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At least 1,783 records · Page 99
All sourcesNASA NTRSDOE OSTI
DOE OSTI2015

Efficient algorithms for Hirshfeld-I charges

A new viewpoint on iterative Hirshfeld charges is presented, whereby the atomic populations obtained from such a scheme are interpreted as such populations which reproduce themselves. This viewpoint yields a self-consistent requirement for the Hirshfeld-I populations rather than being understood as the result of an iterative procedure. Based on this self-consistent requirement, much faster algorithms for Hirshfeld-I charges have been developed. In addition, new atomic reference densities for the Hirshfeld-I procedure are presented. The proposed reference densities are N-representable, display proper atomic shell structure and can be computed for any charged species.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2016

Probing the Crystal Structure and Formation Mechanism of Lanthanide-Doped Upconverting Nanocrystals

Lanthanide (Ln)-doped upconverting nanocrystals (UCNCs), such as NaLnF 4 (with Ln = lanthanide), constitute an important class of nanoscale materials due to their capacity to convert near-infrared photons into near-ultraviolet or visible light. Although under intense investigation for more than a decade, UCNCs have been relatively underexplored especially regarding their crystal structure and mechanisms of formation in organic media. The former is needed to explain the relationship between atomic scale structure and upconversion (UC) properties of UCNCs (i.e., local symmetry for 4f–4f transition probability, Ln 3+ distances for energy migration), while the latter is essential to finely tune the size, morphology, chemical composition, and architecture of well-defined upconverting nanostructures, which constitute the experimental levers to modify the optical properties. In this contribution, we use synchrotron-based diffraction experiments coupled to Rietveld and pair distribution function (PDF) analyses to understand the formation of NaGdF 4 :Yb:Er UCNCs in organic media and to investigate their crystal structure. Our results reveal a complex mechanism of the formation of NaGdF 4 :Yb:Er UCNCs based on chemical reactions involving molecular clusters and in situ-generated, crystalline sodium fluoride at high temperature. Additionally, a detailed crystallographic investigation of NaGdF 4 :Yb:Er UCNCs is presented. Our Rietveld and PDF analyses show that the space group P$\bar{6}$ is the one that best describes the crystal structure of NaGdF 4 :Yb:Er UCNCs contrary to what has been recently proposed. Further, our Rietveld and PDF data reveal the formation of bulk-like crystal structure down to 10 nm with limited distortions. Finally, the results presented in this paper constitute an important step toward the comprehensive understanding of the underlying picture that governs UC properties of lanthanide-doped nanostructures.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2016

Stabilization of a Metastable Fibrous Bi 21.2(1) (Mn 1– x Co x ) 20 Phase with Pseudo-Pentagonal Symmetry Prepared Using a Bi Self-Flux

Bi 21.2(1) (Mn 1– x Co x ) 20 is a new metastable phase which is synthesized via Bi self-flux, adopts a highly fibrous morpholo-gy, and decomposes endothermically near 168 °C. It crystallizes in the orthorhombic space group Imma with unit cell parameters α = 19.067(4) Å, $b$ = 4.6071(10) Å and c = 11.583(4) Å, adopting a low-temperature modification of BiNi-type structure by forming columns along the b-axis. Wave-length-dispersive X-ray spectroscopy (WDS) confirms the presence of Co in the structure, which is found to be 7 at.%. In each column, the transition metal (T) and Bi atoms construct a double-walled nanotubular arrangement of atoms around the disordered central Bi atoms. Electronic structure calculations (LMTO-ASA, LSDA) show that the calculated Fermi level falls into a pseudogap and also indicate a possible low-temperature magnetic ordering in the phase.

36 MATERIALS SCIENCE↗
DOE OSTI2019

CHARMM-GUI Membrane Builder for Complex Biological Membrane Simulations with Glycolipids and Lipoglycans

Glycolipids (such as glycoglycerolipids, glycosphingolipids, and glycosylphosphatidylinositol) and lipoglycans (such as lipopolysaccharides (LPS), lipooligosaccharides (LOS), mycobacterial lipoarabinomannan, and mycoplasma lipoglycans) are typically found on the surface of cell membranes and play crucial roles in various cellular functions. Characterizing their structure and dynamics at the molecular level is essential to understand their biological roles, but systematic generation of glycolipid and lipoglycan structures is challenging because of great variations in lipid structures and glycan sequences (i.e., carbohydrate types and their linkages). To facilitate the generation of all-atom glycolipid/LPS/LOS structures, we have developed Glycolipid Modeler and LPS Modeler in CHARMM-GUI (http://www.charmm-gui.org), a web-based interface that simplifies building of complex biological simulation systems. In addition, we have incorporated these modules into Membrane Builder so that users can readily build a complex symmetric or asymmetric biological membrane system with various glycolipids and LPS/LOS. These tools are expected to be useful in innovative and novel glycolipid/LPS/LOS modeling and simulation research by easing tedious and intricate steps in modeling complex biological systems and shall provide insight into structures, dynamics, and underlying mechanisms of complex glycolipid-/LPS-/LOS-containing biological membrane systems.

