Krautscheid, Harald

2012-06-18

A series of organometallic trialkylphosphine-stabilized copper gallium phenylchalcogenolate complexes [(R(3)P)(m)Cu(n)Me(2-x)Ga(EPh)(n+x+1)] (R = Me, Et, (i)Pr, (t)Bu; E = S, Se, Te; x = 0, 1) has been prepared and structurally characterized by X-ray diffraction. From their molecular structures three groups of compounds can be distinguished: ionic compounds, ring systems, and cage structures. All these complexes contain one gallium atom bound to one or two methyl groups, whereas the number of copper atoms, and therefore the nuclearity of the complexes, is variable and depends mainly on size and amount of phosphine ligand used in synthesis. The Ga-E bonds are relatively rigid, in contrast to flexible Cu-E bonds. The lengths of the latter are controlled by the coordination number and steric influences. The Ga-E bond lengths depend systematically on the number of methyl groups bound to the gallium atom, with somewhat shorter bonds in monomethyl compounds compared to dimethyl compounds. Quantum chemical computations reproduce this trend and show furthermore that the rotation of one phenyl group around the Ga-E bond is a low energy process with two distinct minima, corresponding to two different conformations found experimentally. Mixtures of different types of chalcogen atoms on molecular scale are possible, and then ligand exchange reactions in solution lead to mixed site occupation. In thermogravimetric studies the complexes were converted into the ternary semiconductors CuGaE(2). The thermolysis reaction is completed at temperatures between 250 and 400 °C, typically with lower temperatures for the heavier chalcogens. Because of significant release of Me(3)Ga during the thermolysis process, and especially in case of copper excess in the precursor complexes, binary copper chalcogenides are obtained as additional thermolysis products. Quaternary semiconductors can be obtained from mixed chalcogen precursors.

TiS2 and ZrS2 single- and double-wall nanotubes: first-principles study.

PubMed

Bandura, Andrei V; Evarestov, Robert A

2014-02-15

Hybrid density functional theory has been applied for investigations of the electronic and atomic structure of bulk phases, nanolayers, and nanotubes based on titanium and zirconium disulfides. Calculations have been performed on the basis of the localized atomic functions by means of the CRYSTAL-2009 computer code. The full optimization of all atomic positions in the regarded systems has been made to study the atomic relaxation and to determine the most favorable structures. The different layered and isotropic bulk phases have been considered as the possible precursors of the nanotubes. Calculations on single-walled TiS2 and ZrS2 nanotubes confirmed that the nanotubes obtained by rolling up the hexagonal crystalline layers with octahedral 1T morphology are the most stable. The strain energy of TiS2 and ZrS2 nanotubes is small, does not depend on the tube chirality, and approximately obeys to D(-2) law (D is nanotube diameter) of the classical elasticity theory. It is greater than the strain energy of the similar TiO2 and ZrO2 nanotubes; however, the formation energy of the disulfide nanotubes is considerably less than the formation energy of the dioxide nanotubes. The distance and interaction energy between the single-wall components of the double-wall nanotubes is proved to be close to the distance and interaction energy between layers in the layered crystals. Analysis of the relaxed nanotube shape using radial coordinate of the metal atoms demonstrates a small but noticeable deviation from completely cylindrical cross-section of the external walls in the armchair-like double-wall nanotubes. Copyright © 2013 Wiley Periodicals, Inc.

Dipole-Guided Electron Capture Causes Abnormal Dissociations of Phosphorylated Pentapeptides

NASA Astrophysics Data System (ADS)

Moss, Christopher L.; Chung, Thomas W.; Wyer, Jean A.; Nielsen, Steen Brøndsted; Hvelplund, Preben; Tureček, František

2011-04-01

Electron transfer and capture mass spectra of a series of doubly charged ions that were phosphorylated pentapeptides of a tryptic type (pS,A,A,A,R) showed conspicuous differences in dissociations of charge-reduced ions. Electron transfer from both gaseous cesium atoms at 100 keV kinetic energies and fluoranthene anion radicals in an ion trap resulted in the loss of a hydrogen atom, ammonia, and backbone cleavages forming complete series of sequence z ions. Elimination of phosphoric acid was negligible. In contrast, capture of low-energy electrons by doubly charged ions in a Penning ion trap induced loss of a hydrogen atom followed by elimination of phosphoric acid as the dominant dissociation channel. Backbone dissociations of charge-reduced ions also occurred but were accompanied by extensive fragmentation of the primary products. z-Ions that were terminated with a deaminated phosphoserine radical competitively eliminated phosphoric acid and H2PO4 radicals. A mechanism is proposed for this novel dissociation on the basis of a computational analysis of reaction pathways and transition states. Electronic structure theory calculations in combination with extensive molecular dynamics mapping of the potential energy surface provided structures for the precursor phosphopeptide dications. Electron attachment produces a multitude of low lying electronic states in charge-reduced ions that determine their reactivity in backbone dissociations and H- atom loss. The predominant loss of H atoms in ECD is explained by a distortion of the Rydberg orbital space by the strong dipolar field of the peptide dication framework. The dipolar field steers the incoming electron to preferentially attach to the positively charged arginine side chain to form guanidinium radicals and trigger their dissociations.

Direct Determination of Atomic Structure and Magnetic Coupling of Magnetite Twin Boundaries.

PubMed

Chen, Chunlin; Li, Hongping; Seki, Takehito; Yin, Deqiang; Sanchez-Santolino, Gabriel; Inoue, Kazutoshi; Shibata, Naoya; Ikuhara, Yuichi

2018-03-27

Clarifying how the atomic structure of interfaces/boundaries in materials affects the magnetic coupling nature across them is of significant academic value and will facilitate the development of state-of-the-art magnetic devices. Here, by combining atomic-resolution transmission electron microscopy, atomistic spin-polarized first-principles calculations, and differential phase contrast imaging, we conduct a systematic investigation of the atomic and electronic structures of individual Fe 3 O 4 twin boundaries (TBs) and determine their concomitant magnetic couplings. We demonstrate that the magnetic coupling across the Fe 3 O 4 TBs can be either antiferromagnetic or ferromagnetic, which directly depends on the TB atomic core structures and resultant electronic structures within a few atomic layers. Revealing the one-to-one correspondence between local atomic structures and magnetic properties of individual grain boundaries will shed light on in-depth understanding of many interesting magnetic behaviors of widely used polycrystalline magnetic materials, which will surely promote the development of advanced magnetic materials and devices.

Astronomy-inspired Atomic and Molecular Physics

NASA Astrophysics Data System (ADS)

Rau, A. R. P.

2002-02-01

Aimed at senior undergraduate and first-year graduate students in departments of physics and astronomy, this textbook gives a systematic treatment of atomic and molecular structure and spectra, together with the effect of weak and strong external electromagnetic fields. Topics chosen are those of interest in astronomy and indeed many were inspired by specific astronomical contexts. Examples include the negative ion of hydrogen and the effects of strong magnetic fields such as those occurring on certain white dwarfs and neutron stars. Adiabatic and non-adiabatic handling of electron correlations and application to processes such as dielectronic recombination are included. Astronomical examples are provided throughout as well as end-of-the chapter problems and exercises. Over seventy illustrative diagrams complete this unique and comprehensive volume. Link: http://www.wkap.nl/prod/b/1-4020-0467-2

Mechanism of Phosphine Dissociation on the Si(001) Surface

NASA Astrophysics Data System (ADS)

Warschkow, Oliver; Schofield, Steven R.; Smith, Phil V.

2005-03-01

The continued down-scaling of electronic devices to the atomic scale increasingly requires an atomic-level understanding of the elementary processes of semiconductor doping. We present a combined experimental and theoretical investigation into the dissociation mechanism of phosphine (PH3) on the Si(001) surface. As reported by us elsewhere in this conference, a number of prominent intermediate species of PH3 dissociation observed in STM experiments have been structurally characterized as PH2+H, PH+2H and P+3H species respectively. In this poster we present detailed quantum chemical calculations of these and other short-lived intermediates as well as the transition (kinetic) barriers between them. This leads us to formulate a step-by-step mechanism for the complete dissociation of PH3 on the Si(001) surface.

N(+)-N and O(+)-O interaction energies, dipole transition moments, and transport cross sections

NASA Technical Reports Server (NTRS)

Partridge, H.; Stallcop, J. R.

1986-01-01

Complete sets of ion-atom interaction energies have been computed for nitrogen and oxygen with accurate large scale structure calculations. The computed energies agree well with the accurate potential curves available from spectroscopic measurement. The state functions from the nitrogen calculations have been applied to determine the transition moment for all allowed dipole transitions. These results can be combined to compute a detailed radiation spectrum such as that required to define the highly nonequilibrium environment of aeroassisted orbital transfer vehicle (AOTV). The long-range interaction energies have been used to determine the ion-atom resonance charge exchange cross sections that are important for transport processes such as diffusion. A calculation to determine reliable transport properties for energies that include the AOTV temperature range from these computed properties is described.

Lithium doping and vacancy effects on the structural, electronic and magnetic properties of hexagonal boron nitride sheet: A first-principles calculation

NASA Astrophysics Data System (ADS)

Fartab, Dorsa S.; Kordbacheh, Amirhossein Ahmadkhan

2018-06-01

The first-principles calculations based on spin-polarized density functional theory is carried out to investigate the structural, electronic and magnetic properties of a hexagonal boron nitride sheet (h-BNS) doped by one or two lithium atom(s). Moreover, a vacancy in the neighborhood of one Li-substituted atom is introduced into the system. All optimized structures indicate significant local deformations with Li atom(s) protruded to the exterior of the sheet. The defects considered at N site are energetically more favorable than their counterpart structures at B site. The spin-polarized impurity states appear within the bandgap region of the pristine h-BNS, which lead to a spontaneous magnetization with the largest magnetic moments of about 2 μB in where a single or two B atom(s) are replaced by Li atom(s). Furthermore, the Li substitution for a single B atom increases the density of holes compared to that of electrons forming a p-type semiconductor. More interestingly, the structure in which two Li are substituted two neighboring B atoms appears to show desired half-metallic behavior that may be applicable in spintronic. The results provide a way to enhance the conductivity and magnetism of the pristine h-BNS for potential applications in BN-based nanoscale devices.

Accelerating atomic structure search with cluster regularization

NASA Astrophysics Data System (ADS)

Sørensen, K. H.; Jørgensen, M. S.; Bruix, A.; Hammer, B.

2018-06-01

We present a method for accelerating the global structure optimization of atomic compounds. The method is demonstrated to speed up the finding of the anatase TiO2(001)-(1 × 4) surface reconstruction within a density functional tight-binding theory framework using an evolutionary algorithm. As a key element of the method, we use unsupervised machine learning techniques to categorize atoms present in a diverse set of partially disordered surface structures into clusters of atoms having similar local atomic environments. Analysis of more than 1000 different structures shows that the total energy of the structures correlates with the summed distances of the atomic environments to their respective cluster centers in feature space, where the sum runs over all atoms in each structure. Our method is formulated as a gradient based minimization of this summed cluster distance for a given structure and alternates with a standard gradient based energy minimization. While the latter minimization ensures local relaxation within a given energy basin, the former enables escapes from meta-stable basins and hence increases the overall performance of the global optimization.

Structural and computational characterization of 4‧,4‧,6‧,6‧-tetrachloro-3-(2-methoxyethyl)-3H,4H-spiro-1,3,2-benzoxaza phosphinine-2,2‧- [1,3,5,2,4,6] triazatriphosphinine

NASA Astrophysics Data System (ADS)

Işıklan, Muhammet; Yıldırım, Erdem Kamil; Atiş, Murat; Sonkaya, Ömer; Çoşut, Bünyemin

2016-08-01

In this study a new monospirocyclic phosphazene derivative, 4‧,4‧,6‧,6‧-tetrachloro-3-(2-methoxyethyl)-3H,4H-spiro [1,3,2-benzoxazaphosphinine-2,2‧- [1,3,5,2,4,6] triazatriphosphinine] (SP1) was synthesized from the reaction of hexachlorocyclotriphosphazene (N3P3Cl6) with N/O donor-type, 2-{[(2-Metoxyethyl) amino]methyl}phenol. The structural investigations of the compound were verified by elemental analyses, MS, FTIR, 1H, 13C, 31P NMR spectroscopy and the single crystal X-ray diffraction analysis. The structural and spectroscopic data of the molecule in the ground state were calculated by using density functional method (DFT) using 6-311++G (d, p) basis set. The complete assignments of all vibrational modes were performed on the basis of the total energy distributions (TED). Isotropic chemical shifts (31P, 1H and 13C NMR) were calculated using the gauge-invariant atomic orbital (GIAO) method. Theoretical calculations of bond parameters, harmonic vibration frequencies and nuclear magnetic resonance are in good agreement with experimental results. The electrophilic and nucleophilic attack centers in SP1 were predicted with the local softness values (sk+, and sk-) of individual atoms and it is confirmed that P atoms of the PCl2 groups are nucleophilic attack centers.

Understanding Atomic Structure: Is There a More Direct and Compelling Connection between Atomic Line Spectra and the Quantization of an Atom's Energy?

ERIC Educational Resources Information Center

Rittenhouse, Robert C.

2015-01-01

The "atoms first" philosophy, adopted by a growing number of General Chemistry textbook authors, places greater emphasis on atomic structure as a key to a deeper understanding of the field of chemistry. A pivotal concept needed to understand the behavior of atoms is the restriction of an atom's energy to specific allowed values. However,…

DFT analysis on the molecular structure, vibrational and electronic spectra of 2-(cyclohexylamino)ethanesulfonic acid

NASA Astrophysics Data System (ADS)

Renuga Devi, T. S.; Sharmi kumar, J.; Ramkumaar, G. R.

2015-02-01

The FTIR and FT-Raman spectra of 2-(cyclohexylamino)ethanesulfonic acid were recorded in the regions 4000-400 cm-1 and 4000-50 cm-1 respectively. The structural and spectroscopic data of the molecule in the ground state were calculated using Hartee-Fock and Density functional method (B3LYP) with the correlation consistent-polarized valence double zeta (cc-pVDZ) basis set and 6-311++G(d,p) basis set. The most stable conformer was optimized and the structural and vibrational parameters were determined based on this. The complete assignments were performed based on the Potential Energy Distribution (PED) of the vibrational modes, calculated using Vibrational Energy Distribution Analysis (VEDA) 4 program. With the observed FTIR and FT-Raman data, a complete vibrational assignment and analysis of the fundamental modes of the compound were carried out. Thermodynamic properties and Atomic charges were calculated using both Hartee-Fock and density functional method using the cc-pVDZ basis set and compared. The calculated HOMO-LUMO energy gap revealed that charge transfer occurs within the molecule. 1H and 13C NMR chemical shifts of the molecule were calculated using Gauge Including Atomic Orbital (GIAO) method and were compared with experimental results. Stability of the molecule arising from hyperconjugative interactions, charge delocalization have been analyzed using Natural Bond Orbital (NBO) analysis. The first order hyperpolarizability (β) and Molecular Electrostatic Potential (MEP) of the molecule was computed using DFT calculations. The electron density based local reactivity descriptor such as Fukui functions were calculated to explain the chemical reactivity site in the molecule.

77 FR 42483 - Application(s) for Duty-Free Entry of Scientific Instruments

Federal Register 2010, 2011, 2012, 2013, 2014

2012-07-19

... creating artificial nanoscale structures on an atom-by- atom basis using nascent atom manipulation techniques. The instrument will be used to investigate the amount of force required to move one atom on a materials surface while simultaneously measuring local electronic structural changes during atom movement...

Crystal Structure and Theoretical Analysis of Green Gold Au 30 (S- t Bu) 18 Nanomolecules and Their Relation to Au 30 S(S- t Bu) 18

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

Dass, Amala; Jones, Tanya; Rambukwella, Milan

We report the complete X-ray crystallographic structure as determined through single crystal X-ray diffraction and a thorough theoretical analysis of the green gold Au30(S-tBu)18. While the structure of Au30S(S-tBu)18 with 19 sulfur atoms has been reported, the crystal structure of Au30(S-tBu)18 without the μ3-sulfur has remained elusive until now, though matrix-assisted laser desorption ionization mass spectrometry (MALDI-MS) and electrospray ionization mass spectrometry (ESI-MS) data unequivocally shows its presence in abundance. The Au30(S-tBu)18 nanomolecule is not only distinct in its crystal structure but has unique temperature dependent optical properties. Structure determination allows a rigorous comparison and an excellent agreement with theoreticalmore » predictions of structure, stability, and optical response.« less

Electrical, structural and optical properties of tellurium thin films on silicon substrate

NASA Astrophysics Data System (ADS)

Arora, Swati; Vijay, Y. K.

2018-05-01

Tellurium (Te) thin films of various thicknesses (200nm, 275nm, 350nm & 500nm) were prepared on Silicon (Si) using thermal evaporation at vacuum of 10-5 torr. It is observed that the resistivity decreases exponentially with the Increases Temperature. A direct band gap between 0.368 eV to 0.395 eV is obtained at different temperatures with Four Probe Method which shows that when we increase the thickness of material the band gap will exponentially decreases. Samples were analysed through X-ray diffraction and atomic force microscopy to attain complete and reliable micro structural in order.

Integrative Structure Determination of Protein Assemblies by Satisfaction of Spatial Restraints

NASA Astrophysics Data System (ADS)

Alber, Frank; Chait, Brian T.; Rout, Michael P.; Sali, Andrej

To understand the cell, we need to determine the structures of macromolecular assemblies, many of which consist of tens to hundreds of components. A great variety of experimental data can be used to characterize the assemblies at several levels of resolution, from atomic structures to component configurations. To maximize completeness, resolution, accuracy, precision and efficiency of the structure determination, a computational approach is needed that can use spatial information from a variety of experimental methods. We propose such an approach, defined by its three main components: a hierarchical representation of the assembly, a scoring function consisting of spatial restraints derived from experimental data, and an optimization method that generates structures consistent with the data. We illustrate the approach by determining the configuration of the 456 proteins in the nuclear pore complex from Baker's yeast.

Ab initio conformational analysis of N-formyl ?-alanine amide including electron correlation

NASA Astrophysics Data System (ADS)

Yu, Ching-Hsing; Norman, Mya A.; Schäfer, Lothar; Ramek, Michael; Peeters, Anik; van Alsenoy, Christian

2001-06-01

The conformational properties of N-formyl L-alanine amide (ALA) were investigated using RMP2/6-311G∗∗ ab initio gradient geometry optimization. One hundred forty four structures of ALA were optimized at 30° grid points in its φ(N-C(α)), ψ(C(α)-C‧) conformational space. Using cubic spline functions, the grid structures were then used to construct analytical representations of complete surfaces, in φ,ψ-space, of bond lengths, bond angles, torsional sensitivity and electrostatic atomic charges. Analyses show that, in agreement with previous studies, the right-handed helical conformation, αR, is not a local energy minimum of the potential energy surface of ALA. Comparisons with protein crystallographic data show that the characteristic differences between geometrical trends in dipeptides and proteins, previously found for ab initio dipeptide structures obtained without electron correlation, are also found in the electron-correlated geometries. In contrast to generally accepted features of force fields used in empirical molecular modeling, partial atomic charges obtained by the CHELPG method are found to be not constant, but to vary significantly throughout the φ,ψ-space. By comparing RHF and MP2 structures, the effects of dispersion forces on ALA were studied, revealing molecular contractions for those conformations, in which small adjustments of torsional angles entail large changes in non-bonded distances.

Effect of disorder on the magnetic and electronic structure of a prospective spin-gapless semiconductor MnCrVAl

DOE PAGES

Kharel, P.; Herran, J.; Lukashev, P.; ...

2016-12-19

Recent discovery of a new class of materials, spin-gapless semiconductors (SGS), has attracted considerable attention in the last few years, primarily due to potential applications in the emerging field of spin-based electronics (spintronics). Here, we investigate structural, electronic, and magnetic properties of one potential SGS compound, MnCrVAl, using various experimental and theoretical techniques. Our calculations show that this material exhibits ≈ 0.5 eV band gap for the majority-spin states, while for the minority-spin it is nearly gapless. The calculated magnetic moment for the completely ordered structure is 2.9 μB/f.u., which is different from our experimentally measured value of almost zero.more » Here, this discrepancy is explained by the structural disorder. In particular, A2 type disorder, where Mn or Cr atoms exchange their positions with Al atoms, results in induced antiferromagnetic exchange coupling, which, at a certain level of disorder, effectively reduces the total magnetic moment to zero. This is consistent with our x-ray diffraction measurements which indicate the presence of A2 disorder in all of our samples. In addition, we also show that B2 disorder does not result in antiferromagnetic exchange coupling and therefore does not significantly reduce the total magnetic moment.« less

Atomic Fuel, Understanding the Atom Series. Revised.

ERIC Educational Resources Information Center

Hogerton, John F.

This publication is part of the "Understanding the Atom" series. Complete sets of the series are available free to teachers, schools, and public librarians who can make them available for reference or use by groups. Among the topics discussed are: What Atomic Fuel Is; The Odyssey of Uranium; Production of Uranium; Fabrication of Reactor…

Electronic structure and surface properties of MgB2(0001) upon oxygen adsorption

NASA Astrophysics Data System (ADS)

Kim, Chang-Eun; Ray, Keith G.; Bahr, David F.; Lordi, Vincenzo

2018-05-01

We use density-functional theory to investigate the bulk and surface properties of MgB2. The unique bonding structure of MgB2 is investigated by Bader's atoms-in-molecules, charge density difference, and occupancy projected band structure analyses. Oxygen adsorption on the charge-depleted surfaces of MgB2 is studied by a surface potential energy mapping method, reporting a complete map including low-symmetry binding sites. The B-terminated MgB2(0001) demonstrates reconstruction of the graphenelike B layer, and the reconstructed geometry exposes a threefold site of the subsurface Mg, making it accessible from the surface. Detailed reconstruction mechanisms are studied by simulated annealing method based on ab initio molecular dynamics and nudged elastic band calculations. The surface clustering of B atoms significantly modifies the B 2 p states to occupy low energy valence states. The present paper emphasizes that a thorough understanding of the surface phase may explain an apparent inconsistency in the experimental surface characterization of MgB2. Furthermore, these results suggest that the surface passivation can be an important technical challenge when it comes to development of a superconducting device using MgB2.

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

Kharel, P.; Herran, J.; Lukashev, P.

Recent discovery of a new class of materials, spin-gapless semiconductors (SGS), has attracted considerable attention in the last few years, primarily due to potential applications in the emerging field of spin-based electronics (spintronics). Here, we investigate structural, electronic, and magnetic properties of one potential SGS compound, MnCrVAl, using various experimental and theoretical techniques. Our calculations show that this material exhibits ≈ 0.5 eV band gap for the majority-spin states, while for the minority-spin it is nearly gapless. The calculated magnetic moment for the completely ordered structure is 2.9 μB/f.u., which is different from our experimentally measured value of almost zero.more » Here, this discrepancy is explained by the structural disorder. In particular, A2 type disorder, where Mn or Cr atoms exchange their positions with Al atoms, results in induced antiferromagnetic exchange coupling, which, at a certain level of disorder, effectively reduces the total magnetic moment to zero. This is consistent with our x-ray diffraction measurements which indicate the presence of A2 disorder in all of our samples. In addition, we also show that B2 disorder does not result in antiferromagnetic exchange coupling and therefore does not significantly reduce the total magnetic moment.« less

Vibrational and structural study of onopordopicrin based on the FTIR spectrum and DFT calculations.

PubMed

Chain, Fernando E; Romano, Elida; Leyton, Patricio; Paipa, Carolina; Catalán, César A N; Fortuna, Mario; Brandán, Silvia Antonia

2015-01-01

In the present work, the structural and vibrational properties of the sesquiterpene lactone onopordopicrin (OP) were studied by using infrared spectroscopy and density functional theory (DFT) calculations together with the 6-31G(∗) basis set. The harmonic vibrational wavenumbers for the optimized geometry were calculated at the same level of theory. The complete assignment of the observed bands in the infrared spectrum was performed by combining the DFT calculations with Pulay's scaled quantum mechanical force field (SQMFF) methodology. The comparison between the theoretical and experimental infrared spectrum demonstrated good agreement. Then, the results were used to predict the Raman spectrum. Additionally, the structural properties of OP, such as atomic charges, bond orders, molecular electrostatic potentials, characteristics of electronic delocalization and topological properties of the electronic charge density were evaluated by natural bond orbital (NBO), atoms in molecules (AIM) and frontier orbitals studies. The calculated energy band gap and the chemical potential (μ), electronegativity (χ), global hardness (η), global softness (S) and global electrophilicity index (ω) descriptors predicted for OP low reactivity, higher stability and lower electrophilicity index as compared with the sesquiterpene lactone cnicin containing similar rings. Copyright © 2015 Elsevier B.V. All rights reserved.

A Branch-and-Bound Approach for Tautomer Enumeration.

PubMed

Thalheim, Torsten; Wagner, Barbara; Kühne, Ralph; Middendorf, Martin; Schüürmann, Gerrit

2015-05-01

Knowledge about tautomer forms of a structure is important since, e.g., a property prediction for a molecule can yield to different results which depend on the individual tautomer. Tautomers are isomers that can be transformed to each other through chemical equilibrium reactions. In this paper the first exact Branch-and-Bound (B&B) algorithm to calculate tautomer structures is proposed. The algorithm is complete in the sense of tautomerism and generates all possible tautomers of a structure according to the tautomer definition, it is initialized with. To be efficient, the algorithm takes advantage of symmetric and formation properties. Some restrictions are used to enable an early pruning of some branches of the B&B tree. This is important, since a simple enumeration strategy would lead to number of candidate tautomers that is exponentially increasing with the number of hydrogen atoms and their attachment sites. The proposed implementation of the B&B algorithm covers the majority of the prototropic tautomer cases, but can be adapted to other kinds of tautomerism too. Furthermore, a computer processable definition of tautomerism is given in the form of the moving hydrogen atom problem. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Photoexcitation and photoionization of argon atom and chlorine molecule using the Advanced Light Source

NASA Astrophysics Data System (ADS)

Nayandin, Oleg

2001-08-01

The use of a third generation Synchrotron Radiation source combined with time-of-flight (TOF) electron spectrometers and a two-dimensional (2D) imaging technique makes it possible to investigate and reveal new aspects of atomic and molecular structure, and allows a better understanding of electron correlation. This dissertation concentrates on the experimental study of the interaction of synchrotron radiation with argon atoms and chlorine molecules in the gas phase. The measurements were performed using a two-dimensional photoelectron spectroscopy technique in combination with the high resolution Atomic, Molecular and Optical Physics undulator beam line at the Advanced Light Source at the Lawrence Berkeley National Laboratory. The complete angle-resolved 2D experimental images of the electron emission following photoexcitation and photoionization of the 2p inner-shell in Ar and Cl2 were measured. For argon, the intensity profiles as a function of photon energy for all accessible Auger decay channels were studied for the first time. Significant asymmetries are observed in these various partial cross-sections, due to the interference between direct photoionization and resonant photoexcitation leading to the same final ionic state. For chlorine, Auger electron spectra following the decay of the 2p --> σ* and 2p --> nl resonances were analyzed. It was found that valence photoionization channels do not resonate strongly for photon energies equal to the coreto-Rydberg excitation, in contrast to the strongly resonating ones observed in the HCl molecule. Auger decay spectra of the 2p-1σ* resonances showed no evidence of atomic transitions in Cl2, indicative of no significant dissociation, also in contrast to HCl. In addition, angular distributions of the photo- and Auger electron lines were derived. These results contribute to a better understanding of atomic and molecular structure and dynamics of inner shell processes and hopefully will stimulate further experimental and theoretical work.

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

PubMed

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

2009-11-17

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

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

Hu Qiang; Zeng Xierong; Shenzhen Key Laboratory of Special Functional Materials, Shenzhen 518060

This paper reports the observation of the clear Invar effects of (Fe{sub 71.2}B{sub 24}Y{sub 4.8}){sub 96}Nb{sub 4} bulk metallic glass. The Invar effects of (Fe{sub 71.2}B{sub 24}Y{sub 4.8}){sub 96}Nb{sub 4} alloys in different structural states are also investigated in situ through cyclic thermal dilation tests at different cyclic temperatures. The results show that these Invar effects are strengthened in the relaxation amorphous state, weakened in the nanocrystalline state, and absent in the complete crystalline state. X-ray diffraction and Moessbauer spectroscopy demonstrate that the structural influences on Invar effects can be explained by the different local atomic arrangements around Fe atomsmore » in different structural states.« less

Phase identification in boron-containing powder metallurgy steel using EBSD in combination with EPMA

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

Wu, Ming-Wei, E-mail: mwwu@ntut.edu.tw; Cai, Wen-Zhang

2016-03-15

Boron (B) is extensively used to induce liquid phase sintering (LPS) in powder metallurgy (PM) steels and thereby increase the densification. The alloying elements in B-containing PM steels affect the boride phase, stability of the boride, the temperature of liquid formation, and the progress of LPS. However, the boride phase has not been systematically identified yet. The main objective of this study was to clarify the influences of alloying elements, including C, Cr, and Ni, on the boride phases using electron backscatter diffraction (EBSD) in combination with electron probe microanalysis (EPMA). Network structures consisting of ferrite, Fe{sub 2}B boride, andmore » Fe{sub 3}C carbide were extensively observed in the Fe–0.4B–0.5C steel. The portions of Fe{sub 2}B were sufficiently larger than those of Fe{sub 3}C, and Fe{sub 3}C was mostly distributed at the interfaces between ferrite and Fe{sub 2}B. Adding 1.5 wt.% Cr or 1.8 wt.% Ni to Fe–0.4B–0.5C steel completely changes the Fe{sub 2}B and Fe{sub 3}C phases to a M{sub 3}(B,C) phase, where M represents the metallic elements, including Fe, Cr, Mo, and Ni. Furthermore, Cr, Mo, B, and C atoms tend to concentrate on the M{sub 3}(B,C) phase, but Ni atoms do not. - Highlights: • Network structures consisting of ferrite, Fe{sub 2}B boride, and Fe{sub 3}C carbide were extensively observed in the Fe–0.4B–0.5C steel. • Adding 1.5 wt.% Cr or 1.8 wt.% Ni to Fe–0.4B–0.5C steel completely transforms the Fe{sub 2}B and Fe{sub 3}C phases to a M{sub 3}(B,C) phase. • Cr, Mo, B, and C atoms tend to concentrate on the M{sub 3}(B,C) phase, but Ni atoms do not.« less

Structures of 38-atom gold-platinum nanoalloy clusters

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

Ong, Yee Pin; Yoon, Tiem Leong; Lim, Thong Leng

2015-04-24

Bimetallic nanoclusters, such as gold-platinum nanoclusters, are nanomaterials promising wide range of applications. We perform a numerical study of 38-atom gold-platinum nanoalloy clusters, Au{sub n}Pt{sub 38−n} (0 ≤ n ≤ 38), to elucidate the geometrical structures of these clusters. The lowest-energy structures of these bimetallic nanoclusters at the semi-empirical level are obtained via a global-minimum search algorithm known as parallel tempering multi-canonical basin hopping plus genetic algorithm (PTMBHGA), in which empirical Gupta many-body potential is used to describe the inter-atomic interactions among the constituent atoms. The structures of gold-platinum nanoalloy clusters are predicted to be core-shell segregated nanoclusters. Gold atomsmore » are observed to preferentially occupy the surface of the clusters, while platinum atoms tend to occupy the core due to the slightly smaller atomic radius of platinum as compared to gold’s. The evolution of the geometrical structure of 38-atom Au-Pt clusters displays striking similarity with that of 38-atom Au-Cu nanoalloy clusters as reported in the literature.« less

Chemical reactivity indices for the complete series of chlorinated benzenes: solvent effect.

PubMed

Padmanabhan, J; Parthasarathi, R; Subramanian, V; Chattaraj, P K

2006-03-02

We present a comprehensive analysis to probe the effect of solvation on the reactivity of the complete series of chlorobenzenes through the conceptual density functional theory (DFT)-based global and local descriptors. We propose a multiphilic descriptor in this study to explore the nature of attack at a particular site in a molecule. It is defined as the difference between nucleophilic and electrophilic condensed philicity functions. This descriptor is capable of explaining both the nucleophilicity and electrophilicity of the given atomic sites in the molecule simultaneously. The predictive ability of this descriptor is tested on the complete series of chlorobenzenes in gas and solvent media. A structure-toxicity analysis of these entire sets of chlorobenzenes toward aquatic organisms demonstrates the importance of the electrophilicity index in the prediction of the reactivity/toxicity.

Placement of molecules in (not out of) the cell

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

Dauter, Zbigniew, E-mail: dauter@anl.gov

2013-01-01

The importance of presenting macromolecular structures in unified, standard ways is discussed. To uniquely describe a crystal structure, it is sufficient to specify the crystal unit cell and symmetry, and describe the unique structural motif which is repeated by the space-group symmetry throughout the whole crystal. It is somewhat arbitrary how such a unique motif can be defined and positioned with respect to the unit-cell origin. As a result of such freedom, some isomorphous structures are presented in the Protein Data Bank in different locations and appear as if they have different atomic coordinates, despite being completely equivalent structurally. Thismore » may easily confuse those users of the PDB who are less familiar with crystallographic symmetry transformations. It would therefore be beneficial for the community of PDB users to introduce standard rules for locating crystal structures of macromolecules in the unit cells of various space groups.« less

Structures of small Pd Pt bimetallic clusters by Monte Carlo simulation

NASA Astrophysics Data System (ADS)

Cheng, Daojian; Huang, Shiping; Wang, Wenchuan

2006-11-01

Segregation phenomena of Pd-Pt bimetallic clusters with icosahedral and decahedral structures are investigated by using Monte Carlo method based on the second-moment approximation of the tight-binding (TB-SMA) potentials. The simulation results indicate that the Pd atoms generally lie on the surface of the smaller clusters. The three-shell onion-like structures are observed in 55-atom Pd-Pt bimetallic clusters, in which a single Pd atom is located in the center, and the Pt atoms are in the middle shell, while the Pd atoms are enriched on the surface. With the increase of Pd mole fraction in 55-atom Pd-Pt bimetallic clusters, the Pd atoms occupy the vertices of clusters first, then edge and center sites, and finally the interior shell. It is noticed that some decahedral structures can be transformed into the icosahedron-like structure at 300 and 500 K. Comparisons are made with previous experiments and theoretical studies of Pd-Pt bimetallic clusters.

Atomic Mass and Nuclear Binding Energy for I-131 (Iodine)

NASA Astrophysics Data System (ADS)

Sukhoruchkin, S. I.; Soroko, Z. N.

This document is part of the Supplement containing the complete sets of data of Subvolume A `Nuclei with Z = 1 - 54' of Volume 22 `Nuclear Binding Energies and Atomic Masses' of Landolt-Börnstein - Group I `Elementary Particles, Nuclei and Atoms'. It provides atomic mass, mass excess, nuclear binding energy, nucleon separation energies, Q-values, and nucleon residual interaction parameters for atomic nuclei of the isotope I-131 (Iodine, atomic number Z = 53, mass number A = 131).

Atomic Mass and Nuclear Binding Energy for F-22 (Fluorine)

NASA Astrophysics Data System (ADS)

Sukhoruchkin, S. I.; Soroko, Z. N.

This document is part of the Supplement containing the complete sets of data of Subvolume A `Nuclei with Z = 1 - 54' of Volume 22 `Nuclear Binding Energies and Atomic Masses' of Landolt-Börnstein - Group I `Elementary Particles, Nuclei and Atoms'. It provides atomic mass, mass excess, nuclear binding energy, nucleon separation energies, Q-values, and nucleon residual interaction parameters for atomic nuclei of the isotope F-22 (Fluorine, atomic number Z = 9, mass number A = 22).

pdb-care (PDB carbohydrate residue check): a program to support annotation of complex carbohydrate structures in PDB files.

PubMed

Lütteke, Thomas; von der Lieth, Claus-W

2004-06-04

Carbohydrates are involved in a variety of fundamental biological processes and pathological situations. They therefore have a large pharmaceutical and diagnostic potential. Knowledge of the 3D structure of glycans is a prerequisite for a complete understanding of their biological functions. The largest source of biomolecular 3D structures is the Protein Data Bank. However, about 30% of all 1663 PDB entries (version September 2003) containing carbohydrates comprise errors in glycan description. Unfortunately, no software is currently available which aligns the 3D information with the reported assignments. It is the aim of this work to fill this gap. The pdb-care program http://www.glycosciences.de/tools/pdb-care/ is able to identify and assign carbohydrate structures using only atom types and their 3D atom coordinates given in PDB-files. Looking up a translation table where systematic names and the respective PDB residue codes are listed, both assignments are compared and inconsistencies are reported. Additionally, the reliability of reported and calculated connectivities for molecules listed within the HETATOM records is checked and unusual values are reported. Frequent use of pdb-care will help to improve the quality of carbohydrate data contained in the PDB. Automatic assignment of carbohydrate structures contained in PDB entries will enable the cross-linking of glycobiology resources with genomic and proteomic data collections.

Theoretical investigations of two adamantane derivatives: A combined X-ray, DFT, QTAIM analysis and molecular docking

NASA Astrophysics Data System (ADS)

Al-Wahaibi, Lamya H.; Sujay, Subramaniam; Muthu, Gangadharan Ganesh; El-Emam, Ali A.; Venkataramanan, Natarajan S.; Al-Omary, Fatmah A. M.; Ghabbour, Hazem A.; Percino, Judith; Thamotharan, Subbiah

2018-05-01

A detailed structural analysis of two adamantane derivatives namely, ethyl 2-[(Z)-1-(adamantan-1-yl)-3-(phenyl)isothioureido]acetate I and ethyl 2-[(Z)-1-(adamantan-1-yl)-3-(4-fluorophenyl)isothioureido]acetate II is carried out to understand the effect of fluorine substitution. The introduction of fluorine atom alters the crystal packing and is completely different from its parent compound. The fluorine substitution drastically reduced the intermolecular H⋯H contacts and this reduction is compensated by intermolecular F⋯H and F⋯F contacts. The relative contributions of various intermolecular contacts present in these structures were quantified using Hirshfeld surface analysis. Energetically significant molecular pairs were identified from the crystal structures of these compounds using PIXEL method. The structures of I and II are optimized in gas and solvent phases using the B3LYP-D3/6-311++G(d,p) level of theory. The quantum theory of atoms-in-molecules (QTAIM) analysis was carried out to estimate the strengths of various intermolecular contacts present in these molecular dimers. The results suggest that the Hsbnd H bonding take part in the stabilization of crystal structures. The experimental and theoretical UV-Vis results show the variations in HOMO and LUMO energy levels. In silico docking analysis indicates that both compounds I and II may exhibit inhibitory activity against 11-β-hydroxysteroid dehydrogenase 1 (11-β-HSD1).

Improved hopcalite procedure for the determination of mercury vapor in air by flameless atomic absorption.

PubMed

Rathje, A O; Marcero, D H

1976-05-01

Mercury vapor is efficiently trapped from air by passage through a small glass tube filled with hopcalite. The hopcalite and adsorbed mercury are dissolved in a mixture of nitric and hydrochloric acids. Solution is rapid and complete, with no loss of mercury. Analysis is completed by flameless atomic absorption.

Solid-solution thermodynamics in Al-Li alloys

NASA Astrophysics Data System (ADS)

Alekseev, A. A.; Lukina, E. A.

2016-05-01

The relative equilibrium concentrations of lithium atoms distributed over different electron-structural states has been estimated. The possibility of the existence of various nonequilibrium electron-structural states of Li atoms in the solid solution in Al has been substantiated thermodynamically. Upon the decomposition of the supersaturated solid solution, the supersaturation on three electron-structural states of Li atoms that arises upon the quenching of the alloy can lead to the formation of lithium-containing phases in which the lithium atoms enter in one electron-structural state.

Paramagnetic Attraction of Impurity-Helium Solids

NASA Technical Reports Server (NTRS)

Bernard, E. P.; Boltnev, R. E.; Khmelenko, V. V.; Lee, D. M.

2003-01-01

Impurity-helium solids are formed when a mixture of impurity and helium gases enters a volume of superfluid helium. Typical choices of impurity gas are hydrogen deuteride, deuterium, nitrogen, neon and argon, or a mixture of these. These solids consist of individual impurity atoms and molecules as well as clusters of impurity atoms and molecules covered with layers of solidified helium. The clusters have an imperfect crystalline structure and diameters ranging up to 90 angstroms, depending somewhat on the choice of impurity. Immediately following formation the clusters aggregate into loosely connected porous solids that are submerged in and completely permeated by the liquid helium. Im-He solids are extremely effective at stabilizing high concentrations of free radicals, which can be introduced by applying a high power RF dis- charge to the impurity gas mixture just before it strikes the super fluid helium. Average concentrations of 10(exp 19) nitrogen atoms/cc and 5 x 10(exp 18) deuterium atoms/cc can be achieved this way. It shows a typical sample formed from a mixture of atomic and molecular hydrogen and deuterium. It shows typical sample formed from atomic and molecular nitrogen. Much of the stability of Im-He solids is attributed to their very large surface area to volume ratio and their permeation by super fluid helium. Heat resulting from a chance meeting and recombination of free radicals is quickly dissipated by the super fluid helium instead of thermally promoting the diffusion of other nearby free radicals.

Resilience among Japanese atomic bomb survivors.

PubMed

Knowles, A

2011-03-01

The purpose of the study was to explore the experience of atomic bomb survivors from Hiroshima and Nagasaki. Never has the world experienced such extreme devastation as with the atomic bombings of Hiroshima and Nagasaki, Japan, in August 1945. Although significant quantitative research has been completed about the medical effects following radiation, the literature lacks qualitative exploration from a holistic health perspective. This was a qualitative descriptive study, using methods of narrative analysis, oral history and ethnography. The sample for this research included eight individuals who were exposed to the atomic bombings in Japan and currently reside in the United States. Findings provide insight to the resilience that the survivors exhibited immediately following the bomb, as well as throughout the 65 years following the event. From ethnographic data and interviews with survivors, a thematic structure was developed that depicts the essential elements of the atomic bomb experience. Two ways of being in the world followed the bombing: surviving and thriving, with resilience serving as a lever, allowing for fluid movement over time across the continuum. Individuals experiencing surviving exhibited anxiety about their personal and family members' health, expressed mistrust, and felt a stigma associated with being a survivor. For those who were thriving, peace activism, overcoming and forgiveness were typically displayed. Findings from this study add to the disaster nursing literature and highlight the role resilience plays in the atomic bomb survivors' life perspective. © 2011 The Author. International Nursing Review © 2011 International Council of Nurses.

Correlations between dynamics and atomic structures in Cu64.5Zr35.5 metallic glass

NASA Astrophysics Data System (ADS)

Wang, C. Z.; Zhang, Y.; Zhang, F.; Mendelev, M. I.; Kramer, M. J.; Ho, K. M.

2015-03-01

The atomic structure of Cu-Zr metallic glasses (MGs) has been widely accepted to be heterogeneous and dominated by icosahedral short range order (ISRO). However, the correlations between dynamics and atomic structures in Cu-Zr MGs remain an enigma. Using molecular dynamics (MD) simulations, we investigated the correlations between dynamics and atomic structures in Cu64.5Zr35.5 MG. The atomic structures are characterized using ISRO and the Bergman-type medium range order (BMRO). The simulation and analysis results show that the majority of the mobile atoms are not involved in ISRO or BMRO, indicating that the dynamical heterogeneity has a strong correlation to structural heterogeneity. Moreover, we found that the localized soft vibration modes below 1.0 THz are mostly concentrated on the mobile atoms. The diffusion was studied using the atomic trajectory collected in an extended time interval of 1.2 μs at 700 K in MD simulations. It was found that the long range diffusion in MGs is highly heterogeneous, which is confined to the liquid-like regions and strongly avoids the ISRO and the Bergman-type MRO. All These results clearly demonstrate strong correlations between dynamics (in terms of dynamical heterogeneity and diffusion) and atomic structures in Cu64.5Zr35.5 MGs. This work was supported by the U.S. Department of Energy, Basic Energy Sciences, Division of Materials Science and Engineering under the Contract No. DE-AC02-07CH11358.

Classical And Quantum Rainbow Scattering From Surfaces

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

Winter, H.; Schueller, A.; Busch, M.