Lee, Jumin↗
DOE OSTI2019

Length-Dependent Evolution of Type II Heterojunctions in Bottom-Up-Synthesized Graphene Nanoribbons

The ability to tune the band-edge energies of bottom-up graphene nanoribbons (GNRs) via edge dopants creates new opportunities for designing tailor-made GNR heterojunctions and related nanoscale electronic devices. Here we report the local electronic characterization of type II GNR heterojunctions composed of two different nitrogen edge-doping configurations (carbazole and phenanthridine) that separately exhibit electron-donating and electron-withdrawing behavior. Atomically resolved structural characterization of phenanthridine/carbazole GNR heterojunctions was performed using bond-resolved scanning tunneling microscopy and noncontact atomic force microscopy. Scanning tunneling spectroscopy and first-principles calculations reveal that carbazole and phenanthridine dopant configurations induce opposite upward and downward orbital energy shifts owing to their different electron affinities. Here, the magnitude of the energy offsets observed in carbazole/phenanthridine heterojunctions is dependent on the length of the GNR segments comprising each heterojunction with longer segments leading to larger heterojunction energy offsets. Using a new on-site energy analysis based on Wannier functions, we find that the origin of this behavior is a charge transfer process that reshapes the electrostatic potential profile over a long distance within the GNR heterojunction.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2018

Two-dimensional ferroelectric topological insulators in functionalized atomically thin bismuth layers

We introduce a class of two-dimensional (2D) materials that possess coexisting ferroelectric and topologically insulating orders. Such ferroelectric topological insulators (FETIs) occur in noncentrosymmetric atomic layer structures with strong spin-orbit coupling (SOC). Here, we showcase a prototype 2D FETI in an atomically thin bismuth layer functionalized by CH 2 OH, which exhibits a large ferroelectric polarization that is switchable by a ligand molecule rotation mechanism and a strong SOC that drives a band inversion leading to the topologically insulating state. An external electric field that switches the ferroelectric polarization also tunes the spin texture in the underlying atomic lattice. Moreover, the functionalized bismuth layer exhibits an additional quantum order driven by the valley splitting at the K and K' points in the Brillouin zone stemming from the symmetry breaking and strong SOC in the system, resulting in a remarkable state of matter with the simultaneous presence of the quantum spin Hall and quantum valley Hall effect. These phenomena are predicted to exist in other similarly constructed 2D FETIs, thereby offering a unique quantum material platform for discovering novel physics and exploring innovative applications.

2-dimensional systems↗
DOE OSTI2015

Structural properties of small rhodium clusters

We report a systematic study of the structural properties of rhodium clusters at the atomistic level. A novel global-minimum search algorithm, known as parallel tempering multicanonical basin hopping plus genetic algorithm (PTMBHGA), is used to obtain the geometrical structures with lowest minima at the semi-empirical level where Gupta potential is used to describe the atomic interaction among the rhodium atoms. These structures are then re-optimized at the density functional theory (DFT) level with exchange-correlation energy approximated by Perdew-Burke-Ernzerhof (PBE) generalized gradient approximation (GGA). The structures are optimized for different spin multiplicities. The ones with lowest energies will be taken as ground-state structures. In most cases, we observe only minor changes in the geometry and bond length of the clusters as a result of DFT-level re-optimization. Only in some limited cases, the initial geometries obtained from the PTMBHGA are modified by the re-optimization. The variation of structural properties, such as ground-state geometry, symmetry and binding energy, with respect to the cluster size is studied and agreed well with other results available in the literature.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2026

Exploration of the Electronic and Catalytic Properties of [Co 5 MS 8 (PEt 3 ) 5 ] 1+ Nanoclusters: A Computational Study