2011-06-01

The structure of clean and adsorbate covered surfaces as well as of ultrathin films can be investigated by grazing scattering of fast atoms. We present two recent experimental techniques which allow one to study the structure of ordered arrangements of surface atoms in detail. (1) Rainbow scattering under axial surface channeling conditions, and (2) fast atom diffraction. Our examples demonstrate the attractive features of grazing fast atom scattering as a powerful analytical tool in studies on the structure of surfaces. We will concentrate our discussion on the structure of ultrathin silica films on a Mo(112) surface and of adsorbed oxygenmore » atoms on a Fe(110) surface.« less

Comparing postdeposition reactions of electrons and radicals with Pt nanostructures created by focused electron beam induced deposition.

PubMed

Spencer, Julie A; Barclay, Michael; Gallagher, Miranda J; Winkler, Robert; Unlu, Ilyas; Wu, Yung-Chien; Plank, Harald; McElwee-White, Lisa; Fairbrother, D Howard

2017-01-01

The ability of electrons and atomic hydrogen (AH) to remove residual chlorine from PtCl 2 deposits created from cis -Pt(CO) 2 Cl 2 by focused electron beam induced deposition (FEBID) is evaluated. Auger electron spectroscopy (AES) and energy-dispersive X-ray spectroscopy (EDS) measurements as well as thermodynamics calculations support the idea that electrons can remove chlorine from PtCl 2 structures via an electron-stimulated desorption (ESD) process. It was found that the effectiveness of electrons to purify deposits greater than a few nanometers in height is compromised by the limited escape depth of the chloride ions generated in the purification step. In contrast, chlorine atoms can be efficiently and completely removed from PtCl 2 deposits using AH, regardless of the thickness of the deposit. Although AH was found to be extremely effective at chemically purifying PtCl 2 deposits, its viability as a FEBID purification strategy is compromised by the mobility of transient Pt-H species formed during the purification process. Scanning electron microscopy data show that this results in the formation of porous structures and can even cause the deposit to lose structural integrity. However, this phenomenon suggests that the use of AH may be a useful strategy to create high surface area Pt catalysts and may reverse the effects of sintering. In marked contrast to the effect observed with AH, densification of the structure was observed during the postdeposition purification of PtC x deposits created from MeCpPtMe 3 using atomic oxygen (AO), although the limited penetration depth of AO restricts its effectiveness as a purification strategy to relatively small nanostructures.

FT-IR, FT-Raman, UV-visible, and NMR spectroscopy and vibrational properties of the labdane-type diterpene 13-epi-sclareol.

PubMed

Chain, Fernando E; Leyton, Patricio; Paipa, Carolina; Fortuna, Mario; Brandán, Silvia A

2015-03-05

In this work, FT-IR, FT-Raman, UV-Visible and NMR spectroscopies and density functional theory (DFT) calculations were employed to study the structural and vibrational properties of the labdane-type diterpene 13-epi-sclareol using the hybrid B3LYP method together with the 6-31G(∗) basis set. Three stable structures with minimum energy found on the potential energy curves (PES) were optimized, and the corresponding molecular electrostatic potentials, atomic charges, bond orders, stabilization energies and topological properties were computed at the same approximation level. The complete assignment of the bands observed in the vibrational spectrum of 13-epi-sclareol was performed taking into account the internal symmetry coordinates for the three structures using the scaled quantum mechanical force field (SQMFF) methodology at the same level of theory. In addition, the force constants were calculated and compared with those reported in the literature for similar compounds. The predicted vibrational spectrum and the calculated (1)H NMR and (13)C NMR chemical shifts are in good agreement with the corresponding experimental results. The theoretical UV-Vis spectra for the most stable structure of 13-epi-sclareol demonstrate a better correlation with the corresponding experimental spectrum. The study of the three conformers by means of the theory of atoms in molecules (AIM) revealed different H bond interactions and a strong dependence of the interactions on the distance between the involved atoms. Furthermore, the natural bond orbital (NBO) calculations showed the characteristics of the electronic delocalization for the two six-membered rings with chair conformations. Copyright © 2014 Elsevier B.V. All rights reserved.

Comparing postdeposition reactions of electrons and radicals with Pt nanostructures created by focused electron beam induced deposition

PubMed Central

Spencer, Julie A; Barclay, Michael; Gallagher, Miranda J; Winkler, Robert; Unlu, Ilyas; Wu, Yung-Chien; Plank, Harald; McElwee-White, Lisa

2017-01-01

The ability of electrons and atomic hydrogen (AH) to remove residual chlorine from PtCl2 deposits created from cis-Pt(CO)2Cl2 by focused electron beam induced deposition (FEBID) is evaluated. Auger electron spectroscopy (AES) and energy-dispersive X-ray spectroscopy (EDS) measurements as well as thermodynamics calculations support the idea that electrons can remove chlorine from PtCl2 structures via an electron-stimulated desorption (ESD) process. It was found that the effectiveness of electrons to purify deposits greater than a few nanometers in height is compromised by the limited escape depth of the chloride ions generated in the purification step. In contrast, chlorine atoms can be efficiently and completely removed from PtCl2 deposits using AH, regardless of the thickness of the deposit. Although AH was found to be extremely effective at chemically purifying PtCl2 deposits, its viability as a FEBID purification strategy is compromised by the mobility of transient Pt–H species formed during the purification process. Scanning electron microscopy data show that this results in the formation of porous structures and can even cause the deposit to lose structural integrity. However, this phenomenon suggests that the use of AH may be a useful strategy to create high surface area Pt catalysts and may reverse the effects of sintering. In marked contrast to the effect observed with AH, densification of the structure was observed during the postdeposition purification of PtCx deposits created from MeCpPtMe3 using atomic oxygen (AO), although the limited penetration depth of AO restricts its effectiveness as a purification strategy to relatively small nanostructures. PMID:29234576

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

Thayer, K.J.

The past year has seen several of the Physics Division`s new research projects reach major milestones with first successful experiments and results: the atomic physics station in the Basic Energy Sciences Research Center at the Argonne Advanced Photon Source was used in first high-energy, high-brilliance x-ray studies in atomic and molecular physics; the Short Orbit Spectrometer in Hall C at the Thomas Jefferson National Accelerator (TJNAF) Facility that the Argonne medium energy nuclear physics group was responsible for, was used extensively in the first round of experiments at TJNAF; at ATLAS, several new beams of radioactive isotopes were developed andmore » used in studies of nuclear physics and nuclear astrophysics; the new ECR ion source at ATLAS was completed and first commissioning tests indicate excellent performance characteristics; Quantum Monte Carlo calculations of mass-8 nuclei were performed for the first time with realistic nucleon-nucleon interactions using state-of-the-art computers, including Argonne`s massively parallel IBM SP. At the same time other future projects are well under way: preparations for the move of Gammasphere to ATLAS in September 1997 have progressed as planned. These new efforts are imbedded in, or flowing from, the vibrant ongoing research program described in some detail in this report: nuclear structure and reactions with heavy ions; measurements of reactions of astrophysical interest; studies of nucleon and sub-nucleon structures using leptonic probes at intermediate and high energies; atomic and molecular structure with high-energy x-rays. The experimental efforts are being complemented with efforts in theory, from QCD to nucleon-meson systems to structure and reactions of nuclei. Finally, the operation of ATLAS as a national users facility has achieved a new milestone, with 5,800 hours beam on target for experiments during the past fiscal year.« less

Photoionization microscopy: Hydrogenic theory in semiparabolic coordinates and comparison with experimental results

NASA Astrophysics Data System (ADS)

Kalaitzis, P.; Danakas, S.; Lépine, F.; Bordas, C.; Cohen, S.

2018-05-01

Photoionization microscopy (PM) is an experimental method allowing for high-resolution measurements of the electron current probability density in the case of photoionization of an atom in an external uniform static electric field. PM is based on high-resolution velocity-map imaging and offers the unique opportunity to observe the quantum oscillatory spatial structure of the outgoing electron flux. We present the basic elements of the quantum-mechanical theoretical framework of PM for hydrogenic systems near threshold. Our development is based on the computationally more convenient semiparabolic coordinate system. Theoretical results are first subjected to a quantitative comparison with hydrogenic images corresponding to quasibound states and a qualitative comparison with nonresonant images of multielectron atoms. Subsequently, particular attention is paid on the structure of the electron's momentum distribution transversely to the static field (i.e., of the angularly integrated differential cross-section as a function of electron energy and radius of impact on the detector). Such 2D maps provide at a glance a complete picture of the peculiarities of the differential cross-section over the entire near-threshold energy range. Hydrogenic transverse momentum distributions are computed for the cases of the ground and excited initial states and single- and two-photon ionization schemes. Their characteristics of general nature are identified by comparing the hydrogenic distributions among themselves, as well as with a presently recorded experimental distribution concerning the magnesium atom. Finally, specificities attributed to different target atoms, initial states, and excitation scenarios are also discussed, along with directions of further work.

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

A Variational Monte Carlo Approach to Atomic Structure

ERIC Educational Resources Information Center

Davis, Stephen L.

2007-01-01

The practicality and usefulness of variational Monte Carlo calculations to atomic structure are demonstrated. It is found to succeed in quantitatively illustrating electron shielding, effective nuclear charge, l-dependence of the orbital energies, and singlet-tripetenergy splitting and ionization energy trends in atomic structure theory.

Adhesion and Atomic Structures of Gold on Ceria Nanostructures:The Role of Surface Structure and Oxidation State of Ceria Supports

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

Lin, Yuyuan; Wu, Zili; Wen, Jianguo

2015-01-01

Recent advances in heterogeneous catalysis have demonstrated that oxides supports with the same material but different shapes can result in metal catalysts with distinct catalytic properties. The shape-dependent catalysis was not well-understood owing to the lack of direct visualization of the atomic structures at metal-oxide interface. Herein, we utilized aberration-corrected electron microscopy and revealed the atomic structures of gold particles deposited on ceria nanocubes and nanorods with {100} or {111} facets exposed. For the ceria nanocube support, gold nanoparticles have extended atom layers at the metal-support interface. In contrast, regular gold nanoparticles and rafts are present on the ceria nanorodmore » support. After hours of water gas shift reaction, the extended gold atom layers and rafts vanish, which is associated with the decrease of the catalytic activities. By understanding the atomic structures of the support surfaces, metal-support interfaces, and morphologies of the gold particles, a direct structure-property relationship is established.« 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

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

First principles calculation of the structural, electronic, and magnetic properties of Au-Pd atomic chains

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

Dave, Mudra R., E-mail: mdave-phy@yahoo.co.in; Sharma, A. C.

2015-06-24

The structural, electronic and magnetic properties of free standing Au-Pd bimetallic atomic chain is studied using ab-initio method. It is found that electronic and magnetic properties of chains depend on position of atoms and number of atoms. Spin polarization factor for different atomic configuration of atomic chain is calculated predicting a half metallic behavior. It suggests a total spin polarised transport in these chains.

Big Atoms for Small Children: Building Atomic Models from Common Materials to Better Visualize and Conceptualize Atomic Structure

ERIC Educational Resources Information Center

Cipolla, Laura; Ferrari, Lia A.

2016-01-01

A hands-on approach to introduce the chemical elements and the atomic structure to elementary/middle school students is described. The proposed classroom activity presents Bohr models of atoms using common and inexpensive materials, such as nested plastic balls, colored modeling clay, and small-sized pasta (or small plastic beads).

Cryogenic STM in 3D vector magnetic fields realized through a rotatable insert.

PubMed

Trainer, C; Yim, C M; McLaren, M; Wahl, P

2017-09-01

Spin-polarized scanning tunneling microscopy (SP-STM) performed in vector magnetic fields promises atomic scale imaging of magnetic structure, providing complete information on the local spin texture of a sample in three dimensions. Here, we have designed and constructed a turntable system for a low temperature STM which in combination with a 2D vector magnet provides magnetic fields of up to 5 T in any direction relative to the tip-sample geometry. This enables STM imaging and spectroscopy to be performed at the same atomic-scale location and field-of-view on the sample, and most importantly, without experiencing any change on the tip apex before and after field switching. Combined with a ferromagnetic tip, this enables us to study the magnetization of complex magnetic orders in all three spatial directions.

Structural and magnetic properties of FeGen-/0 (n = 3-12) clusters: Mass-selected anion photoelectron spectroscopy and density functional theory calculations

NASA Astrophysics Data System (ADS)

Deng, Xiao-Jiao; Kong, Xiang-Yu; Liang, Xiaoqing; Yang, Bin; Xu, Hong-Guang; Xu, Xi-Ling; Feng, Gang; Zheng, Wei-Jun

2017-12-01

The structural, electronic, and magnetic properties of FeGen-/0 (n = 3-12) clusters were investigated by using anion photoelectron spectroscopy in combination with density functional theory calculations. For both anionic and neutral FeGen (n = 3-12) clusters with n ≤ 7, the dominant structures are exohedral. The FeGe8-/0 clusters have half-encapsulated boat-shaped structures, and the opening of the boat-shaped structure is gradually covered by the additional Ge atoms to form Gen cage from n = 9 to 11. The structures of FeGe10-/0 can be viewed as two Ge atoms symmetrically capping the opening of the boat-shaped structure of FeGe8, and those of FeGe12-/0 are distorted hexagonal prisms with the Fe atom at the center. Natural population analysis shows that there is an electron transfer from the Ge atoms to the Fe atom at n = 8-12. The total magnetic moment of FeGen-/0 and local magnetic moment of the Fe atom have not been quenched.

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.

Name that compound: The numbers game for CFCs, HFCs, HCFCs, and Halons

DOE Data Explorer

Blasing, T. J.; Jones, Sonja

2012-02-01

Chlorofluorocarbons (CFCs) contain Carbon and some combination of Fluorine and Chlorine atoms. Hydrofluorocarbons (HFCs) contain Hydrogen, Fluorine, and Carbon (no chlorine). Hydrochlorofluorocarbons (HCFCs) contain Hydrogen, Chlorine, Fluorine, and Carbon atoms. Hydrobromofluorocarbons (HBFCs) contain Hydrogen, Bromine, Fluorine, and Carbon atoms. Perfluorocarbons contain Fluorine, Carbon, and Bromine atoms, and some contain Chlorine and/or Hydrogen atoms. These compounds are often designated by a combination of letters and numbers (e.g., CFC-11, HCFC-142b). In the latter example, the lower-case b refers to an isomer, which has no relationship to the chemical formula (C2H3F2Cl), but designates a particular structural arrangement of the atoms included. For example, HCFC-142b identifies the isomer in which all three hydrogen atoms are attached to the same carbon atom, and the structural formula is written as CH3CF2Cl. By contrast, HCFC-142 (without the b) refers to an arrangement in which one carbon atom is attached to two hydrogen atoms and one chlorine atom, while the other carbon atom is attached to the third hydrogen atom and two fluorine atoms. Hence, it has a different structural formula (CH2ClCHF2).

Unique atom hyper-kagome order in Na4Ir3O8 and in low-symmetry spinel modifications.

PubMed

Talanov, V M; Shirokov, V B; Talanov, M V

2015-05-01

Group-theoretical and thermodynamic methods of the Landau theory of phase transitions are used to investigate the hyper-kagome atomic order in structures of ordered spinels and a spinel-like Na4Ir3O8 crystal. The formation of an atom hyper-kagome sublattice in Na4Ir3O8 is described theoretically on the basis of the archetype (hypothetical parent structure/phase) concept. The archetype structure of Na4Ir3O8 has a spinel-like structure (space group Fd\\bar 3m) and composition [Na1/2Ir3/2](16d)[Na3/2](16c)O(32e)4. The critical order parameter which induces hypothetical phase transition has been stated. It is shown that the derived structure of Na4Ir3O8 is formed as a result of the displacements of Na, Ir and O atoms, and ordering of Na, Ir and O atoms, ordering dxy, dxz, dyz orbitals as well. Ordering of all atoms takes place according to the type 1:3. Ir and Na atoms form an intriguing atom order: a network of corner-shared Ir triangles called a hyper-kagome lattice. The Ir atoms form nanoclusters which are named decagons. The existence of hyper-kagome lattices in six types of ordered spinel structures is predicted theoretically. The structure mechanisms of the formation of the predicted hyper-kagome atom order in some ordered spinel phases are established. For a number of cases typical diagrams of possible crystal phase states are built in the framework of the Landau theory of phase transitions. Thermodynamical conditions of hyper-kagome order formation are discussed by means of these diagrams. The proposed theory is in accordance with experimental data.

Structural Characterization of Am(III)- and Pu(III)-DOTA Complexes.

PubMed

Audras, Matthieu; Berthon, Laurence; Berthon, Claude; Guillaumont, Dominique; Dumas, Thomas; Illy, Marie-Claire; Martin, Nicolas; Zilbermann, Israel; Moiseev, Yulia; Ben-Eliyahu, Yeshayahu; Bettelheim, Armand; Cammelli, Sebastiano; Hennig, Christoph; Moisy, Philippe

2017-10-16

The complexation of 1,4,7,10-tetrazacyclodecane-1,4,7,10-tetraacetic acid (DOTA) ligand with two trivalent actinides (Am 3+ and Pu 3+ ) was investigated by UV-visible spectrophotometry, NMR spectroscopy, and extended X-ray absorption fine structure in conjunction with computational methods. The complexation process of these two cations is similar to what has been previously observed with lanthanides(III) of similar ionic radius. The complexation takes place in different steps and ends with the formation of a (1:1) complex [(An(III)DOTA)(H 2 O)] - , where the cation is bonded to the nitrogen atoms of the ring, the four carboxylate arms, and a water molecule to complete the coordination sphere. The formation of An(III)-DOTA complexes is faster than the Ln(III)-DOTA systems of equivalent ionic radius. Furthermore, it is found that An-N distances are slightly shorter than Ln-N distances. Theoretical calculations showed that the slightly higher affinity of DOTA toward Am over Nd is correlated with slightly enhanced ligand-to-metal charge donation arising from oxygen and nitrogen atoms.

Physical nature of surface structure degradation in long term operated rails

NASA Astrophysics Data System (ADS)

Gromov, V. E.; Yuriev, A. A.; Peregudov, O. A.; Konovalov, S. V.; Ivanov, Yu. F.; Glezer, A. M.; Semin, A. P.

2017-12-01

Here we present research data on the structural-phase state and surface properties of rails after long-term operation with a transported tonnage of gross weight 500 and 1000 mln tons. Using optical, scanning, and transmission electron diffraction microscopy, and measurements of microhardness and tribological parameters, it is shown that the wear rate of the material after transport of 500 and 1000 mln tons increases 3 and 3.4 times, respectively, and the friction coefficient decreases 1.4 and 1.1 times. After transport of 500 mln tons, complete failure of cementite plates occurs resulting in round cementite particles of size 10-50 nm. After transport of 1000 mln tons, dynamic recrystallization develops in the material. Two competitive mechanisms are suggested for such evolution: (1) decomposition of cementite particles with their transfer to the volume of ferrite grains or plates in pearlite and (2) decomposition and dissolution of cementite particles, transition of carbon atoms to dislocations (to Cottrell atmospheres), transfer of carbon atoms by dislocations to the volume of ferrite grains or plates, and formation of nano-sized cementite particles.

F-RAG: Generating Atomic Coordinates from RNA Graphs by Fragment Assembly.

PubMed

Jain, Swati; Schlick, Tamar

2017-11-24

Coarse-grained models represent attractive approaches to analyze and simulate ribonucleic acid (RNA) molecules, for example, for structure prediction and design, as they simplify the RNA structure to reduce the conformational search space. Our structure prediction protocol RAGTOP (RNA-As-Graphs Topology Prediction) represents RNA structures as tree graphs and samples graph topologies to produce candidate graphs. However, for a more detailed study and analysis, construction of atomic from coarse-grained models is required. Here we present our graph-based fragment assembly algorithm (F-RAG) to convert candidate three-dimensional (3D) tree graph models, produced by RAGTOP into atomic structures. We use our related RAG-3D utilities to partition graphs into subgraphs and search for structurally similar atomic fragments in a data set of RNA 3D structures. The fragments are edited and superimposed using common residues, full atomic models are scored using RAGTOP's knowledge-based potential, and geometries of top scoring models is optimized. To evaluate our models, we assess all-atom RMSDs and Interaction Network Fidelity (a measure of residue interactions) with respect to experimentally solved structures and compare our results to other fragment assembly programs. For a set of 50 RNA structures, we obtain atomic models with reasonable geometries and interactions, particularly good for RNAs containing junctions. Additional improvements to our protocol and databases are outlined. These results provide a good foundation for further work on RNA structure prediction and design applications. Copyright © 2017 Elsevier Ltd. All rights reserved.

Clustering algorithms for identifying core atom sets and for assessing the precision of protein structure ensembles.

PubMed

Snyder, David A; Montelione, Gaetano T

2005-06-01

An important open question in the field of NMR-based biomolecular structure determination is how best to characterize the precision of the resulting ensemble of structures. Typically, the RMSD, as minimized in superimposing the ensemble of structures, is the preferred measure of precision. However, the presence of poorly determined atomic coordinates and multiple "RMSD-stable domains"--locally well-defined regions that are not aligned in global superimpositions--complicate RMSD calculations. In this paper, we present a method, based on a novel, structurally defined order parameter, for identifying a set of core atoms to use in determining superimpositions for RMSD calculations. In addition we present a method for deciding whether to partition that core atom set into "RMSD-stable domains" and, if so, how to determine partitioning of the core atom set. We demonstrate our algorithm and its application in calculating statistically sound RMSD values by applying it to a set of NMR-derived structural ensembles, superimposing each RMSD-stable domain (or the entire core atom set, where appropriate) found in each protein structure under consideration. A parameter calculated by our algorithm using a novel, kurtosis-based criterion, the epsilon-value, is a measure of precision of the superimposition that complements the RMSD. In addition, we compare our algorithm with previously described algorithms for determining core atom sets. The methods presented in this paper for biomolecular structure superimposition are quite general, and have application in many areas of structural bioinformatics and structural biology.

Unbiased, scalable sampling of protein loop conformations from probabilistic priors.

PubMed

Zhang, Yajia; Hauser, Kris

2013-01-01

Protein loops are flexible structures that are intimately tied to function, but understanding loop motion and generating loop conformation ensembles remain significant computational challenges. Discrete search techniques scale poorly to large loops, optimization and molecular dynamics techniques are prone to local minima, and inverse kinematics techniques can only incorporate structural preferences in adhoc fashion. This paper presents Sub-Loop Inverse Kinematics Monte Carlo (SLIKMC), a new Markov chain Monte Carlo algorithm for generating conformations of closed loops according to experimentally available, heterogeneous structural preferences. Our simulation experiments demonstrate that the method computes high-scoring conformations of large loops (>10 residues) orders of magnitude faster than standard Monte Carlo and discrete search techniques. Two new developments contribute to the scalability of the new method. First, structural preferences are specified via a probabilistic graphical model (PGM) that links conformation variables, spatial variables (e.g., atom positions), constraints and prior information in a unified framework. The method uses a sparse PGM that exploits locality of interactions between atoms and residues. Second, a novel method for sampling sub-loops is developed to generate statistically unbiased samples of probability densities restricted by loop-closure constraints. Numerical experiments confirm that SLIKMC generates conformation ensembles that are statistically consistent with specified structural preferences. Protein conformations with 100+ residues are sampled on standard PC hardware in seconds. Application to proteins involved in ion-binding demonstrate its potential as a tool for loop ensemble generation and missing structure completion.

Unbiased, scalable sampling of protein loop conformations from probabilistic priors

PubMed Central

2013-01-01

Background Protein loops are flexible structures that are intimately tied to function, but understanding loop motion and generating loop conformation ensembles remain significant computational challenges. Discrete search techniques scale poorly to large loops, optimization and molecular dynamics techniques are prone to local minima, and inverse kinematics techniques can only incorporate structural preferences in adhoc fashion. This paper presents Sub-Loop Inverse Kinematics Monte Carlo (SLIKMC), a new Markov chain Monte Carlo algorithm for generating conformations of closed loops according to experimentally available, heterogeneous structural preferences. Results Our simulation experiments demonstrate that the method computes high-scoring conformations of large loops (>10 residues) orders of magnitude faster than standard Monte Carlo and discrete search techniques. Two new developments contribute to the scalability of the new method. First, structural preferences are specified via a probabilistic graphical model (PGM) that links conformation variables, spatial variables (e.g., atom positions), constraints and prior information in a unified framework. The method uses a sparse PGM that exploits locality of interactions between atoms and residues. Second, a novel method for sampling sub-loops is developed to generate statistically unbiased samples of probability densities restricted by loop-closure constraints. Conclusion Numerical experiments confirm that SLIKMC generates conformation ensembles that are statistically consistent with specified structural preferences. Protein conformations with 100+ residues are sampled on standard PC hardware in seconds. Application to proteins involved in ion-binding demonstrate its potential as a tool for loop ensemble generation and missing structure completion. PMID:24565175

An atomic model for neutral and singly ionized uranium

NASA Technical Reports Server (NTRS)

Maceda, E. L.; Miley, G. H.

1979-01-01

A model for the atomic levels above ground state in neutral, U(0), and singly ionized, U(+), uranium is described based on identified atomic transitions. Some 168 states in U(0) and 95 in U(+) are found. A total of 1581 atomic transitions are used to complete this process. Also discussed are the atomic inverse lifetimes and line widths for the radiative transitions as well as the electron collisional cross sections.

Atoms in molecules, an axiomatic approach. I. Maximum transferability

NASA Astrophysics Data System (ADS)

Ayers, Paul W.

2000-12-01

Central to chemistry is the concept of transferability: the idea that atoms and functional groups retain certain characteristic properties in a wide variety of environments. Providing a completely satisfactory mathematical basis for the concept of atoms in molecules, however, has proved difficult. The present article pursues an axiomatic basis for the concept of an atom within a molecule, with particular emphasis devoted to the definition of transferability and the atomic description of Hirshfeld.

Symmetry and electronic structure of noble-metal nanoparticles and the role of relativity.

PubMed

Häkkinen, Hannu; Moseler, Michael; Kostko, Oleg; Morgner, Nina; Hoffmann, Margarita Astruc; von Issendorff, Bernd

2004-08-27

We present high resolution UV-photoelectron spectra of cold mass selected Cun-, Agn-, and Aun- with n=53-58. The observed electron density of states is not the expected simple electron shell structure, but is strongly influenced by electron-lattice interactions. Only Cu55- and Ag55- exhibit highly degenerate states. This is a direct consequence of their icosahedral symmetry, as is confirmed by density functional theory calculations. Neighboring sizes exhibit perturbed electronic structures, as they are formed by removal or addition of atoms to the icosahedron and therefore have lower symmetries. Gold clusters in the same size range show completely different spectra with almost no degeneracy, which indicates that they have structures of much lower symmetry. This behavior is related to strong relativistic bonding effects in gold, as demonstrated by ab initio calculations for Au55-.

Principle and Reconstruction Algorithm for Atomic-Resolution Holography

NASA Astrophysics Data System (ADS)

Matsushita, Tomohiro; Muro, Takayuki; Matsui, Fumihiko; Happo, Naohisa; Hosokawa, Shinya; Ohoyama, Kenji; Sato-Tomita, Ayana; Sasaki, Yuji C.; Hayashi, Kouichi

2018-06-01

Atomic-resolution holography makes it possible to obtain the three-dimensional (3D) structure around a target atomic site. Translational symmetry of the atomic arrangement of the sample is not necessary, and the 3D atomic image can be measured when the local structure of the target atomic site is oriented. Therefore, 3D local atomic structures such as dopants and adsorbates are observable. Here, the atomic-resolution holography comprising photoelectron holography, X-ray fluorescence holography, neutron holography, and their inverse modes are treated. Although the measurement methods are different, they can be handled with a unified theory. The algorithm for reconstructing 3D atomic images from holograms plays an important role. Although Fourier transform-based methods have been proposed, they require the multiple-energy holograms. In addition, they cannot be directly applied to photoelectron holography because of the phase shift problem. We have developed methods based on the fitting method for reconstructing from single-energy and photoelectron holograms. The developed methods are applicable to all types of atomic-resolution holography.

Density functional theory calculations establish the experimental evidence of the DX center atomic structure in CdTe.

PubMed

Lany, Stephan; Wolf, Herbert; Wichert, Thomas

2004-06-04

The In DX center and the DX-like configuration of the Cd host atom in CdTe are investigated using density functional theory. The simultaneous calculation of the atomic structure and the electric field gradient (EFG) allows one to correlate the theoretically predicted structure of the DX center with an experimental observable, namely, the EFG obtained from radioactive 111In/111Cd probe atoms in In doped CdTe. In this way, the experimental identification of the DX center structure is established.

Exploring the atomic structure of 1.8nm monolayer-protected gold clusters with aberration-corrected STEM.

PubMed

Liu, Jian; Jian, Nan; Ornelas, Isabel; Pattison, Alexander J; Lahtinen, Tanja; Salorinne, Kirsi; Häkkinen, Hannu; Palmer, Richard E

2017-05-01

Monolayer-protected (MP) Au clusters present attractive quantum systems with a range of potential applications e.g. in catalysis. Knowledge of the atomic structure is needed to obtain a full understanding of their intriguing physical and chemical properties. Here we employed aberration-corrected scanning transmission electron microscopy (ac-STEM), combined with multislice simulations, to make a round-robin investigation of the atomic structure of chemically synthesised clusters with nominal composition Au 144 (SCH 2 CH 2 Ph) 60 provided by two different research groups. The MP Au clusters were "weighed" by the atom counting method, based on their integrated intensities in the high angle annular dark field (HAADF) regime and calibrated exponent of the Z dependence. For atomic structure analysis, we compared experimental images of hundreds of clusters, with atomic resolution, against a variety of structural models. Across the size range 123-151 atoms, only 3% of clusters matched the theoretically predicted Au 144 (SR) 60 structure, while a large proportion of the clusters were amorphous (i.e. did not match any model structure). However, a distinct ring-dot feature, characteristic of local icosahedral symmetry, was observed in about 20% of the clusters. Copyright © 2017. Published by Elsevier B.V.

‘Pd20Sn13’ revisited: crystal structure of Pd6.69Sn4.31

PubMed Central

Klein, Wilhelm; Jin, Hanpeng; Hlukhyy, Viktor; Fässler, Thomas F.

2015-01-01

The crystal structure of the title compound was previously reported with composition ‘Pd20Sn13’ [Sarah et al. (1981 ▸). Z. Metallkd, 72, 517–520]. For the original structure model, as determined from powder X-ray data, atomic coordinates from the isostructural compound Ni13Ga3Ge6 were transferred. The present structure determination, resulting in a composition Pd6.69Sn4.31, is based on single crystal X-ray data and includes anisotropic displacement parameters for all atoms as well as standard uncertainties for the atomic coordinates, leading to higher precision and accuracy for the structure model. Single crystals of the title compound were obtained via a solid-state reaction route, starting from the elements. The crystal structure can be derived from the AlB2 type of structure after removing one eighth of the atoms at the boron positions and shifting adjacent atoms in the same layer in the direction of the voids. One atomic site is partially occupied by both elements with a Pd:Sn ratio of 0.38 (3):0.62 (3). One Sn and three Pd atoms are located on special positions with site symmetry 2. (Wyckoff letter 3a and 3b). PMID:26279872

Atomic scale structure and chemistry of interfaces by Z-contrast imaging and electron energy loss spectroscopy in the stem

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

McGibbon, M.M.; Browning, N.D.; Chisholm, M.F.

The macroscopic properties of many materials are controlled by the structure and chemistry at grain boundaries. A basic understanding of the structure-property relationship requires a technique which probes both composition and chemical bonding on an atomic scale. High-resolution Z-contrast imaging in the scanning transmission electron microscope (STEM) forms an incoherent image in which changes in atomic structure and composition across an interface can be interpreted directly without the need for preconceived atomic structure models. Since the Z-contrast image is formed by electrons scattered through high angles, parallel detection electron energy loss spectroscopy (PEELS) can be used simultaneously to provide complementarymore » chemical information on an atomic scale. The fine structure in the PEEL spectra can be used to investigate the local electronic structure and the nature of the bonding across the interface. In this paper we use the complimentary techniques of high resolution Z-contrast imaging and PEELS to investigate the atomic structure and chemistry of a 25{degree} symmetric tilt boundary in a bicrystal of the electroceramic SrTiO{sub 3}.« less

Quantitative determination of the conformational properties of partially folded and intrinsically disordered proteins using NMR dipolar couplings.

PubMed

Jensen, Malene Ringkjøbing; Markwick, Phineus R L; Meier, Sebastian; Griesinger, Christian; Zweckstetter, Markus; Grzesiek, Stephan; Bernadó, Pau; Blackledge, Martin

2009-09-09

Intrinsically disordered proteins (IDPs) inhabit a conformational landscape that is too complex to be described by classical structural biology, posing an entirely new set of questions concerning the molecular understanding of functional biology. The characterization of the conformational properties of IDPs, and the elucidation of the role they play in molecular function, is therefore one of the major challenges remaining for modern structural biology. NMR is the technique of choice for studying this class of proteins, providing information about structure, flexibility, and interactions at atomic resolution even in completely disordered states. In particular, residual dipolar couplings (RDCs) have been shown to be uniquely sensitive and powerful tools for characterizing local and long-range structural behavior in disordered proteins. In this review we describe recent applications of RDCs to quantitatively describe the level of local structure and transient long-range order in IDPs involved in viral replication, neurodegenerative disease, and cancer.

The Influence of Milling and Spark Plasma Sintering on the Microstructure and Properties of the Al7075 Alloy

PubMed Central

Málek, Přemysl; Minárik, Peter; Novák, Pavel; Průša, Filip

2018-01-01

The compact samples of an Al7075 alloy were prepared by a combination of gas atomization, high energy milling, and spark plasma sintering. The predominantly cellular morphology observed in gas atomized powder particles was completely changed by mechanical milling. The continuous-like intermetallic phases present along intercellular boundaries were destroyed; nevertheless, a small amount of Mg(Zn,Cu,Al)2 phase was observed also in the milled powder. Milling resulted in a severe plastic deformation of the material and led to a reduction of grain size from several µm into the nanocrystalline region. The combination of these microstructural characteristics resulted in abnormally high microhardness values exceeding 300 HV. Consolidation through spark plasma sintering (SPS) resulted in bulk samples with negligible porosity. The heat exposition during SPS led to precipitation of intermetallic phases from the non-equilibrium microstructure of both gas atomized and milled powders. SPS of the milled powder resulted in a recrystallization of the severely deformed structure. An ultra-fine grained structure (grain size close to 500 nm) with grains divided primarily by high-angle boundaries was formed. A simultaneous release of stored deformation energy and an increase in the grain size caused a drop of microhardness to values close to 150 HV. This value was retained even after annealing at 425 °C. PMID:29614046

Lattice instability and elastic response of metastable Mo1-xSix thin films

NASA Astrophysics Data System (ADS)

Fillon, A.; Jaouen, C.; Michel, A.; Abadias, G.; Tromas, C.; Belliard, L.; Perrin, B.; Djemia, Ph.

2013-11-01

We present a detailed experimental study on Mo1-xSix thin films, an archetypal alloy system combining metallic and semiconductor materials. The correlations between structure and elastic response are comprehensively investigated. We focus on assessing trends for understanding the evolution of elastic properties upon Si alloying in relation to the structural state (crystalline vs amorphous), bonding character (metallic vs covalent), and local atomic environment. By combining picosecond ultrasonics and Brillouin light scattering techniques, a complete set of effective elastic constants and mechanical moduli (B, G, E) is provided in the whole compositional range, covering bcc solid solutions (x < 0.20) and the amorphous phase (0.20 < x < 1.0). A softening of the shear and Young moduli and a concomitant decrease of the Debye temperature is revealed for crystalline alloys, with a significant drop being observed at x ˜ 0.2 corresponding to the limit of crystal lattice stability. Amorphous alloys exhibit a more complex elastic response, related to variations in coordination number, atomic volume, and bonding state, depending on Si content. Finally, distinct evolutions of the G/B ratio as a function of Cauchy pressure are reported for crystalline and amorphous alloys, enabling us to identify signatures of ductility vs brittleness in the features of the local atomic environment. This work paves the way to design materials with improved mechanical properties by appropriate chemical substitution or impurity incorporation during thin-film growth.

Local Structures of High-Entropy Alloys (HEAs) on Atomic Scales: An Overview

DOE PAGES

Diao, Haoyan; Santodonato, Louis J.; Tang, Zhi; ...

2015-08-29

The high-entropy alloys (HEAs), containing several elements mixed in equimolar or near-equimolar ratios, have shown exceptional engineering properties. Local structures on atomic level are essential to understand the mechanical behaviors and related mechanisms. In this paper, the local structure and stress on the atomic level are reviewed by the pair-distribution function (PDF) of neutron-diffraction data, ab-initio-molecular-dynamics (AIMD) simulations, and atomic-probe microscopy (APT).

A complete vibrational study on a potential environmental toxicant agent, the 3,3',4,4'-tetrachloroazobenzene combining the FTIR, FTRaman, UV-Visible and NMR spectroscopies with DFT calculations.

PubMed

Castillo, María V; Pergomet, Jorgelina L; Carnavale, Gustavo A; Davies, Lilian; Zinczuk, Juan; Brandán, Silvia A

2015-01-05

In this study 3,3',4,4'-tetrachloroazobenzene (TCAB) was prepared and then characterized by infrared, Raman, multidimensional nuclear magnetic resonance (NMR) and ultraviolet-visible spectroscopies. The density functional theory (DFT) together with the 6-31G(*) and 6-311++G(**) basis sets were used to study the structures and vibrational properties of the two cis and trans isomers of TCAB. The harmonic vibrational wavenumbers for the optimized geometries were calculated at the same theory levels. A complete assignment of all the observed bands in the vibrational spectra of TCAB was performed combining the DFT calculations with the scaled quantum mechanical force field (SQMFF) methodology. The molecular electrostatic potentials, atomic charges, bond orders and frontier orbitals for the two isomers of TCAB were compared and analyzed. The comparison of the theoretical ultraviolet-visible spectrum with the corresponding experimental demonstrates a good concordance while the calculated (1)H and (13)C chemicals shifts are in good conformity with the corresponding experimental NMR spectra of TCAB in solution. The npp(*) transitions for both forms were studied by natural bond orbital (NBO) while the topological properties were calculated by employing Bader's Atoms in the Molecules (AIM) theory. This study shows that the cis and trans isomers exhibit different structural and vibrational properties and absorption bands. Copyright © 2014. Published by Elsevier B.V.

Atomic and electronic structure of Pd40Ni40P20 bulk metallic glass from ab initio simulations

NASA Astrophysics Data System (ADS)

Kumar, Vijay; Fujita, T.; Konno, K.; Matsuura, M.; Chen, M. W.; Inoue, A.; Kawazoe, Y.

2011-10-01

The atomic structure of Pd40Ni40P20 bulk metallic glass has been simulated using an ab initio molecular dynamics method with projector-augmented wave pseudopotentials for electron-ion interaction and generalized gradient approximation for exchange-correlation energy. The calculated extended x-ray absorption fine structure (EXAFS) spectra of Pd-K and Ni-K edges, the mass density, and the electronic structure agree remarkably well with the available experimental data and the EXAFS spectra measured at the SPring-8 synchrotron radiation facility. Our results show that the atomic structure can be described in terms of P-centered polyhedra. There are no two P atoms that are nearest neighbors at this composition, and this could be a reason for the observed optimal P concentration of about 20 at.%. The neighboring polyhedra share metal (M) atoms and form a polar covalently bonded random network of P-M-P favoring certain angles. The remaining M atoms act as metallic glue with a tendency of nanoscale clustering of Pd-Pd and Ni-Ni atoms.

A New Method for Studying the Atom: Optical spectra for multiply ionized atoms are produced by means of nuclear-physics techniques.

PubMed

Bashkin, S

1965-05-21

The new spectroscopy is in its infancy, and many fascinating aspects are yet to be studied. The properties of thin films may be studied by means of the excitation they induce in a given kind of beam. The production of ions with but a single electron offers a means of carefully mapping the nuclear charge distribution without the complications introduced by the normal complement of electrons. The study of high-purity, multiply ionized particles should make for better temperature determinations in hot plasmas. Possibly the data on lifetimes and modes of decay of excited energy levels may assist in the quantitative assignment of element abundances in the stars. One can even attempt to use the glowing beams as sources for absorption spectroscopy. The method seems to permit study of every stage of excitation for every stage of ionization for every element in the periodic table. Practical problems may interfere with so complete a study, but a major extension of our knowledge of atomic structure seems to be at hand.

An overview of ALARA considerations during Yankee Atomic`s Component Removal Project

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

Granados, B.; Babineau, G.; Colby, B.

1995-03-01

In Februrary 1992, Yankee Atomic Electric Company (YAEC) permanently shutdown Yankee Nuclear Power Station in Rowe, Massachusetts, after thirty-two years of efficient operation. Yankee`s plan decommissioning is to defer dismantlement until a low level radioactive waste (LLRW) disposal facility is available. The plant will be maintained in a safe storage condition until a firm contract for the disposal of LLRW generated during decommissioning can be secured. Limited access to a LLRW disposal facility may occur during the safe storage period. Yankee intends to use these opportunities to remove components and structures. A Component Removal Project (CRP) was initiated in 1993more » to take advantage of one of these opportunities. A Componenet Removal Project (CRP) was initiated in 1993 to take advantage of one of these opportunities. The CRP includes removal of four steam generators, the pressurizer, and segmentation of reactor vessel internals and preparation of LLRW for shipment and disposal at Chem-Nuclear`s Barnwell, South Carolina facility. The CRP is projected to be completed by June 1994 at an estimated total worker exposure of less than 160 person-rem.« less

DFT analysis on the molecular structure, vibrational and electronic spectra of 2-(cyclohexylamino)ethanesulfonic acid.

PubMed

Renuga Devi, T S; Sharmi kumar, J; Ramkumaar, G R

2015-02-25

The FTIR and FT-Raman spectra of 2-(cyclohexylamino)ethanesulfonic acid were recorded in the regions 4000-400 cm(-1) and 4000-50 cm(-1) respectively. The structural and spectroscopic data of the molecule in the ground state were calculated using Hartee-Fock and Density functional method (B3LYP) with the correlation consistent-polarized valence double zeta (cc-pVDZ) basis set and 6-311++G(d,p) basis set. The most stable conformer was optimized and the structural and vibrational parameters were determined based on this. The complete assignments were performed based on the Potential Energy Distribution (PED) of the vibrational modes, calculated using Vibrational Energy Distribution Analysis (VEDA) 4 program. With the observed FTIR and FT-Raman data, a complete vibrational assignment and analysis of the fundamental modes of the compound were carried out. Thermodynamic properties and Atomic charges were calculated using both Hartee-Fock and density functional method using the cc-pVDZ basis set and compared. The calculated HOMO-LUMO energy gap revealed that charge transfer occurs within the molecule. (1)H and (13)C NMR chemical shifts of the molecule were calculated using Gauge Including Atomic Orbital (GIAO) method and were compared with experimental results. Stability of the molecule arising from hyperconjugative interactions, charge delocalization have been analyzed using Natural Bond Orbital (NBO) analysis. The first order hyperpolarizability (β) and Molecular Electrostatic Potential (MEP) of the molecule was computed using DFT calculations. The electron density based local reactivity descriptor such as Fukui functions were calculated to explain the chemical reactivity site in the molecule. Copyright © 2014 Elsevier B.V. All rights reserved.

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

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

Bindi, Luca; Garavelli, Anna; Pinto, Daniela

2008-02-15

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

CFD Growth of 3C-SiC on 4H/6H Mesas

NASA Technical Reports Server (NTRS)

Neudeck, Philip G.; Trunek, Andrew J.; Spry, David J.; Powell, J. Anthony; Du, Hui; Skowronski, Marek; Huang, XianRong; Dudley, Michael

2006-01-01

This article describes growth and characterization of the highest quality reproducible 3C-SiC heteroepitaxial films ever reported. By properly nucleating 3C-SiC growth on top of perfectly on-axis (0001) 4H-SiC mesa surfaces completely free of atomic scale steps and extended defects, growth of 3C-SiC mesa heterofilms completely free of extended crystal defects can be achieved. In contrast, nucleation and growth of 3C-SiC mesa heterofilms on top of 4H-SiC mesas with atomic-scale steps always results in numerous observable dislocations threading through the 3C-SiC epilayer. High-resolution X-ray diffraction and transmission electron microscopy measurements indicate non-trivial in-plane lattice mismatch between the 3C and 4H layers. This mismatch is somewhat relieved in the step-free mesa case via misfit dislocations confined to the 3C/4H interfacial region without dislocations threading into the overlying 3C-SiC layer. These results indicate that the presence or absence of steps at the 3C/4H heteroepitaxial interface critically impacts the quality, defect structure, and relaxation mechanisms of single-crystal heteroepitaxial 3C-SiC films.