Recent studies have demonstrated the relative stability of undercoordinated hexanuclear cobalt sulfide nanoclusters (NCs) with different charge states. Considering that these small metal NCs have atomically precise structures and high reactivity due to the open shell of the transition metals, and provide selectivity toward ligand loss, they are a vital model for catalysis. In this paper, the electronic structures of these NCs are investigated. These NCs are then used as the reference state to analyze the catalytic properties with respect to hydrogen evolution reaction (HER) and CO 2 reduction (CO 2 R). Further, to understand the effect of heteroatom incorporation, the geometry and reactivity of ten different metal dopants are analyzed. This work shows that the type of metal incorporation greatly affects the electronic structure and formation energies for ligand binding and catalysis. Particularly, the d-orbital occupancy in the cobalt atoms remains largely unchanged, while the heteroatom greatly influences the reactivity of the undercoordinated NCs. Most notably, this work highlights that transition metals in [Co 5 MS 8 (PEt 3 ) 5 ] 1+ NCs would competitively prefer electrochemical adsorption of H over COOH, while the main group metals prefer COOH adsorption.

catalysis↗
DOE OSTI2015

Roles of dynamical symmetry breaking in driving oblate-prolate transitions of atomic clusters

This paper explores the driving mechanisms for structural transitions of atomic clusters between oblate and prolate isomers. We employ the hyperspherical coordinates to investigate structural dynamics of a seven-atom cluster at a coarse-grained level in terms of the dynamics of three gyration radii and three principal axes, which characterize overall mass distributions of the cluster. Dynamics of gyration radii is governed by two kinds of forces. One is the potential force originating from the interactions between atoms. The other is the dynamical forces called the internal centrifugal forces, which originate from twisting and shearing motions of the system. The internal centrifugal force arising from twisting motions has an effect of breaking the symmetry between two gyration radii. As a result, in an oblate isomer, activation of the internal centrifugal force that has the effect of breaking the symmetry between the two largest gyration radii is crucial in triggering structural transitions into prolate isomers. In a prolate isomer, on the other hand, activation of the internal centrifugal force that has the effect of breaking the symmetry between the two smallest gyration radii is crucial in triggering structural transitions into oblate isomers. Activation of a twisting motion that switches the movement patterns of three principal axes is also important for the onset of structural transitions between oblate and prolate isomers. Based on these trigger mechanisms, we finally show that selective activations of specific gyration radii and twisting motions, depending on the isomer of the cluster, can effectively induce structural transitions of the cluster. The results presented here could provide further insights into the control of molecular reactions.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2015

Evolution Of Lattice Structure And Chemical Composition Of The Surface Reconstruction Layer In Li1.2Ni0.2Mn0.6O2 Cathode Material For Lithium Ion Batteries

Voltage and capacity fading of layer structured lithium and manganese rich (LMR) transition metal oxide is directly related to the structural and composition evolution of the material during the cycling of the battery. However, understanding such evolution at atomic level remains elusive. Based on atomic level structural imaging, elemental mapping of the pristine and cycled samples and density functional theory calculations, it is found that accompanying the hoping of Li ions is the simultaneous migration of Ni ions towards the surface from the bulk lattice, leading to the gradual depletion of Ni in the bulk lattice and thickening of a Ni enriched surface reconstruction layer (SRL). Furthermore, Ni and Mn also exhibit concentration partitions within the thin layer of SRL in the cycled samples where Ni is almost depleted at the very surface of the SRL, indicating the preferential dissolution of Ni ions in the electrolyte. Accompanying the elemental composition evolution, significant structural evolution is also observed and identified as a sequential phase transition of C2/m →I41→Spinel. For the first time, it is found that the surface facet terminated with pure cation is more stable than that with a mixture of cation and anion. These findings firmly established how the elemental species in the lattice of LMR cathode transfer from the bulk lattice to surface layer and further into the electrolyte, clarifying the long standing confusion and debate on the structure and chemistry of the surface layer and their correlation with the voltage fading and capacity decaying of LMR cathode. Therefore, this work provides critical insights for designing of cathode materials with both high capacity and voltage stability during cycling.