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

NASA Astrophysics Data System (ADS)

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

2018-04-01

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

Bis(dicyclo-hexyl-ammonium) μ-oxalato-κO,O:O,O-bis-[aqua-(oxalato-κO,O)diphenyl-stannate(IV)].

PubMed

Gueye, Ndongo; Diop, Libasse; Molloy, K C Kieran; Kociok-Köhn, Gabrielle

2010-11-24

The structure of the title compound, (C(12)H(24)N)(2)[Sn(2)(C(6)H(5))(4)(C(2)O(4))(3)(H(2)O)(2)], consists of a bischelating oxalate ion, located on an inversion center, which is linked to two SnPh(2) groups. The coordination sphere of the Sn(IV) ion is completed by a monochelating oxalate anion and a water mol-ecule. The Sn(IV) atoms are thus seven-coordinated. The discrete binuclear units are further connected by hydrogen bonds, leading to a supra-molecular crystal structure. The asymmetric unit contains one half dianion and one (Cy(2)NH(2))(+) cation.

On the relationship between residue structural environment and sequence conservation in proteins.

PubMed

Liu, Jen-Wei; Lin, Jau-Ji; Cheng, Chih-Wen; Lin, Yu-Feng; Hwang, Jenn-Kang; Huang, Tsun-Tsao

2017-09-01

Residues that are crucial to protein function or structure are usually evolutionarily conserved. To identify the important residues in protein, sequence conservation is estimated, and current methods rely upon the unbiased collection of homologous sequences. Surprisingly, our previous studies have shown that the sequence conservation is closely correlated with the weighted contact number (WCN), a measure of packing density for residue's structural environment, calculated only based on the C α positions of a protein structure. Moreover, studies have shown that sequence conservation is correlated with environment-related structural properties calculated based on different protein substructures, such as a protein's all atoms, backbone atoms, side-chain atoms, or side-chain centroid. To know whether the C α atomic positions are adequate to show the relationship between residue environment and sequence conservation or not, here we compared C α atoms with other substructures in their contributions to the sequence conservation. Our results show that C α positions are substantially equivalent to the other substructures in calculations of various measures of residue environment. As a result, the overlapping contributions between C α atoms and the other substructures are high, yielding similar structure-conservation relationship. Take the WCN as an example, the average overlapping contribution to sequence conservation is 87% between C α and all-atom substructures. These results indicate that only C α atoms of a protein structure could reflect sequence conservation at the residue level. © 2017 Wiley Periodicals, Inc.

Resonance of an unshared electron pair between two atoms connected by a single bond

PubMed Central

Pauling, Linus

1983-01-01

The reported structure of the dimer of a compound of bicovalent tin indicates that the tin-tin bond is of a new type. It can be described as involving resonance between two structures in which there is transfer of an electron pair from one tin atom to the other. The tin atoms are connected by a single covalent bond (each also forms two covalent bonds with carbon atoms), and an unshared electron pair resonates between the fourth sp3 orbitals of the two atoms. Similar structures probably occur in digermene and distannene. PMID:16593329

Nano Electronics on Atomically Controlled van der Waals Quantum Heterostructures

DTIC Science & Technology

2015-03-30

for the structural of the atomically sharp interface between hBN and Bi2Te3. Finally, we have developed unprecedentedly clean graphene supercoductor...crystals by MBE method. We also use transmission electron microscopy (TEM) analysis for the structural of the atomically sharp interface between hBN and...by MBE method. We also use transmission electron microscopy (TEM) analysis for the structural of the atomically sharp interface between hBN and Bi2Te3

First-principles study on silicon atom doped monolayer graphene

NASA Astrophysics Data System (ADS)

Rafique, Muhammad; Shuai, Yong; Hussain, Nayyar

2018-01-01

This paper illustrates the structural, electronic and optical properties of individual silicon (Si) atom-doped single layer graphene using density functional theory method. Si atom forms tight bonding with graphene layer. The effect of doping has been investigated by varying the concentration of Si atoms from 3.125% to 9.37% (i.e. From one to three Si atoms in 4 × 4 pure graphene supercell containing 32 carbon atoms), respectively. Electronic structure, partial density of states (PDOS) and optical properties of pure and Si atom-doped graphene sheet were calculated using VASP (Vienna ab-initio Simulation Package). The calculated results for pure graphene sheet were then compared with Si atom doped graphene. It is revealed that upon Si doping in graphene, a finite band gap appears at the high symmetric K-point, thereby making graphene a direct band gap semiconductor. Moreover, the band gap value is directly proportional to the concentration of impurity Si atoms present in graphene lattice. Upon analyzing the optical properties of Si atom-doped graphene structures, it is found that, there is significant change in the refractive index of the graphene after Si atom substitution in graphene. In addition, the overall absorption spectrum of graphene is decreased after Si atom doping. Although a significant red shift in absorption is found to occur towards visible range of radiation when Si atom is substituted in its lattice. The reflectivity of graphene improves in low energy region after Si atom substitution in graphene. These results can be useful for tuning the electronic structure and to manipulate the optical properties of graphene layer in the visible region.

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

MicroED Structure of Au146(p-MBA)57 at Subatomic Resolution Reveals a Twinned FCC Cluster.

PubMed

Vergara, Sandra; Lukes, Dylan A; Martynowycz, Michael W; Santiago, Ulises; Plascencia-Villa, Germán; Weiss, Simon C; de la Cruz, M Jason; Black, David M; Alvarez, Marcos M; López-Lozano, Xochitl; Barnes, Christopher O; Lin, Guowu; Weissker, Hans-Christian; Whetten, Robert L; Gonen, Tamir; Yacaman, Miguel Jose; Calero, Guillermo

2017-11-16

Solving the atomic structure of metallic clusters is fundamental to understanding their optical, electronic, and chemical properties. Herein we present the structure of the largest aqueous gold cluster, Au 146 (p-MBA) 57 (p-MBA: para-mercaptobenzoic acid), solved by electron micro-diffraction (MicroED) to subatomic resolution (0.85 Å) and by X-ray diffraction at atomic resolution (1.3 Å). The 146 gold atoms may be decomposed into two constituent sets consisting of 119 core and 27 peripheral atoms. The core atoms are organized in a twinned FCC structure, whereas the surface gold atoms follow a C 2 rotational symmetry about an axis bisecting the twinning plane. The protective layer of 57 p-MBAs fully encloses the cluster and comprises bridging, monomeric, and dimeric staple motifs. Au 146 (p-MBA) 57 is the largest cluster observed exhibiting a bulk-like FCC structure as well as the smallest gold particle exhibiting a stacking fault.

MicroED structure of Au146(p-MBA)57 at subatomic resolution reveals a twinned FCC cluster

PubMed Central

Vergara, Sandra; Lukes, Dylan A.; Martynowycz, Michael W.; Santiago, Ulises; Plascencia-Villa, German; Weiss, Simon C.; de la Cruz, M. Jason; Black, David M.; Alvarez, Marcos M.; Lopez-Lozano, Xochitl; Barnes, Christopher O.; Lin, Guowu; Weissker, Hans-Christian; Whetten, Robert L.; Gonen, Tamir; Jose-Yacaman, Miguel; Calero, Guillermo

2018-01-01

Solving the atomic structure of metallic clusters is fundamental to understanding their optical, electronic, and chemical properties. Herein we present the structure of the largest aqueous gold cluster, Au146(p-MBA)57 (p-MBA: para-mercaptobenzoic acid), solved by electron diffraction (MicroED) to subatomic resolution (0.85 Å) and by X-ray diffraction at atomic resolution (1.3 Å). The 146 gold atoms may be decomposed into two constituent sets consisting of 119 core and 27 peripheral atoms. The core atoms are organized in a twinned FCC structure whereas the surface gold atoms follow a C2 rotational symmetry about an axis bisecting the twinning plane. The protective layer of 57 p-MBAs fully encloses the cluster and comprises bridging, monomeric, and dimeric staple motifs. Au146(p-MBA)57 is the largest cluster observed exhibiting a bulk-like FCC structure as well as the smallest gold particle exhibiting a stacking fault. PMID:29072840

Simulation of Rutherford backscattering spectrometry from arbitrary atom structures.

PubMed

Zhang, S; Nordlund, K; Djurabekova, F; Zhang, Y; Velisa, G; Wang, T S

2016-10-01

Rutherford backscattering spectrometry in a channeling direction (RBS/C) is a powerful tool for analysis of the fraction of atoms displaced from their lattice positions. However, it is in many cases not straightforward to analyze what is the actual defect structure underlying the RBS/C signal. To reveal insights of RBS/C signals from arbitrarily complex defective atomic structures, we develop here a method for simulating the RBS/C spectrum from a set of arbitrary read-in atom coordinates (obtained, e.g., from molecular dynamics simulations). We apply the developed method to simulate the RBS/C signals from Ni crystal structures containing randomly displaced atoms, Frenkel point defects, and extended defects, respectively. The RBS/C simulations show that, even for the same number of atoms in defects, the RBS/C signal is much stronger for the extended defects. Comparison with experimental results shows that the disorder profile obtained from RBS/C signals in ion-irradiated Ni is due to a small fraction of extended defects rather than a large number of individual random atoms.

Molecules Without Atoms

NASA Astrophysics Data System (ADS)

Ruth, Anthony; Collins, Laura; Gomes, Kenjiro; Janko, Boldizsar

We present a real-space representation of molecules which results in the normal bonding rules and electronic structure of chemistry without atom-centered coulomb potentials. Using a simple mapping, we can generate atomless molecules from the structure of real molecules. Additionally, molecules without atoms show similar covalent bonding energies and transfer of charge in ionic bonds as real molecules. The atomless molecules contain only the valence and conduction electronic structure of the real molecule. Using the framework of the Atoms in Molecules (AIM) theory of Bader, we prove that the topological features of the valence charge distribution of molecules without atoms are identical to that of real molecules. In particular, the charge basins of atomless molecules show identical location and quantities of representative charge. We compare the accuracy, computational cost, and intuition gained from electronic structure calculations of molecules without atoms with the use of pseudopotentials to represent atomic cores in density functional theory. A. R. acknowledges support from a NASA Space Technology Research Fellowship.

An atomic finite element model for biodegradable polymers. Part 1. Formulation of the finite elements.

PubMed

Gleadall, Andrew; Pan, Jingzhe; Ding, Lifeng; Kruft, Marc-Anton; Curcó, David

2015-11-01

Molecular dynamics (MD) simulations are widely used to analyse materials at the atomic scale. However, MD has high computational demands, which may inhibit its use for simulations of structures involving large numbers of atoms such as amorphous polymer structures. An atomic-scale finite element method (AFEM) is presented in this study with significantly lower computational demands than MD. Due to the reduced computational demands, AFEM is suitable for the analysis of Young's modulus of amorphous polymer structures. This is of particular interest when studying the degradation of bioresorbable polymers, which is the topic of an accompanying paper. AFEM is derived from the inter-atomic potential energy functions of an MD force field. The nonlinear MD functions were adapted to enable static linear analysis. Finite element formulations were derived to represent interatomic potential energy functions between two, three and four atoms. Validation of the AFEM was conducted through its application to atomic structures for crystalline and amorphous poly(lactide). Copyright © 2015 Elsevier Ltd. All rights reserved.

Simulation of Rutherford backscattering spectrometry from arbitrary atom structures

NASA Astrophysics Data System (ADS)

Zhang, S.; Nordlund, K.; Djurabekova, F.; Zhang, Y.; Velisa, G.; Wang, T. S.

2016-10-01

Rutherford backscattering spectrometry in a channeling direction (RBS/C) is a powerful tool for analysis of the fraction of atoms displaced from their lattice positions. However, it is in many cases not straightforward to analyze what is the actual defect structure underlying the RBS/C signal. To reveal insights of RBS/C signals from arbitrarily complex defective atomic structures, we develop here a method for simulating the RBS/C spectrum from a set of arbitrary read-in atom coordinates (obtained, e.g., from molecular dynamics simulations). We apply the developed method to simulate the RBS/C signals from Ni crystal structures containing randomly displaced atoms, Frenkel point defects, and extended defects, respectively. The RBS/C simulations show that, even for the same number of atoms in defects, the RBS/C signal is much stronger for the extended defects. Comparison with experimental results shows that the disorder profile obtained from RBS/C signals in ion-irradiated Ni is due to a small fraction of extended defects rather than a large number of individual random atoms.

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

Atomic Mass and Nuclear Binding Energy for U-287 (Uranium)

NASA Astrophysics Data System (ADS)

Sukhoruchkin, S. I.; Soroko, Z. N.

This document is part of the Supplement containing the complete sets of data of Subvolume B `Nuclei with Z = 55 - 100' of Volume 22 `Nuclear Binding Energies and Atomic Masses' of Landolt-Börnstein - Group I `Elementary Particles, Nuclei and Atoms', and additionally including data for nuclei with Z = 101 - 130. It provides atomic mass, mass excess, nuclear binding energy, nucleon separation energies, Q-values, and nucleon residual interaction parameters for atomic nuclei of the isotope U-287 (Uranium, atomic number Z = 92, mass number A = 287).

Atomic Mass and Nuclear Binding Energy for Ac-212 (Actinium)

NASA Astrophysics Data System (ADS)

Sukhoruchkin, S. I.; Soroko, Z. N.

This document is part of the Supplement containing the complete sets of data of Subvolume B `Nuclei with Z = 55 - 100' of Volume 22 `Nuclear Binding Energies and Atomic Masses' of Landolt-Börnstein - Group I `Elementary Particles, Nuclei and Atoms', and additionally including data for nuclei with Z = 101 - 130. It provides atomic mass, mass excess, nuclear binding energy, nucleon separation energies, Q-values, and nucleon residual interaction parameters for atomic nuclei of the isotope Ac-212 (Actinium, atomic number Z = 89, mass number A = 212).

Doping Scheme in Atomic Chain Electronics

NASA Technical Reports Server (NTRS)

Toshishige, Yamada

1997-01-01

Due to the dramatic reduction in MOS size, there appear many unwanted effects. In these small devices, the number of dopant atoms in the channel is not macroscopic and electrons may suffer significantly different scattering from device to device since the spatial distribution of dopant atoms is no longer regarded as continuous. This prohibits integration, while it is impossible to control such dopant positions within atomic scale. A fundamental solution is to create electronics with simple but atomically precise structures, which could be fabricated with recent atom manipulation technology. All the constituent atoms are placed as planned, and then the device characteristics are deviation-free, which is mandatory for integration. Atomic chain electronics belongs to this category. Foreign atom chains or arrays form devices, and they are placed on the atomically flat substrate surface. We can design the band structure and the resultant Fermi energy of these structures by manipulating the lattice constant. Using the tight-binding theory with universal parameters, it has been predicted that isolated Si chains and arrays are metallic, Mg chains are insulating, and Mg arrays have metallic and insulating phases [1]. The transport properties along a metallic chain have been studied, emphasizing the role of the contact to electrodes [2]. For electronic applications, it is essential to establish a method to dope a semiconducting chain, which is to control the Fermi energy position without altering the original band structure. If we replace some of the chain atoms with dopant atoms randomly, the electrons will see random potential along die chain and will be localized strongly in space (Anderson localization). However, if we replace periodically, although the electrons can spread over the chain, there will generally appear new bands and band gaps reflecting the new periodicity of dopant atoms. This will change the original band structure significantly. In order to overcome this dilemma, we may place a dopant atom beside the chain at every N lattice periods (N > 1). Because of the periodic arrangement of pant atoms, we can avoid the unwanted Anderson localization. Moreover, since the dopant atoms do not constitute the chain, the overlap interaction between them is minimized, and the band structure modification can be made smallest. Some tight-binding results will be discussed to demonstrate the present idea.

Structural investigation of the (010) surface of the Al13 Fe4 catalyst.

PubMed

Ledieu, J; Gaudry, É; Loli, L N Serkovic; Villaseca, S Alarcón; de Weerd, M-C; Hahne, M; Gille, P; Grin, Y; Dubois, J-M; Fournée, V

2013-02-15

We have investigated the structure of the Al(13)Fe(4)(010) surface using both experimental and ab initio computational methods. The results indicate that the topmost surface layers correspond to incomplete puckered (P) planes present in the bulk crystal structure. The main building block of the corrugated termination consists of two adjacent pentagons of Al atoms, each centered by a protruding Fe atom. These motifs are interconnected via additional Al atoms referred to as "glue" atoms which partially desorb above 873 K. The surface structure of lower atomic density compared to the bulk P plane is explained by a strong Fe-Al-Fe covalent polar interaction that preserves intact clusters at the surface. The proposed surface model with identified Fe-containing atomic ensembles could explain the Al(13)Fe(4) catalytic properties recently reported in line with the site-isolation concept [M. Armbrüster et al., Nat. Mater. 11, 690 (2012)].

On the Roles of Substrate Binding and Hinge Unfolding in Conformational Changes of Adenylate Kinase

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

Brokaw, Jason B.; Chu, Jhih-wei

2010-11-17

We characterized the conformational change of adenylate kinase (AK) between open and closed forms by conducting five all-atom molecular-dynamics simulations, each of 100 ns duration. Different initial structures and substrate binding configurations were used to probe the pathways of AK conformational change in explicit solvent, and no bias potential was applied. A complete closed-to-open and a partial open-to-closed transition were observed, demonstrating the direct impact of substrate-mediated interactions on shifting protein conformation. The sampled configurations suggest two possible pathways for connecting the open and closed structures of AK, affirming the prediction made based on available x-ray structures and earlier worksmore » of coarse-grained modeling. The trajectories of the all-atom molecular-dynamics simulations revealed the complexity of protein dynamics and the coupling between different domains during conformational change. Calculations of solvent density and density fluctuations surrounding AK did not show prominent variation during the transition between closed and open forms. Finally, we characterized the effects of local unfolding of an important hinge near Pro177 on the closed-to-open transition of AK and identified a novel mechanism by which hinge unfolding modulates protein conformational change. The local unfolding of Pro177 hinge induces alternative tertiary contacts that stabilize the closed structure and prevent the opening transition.« less

The table of isotopes-8th edition and beyond

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

Firestone, R.B.

A new edition of the Table of Isotopes has been published this year by John Wiley and Sons, Inc. This edition is the eighth in a series started by Glenn T. Seaborg in 1940. The two-volume, 3168-page, cloth-bound edition is twice the size of the previous edition published in 1978. It contains nuclear structure and decay data, based mainly on the Evaluated Nuclear Structure Data File (ENSDF), for >3100 isotopes and isomers. Approximately 24000 references are cited, and the appendices have been updated and extended. The book is packaged with an interactive CD-ROM that contains the Table of Isotopes inmore » Adobe Acrobat Portable Document Format for convenient viewing on personal computer (PC) and UNIX workstations. The CD-ROM version contains a chart of the nuclides graphical index and separate indices organized for radioisotope users and nuclear structure physicists. More than 100000 hypertext links are provided to move the user quickly through related information free from the limitations of page size. Complete references with keyword abstracts are provided. The CD-ROM also contains the Table of Super-deformed Nuclear Bands and Fission Isomers; Tables of Atoms, Atomic Nuclei, and Subatomic Particles by Ivan P. Selinov; the ENSDF and nuclear structure reference (NSR) databases; the ENSDF manual by Jagdish K. Tuli; and Abode Acrobat Reader software.« less

Closing the door on flaviviruses: entry as a target for antiviral drug design.

PubMed

Perera, Rushika; Khaliq, Mansoora; Kuhn, Richard J

2008-10-01

With the emergence and rapid spread of West Nile virus in the United States since 1999, and the 50-100 million infections per year caused by dengue virus globally, the threat of flaviviruses as re-emerging human pathogens has become a reality. To support the efforts that are currently being pursued to develop effective vaccines against these viruses, researchers are also actively pursuing the development of small molecule compounds that target various aspects of the virus life cycle. Recent advances in the structural characterization of the flaviviruses have provided a strong foundation towards these efforts. These studies have provided the pseudo-atomic structures of virions from several members of the genus as well as atomic resolution structures of several viral proteins. Most importantly, these studies have highlighted specific structural rearrangements that occur within the virion that are necessary for the virus to complete its life cycle. These rearrangements occur when the virus must transition from immature, to mature, to fusion-active states and rely heavily on the conformational flexibility of the envelope (E) protein that forms the outer glycoprotein shell of the virus. Analysis of these conformational changes can suggest promising targets for structure-based antiviral design. For instance, by targeting the flexibility of the E protein, it might be possible to inhibit required rearrangements of this protein and trap the virus in a specific state. This would interfere with a productive flaviviral infection. This review presents a structural perspective of the flavivirus life cycle and focuses on the role of the E protein as an opportune target for structure-based antiviral drug design.

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

NASA Astrophysics Data System (ADS)

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

2018-05-01

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

Atomic level structural modulation during the structural relaxation and its effect on magnetic properties of Fe81Si4B10P4Cu1 nanocrystalline alloy

NASA Astrophysics Data System (ADS)

Cao, C. C.; Zhu, L.; Meng, Y.; Zhai, X. B.; Wang, Y. G.

2018-06-01

The evolution of local structure and defects in the Fe81Si4B10P4Cu1 amorphous alloy during the structural relaxation has been investigated by Mössbauer spectroscopy, positron annihilation lifetime spectroscopy and transmission electron microscopy to explore their effects on magnetic properties of the nanocrystalline. The atomic rearrangements at the early stage of the structural relaxation cause the density increase of the amorphous matrix, but the subsequent atomic rearrangements contribute to the transformation of Fe3B-like atomic arrangements to FeB-like ones with the temperature increasing. As the structural relaxation processes, the released Fe atoms both from Fe3B- and Fe3P-like atomic arrangements result in the formation of new Fe clusters and the increase of Fe-Fe coordination number in the existing Fe clusters and the nucleation sites for α-Fe gradually increase, both of which promote the crystallization. However, the homogeneity of amorphous matrix will be finally destroyed under excessive relaxation temperature, which coarsens nanograins during the crystallization instead. Therefore, soft magnetic properties of the Fe81Si4B10P4Cu1 nanocrystalline alloy can be improved by pre-annealing the amorphous precursor at an appropriate temperature due to the atomic level structural optimization.

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.

Robust procedure for creating and characterizing the atomic structure of scanning tunneling microscope tips.

PubMed

Tewari, Sumit; Bastiaans, Koen M; Allan, Milan P; van Ruitenbeek, Jan M

2017-01-01

Scanning tunneling microscopes (STM) are used extensively for studying and manipulating matter at the atomic scale. In spite of the critical role of the STM tip, procedures for controlling the atomic-scale shape of STM tips have not been rigorously justified. Here, we present a method for preparing tips in situ while ensuring the crystalline structure and a reproducibly prepared tip structure up to the second atomic layer. We demonstrate a controlled evolution of such tips starting from undefined tip shapes.

X-ray Crystal Structures Elucidate the Nucleotidyl Transfer Reaction of Transcript Initiation Using Two Nucleotides

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

M Gleghorn; E Davydova; R Basu

2011-12-31

We have determined the X-ray crystal structures of the pre- and postcatalytic forms of the initiation complex of bacteriophage N4 RNA polymerase that provide the complete set of atomic images depicting the process of transcript initiation by a single-subunit RNA polymerase. As observed during T7 RNA polymerase transcript elongation, substrate loading for the initiation process also drives a conformational change of the O helix, but only the correct base pairing between the +2 substrate and DNA base is able to complete the O-helix conformational transition. Substrate binding also facilitates catalytic metal binding that leads to alignment of the reactive groupsmore » of substrates for the nucleotidyl transfer reaction. Although all nucleic acid polymerases use two divalent metals for catalysis, they differ in the requirements and the timing of binding of each metal. In the case of bacteriophage RNA polymerase, we propose that catalytic metal binding is the last step before the nucleotidyl transfer reaction.« less

Formation and structural phase transition in Co atomic chains on a Cu(775) surface

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

Syromyatnikov, A. G.; Kabanov, N. S.; Saletsky, A. M.

The formation of Co atomic chains on a Cu(775) surface is investigated by the kinetic Monte Carlo method. It is found that the length of Co atomic chains formed as a result of self-organization during epitaxial growth is a random quantity and its mean value depends on the parameters of the experiment. The existence of two structural phases in atomic chains is detected using the density functional theory. In the first phase, the separations between an atom and its two nearest neighbors in a chain are 0.230 and 0.280 nm. In the second phase, an atomic chain has identical atomicmore » spacings of 0.255 nm. It is shown that the temperature of the structural phase transition depends on the length of the atomic chain.« less

Structural disorder within sendai virus nucleoprotein and phosphoprotein: insight into the structural basis of molecular recognition.

PubMed

Jensen, Malene Ringkjøbing; Bernadó, Pau; Houben, Klaartje; Blanchard, Laurence; Marion, Dominque; Ruigrok, Rob W H; Blackledge, Martin

2010-08-01

Intrinsically disordered regions of significant length are present throughout eukaryotic genomes, and are particularly prevalent in viral proteins. Due to their inherent flexibility, these proteins inhabit a conformational landscape that is too complex to be described by classical structural biology. The elucidation of the role that conformational flexibility plays in molecular function will redefine our understanding of the molecular basis of biological function, and the development of appropriate technology to achieve this aim remains one of the major challenges for the future of structural biology. NMR is the technique of choice for studying intrinsically disordered proteins, providing information about structure, flexibility and interactions at atomic resolution even in completely disordered proteins. In particular residual dipolar couplings (RDCs) are sensitive and powerful tools for determining local and long-range structural behaviour in flexible proteins. Here we describe recent applications of the use of RDCs to quantitatively describe the level of local structure in intrinsically disordered proteins involved in replication and transcription in Sendai virus.

Time to face the fats: what can mass spectrometry reveal about the structure of lipids and their interactions with proteins?

PubMed

Brown, Simon H J; Mitchell, Todd W; Oakley, Aaron J; Pham, Huong T; Blanksby, Stephen J

2012-09-01

Since the 1950s, X-ray crystallography has been the mainstay of structural biology, providing detailed atomic-level structures that continue to revolutionize our understanding of protein function. From recent advances in this discipline, a picture has emerged of intimate and specific interactions between lipids and proteins that has driven renewed interest in the structure of lipids themselves and raised intriguing questions as to the specificity and stoichiometry in lipid-protein complexes. Herein we demonstrate some of the limitations of crystallography in resolving critical structural features of ligated lipids and thus determining how these motifs impact protein binding. As a consequence, mass spectrometry must play an important and complementary role in unraveling the complexities of lipid-protein interactions. We evaluate recent advances and highlight ongoing challenges towards the twin goals of (1) complete structure elucidation of low, abundant, and structurally diverse lipids by mass spectrometry alone, and (2) assignment of stoichiometry and specificity of lipid interactions within protein complexes.

Time to Face the Fats: What Can Mass Spectrometry Reveal about the Structure of Lipids and Their Interactions with Proteins?

NASA Astrophysics Data System (ADS)

Brown, Simon H. J.; Mitchell, Todd W.; Oakley, Aaron J.; Pham, Huong T.; Blanksby, Stephen J.

2012-09-01

Since the 1950s, X-ray crystallography has been the mainstay of structural biology, providing detailed atomic-level structures that continue to revolutionize our understanding of protein function. From recent advances in this discipline, a picture has emerged of intimate and specific interactions between lipids and proteins that has driven renewed interest in the structure of lipids themselves and raised intriguing questions as to the specificity and stoichiometry in lipid-protein complexes. Herein we demonstrate some of the limitations of crystallography in resolving critical structural features of ligated lipids and thus determining how these motifs impact protein binding. As a consequence, mass spectrometry must play an important and complementary role in unraveling the complexities of lipid-protein interactions. We evaluate recent advances and highlight ongoing challenges towards the twin goals of (1) complete structure elucidation of low, abundant, and structurally diverse lipids by mass spectrometry alone, and (2) assignment of stoichiometry and specificity of lipid interactions within protein complexes.

Student perception and conceptual development as represented by student mental models of atomic structure

NASA Astrophysics Data System (ADS)

Park, Eun Jung

The nature of matter based upon atomic theory is a principal concept in science; hence, how to teach and how to learn about atoms is an important subject for science education. To this end, this study explored student perceptions of atomic structure and how students learn about this concept by analyzing student mental models of atomic structure. Changes in student mental models serve as a valuable resource for comprehending student conceptual development. Data was collected from students who were taking the introductory chemistry course. Responses to course examinations, pre- and post-questionnaires, and pre- and post-interviews were used to analyze student mental models of atomic structure. First, this study reveals that conceptual development can be achieved, either by elevating mental models toward higher levels of understanding or by developing a single mental model. This study reinforces the importance of higher-order thinking skills to enable students to relate concepts in order to construct a target model of atomic structure. Second, Bohr's orbital structure seems to have had a strong influence on student perceptions of atomic structure. With regard to this finding, this study suggests that it is instructionally important to teach the concept of "orbitals" related to "quantum theory." Third, there were relatively few students who had developed understanding at the level of the target model, which required student understanding of the basic ideas of quantum theory. This study suggests that the understanding of atomic structure based on the idea of quantum theory is both important and difficult. Fourth, this study included different student assessments comprised of course examinations, questionnaires, and interviews. Each assessment can be used to gather information to map out student mental models. Fifth, in the comparison of the pre- and post-interview responses, this study showed that high achieving students moved toward more improved models or to advanced levels of understanding. The analysis of mental models in this study has provided information describing student understanding of the nature and structure of an atom. In addition to an assessment of student cognition, information produced from this study can serve as an important resource for curriculum development, teacher education, and instruction.

Atomic Structure. Independent Learning Project for Advanced Chemistry (ILPAC). Unit S2.

ERIC Educational Resources Information Center

Inner London Education Authority (England).

This unit on atomic structure is one of 10 first year units produced by the Independent Learning Project for Advanced Chemistry (ILPAC). The unit consists of two levels. Level one focuses on the atomic nucleus. Level two focuses on the arrangement of extranuclear electrons, approaching atomic orbitals through both electron bombardment and spectra.…

MATCH: An Atom- Typing Toolset for Molecular Mechanics Force Fields

PubMed Central

Yesselman, Joseph D.; Price, Daniel J.; Knight, Jennifer L.; Brooks, Charles L.

2011-01-01

We introduce a toolset of program libraries collectively titled MATCH (Multipurpose Atom-Typer for CHARMM) for the automated assignment of atom types and force field parameters for molecular mechanics simulation of organic molecules. The toolset includes utilities for the conversion from multiple chemical structure file formats into a molecular graph. A general chemical pattern-matching engine using this graph has been implemented whereby assignment of molecular mechanics atom types, charges and force field parameters is achieved by comparison against a customizable list of chemical fragments. While initially designed to complement the CHARMM simulation package and force fields by generating the necessary input topology and atom-type data files, MATCH can be expanded to any force field and program, and has core functionality that makes it extendable to other applications such as fragment-based property prediction. In the present work, we demonstrate the accurate construction of atomic parameters of molecules within each force field included in CHARMM36 through exhaustive cross validation studies illustrating that bond increment rules derived from one force field can be transferred to another. In addition, using leave-one-out substitution it is shown that it is also possible to substitute missing intra and intermolecular parameters with ones included in a force field to complete the parameterization of novel molecules. Finally, to demonstrate the robustness of MATCH and the coverage of chemical space offered by the recent CHARMM CGENFF force field (Vanommeslaeghe, et al., JCC., 2010, 31, 671–690), one million molecules from the PubChem database of small molecules are typed, parameterized and minimized. PMID:22042689

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

PubMed

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

2018-02-24

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

Study of TiO2 anatase nano and microstructures with dominant {001} facets for NO oxidation.

PubMed

Sofianou, Maria-Veronica; Trapalis, Christos; Psycharis, Vassils; Boukos, Nikos; Vaimakis, Tiverios; Yu, Jiaguo; Wang, Wenguang

2012-11-01

TiO(2) anatase nanoplates and hollow microspheres were fabricated by a solvothermal-hydrothermal method using titanium isopropoxide as a titanium precursor and hydrofluoric acid as a capping agent in order to enhance the formation of the {001} crystal facets of the anatase nanocrystals. These different morphological structures of TiO(2) anatase can be achieved by only changing the solvent, keeping the amount of the precursor and of the capping agent identical during the solvothermal-hydrothermal process. After calcination of the samples, the adsorbed fluoride atoms on the {001} crystal facets of the TiO(2) anatase nanocrystals were completely removed from their surface according to XPS analysis. The calcined TiO(2) anatase structures were higher crystallized and the specific surface area of the catalysts increased, enhancing their photocatalytic activity in comparison to the non-calcined TiO(2) anatase structures. All TiO(2) anatase samples with adsorbed as well as non-adsorbed fluoride atoms on their {001} crystal facets, exhibited a higher photonic efficiency than Degussa P25, which was used as a reference. The fluoride free TiO(2) anatase nanoplates exhibited the best photocatalytic activity in oxidizing the NO gas to NO(2) and NO(3) (-).

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

PubMed Central

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

2018-01-01

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

ProQ3: Improved model quality assessments using Rosetta energy terms

PubMed Central

Uziela, Karolis; Shu, Nanjiang; Wallner, Björn; Elofsson, Arne

2016-01-01

Quality assessment of protein models using no other information than the structure of the model itself has been shown to be useful for structure prediction. Here, we introduce two novel methods, ProQRosFA and ProQRosCen, inspired by the state-of-art method ProQ2, but using a completely different description of a protein model. ProQ2 uses contacts and other features calculated from a model, while the new predictors are based on Rosetta energies: ProQRosFA uses the full-atom energy function that takes into account all atoms, while ProQRosCen uses the coarse-grained centroid energy function. The two new predictors also include residue conservation and terms corresponding to the agreement of a model with predicted secondary structure and surface area, as in ProQ2. We show that the performance of these predictors is on par with ProQ2 and significantly better than all other model quality assessment programs. Furthermore, we show that combining the input features from all three predictors, the resulting predictor ProQ3 performs better than any of the individual methods. ProQ3, ProQRosFA and ProQRosCen are freely available both as a webserver and stand-alone programs at http://proq3.bioinfo.se/. PMID:27698390

Protein and gene structure of a blue laccase from Pleurotus ostreatus1.

PubMed Central

Giardina, P; Palmieri, G; Scaloni, A; Fontanella, B; Faraco, V; Cennamo, G; Sannia, G

1999-01-01

A new laccase isoenzyme (POXA1b, where POX is phenol oxidase), produced by Pleurotus ostreatus in cultures supplemented with copper sulphate, has been purified and fully characterized. The main characteristics of this protein (molecular mass in native and denaturing conditions, pI and catalytic properties) are almost identical to the previously studied laccase POXA1w. However, POXA1b contains four copper atoms per molecule instead of one copper, two zinc and one iron atom per molecule of POXA1w. Furthermore, POXA1b shows an unusually high stability at alkaline pH. The gene and cDNA coding for POXA1b have been cloned and sequenced. The gene coding sequence contains 1599 bp, interrupted by 15 introns. Comparison of the structure of the poxa1b gene with the two previously studied P. ostreatus laccase genes (pox1 and poxc) suggests that these genes belong to two different subfamilies. The amino acid sequence of POXA1b deduced from the cDNA sequence has been almost completely verified by means of matrix-assisted laser desorption ionization MS. It has been demonstrated that three out of six putative glycosylation sites are post-translationally modified and the structure of the bound glycosidic moieties has been determined, whereas two other putative glycosylation sites are unmodified. PMID:10417329

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.

Exploring the structure-activity relations of N-carbethoxyphthalimide by combining FTIR, FT-Raman and NMR spectroscopy with DFT electronic structure method.

PubMed

Arjunan, V; Govindaraja, S Thillai; Ravindran, P; Mohan, S

2014-01-01

The complete vibrational assignment and analysis of N-carbethoxyphthalimide were carried out using the experimental FTIR and FT-Raman data in the range 4000-450 and 4000-100 cm(-1), respectively along with quantum chemical studies of the compound using DFT-B3LYP gradient calculations employing the 6-31G**, 6-311++G** and cc-pVDZ basis sets. The 1H (400 MHz; CDCl3) and 13C (100 MHz;CDCl3) nuclear magnetic resonance (NMR) spectra were also recorded. Due to the partial ionic nature of the carbonyl group, the carbon atoms C1 and C3 in NCEP show downfield effect and the corresponding observed chemical shift of both are observed at 163.76 ppm and the carbon atom C16 in the carbethoxy group also give signal in the downfield at 148.45 ppm. The active sites are determined by molecular electrostatic potential. The possible electronic transitions are determined by HOMO and LUMO orbital shapes and their energies. The structure-chemical reactivity relations of the compound were determined through chemical potential, global hardness, global softness, electronegativity, electrophilicity and local reactivity descriptors by conceptual DFT methods. Copyright © 2013 Elsevier B.V. All rights reserved.

Theoretical discovery of stable structures of group III-V monolayers: The materials for semiconductor devices

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

Suzuki, Tatsuo, E-mail: dr.tatsuosuzuki@gmail.com

Group III-V compounds are very important as the materials of semiconductor devices. Stable structures of the monolayers of group III-V binary compounds have been discovered by using first-principles calculations. The primitive unit cell of the discovered structures is a rectangle, which includes four group-III atoms and four group-V atoms. A group-III atom and its three nearest-neighbor group-V atoms are placed on the same plane; however, these connections are not the sp{sup 2} hybridization. The bond angles around the group-V atoms are less than the bond angle of sp{sup 3} hybridization. The discovered structure of GaP is an indirect transition semiconductor,more » while the discovered structures of GaAs, InP, and InAs are direct transition semiconductors. Therefore, the discovered structures of these compounds have the potential of the materials for semiconductor devices, for example, water splitting photocatalysts. The discovered structures may become the most stable structures of monolayers which consist of other materials.« less

Picture this: The value of multiple visual representations for student learning of quantum concepts in general chemistry

NASA Astrophysics Data System (ADS)

Allen, Emily Christine

Mental models for scientific learning are often defined as, "cognitive tools situated between experiments and theories" (Duschl & Grandy, 2012). In learning, these cognitive tools are used to not only take in new information, but to help problem solve in new contexts. Nancy Nersessian (2008) describes a mental model as being "[loosely] characterized as a representation of a system with interactive parts with representations of those interactions. Models can be qualitative, quantitative, and/or simulative (mental, physical, computational)" (p. 63). If conceptual parts used by the students in science education are inaccurate, then the resulting model will not be useful. Students in college general chemistry courses are presented with multiple abstract topics and often struggle to fit these parts into complete models. This is especially true for topics that are founded on quantum concepts, such as atomic structure and molecular bonding taught in college general chemistry. The objectives of this study were focused on how students use visual tools introduced during instruction to reason with atomic and molecular structure, what misconceptions may be associated with these visual tools, and how visual modeling skills may be taught to support students' use of visual tools for reasoning. The research questions for this study follow from Gilbert's (2008) theory that experts use multiple representations when reasoning and modeling a system, and Kozma and Russell's (2005) theory of representational competence levels. This study finds that as students developed greater command of their understanding of abstract quantum concepts, they spontaneously provided additional representations to describe their more sophisticated models of atomic and molecular structure during interviews. This suggests that when visual modeling with multiple representations is taught, along with the limitations of the representations, it can assist students in the development of models for reasoning about abstract topics such as atomic and molecular structure. There is further gain if students' difficulties with these representations are targeted through the use additional instruction such as a workbook that requires the students to exercise their visual modeling skills.

Atomic data and line intensities for the S V ion

NASA Astrophysics Data System (ADS)

Iorga, C.; Stancalie, V.

2017-05-01

The energy levels, oscillator strengths, spontaneous radiative decay rates, lifetimes and electron impact collision strengths have been obtained for the [ Ne ] 3s nl, [ Ne ] 3p nl, [ Ne ] 3d nl configurations belonging to S V ion, with n ≤ 7 and l ≤ 4, resulting in 567 fine-structure levels. The calculations have been performed within the fully relativistic Flexible Atomic Code (FAC, Gu, 2008) framework and the distorted wave approximation. To attain the desired accuracy for the levels energy, the valence-valence and valence-core correlations have been taken care of by including 96 configuration state functions (CSFs) in the model, reaching a total of 3147 fine-structure levels. Two separate calculations have been performed with the local central potential computed for two different average configurations. A third calculation is also performed without the addition of the core-excited states in the atomic model for completeness. The effects of slightly different mean configurations and valence-core correlations on the energy levels and decay rates are investigated. The collision data have been computed employing the relativistic distorted-wave method along with the atomic model containing the 96 CSFs and corresponding to the ground state mean configuration. The collision strengths corresponding to excitation from the first four fine-structure levels are given for five energy values of the scattered electron 2.65, 6.18, 11.02, 17.36, 25.43 Rydberg, plus an additional variable small energy value near the threshold. A collisional-radiative model has been employed to solve the rate equations for the populations of the 567 fine-structure levels, for a temperature of LogTE(K) = 5.2 corresponding to the maximum abundance of S V, and at densities 106-1016cm-3, assuming a Maxwellian electron energy distribution function and black body radiation of temperature 6000 K and dilution factor 0.35 for the photon distribution function. The main processes responsible for the level population variations are the electron-impact collisional excitation and the radiative decay along with their inverse processes. As a result, the level populations along with the spectral high-line intensity ratios are provided.

Architecture of Pd-Au bimetallic nanoparticles in sodium bis(2-ethylhexyl)sulfosuccinate reverse micelles as investigated by X-ray absorption spectroscopy.

PubMed

Chen, Ching-Hsiang; Sarma, Loka Subramanyam; Chen, Jium-Ming; Shih, Shou-Chu; Wang, Guo-Rung; Liu, Din-Goa; Tang, Mau-Tsu; Lee, Jyh-Fu; Hwang, Bing-Joe

2007-09-01

In this study, we demonstrate the unique application of X-ray absorption spectroscopy (XAS) as a fundamental characterization tool to help in designing and controlling the architecture of Pd-Au bimetallic nanoparticles within a water-in-oil microemulsion system of water/sodium bis(2-ethylhexyl)sulfosuccinate (AOT)/n-heptane. Structural insights obtained from the in situ XAS measurements recorded at each step during the formation process revealed that Pd-Au bimetallic clusters with various Pd-Au atomic stackings are formed by properly performing hydrazine reduction and redox transmetalation reactions sequentially within water-in-oil microemulsions. A structural model is provided to explain reasonably each reaction step and to give detailed insight into the nucleation and growth mechanism of Pd-Au bimetallic clusters. The combination of in situ XAS analysis at both the Pd K-edge and the Au L(III)-edge and UV-vis absorption spectral features confirms that the formation of Pd-Au bimetallic clusters follows a (Pd(nuclei)-Au(stack))-Pd(surf) stacking. This result further implies that the thickness of Au(stack) and Pd(surf) layers may be modulated by varying the dosage of the Au precursor and hydrazine, respectively. In addition, a bimetallic (Pd-Au)(alloy) nanocluster with a (Pd(nuclei)-Au(stack))-(Pd-Au(alloy))(surf) stacking was also designed and synthesized in order to check the feasibility of Pd(surf) layer modification. The result reveals that the Pd(surf) layer of the stacked (Pd(nuclei)-Au)(stack) bimetallic clusters can be successfully modified to form a (Au-Pd alloy)(surf) layer by a co-reduction of Pd and Au ions by hydrazine. Further, we demonstrate the alloying extent or atomic distribution of Pd and Au in Pd-Au bimetallic nanoparticles from the derived XAS structural parameters. The complete XAS-based methodology, demonstrated here on the Pd-Au bimetallic system, can easily be extended to design and control the alloying extent or atomic distribution, atomic stacking, and electronic structure to construct many other types of bimetallic systems for interesting applications.

Two Series of Homodinuclear Lanthanide Complexes: Greatly Enhancing Energy Barriers through Tuning Terminal Solvent Ligands in Dy2 Single-Molecule Magnets.

PubMed

Qin, Yaru; Zhang, Haifeng; Sun, Hao; Pan, Yangdan; Ge, Yu; Li, Yahong; Zhang, Yi-Quan

2017-11-02

The utilization of 2-ethoxy-6-{[(2-hydroxy-3-methoxybenzyl)imino]methyl}phenol (H 2 L) as a chelating ligand, in combination with the employment of alcohols (EtOH and MeOH) as auxiliary ligands, in 4 f-metal chemistry afforded two series of dinuclear lanthanide complexes of compositions [Ln 2 L 2 (NO 3 ) 2 (EtOH) 2 ] (Ln=Sm (1), Eu (2), Gd (3), Tb (4), Dy (5), Ho (6), Er (7)) and [Ln 2 L 2 (NO 3 ) 2 (MeOH) 2 ] (Ln=Sm (8), Eu (9), Gd (10), Tb (11), Dy (12), Ho (13), Er (14)). The structures of 1-14 were determined by single-crystal X-ray crystallography. Complexes 1-7 are isomorphous. The two lanthanide(III) ions in 1-7 are doubly bridged by two deprotonated aminophenoxide oxygen atoms of two μ 2 :η 0 :η 1 :η 2 :η 1 :η 1 :η 0 -L 2- ligands. One nitrogen atom, two oxygen atoms of the NO 3 - anion, two methoxide oxygen atoms of two ligand sets, and one oxygen atom of the terminally coordinated EtOH molecule complete the distorted dodecahedron geometry of each lanthanide(III) ion. Compounds 8-14 are isomorphous and their structures are similar to those of 1-7. The slight difference between 1-7 and 8-14 stems from purposefully replacing the EtOH ligands in 1-7 with MeOH in 8-14. Direct-current magnetic susceptibility studies in the 2-300 K range reveal weak antiferromagnetic interactions for 3, 4, 7, 10, 11, and 14, and ferromagnetic interactions at low temperature for 5, 6, 12, and 13. Complexes 5 and 12 exhibit single-molecule magnet (SMM) behavior with energy barriers of 131.3 K for 5 and 198.8 K for 12. The energy barrier is significantly enhanced by dexterously regulating the terminal ligands. To rationalize the observed difference in the magnetic behavior, complete-active-space self-consistent field (CASSCF) calculations were performed on two Dy 2 complexes. Subtle variation in the angle between the magnetic axes and the vector connecting two dysprosium(III) ions results in a weaker influence on the tunneling gap of individual dysprosium(III) ions by the dipolar field in 12. This work proposes an efficient strategy for synthesizing Dy 2 SMMs with high energy barriers. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Determination of functional collective motions in a protein at atomic resolution using coherent neutron scattering

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

Hong, Liang; Jain, Nitin; Cheng, Xiaolin

Protein function often depends on global, collective internal motions. However, the simultaneous quantitative experimental determination of the forms, amplitudes, and time scales of these motions has remained elusive. We demonstrate that a complete description of these large-scale dynamic modes can be obtained using coherent neutron-scattering experiments on perdeuterated samples. With this approach, a microscopic relationship between the structure, dynamics, and function in a protein, cytochrome P450cam, is established. The approach developed here should be of general applicability to protein systems.

Determination of functional collective motions in a protein at atomic resolution using coherent neutron scattering

DOE PAGES

Hong, Liang; Jain, Nitin; Cheng, Xiaolin; ...

2016-10-14

Protein function often depends on global, collective internal motions. However, the simultaneous quantitative experimental determination of the forms, amplitudes, and time scales of these motions has remained elusive. We demonstrate that a complete description of these large-scale dynamic modes can be obtained using coherent neutron-scattering experiments on perdeuterated samples. With this approach, a microscopic relationship between the structure, dynamics, and function in a protein, cytochrome P450cam, is established. The approach developed here should be of general applicability to protein systems.

Atomistic insight into the adsorption site selectivity of stepped Au(111) surfaces

NASA Astrophysics Data System (ADS)

Gaspari, Roberto; Pignedoli, Carlo A.; Fasel, Roman; Treier, Matthias; Passerone, Daniele

2010-07-01

Using classical and ab initio simulations, we study the interplay between the Au(111) surface reconstruction and monoatomic steps on a vicinal face. The experimentally observed discommensuration line patterns on a specific vicinal are reproduced and explained, and a complete description of the structure is given. An unusual atomic arrangement is shown to be responsible for the lower reactivity of hcp segments of step edges compared to the one of fcc segments. Our results provide an unprecedented understanding of the electronic and geometric properties of the complex Au(111) surface.

Experimental observation of boron nitride chains.

PubMed

Cretu, Ovidiu; Komsa, Hannu-Pekka; Lehtinen, Ossi; Algara-Siller, Gerardo; Kaiser, Ute; Suenaga, Kazu; Krasheninnikov, Arkady V

2014-12-23

We report the formation and characterization of boron nitride atomic chains. The chains were made from hexagonal boron nitride sheets using the electron beam inside a transmission electron microscope. We find that the stability and lifetime of the chains are significantly improved when they are supported by another boron nitride layer. With the help of first-principles calculations, we prove the heteroatomic structure of the chains and determine their mechanical and electronic properties. Our study completes the analogy between various boron nitride and carbon polymorphs, in accordance with earlier theoretical predictions.

Atomic structure of granulin determined from native nanocrystalline granulovirus using an X-ray free-electron laser

PubMed Central

Gati, Cornelius; Oberthuer, Dominik; Yefanov, Oleksandr; Stellato, Francesco; Chiu, Elaine; Yeh, Shin-Mei; Aquila, Andrew; Basu, Shibom; Bean, Richard; Beyerlein, Kenneth R.; Botha, Sabine; Boutet, Sébastien; DePonte, Daniel P.; Doak, R. Bruce; Fromme, Raimund; Galli, Lorenzo; Grotjohann, Ingo; James, Daniel R.; Kupitz, Christopher; Lomb, Lukas; Messerschmidt, Marc; Nass, Karol; Rendek, Kimberly; Shoeman, Robert L.; Wang, Dingjie; Weierstall, Uwe; White, Thomas A.; Williams, Garth J.; Zatsepin, Nadia A.; Fromme, Petra; Spence, John C. H.; Goldie, Kenneth N.; Jehle, Johannes A.; Metcalf, Peter; Barty, Anton

2017-01-01

To understand how molecules function in biological systems, new methods are required to obtain atomic resolution structures from biological material under physiological conditions. Intense femtosecond-duration pulses from X-ray free-electron lasers (XFELs) can outrun most damage processes, vastly increasing the tolerable dose before the specimen is destroyed. This in turn allows structure determination from crystals much smaller and more radiation sensitive than previously considered possible, allowing data collection from room temperature structures and avoiding structural changes due to cooling. Regardless, high-resolution structures obtained from XFEL data mostly use crystals far larger than 1 μm3 in volume, whereas the X-ray beam is often attenuated to protect the detector from damage caused by intense Bragg spots. Here, we describe the 2 Å resolution structure of native nanocrystalline granulovirus occlusion bodies (OBs) that are less than 0.016 μm3 in volume using the full power of the Linac Coherent Light Source (LCLS) and a dose up to 1.3 GGy per crystal. The crystalline shell of granulovirus OBs consists, on average, of about 9,000 unit cells, representing the smallest protein crystals to yield a high-resolution structure by X-ray crystallography to date. The XFEL structure shows little to no evidence of radiation damage and is more complete than a model determined using synchrotron data from recombinantly produced, much larger, cryocooled granulovirus granulin microcrystals. Our measurements suggest that it should be possible, under ideal experimental conditions, to obtain data from protein crystals with only 100 unit cells in volume using currently available XFELs and suggest that single-molecule imaging of individual biomolecules could almost be within reach. PMID:28202732

3DIANA: 3D Domain Interaction Analysis: A Toolbox for Quaternary Structure Modeling

PubMed Central

Segura, Joan; Sanchez-Garcia, Ruben; Tabas-Madrid, Daniel; Cuenca-Alba, Jesus; Sorzano, Carlos Oscar S.; Carazo, Jose Maria

2016-01-01

Electron microscopy (EM) is experiencing a revolution with the advent of a new generation of Direct Electron Detectors, enabling a broad range of large and flexible structures to be resolved well below 1 nm resolution. Although EM techniques are evolving to the point of directly obtaining structural data at near-atomic resolution, for many molecules the attainable resolution might not be enough to propose high-resolution structural models. However, accessing information on atomic coordinates is a necessary step toward a deeper understanding of the molecular mechanisms that allow proteins to perform specific tasks. For that reason, methods for the integration of EM three-dimensional maps with x-ray and NMR structural data are being developed, a modeling task that is normally referred to as fitting, resulting in the so called hybrid models. In this work, we present a novel application—3DIANA—specially targeted to those cases in which the EM map resolution is medium or low and additional experimental structural information is scarce or even lacking. In this way, 3DIANA statistically evaluates proposed/potential contacts between protein domains, presents a complete catalog of both structurally resolved and predicted interacting regions involving these domains and, finally, suggests structural templates to model the interaction between them. The evaluation of the proposed interactions is computed with DIMERO, a new method that scores physical binding sites based on the topology of protein interaction networks, which has recently shown the capability to increase by 200% the number of domain-domain interactions predicted in interactomes as compared to previous approaches. The new application displays the information at a sequence and structural level and is accessible through a web browser or as a Chimera plugin at http://3diana.cnb.csic.es. PMID:26772592

Atomic structure of granulin determined from native nanocrystalline granulovirus using an X-ray free-electron laser

DOE PAGES

Gati, Cornelius; Oberthuer, Dominik; Yefanov, Oleksandr; ...

2017-02-15

To understand how molecules function in biological systems, new methods are required to obtain atomic resolution structures from biological material under physiological conditions. Intense femtosecond-duration pulses from X-ray free-electron lasers (XFELs) can outrun most damage processes, vastly increasing the tolerable dose before the specimen is destroyed. This in turn allows structure determination from crystals much smaller and more radiation sensitive than previously considered possible, allowing data collection from room temperature structures and avoiding structural changes due to cooling. Regardless, high-resolution structures obtained from XFEL data mostly use crystals far larger than 1 μm3 in volume, whereas the X-ray beam ismore » often attenuated to protect the detector from damage caused by intense Bragg spots. Here, we describe the 2 Å resolution structure of native nanocrystalline granulovirus occlusion bodies (OBs) that are less than 0.016 μm3 in volume using the full power of the Linac Coherent Light Source (LCLS) and a dose up to 1.3 GGy per crystal. The crystalline shell of granulovirus OBs consists, on average, of about 9,000 unit cells, representing the smallest protein crystals to yield a high-resolution structure by X-ray crystallography to date. The XFEL structure shows little to no evidence of radiation damage and is more complete than a model determined using synchrotron data from recombinantly produced, much larger, cryocooled granulovirus granulin microcrystals. Furthermore, our measurements suggest that it should be possible, under ideal experimental conditions, to obtain data from protein crystals with only 100 unit cells in volume using currently available XFELs and suggest that single-molecule imaging of individual biomolecules could almost be within reach.« less

Long-range empirical potential model: extension to hexagonal close-packed metals.

PubMed

Dai, Y; Li, J H; Liu, B X

2009-09-23

An n-body potential is developed and satisfactorily applied to hcp metals, Co, Hf, Mg, Re, Ti, and Zr, in the form of long-range empirical potential. The potential can well reproduce the lattice constants, c/a ratios, cohesive energies, and the bulk modulus for their stable structures (hcp) and metastable structures (bcc or fcc). Meanwhile, the potential can correctly predict the order of structural stability and distinguish the energy differences between their stable hcp structure and other structures. The energies and forces derived by the potential can smoothly go to zero at cutoff radius, thus completely avoiding the unphysical behaviors in the simulations. The developed potential is applied to study the vacancy, surface fault, stacking fault and self-interstitial atom in the hcp metals. The calculated formation energies of vacancy and divacancy and activation energies of self-diffusion by vacancies are in good agreement with the values in experiments and in other works. The calculated surface energies and stacking fault energies are also consistent with the experimental data and those obtained in other theoretical works. The calculated formation energies generally agree with the results in other works, although the stable configurations of self-interstitial atoms predicted in this work somewhat contrast with those predicted by other methods. The proposed potential is shown to be relevant for describing the interaction of bcc, fcc and hcp metal systems, bringing great convenience for researchers in constructing potentials for metal systems constituted by any combination of bcc, fcc and hcp metals.

Progress in Visualizing Atomic Size Effects with DFT-Chemical Pressure Analysis: From Isolated Atoms to Trends in AB5 Intermetallics.

PubMed

Berns, Veronica M; Engelkemier, Joshua; Guo, Yiming; Kilduff, Brandon J; Fredrickson, Daniel C

2014-08-12

The notion of atomic size poses an important challenge to chemical theory: empirical evidence has long established that atoms have spatial requirements, which are summarized in tables of covalent, ionic, metallic, and van der Waals radii. Considerations based on these radii play a central role in the design and interpretation of experiments, but few methods are available to directly support arguments based on atomic size using electronic structure methods. Recently, we described an approach to elucidating atomic size effects using theoretical calculations: the DFT-Chemical Pressure analysis, which visualizes the local pressures arising in crystal structures from the interactions of atomic size and electronic effects. Using this approach, a variety of structural phenomena in intermetallic phases have already been understood in terms that provide guidance to new synthetic experiments. However, the applicability of the DFT-CP method to the broad range of the structures encountered in the solid state is limited by two issues: (1) the difficulty of interpreting the intense pressure features that appear in atomic core regions and (2) the need to divide space among pairs of interacting atoms in a meaningful way. In this article, we describe general solutions to these issues. In addressing the first issue, we explore the CP analysis of a test case in which no core pressures would be expected to arise: isolated atoms in large boxes. Our calculations reveal that intense core pressures do indeed arise in these virtually pressure-less model systems and allow us to trace the issue to the shifts in the voxel positions relative to atomic centers upon expanding and contracting the unit cell. A compensatory grid unwarping procedure is introduced to remedy this artifact. The second issue revolves around the difficulty of interpreting the pressure map in terms of interatomic interactions in a way that respects the size differences of the atoms and avoids artificial geometrical constraints. In approaching this challenge, we have developed a scheme for allocating the grid pressures to contacts inspired by the Hirshfeld charge analysis. Here, each voxel is allocated to the contact between the two atoms whose free atom electron densities show the largest values at that position. In this way, the differing sizes of atoms are naturally included in the division of space without resorting to empirical radii. The use of the improved DFT-CP method is illustrated through analyses of the applicability of radius ratio arguments to Laves phase structures and the structural preferences of AB5 intermetallics between the CaCu5 and AuBe5 structure types.

Informing, involving or engaging? Science communication, in the ages of atom-, bio- and nanotechnology.

PubMed

Kurath, Monika; Gisler, Priska

2009-09-01

Science communication has shifted considerably in Europe over the last decades. Three technology controversies on atoms, genes, and nanoscale sciences and nanotechnologies (NST) turned the style of communication from one-way information, participation and dialogues to the idea of an early and more democratic engagement of the public. Analyzing science communication developing over the three controversies, this article shows that what happened in one technology field fed forward to and contributed to shaping the subsequent field and that communication was initiated at a progressively earlier stage of technology development. The article concludes with an empirical analysis of six public engagement projects in NST, saying that the shift towards more democratic engagement of the public hasn't been as profound and complete as has been thought. This is particularly due to the continuing adoption of a simplistic contrast structure that opposes science and the public as two self-contained, antagonistic social entities.

The standard calibration instrument automation system for the atomic absorption spectrophotometer. Part 3: Program documentation

NASA Astrophysics Data System (ADS)

Ryan, D. P.; Roth, G. S.

1982-04-01

Complete documentation of the 15 programs and 11 data files of the EPA Atomic Absorption Instrument Automation System is presented. The system incorporates the following major features: (1) multipoint calibration using first, second, or third degree regression or linear interpolation, (2) timely quality control assessments for spiked samples, duplicates, laboratory control standards, reagent blanks, and instrument check standards, (3) reagent blank subtraction, and (4) plotting of calibration curves and raw data peaks. The programs of this system are written in Data General Extended BASIC, Revision 4.3, as enhanced for multi-user, real-time data acquisition. They run in a Data General Nova 840 minicomputer under the operating system RDOS, Revision 6.2. There is a functional description, a symbol definitions table, a functional flowchart, a program listing, and a symbol cross reference table for each program. The structure of every data file is also detailed.

Cytocompatibility evaluation of gum Arabic-coated ultra-pure boron nitride nanotubes on human cells.

PubMed

Ciofani, Gianni; Del Turco, Serena; Rocca, Antonella; de Vito, Giuseppe; Cappello, Valentina; Yamaguchi, Maho; Li, Xia; Mazzolai, Barbara; Basta, Giuseppina; Gemmi, Mauro; Piazza, Vincenzo; Golberg, Dmitri; Mattoli, Virgilio

2014-05-01

Boron nitride nanotubes (BNNTs) are tubular nanoparticles with a structure analogous to that of carbon nanotubes, but with B and N atoms that completely replace the C atoms. Many favorable results indicate BNNTs as safe nanomaterials; however, important concerns have recently been raised about ultra-pure, long (~10 µm) BNNTs tested on several cell types. Here, we propose additional experiments with the same BNNTs, but shortened (~1.5 µm) with a homogenization/sonication treatment that allows for their dispersion in gum Arabic aqueous solutions. Obtained BNNTs are tested on human endothelial and neuron-like cells with several independent biocompatibility assays. Moreover, for the first time, their strong sum-frequency generation signal is exploited to assess the cellular uptake. Our data demonstrate no toxic effects up to concentrations of 20 µg/ml, once more confirming biosafety of BNNTs, and again highlighting that nanoparticle aspect ratio plays a key role in the biocompatibility evaluation.

Ab-initio atomic level stress and role of d-orbitals in CuZr, CuZn and CuY

NASA Astrophysics Data System (ADS)

Ojha, Madhusudan; Nicholson, Don M.; Egami, Takeshi

2015-03-01

Atomic level stress offers a new tool to characterize materials within the local approximation to density functional theory (DFT). Ab-initio atomic level stresses in B2 structures of CuZr, CuZn and CuY are calculated and results are explained on the basis of d-orbital contributions to Density of States (DOS). The overlap of d-orbital DOS plays an important role in the relative magnitude of atomic level stresses in these structures. The trends in atomic level stresses that we observed in these simple B2 structures are also seen in complex structures such as liquids, glasses and solid solutions. The stresses are however modified by the different coordination and relaxed separation distances in these complex structures. We used the Locally Self-Consistent Multiple Scattering (LSMS) code and Vienna Ab-initio Simulation Package (VASP) for ab-initio calculations.

First-principles study of low-spin LaCoO3 with structurally consistent Hubbard U

NASA Astrophysics Data System (ADS)

Hsu, H.; Umemoto, K.; Cococcioni, M.; Wentzcovitch, R.

2008-12-01

We use the local density approximation + Hubbard U (LDA+U) method to calculate the structural and electronic properties of low-spin LaCoO3. The Hubbard U is obtained by first principles and consistent with each fully-optimized atomic structure at different pressures. With structurally consistent U, the fully-optimized atomic structure agrees with experimental data better than the calculations with fixed or vanishing U. A discussion on how the Hubbard U affects the electronic and atomic structure of LaCoO3 is also given.

Superimposition of protein structures with dynamically weighted RMSD.

PubMed

Wu, Di; Wu, Zhijun

2010-02-01

In protein modeling, one often needs to superimpose a group of structures for a protein. A common way to do this is to translate and rotate the structures so that the square root of the sum of squares of coordinate differences of the atoms in the structures, called the root-mean-square deviation (RMSD) of the structures, is minimized. While it has provided a general way of aligning a group of structures, this approach has not taken into account the fact that different atoms may have different properties and they should be compared differently. For this reason, when superimposed with RMSD, the coordinate differences of different atoms should be evaluated with different weights. The resulting RMSD is called the weighted RMSD (wRMSD). Here we investigate the use of a special wRMSD for superimposing a group of structures with weights assigned to the atoms according to certain thermal motions of the atoms. We call such an RMSD the dynamically weighted RMSD (dRMSD). We show that the thermal motions of the atoms can be obtained from several sources such as the mean-square fluctuations that can be estimated by Gaussian network model analysis. We show that the superimposition of structures with dRMSD can successfully identify protein domains and protein motions, and that it has important implications in practice, e.g., in aligning the ensemble of structures determined by nuclear magnetic resonance.

Galactic politics

NASA Image and Video Library

2015-12-07

Only rarely does an astronomical object have a political association. However, the spiral galaxy NGC 7252 acquired exactly that when it was given an unusual nickname. In December 1953, the US President Dwight D. Eisenhower gave a speech advocating the use of nuclear power for peaceful purposes. This  “Atoms for Peace” speech was significant for the scientific community, as it brought nuclear research into the public domain, and NGC 7252, which has a superficial resemblance to an atomic nucleus surrounded by the loops of electronic orbits, was dubbed the Atoms for Peace galaxy in honour of this. These loops are well visible in a wider field of view image. This nickname is quite ironic, as the galaxy’s past was anything but peaceful. Its peculiar appearance is the result of a collision between two galaxies that took place about a billion years ago, which ripped both galaxies apart. The loop-like outer structures, likely made up of dust and stars flung outwards by the crash, but recalling orbiting electrons in an atom, are partly responsible for the galaxy’s nickname. This NASA/ESA Hubble Space Telescope image shows the inner parts of the galaxy, revealing a pinwheel-shaped disc that is rotating in a direction opposite to the rest of the galaxy. This disc resembles a spiral galaxy like our own galaxy, the Milky Way, but is only about 10 000 light-years across — about a tenth of the size of the Milky Way. It is believed that this whirling structure is a remnant of the galactic collision. It will most likely have vanished in a few billion years’ time, when NGC 7252 will have completed its merging process.

Hubble View of a Galaxy Resembling an Atomic Nucleus

NASA Image and Video Library

2017-12-08

The spiral galaxy NGC 7252 has a superficial resemblance to an atomic nucleus surrounded by the loops of electronic orbits, and was informally dubbed the "Atoms for Peace" galaxy. These loops are well visible in a wider field of view image. This nickname is quite ironic, as the galaxy’s past was anything but peaceful. Its peculiar appearance is the result of a collision between two galaxies that took place about a billion years ago, which ripped both galaxies apart. The loop-like outer structures, likely made up of dust and stars flung outwards by the crash, but recalling orbiting electrons in an atom, are partly responsible for the galaxy’s nickname. This NASA/ESA Hubble Space Telescope image shows the inner parts of the galaxy, revealing a pinwheel-shaped disk that is rotating in a direction opposite to the rest of the galaxy. This disk resembles a spiral galaxy like our own galaxy, the Milky Way, but is only about 10,000 light-years across — about a tenth of the size of the Milky Way. It is believed that this whirling structure is a remnant of the galactic collision. It will most likely have vanished in a few billion years’ time, when NGC 7252 will have completed its merging process. Image credit: NASA & ESA, Acknowledgements: Judy Schmidt NASA image use policy. NASA Goddard Space Flight Center enables NASA’s mission through four scientific endeavors: Earth Science, Heliophysics, Solar System Exploration, and Astrophysics. Goddard plays a leading role in NASA’s accomplishments by contributing compelling scientific knowledge to advance the Agency’s mission. Follow us on Twitter Like us on Facebook Find us on Instagram

Electronic, magnetic and transport properties of transition metal-doped holely C2N-h2D nanoribbons

NASA Astrophysics Data System (ADS)

He, Jing-Jing; Guo, Yan-Dong; Yan, Xiao-Hong; Zeng, Hong-Li

2018-01-01

A novel layered two-dimensional graphene-like material C2N-h2D with evenly distributed holes and nitrogen atoms has been synthesized via a bottom-up wet-chemical reaction [Nat. Commun. 6, 6486 (2015)]. The presence of holes provides a ground for further functionalization by doping. By performing a first-principles study, we have doped transition metals at the center of the holes of C2N-h2D nanoribbons and explored their doping effects on electronic, magnetic and transport properties. It is found that the doping can essentially regulate the electronic properties of C2N-h2D nanoribbons. The metallic zigzag ribbon is tuned into a semiconductor for Mn, Fe and Co-doped cases, but half-metal for Ni-doping. This transition is derived from the peculiar band morphology which has a big band gap between the edge state and the higher band, so when the energy of the edge state is reduced by the impurity state, the band gap falls too and crosses the Fermi level. In contrast, the pristine semiconducting armchair C2N-h2D nanoribbon is changed into metallic. Different from the zigzag case, its physical mechanism originates from the hybridization of 3 d orbitals of transition metal atoms and the p orbitals of carbon and nitrogen atoms which introduces several resonant peaks at the Fermi level in the density of states. Furthermore, the magnetic moments of all doped materials are enhanced compared to the pristine structures but decrease as the atomic number of the transition metal atom increases. And the spin polarization of armchair C2N-h2D nanoribbon is increased, while that of the zigzag structure is decreased except the Ni-doped one which is completely spin-polarized suggesting great prospects in the future of spintronics and nanoelectronics.

Atomic resolution holography.

PubMed

Hayashi, Kouichi

2014-11-01

Atomic resolution holography, such as X-ray fluorescence holography (XFH)[1] and photoelectron holography (PH), has the attention of researcher as an informative local structure analysis, because it provides three dimensional atomic images around specific elements within a range of a few nanometers. It can determine atomic arrangements around a specific element without any prior knowledge of structures. It is considered that the atomic resolution holographic is a third method of structural analysis at the atomic level after X-ray diffraction (XRD) and X-ray absorption fine structure (XAFS). As known by many researchers, XRD and XAFS are established methods that are widespread use in various fields. XRD and XAFS provide information on long-range translational periodicities and very local environments, respectively, whereas the atomic resolution holography gives 3D information on the local order and can visualize surrounding atoms with a large range of coordination shells. We call this feature "3D medium-range local structure observation".In addition to this feature, the atomic resolution holography is very sensitive to the displacement of atoms from their ideal positions, and one can obtain quantitative information about local lattice distortions by analyzing reconstructed atomic images[2] When dopants with different atomic radii from the matrix elements are present, the lattices around the dopants are distorted. However, using the conventional methods of structural analysis, one cannot determine the extent to which the local lattice distortions are preserved from the dopants. XFH is a good tool for solving this problem.Figure 1 shows a recent achievement on a relaxor ferroelectric of Pb(Mg1/3Nb2/3)O3 (PMN) using XFH. The structural studies of relaxor ferroelectrics have been carried out by X-ray or neutron diffractions, which suggested rhombohedral distortions of their lattices. However, their true pictures have not been obtained, yet. The Nb Kα holograms showed four separate Pb images, as shown in Fig.1. Using these images, we could obtain acute and obtuse rhombohedral structures of the crystal unit cells. Moreover, the Pb-Pb correlated images reconstructed from Pb Lα holograms showed a local structure of body center-like 2a0 ×2a0 × 2a0 superlattice, proving a rigid 3D network structural model combining the two kinds of rhombohedrons. This superstructure are believed to play an important role in the relaxor behaviour of PMN at atomic level[3].jmicro;63/suppl_1/i13/DFU047F1F1DFU047F1Fig. 1.3D images of the nearest Pb and O atoms around Nb in Pb(Mg1/3Nb2/3)O3. The cube represents 1/8 of the unit cell. © The Author 2014. Published by Oxford University Press on behalf of The Japanese Society of Microscopy. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Local structure and polarization resistance of Ce doped SrMnO{sub 3} using extended x-ray fine structure analysis

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

Ryu, Jiseung; Lee, Heesoo, E-mail: heesoo@pusan.ac.kr

2014-09-15

Changes to the local structure of Sr and Mn atoms in Sr{sub 1−x}Ce{sub x}MnO{sub 3} (SCM) according to increasing Ce content and the effect of the structural change on the polarization resistance of SCM were investigated. The reduction of manganese was confirmed by the absorption edge shift of the Mn K-edge toward lower energies. The noise of oscillation in extended X-ray absorption fine structure k{sup 3}χ data at Mn K-edge reveals the distortion of the local structure of Mn atoms, and the peak that indicates the bonding length of Mn-O, Sr/Ce, and -Mn decreased with the addition of Ce contentmore » in Fourier transformations of the Mn K-edge. The distortion of the local structure at Mn atoms was affected by the reduced manganese ions having larger ionic radii than Mn{sup 4+}. Meanwhile, few distortions of local atomic structures of Sr atoms occurred, and the average nearest neighboring distances of Sr-O and Sr-Mn are ∼2.13 Å and ∼2.95 Å, respectively. The average bonding lengths of the Ce-O and Ce-Mn increased because the ionic radius of substituted Ce ion with 12 coordination number is smaller than that of Sr ion, which leads the reduction of Mn ions and the distortion of local structure at the substituted A-site. Therefore, we reasoned that the distortion of the local atomic structure at Mn atoms in MnO{sub 6} and Ce atoms in A-site is one of the causes for interrupting oxygen ion transfers as a geometric factor, which results in an increase in the polarization resistance of SCM within the Ce composition range from 10 mol. % to 30 mol. %.« less

A basin-hopping Monte Carlo investigation of the structural and energetic properties of 55- and 561-atom bimetallic nanoclusters: the examples of the ZrCu, ZrAl, and CuAl systems.

PubMed

De Souza, Douglas G; Cezar, Henrique M; Rondina, Gustavo G; de Oliveira, Marcelo F; Da Silva, Juarez L F

2016-05-05

We report a basin-hopping Monte Carlo investigation within the embedded-atom method of the structural and energetic properties of bimetallic ZrCu, ZrAl, and CuAl nanoclusters with 55 and 561 atoms. We found that unary Zr55, Zr561, Cu55, Cu561, Al55, and Al561 systems adopt the well known compact icosahedron (ICO) structure. The excess energy is negative for all systems and compositions, which indicates an energetic preference for the mixing of both chemical species. The ICO structure is preserved if a few atoms of the host system are replaced by different species, however, the composition limit in which the ICO structure is preserved depends on both the host and new chemical species. Using several structural analyses, three classes of structures, namely ideal ICO, nearly ICO, and distorted ICO structures, were identified. As the amounts of both chemical species change towards a more balanced composition, configurations far from the ICO structure arise and the dominant structures are nearly spherical, which indicates a strong minimization of the surface energy by decreasing the number of atoms with lower coordination on the surface. The average bond lengths follow Vegard's law almost exactly for ZrCu and ZrAl, however, this is not the case for CuAl. Furthermore, the radial distribution allowed us to identify the presence of an onion-like behavior in the surface of the 561-atom CuAl nanocluster with the Al atoms located in the outermost surface shell, which can be explained by the lower surface energies of the Al surfaces compared with the Cu surfaces. In ZrCu and ZrAl the radial distribution indicates a nearly homogeneous distribution for the chemical species, however, with a slightly higher concentration of Al atoms on the ZrAl surface, which can also be explained by the lower surface energy.

Voronoi analysis of the short–range atomic structure in iron and iron–carbon melts

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

Sobolev, Andrey; Mirzoev, Alexander

2015-08-17

In this work, we simulated the atomic structure of liquid iron and iron–carbon alloys by means of ab initio molecular dynamics. Voronoi analysis was used to highlight changes in the close environments of Fe atoms as carbon concentration in the melt increases. We have found, that even high concentrations of carbon do not affect short–range atomic order of iron atoms — it remains effectively the same as in pure iron melts.

Investigation on the neutral and anionic BxAlyH2 (x + y = 7, 8, 9) clusters using density functional theory combined with photoelectron spectroscopy.

PubMed

Ding, Li-Ping; Shao, Peng; Lu, Cheng; Zhang, Fang-Hui; Ding, Lei; Yuan, Tao Li

2016-08-17

The structure and bonding nature of neutral and negatively charged BxAlyH2 (x + y = 7, 8, 9) clusters are investigated with the aid of previously published experimental photoelectron spectra combined with the present density functional theory calculations. The comparison between the experimental photoelectron spectra and theoretical simulated spectra helps to identify the ground state structures. The accuracy of the obtained ground state structures is further verified by calculating their adiabatic electron affinities and vertical detachment energies and comparing them against available experimental data. The results show that the structures of BxAlyH2 transform from three-dimensional to planar structures as the number of boron atoms increases. Moreover, boron atoms tend to bind together forming Bn units. The hydrogen atoms prefer to bind with boron atoms rather than aluminum atoms. The analyses of the molecular orbital on the ground state structures further support the abovementioned results.

Structure of a low-population intermediate state in the release of an enzyme product.

PubMed

De Simone, Alfonso; Aprile, Francesco A; Dhulesia, Anne; Dobson, Christopher M; Vendruscolo, Michele

2015-01-09

Enzymes can increase the rate of biomolecular reactions by several orders of magnitude. Although the steps of substrate capture and product release are essential in the enzymatic process, complete atomic-level descriptions of these steps are difficult to obtain because of the transient nature of the intermediate conformations, which makes them largely inaccessible to standard structure determination methods. We describe here the determination of the structure of a low-population intermediate in the product release process by human lysozyme through a combination of NMR spectroscopy and molecular dynamics simulations. We validate this structure by rationally designing two mutations, the first engineered to destabilise the intermediate and the second to stabilise it, thus slowing down or speeding up, respectively, product release. These results illustrate how product release by an enzyme can be facilitated by the presence of a metastable intermediate with transient weak interactions between the enzyme and product.

Coordination radii in diamond, zinc blende, and CaF2 structures

NASA Astrophysics Data System (ADS)

Hall, George L.

1982-07-01

The radii of all ''shells'' of atoms about any lattice point are given for these three structures, and for the zinc blende (AB) and CaF2 (AB2) structures it is shown that all shells about an A origin and all shells about a B origin are of pure type, i.e., contain only A's or only B's. The initial sequence (small radii) of shell types does not continue indefinitely and is broken according to rules completely specified. These results are analogous to those reported by Hall and Christy earlier for the NaCl and CsCl structures in which the ABABABṡṡṡ sequence for NaCl and the ABAABAABAAṡṡṡ for CsCl, both taken about an A origin, do not continue indefinitely. It is shown that Ferris-Prabhu's results for diamond violate theorem 1 of Hall and Christy.

Crossover from disordered to core-shell structures of nano-oxide Y{sub 2}O{sub 3} dispersed particles in Fe

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

Higgins, M. P.; Wang, L. M.; Gao, F., E-mail: gaofeium@umich.edu

Molecular dynamic simulations of Y{sub 2}O{sub 3} in bcc Fe and transmission electron microscopy (TEM) observations were used to understand the structure of Y{sub 2}O{sub 3} nano-clusters in an oxide dispersion strengthened steel matrix. The study showed that Y{sub 2}O{sub 3} nano-clusters below 2 nm were completely disordered. Y{sub 2}O{sub 3} nano-clusters above 2 nm, however, form a core-shell structure, with a shell thickness of 0.5–0.7 nm that is independent of nano-cluster size. Y{sub 2}O{sub 3} nano-clusters were surrounded by off-lattice Fe atoms, further increasing the stability of these nano-clusters. TEM was used to corroborate our simulation results and showed a crossover frommore » a disordered nano-cluster to a core-shell structure.« less

Unusual Features of Crystal Structures of Some Simple Copper Compounds

ERIC Educational Resources Information Center

Douglas, Bodie

2009-01-01

Some simple copper compounds have unusual crystal structures. Cu[subscript 3]N is cubic with N atoms at centers of octahedra formed by 6 Cu atoms. Cu[subscript 2]O (cuprite) is also cubic; O atoms are in tetrahedra formed by 4 Cu atoms. These tetrahedra are linked by sharing vertices forming two independent networks without linkages between them.…

Colloquium: Laser probing of neutron-rich nuclei in light atoms

NASA Astrophysics Data System (ADS)

Lu, Z.-T.; Mueller, P.; Drake, G. W. F.; Nörtershäuser, W.; Pieper, Steven C.; Yan, Z.-C.

2013-10-01

The neutron-rich He6 and He8 isotopes exhibit an exotic nuclear structure that consists of a tightly bound He4-like core with additional neutrons orbiting at a relatively large distance, forming a halo. Recent experimental efforts have succeeded in laser trapping and cooling these short-lived, rare helium atoms and have measured the atomic isotope shifts along the He4-He6-He8 chain by performing laser spectroscopy on individual trapped atoms. Meanwhile, the few-electron atomic structure theory, including relativistic and QED corrections, has reached a comparable degree of accuracy in the calculation of the isotope shifts. In parallel efforts, also by measuring atomic isotope shifts, the nuclear charge radii of lithium and beryllium isotopes have been studied. The techniques employed were resonance ionization spectroscopy on neutral, thermal lithium atoms and collinear laser spectroscopy on beryllium ions. Combining advances in both atomic theory and laser spectroscopy, the charge radii of these light halo nuclei have now been determined for the first time independent of nuclear structure models. The results are compared with the values predicted by a number of nuclear structure calculations and are used to guide our understanding of the nuclear forces in the extremely neutron-rich environment.

Classification Order of Surface-Confined Intermixing at Epitaxial Interface

NASA Astrophysics Data System (ADS)

Michailov, M.

The self-organization phenomena at epitaxial interface hold special attention in contemporary material science. Being relevant to the fundamental physical problem of competing, long-range and short-range atomic interactions in systems with reduced dimensionality, these phenomena have found exacting academic interest. They are also of great technological importance for their ability to bring spontaneous formation of regular nanoscale surface patterns and superlattices with exotic properties. The basic phenomenon involved in this process is surface diffusion. That is the motivation behind the present study which deals with important details of diffusion scenarios that control the fine atomic structure of epitaxial interface. Consisting surface imperfections (terraces, steps, kinks, and vacancies), the interface offers variety of barriers for surface diffusion. Therefore, the adatoms and clusters need a certain critical energy to overcome the corresponding diffusion barriers. In the most general case the critical energies can be attained by variation of the system temperature. Hence, their values define temperature limits of system energy gaps associated with different diffusion scenarios. This systematization imply classification order of surface alloying: blocked, incomplete, and complete. On that background, two diffusion problems, related to the atomic-scale surface morphology, will be discussed. The first problem deals with diffusion of atomic clusters on atomically smooth interface. On flat domains, far from terraces and steps, we analyzed the impact of size, shape, and cluster/substrate lattice misfit on the diffusion behavior of atomic clusters (islands). We found that the lattice constant of small clusters depends on the number N of building atoms at 1 < N ≤ 10. In heteroepitaxy, this effect of variable lattice constant originates from the enhanced charge transfer and the strong influence of the surface potential on cluster atomic arrangement. At constant temperature, the variation of the lattice constant leads to variable misfit which affects the island migration. The cluster/substrate commensurability influences the oscillation behavior of the diffusion coefficient caused by variation in the cluster shape. We discuss the results in a physical model that implies cluster diffusion with size-dependent cluster/substrate misfit. The second problem is devoted to diffusion phenomena in the vicinity of atomic terraces on stepped or vicinal surfaces. Here, we develop a computational model that refines important details of diffusion behavior of adatoms accounting for the energy barriers at specific atomic sites (smooth domains, terraces, and steps) located on the crystal surface. The dynamic competition between energy gained by mixing and substrate strain energy results in diffusion scenario where adatoms form alloyed islands and alloyed stripes in the vicinity of terrace edges. Being in agreement with recent experimental findings, the observed effect of stripe and island alloy formation opens up a way regular surface patterns to be configured at different atomic levels on the crystal surface. The complete surface alloying of the entire interface layer is also briefly discussed with critical analysis and classification of experimental findings and simulation data.

Selective Reflection of Potassium Vapor Nanolayers in a Magnetic Field

NASA Astrophysics Data System (ADS)

Sargsyan, A.; Tonoyan, A.; Keaveney, J.; Hughes, I. G.; Adams, C. S.; Sarkisyan, D.

2018-03-01

The selective reflection of laser radiation from the interface between a dielectric window and the atomic vapors confined in a nanocell of thickness L ≈ 350 nm is used to develop effective Doppler-broadening- free spectroscopy of potassium atoms. A small atomic line width and a relation between the signal intensity and the transition probability allowed us to resolve four lines of atomic transitions responsible for the D1 lines of the 39K and 41K isotopes. Two groups containing four atomic transitions form in an applied magnetic field upon pumping by radiation with circular polarization σ+ or σ-. Different intensities (probabilities) of transitions for the σ+ and σ- excitations are detected in magnetic field B 0 ≈ A hfs /μB ≈ 165 G ( A hfs is the magnetic dipole constant for the ground state and μB is the Bohr magneton). A substantially different situation is observed at B ≫ B 0, since high symmetry appears for the two groups formed by radiation with circular polarization σ+ or σ-. Each group is the mirror image of the other group with respect to the frequency of the 42 S 1/2-42 P 1/2 transition, which additionally proves the occurrence of the complete Paschen-Back regime of the hyperfine structure at B ≈ 2.5 kG. A developed theoretical model well reproduces the experimental results. Possible practical applications are described. The results obtained can also be applied to the D 1 lines of 87Rb and 23Na.

Further along the Road Less Traveled: AMBER ff15ipq, an Original Protein Force Field Built on a Self-Consistent Physical Model

PubMed Central

2016-01-01

We present the AMBER ff15ipq force field for proteins, the second-generation force field developed using the Implicitly Polarized Q (IPolQ) scheme for deriving implicitly polarized atomic charges in the presence of explicit solvent. The ff15ipq force field is a complete rederivation including more than 300 unique atomic charges, 900 unique torsion terms, 60 new angle parameters, and new atomic radii for polar hydrogens. The atomic charges were derived in the context of the SPC/Eb water model, which yields more-accurate rotational diffusion of proteins and enables direct calculation of nuclear magnetic resonance (NMR) relaxation parameters from molecular dynamics simulations. The atomic radii improve the accuracy of modeling salt bridge interactions relative to contemporary fixed-charge force fields, rectifying a limitation of ff14ipq that resulted from its use of pair-specific Lennard-Jones radii. In addition, ff15ipq reproduces penta-alanine J-coupling constants exceptionally well, gives reasonable agreement with NMR relaxation rates, and maintains the expected conformational propensities of structured proteins/peptides, as well as disordered peptides—all on the microsecond (μs) time scale, which is a critical regime for drug design applications. These encouraging results demonstrate the power and robustness of our automated methods for deriving new force fields. All parameters described here and the mdgx program used to fit them are included in the AmberTools16 distribution. PMID:27399642

Quantum conductance oscillation in linear monatomic silicon chains

NASA Astrophysics Data System (ADS)

Liu, Fu-Ti; Cheng, Yan; Yang, Fu-Bin; Chen, Xiang-Rong

2014-02-01

The conductance of linear silicon atomic chains with n=1-8 atoms sandwiched between Au electrodes is investigated by using the density functional theory combined with non-equilibrium Green's function. The results show that the conductance oscillates with a period of two atoms as the number of atoms in the chain is varied. We optimize the geometric structure of nanoscale junctions in different distances, and obtain that the average bond-length of silicon atoms in each chain at equilibrium positions is 2.15±0.03 Å. The oscillation of average Si-Si bond-length can explain the conductance oscillation from the geometric structure of atomic chains. We calculate the transmission spectrum of the chains in the equilibrium positions, and explain the conductance oscillation from the electronic structure. The transport channel is mainly contributed by px and py orbital electrons of silicon atoms. The even-odd oscillation is robust under external voltage up to 1.2 V.

Interplay of weak interactions in the atom-by-atom condensation of xenon within quantum boxes

PubMed Central

Nowakowska, Sylwia; Wäckerlin, Aneliia; Kawai, Shigeki; Ivas, Toni; Nowakowski, Jan; Fatayer, Shadi; Wäckerlin, Christian; Nijs, Thomas; Meyer, Ernst; Björk, Jonas; Stöhr, Meike; Gade, Lutz H.; Jung, Thomas A.

2015-01-01

Condensation processes are of key importance in nature and play a fundamental role in chemistry and physics. Owing to size effects at the nanoscale, it is conceptually desired to experimentally probe the dependence of condensate structure on the number of constituents one by one. Here we present an approach to study a condensation process atom-by-atom with the scanning tunnelling microscope, which provides a direct real-space access with atomic precision to the aggregates formed in atomically defined ‘quantum boxes’. Our analysis reveals the subtle interplay of competing directional and nondirectional interactions in the emergence of structure and provides unprecedented input for the structural comparison with quantum mechanical models. This approach focuses on—but is not limited to—the model case of xenon condensation and goes significantly beyond the well-established statistical size analysis of clusters in atomic or molecular beams by mass spectrometry. PMID:25608225

Atomic oxygen protective coating with resistance to undercutting at defect sites

NASA Technical Reports Server (NTRS)

Banks, Bruce A. (Inventor); Rutledge, Sharon K. (Inventor)

1994-01-01

Structures composed at least partially of an organic substrate may be protected from oxidation by applying a catalyst onto said substrate for promoting the combination of atomic oxygen to molecular oxygen. The structure may also be protected by applying both a catalyst and an atomic oxygen shielding layer onto the substrate. The structures to be protected include spacecraft surfaces.

Atomic Structure of Au 329(SR) 84 Faradaurate Plasmonic Nanomolecules

DOE PAGES

Kumara, Chanaka; Zuo, Xiaobing; Ilavsky, Jan; ...

2015-04-03

To design novel nanomaterials, it is important to precisely control the composition, determine the atomic structure, and manipulate the structure to tune the materials property. Here we present a comprehensive characterization of the material whose composition is Au 329(SR) 84 precisely, therefore referred to as a nanomolecule. The size homogeneity was shown by electron microscopy, solution X-ray scattering, and mass spectrometry. We proposed its atomic structure to contain the Au 260 core using experiments and modeling of a total-scattering-based atomic-pair distribution functional analysis. HAADF-STEM images shows fcc-like 2.0 ± 0.1 nm diameter nanomolecules.

NC-AFM observation of atomic scale structure of rutile-type TiO2(110) surface prepared by wet chemical process.

PubMed

Namai, Yoshimichi; Matsuoka, Osamu

2006-04-06

We succeeded in observing the atomic scale structure of a rutile-type TiO2(110) single-crystal surface prepared by the wet chemical method of chemical etching in an acid solution and surface annealing in air. Ultrahigh vacuum noncontact atomic force microscopy (UHV-NC-AFM) was used for observing the atomic scale structures of the surface. The UHV-NC-AFM measurements at 450 K, which is above a desorption temperature of molecularly adsorbed water on the TiO2(110) surface, enabled us to observe the atomic scale structure of the TiO2(110) surface prepared by the wet chemical method. In the UHV-NC-AFM measurements at room temperature (RT), however, the atomic scale structure of the TiO2(110) surface was not observed. The TiO2(110) surface may be covered with molecularly adsorbed water after the surface was prepared by the wet chemical method. The structure of the TiO2(110) surface that was prepared by the wet chemical method was consistent with the (1 x 1) bulk-terminated model of the TiO2(110) surface.

Atomic scale chemical tomography of human bone

NASA Astrophysics Data System (ADS)

Langelier, Brian; Wang, Xiaoyue; Grandfield, Kathryn

2017-01-01

Human bone is a complex hierarchical material. Understanding bone structure and its corresponding composition at the nanometer scale is critical for elucidating mechanisms of biomineralization under healthy and pathological states. However, the three-dimensional structure and chemical nature of bone remains largely unexplored at the nanometer scale due to the challenges associated with characterizing both the structural and chemical integrity of bone simultaneously. Here, we use correlative transmission electron microscopy and atom probe tomography for the first time, to our knowledge, to reveal structures in human bone at the atomic level. This approach provides an overlaying chemical map of the organic and inorganic constituents of bone on its structure. This first use of atom probe tomography on human bone reveals local gradients, trace element detection of Mg, and the co-localization of Na with the inorganic-organic interface of bone mineral and collagen fibrils, suggesting the important role of Na-rich organics in the structural connection between mineral and collagen. Our findings provide the first insights into the hierarchical organization and chemical heterogeneity in human bone in three-dimensions at its smallest length scale - the atomic level. We demonstrate that atom probe tomography shows potential for new insights in biomineralization research on bone.

Fluorescence detection of white-beam X-ray absorption anisotropy: towards element-sensitive projections of local atomic structure

PubMed Central

Korecki, P.; Tolkiehn, M.; Dąbrowski, K. M.; Novikov, D. V.

2011-01-01

Projections of the atomic structure around Nb atoms in a LiNbO3 single crystal were obtained from a white-beam X-ray absorption anisotropy (XAA) pattern detected using Nb K fluorescence. This kind of anisotropy results from the interference of X-rays inside a sample and, owing to the short coherence length of a white beam, is visible only at small angles around interatomic directions. Consequently, the main features of the recorded XAA corresponded to distorted real-space projections of dense-packed atomic planes and atomic rows. A quantitative analysis of XAA was carried out using a wavelet transform and allowed well resolved projections of Nb atoms to be obtained up to distances of 10 Å. The signal of nearest O atoms was detected indirectly by a comparison with model calculations. The measurement of white-beam XAA using characteristic radiation indicates the possibility of obtaining element-sensitive projections of the local atomic structure in more complex samples. PMID:21997909

Light element opacities of astrophysical interest from ATOMIC

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

Colgan, J.; Kilcrease, D. P.; Magee, N. H. Jr.

We present new calculations of local-thermodynamic-equilibrium (LTE) light element opacities from the Los Alamos ATOMIC code for systems of astrophysical interest. ATOMIC is a multi-purpose code that can generate LTE or non-LTE quantities of interest at various levels of approximation. Our calculations, which include fine-structure detail, represent a systematic improvement over previous Los Alamos opacity calculations using the LEDCOP legacy code. The ATOMIC code uses ab-initio atomic structure data computed from the CATS code, which is based on Cowan's atomic structure codes, and photoionization cross section data computed from the Los Alamos ionization code GIPPER. ATOMIC also incorporates a newmore » equation-of-state (EOS) model based on the chemical picture. ATOMIC incorporates some physics packages from LEDCOP and also includes additional physical processes, such as improved free-free cross sections and additional scattering mechanisms. Our new calculations are made for elements of astrophysical interest and for a wide range of temperatures and densities.« less

{μ-2-[(3-Amino-2,2-dimethyl-prop-yl)imino-meth-yl]-6-meth-oxy-phenolato-1:2κ(5)O(1),O(6):N,N',O(1)}{2-[(3-amino-2,2-dimethyl-prop-yl)imino-meth-yl]-6-meth-oxy-phenolato-1κ(3)N,N',O(1)}-μ-azido-1:2κ(2)N:N-azido-2κN-methanol-2κO-dinickel(II).

PubMed

Ghaemi, Akbar; Rayati, Saeed; Fayyazi, Kazem; Ng, Seik Weng; Tiekink, Edward R T

2012-08-01

Two distinct coordination geometries are found in the binuclear title complex, [Ni(2)(C(13)H(19)N(2)O(2))(2)(N(3))(2)(CH(3)OH)], as one Schiff base ligand is penta-dentate, coordinating via the anti-cipated oxide O, imine N and amine N atoms (as for the second, tridentate, ligand) but the oxide O is bridging and coordination also occurs through the meth-oxy O atom. The Ni(II) atoms are linked by a μ(2)-oxide atom and one end of a μ(2)-azide ligand, forming an Ni(2)ON core. The coordination geometry for the Ni(II) atom coordinated by the tridentate ligand is completed by the meth-oxy O atom derived from the penta-dentate ligand, with the resulting N(3)O(3) donor set defining a fac octa-hedron. The second Ni(II) atom has its cis-octa-hedral N(4)O(2) coordination geometry completed by the imine N and amine N atoms of the penta-dentate Schiff base ligand, a terminally coordinated azide N and a methanol O atom. The arrangement is stabilized by an intra-molecular hydrogen bond between the methanol H and the oxide O atom. Linear supra-molecular chains along the a axis are formed in the crystal packing whereby two amine H atoms from different amine atoms hydrogen bond to the terminal N atom of the monodentate azide ligand.

IR investigation on silicon oxycarbide structure obtained from precursors with 1:1 silicon to carbon atoms ratio and various carbon atoms distribution

NASA Astrophysics Data System (ADS)

Niemiec, Wiktor; Szczygieł, Przemysław; Jeleń, Piotr; Handke, Mirosław

2018-07-01

Silicon oxycarbide is a material with a number of advantageous properties that strongly depend on its structure. The most common approach to its tailoring is based on varying the silicon to carbon atoms ratio in the preceramic polymeric precursor. This work is the first comparison of the materials obtained from precursors with the same Si to C atoms ratio, but with various distribution of these atoms in the preceramic polymer. In addition to standard mixtures of monomers containing single silicon atom, a number of monomers with high molar masses and well defined structure was used. The IR was used to investigate the structure of the precursors and materials obtained after their annealing in 800 °C. The results show, that not only the distribution of carbon containing groups among the monomers is important, but also the (in)ability of these groups to end up in each other vicinity in the precursor as well as the degree of condensation of each structural unit.

Simulation of Rutherford backscattering spectrometry from arbitrary atom structures

DOE PAGES

Zhang, S.; Univ. of Helsinki; Nordlund, Kai; ...

2016-10-25

Rutherford backscattering spectrometry in a channeling direction (RBS/C) is a powerful tool for analysis of the fraction of atoms displaced from their lattice positions. However, it is in many cases not straightforward to analyze what is the actual defect structure underlying the RBS/C signal. To reveal insights of RBS/C signals from arbitrarily complex defective atomic structures, we develop in this paper a method for simulating the RBS/C spectrum from a set of arbitrary read-in atom coordinates (obtained, e.g., from molecular dynamics simulations). We apply the developed method to simulate the RBS/C signals from Ni crystal structures containing randomly displaced atoms,more » Frenkel point defects, and extended defects, respectively. The RBS/C simulations show that, even for the same number of atoms in defects, the RBS/C signal is much stronger for the extended defects. Finally, comparison with experimental results shows that the disorder profile obtained from RBS/C signals in ion-irradiated Ni is due to a small fraction of extended defects rather than a large number of individual random atoms.« less

Atomic structures of B20 FeGe thin films grown on the Si(111) surface

NASA Astrophysics Data System (ADS)

Kim, Wondong; Noh, Seungkyun; Yoon, Jisoo; Kim, Young Heon; Lee, Inho; Kim, Jae-Sung; Hwang, Chanyong

We investigated the growth and atomic structures of FeGe thin films on the Si (111) surface by using scanning tunneling microscopy (STM) and transmission electron microscopy (TEM). The 2 5nm- thick FeGe thin films were prepared on the clean Si(111) 7x7 surface by co-deposition of Fe and Ge from separated electron-beam evaporators. With direct deposition on the substrate at the temperature above 550 K, the surface of FeGe films was not smooth and consisted of coarse grains. By the combination of room-temperature annealing and post-annealing process around 800 K, the structure of FeGe thin films evolved into the well crystalized structures. Atom-resolved STM images revealed that there are at least four different surface terminations. We constructed atomic models for each surface terminations based on the bulk atomic arrangement of a B20 chiral structure and confirmed that the observed STM images are successfully reproduced by using computational simulations employing Vienna Ab Initio Simulation package (VASP) with a B20 chiral structure model. TEM cross-sectional images also support our atomic models by revealing clearly the characteristic zigzag features of B20 structures of FeGe(111) thin films.

Mechanistic Details and Reactivity Descriptors in Oxidation and Acid Catalysis of Methanol

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

Deshlahra, Prashant; Carr, Robert T.; Chai, Song-Hai

2015-02-06

Acid and redox reaction rates of CH₃OH-O₂ mixtures on polyoxometalate (POM) clusters, together with isotopic, spectroscopic, and theoretical assessments of catalyst properties and reaction pathways, were used to define rigorous descriptors of reactivity and to probe the compositional effects for oxidative dehydrogenation (ODH) and dehydration reactions. ³¹P-MAS NMR, transmission electron microscopy and titrations of protons with di-tert-butylpyridine during catalysis showed that POM clusters retained their Keggin structure upon dispersion on SiO₂ and after use in CH₃OH reactions. The effects of CH₃OH and O₂ pressures and of D-substitution on ODH rates show that C-H activation in molecularly adsorbed CH₃OH is themore » sole kinetically relevant step and leads to reduced centers as intermediates present at low coverages; their concentrations, measured from UV-vis spectra obtained during catalysis, are consistent with the effects of CH₃OH/O₂ ratios predicted from the elementary steps proposed. First-order ODH rate constants depend strongly on the addenda atoms (Mo vs W) but weakly on the central atom (P vs Si) in POM clusters, because C-H activation steps inject electrons into the lowest unoccupied molecular orbitals (LUMO) of the clusters, which are the d-orbitals at Mo⁶⁺ and W⁶⁺ centers. H-atom addition energies (HAE) at O-atoms in POM clusters represent the relevant theoretical probe of the LUMO energies and of ODH reactivity. The calculated energies of ODH transition states at each O-atom depend linearly on their HAE values with slopes near unity, as predicted for late transition states in which electron transfer and C-H cleavage are essentially complete. HAE values averaged over all accessible O-atoms in POM clusters provide the appropriate reactivity descriptor for oxides whose known structures allow accurate HAE calculations. CH₃OH dehydration proceeds via parallel pathways mediated by late carbenium-ion transition states; effects of composition on dehydration reactivity reflect changes in charge reorganizations and electrostatic forces that stabilize protons at Brønsted acid sites.« less

Methanol oxidation reaction on core-shell structured Ruthenium-Palladium nanoparticles: Relationship between structure and electrochemical behavior

NASA Astrophysics Data System (ADS)

Kübler, Markus; Jurzinsky, Tilman; Ziegenbalg, Dirk; Cremers, Carsten

2018-01-01

In this work the relationship between structural composition and electrochemical characteristics of Palladium(Pd)-Ruthenium(Ru) nanoparticles during alkaline methanol oxidation reaction is investigated. The comparative study of a standard alloyed and a precisely Ru-core-Pd-shell structured catalyst allows for a distinct investigation of the electronic effect and the bifunctional mechanism. Core-shell catalysts benefit from a strong electronic effect and an efficient Pd utilization. It is found that core-shell nanoparticles are highly active towards methanol oxidation reaction for potentials ≥0.6 V, whereas alloyed catalysts show higher current outputs in the lower potential range. However, differential electrochemical mass spectrometry (DEMS) experiments reveal that the methanol oxidation reaction on core-shell structured catalysts proceeds via the incomplete oxidation pathway yielding formaldehyde, formic acid or methyl formate. Contrary, the alloyed catalyst benefits from the Ru atoms at its surface. Those are found to be responsible for high methanol oxidation activity at lower potentials as well as for complete oxidation of CH3OH to CO2 via the bifunctional mechanism. Based on these findings a new Ru-core-Pd-shell-Ru-terrace catalyst was synthesized, which combines the advantages of the core-shell structure and the alloy. This novel catalyst shows high methanol electrooxidation activity as well as excellent selectivity for the complete oxidation pathway.

Atomic structure and dynamics properties of Cu50Zr50 films

NASA Astrophysics Data System (ADS)

Chen, Heng; Qu, Bingyan; Li, Dongdong; Zhou, Rulong; Zhang, Bo

2018-01-01

In this paper, the structural and dynamic properties of Cu50Zr50 films are investigated by molecular dynamics simulations. Our results show that the dynamics of the surface atoms are much faster than those of the bulk. Especially, the diffusion coefficient of the surface atoms is about forty times larger than that of the bulk at 600 K, which qualitatively agrees with the experimental results. Meanwhile, we find that the population of the icosahedral (-like) clusters in the surface region is obviously higher than that of the bulk, which prevents the surface from crystallization. A new method to determine the string-like collective atomic motion is introduced in the paper, and it suggests a possible connection between the glass formation ability and collective atomic motion. By using the method, the effects of surface on collective motion are illustrated. Our results show that the string-like collective atomic motion of surface atoms is weakened while that of the interior atoms is strengthened. The studies clearly explain the effects of surface on the structural and dynamic properties of Cu50Zr50 films from the atomic scale.

THESEUS: maximum likelihood superpositioning and analysis of macromolecular structures

PubMed Central

Theobald, Douglas L.; Wuttke, Deborah S.

2008-01-01

Summary THESEUS is a command line program for performing maximum likelihood (ML) superpositions and analysis of macromolecular structures. While conventional superpositioning methods use ordinary least-squares (LS) as the optimization criterion, ML superpositions provide substantially improved accuracy by down-weighting variable structural regions and by correcting for correlations among atoms. ML superpositioning is robust and insensitive to the specific atoms included in the analysis, and thus it does not require subjective pruning of selected variable atomic coordinates. Output includes both likelihood-based and frequentist statistics for accurate evaluation of the adequacy of a superposition and for reliable analysis of structural similarities and differences. THESEUS performs principal components analysis for analyzing the complex correlations found among atoms within a structural ensemble. PMID:16777907

An all-atom structure-based potential for proteins: bridging minimal models with all-atom empirical forcefields.

PubMed

Whitford, Paul C; Noel, Jeffrey K; Gosavi, Shachi; Schug, Alexander; Sanbonmatsu, Kevin Y; Onuchic, José N

2009-05-01

Protein dynamics take place on many time and length scales. Coarse-grained structure-based (Go) models utilize the funneled energy landscape theory of protein folding to provide an understanding of both long time and long length scale dynamics. All-atom empirical forcefields with explicit solvent can elucidate our understanding of short time dynamics with high energetic and structural resolution. Thus, structure-based models with atomic details included can be used to bridge our understanding between these two approaches. We report on the robustness of folding mechanisms in one such all-atom model. Results for the B domain of Protein A, the SH3 domain of C-Src Kinase, and Chymotrypsin Inhibitor 2 are reported. The interplay between side chain packing and backbone folding is explored. We also compare this model to a C(alpha) structure-based model and an all-atom empirical forcefield. Key findings include: (1) backbone collapse is accompanied by partial side chain packing in a cooperative transition and residual side chain packing occurs gradually with decreasing temperature, (2) folding mechanisms are robust to variations of the energetic parameters, (3) protein folding free-energy barriers can be manipulated through parametric modifications, (4) the global folding mechanisms in a C(alpha) model and the all-atom model agree, although differences can be attributed to energetic heterogeneity in the all-atom model, and (5) proline residues have significant effects on folding mechanisms, independent of isomerization effects. Because this structure-based model has atomic resolution, this work lays the foundation for future studies to probe the contributions of specific energetic factors on protein folding and function.

An All-atom Structure-Based Potential for Proteins: Bridging Minimal Models with All-atom Empirical Forcefields

PubMed Central

Whitford, Paul C.; Noel, Jeffrey K.; Gosavi, Shachi; Schug, Alexander; Sanbonmatsu, Kevin Y.; Onuchic, José N.

2012-01-01

Protein dynamics take place on many time and length scales. Coarse-grained structure-based (Gō) models utilize the funneled energy landscape theory of protein folding to provide an understanding of both long time and long length scale dynamics. All-atom empirical forcefields with explicit solvent can elucidate our understanding of short time dynamics with high energetic and structural resolution. Thus, structure-based models with atomic details included can be used to bridge our understanding between these two approaches. We report on the robustness of folding mechanisms in one such all-atom model. Results for the B domain of Protein A, the SH3 domain of C-Src Kinase and Chymotrypsin Inhibitor 2 are reported. The interplay between side chain packing and backbone folding is explored. We also compare this model to a Cα structure-based model and an all-atom empirical forcefield. Key findings include 1) backbone collapse is accompanied by partial side chain packing in a cooperative transition and residual side chain packing occurs gradually with decreasing temperature 2) folding mechanisms are robust to variations of the energetic parameters 3) protein folding free energy barriers can be manipulated through parametric modifications 4) the global folding mechanisms in a Cα model and the all-atom model agree, although differences can be attributed to energetic heterogeneity in the all-atom model 5) proline residues have significant effects on folding mechanisms, independent of isomerization effects. Since this structure-based model has atomic resolution, this work lays the foundation for future studies to probe the contributions of specific energetic factors on protein folding and function. PMID:18837035

Tailor-made force fields for crystal-structure prediction.

PubMed

Neumann, Marcus A

2008-08-14

A general procedure is presented to derive a complete set of force-field parameters for flexible molecules in the crystalline state on a case-by-case basis. The force-field parameters are fitted to the electrostatic potential as well as to accurate energies and forces generated by means of a hybrid method that combines solid-state density functional theory (DFT) calculations with an empirical van der Waals correction. All DFT calculations are carried out with the VASP program. The mathematical structure of the force field, the generation of reference data, the choice of the figure of merit, the optimization algorithm, and the parameter-refinement strategy are discussed in detail. The approach is applied to cyclohexane-1,4-dione, a small flexible ring. The tailor-made force field obtained for cyclohexane-1,4-dione is used to search for low-energy crystal packings in all 230 space groups with one molecule per asymmetric unit, and the most stable crystal structures are reoptimized in a second step with the hybrid method. The experimental crystal structure is found as the most stable predicted crystal structure both with the tailor-made force field and the hybrid method. The same methodology has also been applied successfully to the four compounds of the fourth CCDC blind test on crystal-structure prediction. For the five aforementioned compounds, the root-mean-square deviations between lattice energies calculated with the tailor-made force fields and the hybrid method range from 0.024 to 0.053 kcal/mol per atom around an average value of 0.034 kcal/mol per atom.

All-atom four-body knowledge-based statistical potential to distinguish native tertiary RNA structures from nonnative folds.

PubMed

Masso, Majid

2018-09-14

Scientific breakthroughs in recent decades have uncovered the capability of RNA molecules to fulfill a wide array of structural, functional, and regulatory roles in living cells, leading to a concomitantly significant increase in both the number and diversity of experimentally determined RNA three-dimensional (3D) structures. Atomic coordinates from a representative training set of solved RNA structures, displaying low sequence and structure similarity, facilitate derivation of knowledge-based energy functions. Here we develop an all-atom four-body statistical potential and evaluate its capacity to distinguish native RNA 3D structures from nonnative folds based on calculated free energy scores. Atomic four-body nearest-neighbors are objectively identified by their occurrence as tetrahedral vertices in the Delaunay tessellations of RNA structures, and rates of atomic quadruplet interactions expected by chance are obtained from a multinomial reference distribution. Our four-body energy function, referred to as RAMP (ribonucleic acids multibody potential), is subsequently derived by applying the inverted Boltzmann principle to the frequency data, yielding an energy score for each type of atomic quadruplet interaction. Several well-known benchmark datasets reveal that RAMP is comparable with, and often outperforms, existing knowledge- and physics-based energy functions. To the best of our knowledge, this is the first study detailing an RNA tertiary structure-based multibody statistical potential and its comparative evaluation. Copyright © 2018 Elsevier Ltd. All rights reserved.

Probing Single Pt Atoms in Complex Intermetallic Al13Fe4.

PubMed

Yamada, Tsunetomo; Kojima, Takayuki; Abe, Eiji; Kameoka, Satoshi; Murakami, Yumi; Gille, Peter; Tsai, An Pang

2018-03-21

The atomic structure of a 0.2 atom % Pt-doped complex metallic alloy, monoclinic Al 13 Fe 4 , was investigated using a single crystal prepared by the Czochralski method. High-angle annular dark-field scanning transmission electron microscopy showed that the Pt atoms were dispersed as single atoms and substituted at Fe sites in Al 13 Fe 4 . Single-crystal X-ray structural analysis revealed that the Pt atoms preferentially substitute at Fe(1). Unlike those that have been reported, Pt single atoms in the surface layers showed lower activity and selectivity than those of Al 2 Pt and bulk Pt for propyne hydrogenation, indicating that the active state of a given single-atom Pt site is strongly dominated by the bonding to surrounding Al atoms.

Pb chains on reconstructed Si(335) surface

NASA Astrophysics Data System (ADS)

Krawiec, Mariusz

2009-04-01

The structural and electronic properties of Si(335)-Au surface decorated with Pb atoms are studied by means of density-functional theory. The resulting structural model features Pb atoms bonded to neighboring Si and Au surface atoms, forming monoatomic chain located 0.2 nm above the surface. The presence of Pb chain leads to a strong rebonding of Si atoms at the step edge. The fact that Pb atoms occupy positions in the middle of terrace is consistent with scanning tunneling microscopy (STM) data and also confirmed by simulated STM images. The calculated band structure clearly shows one-dimensional metallic character. The calculated electronic bands remain in very good agreement with photoemission data.

Optimal atomic structure of amorphous silicon obtained from density functional theory calculations

NASA Astrophysics Data System (ADS)

Pedersen, Andreas; Pizzagalli, Laurent; Jónsson, Hannes

2017-06-01

Atomic structure of amorphous silicon consistent with several reported experimental measurements has been obtained from annealing simulations using electron density functional theory calculations and a systematic removal of weakly bound atoms. The excess energy and density with respect to the crystal are well reproduced in addition to radial distribution function, angular distribution functions, and vibrational density of states. No atom in the optimal configuration is locally in a crystalline environment as deduced by ring analysis and common neighbor analysis, but coordination defects are present at a level of 1%-2%. The simulated samples provide structural models of this archetypal disordered covalent material without preconceived notion of the atomic ordering or fitting to experimental data.

Atomic Chain Electronics

NASA Technical Reports Server (NTRS)

Yamada, Toshishige; Saini, Subhash (Technical Monitor)

1998-01-01

Adatom chains, precise structures artificially created on an atomically regulated surface, are the smallest possible candidates for future nanoelectronics. Since all the devices are created by combining adatom chains precisely prepared with atomic precision, device characteristics are predictable, and free from deviations due to accidental structural defects. In this atomic dimension, however, an analogy to the current semiconductor devices may not work. For example, Si structures are not always semiconducting. Adatom states do not always localize at the substrate surface when adatoms form chemical bonds to the substrate atoms. Transport properties are often determined for the entire system of the chain and electrodes, and not for chains only. These fundamental issues are discussed, which will be useful for future device considerations.

Dislocation imaging for orthopyroxene using an atom-resolved scanning transmission electron microscopy.

PubMed

Kumamoto, Akihito; Kogure, Toshihiro; Raimbourg, Hugues; Ikuhara, Yuichi

2014-11-01

Dislocations, one-dimensional lattice defects, appear as a microscopic phenomenon while they are formed in silicate minerals by macroscopic dynamics of the earth crust such as shear stress. To understand ductile deformation mechanisms of silicates, atomic structures of the dislocations have been examined using transmission electron microscopy (TEM). Among them, it has been proposed that {100}<001> primary slip system of orthopyroxene (Opx) is dissociated into partial dislocations, and a stacking fault with the clinopyroxene (Cpx) structure is formed between the dislocations. This model, however, has not been determined completely due to the complex structures of silicates. Scanning transmission electron microscopy (STEM) has a potential to determine the structure of dislocations with single-atomic column sensitivity, particularly by using high-angle annular dark field (HAADF) and annular bright field (ABF) imaging with a probing aberration corrector.[1] Furthermore, successive analyses from light microscopy to atom-resolved STEM have been achieved by focused ion beam (FIB) sampling techniques.[2] In this study, we examined dislocation arrays at a low-angle grain boundary of ∼1° rotation about the b-axis in natural deformed Opx using a simultaneous acquisition of HAADF/ABF (JEM-ARM200F, JEOL) equipped with 100 mm2 silicon drift detector (SDD) for energy dispersive X-ray spectroscopy (EDS). Figure 1 shows averaged STEM images viewed along the b- axis of Opx extracted from repeating units. HAADF provides the cation-site arrangement, and ABF distinguishes the difference of slightly rotated SiO4 tetrahedron around the a- axis. This is useful to distinguish the change of stacking sequence between the partial dislocations. Two types of stacking faults with Cpx and protopyroxene (Ppx) structures were identified between three partial dislocations. Furthermore, Ca accumulation in M2 (Fe) site around the stacking faults was detected by STEM-EDS. Interestingly, Ca is distributed not only in these stacking faults but also Opx matrix around the faults. jmicro;63/suppl_1/i17/DFU063F1F1DFU063F1Fig. 1. (a) HAADF and (b) ABF of Opx view of [010] direction with inset simulation images and models of its unit cell (a = 0.52, c = 1.83 nm). © The Author 2014. Published by Oxford University Press on behalf of The Japanese Society of Microscopy. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

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

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

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

1996-06-01

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

Structural Investigation of the (010) Surface of the Al13Fe4 Catalyst

NASA Astrophysics Data System (ADS)

Ledieu, J.; Gaudry, É.; Loli, L. N. Serkovic; Villaseca, S. Alarcón; de Weerd, M.-C.; Hahne, M.; Gille, P.; Grin, Y.; Dubois, J.-M.; Fournée, V.

2013-02-01

We have investigated the structure of the Al13Fe4(010) surface using both experimental and ab initio computational methods. The results indicate that the topmost surface layers correspond to incomplete puckered (P) planes present in the bulk crystal structure. The main building block of the corrugated termination consists of two adjacent pentagons of Al atoms, each centered by a protruding Fe atom. These motifs are interconnected via additional Al atoms referred to as “glue” atoms which partially desorb above 873 K. The surface structure of lower atomic density compared to the bulk P plane is explained by a strong Fe-Al-Fe covalent polar interaction that preserves intact clusters at the surface. The proposed surface model with identified Fe-containing atomic ensembles could explain the Al13Fe4 catalytic properties recently reported in line with the site-isolation concept [M. Armbrüster , Nat. Mater. 11, 690 (2012)NMAACR1476-1122].

Changing optical band structure with single photons

NASA Astrophysics Data System (ADS)

Albrecht, Andreas; Caneva, Tommaso; Chang, Darrick E.

2017-11-01

Achieving strong interactions between individual photons enables a wide variety of exciting possibilities in quantum information science and many-body physics. Cold atoms interfaced with nanophotonic structures have emerged as a platform to realize novel forms of nonlinear interactions. In particular, when atoms are coupled to a photonic crystal waveguide, long-range atomic interactions can arise that are mediated by localized atom-photon bound states. We theoretically show that in such a system, the absorption of a single photon can change the band structure for a subsequent photon. This occurs because the first photon affects the atoms in the chain in an alternating fashion, thus leading to an effective period doubling of the system and a new optical band structure for the composite atom-nanophotonic system. We demonstrate how this mechanism can be engineered to realize a single-photon switch, where the first incoming photon switches the system from being highly transmissive to highly reflective, and analyze how signatures can be observed via non-classical correlations of the outgoing photon field.

A microscopic study investigating the structure of SnSe surfaces

NASA Astrophysics Data System (ADS)

Kim, Sang-ui; Duong, Anh-Tuan; Cho, Sunglae; Rhim, S. H.; Kim, Jungdae

2016-09-01

SnSe has been widely studied due to its many potential applications that take advantage of its excellent thermoelectric, photovoltaic, and optoelectronic properties. However, experimental investigations into the microscopic structure of SnSe remain largely unexplored. Herein, for the first time, the atomic and electronic structures of SnSe surfaces are studied by a home-built low temperature scanning tunneling microscope (STM) and density functional theory (DFT) calculations. The cleaved surface of SnSe is comprised of covalently bonded Se and Sn atoms in zigzag patterns. However, rectangular periodicity was observed in the atomic images of SnSe surfaces for filled and empty state probing. Detailed atomic structures are analyzed by DFT calculations, indicating that the bright extrusions of both filled and empty state images are mostly located at the positions of Sn atoms.

MolProbity: More and better reference data for improved all-atom structure validation.

PubMed

Williams, Christopher J; Headd, Jeffrey J; Moriarty, Nigel W; Prisant, Michael G; Videau, Lizbeth L; Deis, Lindsay N; Verma, Vishal; Keedy, Daniel A; Hintze, Bradley J; Chen, Vincent B; Jain, Swati; Lewis, Steven M; Arendall, W Bryan; Snoeyink, Jack; Adams, Paul D; Lovell, Simon C; Richardson, Jane S; Richardson, David C

2018-01-01

This paper describes the current update on macromolecular model validation services that are provided at the MolProbity website, emphasizing changes and additions since the previous review in 2010. There have been many infrastructure improvements, including rewrite of previous Java utilities to now use existing or newly written Python utilities in the open-source CCTBX portion of the Phenix software system. This improves long-term maintainability and enhances the thorough integration of MolProbity-style validation within Phenix. There is now a complete MolProbity mirror site at http://molprobity.manchester.ac.uk. GitHub serves our open-source code, reference datasets, and the resulting multi-dimensional distributions that define most validation criteria. Coordinate output after Asn/Gln/His "flip" correction is now more idealized, since the post-refinement step has apparently often been skipped in the past. Two distinct sets of heavy-atom-to-hydrogen distances and accompanying van der Waals radii have been researched and improved in accuracy, one for the electron-cloud-center positions suitable for X-ray crystallography and one for nuclear positions. New validations include messages at input about problem-causing format irregularities, updates of Ramachandran and rotamer criteria from the million quality-filtered residues in a new reference dataset, the CaBLAM Cα-CO virtual-angle analysis of backbone and secondary structure for cryoEM or low-resolution X-ray, and flagging of the very rare cis-nonProline and twisted peptides which have recently been greatly overused. Due to wide application of MolProbity validation and corrections by the research community, in Phenix, and at the worldwide Protein Data Bank, newly deposited structures have continued to improve greatly as measured by MolProbity's unique all-atom clashscore. © 2017 The Protein Society.

Novel highly ordered core–shell nanoparticles

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

Dey, Sonal; Hossain, Mohammad D.; Mayanovic, Robert A.

2016-10-26

Core–shell nanoparticles have potential for a wide range of applications due to the tunability of their magnetic, catalytic, electronic, optical, and other physicochemical properties. A frequent drawback in the design of core–shell nanoparticles and nanocrystals is the lack of control over an extensive, disordered, and compositionally distinct interface that occurs due to the dissimilarity of structural and compositional phases of the core and shell. In this work, we demonstrate a new hydrothermal nanophase epitaxy (HNE) technique to synthesize highly structurally ordered α-Cr 2O 3@α-Co 0.38Cr 1.62O 2.92 inverted core–shell nanoparticles (CSNs) with evidence for the nanoscale growth of corundum structuremore » beginning from the core and extending completely into the shell of the CSNs with minimal defects at the interface. The high-resolution TEM results show a sharp interface exhibiting epitaxial atomic registry of shell atoms over highly ordered core atoms. The XPS and Co K-edge XANES analyses indicate the +2 oxidation state of cobalt is incorporated in the shell of the CSNs. Our XPS and EXAFS results are consistent with oxygen vacancy formation in order to maintain charge neutrality upon substitution of the Co 2+ ion for the Cr 3+ ion in the α-Co 0.38Cr 1.62O 2.92 shell. Furthermore, the CSNs exhibit the magnetic exchange bias effect, which is attributed to the exchange anisotropy at the interface made possible by the nanophase epitaxial growth of the α-Co 0.38Cr 1.62O 2.92 shell on the α-Cr 2O 3 core of the nanoparticles. The combination of a well-structured, sharp interface and novel nanophase characteristics is highly desirable for nanostructures having enhanced magnetic properties.« less

Index to the Understanding the Atom Series.

ERIC Educational Resources Information Center

Atomic Energy Commission, Oak Ridge, TN. Div. of Technical Information.

This index was prepared for the set of 51 booklets in the "Understanding the Atom Series" published by the U. S. Atomic Energy Commission for high school students and their teachers. In addition to the index, a complete list of the series is provided in which the booklets are grouped into the categories of physics, chemistry, biology, nuclear…

Atomic and electronic structure of the silicon and silicon-metal Si{sub 20}, Si{sub 20}{sup -}, NaSi{sub 20}, KSi{sub 20} nanoparticles

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

Borshch, N. A., E-mail: ssd18@phys.vsu.ru; Pereslavtseva, N. S.; Kurganskii, S. I.

The results of atomic-structure optimization and calculation of the electronic structure of the Si{sub 20}, Si{sub 20}{sup -}, NaSi{sub 20}, and KSi{sub 20} clusters are reported. The PM3 and AM1 semiempirical methods were used in the calculations. It is shown that the Na and K atoms stabilize the fullerene-like silicon structure. The effect of configuration of the clusters on their electronic structure is analyzed.

All-Atom Four-Body Knowledge-Based Statistical Potentials to Distinguish Native Protein Structures from Nonnative Folds

PubMed Central

2017-01-01

Recent advances in understanding protein folding have benefitted from coarse-grained representations of protein structures. Empirical energy functions derived from these techniques occasionally succeed in distinguishing native structures from their corresponding ensembles of nonnative folds or decoys which display varying degrees of structural dissimilarity to the native proteins. Here we utilized atomic coordinates of single protein chains, comprising a large diverse training set, to develop and evaluate twelve all-atom four-body statistical potentials obtained by exploring alternative values for a pair of inherent parameters. Delaunay tessellation was performed on the atomic coordinates of each protein to objectively identify all quadruplets of interacting atoms, and atomic potentials were generated via statistical analysis of the data and implementation of the inverted Boltzmann principle. Our potentials were evaluated using benchmarking datasets from Decoys-‘R'-Us, and comparisons were made with twelve other physics- and knowledge-based potentials. Ranking 3rd, our best potential tied CHARMM19 and surpassed AMBER force field potentials. We illustrate how a generalized version of our potential can be used to empirically calculate binding energies for target-ligand complexes, using HIV-1 protease-inhibitor complexes for a practical application. The combined results suggest an accurate and efficient atomic four-body statistical potential for protein structure prediction and assessment. PMID:29119109

Crystal structure of the ternary silicide Gd2Re3Si5.

PubMed

Fedyna, Vitaliia; Kozak, Roksolana; Gladyshevskii, Roman

2014-12-01

A single crystal of the title compound, the ternary silicide digadolinium trirhenium penta-silicide, Gd2Re3Si5, was isolated from an alloy of nominal composition Gd20Re30Si50 synthesized by arc melting and investigated by X-ray single-crystal diffraction. Its crystal structure belongs to the U2Mn3Si5 structure type. All atoms in the asymmetric lie on special positions. The Gd site has site symmetry m..; the two Mn atoms have site symmetries m.. and 2.22; the three Si atoms have site symmetries m.., ..2 and 4.. . The coordination polyhedra of the Gd atoms have 21 vertices, while those of the Re atoms are cubo-octa-hedra and 13-vertex polyhedra. The Si atoms are arranged as tricapped trigonal prisms, bicapped square anti-prisms, or 11-vertex polyhedra. The crystal structure of the title compound is also related to the structure types CaBe2Ge2 and W5Si3. It can be represented as a stacking of Gd-centred polyhedra of composition [GdSi9]. The Re atoms form infinite chains with an Re-Re distance of 2.78163 (5) Å and isolated squares with an Re-Re distance of 2.9683 (6) Å.

Crystal structure of the ternary silicide Gd2Re3Si5

PubMed Central

Fedyna, Vitaliia; Kozak, Roksolana; Gladyshevskii, Roman

2014-01-01

A single crystal of the title compound, the ternary silicide digadolinium trirhenium penta­silicide, Gd2Re3Si5, was isolated from an alloy of nominal composition Gd20Re30Si50 synthesized by arc melting and investigated by X-ray single-crystal diffraction. Its crystal structure belongs to the U2Mn3Si5 structure type. All atoms in the asymmetric lie on special positions. The Gd site has site symmetry m..; the two Mn atoms have site symmetries m.. and 2.22; the three Si atoms have site symmetries m.., ..2 and 4.. . The coordination polyhedra of the Gd atoms have 21 vertices, while those of the Re atoms are cubo­octa­hedra and 13-vertex polyhedra. The Si atoms are arranged as tricapped trigonal prisms, bicapped square anti­prisms, or 11-vertex polyhedra. The crystal structure of the title compound is also related to the structure types CaBe2Ge2 and W5Si3. It can be represented as a stacking of Gd-centred polyhedra of composition [GdSi9]. The Re atoms form infinite chains with an Re—Re distance of 2.78163 (5) Å and isolated squares with an Re—Re distance of 2.9683 (6) Å. PMID:25552967

Chemical Trends in Solid Alkali Pertechnetates.

PubMed

Weaver, Jamie; Soderquist, Chuck Z; Washton, Nancy M; Lipton, Andrew S; Gassman, Paul L; Lukens, Wayne W; Kruger, Albert A; Wall, Nathalie A; McCloy, John S

2017-03-06

Insight into the solid-state chemistry of pure technetium-99 ( 99 Tc) oxides is required in the development of a robust immobilization and disposal system for nuclear waste stemming from the radiopharmaceutical industry, from the production of nuclear weapons, and from spent nuclear fuel. However, because of its radiotoxicity and the subsequent requirement of special facilities and handling procedures for research, only a few studies have been completed, many of which are over 20 years old. In this study, we report the synthesis of pure alkali pertechnetates (sodium, potassium, rubidium, and cesium) and analysis of these compounds by Raman spectroscopy, X-ray absorption spectroscopy (XANES and EXAFS), solid-state nuclear magnetic resonance (static and magic angle spinning), and neutron diffraction. The structures and spectral signatures of these compounds will aid in refining the understanding of 99 Tc incorporation into and release from nuclear waste glasses. NaTcO 4 shows aspects of the relatively higher electronegativity of the Na atom, resulting in large distortions of the pertechnetate tetrahedron and deshielding of the 99 Tc nucleus relative to the aqueous TcO 4 - . At the other extreme, the large Cs and Rb atoms interact only weakly with the pertechnetate, have closer to perfect tetrahedral symmetry at the Tc atom, and have very similar vibrational spectra, even though the crystal structure of CsTcO 4 is orthorhombic while that of RbTcO 4 is tetragonal. Further trends are observed in the cell volume and quadrupolar coupling constant.

Chemical Trends in Solid Alkali Pertechnetates

DOE PAGES

Weaver, Jamie; Soderquist, Chuck Z.; Washton, Nancy M.; ...

2017-02-21

Insight into the solid-state chemistry of pure technetium-99 ( 99Tc) oxides is required in the development of a robust immobilization and disposal system for nuclear waste stemming from the radiopharmaceutical industry, from the production of nuclear weapons, and from spent nuclear fuel. However, because of its radiotoxicity and the subsequent requirement of special facilities and handling procedures for research, only a few studies have been completed, many of which are over 20 years old. In this study, we report the synthesis of pure alkali pertechnetates (sodium, potassium, rubidium, and cesium) and analysis of these compounds by Raman spectroscopy, X-ray absorptionmore » spectroscopy (XANES and EXAFS), solid-state nuclear magnetic resonance (static and magic angle spinning), and neutron diffraction. The structures and spectral signatures of these compounds will aid in refining the understanding of 99Tc incorporation into and release from nuclear waste glasses. NaTcO 4 shows aspects of the relatively higher electronegativity of the Na atom, resulting in large distortions of the pertechnetate tetrahedron and deshielding of the 99Tc nucleus relative to the aqueous TcO 4 –. At the other extreme, the large Cs and Rb atoms interact only weakly with the pertechnetate, have closer to perfect tetrahedral symmetry at the Tc atom, and have very similar vibrational spectra, even though the crystal structure of CsTcO 4 is orthorhombic while that of RbTcO 4 is tetragonal. Further trends are observed in the cell volume and quadrupolar coupling constant.« less

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

Weaver, Jamie; Soderquist, Chuck Z.; Washton, Nancy M.

Insight into the solid-state chemistry of pure technetium-99 ( 99Tc) oxides is required in the development of a robust immobilization and disposal system for nuclear waste stemming from the radiopharmaceutical industry, from the production of nuclear weapons, and from spent nuclear fuel. However, because of its radiotoxicity and the subsequent requirement of special facilities and handling procedures for research, only a few studies have been completed, many of which are over 20 years old. In this study, we report the synthesis of pure alkali pertechnetates (sodium, potassium, rubidium, and cesium) and analysis of these compounds by Raman spectroscopy, X-ray absorptionmore » spectroscopy (XANES and EXAFS), solid-state nuclear magnetic resonance (static and magic angle spinning), and neutron diffraction. The structures and spectral signatures of these compounds will aid in refining the understanding of 99Tc incorporation into and release from nuclear waste glasses. NaTcO 4 shows aspects of the relatively higher electronegativity of the Na atom, resulting in large distortions of the pertechnetate tetrahedron and deshielding of the 99Tc nucleus relative to the aqueous TcO 4 –. At the other extreme, the large Cs and Rb atoms interact only weakly with the pertechnetate, have closer to perfect tetrahedral symmetry at the Tc atom, and have very similar vibrational spectra, even though the crystal structure of CsTcO 4 is orthorhombic while that of RbTcO 4 is tetragonal. Further trends are observed in the cell volume and quadrupolar coupling constant.« less

Endohedral beryllium atoms in germanium clusters with eight and fewer vertices: how small can a cluster be and still encapsulate a central atom?

PubMed

Uţă, M M; King, R B

2012-05-31

Structures of the beryllium-centered germanium clusters Be@Ge(n)(z) (n = 8, 7, 6; z = -4, -2, 0, +2) have been investigated by density functional theory to provide some insight regarding the smallest metal cluster that can encapsulate an interstitial atom. The lowest energy structures of the eight-vertex Be@Ge(8)(z) clusters (z = -4, -2, 0, +2) all have the Be atom at the center of a closed polyhedron, namely, a D(4d) square antiprism for Be@Ge(8)(4-), a D(2d) bisdisphenoid for Be@Ge(8)(2-), an ideal O(h) cube for Be@Ge(8), and a C(2v) distorted cube for Be@Ge(8)(2+). The Be-centered cubic structures predicted for Be@Ge(8) and Be@Ge(8)(2+) differ from the previously predicted lowest energy structures for the isoelectronic Ge(8)(2-) and Ge(8). This appears to be related to the larger internal volume of the cube relative to other closed eight-vertex polyhedra. The lowest energy structures for the smaller seven- and six-vertex clusters Be@Ge(n)(z) (n = 7, 6; z = -4, -2, 0, +2) no longer have the Be atom at the center of a closed Ge(n) polyhedron. Instead, either the Ge(n) polyhedron has opened up to provide a larger volume for the Be atom or the Be atom has migrated to the surface of the polyhedron. However, higher energy structures are found in which the Be atom is located at the center of a Ge(n) (n = 7, 6) polyhedron. Examples of such structures are a centered C(2v) capped trigonal prismatic structure for Be@Ge(7)(2-), a centered D(5h) pentagonal bipyramidal structure for Be@Ge(7), a centered D(3h) trigonal prismatic structure for Be@Ge(6)(4-), and a centered octahedral structure for Be@Ge(6). Cluster buildup reactions of the type Be@Ge(n)(z) + Ge(2) → Be@Ge(n+2)(z) (n = 6, 8; z = -4, -2, 0, +2) are all predicted to be highly exothermic. This suggests that interstitial clusters having an endohedral atom inside a bare post transition element polyhedron with eight or fewer vertices are less than the optimum size. This is consistent with the experimental observation of several types of 10-vertex polyhedral bare post transition element clusters with interstitial atoms but the failure to observe such clusters with external polyhedra having eight or fewer vertices.

Nanoparticle layer deposition for highly controlled multilayer formation based on high- coverage monolayers of nanoparticles

PubMed Central

Liu, Yue; Williams, Mackenzie G.; Miller, Timothy J.; Teplyakov, Andrew V.

2015-01-01

This paper establishes a strategy for chemical deposition of functionalized nanoparticles onto solid substrates in a layer-by-layer process based on self-limiting surface chemical reactions leading to complete monolayer formation within the multilayer system without any additional intermediate layers – nanoparticle layer deposition (NPLD). This approach is fundamentally different from previously established traditional layer-by-layer deposition techniques and is conceptually more similar to well-known atomic and molecular – layer deposition processes. The NPLD approach uses efficient chemical functionalization of the solid substrate material and complementary functionalization of nanoparticles to produce a nearly 100% coverage of these nanoparticles with the use of “click chemistry”. Following this initial deposition, a second complete monolayer of nanoparticles is deposited using a copper-catalyzed “click reaction” with the azide-terminated silica nanoparticles of a different size. This layer-by-layer growth is demonstrated to produce stable covalently-bound multilayers of nearly perfect structure over macroscopic solid substrates. The formation of stable covalent bonds is confirmed spectroscopically and the stability of the multilayers produced is tested by sonication in a variety of common solvents. The 1-, 2- and 3-layer structures are interrogated by electron microscopy and atomic force microscopy and the thickness of the multilayers formed is fully consistent with that expected for highly efficient monolayer formation with each cycle of growth. This approach can be extended to include a variety of materials deposited in a predesigned sequence on different substrates with a highly conformal filling. PMID:26726273

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

Nahar, Sultana N., E-mail: nahar@astronomy.ohio-state.edu

The atomic parameters–oscillator strengths, line strengths, radiative decay rates (A), and lifetimes–for fine structure transitions of electric dipole (E1) type for the astrophysically abundant ion Ne IV are presented. The results include 868 fine structure levels with n≤ 10, l≤ 9, and 1/2≤J≤ 19/2 of even and odd parities, and the corresponding 83,767 E1 transitions. The calculations were carried out using the relativistic Breit–Pauli R-matrix method in the close coupling approximation. The transitions have been identified spectroscopically using an algorithm based on quantum defect analysis and other criteria. The calculated energies agree with the 103 observed and identified energies to withinmore » 3% or better for most of the levels. Some larger differences are also noted. The A-values show good to fair agreement with the very limited number of available transitions in the table compiled by NIST, but show very good agreement with the latest published multi-configuration Hartree–Fock calculations. The present transitions should be useful for diagnostics as well as for precise and complete spectral modeling in the soft X-ray to infra-red regions of astrophysical and laboratory plasmas. -- Highlights: •The first application of BPRM method for accurate E1 transitions in Ne IV is reported. •Amount of atomic data (n going up to 10) is complete for most practical applications. •The calculated energies are in very good agreement with most observed levels. •Very good agreement of A-values and lifetimes with other relativistic calculations. •The results should provide precise nebular abundances, chemical evolution etc.« less

Thorium Copper Phosphides: More Diverse Metal-Phosphorus and Phosphorus-Phosphorus Interactions than U analogues

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

Jin, Geng Bang; Malliakas, Christos D.; Lin, Jian

To explore the chemical analogy between thorium and heavier actinides in soft anionic environments, three new thorium phosphides (ThCuP 2, beta-ThCu 2P 2, and ThCu 5P 3) have been prepared through solid-state reactions using CuI as a reaction promoter. The structure of ThCuP 2 can be described as a filled UTe 2-type with both dimeric P 2 4- and monomeric P 3- anions, in which Th is coordinated by eight P atoms in a bicapped trigonal prismatic arrangement and Cu is tetrahedrally coordinated by four P atoms. β-ThCu 2P 2 contains only P 3- anions and is isostructural with BaCumore » 2S 2. In this structure, Th is coordinated by seven P atoms in monocapped trigonal prismatic geometry and Cu is tetrahedrally coordinated by four P atoms. ThCu 5P 3 adopts the YCo 5P 3-type structure consisting of P 3- anions. This structure contains Th atoms coordinated by six P atoms in a trigonal prismatic arrangement and Cu atoms that are either tetrahedrally coordinated by four P atoms or square pyramidally coordinated by five P atoms. Electric resistivity measurements and electronic structure calculations on β-ThCu 2P 2 indicate a metal. These new compounds may be charge-balanced and formulated as Th 4+Cu +(P 2 4-) 1/2P 3-, Th 4+(Cu +) 2(P 3-) 2, and Th 4+(Cu +) 5(P 3-) 3, respectively. The structural, bonding, and property relationships between these Th compounds and related actinide and rare-earth phases are discussed. In conclusion, titled compounds display more diverse ion-ion interactions and different electronic structures from those in UCuP 2 and UCu 2P 2 that were synthesized under similar experimental conditions, suggesting divergence of thorium-phosphide chemistry from uranium-phosphide chemistry.« less

Thorium Copper Phosphides: More Diverse Metal-Phosphorus and Phosphorus-Phosphorus Interactions than U analogues

DOE PAGES

Jin, Geng Bang; Malliakas, Christos D.; Lin, Jian

2017-09-28

To explore the chemical analogy between thorium and heavier actinides in soft anionic environments, three new thorium phosphides (ThCuP 2, beta-ThCu 2P 2, and ThCu 5P 3) have been prepared through solid-state reactions using CuI as a reaction promoter. The structure of ThCuP 2 can be described as a filled UTe 2-type with both dimeric P 2 4- and monomeric P 3- anions, in which Th is coordinated by eight P atoms in a bicapped trigonal prismatic arrangement and Cu is tetrahedrally coordinated by four P atoms. β-ThCu 2P 2 contains only P 3- anions and is isostructural with BaCumore » 2S 2. In this structure, Th is coordinated by seven P atoms in monocapped trigonal prismatic geometry and Cu is tetrahedrally coordinated by four P atoms. ThCu 5P 3 adopts the YCo 5P 3-type structure consisting of P 3- anions. This structure contains Th atoms coordinated by six P atoms in a trigonal prismatic arrangement and Cu atoms that are either tetrahedrally coordinated by four P atoms or square pyramidally coordinated by five P atoms. Electric resistivity measurements and electronic structure calculations on β-ThCu 2P 2 indicate a metal. These new compounds may be charge-balanced and formulated as Th 4+Cu +(P 2 4-) 1/2P 3-, Th 4+(Cu +) 2(P 3-) 2, and Th 4+(Cu +) 5(P 3-) 3, respectively. The structural, bonding, and property relationships between these Th compounds and related actinide and rare-earth phases are discussed. In conclusion, titled compounds display more diverse ion-ion interactions and different electronic structures from those in UCuP 2 and UCu 2P 2 that were synthesized under similar experimental conditions, suggesting divergence of thorium-phosphide chemistry from uranium-phosphide chemistry.« less

Structural stability and electronic properties of β-tetragonal boron: A first-principles study

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

Hayami, Wataru, E-mail: hayami.wataru@nims.go.jp

2015-01-15

It is known that elemental boron has five polymorphs: α- and β-rhombohedral, α- and β-tetragonal, and the high-pressure γ phase. β-tetragonal (β-t) boron was first discovered in 1960, but there have been only a few studies since then. We have thoroughly investigated, using first-principles calculations, the atomic and electronic structures of β-t boron, the details of which were not known previously. The difficulty of calculation arises from the fact that β-t boron has a large unit cell that contains between 184 and 196 atoms, with 12 partially-occupied interstitial sites. This makes the number of configurations of interstitial atoms too greatmore » to calculate them all. By introducing assumptions based on symmetry and preliminary calculations, the number of configurations to calculate can be greatly reduced. It was eventually found that β-t boron has the lowest total energy, with 192 atoms (8 interstitial atoms) in an orthorhombic lattice. The total energy per atom was between those of α- and β-rhombohedral boron. Another tetragonal structure with 192 atoms was found to have a very close energy. The valence bands were fully filled and the gaps were about 1.16 to 1.54 eV, making it comparable to that of β-rhombohedral boron. - Graphical abstract: Electronic density distribution for the lowest-energy configuration (N=192) viewed from the 〈1 0 0〉 direction. Left: isosurface (yellow) at d=0.09 electrons/a.u.{sup 3} Right: isosurface (orange) at d=0.12 electrons/a.u.{sup 3}. - Highlights: • β-tetragonal boron was thoroughly investigated using first-principles calculations. • The lowest energy structure contains 192 atoms in an orthorhombic lattice. • Another tetragonal structure with 192 atoms has a very close energy. • The total energy per atom is between those of α- and β-rhombohedral boron. • The band gap of the lowest energy structure is about 1.16 to 1.54 eV.« less

Correlation between morphology, electron band structure, and resistivity of Pb atomic chains on the Si(5 5 3)-Au surface

NASA Astrophysics Data System (ADS)

Jałochowski, M.; Kwapiński, T.; Łukasik, P.; Nita, P.; Kopciuszyński, M.

2016-07-01

Structural and electron transport properties of multiple Pb atomic chains fabricated on the Si(5 5 3)-Au surface are investigated using scanning tunneling spectroscopy, reflection high electron energy diffraction, angular resolved photoemission electron spectroscopy and in situ electrical resistance. The study shows that Pb atomic chains growth modulates the electron band structure of pristine Si(5 5 3)-Au surface and hence changes its sheet resistivity. Strong correlation between chains morphology, electron band structure and electron transport properties is found. To explain experimental findings a theoretical tight-binding model of multiple atomic chains interacting on effective substrate is proposed.

About the atomic structures of icosahedral quasicrystals

NASA Astrophysics Data System (ADS)

Quiquandon, Marianne; Gratias, Denis

2014-01-01

This paper is a survey of the crystallographic methods that have been developed these last twenty five years to decipher the atomic structures of the icosahedral stable quasicrystals since their discovery in 1982 by D. Shechtman. After a brief recall of the notion of quasiperiodicity and the natural description of Z-modules in 3-dim as projection of regular lattices in N>3-dim spaces, we give the basic geometrical ingredients useful to describe icosahedral quasicrystals as irrational 3-dim cuts of ordinary crystals in 6-dim space. Atoms are described by atomic surfaces (ASs) that are bounded volumes in the internal (or perpendicular) 3-dim space and the intersections of which with the physical space are the actual atomic positions. The main part of the paper is devoted to finding the major properties of quasicrystalline icosahedral structures. As experimentally demonstrated, they can be described with a surprisingly few high symmetry ASs located at high symmetry special points in 6-dim space. The atomic structures are best described by aggregations and intersections of high symmetry compact interpenetrating atomic clusters. We show here that the experimentally relevant clusters are derived from one generic cluster made of two concentric triacontahedra scaled by τ and an external icosidodecahedron. Depending on which ones of the orbits of this cluster are eventually occupied by atoms, the actual atomic clusters are of type Bergman, Mackay, Tsai and others….

Ion beam processing and characterization of advanced optical materials

NASA Astrophysics Data System (ADS)

Zhu, Jie

Ion beams have been extensively applied for materials modification and characterization. In this dissertation, I will focus on the applications of ion beams for advanced optical materials. The first part of my work addresses the effects of 1.0 MeV proton irradiation on photoluminescence (PL) properties of self-assembled InAs QDs. Compared to the QDs grown in a GaAs thin film, the QDs embedded in an AlAs/GaAs superlattice structure exhibits much higher photoluminescence degradation resistance to proton irradiation. Proton irradiation combined with thermal annealing results in significant blueshifts in PL spectra of QDs embedded in GaAs, suggesting enhanced atomic intermixing in the QD systems due to point defects introduced by ion irradiation. In the second part of my work, ion channeling combined with Rutherford backscattering is applied to investigate In-Ga atomic intermixing processes in the proton irradiated InAs QD system. Ion channeling along the growth (<100>) direction shows evidence of In atoms with small displacement from the atomic row, which gives direct signature of QD lattice structures, allowing us to monitor atomic intermixing between In and Ga. Based on the channeling data, a model for In-Ga atomic intermixing in InAs/GaAs QD system is proposed, in which In-Ga atomic intermixing can take place along both the growth direction and the lateral direction in the QD layer. The third part of my dissertation is the elemental mapping of silica-based optical cross section using micron-ion-beam imaging techniques. This work is intended to examine the thermal stability of Ge-doped fiber cores in high-temperature environments. Our measurements show that Ge completely diffuses out of the core region following thermal annealing at 1000°C. This indicates that silica-based optical fibers cannot be used for applications at extreme high temperatures. The final part is the study of the effects of various wet treatment on GaN surface, which is a necessary step during the GaN device fabrication. In our work, the HCL treatment has reduced the Ga concentration on the surface for N type GaN. However, for samples with lower concentration of Si doping or P type GaN samples, this effect does not occur.

Direct Visualization of Local Electromagnetic Field Structures by Scanning Transmission Electron Microscopy.

PubMed

Shibata, Naoya; Findlay, Scott D; Matsumoto, Takao; Kohno, Yuji; Seki, Takehito; Sánchez-Santolino, Gabriel; Ikuhara, Yuichi

2017-07-18

The functional properties of materials and devices are critically determined by the electromagnetic field structures formed inside them, especially at nanointerface and surface regions, because such structures are strongly associated with the dynamics of electrons, holes and ions. To understand the fundamental origin of many exotic properties in modern materials and devices, it is essential to directly characterize local electromagnetic field structures at such defect regions, even down to atomic dimensions. In recent years, rapid progress in the development of high-speed area detectors for aberration-corrected scanning transmission electron microscopy (STEM) with sub-angstrom spatial resolution has opened new possibilities to directly image such electromagnetic field structures at very high-resolution. In this Account, we give an overview of our recent development of differential phase contrast (DPC) microscopy for aberration-corrected STEM and its application to many materials problems. In recent years, we have developed segmented-type STEM detectors which divide the detector plane into 16 segments and enable simultaneous imaging of 16 STEM images which are sensitive to the positions and angles of transmitted/scattered electrons on the detector plane. These detectors also have atomic-resolution imaging capability. Using these segmented-type STEM detectors, we show DPC STEM imaging to be a very powerful tool for directly imaging local electromagnetic field structures in materials and devices in real space. For example, DPC STEM can clearly visualize the local electric field variation due to the abrupt potential change across a p-n junction in a GaAs semiconductor, which cannot be observed by normal in-focus bright-field or annular type dark-field STEM imaging modes. DPC STEM is also very effective for imaging magnetic field structures in magnetic materials, such as magnetic domains and skyrmions. Moreover, real-time imaging of electromagnetic field structures can now be realized through very fast data acquisition, processing, and reconstruction algorithms. If we use DPC STEM for atomic-resolution imaging using a sub-angstrom size electron probe, it has been shown that we can directly observe the atomic electric field inside atoms within crystals and even inside single atoms, the field between the atomic nucleus and the surrounding electron cloud, which possesses information about the atomic species, local chemical bonding and charge redistribution between bonded atoms. This possibility may open an alternative way for directly visualizing atoms and nanostructures, that is, seeing atoms as an entity of electromagnetic fields that reflect the intra- and interatomic electronic structures. In this Account, the current status of aberration-corrected DPC STEM is highlighted, along with some applications in real material and device studies.

Trapped atoms along nanophotonic resonators

NASA Astrophysics Data System (ADS)

Fields, Brian; Kim, May; Chang, Tzu-Han; Hung, Chen-Lung

2017-04-01

Many-body systems subject to long-range interactions have remained a very challenging topic experimentally. Ultracold atoms trapped in extreme proximity to the surface of nanophotonic structures provides a dynamic system combining the strong atom-atom interactions mediated by guided mode photons with the exquisite control implemented with trapped atom systems. The hybrid system promises pair-wise tunability of long-range interactions between atomic pseudo spins, allowing studies of quantum magnetism extending far beyond nearest neighbor interactions. In this talk, we will discuss our current status developing high quality nanophotonic ring resonators, engineered on CMOS compatible optical chips with integrated nanostructures that, in combination with a side illuminating beam, can realize stable atom traps approximately 100nm above the surface. We will report on our progress towards loading arrays of cold atoms near the surface of these structures and studying atom-atom interaction mediated by photons with high cooperativity.

Microfabricated Waveguide Atom Traps.

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

Jau, Yuan-Yu

A nanoscale , microfabricated waveguide structure can in - principle be used to trap atoms in well - defined locations and enable strong photon-atom interactions . A neutral - atom platform based on this microfabrication technology will be prealigned , which is especially important for quantum - control applications. At present, there is still no reported demonstration of evanescent - field atom trapping using a microfabricated waveguide structure. We described the capabilities established by our team for future development of the waveguide atom - trapping technology at SNL and report our studies to overcome the technical challenges of loading coldmore » atoms into the waveguide atom traps, efficient and broadband optical coupling to a waveguide, and the waveguide material for high - power optical transmission. From the atomic - physics and the waveguide modeling, w e have shown that a square nano-waveguide can be utilized t o achieve better atomic spin squeezing than using a nanofiber for first time.« less

Uncovering the Connection Between Low-Frequency Dynamics and Phase Transformation Phenomena in Molecular Solids

NASA Astrophysics Data System (ADS)

Ruggiero, Michael T.; Zhang, Wei; Bond, Andrew D.; Mittleman, Daniel M.; Zeitler, J. Axel

2018-05-01

The low-frequency motions of molecules in the condensed phase have been shown to be vital to a large number of physical properties and processes. However, in the case of disordered systems, it is often difficult to elucidate the atomic-level details surrounding these phenomena. In this work, we have performed an extensive experimental and computational study on the molecular solid camphor, which exhibits a rich and complex structure-dynamics relationship, and undergoes an order-disorder transition near ambient conditions. The combination of x-ray diffraction, variable temperature and pressure terahertz time-domain spectroscopy, ab initio molecular dynamics, and periodic density functional theory calculations enables a complete picture of the phase transition to be obtained, inclusive of mechanistic, structural, and thermodynamic phenomena. Additionally, the low-frequency vibrations of a disordered solid are characterized for the first time with atomic-level precision, uncovering a clear link between such motions and the phase transformation. Overall, this combination of methods allows for significant details to be obtained for disordered solids and the associated transformations, providing a framework that can be directly applied for a wide range of similar systems.

Spectroscopic (FT-IR and FT-Raman) investigation, first order hyperpolarizability, NBO, HOMO-LUMO and MEP analysis of 6-nitrochromone by ab initio and density functional theory calculations

NASA Astrophysics Data System (ADS)

Senthil kumar, J.; Jeyavijayan, S.; Arivazhagan, M.

2015-02-01

The vibrational spectral analysis is carried out using FT-Raman and FT-IR spectroscopy in the range 3500-50 cm-1 and 4000-400 cm-1, respectively, for 6-nitrochromone (6NC). The molecular structure, fundamental vibrational frequencies and intensity of the vibrational bands are interpreted with the aid of structure optimization and normal coordinates force field calculation based on ab initio HF and DFT gradient calculations employing the HF/6-311++G(d,p) and B3LYP/6-311++G(d,p) basis set. Stability of the molecule has been analyzed using NBO analysis. The calculated HOMO and LUMO energies show that charge transfer occurs within the molecule. Thermodynamic properties like entropy, heat capacity, zero-point energy and Mulliken's charge analysis have been calculated for the 6NC. The complete assignments were performed on the basis of total energy distribution (TED) of the vibrational modes with scaled quantum mechanical (SQM) method. The MEP map shows the negative potential sites are on oxygen atoms as well as the positive potential sites are around the hydrogen atoms.

Uncovering the Connection Between Low-Frequency Dynamics and Phase Transformation Phenomena in Molecular Solids.

PubMed

Ruggiero, Michael T; Zhang, Wei; Bond, Andrew D; Mittleman, Daniel M; Zeitler, J Axel

2018-05-11

The low-frequency motions of molecules in the condensed phase have been shown to be vital to a large number of physical properties and processes. However, in the case of disordered systems, it is often difficult to elucidate the atomic-level details surrounding these phenomena. In this work, we have performed an extensive experimental and computational study on the molecular solid camphor, which exhibits a rich and complex structure-dynamics relationship, and undergoes an order-disorder transition near ambient conditions. The combination of x-ray diffraction, variable temperature and pressure terahertz time-domain spectroscopy, ab initio molecular dynamics, and periodic density functional theory calculations enables a complete picture of the phase transition to be obtained, inclusive of mechanistic, structural, and thermodynamic phenomena. Additionally, the low-frequency vibrations of a disordered solid are characterized for the first time with atomic-level precision, uncovering a clear link between such motions and the phase transformation. Overall, this combination of methods allows for significant details to be obtained for disordered solids and the associated transformations, providing a framework that can be directly applied for a wide range of similar systems.

Unreal perpetual motion machine, Rydberg constant and Carnot non-unitary efficiency as a consequence of the atomic irreversibility

NASA Astrophysics Data System (ADS)

Lucia, Umberto

2018-02-01

A perpetual motion machine is a completely ideal engine which cannot be realized. Carnot introduced the concept of the ideal engine which operates on a completely reversible cycle, without any dissipation, but with an upper limit in it. So, even in ideal condition without any dissipation, there is something that prevents the conversion of all the energy absorbed by an ideal reservoir into work. But what is the cause of irreversibility? Here we highlight the atomic nature of this irreversibility, proving that it is no more than the continuous interaction of the atoms with the surrounding field. The macroscopic irreversibility is the consequence of the microscopic irreversibility.

Sc20C60: a volleyballene

NASA Astrophysics Data System (ADS)

Wang, Jing; Ma, Hong-Man; Liu, Ying

2016-06-01

An exceptionally stable hollow cage containing 20 scandium atoms and 60 carbon atoms has been identified. This Sc20C60 molecular cluster has a Th point group symmetry and a volleyball-like shape that we refer to below as ``Volleyballene''. Electronic structure analysis shows that the formation of delocalized π bonds between Sc atoms and the neighboring pentagonal rings made of carbon atoms is crucial for stabilizing the cage structure. A relatively large HOMO-LUMO gap (~1.4 eV) was found. The results of vibrational frequency analysis and molecular dynamics simulations both demonstrate that this Volleyballene molecule is exceptionally stable.An exceptionally stable hollow cage containing 20 scandium atoms and 60 carbon atoms has been identified. This Sc20C60 molecular cluster has a Th point group symmetry and a volleyball-like shape that we refer to below as ``Volleyballene''. Electronic structure analysis shows that the formation of delocalized π bonds between Sc atoms and the neighboring pentagonal rings made of carbon atoms is crucial for stabilizing the cage structure. A relatively large HOMO-LUMO gap (~1.4 eV) was found. The results of vibrational frequency analysis and molecular dynamics simulations both demonstrate that this Volleyballene molecule is exceptionally stable. Electronic supplementary information (ESI) available: Sc20C60: a Volleyballene_SI. See DOI: 10.1039/c5nr07784b

Ab initio calculations of ionic hydrocarbon compounds with heptacoordinate carbon.

PubMed

Wang, George; Rahman, A K Fazlur; Wang, Bin

2018-04-25

Ionic hydrocarbon compounds that contain hypercarbon atoms, which bond to five or more atoms, are important intermediates in chemical synthesis and may also find applications in hydrogen storage. Extensive investigations have identified hydrocarbon compounds that contain a five- or six-coordinated hypercarbon atom, such as the pentagonal-pyramidal hexamethylbenzene, C 6 (CH 3 ) 6 2+ , in which a hexacoordinate carbon atom is involved. It remains challenging to search for further higher-coordinated carbon in ionic hydrocarbon compounds, such as seven- and eight-coordinated carbon. Here, we report ab initio density functional calculations that show a stable 3D hexagonal-pyramidal configuration of tropylium trication, (C 7 H 7 ) 3+ , in which a heptacoordinate carbon atom is involved. We show that this tropylium trication is stable against deprotonation, dissociation, and structural deformation. In contrast, the pyramidal configurations of ionic C 8 H 8 compounds, which would contain an octacoordinate carbon atom, are unstable. These results provide insights for developing new molecular structures containing hypercarbon atoms, which may have potential applications in chemical synthesis and in hydrogen storage. Graphical abstract Possible structural transformations of stable configurations of (C 7 H 7 ) 3+ , which may result in the formation of the pyramidal structure that involves a heptacoordinate hypercarbon atom.

Au102(p-MBA)44 nanocluster, a superatom suitable for bio-applications

NASA Astrophysics Data System (ADS)

Häkkinen, Hannu

2016-12-01

Inorganic nanoparticles, including metals, semiconductors and metal oxides, comprise a common set of structures exhibiting an inorganic core `passivated' by an organic shell. Ligated inorganic nanoparticles currently provoke widespread fundamental interest in their structural, optical and magnetic properties, which differ fundamentally from bulk counterparts. These nanomaterials are already finding applications in biology, medicine, solar energy, and display panels. 1-6 Conjugating inorganic nanoparticles with organic (biological) material for applications in nanobiology and nanomedicine creates significant challenges for controlling the effects on the environment, particularly regarding toxicity. Chemical reactions of almost identical substances can lead to drastically different outcomes in a biological environment. As a simplistic example one can consider the case of ethanol vs. methanol. Ethanol (CH3CH2OH) can be consumed by humans while even a small dose of methanol (CH3OH) can be fatal, yet the difference between the molecular formulas of these substances is just the smallest meaningful hydrocarbon unit CH2. This illuminates the fact that minute differences in the size and structure of molecular compounds can have drastically different end effects in a biological environment due to the way the compounds start to react with the environment. In recent years, gold nanoparticles covered by ligands that make them water-soluble have become a popular target for research in nanobiology and nanomedicine. 1,2 In most cases up to now, colloidal nanoparticles (5 nm and larger) have been used for sensing and photothermal applications. However, this class of gold-based nanomaterials still has large uncertainties regarding the atomic composition of the nanoparticle surface and particularly the metal-ligand interface. A simple example illuminates the facts. The density of atoms in the fcc lattice of macrosocopic gold metal is about 59 atoms/nm3. This means that a spherical colloidal gold nanoparticle with radius of 5 nm has about 3850 atoms. Even in a sample of extremely narrow range of diameters ranging from 5.25 nm to 4.75 nm (+/- 5% of the mean) the particles will have anywhere between 3300 and 4750 atoms, and their surface area can differ up to 20%. It is clear that such particles are not suitable for applications that would need molecularly precise size, structure and shape of the metal nanoparticle and precise knowledge of the composition of its organic surface. In 1994, Brust, Schiffrin and coworkers published a landmark synthesis recipe on how to prepare thiol(ate)-stabilized small gold nanoparticles of about 2 nm in size. 7 This paper started a completely new field which has now matured to studies of several "atom-precise" or "molecularly precise" gold-thiolate compounds for which molecular formulas Aux(SR)y can be written and the substances in most cases have a good ambient stability allowing for storage and later use.8 Atomic structures of the gold core and the thiolate layer have been resolved for many of these compounds, opening doors for detailed density functional theory (DFT) simulations of their properties. This Perspective discusses developments in understanding the structure and properties of one of such compounds, which can be used for site-specific (or "molecularly precise") targeting of capsid proteins on a viral surface.

Defect Induced Electronic Structure of Uranofullerene

PubMed Central

Dai, Xing; Cheng, Cheng; Zhang, Wei; Xin, Minsi; Huai, Ping; Zhang, Ruiqin; Wang, Zhigang

2013-01-01

The interaction between the inner atoms/cluster and the outer fullerene cage is the source of various novel properties of endohedral metallofullerenes. Herein, we introduce an adatom-type spin polarization defect on the surface of a typical endohedral stable U2@C60 to predict the associated structure and electronic properties of U2@C61 based on the density functional theory method. We found that defect induces obvious changes in the electronic structure of this metallofullerene. More interestingly, the ground state of U2@C61 is nonet spin in contrast to the septet of U2@C60. Electronic structure analysis shows that the inner U atoms and the C ad-atom on the surface of the cage contribute together to this spin state, which is brought about by a ferromagnetic coupling between the spin of the unpaired electrons of the U atoms and the C ad-atom. This discovery may provide a possible approach to adapt the electronic structure properties of endohedral metallofullerenes. PMID:23439318

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.

Core–Shell to Doped Quantum Dots: Evolution of the Local Environment Using XAFS

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

Saha, Avijit; Chattopadhyay, Soma; Shibata, Tomohiro

2016-09-30

Internal structure study at an atomic level is a challenging task with far reaching consequences to its material properties, specifically in the field of transition metal doping in quantum dots. Diffusion of transition metal ions in and out of quantum dots forming magnetic clusters has been a major bottleneck in this class of materials. Diffusion of the magnetic ions from the core into the nonmagnetic shell in a core/shell heterostructure architecture to attain uniform doping has been recently introduced and yet to be understood. In this work, we have studied the local structure variation of Fe as a function ofmore » CdS matrix thickness and annealing time during the overcoating of Fe 3O 4 core with CdS using X-ray absorption spectroscopy. The data reveals that Fe 3O 4 core initially forms a core/shell structure with CdS followed by alloying at the interface eventually completely diffusing all the way through the CdS matrix to form homogeneously Fe-doped CdS QDs with excellent control over size and size distribution. Study of Fe K-edge shows a complete change of Fe local environment from Fe–O to FeS.« less

Standard deviations of composition measurements in atom probe analyses. Part I conventional 1D atom probe.

PubMed

Danoix, F; Grancher, G; Bostel, A; Blavette, D

2007-09-01

Atom probe is a very powerful instrument to measure concentrations on a sub nanometric scale [M.K. Miller, G.D.W. Smith, Atom Probe Microanalysis, Principles and Applications to Materials Problems, Materials Research Society, Pittsburgh, 1989]. Atom probe is therefore a unique tool to study and characterise finely decomposed metallic materials. Composition profiles or 3D mapping can be realised by gathering elemental composition measurements. As the detector efficiency is generally not equal to 1, the measured compositions are only estimates of actual values. The variance of the estimates depends on which information is to be estimated. It can be calculated when the detection process is known. These two papers are devoted to give complete analytical derivation and expressions of the variance on composition measurements in several situations encountered when using atom probe. In the first paper, we will concentrate on the analytical derivation of the variance when estimation of compositions obtained from a conventional one dimension (1D) atom probe is considered. In particular, the existing expressions, and the basic hypotheses on which they rely, will be reconsidered, and complete analytical demonstrations established. In the second companion paper, the case of 3D atom probe will be treated, highlighting how the knowledge of the 3D position of detected ions modifies the analytical derivation of the variance of local composition data.

Structural, electronic and magnetic properties of chevron-type graphene, BN and BC2N nanoribbons

NASA Astrophysics Data System (ADS)

Guerra, T.; Azevedo, S.; Kaschny, J. R.

2017-04-01

Graphene nanoribbons are predicted to be essential components in future nanoelectronics. The size, edge type, arrangement of atoms and width of nanoribbons drastically change their properties. Boronnitrogencarbon nanoribbons properties are not fully understood so far. In the present contribution it was investigated the structural, electronic and magnetic properties of chevron-type carbon, boron nitride and BC2N nanoribbons, using first-principles calculations. The results indicate that the structural stability is closely related to the discrepancies in the bond lengths, which can induce structural deformations and stress. Such nanoribbons present a wide range of electronic behaviors, depending on their composition and particularities of the atomic arrangement. A net magnetic moment is found for structures that present carbon atoms at the nanoribbon borders. Nevertheless, the calculated magnetic moment depends on the peculiarities of the symmetric arrangement of atoms and imbalance of carbon atoms between different sublattices. It was found that all structures which have a significant energy gap do not present magnetic moment, and vice-versa. Such result indicates the strong correlation between the electronic and magnetic properties of the chevron-type nanoribbons.

Synthesis, crystal structure and electronic structure of the binary phase Rh{sub 2}Cd{sub 5}

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

Koley, Biplab; Chatterjee, S.; Jana, Partha P., E-mail: ppj@chem.iitkgp.ernet.in

2017-02-15

A new phase in the Rh-Cd binary system - Rh{sub 2}Cd{sub 5} has been identified and characterized by single crystal X-ray diffraction and Energy dispersive X-ray analysis. The stoichiometric compound Rh{sub 2}Cd{sub 5} crystallizes with a unit cell containing 14 atoms, in the orthorhombic space group Pbam (55). The crystal structure of Rh{sub 2}Cd{sub 5} can be described as a defect form of the In{sub 3}Pd{sub 5} structure with ordered vacancies, formed of two 2D atomic layers with the stacking sequence: ABAB. The A type layers consist of (3.6.3.6)-Kagomé nets of Cd atoms while the B type layers consist ofmore » (3{sup 5}) (3{sup 7})- nets of both Cd and Rh atoms. The stability of this line phase is investigated by first principle electronic structure calculations on the model of ordered Rh{sub 2}Cd{sub 5}. - Graphical abstract: (3.6.3.6)-Kagomé nets of cadmium atoms (top) and (3{sup 5}) (3{sup 7})- nets of both cadmium and rhodium atoms (bottom) in the structure of Rh{sub 2}Cd{sub 5}.« less

Structural stability and O{sub 2} dissociation on nitrogen-doped graphene with transition metal atoms embedded: A first-principles study

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

Yang, Mingye; Wang, Lu, E-mail: lwang22@suda.edu.cn, E-mail: yyli@suda.edu.cn; Li, Min

2015-06-15

By using first-principles calculations, we investigate the structural stability of nitrogen-doped (N-doped) graphene with graphitic-N, pyridinic-N and pyrrolic-N, and the transition metal (TM) atoms embedded into N-doped graphene. The structures and energetics of TM atoms from Sc to Ni embedded into N-doped graphene are studied. The TM atoms at N{sub 4}V {sub 2} forming a 4N-centered structure shows the strongest binding and the binding energies are more than 7 eV. Finally, we investigate the catalytic performance of N-doped graphene with and without TM embedding for O{sub 2} dissociation, which is a fundamental reaction in fuel cells. Compared to the pyridinic-N,more » the graphitic-N is more favorable to dissociate O{sub 2} molecules with a relatively low reaction barrier of 1.15 eV. However, the catalytic performance on pyridinic-N doped structure can be greatly improved by embedding TM atoms, and the energy barrier can be reduced to 0.61 eV with V atom embedded. Our results provide the stable structure of N-doped graphene and its potential applications in the oxygen reduction reactions.« less

The Chemical Structure and Acid Deterioration of Paper.

ERIC Educational Resources Information Center

Hollinger, William K., Jr.

1984-01-01

Describes the chemical structure of paper, including subatomic particles, atoms and molecules, and the forces that bond atoms into molecules, molecules into chains, chains into sheets, and sheets into layers. Acid is defined, and the deleterious role of acid in breaking the forces that bond atoms into molecules is detailed. (EJS)

GENERAL VIEW, LOOKING NORTH, OF ATOMIC PHYSICS OBSERVATORY WHICH CONTAINS ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

GENERAL VIEW, LOOKING NORTH, OF ATOMIC PHYSICS OBSERVATORY WHICH CONTAINS THE WHITE DOME STRUCTURE. THE SHED-LIKE STRUCTURE TO THE LEFT IS THE SEARCH-LIGHT BUILDING. - Carnegie Institution of Washington, Department of Terrestrial Magnetism, Atomic Physics Observatory, 5241 Broad Branch Drive Northwest, Washington, District of Columbia, DC

Understanding complete oxidation of methane on spinel oxides at a molecular level

DOE PAGES

Tao, Franklin Feng; Shan, Jun-jun; Nguyen, Luan; ...

2015-08-04

It is crucial to develop a catalyst made of earth-abundant elements highly active for a complete oxidation of methane at a relatively low temperature. NiCo 2O 4 consisting of earth-abundant elements which can completely oxidize methane in the temperature range of 350-550 °C. Being a cost-effective catalyst, NiCo 2O 4 exhibits activity higher than precious-metal-based catalysts. Here we report that the higher catalytic activity at the relatively low temperature results from the integration of nickel cations, cobalt cations and surface lattice oxygen atoms/oxygen vacancies at the atomic scale. Finally, in situ studies of complete oxidation of methane on NiCo 2Omore » 4 and theoretical simulations show that methane dissociates to methyl on nickel cations and then couple with surface lattice oxygen atoms to form -CH 3O with a following dehydrogenation to -CH 2O; a following oxidative dehydrogenation forms CHO; CHO is transformed to product molecules through two different sub-pathways including dehydrogenation of OCHO and CO oxidation.« less

Complete wavelength mismatching effect in a Doppler broadened Y-type six-level EIT atomic medium

NASA Astrophysics Data System (ADS)

Bharti, Vineet; Wasan, Ajay

We present a theoretical study of the Doppler broadened Y-type six-level atomic system, using a density matrix approach, to investigate the effect of varying control field wavelengths and closely spaced hyperfine levels in the 5P state of 87Rb. The closely spaced hyperfine levels in our six-level system affect the optical properties of Y-type system and cause asymmetry in absorption profiles. Depending upon the choices of π-probe, σ+-control and σ--control fields transitions, we consider three regimes: (i) perfect wavelength matching regime (λp=λ=λ), (ii) partial wavelength mismatching regime (λp≠λ=λ), and (iii) complete wavelength mismatching regime (λp≠λ≠λ). The complete wavelength mismatching regime is further distinguished into two situations, i.e., λ<λ and λ>λ. We have shown that in the room temperature atomic vapor, the asymmetric transparency window gets broadened in the partial wavelength mismatching regime as compared to the perfect wavelength matching regime. This broad transparency window also splits at the line center in the complete wavelength mismatching regime.

Forging Fast Ion Conducting Nanochannels with Swift Heavy Ions: The Correlated Role of Local Electronic and Atomic Structure

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

Sachan, Ritesh; Cooper, Valentino R.; Liu, Bin

2016-12-19

Atomically disordered oxides have attracted significant attention in recent years due to the possibility of enhanced ionic conductivity. However, the correlation between atomic disorder, corresponding electronic structure, and the resulting oxygen diffusivity is not well understood. The disordered variants of the ordered pyrochlore structure in gadolinium titanate (Gd 2Ti 2O 7) are seen as a particularly interesting prospect due to intrinsic presence of a vacant oxygen site in the unit atomic structure, which could provide a channel for fast oxygen conduction. In this paper, we provide insights into the subangstrom scale on the disordering-induced variations in the local atomic environmentmore » and its effect on the electronic structure in high-energy ion irradiation-induced disordered nanochannels, which can be utilized as pathways for fast oxygen ion transport. With the help of an atomic plane-by-plane-resolved analyses, the work shows how the presence of various types of TiO x polyhedral that exist in the amorphous and disordered crystalline phase modify the electronic structures relative to the ordered pyrochlore phase in Gd 2Ti 2O 7. Finally, the correlated molecular dynamics simulations on the disordered structures show a remarkable enhancement in oxygen diffusivity as compared with ordered pyrochlore lattice and make that a suitable candidate for applications requiring fast oxygen conduction.« less

Structural determination of Bi-doped magnetite multifunctional nanoparticles for contrast imaging.

PubMed

Laguna-Marco, M A; Piquer, C; Roca, A G; Boada, R; Andrés-Vergés, M; Veintemillas-Verdaguer, S; Serna, C J; Iadecola, A; Chaboy, J

2014-09-14

To determine with precision how Bi atoms are distributed in Bi-doped iron oxide nanoparticles their structural characterization has been carried out by X-ray absorption spectroscopy (XAS) recorded at the K edge of Fe and at the L3 edge of Bi. The inorganic nanoparticles are nominally hybrid structures integrating an iron oxide core and a bismuth oxide shell. Fe K-edge XAS indicates the formation of a structurally ordered, non-stoichiometric magnetite (Fe3-δO4) phase for all the nanoparticles. The XAS spectra show that, in the samples synthesized by precipitation in aqueous media and laser pyrolysis, the Bi atoms neither enter into the iron oxide spinel lattice nor form any other mixed Bi-Fe oxides. No modification of the local structure around the Fe atoms induced by the Bi atoms is observed at the Fe K edge. In addition, contrary to expectations, our results indicate that the Bi atoms do not form a well-defined Bi oxide structure. The XAS study at the Bi L3 edge indicates that the environment around Bi atoms is highly disordered and only a first oxygen coordination shell is observed. Indefinite [BiO6-x(OH)x] units (isolated or aggregated forming tiny amorphous clusters) bonded through hydroxyl bridges to the nanoparticle, rather than a well defined Bi2O3 shell, surround the nanoparticle. On the other hand, the XAS study indicates that, in the samples synthesized by thermal decomposition, the Bi atoms are embedded in a longer range ordered structure showing the first and second neighbors.

Short and medium range structures of 80GeSe2–20Ga2Se3 chalcogenide glasses

NASA Astrophysics Data System (ADS)

Petracovschi, Elena; Calvez, Laurent; Cormier, Laurent; Le Coq, David; Du, Jincheng

2018-05-01

The short and medium range structures of 80GeSe2–20Ga2Se3 (or Ge23.5Ga11.8Se64.7) chalcogenide glasses have been studied by combining ab initio molecular dynamics (AIMD) simulations and experimental neutron diffraction studies. The structure factor and total correlation function were calculated from glass structures generated from AIMD simulations and compared with neutron diffraction experiments showing reasonable agreement. The atomic structures of ternary chalcogenide glasses were analyzed in detail, and it was found that gallium atoms are four-fold coordinated by selenium (Se) and form [GaSe4] tetrahedra. Germanium atoms on average also have four-fold coordination, among which Se is 3.5 with the remaining being Ge–Ge homo-nuclear bonds. Ga and Ge tetrahedra link together mainly through corner-sharing and some edge-sharing of Se. No homo-nuclear bonds were observed among Ga atoms or between Ge and Ga. In addition, Se–Se homo-nuclear bonds and Se chains with various lengths were observed. A small fraction of Se atom triclusters that bond to three cations of Ge and Ga were also observed, confirming earlier proposals from 77Se solid state nuclear magnetic resonance studies. Furthermore, the electronic structures of ternary chalcogenide glasses were studied in terms of atomic charge and electronic density of states in order to gain insights into the chemical bonding and electronic properties, as well as to provide an explanation of the observed atomic structures in these ternary chalcogenide glasses.

μ-Hexa-thio-metadiphosphato-bis-[(1,4,7,10,13,16-hexa-oxa-cyclo-octa-decane-κ(6) O)rubidium] aceto-nitrile disolvate.

PubMed

Gjikaj, Mimoza; Pook, Niels-Patrick; Qarri, Flora

2013-12-01

The asymmetric unit of the title compound, [Rb2(P2S6)(C12H24O6)2]·2CH3CN, contains one half of an [Rb(18-crown-6)2]2[P2S6] unit and one aceto-nitrile solvent mol-ecule. The [Rb(18-crown-6)]2[P2S6] unit is completed by inversion symmetry. Its Rb(+) ion is situated near the centre of the macrocyclic cavity, but is displaced by 0.8972 (1) Å from the O atoms of the crown in the direction of the [P2S6](2-) moiety. The overall coordination number of the cation is eight, defined by the six crown ether O atoms and by two terminal S atoms of the [P2S6](2-) anion. The hexa-thio-metadiphosphate anion is built up from two tetra-hedral PS4 units joined together by a common edge. The crystal structure is characterized by alternating layers of [Rb(18-crown-6)]2[P2S6] and aceto-nitrile solvent mol-ecules stacked along [010].

Giant (12 ×12 ) and (4 ×8 ) reconstructions of the 6 H -SiC(0001) surface obtained by progressive enrichment in Si atoms

NASA Astrophysics Data System (ADS)

Martrou, David; Leoni, Thomas; Chaumeton, Florian; Castanié, Fabien; Gauthier, Sébastien; Bouju, Xavier

2018-02-01

Silicon carbide (SiC) is nowadays a major material for applications in high power electronics, quantum optics, or nitride semiconductors growth. Mastering the surface of SiC substrate is crucial to obtain reproducible results. Previous studies on the 6 H -SiC(0001) surface have determined several reconstructions, including the (√{3 }×√{3 }) -R 30∘ and the (3 ×3 ) . Here, we introduce a process of progressive Si enrichment that leads to the formation of two reconstructions, the giant (12 ×12 ) and the (4 ×8 ) . From electron diffraction and tunneling microscopy completed by molecular dynamics simulations, we build models introducing a type of Si adatom bridging two Si surface atoms. Using these Si bridges, we also propose a structure for two other reconstructions, the (2 √{3 }×2 √{3 }) -R 30∘ and the (2 √{3 }×2 √{13 } ). We show that five reconstructions follow each other with Si coverage ranging from 1 and 1.444 monolayer. This result opens the way to greatly improve the control of 6 H -SiC(0001) at the atomic scale.

Mathematical model for Dengue with three states of infection

NASA Astrophysics Data System (ADS)

Hincapie, Doracelly; Ospina, Juan

2012-06-01

A mathematical model for dengue with three states of infection is proposed and analyzed. The model consists in a system of differential equations. The three states of infection are respectively asymptomatic, partially asymptomatic and fully asymptomatic. The model is analyzed using computer algebra software, specifically Maple, and the corresponding basic reproductive number and the epidemic threshold are computed. The resulting basic reproductive number is an algebraic synthesis of all epidemic parameters and it makes clear the possible control measures. The microscopic structure of the epidemic parameters is established using the quantum theory of the interactions between the atoms and radiation. In such approximation, the human individual is represented by an atom and the mosquitoes are represented by radiation. The force of infection from the mosquitoes to the humans is considered as the transition probability from the fundamental state of atom to excited states. The combination of computer algebra software and quantum theory provides a very complete formula for the basic reproductive number and the possible control measures tending to stop the propagation of the disease. It is claimed that such result may be important in military medicine and the proposed method can be applied to other vector-borne diseases.

Direct Imaging and First Principles Studies of Si3N4/SiO2 Interface

NASA Astrophysics Data System (ADS)

Walkosz, Weronika; Klie, Robert; Ogut, Serdar; Mikijelj, Bilijana; Pennycook, Stephen; Idrobo, Juan C.

2010-03-01

It is well known that the composition of the integranular films (IGFs) in sintered polycrystalline silicon nitride (Si3N4) ceramics controls many of their physical and mechanical properties. A considerable effort has been made to characterize these films on the atomic scale using both experimental and theoretical methods. In this talk, we present results from a combined atomic-resolution Z-contrast and annular bright field imaging, electron energy-loss spectroscopy, as well as ab initio studies of the interface between β-Si3N4 (10-10) and SiO2 intergranular film. Our results show that O replaces N at the interface between the two materials in agreement with our theoretical calculations and that N is present in the SiO2 IGF. Moreover, they indicate the presence of atomic columns completing Si3N4 open rings, which have not been observed experimentally at the recently imaged Si3N4/rare-earth oxides interfaces, but have been predicted theoretically on bare Si3N4 surfaces. The structural and electronic variations at the Si3N4/SiO2 interface will be discussed in detail, focusing in particular on bonding characteristics.

Quantitative Subsurface Atomic Structure Fingerprint for 2D Materials and Heterostructures by First-Principles-Calibrated Contact-Resonance Atomic Force Microscopy.

PubMed

Tu, Qing; Lange, Björn; Parlak, Zehra; Lopes, Joao Marcelo J; Blum, Volker; Zauscher, Stefan

2016-07-26

Interfaces and subsurface layers are critical for the performance of devices made of 2D materials and heterostructures. Facile, nondestructive, and quantitative ways to characterize the structure of atomically thin, layered materials are thus essential to ensure control of the resultant properties. Here, we show that contact-resonance atomic force microscopy-which is exquisitely sensitive to stiffness changes that arise from even a single atomic layer of a van der Waals-adhered material-is a powerful experimental tool to address this challenge. A combined density functional theory and continuum modeling approach is introduced that yields sub-surface-sensitive, nanomechanical fingerprints associated with specific, well-defined structure models of individual surface domains. Where such models are known, this information can be correlated with experimentally obtained contact-resonance frequency maps to reveal the (sub)surface structure of different domains on the sample.

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

Tyson, T. A.; Gao, W.; Chen, Y. -S.

Solar cells based on hybrid perovskites have shown high efficiency while possessing simple processing methods. To gain a fundamental understanding of their properties on an atomic level, we investigate single crystals of CH 3NH 3PbI 3 with a narrow transition (~5 K) near 327 K. Temperature dependent structural measurements reveal a persistent tetragonal structure with smooth changes in the atomic displacement parameters (ADPs) on crossing T*. We show that the ADPs for I ions yield extended flat regions in the potential wells consistent with the measured large thermal expansion parameter. Molecular dynamics simulations reveal that this material exhibits significant asymmetriesmore » in the Pb-I pair distribution functions. We also show that the intrinsically enhanced freedom of motion of the iodine atoms enables large deformations. This flexibility (softness) of the atomic structure results in highly localized atomic relaxation about defects and hence accounts for both the high carrier mobility as well as the structural instability.« less

Visualization and automatic detection of defect distribution in GaN atomic structure from sampling Moiré phase.

PubMed

Wang, Qinghua; Ri, Shien; Tsuda, Hiroshi; Kodera, Masako; Suguro, Kyoichi; Miyashita, Naoto

2017-09-19

Quantitative detection of defects in atomic structures is of great significance to evaluating product quality and exploring quality improvement process. In this study, a Fourier transform filtered sampling Moire technique was proposed to visualize and detect defects in atomic arrays in a large field of view. Defect distributions, defect numbers and defect densities could be visually and quantitatively determined from a single atomic structure image at low cost. The effectiveness of the proposed technique was verified from numerical simulations. As an application, the dislocation distributions in a GaN/AlGaN atomic structure in two directions were magnified and displayed in Moire phase maps, and defect locations and densities were detected automatically. The proposed technique is able to provide valuable references to material scientists and engineers by checking the effect of various treatments for defect reduction. © 2017 IOP Publishing Ltd.

Atoms in Action: Observing Atomic Motion with Dynamic in situ X-ray Diffraction

NASA Astrophysics Data System (ADS)

Cox, Jordan Michael

Metal-organic framework (MOF) materials are rich in both structural diversity and application. These materials are comprised of metal atoms or clusters which are connected in a three-dimensional polymer-like network by bridging organic linker molecules. One of the major attractive features in MOFs is their permanent pore space which can potentially be used to adsorb or exchange foreign molecules from/with the surrounding environment. While MOFs are an active area of scientific interest, MOF materials are still relatively new, only 20 years old. As such, there is still much that needs to be understood about these materials before they can be effectively applied to widespread chemical problems like CO2 sequestration or low-pressure hydrogen fuel storage. One of the most important facets of MOF chemistry to understand in order to rationally design MOF materials with tailor-made properties is the relationship between the structural features in a MOF and the chemical and physical properties of that material. By examining in detail the atomic structure of a MOF with known properties under a variety of conditions, scientists can begin to unravel the guiding principles which govern these relationships. X-ray diffraction remains one of the most effective tools for determining the structure of a crystalline material with atomic resolution, and has been applied to the determination of MOF structures for years. Typically these experiments have been carried out using powder X-ray diffraction, but this technique lacks the high-resolution structural information found in single-crystal methods. Some studies have been reported which use specialized devices, sometimes called Environmental Control Cells, to study single crystalline MOFs under non-ambient chemical conditions in situ . However, these in situ studies are performed under static conditions. Even in cases where the ECC provides continued access to the local chemical environment during diffraction data collections, the environment is left static or data is not collected until after the material has equilibrated to its new environment. First, a unique ECC has been designed and constructed which allows continuous access to the local chemical environment of a single-crystal sample while maintaining ease of use, minimizing size, and which is easily adaptable to a wide variety of gaseous and liquid chemical stimuli. Novel methods have been developed and are herein described for utilizing this ECC and in situ X-ray diffraction methods in a dynamic manner for monitoring the structural responses of single crystals to changes in their local chemical environment. These methods provide the opportunity for the determination of changes in unit cell parameters and even complete crystal structures during adsorption, desorption, and exchange processes in MOF materials. The application of these methods to the determination of the dehydration process of a previously reported cobalt-based MOF have revealed surprising structural and dynamics data. Several new intermediate structures have been determined in this process, including one metastable species and several actively transitioning species during the dehydration process. Applying these methods to the ethanol solvation process in the same material again yielded results which were richer in structural information than the previously reported ex situ structures. A computational study of rotational potential energy surfaces in a family of photochromic MOF linkers revealed the important role rotational stereoisomers can play in maintaining light-activated functionality when these linkers are incorporated into next-generation functional MOF materials. Finally, the application of novel photocrystallography techniques were used in conjunction with spectroscopic methods to determine the nature of the anomalous behavior of a photochromic diarylethene single-crystal.

Adaptive local basis set for Kohn–Sham density functional theory in a discontinuous Galerkin framework II: Force, vibration, and molecular dynamics calculations

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

Zhang, Gaigong; Lin, Lin, E-mail: linlin@math.berkeley.edu; Computational Research Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720

Recently, we have proposed the adaptive local basis set for electronic structure calculations based on Kohn–Sham density functional theory in a pseudopotential framework. The adaptive local basis set is efficient and systematically improvable for total energy calculations. In this paper, we present the calculation of atomic forces, which can be used for a range of applications such as geometry optimization and molecular dynamics simulation. We demonstrate that, under mild assumptions, the computation of atomic forces can scale nearly linearly with the number of atoms in the system using the adaptive local basis set. We quantify the accuracy of the Hellmann–Feynmanmore » forces for a range of physical systems, benchmarked against converged planewave calculations, and find that the adaptive local basis set is efficient for both force and energy calculations, requiring at most a few tens of basis functions per atom to attain accuracies required in practice. Since the adaptive local basis set has implicit dependence on atomic positions, Pulay forces are in general nonzero. However, we find that the Pulay force is numerically small and systematically decreasing with increasing basis completeness, so that the Hellmann–Feynman force is sufficient for basis sizes of a few tens of basis functions per atom. We verify the accuracy of the computed forces in static calculations of quasi-1D and 3D disordered Si systems, vibration calculation of a quasi-1D Si system, and molecular dynamics calculations of H{sub 2} and liquid Al–Si alloy systems, where we show systematic convergence to benchmark planewave results and results from the literature.« less

Adaptive local basis set for Kohn–Sham density functional theory in a discontinuous Galerkin framework II: Force, vibration, and molecular dynamics calculations

DOE PAGES

Zhang, Gaigong; Lin, Lin; Hu, Wei; ...

2017-01-27

Recently, we have proposed the adaptive local basis set for electronic structure calculations based on Kohn–Sham density functional theory in a pseudopotential framework. The adaptive local basis set is efficient and systematically improvable for total energy calculations. In this paper, we present the calculation of atomic forces, which can be used for a range of applications such as geometry optimization and molecular dynamics simulation. We demonstrate that, under mild assumptions, the computation of atomic forces can scale nearly linearly with the number of atoms in the system using the adaptive local basis set. We quantify the accuracy of the Hellmann–Feynmanmore » forces for a range of physical systems, benchmarked against converged planewave calculations, and find that the adaptive local basis set is efficient for both force and energy calculations, requiring at most a few tens of basis functions per atom to attain accuracies required in practice. Sin ce the adaptive local basis set has implicit dependence on atomic positions, Pulay forces are in general nonzero. However, we find that the Pulay force is numerically small and systematically decreasing with increasing basis completeness, so that the Hellmann–Feynman force is sufficient for basis sizes of a few tens of basis functions per atom. We verify the accuracy of the computed forces in static calculations of quasi-1D and 3D disordered Si systems, vibration calculation of a quasi-1D Si system, and molecular dynamics calculations of H 2 and liquid Al–Si alloy systems, where we show systematic convergence to benchmark planewave results and results from the literature.« less

Adaptive local basis set for Kohn–Sham density functional theory in a discontinuous Galerkin framework II: Force, vibration, and molecular dynamics calculations

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

Zhang, Gaigong; Lin, Lin; Hu, Wei

Recently, we have proposed the adaptive local basis set for electronic structure calculations based on Kohn–Sham density functional theory in a pseudopotential framework. The adaptive local basis set is efficient and systematically improvable for total energy calculations. In this paper, we present the calculation of atomic forces, which can be used for a range of applications such as geometry optimization and molecular dynamics simulation. We demonstrate that, under mild assumptions, the computation of atomic forces can scale nearly linearly with the number of atoms in the system using the adaptive local basis set. We quantify the accuracy of the Hellmann–Feynmanmore » forces for a range of physical systems, benchmarked against converged planewave calculations, and find that the adaptive local basis set is efficient for both force and energy calculations, requiring at most a few tens of basis functions per atom to attain accuracies required in practice. Sin ce the adaptive local basis set has implicit dependence on atomic positions, Pulay forces are in general nonzero. However, we find that the Pulay force is numerically small and systematically decreasing with increasing basis completeness, so that the Hellmann–Feynman force is sufficient for basis sizes of a few tens of basis functions per atom. We verify the accuracy of the computed forces in static calculations of quasi-1D and 3D disordered Si systems, vibration calculation of a quasi-1D Si system, and molecular dynamics calculations of H 2 and liquid Al–Si alloy systems, where we show systematic convergence to benchmark planewave results and results from the literature.« less

Adaptive local basis set for Kohn-Sham density functional theory in a discontinuous Galerkin framework II: Force, vibration, and molecular dynamics calculations

NASA Astrophysics Data System (ADS)

Zhang, Gaigong; Lin, Lin; Hu, Wei; Yang, Chao; Pask, John E.

2017-04-01

Recently, we have proposed the adaptive local basis set for electronic structure calculations based on Kohn-Sham density functional theory in a pseudopotential framework. The adaptive local basis set is efficient and systematically improvable for total energy calculations. In this paper, we present the calculation of atomic forces, which can be used for a range of applications such as geometry optimization and molecular dynamics simulation. We demonstrate that, under mild assumptions, the computation of atomic forces can scale nearly linearly with the number of atoms in the system using the adaptive local basis set. We quantify the accuracy of the Hellmann-Feynman forces for a range of physical systems, benchmarked against converged planewave calculations, and find that the adaptive local basis set is efficient for both force and energy calculations, requiring at most a few tens of basis functions per atom to attain accuracies required in practice. Since the adaptive local basis set has implicit dependence on atomic positions, Pulay forces are in general nonzero. However, we find that the Pulay force is numerically small and systematically decreasing with increasing basis completeness, so that the Hellmann-Feynman force is sufficient for basis sizes of a few tens of basis functions per atom. We verify the accuracy of the computed forces in static calculations of quasi-1D and 3D disordered Si systems, vibration calculation of a quasi-1D Si system, and molecular dynamics calculations of H2 and liquid Al-Si alloy systems, where we show systematic convergence to benchmark planewave results and results from the literature.

Analysis of structural correlations in a model binary 3D liquid through the eigenvalues and eigenvectors of the atomic stress tensors

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

Levashov, V. A.

2016-03-07

It is possible to associate with every atom or molecule in a liquid its own atomic stress tensor. These atomic stress tensors can be used to describe liquids’ structures and to investigate the connection between structural and dynamic properties. In particular, atomic stresses allow to address atomic scale correlations relevant to the Green-Kubo expression for viscosity. Previously correlations between the atomic stresses of different atoms were studied using the Cartesian representation of the stress tensors or the representation based on spherical harmonics. In this paper we address structural correlations in a 3D model binary liquid using the eigenvalues and eigenvectorsmore » of the atomic stress tensors. This approach allows to interpret correlations relevant to the Green-Kubo expression for viscosity in a simple geometric way. On decrease of temperature the changes in the relevant stress correlation function between different atoms are significantly more pronounced than the changes in the pair density function. We demonstrate that this behaviour originates from the orientational correlations between the eigenvectors of the atomic stress tensors. We also found correlations between the eigenvalues of the same atomic stress tensor. For the studied system, with purely repulsive interactions between the particles, the eigenvalues of every atomic stress tensor are positive and they can be ordered: λ{sub 1} ≥ λ{sub 2} ≥ λ{sub 3} ≥ 0. We found that, for the particles of a given type, the probability distributions of the ratios (λ{sub 2}/λ{sub 1}) and (λ{sub 3}/λ{sub 2}) are essentially identical to each other in the liquids state. We also found that λ{sub 2} tends to be equal to the geometric average of λ{sub 1} and λ{sub 3}. In our view, correlations between the eigenvalues may represent “the Poisson ratio effect” at the atomic scale.« less

Analysis of structural correlations in a model binary 3D liquid through the eigenvalues and eigenvectors of the atomic stress tensors.

PubMed

Levashov, V A

2016-03-07

It is possible to associate with every atom or molecule in a liquid its own atomic stress tensor. These atomic stress tensors can be used to describe liquids' structures and to investigate the connection between structural and dynamic properties. In particular, atomic stresses allow to address atomic scale correlations relevant to the Green-Kubo expression for viscosity. Previously correlations between the atomic stresses of different atoms were studied using the Cartesian representation of the stress tensors or the representation based on spherical harmonics. In this paper we address structural correlations in a 3D model binary liquid using the eigenvalues and eigenvectors of the atomic stress tensors. This approach allows to interpret correlations relevant to the Green-Kubo expression for viscosity in a simple geometric way. On decrease of temperature the changes in the relevant stress correlation function between different atoms are significantly more pronounced than the changes in the pair density function. We demonstrate that this behaviour originates from the orientational correlations between the eigenvectors of the atomic stress tensors. We also found correlations between the eigenvalues of the same atomic stress tensor. For the studied system, with purely repulsive interactions between the particles, the eigenvalues of every atomic stress tensor are positive and they can be ordered: λ1 ≥ λ2 ≥ λ3 ≥ 0. We found that, for the particles of a given type, the probability distributions of the ratios (λ2/λ1) and (λ3/λ2) are essentially identical to each other in the liquids state. We also found that λ2 tends to be equal to the geometric average of λ1 and λ3. In our view, correlations between the eigenvalues may represent "the Poisson ratio effect" at the atomic scale.

From Quasicrystals to Crystals with Interpenetrating Icosahedra in Ca–Au–Al: In Situ Variable-Temperature Transformation

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

Pham, Joyce; Meng, Fanqiang; Lynn, Matthew J.

The irreversible transformation from an icosahedral quasicrystal (i-QC) CaAu 4.39Al 1.61 to its cubic 2/1 crystalline approximant (CA) Ca 13Au 56.31(3)Al 21.69 (CaAu 4.33(1)Al1.67, Pamore » $$\\bar{3}$$ (No. 205); Pearson symbol: cP728; a = 23.8934(4)), starting at ~570 °C and complete by ~650 °C, is discovered from in situ, high-energy, variable-temperature powder X-ray diffraction (PXRD), thereby providing direct experimental evidence for the relationship between QCs and their associated CAs. The new cubic phase crystallizes in a Tsai-type approximant structure under the broader classification of polar intermetallic compounds, in which atoms of different electronegativities, viz., electronegative Au + Al vs electropositive Ca, are arranged in concentric shells. From a structural chemical perspective, the outermost shell of this cubic approximant may be described as interpenetrating and edge-sharing icosahedra, a perspective that is obtained by splitting the traditional structural description of this shell as a 92-atom rhombic triacontahedron into an 80-vertex cage of primarily Au [Au 59.86(2)Al 17.14⟂ 3.00] and an icosahedral shell of only Al [Al 10.5⟂ 1.5]. Following the proposal that the cubic 2/1 CA approximates the structure of the i-QC and on the basis of the observed transformation, an atomic site analysis of the 2/1 CA, which shows a preference to maximize the number of heteroatomic Au–Al nearest neighbor contacts over homoatomic Al–Al contacts, implies a similar outcome for the i-QC structure. Analysis of the most intense reflections in the diffraction pattern of the cubic 2/1 CA that changed during the phase transformation shows correlations with icosahedral symmetry, and the stability of this cubic phase is assessed using valence electron counts. Finally, according to electronic structure calculations, a cubic 1/1 CA, “Ca 24Au 88Al 64” (CaAu 3.67Al 2.67) is proposed.« less

From Quasicrystals to Crystals with Interpenetrating Icosahedra in Ca–Au–Al: In Situ Variable-Temperature Transformation

DOE PAGES

Pham, Joyce; Meng, Fanqiang; Lynn, Matthew J.; ...

2017-12-29

The irreversible transformation from an icosahedral quasicrystal (i-QC) CaAu 4.39Al 1.61 to its cubic 2/1 crystalline approximant (CA) Ca 13Au 56.31(3)Al 21.69 (CaAu 4.33(1)Al1.67, Pamore » $$\\bar{3}$$ (No. 205); Pearson symbol: cP728; a = 23.8934(4)), starting at ~570 °C and complete by ~650 °C, is discovered from in situ, high-energy, variable-temperature powder X-ray diffraction (PXRD), thereby providing direct experimental evidence for the relationship between QCs and their associated CAs. The new cubic phase crystallizes in a Tsai-type approximant structure under the broader classification of polar intermetallic compounds, in which atoms of different electronegativities, viz., electronegative Au + Al vs electropositive Ca, are arranged in concentric shells. From a structural chemical perspective, the outermost shell of this cubic approximant may be described as interpenetrating and edge-sharing icosahedra, a perspective that is obtained by splitting the traditional structural description of this shell as a 92-atom rhombic triacontahedron into an 80-vertex cage of primarily Au [Au 59.86(2)Al 17.14⟂ 3.00] and an icosahedral shell of only Al [Al 10.5⟂ 1.5]. Following the proposal that the cubic 2/1 CA approximates the structure of the i-QC and on the basis of the observed transformation, an atomic site analysis of the 2/1 CA, which shows a preference to maximize the number of heteroatomic Au–Al nearest neighbor contacts over homoatomic Al–Al contacts, implies a similar outcome for the i-QC structure. Analysis of the most intense reflections in the diffraction pattern of the cubic 2/1 CA that changed during the phase transformation shows correlations with icosahedral symmetry, and the stability of this cubic phase is assessed using valence electron counts. Finally, according to electronic structure calculations, a cubic 1/1 CA, “Ca 24Au 88Al 64” (CaAu 3.67Al 2.67) is proposed.« less

Complete titanium substitution by boron in a tetragonal prism: exploring the complex boride series Ti(3-x)Ru(5-y)Ir(y)B(2+x) (0 ≤ x ≤ 1 and 1 < y < 3) by experiment and theory.

PubMed

Fokwa, Boniface P T; Hermus, Martin

2011-04-18

Polycrystalline samples and single crystals of four members of the new complex boride series Ti(3-x)Ru(5-y)Ir(y)B(2+x) (0 ≤ x ≤ 1 and 1 < y < 3) were synthesized by arc-melting the elements in a water-cooled copper crucible under an argon atmosphere. The new silvery phases were structurally characterized by powder and single-crystal X-ray diffraction as well as energy- and wavelength-dispersive X-ray spectroscopy analyses. They crystallize with the tetragonal Ti(3)Co(5)B(2) structure type in space group P4/mbm (No. 127). Tetragonal prisms of Ru/Ir atoms are filled with titanium in the boron-poorest phase (Ti(3)Ru(2.9)Ir(2.1)B(2)). Gradual substitution of titanium by boron then results in the successive filling of this site by a Ti/B mixture en route to the complete boron occupation, leading to the boron-richest phase (Ti(2)Ru(2.8)Ir(2.2)B(3)). Furthermore, both ruthenium and iridium share two sites in these structures, but a clear Ru/Ir site preference is found. First-principles density functional theory calculations (Vienna ab initio simulation package) on appropriate structural models (using a supercell approach) have provided more evidence on the stability of the boron-richest and -poorest phases, and the calculated lattice parameters corroborate very well with the experimentally found ones. Linear muffin-tin orbital atomic sphere approximation calculations further supported these findings through crystal orbital Hamilton population bonding analyses, which also show that the Ru/Ir-B and Ru/Ir-Ti heteroatomic interactions are mainly responsible for the structural stability of these compounds. Furthermore, some stable and unstable phases of this complex series could be predicted using the rigid-band model. According to the density of states analyses, all phases should be metallic conductors, as was expected from these metal-rich borides.

Molecular structure, spectroscopic (FTIR, FT-Raman, 13C and 1H NMR, UV), polarizability and first-order hyperpolarizability, HOMO-LUMO analysis of 2,4-difluoroacetophenone

NASA Astrophysics Data System (ADS)

Jeyavijayan, S.

2015-02-01

The FTIR and FT-Raman spectra of 2,4-difluoroacetophenone (DFAP) have been recorded in the regions 4000-400 cm-1 and 3500-50 cm-1, respectively. Utilizing the observed FTIR and FT-Raman data, a complete vibrational assignment and analysis of the fundamental modes of the compound were carried out. The optimum molecular geometry, harmonic vibrational frequencies, infrared intensities and Raman scattering activities, were calculated by density functional theory (DFT/B3LYP) method with 6-31+G(d,p) and 6-311++G(d,p) basis sets. The difference between the observed and scaled wavenumber values of most of the fundamentals is very small. A detailed interpretation of the infrared and Raman spectra of DFAP is also reported based on total energy distribution (TED). Stability of the molecule arising from hyperconjugative interactions, charge delocalization have been analyzed using natural bond orbital (NBO) analysis. The MEP map shows the negative potential sites are on oxygen atom as well as the positive potential sites are around the hydrogen atoms. The UV-Vis spectral analysis of DFAP has also been done which confirms the charge transfer of DFAP. The chemical shifts of H atoms and C atoms were calculated using NMR analysis. Furthermore, the polarizability, the first hyperpolarizability and total dipole moment of the molecule have been calculated.

Accurate energetics of small molecules containing third-row atoms Ga-Kr: A comparison of advanced ab initio and density functional theory

NASA Astrophysics Data System (ADS)

Yockel, Scott; Mintz, Benjamin; Wilson, Angela K.

2004-07-01

Advanced ab initio [coupled cluster theory through quasiperturbative triple excitations (CCSD(T))] and density functional (B3LYP) computational chemistry approaches were used in combination with the standard and augmented correlation consistent polarized valence basis sets [cc-pVnZ and aug-cc-pVnZ, where n=D(2), T(3), Q(4), and 5] to investigate the energetic and structural properties of small molecules containing third-row (Ga-Kr) atoms. These molecules were taken from the Gaussian-2 (G2) extended test set for third-row atoms. Several different schemes were used to extrapolate the calculated energies to the complete basis set (CBS) limit for CCSD(T) and the Kohn-Sham (KS) limit for B3LYP. Zero point energy and spin orbital corrections were included in the results. Overall, CCSD(T) atomization energies, ionization energies, proton affinities, and electron affinities are in good agreement with experiment, within 1.1 kcal/mol when the CBS limit has been determined using a series of two basis sets of at least triple zeta quality. For B3LYP, the overall mean absolute deviation from experiment for the three properties and the series of molecules is more significant at the KS limit, within 2.3 and 2.6 kcal/mol for the cc-pVnZ and aug-cc-pVnZ basis set series, respectively.

Poly[[(μ2-acetato-κ3 O,O′:O′)aqua­bis­(μ3-isonicotinato-κ3 O:O′:N)samarium(III)silver(I)] perchlorate

PubMed Central

Zhu, Li-Cai; Zhu, Si-Ming

2011-01-01

The title compound, {[AgSm(C6H4NO2)2(CH3CO2)(H2O)]ClO4}n, is a three-dimensional heterobimetallic complex constructed from a repeating dimeric unit. Only half of the dimeric moiety is found in the asymmetric unit; the unit cell is completed by crystallographic inversion symmetry. The SmIII ion is eight-coordinated by four O atoms of four different isonicotinate ligands, three O atoms of two different acetate ligands, and one O atom of a water mol­ecule. The two-coordinate AgI ion is bonded to two N atoms of two different isonicotinate anions, thereby connecting the disamarium units. In addition, the isonicotinate ligands also act as bridging ligands, generating a three-dimensional network. The coordinated water mol­ecules link the carboxyl­ate group and acetate ligands by O—H⋯O hydrogen bonding. Another O—H⋯O hydrogen bond is observed in the crystal structure. The perchlorate ion is disordered over two sites with site-occupancy factors of 0.560 (11) and 0.440 (11), whereas the methyl group of the acetate ligand is disordered over two sites with site-occupancy factors of 0.53 (5) and 0.47 (5). PMID:22090841

Probing structure, thermochemistry, electron affinity, and magnetic moment of thulium-doped silicon clusters TmSi n (n = 3-10) and their anions with density functional theory.

PubMed

Huang, Xintao; Yang, Jucai

2017-12-26

The most stable structures and electronic properties of TmSi n (n = 3-10) clusters and their anions have been probed by using the ABCluster global search technique combined with the PBE, TPSSh, and B3LYP density functional methods. The results revealed that the most stable structures of neutral TmSi n and their anions can be regarded as substituting a Si atom of the ground state structure of Si n + 1 with a Tm atom. The reliable AEAs, VDEs and simulated PES of TmSi n (n = 3-10) are presented. Calculations of HOMO-LUMO gap revealed that introducing Tm atom to Si cluster can improve photochemical reactivity of the cluster. The NPA analyses indicated that the 4f electron of Tm atom in TmSi n (n = 3-10) and their anions do not participate in bonding. The total magnetic moments of TmSi n are mainly provided by the 4f electrons of Tm atom. The dissociation energy of Tm atom from the most stable structure of TmSi n and their anions has been calculated to examine relative stability.

Tailoring characteristic thermal stability of Ni-Au binary nanocrystals via structure and composition engineering: theoretical insights into structural evolution and atomic inter-diffusion

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

Li, Bangquan; Wang, Hailong; Xing, Guozhong

We report on the structural evolution and atomic inter-diffusion characteristics of the bimetallic Ni-Au nanocrystals (NCs) by molecular dynamics simulations studies. Our results reveal that the thermal stability dynamics of Ni-Au NCs strongly depends on the atomic configurations. By engineering the structural construction with Ni:Au = 1:1 atomic composition, compared with core-shell Au@Ni and alloy NCs, the melting point of core-shell Ni@Au NCs is significantly enhanced up to 1215 K. Unexpectedly, with atomic ratio of Au:Ni= 1:9, the melting process initiates from the atoms in the shell of Ni@Au and alloy NCs, while starts from the core of Au@Ni NCs.more » The corresponding features and evolution process of structural motifs, mixing and segregation are illustrated via a series of dynamic simulations videos. Moreover, our results revealed that the face centered cubic phase Au{sub 0.75}Ni{sub 0.25} favorably stabilizes in NCs form but does not exist in the bulk counterpart, which elucidates the anomalies of previously reported experimental results on such bimetallic NCs.« less

Synthesis of two-dimensional TlxBi1−x compounds and Archimedean encoding of their atomic structure

PubMed Central

Gruznev, Dimitry V.; Bondarenko, Leonid V.; Matetskiy, Andrey V.; Mihalyuk, Alexey N.; Tupchaya, Alexandra Y.; Utas, Oleg A.; Eremeev, Sergey V.; Hsing, Cheng-Rong; Chou, Jyh-Pin; Wei, Ching-Ming; Zotov, Andrey V.; Saranin, Alexander A.

2016-01-01

Crystalline atomic layers on solid surfaces are composed of a single building block, unit cell, that is copied and stacked together to form the entire two-dimensional crystal structure. However, it appears that this is not an unique possibility. We report here on synthesis and characterization of the one-atomic-layer-thick TlxBi1−x compounds which display quite a different arrangement. It represents a quasi-periodic tiling structures that are built by a set of tiling elements as building blocks. Though the layer is lacking strict periodicity, it shows up as an ideally-packed tiling of basic elements without any skips or halting. The two-dimensional TlxBi1−x compounds were formed by depositing Bi onto the Tl-covered Si(111) surface where Bi atoms substitute appropriate amount of Tl atoms. Atomic structure of each tiling element as well as arrangement of TlxBi1−x compounds were established in a detail. Electronic properties and spin texture of the selected compounds having periodic structures were characterized. The shown example demonstrates possibility for the formation of the exotic low-dimensional materials via unusual growth mechanisms. PMID:26781340

1D chain formation by coadsorption of Pb and Bi on Cu(001): Determination using low energy electron diffraction

NASA Astrophysics Data System (ADS)

Kabiruzzaman, Md; Ahmed, Rezwan; Nakagawa, Takeshi; Mizuno, Seigi

2017-10-01

Coadsorption of two heavy metals, Pb and Bi, on Cu(001) at room temperature has been studied using low energy electron diffraction (LEED). c(4 × 4), c(2 × 2), and c(9√{ 2}×√{ 2}) phases are obtained at different coverages; here, we have determined the best-fit structure of c(4 × 4) phase. This structure can be described as a 1D substitutional chain arrangement of Pb and Bi atoms between the Cu rows along the [110] direction. The unit cell in the two-dimensional (2D) surface consists of one Bi atom, two Pb atoms, and four Cu atoms with one vacancy at the center. The optimal structure parameters demonstrate that Bi atoms are located at fourfold-hollow sites and that Pb atoms are laterally displaced by 0.78 Å from the fourfold-hollow site toward the vacancy. The reasons for the formation of the c(4 × 4) structure upon deposition of Pb and Bi on Cu(001) are discussed in comparison with a similar structure formed by the individual adsorption of Pb on the same substrate.

Structure cristalline du composé intermétallique Ni18Ge12

PubMed Central

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

2015-01-01

Single crystals of octa­deca­nickel dodeca­germanide were grown by chemical transport reaction. The inter­metallic compound crystallizes in a superstructure of the hexa­gonal NiAs type (B8 type). All atoms in the asymmetric unit lie on special positions except one Ni atom (two Ni atoms have site symmetry -6.. and another one has site symmetry .2. while the Ge atoms have site symmetries 32., m.. and 3..). In the structure, the Ni atoms are arranged in 11- or 13-vertex polyhedra (CN = 11–13). The coordination polyhedra of the Ge atoms are bicapped square anti­prisms (CN = 10) or 11-vertex polyhedra (CN = 11). The structure exhibits strong Ge⋯Ni inter­actions, but no close Ge⋯Ge contacts are observed. The Ni atoms with CN = 13 form infinite chains along [001] with an Ni—Ni distance of 2.491 (2) Å. PMID:25844198

Study of diffusion and local structure of sodium-silicate liquid: the molecular dynamic simulation

NASA Astrophysics Data System (ADS)

Hung, Pham Khac; Noritake, Fumiya; San, Luyen Thi; Van, To Ba; Vinh, Le The

2017-10-01

A systematic analysis on sodium-silicate melt with various silica contents was carried out. The simulation revealed two diffusion mechanisms occurred in the melt: the bond-breaking and hopping between sites. The local structure was analyzed through T-simplexes. It was revealed that T-clusters have a non-spherical shape and represent the diffusion channel, in which Na atoms are dominant, but no any O atoms are located. The SiO2-poor melt acquires a long channel. In contrast, the SiO2-rich melt consists of unconnected short channels. The simulation also revealed the immobile and mobile regions which differ in local structure and constituent composition. We propose a new CL-function to characterizing the spatial distribution of different atom component. The spatial distribution of mobile and immobile atoms is found quite different. In particular, the immobile atoms are concentrated in high-density regions possessing very large density of immobile atoms. The spatial distribution of mobile atoms in contrast is more homogeneous.

First Measurement of the Atomic Electric Dipole Moment of (225)Ra.

PubMed

Parker, R H; Dietrich, M R; Kalita, M R; Lemke, N D; Bailey, K G; Bishof, M; Greene, J P; Holt, R J; Korsch, W; Lu, Z-T; Mueller, P; O'Connor, T P; Singh, J T

2015-06-12

The radioactive radium-225 ((225)Ra) atom is a favorable case to search for a permanent electric dipole moment. Because of its strong nuclear octupole deformation and large atomic mass, (225)Ra is particularly sensitive to interactions in the nuclear medium that violate both time-reversal symmetry and parity. We have developed a cold-atom technique to study the spin precession of (225)Ra atoms held in an optical dipole trap, and demonstrated the principle of this method by completing the first measurement of its atomic electric dipole moment, reaching an upper limit of |d((225)Ra)|<5.0×10(-22)  e cm (95% confidence).

Pressure induced metallization with absence of structural transition in layered molybdenum diselenide

PubMed Central

Zhao, Zhao; Zhang, Haijun; Yuan, Hongtao; Wang, Shibing; Lin, Yu; Zeng, Qiaoshi; Xu, Gang; Liu, Zhenxian; Solanki, G. K.; Patel, K. D.; Cui, Yi; Hwang, Harold Y.; Mao, Wendy L.

2015-01-01

Layered transition-metal dichalcogenides have emerged as exciting material systems with atomically thin geometries and unique electronic properties. Pressure is a powerful tool for continuously tuning their crystal and electronic structures away from the pristine states. Here, we systematically investigated the pressurized behavior of MoSe2 up to ∼60 GPa using multiple experimental techniques and ab-initio calculations. MoSe2 evolves from an anisotropic two-dimensional layered network to a three-dimensional structure without a structural transition, which is a complete contrast to MoS2. The role of the chalcogenide anions in stabilizing different layered patterns is underscored by our layer sliding calculations. MoSe2 possesses highly tunable transport properties under pressure, determined by the gradual narrowing of its band-gap followed by metallization. The continuous tuning of its electronic structure and band-gap in the range of visible light to infrared suggest possible energy-variable optoelectronics applications in pressurized transition-metal dichalcogenides. PMID:26088416

Pressure induced metallization with absence of structural transition in layered molybdenum diselenide

DOE PAGES

Zhao, Zhao; Zhang, Haijun; Yuan, Hongtao; ...

2015-06-19

Layered transition-metal dichalcogenides have emerged as exciting material systems with atomically thin geometries and unique electronic properties. Pressure is a powerful tool for continuously tuning their crystal and electronic structures away from the pristine states. Here, we systematically investigated the pressurized behavior of MoSe 2 up to ~60 GPa using multiple experimental techniques and ab-initio calculations. MoSe 2 evolves from an anisotropic two-dimensional layered network to a three-dimensional structure without a structural transition, which is a complete contrast to MoS 2. The role of the chalcogenide anions in stabilizing different layered patterns is underscored by our layer sliding calculations. MoSemore » 2 possesses highly tunable transport properties under pressure, determined by the gradual narrowing of its band-gap followed by metallization. The continuous tuning of its electronic structure and band-gap in the range of visible light to infrared suggest possible energy-variable optoelectronics applications in pressurized transition-metal dichalcogenides.« less

EXAFS: New tool for study of battery and fuel cell materials

NASA Technical Reports Server (NTRS)

Mcbreen, James; Ogrady, William E.; Pandya, Kaumudi I.

1987-01-01

Extended X ray absorption fine structure (EXAFS) is a powerful technique for probing the local atomic structure of battery and fuel cell materials. The major advantages of EXAFS are that both the probe and the signal are X rays and the technique is element selective and applicable to all states of matter. This permits in situ studies of electrodes and determination of the structure of single components in composite electrodes, or even complete cells. EXAFS specifically probes short range order and yields coordination numbers, bond distances, and chemical identity of nearest neighbors. Thus, it is ideal for structural studies of ions in solution and the poorly crystallized materials that are often the active materials or catalysts in batteries and fuel cells. Studies on typical battery and fuel cell components are used to describe the technique and the capability of EXAFS as a structural tool in these applications. Typical experimental and data analysis procedures are outlined. The advantages and limitations of the technique are also briefly discussed.

Automated Reflectance Measurement System Designed and Fabricated to Determine the Limits of Atomic Oxygen Treatment of Art Through Contrast Optimization

NASA Technical Reports Server (NTRS)

Sechkar, Edward A.; Stueber, Thomas J.; Rutledge, Sharon K.

2000-01-01

Atomic oxygen generated in ground-based research facilities has been used to not only test erosion of candidate spacecraft materials but as a noncontact technique for removing organic deposits from the surfaces of artwork. NASA has patented the use of atomic oxygen to remove carbon-based soot contamination from fire-damaged artwork. The process of cleaning soot-damaged paintings with atomic oxygen requires exposures for variable lengths of time, dependent on the condition of a painting. Care must be exercised while cleaning to prevent the removal of pigment. The cleaning process must be stopped as soon as visual inspection or surface reflectance measurements indicate that cleaning is complete. Both techniques rely on optical comparisons of known bright locations against known dark locations on the artwork being cleaned. Difficulties arise with these techniques when either a known bright or dark location cannot be determined readily. Furthermore, dark locations will lighten with excessive exposure to atomic oxygen. Therefore, an automated test instrument to quantitatively characterize cleaning progression was designed and developed at the NASA Glenn Research Center at Lewis Field to determine when atomic oxygen cleaning is complete.

Gold-promoted structurally ordered intermetallic palladium cobalt nanoparticles for the oxygen reduction reaction.

PubMed

Kuttiyiel, Kurian A; Sasaki, Kotaro; Su, Dong; Wu, Lijun; Zhu, Yimei; Adzic, Radoslav R

2014-11-06

Considerable efforts to make palladium and palladium alloys active catalysts and a possible replacement for platinum have had a marginal success. Here we report on a structurally ordered Au10Pd₄₀Co₅₀ catalyst that exhibits comparable activity to conventional platinum catalysts in both acid and alkaline media. Electron microscopic techniques demonstrate that, at elevated temperatures, palladium cobalt nanoparticles undergo an atomic structural transition from core-shell to a rare intermetallic ordered structure with twin boundaries forming stable {111}, {110} and {100} facets via addition of gold atoms. The superior stability of this catalyst compared with platinum after 10,000 potential cycles in alkaline media is attributed to the atomic structural order of PdCo nanoparticles along with protective effect of clusters of gold atoms on the surface. This strategy of making ordered palladium intermetallic alloy nanoparticles can be used in diverse heterogeneous catalysis where particle size and structural stability matter.

Hydroxyl migration disorders the surface structure of hydroxyapatite nanoparticles

NASA Astrophysics Data System (ADS)

Cheng, Xiajie; Wu, Hong; Zhang, Li; Ma, Xingtao; Zhang, Xingdong; Yang, Mingli

2017-09-01

The surface structure of nano-hydroxyapatite (HAP) was investigated using a combined simulated annealing and molecular dynamics method. The stationary structures of nano-HAP with 4-7 nm in diameter and annealed under different temperatures were analyzed in terms of pair distribution function, structural factor, mean square displacement and atomic coordination number. The particles possess different structures from bulk crystal. A clear radial change in their atomic arrangements was noted. From core to surface the structures change from ordered to disordered. A three-shell model was proposed to describe the structure evolution of nano-HAP. Atoms in the core zone keep their arrangements as in crystal, while atoms in the surface shell are in short-range order and long-range disorder, adopting a typically amorphous structure. Atoms in the middle shell have small displacements and/or deflections but basically retain their original locations as in crystal. The disordered shell is about 1 nm in thickness, in agreement with experimental observations. The disordering mainly stems from hydroxyl migration during which hydroxyls move to the surface and bond with the exposed Ca ions, and their left vacancies bring about a rearrangement of nearby atoms. The disordering is to some extent different for particles unannealed under different temperatures, resulting from fewer number of migrated hydroxyls at lower temperatures. Particles with different sizes have similar surface structures, and their surface energy decreases with increasing size. Moreover, the surface energy is reduced by hydroxyl migration because the exposed Ca ions on the surface are ionically bonded with the migrated hydroxyls. Our calculations proposed a new structure model for nano-HAP, which indicates a surface structure with activities different from those without surface reorganization. This is particularly interesting because most bioactivities of biomaterials are dominated by their surface activity.

Pair distribution function analysis applied to decahedral gold nanoparticles

NASA Astrophysics Data System (ADS)

Nakotte, H.; Silkwood, C.; Page, K.; Wang, H.-W.; Olds, D.; Kiefer, B.; Manna, S.; Karpov, D.; Fohtung, E.; Fullerton, E. E.

2017-11-01

The five-fold symmetry of face-centered cubic (fcc) derived nanoparticles is inconsistent with the translational symmetry of a Bravais lattice and generally explained by multiple twinning of a tetrahedral subunit about a (joint) symmetry axis, with or without structural modification to the fcc motif. Unlike in bulk materials, five-fold twinning in cubic nanoparticles is common and strongly affects their structural, chemical, and electronic properties. To test and verify theoretical approaches, it is therefore pertinent that the local structural features of such materials can be fully characterized. The small size of nanoparticles severely limits the application of traditional analysis techniques, such as Bragg diffraction. A complete description of the atomic arrangement in nanoparticles therefore requires a departure from the concept of translational symmetry, and prevents fully evaluating all the structural features experimentally. We describe how recent advances in instrumentation, together with the increasing power of computing, are shaping the development of alternative analysis methods of scattering data for nanostructures. We present the application of Debye scattering and pair distribution function (PDF) analysis towards modeling of the total scattering data for the example of decahedral gold nanoparticles. PDF measurements provide a statistical description of the pair correlations of atoms within a material, allowing one to evaluate the probability of finding two atoms within a given distance. We explored the sensitivity of existing synchrotron x-ray PDF instruments for distinguishing four different simple models for our gold nanoparticles: a multiply twinned fcc decahedron with either a single gap or multiple distributed gaps, a relaxed body-centered orthorhombic (bco) decahedron, and a hybrid decahedron. The data simulations of the models were then compared with experimental data from synchrotron x-ray total scattering. We present our experimentally derived atomistic models of the gold nanoparticles, with surprising results and a perspective on remaining challenges. Our findings provide evidence for the suitability of PDF analysis in the characterization of other nanosized particles that may have commercial applications.

Atomic electron tomography: 3D structures without crystals

DOE PAGES

Miao, Jianwei; Ercius, Peter; Billinge, S. J. L.

2016-09-23

Crystallography has been fundamental to the development of many fields of science over the last century. However, much of our modern science and technology relies on materials with defects and disorders, and their three-dimensional (3D) atomic structures are not accessible to crystallography. One method capable of addressing this major challenge is atomic electron tomography. By combining advanced electron microscopes and detectors with powerful data analysis and tomographic reconstruction algorithms, it is now possible to determine the 3D atomic structure of crystal defects such as grain boundaries, stacking faults, dislocations, and point defects, as well as to precisely localize the 3Dmore » coordinates of individual atoms in materials without assuming crystallinity. In this work, we review the recent advances and the interdisciplinary science enabled by this methodology. We also outline further research needed for atomic electron tomography to address long-standing unresolved problems in the physical sciences.« less

Self-consistent average-atom scheme for electronic structure of hot and dense plasmas of mixture.

PubMed

Yuan, Jianmin

2002-10-01

An average-atom model is proposed to treat the electronic structures of hot and dense plasmas of mixture. It is assumed that the electron density consists of two parts. The first one is a uniform distribution with a constant value, which is equal to the electron density at the boundaries between the atoms. The second one is the total electron density minus the first constant distribution. The volume of each kind of atom is proportional to the sum of the charges of the second electron part and of the nucleus within each atomic sphere. By this way, one can make sure that electrical neutrality is satisfied within each atomic sphere. Because the integration of the electron charge within each atom needs the size of that atom in advance, the calculation is carried out in a usual self-consistent way. The occupation numbers of electron on the orbitals of each kind of atom are determined by the Fermi-Dirac distribution with the same chemical potential for all kinds of atoms. The wave functions and the orbital energies are calculated with the Dirac-Slater equations. As examples, the electronic structures of the mixture of Au and Cd, water (H2O), and CO2 at a few temperatures and densities are presented.

Attractive interaction between Mn atoms on the GaAs(110) surface observed by scanning tunneling microscopy.

PubMed

Taninaka, Atsushi; Yoshida, Shoji; Kanazawa, Ken; Hayaki, Eiko; Takeuchi, Osamu; Shigekawa, Hidemi

2016-06-16

Scanning tunneling microscopy/spectroscopy (STM/STS) was carried out to investigate the structures of Mn atoms deposited on a GaAs(110) surface at room temperature to directly observe the characteristics of interactions between Mn atoms in GaAs. Mn atoms were paired with a probability higher than the random distribution, indicating an attractive interaction between them. In fact, re-pairing of unpaired Mn atoms was observed during STS measurement. The pair initially had a new structure, which was transformed during STS measurement into one of those formed by atom manipulation at 4 K. Mn atoms in pairs and trimers were aligned in the <110> direction, which is theoretically predicted to produce a high Curie temperature.

Distribution of Al atoms in the clathrate-I phase Ba8AlxSi46-x at x = 6.9.

PubMed

Bobnar, Matej; Böhme, Bodo; Wedel, Michael; Burkhardt, Ulrich; Ormeci, Alim; Prots, Yurii; Drathen, Christina; Liang, Ying; Nguyen, Hong Duong; Baitinger, Michael; Grin, Yuri

2015-07-28

The clathrate-I phase Ba8AlxSi46-x has been structurally characterized at the composition x = 6.9 (space group Pm3[combining macron]n, no. 223, a = 10.4645(2) Å). A crystal structure model comprising the distribution of aluminium and silicon atoms in the clathrate framework was established: 5.7 Al atoms and 0.3 Si atoms occupy the crystallographic site 6c, while 1.2 Al atoms and 22.8 Si atoms occupy site 24k. The atomic distribution was established based on a combination of (27)Al and (29)Si NMR experiments, X-ray single-crystal diffraction and wavelength-dispersive X-ray spectroscopy.

Large scale structural optimization of trimetallic Cu-Au-Pt clusters up to 147 atoms

NASA Astrophysics Data System (ADS)

Wu, Genhua; Sun, Yan; Wu, Xia; Chen, Run; Wang, Yan

2017-10-01

The stable structures of Cu-Au-Pt clusters up to 147 atoms are optimized by using an improved adaptive immune optimization algorithm (AIOA-IC method), in which several motifs, such as decahedron, icosahedron, face centered cubic, sixfold pancake, and Leary tetrahedron, are randomly selected as the inner cores of the starting structures. The structures of Cu8AunPt30-n (n = 1-29), Cu8AunPt47-n (n = 1-46), and partial 75-, 79-, 100-, and 147-atom clusters are analyzed. Cu12Au93Pt42 cluster has onion-like Mackay icosahedral motif. The segregation phenomena of Cu, Au and Pt in clusters are explained by the atomic radius, surface energy, and cohesive energy.

Simulation of Laser Cooling and Trapping in Engineering Applications

NASA Technical Reports Server (NTRS)

Ramirez-Serrano, Jaime; Kohel, James; Thompson, Robert; Yu, Nan; Lunblad, Nathan

2005-01-01

An advanced computer code is undergoing development for numerically simulating laser cooling and trapping of large numbers of atoms. The code is expected to be useful in practical engineering applications and to contribute to understanding of the roles that light, atomic collisions, background pressure, and numbers of particles play in experiments using laser-cooled and -trapped atoms. The code is based on semiclassical theories of the forces exerted on atoms by magnetic and optical fields. Whereas computer codes developed previously for the same purpose account for only a few physical mechanisms, this code incorporates many more physical mechanisms (including atomic collisions, sub-Doppler cooling mechanisms, Stark and Zeeman energy shifts, gravitation, and evanescent-wave phenomena) that affect laser-matter interactions and the cooling of atoms to submillikelvin temperatures. Moreover, whereas the prior codes can simulate the interactions of at most a few atoms with a resonant light field, the number of atoms that can be included in a simulation by the present code is limited only by computer memory. Hence, the present code represents more nearly completely the complex physics involved when using laser-cooled and -trapped atoms in engineering applications. Another advantage that the code incorporates is the possibility to analyze the interaction between cold atoms of different atomic number. Some properties that cold atoms of different atomic species have, like cross sections and the particular excited states they can occupy when interacting with each other and light fields, play important roles not yet completely understood in the new experiments that are under way in laboratories worldwide to form ultracold molecules. Other research efforts use cold atoms as holders of quantum information, and more recent developments in cavity quantum electrodynamics also use ultracold atoms to explore and expand new information-technology ideas. These experiments give a hint on the wide range of applications and technology developments that can be tackled using cold atoms and light fields. From more precise atomic clocks and gravity sensors to the development of quantum computers, there will be a need to completely understand the whole ensemble of physical mechanisms that play a role in the development of such technologies. The code also permits the study of the dynamic and steady-state operations of technologies that use cold atoms. The physical characteristics of lasers and fields can be time-controlled to give a realistic simulation of the processes involved such that the design process can determine the best control features to use. It is expected that with the features incorporated into the code it will become a tool for the useful application of ultracold atoms in engineering applications. Currently, the software is being used for the analysis and understanding of simple experiments using cold atoms, and for the design of a modular compact source of cold atoms to be used in future research and development projects. The results so far indicate that the code is a useful design instrument that shows good agreement with experimental measurements (see figure), and a Windows-based user-friendly interface is also under development.

Towards a rational approach for heavy-atom derivative screening in protein crystallography

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

Agniswamy, Johnson; Joyce, M. Gordon; Hammer, Carl H.

2008-04-01

Heavy-atom derivatization is routinely used in protein structure determination and is thus of critical importance in structural biology. In order to replace the current trial-and-error heavy-atom derivative screening with a knowledge-based rational derivative-selection method, the reactivity of more than 40 heavy-atom compounds over a wide range of buffer and pH values was systematically examined using peptides which contained a single reactive amino-acid residue. Heavy-atom derivatization is routinely used in protein structure determination and is thus of critical importance in structural biology. In order to replace the current trial-and-error heavy-atom derivative screening with a knowledge-based rational derivative-selection method, the reactivity ofmore » more than 40 heavy-atom compounds over a wide range of buffer and pH values was systematically examined using peptides which contained a single reactive amino-acid residue. Met-, Cys- and His-containing peptides were derivatized against Hg, Au and Pt compounds, while Tyr-, Glu-, Asp-, Asn- and Gln-containing peptides were assessed against Pb compounds. A total of 1668 reactive conditions were examined using mass spectrometry and were compiled into heavy-atom reactivity tables. The results showed that heavy-atom derivatization reactions are highly linked to buffer and pH, with the most accommodating buffer being MES at pH 6. A group of 21 compounds were identified as most successful irrespective of ligand or buffer/pH conditions. To assess the applicability of the peptide heavy-atom reactivity to proteins, lysozyme crystals were derivatized with a list of peptide-reactive compounds that included both known and new compounds for lysozyme derivatization. The results showed highly consistent heavy-atom reactivities between the peptides and lysozyme.« less

Free-Energy Landscape of Protein-Ligand Interactions Coupled with Protein Structural Changes.

PubMed

Moritsugu, Kei; Terada, Tohru; Kidera, Akinori

2017-02-02

Protein-ligand interactions are frequently coupled with protein structural changes. Focusing on the coupling, we present the free-energy surface (FES) of the ligand-binding process for glutamine-binding protein (GlnBP) and its ligand, glutamine, in which glutamine binding accompanies large-scale domain closure. All-atom simulations were performed in explicit solvents by multiscale enhanced sampling (MSES), which adopts a multicopy and multiscale scheme to achieve enhanced sampling of systems with a large number of degrees of freedom. The structural ensemble derived from the MSES simulation yielded the FES of the coupling, described in terms of both the ligand's and protein's degrees of freedom at atomic resolution, and revealed the tight coupling between the two degrees of freedom. The derived FES led to the determination of definite structural states, which suggested the dominant pathways of glutamine binding to GlnBP: first, glutamine migrates via diffusion to form a dominant encounter complex with Arg75 on the large domain of GlnBP, through strong polar interactions. Subsequently, the closing motion of GlnBP occurs to form ligand interactions with the small domain, finally completing the native-specific complex structure. The formation of hydrogen bonds between glutamine and the small domain is considered to be a rate-limiting step, inducing desolvation of the protein-ligand interface to form the specific native complex. The key interactions to attain high specificity for glutamine, the "door keeper" existing between the two domains (Asp10-Lys115) and the "hydrophobic sandwich" formed between the ligand glutamine and Phe13/Phe50, have been successfully mapped on the pathway derived from the FES.

Crystal structure of a trapped catalytic intermediate suggests that forced atomic proximity drives the catalysis of mIPS.

PubMed

Neelon, Kelly; Roberts, Mary F; Stec, Boguslaw

2011-12-07

1-L-myo-inositol-phosphate synthase (mIPS) catalyzes the first step of the unique, de novo pathway of inositol biosynthesis. However, details about the complex mIPS catalytic mechanism, which requires oxidation, enolization, intramolecular aldol cyclization, and reduction, are not fully known. To gain further insight into this mechanism, we determined the crystal structure of the wild-type mIPS from Archaeoglobus fulgidus at 1.7 Å, as well as the crystal structures of three active-site mutants. Additionally, we obtained the structure of mIPS with a trapped 5-keto-glucose-6-phosphate intermediate at 2 Å resolution by a novel (to our knowledge) process of activating the crystal at high temperature. A comparison of all of the crystal structures of mIPS described in this work suggests a novel type of catalytic mechanism that relies on the forced atomic proximity of functional groups. The lysine cluster is contained in a small volume in the active site, where random motions of these side chains are responsible for the progress of the complex multistep reaction as well as for the low rate of catalysis. The mechanism requires that functional groups of Lys-274, Lys-278, Lys-306, and Lys-367 assume differential roles in the protonation/deprotonation steps that must occur during the mIPS reaction. This mechanism is supported by the complete loss of activity of the enzyme caused by the Leu-257 mutation to Ala that releases the lysine containment. Copyright © 2011 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Microporous structure with layered interstitial surface treatment, and method and apparatus for preparation thereof

NASA Technical Reports Server (NTRS)

Koontz, Steven L. (Inventor)

1994-01-01

A microporous structure with layered interstitial surface treatments, and method and apparatus for preparation thereof is presented. The structure is prepared by sequentially subjecting a uniformly surface-treated structure to atomic oxygen treatment to remove an outer layer of surface treatment to a generally uniform depth, and then surface treating the so exposed layer with another surface treating agent. The atomic oxygen/surface treatment steps may optionally be repeated, each successive time to a lesser depth, to produce a microporous structure having multilayered surface treatments. The apparatus employs at least one side arm from a main atomic oxygen-containing chamber. The side arm has characteristic relaxation times such that a uniform atomic oxygen dose rate is delivered to a specimen positioned transversely in the side arm spaced from the main gas chamber.

Presentation of Atomic Structure in Turkish General Chemistry Textbooks

ERIC Educational Resources Information Center

Niaz, Mansoor; Costu, Bayram

2009-01-01

Research in science education has recognized the importance of teaching atomic structure within a history and philosophy of science perspective. The objective of this study is to evaluate general chemistry textbooks published in Turkey based on the eight criteria developed in previous research. Criteria used referred to the atomic models of…

Arguments, Contradictions, Resistances, and Conceptual Change in Students' Understanding of Atomic Structure.

ERIC Educational Resources Information Center

Niaz, Mansoor; Aguilera, Damarys; Maza, Arelys; Liendo, Gustavo

2002-01-01

Reports on a study aimed at facilitating freshman general chemistry students' understanding of atomic structure based on the work of Thomson, Rutherford, and Bohr. Hypothesizes that classroom discussions based on arguments/counterarguments of the heuristic principles on which these scientists based their atomic models can facilitate students'…

Key experimental information on intermediate-range atomic structures in amorphous Ge2Sb2Te5 phase change material

NASA Astrophysics Data System (ADS)

Hosokawa, Shinya; Pilgrim, Wolf-Christian; Höhle, Astrid; Szubrin, Daniel; Boudet, Nathalie; Bérar, Jean-François; Maruyama, Kenji

2012-04-01

Laser-induced crystalline-amorphous phase change of Ge-Sb-Te alloys is the key mechanism enabling the fast and stable writing/erasing processes in rewritable optical storage devices, such as digital versatile disk (DVD) or blu-ray disk. Although the structural information in the amorphous phase is essential for clarifying this fast process, as well as long lasting stabilities of both the phases, experimental works were mostly limited to the short-range order by x ray absorption fine structure. Here we show both the short and intermediate-range atomic structures of amorphous DVD material, Ge2Sb2Te5 (GST), investigated by a combination of anomalous x ray scattering and reverse Monte Carlo modeling. From the obtained atomic configurations of amorphous GST, we have found that the Sb atoms and half of the Ge atoms play roles in the fast phase change process of order-disorder transition, while the remaining Ge atoms act for the proper activation energy of barriers between the amorphous and crystalline phases.

Biexciton emission from single isoelectronic traps formed by nitrogen-nitrogen pairs in GaAs

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

Takamiya, Kengo; Fukushima, Toshiyuki; Yagi, Shuhei

2013-12-04

We have studied photoluminescence (PL) from individual isoelectronic traps formed by nitrogen-nitrogen (NN) pairs in GaAs. Sharp emission lines due to exciton and biexciton were observed from individual isoelectronic traps in nitrogen atomic-layer doped (ALD) GaAs. The binding energy of biexciton bound to individual isoelectronic traps was approximately 8 meV. Both the exciton and biexciton luminescence lines show completely random polarization and no fine-structure splitting. These results are desirable to the application to the quantum cryptography used in the field of quantum information technology.

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

Structural, electronic, topological and vibrational properties of a series of N-benzylamides derived from Maca (Lepidium meyenii) combining spectroscopic studies with ONION calculations

NASA Astrophysics Data System (ADS)

Chain, Fernando E.; Ladetto, María Florencia; Grau, Alfredo; Catalán, César A. N.; Brandán, Silvia Antonia

2016-02-01

In the present work, the structural, topological and vibrational properties of four members of the N-benzylamides series derived from Maca (Lepidium meyenii) whose names are, N-benzylpentadecanamide, N-benzylhexadecanamide, N-benzylheptadecanamide and N-benzyloctadecanamide, were studied combining the FTIR, FT-Raman and 1H and 13C-NMR spectroscopies with density functional theory (DFT) and ONION calculations. Furthermore, the N-benzylacetamide, N-benzylpropilamide and N-benzyl hexanamide derivatives were also studied in order to compare their properties with those computed for the four macamides. These seven N-benzylamides series have a common structure, C8H8NO-R, being R the side chain [-(CH2)n-CH3] with a variable n number of CH2 groups. Here, the atomic charges, molecular electrostatic potentials, stabilization energies, topological properties of those macamides were analyzed as a function of the number of C atoms of the side chain while the frontier orbitals were used to compute the gap energies and some descriptors in order to predict their reactivities and behaviors in function of the longitude of the side chain. Here, the force fields, the complete vibrational assignments and the corresponding force constants were only reported for N-benzylacetamide, N-benzyl hexanamide and N-benzylpentadecanamide due to the high number of vibration normal modes that present the remains macamides.

Structure of 3,4-dihydroxy-2-butanone 4-phosphate synthase from Methanococcus jannaschii in complex with divalent metal ions and the substrate ribulose 5-phosphate: implications for the catalytic mechanism.

PubMed

Steinbacher, Stefan; Schiffmann, Susanne; Richter, Gerald; Huber, Robert; Bacher, Adelbert; Fischer, Markus

2003-10-24

Skeletal rearrangements of carbohydrates are crucial for many biosynthetic pathways. In riboflavin biosynthesis ribulose 5-phosphate is converted into 3,4-dihydroxy-2-butanone 4-phosphate while its C4 atom is released as formate in a sequence of metal-dependent reactions. Here, we present the crystal structure of Methanococcus jannaschii 3,4-dihydroxy-2-butanone 4-phosphate synthase in complex with the substrate ribulose 5-phosphate at a dimetal center presumably consisting of non-catalytic zinc and calcium ions at 1.7-A resolution. The carbonyl group (O2) and two out of three free hydroxyl groups (OH3 and OH4) of the substrate are metal-coordinated. We correlate previous mutational studies on this enzyme with the present structural results. Residues of the first coordination sphere involved in metal binding are indispensable for catalytic activity. Only Glu-185 of the second coordination sphere cannot be replaced without complete loss of activity. It contacts the C3 hydrogen atom directly and probably initiates enediol formation in concert with both metal ions to start the reaction sequence. Mechanistic similarities to Rubisco acting on the similar substrate ribulose 1,5-diphosphate in carbon dioxide fixation as well as other carbohydrate (reducto-) isomerases are discussed.

Electronic structure of trioxide, oxoperoxide, oxosuperoxide, and ozonide clusters of the 3d elements: density functional theory study.

PubMed

Uzunova, Ellie L

2011-03-03

The trioxide clusters with stoichiometry MO3, and the structural isomers with side-on and end-on bonded oxygen atoms, are studied by DFT with the B1LYP functional. For the first half of the 3d elements row (Sc to Cr), pyramidal or distorted pyramidal structures dominate among the trioxide and oxoperoxide ground states, while the remaining elements form planar trioxides, oxoperoxides, oxosuperoxides, and ozonides. Low-lying trioxide clusters are formed by Ti, V, Cr, and Mn, among which the distorted pyramidal VO3 in the (2)A'' state, the pyramidal CrO3 in the (1)A1 state, and the planar MnO3 in the (2)A1' state are global minima. With the exception of the middle-row elements Mn, Fe, and Co, the magnetic moment of the ground-state clusters is formed with a major contribution from unpaired electrons located at the oxygen atoms. The stability of trioxides and oxoperoxides toward release of molecular oxygen is significantly higher for Sc, Ti, and V than for the remaining elements of the row. A trend of increasing the capability to dissociate one oxygen molecule is observed from Cr to Cu, with the exception of OFe(O2) being more reactive than OCo(O2). A gradual increase of reactivity from Ti to Cu is observed for the complete fragmentation reaction M + O + O2.

Theoretical Study of tip apex electronic structure in Scanning Tunneling Microscope

NASA Astrophysics Data System (ADS)

Choi, Heesung; Huang, Min; Randall, John; Cho, Kyeongjae

2011-03-01

Scanning Tunneling Microscope (STM) has been widely used to explore diverse surface properties with an atomic resolution, and STM tip has played a critical role in controlling surface structures. However, detailed information of atomic and electronic structure of STM tip and the fundamental understanding of STM images are still incomplete. Therefore, it is important to develop a comprehensive understanding of the electronic structure of STM tip. We have studied the atomic and electronic structures of STM tip with various transition metals (TMs) by DFT method. The d-electrons of TM tip apex atoms show different orbital states near the Fermi level. We will present comprehensive data of STM tips from our DFT calculation. Verified quantification of the tip electronic structures will lead to fundamental understanding of STM tip structure-property relationship. This work is supported by the DARPA TBN Program and the Texas ETF. DARPA Tip Based Nanofabrication Program and the Emerging Technology Fund of the State of Texas.

Quantum Monte Carlo study of the phase diagram of solid molecular hydrogen at extreme pressures

PubMed Central

Drummond, N. D.; Monserrat, Bartomeu; Lloyd-Williams, Jonathan H.; Ríos, P. López; Pickard, Chris J.; Needs, R. J.

2015-01-01

Establishing the phase diagram of hydrogen is a major challenge for experimental and theoretical physics. Experiment alone cannot establish the atomic structure of solid hydrogen at high pressure, because hydrogen scatters X-rays only weakly. Instead, our understanding of the atomic structure is largely based on density functional theory (DFT). By comparing Raman spectra for low-energy structures found in DFT searches with experimental spectra, candidate atomic structures have been identified for each experimentally observed phase. Unfortunately, DFT predicts a metallic structure to be energetically favoured at a broad range of pressures up to 400 GPa, where it is known experimentally that hydrogen is non-metallic. Here we show that more advanced theoretical methods (diffusion quantum Monte Carlo calculations) find the metallic structure to be uncompetitive, and predict a phase diagram in reasonable agreement with experiment. This greatly strengthens the claim that the candidate atomic structures accurately model the experimentally observed phases. PMID:26215251

Chemical shielding properties for BN, BP, AlN, and AlP nanocones: DFT studies

NASA Astrophysics Data System (ADS)

Mirzaei, Mahmoud; Yousefi, Mohammad; Meskinfam, Masoumeh

2012-06-01

The properties of boron nitride (BN), boron phosphide (BP), aluminum nitride (AlN), and aluminum phosphide (AlP) nanocones were investigated by density functional theory (DFT) calculations. The investigated structures were optimized and chemical shielding (CS) properties including isotropic and anisotropic CS parameters were calculated for the atoms of the optimized structures. The magnitudes of CS parameters were observed to be mainly dependent on the bond lengths of considered atoms. The results indicated that the atoms could be divided into atomic layers due to the similarities of their CS properties for the atoms of each layer. The trend means that the atoms of each layer detect almost similar electronic environments. Moreover, the atoms at the apex and mouth of nanocones exhibit different properties with respect to the other atomic layers.

Doping of Semiconducting Atomic Chains

NASA Technical Reports Server (NTRS)

Toshishige, Yamada; Kutler, Paul (Technical Monitor)

1997-01-01

Due to the rapid progress in atom manipulation technology, atomic chain electronics would not be a dream, where foreign atoms are placed on a substrate to form a chain, and its electronic properties are designed by controlling the lattice constant d. It has been shown theoretically that a Si atomic chain is metallic regardless of d and that a Mg atomic chain is semiconducting or insulating with a band gap modified with d. For electronic applications, it is essential to establish a method to dope a semiconducting chain, which is to control the Fermi energy position without altering the original band structure. If we replace some of the chain atoms with dopant atoms randomly, the electrons will see random potential along the chain and will be localized strongly in space (Anderson localization). However, if we replace periodically, although the electrons can spread over the chain, there will generally appear new bands and band gaps reflecting the new periodicity of dopant atoms. This will change the original band structure significantly. In order to overcome this dilemma, we may place a dopant atom beside the chain at every N lattice periods (N > 1). Because of the periodic arrangement of dopant atoms, we can avoid the unwanted Anderson localization. Moreover, since the dopant atoms do not constitute the chain, the overlap interaction between them is minimized, and the band structure modification can be made smallest. Some tight-binding results will be discussed to demonstrate the present idea.

Research on Spectroscopy, Opacity, and Atmospheres

NASA Technical Reports Server (NTRS)

Kurucz, Robert L.; West, Donald (Technical Monitor)

2001-01-01

With this funding I produced a web site kurucz.harvard.edu that can also be accessed by FTP. it has a 73GB disk that holds all of my atomic and diatomic molecular data, my tables of distribution function opacities, my grids of model atmospheres, colors, fluxes, etc., my programs that are ready for distribution, and most of my recent papers. Atlases and computed spectra will be added as they are completed. New atomic and molecular calculations will be added as they are completed.

Structure determination of the ordered (2 × 1) phase of NiSi surface alloy on Ni(111) using low-energy electron diffraction

NASA Astrophysics Data System (ADS)

Sazzadur Rahman, Md.; Amirul Islam, Md.; Saha, Bidyut Baran; Nakagawa, Takeshi; Mizuno, Seigi

2015-12-01

The (2 × 1) structure of the two-dimensional nickel silicide surface alloy on Ni(111) was investigated using quantitative low-energy electron diffraction analysis. The unit cell of the determined silicide structure contains one Si and one Ni atom, corresponding to a chemical formula of NiSi. The Si atoms adopt substitutional face-centered cubic hollow sites on the Ni(111) substrate. The Ni-Si bond lengths were determined to be 2.37 and 2.34 Å. Both the alloy surface and the underlying first layers of Ni atoms exhibit slight corrugation. The Ni-Si interlayer distance is smaller than the Ni-Ni interlayer distance, which indicates that Si atoms and underlying Ni atoms strongly interact.

Structural plasticity: how intermetallics deform themselves in response to chemical pressure, and the complex structures that result.

PubMed

Berns, Veronica M; Fredrickson, Daniel C

2014-10-06

Interfaces between periodic domains play a crucial role in the properties of metallic materials, as is vividly illustrated by the way in which the familiar malleability of many metals arises from the formation and migration of dislocations. In complex intermetallics, such interfaces can occur as an integral part of the ground-state crystal structure, rather than as defects, resulting in such marvels as the NaCd2 structure (whose giant cubic unit cell contains more than 1000 atoms). However, the sources of the periodic interfaces in intermetallics remain mysterious, unlike the dislocations in simple metals, which can be associated with the exertion of physical stresses. In this Article, we propose and explore the concept of structural plasticity, the hypothesis that interfaces in complex intermetallic structures similarly result from stresses, but ones that are inherent in a defect-free parent structure, rather than being externally applied. Using DFT-chemical pressure analysis, we show how the complex structures of Ca2Ag7 (Yb2Ag7 type), Ca14Cd51 (Gd14Ag51 type), and the 1/1 Tsai-type quasicrystal approximant CaCd6 (YCd6 type) can all be traced to large negative pressures around the Ca atoms of a common progenitor structure, the CaCu5 type with its simple hexagonal 6-atom unit cell. Two structural paths are found by which the compounds provide relief to the Ca atoms' negative pressures: a Ca-rich pathway, where lower coordination numbers are achieved through defects eliminating transition metal (TM) atoms from the structure; and a TM-rich path, along which the addition of spacer Cd atoms provides the Ca coordination environments greater independence from each other as they contract. The common origins of these structures in the presence of stresses within a single parent structure highlights the diverse paths by which intermetallics can cope with competing interactions, and the role that structural plasticity may play in navigating this diversity.

Challenges in NMR-based structural genomics

NASA Astrophysics Data System (ADS)

Sue, Shih-Che; Chang, Chi-Fon; Huang, Yao-Te; Chou, Ching-Yu; Huang, Tai-huang

2005-05-01

Understanding the functions of the vast number of proteins encoded in many genomes that have been completely sequenced recently is the main challenge for biologists in the post-genomics era. Since the function of a protein is determined by its exact three-dimensional structure it is paramount to determine the 3D structures of all proteins. This need has driven structural biologists to undertake the structural genomics project aimed at determining the structures of all known proteins. Several centers for structural genomics studies have been established throughout the world. Nuclear magnetic resonance (NMR) spectroscopy has played a major role in determining protein structures in atomic details and in a physiologically relevant solution state. Since the number of new genes being discovered daily far exceeds the number of structures determined by both NMR and X-ray crystallography, a high-throughput method for speeding up the process of protein structure determination is essential for the success of the structural genomics effort. In this article we will describe NMR methods currently being employed for protein structure determination. We will also describe methods under development which may drastically increase the throughput, as well as point out areas where opportunities exist for biophysicists to make significant contribution in this important field.

Atomic moments in Mn 2CoAl thin films analyzed by X-ray magnetic circular dichroism

DOE PAGES

Jamer, M. E.; Assaf, B. A.; Sterbinsky, G. E.; ...

2014-12-05

Spin gapless semiconductors are known to be strongly affected by structural disorder when grown epitaxially as thin films. The magnetic properties of Mn 2CoAl thin films grown on GaAs (001) substrates are investigated here as a function of annealing. This study investigates the atomic-specific magnetic moments of Mn and Co atoms measured through X-ray magnetic circular dichroism as a function of annealing and the consequent structural ordering. Results indicate that the structural distortion mainly affects the Mn atoms as seen by the reduction of the magnetic moment from its predicted value.

Validation and extraction of molecular-geometry information from small-molecule databases.

PubMed

Long, Fei; Nicholls, Robert A; Emsley, Paul; Graǽulis, Saulius; Merkys, Andrius; Vaitkus, Antanas; Murshudov, Garib N

2017-02-01

A freely available small-molecule structure database, the Crystallography Open Database (COD), is used for the extraction of molecular-geometry information on small-molecule compounds. The results are used for the generation of new ligand descriptions, which are subsequently used by macromolecular model-building and structure-refinement software. To increase the reliability of the derived data, and therefore the new ligand descriptions, the entries from this database were subjected to very strict validation. The selection criteria made sure that the crystal structures used to derive atom types, bond and angle classes are of sufficiently high quality. Any suspicious entries at a crystal or molecular level were removed from further consideration. The selection criteria included (i) the resolution of the data used for refinement (entries solved at 0.84 Å resolution or higher) and (ii) the structure-solution method (structures must be from a single-crystal experiment and all atoms of generated molecules must have full occupancies), as well as basic sanity checks such as (iii) consistency between the valences and the number of connections between atoms, (iv) acceptable bond-length deviations from the expected values and (v) detection of atomic collisions. The derived atom types and bond classes were then validated using high-order moment-based statistical techniques. The results of the statistical analyses were fed back to fine-tune the atom typing. The developed procedure was repeated four times, resulting in fine-grained atom typing, bond and angle classes. The procedure will be repeated in the future as and when new entries are deposited in the COD. The whole procedure can also be applied to any source of small-molecule structures, including the Cambridge Structural Database and the ZINC database.

Atomic and electronic structures of Si(1 1 1)-(√3 x √3)R30°-Au and (6 × 6)-Au surfaces.

PubMed

Patterson, C H

2015-12-02

Si(1 1 1)-Au surfaces with around one monolayer of Au exhibit many ordered structures and structures containing disordered domain walls. Hybrid density functional theory (DFT) calculations presented here reveal the origin of these complex structures and tendency to form domain walls. The conjugate honeycomb chain trimer (CHCT) structure of the [Formula: see text]-Au phase contains Si atoms with non-bonding surface states which can bind Au atoms in pairs in interstices of the CHCT structure and make this surface metallic. Si adatoms adsorbed on the [Formula: see text]-Au surface induce a gapped surface through interaction with the non-bonding states. Adsorption of extra Au atoms in interstitial sites of the [Formula: see text]-Au surface is stabilized by interaction with the non-bonding orbitals and leads to higher coverage ordered structures including the [Formula: see text]-Au phase. Extra Au atoms bound in interstitial sites of the [Formula: see text]-Au surface result in top layer Si atoms with an SiAu4 butterfly wing configuration. The structure of a [Formula: see text]-Au phase, whose in-plane top atomic layer positions were previously determined by an electron holography technique (Grozea et al 1998 Surf. Sci. 418 32), is calculated using total energy minimization. The Patterson function for this structure is calculated and is in good agreement with data from an in-plane x-ray diffraction study (Dornisch et al 1991 Phys. Rev. B 44 11221). Filled and empty state scanning tunneling microscopy (STM) images are calculated for domain walls and the [Formula: see text]-Au structure. The [Formula: see text]-Au phase is 2D chiral and this is evident in computed and actual STM images. [Formula: see text]-Au and domain wall structures contain the SiAu4 motif with a butterfly wing shape. Chemical bonding within the Si-Au top layers of the [Formula: see text]-Au and [Formula: see text]-Au surfaces is analyzed and an explanation for the SiAu4 motif structure is given.

Molecular dynamics investigation of dynamical heterogeneity and local structure in the supercooled liquid and glass states of Al

NASA Astrophysics Data System (ADS)

Li, Maozhi; Wang, Cai-Zhuang; Mendelev, Mikhail I.; Ho, Kai-Ming

2008-05-01

Molecular dynamics simulations are performed to study the structure and dynamical heterogeneity in the liquid and glass states of Al using a frequently employed embedded atom potential. While the pair correlation function of the glass and liquid states displays only minor differences, the icosahedral short-range order (ISRO) and the dynamics of the two states are very different. The ISRO is much stronger in the glass than in the liquid. It is also found that both the most mobile and the most immobile atoms in the glass state tend to form clusters, and the clusters formed by the immobile atoms are more compact. In order to investigate the local environment of each atom in the liquid and glass states, a local density is defined to characterize the local atomic packing. There is a strong correlation between the local packing density and the mobility of the atoms. These results indicate that dynamical heterogeneity in glasses is directly correlated to the local structure. We also analyze the diffusion mechanisms of atoms in the liquid and glass states. It is found that for the mobile atoms in the glass state, initially they are confined in the cages formed by their nearest neighbors and vibrating. On the time scale of β relaxation, the mobile atoms try to break up the cage confinement and hop into new cages. In the supercooled liquid states, however, atoms continuously diffuse. Furthermore, it is found that on the time scale of β relaxation, some of the mobile atoms in the glass state cooperatively hop, which is facilitated by the stringlike cluster structures. On the longer time scale, it is found that a certain fraction of atoms can simultaneously hop, although they are not nearest neighbors. Further analysis shows that these hopping atoms form big and more compact clusters than the characterized most mobile atoms. The cooperative rearrangement of these big compact clusters might facilitate the simultaneous hopping of atoms in the glass states on the long time scale.

Single crystal synthesis and magnetism of the Ba Ln 2O 4 family ( Ln = lanthanide)

DOE PAGES

Besara, Tiglet; Lundberg, Matthew S.; Sun, Jifeng; ...

2014-05-27

The series of compounds in the Ba Ln 2O 4 family (Ln = La–Lu, Y) has been synthesized for the first time in single crystalline form, using a molten metal flux. The series crystallizes in the CaV 2O 4 structure type with primitive orthorhombic symmetry (space group Pnma, #62), and a complete structural study of atomic positions, bonds, angles, and distortions across the lanthanide series is presented. With the exception of the Y, La, Eu, and Lu members, magnetic susceptibility measurements were performed between 2 K and 300 K. BaCe 2O 4 and BaYb 2O 4 display large crystal fieldsmore » effects and suppression of magnetic ordering. As a result, all compounds show signs of magnetic frustration due to the trigonal arrangements of the trivalent lanthanide cations in the structure.« less

Synaptic Neurotransmitter-Gated Receptors

PubMed Central

Smart, Trevor G.; Paoletti, Pierre

2012-01-01

Since the discovery of the major excitatory and inhibitory neurotransmitters and their receptors in the brain, many have deliberated over their likely structures and how these may relate to function. This was initially satisfied by the determination of the first amino acid sequences of the Cys-loop receptors that recognized acetylcholine, serotonin, GABA, and glycine, followed later by similar determinations for the glutamate receptors, comprising non-NMDA and NMDA subtypes. The last decade has seen a rapid advance resulting in the first structures of Cys-loop receptors, related bacterial and molluscan homologs, and glutamate receptors, determined down to atomic resolution. This now provides a basis for determining not just the complete structures of these important receptor classes, but also for understanding how various domains and residues interact during agonist binding, receptor activation, and channel opening, including allosteric modulation. This article reviews our current understanding of these mechanisms for the Cys-loop and glutamate receptor families. PMID:22233560

Structure and effective interactions in three-component hard sphere liquids.

PubMed

König, A; Ashcroft, N W

2001-04-01

Complete and simple analytical expressions for the partial structure factors of the ternary hard sphere mixture are obtained within the Percus-Yevick approximation and presented as functions of relative packing fractions and relative hard sphere diameters. These solutions follow from the Laplace transform method as applied to multicomponent systems by Lebowitz [Phys. Rev. 133, A895 (1964)]. As an important application, we examine effective interactions in hard sphere liquid mixtures using the microscopic information contained in their partial structure factors. Thus the ensuring pair potential for an effective one-component system is obtained from the correlation functions by using an approximate inversion, and examples of effective potentials for three-component hard sphere mixtures are given. These mixtures may be of particular interest for the study of the packing aspects of melts that form glasses or quasicrystals, since noncrystalline solids often emerge from melts with at least three atomic constituents.

Magic-angle spinning NMR of intact bacteriophages: Insights into the capsid, DNA and their interface

NASA Astrophysics Data System (ADS)

Abramov, Gili; Morag, Omry; Goldbourt, Amir

2015-04-01

Bacteriophages are viruses that infect bacteria. They are complex macromolecular assemblies, which are composed of multiple protein subunits that protect genomic material and deliver it to specific hosts. Various biophysical techniques have been used to characterize their structure in order to unravel phage morphogenesis. Yet, most bacteriophages are non-crystalline and have very high molecular weights, in the order of tens of MegaDaltons. Therefore, complete atomic-resolution characterization on such systems that encompass both capsid and DNA is scarce. In this perspective article we demonstrate how magic-angle spinning solid-state NMR has and is used to characterize in detail bacteriophage viruses, including filamentous and icosahedral phage. We discuss the process of sample preparation, spectral assignment of both capsid and DNA and the use of chemical shifts and dipolar couplings to probe the capsid-DNA interface, describe capsid structure and dynamics and extract structural differences between viruses.

Carbon protrusions on PTFE surface prepared by ion irradiation and chemical defluorination

NASA Astrophysics Data System (ADS)

Kobayashi, T.; Iwaki, M.

2006-01-01

A surface of PTFE was covered with small protrusions by ion-beam irradiation. In this study, we converted PTFE protrusions into carbon protrusions by a defluorination (carbonization) process using sodium vapor. The morphology, composition and structure were analyzed by SEM-EDX, Raman spectroscopy and TEM. The irradiated PTFE sheets were packed in evacuated glass tubes with a sodium block and kept at 473 K for 2-48 h. The samples were then rinsed in HCl and distilled water to remove NaF precipitates. The EDX measurement showed that the NaF precipitates were completely removed by washing, and the percentage of carbon atoms was controlled from 60% to 99% by the treatment. Raman spectra showed that graphite structures grow during the defluorination process. TEM micrographs showed that the protrusions have a bubble structure and are covered with a thin wall. The carbonized protrusions were conductive and grew perpendicular to the substrate.

ShelXle: a Qt graphical user interface for SHELXL.

PubMed

Hübschle, Christian B; Sheldrick, George M; Dittrich, Birger

2011-12-01

ShelXle is a graphical user interface for SHELXL [Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122], currently the most widely used program for small-molecule structure refinement. It combines an editor with syntax highlighting for the SHELXL-associated .ins (input) and .res (output) files with an interactive graphical display for visualization of a three-dimensional structure including the electron density (F(o)) and difference density (F(o)-F(c)) maps. Special features of ShelXle include intuitive atom (re-)naming, a strongly coupled editor, structure visualization in various mono and stereo modes, and a novel way of displaying disorder extending over special positions. ShelXle is completely compatible with all features of SHELXL and is written entirely in C++ using the Qt4 and FFTW libraries. It is available at no cost for Windows, Linux and Mac-OS X and as source code.

Efficient accesses of data structures using processing near memory

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

Jayasena, Nuwan S.; Zhang, Dong Ping; Diez, Paula Aguilera

Systems, apparatuses, and methods for implementing efficient queues and other data structures. A queue may be shared among multiple processors and/or threads without using explicit software atomic instructions to coordinate access to the queue. System software may allocate an atomic queue and corresponding queue metadata in system memory and return, to the requesting thread, a handle referencing the queue metadata. Any number of threads may utilize the handle for accessing the atomic queue. The logic for ensuring the atomicity of accesses to the atomic queue may reside in a management unit in the memory controller coupled to the memory wheremore » the atomic queue is allocated.« less

Size effect on atomic structure in low-dimensional Cu-Zr amorphous systems.

PubMed

Zhang, W B; Liu, J; Lu, S H; Zhang, H; Wang, H; Wang, X D; Cao, Q P; Zhang, D X; Jiang, J Z

2017-08-04

The size effect on atomic structure of a Cu 64 Zr 36 amorphous system, including zero-dimensional small-size amorphous particles (SSAPs) and two-dimensional small-size amorphous films (SSAFs) together with bulk sample was investigated by molecular dynamics simulations. We revealed that sample size strongly affects local atomic structure in both Cu 64 Zr 36 SSAPs and SSAFs, which are composed of core and shell (surface) components. Compared with core component, the shell component of SSAPs has lower average coordination number and average bond length, higher degree of ordering, and lower packing density due to the segregation of Cu atoms on the shell of Cu 64 Zr 36 SSAPs. These atomic structure differences in SSAPs with various sizes result in different glass transition temperatures, in which the glass transition temperature for the shell component is found to be 577 K, which is much lower than 910 K for the core component. We further extended the size effect on the structure and glasses transition temperature to Cu 64 Zr 36 SSAFs, and revealed that the T g decreases when SSAFs becomes thinner due to the following factors: different dynamic motion (mean square displacement), different density of core and surface and Cu segregation on the surface of SSAFs. The obtained results here are different from the results for the size effect on atomic structure of nanometer-sized crystalline metallic alloys.

Multiscale structural changes of atomic order in severely deformed industrial aluminum

NASA Astrophysics Data System (ADS)

Samoilenko, Z. A.; Ivakhnenko, N. N.; Pushenko, E. I.; Pashinskaya, E. G.; Varyukhin, V. N.

2016-02-01

The regularities of multiscale structural changes in the atomic order of the aluminum alloy AD-1 after a severe cold plastic deformation by conventional rolling in smooth rolls or in rolls with relief recesses favorable for shear deformation have been investigated. It has been found that there are four types of structural fractions that differ in scale and perfection of atomic order: crystallographic planes with a long-range order; nanoscale fragments of the planes ( D = 100-300 Å) with an incipient long-range order; smaller groups of atoms ( D = 20-30 Å) of amorphized structure; and the least ordered structural fraction of intercluster medium, keeping only a short-range atomic order (2-3 interatomic distances, 10 Å). The presence of diffuse halo bands in the region of intense Debye lines indicates phase transitions of the order → disorder type with the formation of one to three groups of amorphous clusters with the dominance, in the nanometer scale, of the atomic order characteristic of the family of planes (111), (220), and (311) of crystalline aluminum. We have found a dynamic phase transition with the changing crystallographic order of aluminum, with the matrix structure of a face-centered cubic (FCC) lattice, in the form of nanosized local groups of atoms, that is, the deformation clusters of aluminum with a simple cubic K6 lattice. In the case of conventional rolling, the development of large clusters 50-500 Å in size is observed; however, in the use of rolls with relief recesses, the difference in the sizes of the clusters is one half as much: 50-250 Å. Based on the analysis of the integrated intensity of incoherent X-ray scattering by the samples, we have elucidated the nature of the lowest measured density for the sample subjected to conventional rolling, which consists in the volume concentration of disorderly arranged atoms, the highest of the compared structures, which indicates the formation therein of the greatest amount of fluctuation "voids."

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