Environmental Molecular Sciences Laboratory↗
DOE OSTI2015

Hydrogen reverses the clustering tendency of carbon in amorphous silicon oxycarbide

Amorphous silicon oxycarbide (SiOC) is of great technological interest. However, its atomic-level structure is not well understood. Using density functional theory calculations, we show that the clustering tendency of C atoms in SiOC is extremely sensitive to hydrogen (H): without H, the C-C interaction is attractive, leading to enrichment of aggregated SiC 4 tetrahedral units; with hydrogen, the C-C interaction is repulsive, leading to enrichment of randomly distributed SiCO 3 tetrahedral units. Our results suggest that conflicting experimental characterizations of C distributions may be due to differing amounts of H present in the samples investigated. Our work also opens a path for tailoring the properties of SiOC by using the total H content to control the C distribution.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2015

Crystal Structures and Small-angle X-ray Scattering Analysis of UDP-galactopyranose Mutase from the Pathogenic Fungus Aspergillus fumigatus

UDP-galactopyranose mutase (UGM) is a flavoenzyme that catalyzes the conversion of UDP-galactopyranose to UDP-galactofuranose, which is a central reaction in galactofuranose biosynthesis. Galactofuranose has never been found in humans but is an essential building block of the cell wall and extracellular matrix of many bacteria, fungi, and protozoa. The importance of UGM for the viability of many pathogens and its absence in humans make UGM a potential drug target. Here we report the first crystal structures and small-angle x-ray scattering data for UGM from the fungus Aspergillus fumigatus, the causative agent of aspergillosis. The structures reveal that Aspergillus UGM has several extra secondary and tertiary structural elements that are not found in bacterial UGMs yet are important for substrate recognition and oligomerization. Small-angle x-ray scattering data show that Aspergillus UGM forms a tetramer in solution, which is unprecedented for UGMs. The binding of UDP or the substrate induces profound conformational changes in the enzyme. Two loops on opposite sides of the active site move toward each other by over 10 {angstrom} to cover the substrate and create a closed active site. The degree of substrate-induced conformational change exceeds that of bacterial UGMs and is a direct consequence of the unique quaternary structure of Aspergillus UGM. Galactopyranose binds at the re face of the FAD isoalloxazine with the anomeric carbon atom poised for nucleophilic attack by the FAD N5 atom. The structural data provide new insight into substrate recognition and the catalytic mechanism and thus will aid inhibitor design.

Dhatwalia, Richa↗
DOE OSTI2019

Density-driven ionization potential depression and its effects on material properties

Changes in ionization potential at high density drive changes in material transport properties and often in crystal structure and equation of state. Current models used to describe and predict these effects have not been tested in regimes much beyond ~200 GPa, because of limitations in experimental techniques. Now, however, high-energy laser facilities with flexible pulse-shaping capabilities have made it possible to reach pressures in the 1000 GPa range, while maintaining temperatures below 1 eV. We have used these new methods to ramp-compress cobalt and magnesium and have measured shifts in the k-shell emission lines to infer changes in ionization stage, and x-ray diffraction to measure changes in crystal structure. In the case of cobalt, commonly-used detailed models for effective ionization based on isolated-atom electronic structure are shown to give the wrong answer, while self-consistent density-functional-theory-based models reproduce the data well. In the case of magnesium, zero-kelvin density functional theory predictions of density-driven electron localization in lattice interstitials (so-called electride phases) at high pressure are found to be too simple to describe material evolution along a laser ramp-compression pathway. Instead, by a combination of experiment, first-principles theory and evolutionary structure-searching algorithms, we have discovered several unexpected lower-symmetry metastable structures. First principles results find that the density of localized interstitial charge in the high-pressure magnesium phases is too low to be measurable with x-ray diffraction, and the body of theory work which has predicted high pressure electride phases for many systems, based on analysis of electron localization function, needs to be re-examined.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2015

Tungsten Data for Current and Future Uses in Fusion and Plasma Science

We give a brief overview of our recent experimental and theoretical work involving highly charged tungsten ions in high-temperature magnetically confined plasmas. Our work includes X-ray and extreme ultraviolet spectroscopy, state-of-the-art structure calculations, the generation of dielectronic recombination rate coefficients, collisional-radiative spectral modeling and assessments of the atomic data need for X-ray diagnostics monitoring of the parameters of the core plasma of future tokamaks, such as ITER. We give examples of our recent results in these areas.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2014

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

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 content 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. %.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2018

2-Allyloxy/propargyloxypyridines: synthesis, structure, and biological activity

The alkylation (allylation and propargylation) of 3-cyano-6-dialkylamino-2-pyridones containing a d-annulated ring occurs at the oxygen atom. The structures of the starting compounds and their alkylation products were determined by X-ray diffraction. The neurotropic and antimicrobial activity of alkylation products was examined.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2016

Broadband cross-polarization-based heteronuclear dipolar recoupling for structural and dynamic NMR studies of rigid and soft solids

Dipolar recoupling is an essential part of current solid-state NMR methodology for probing atomic-resolution structure and dynamics in solids and soft matter. Recently described magic-echo amplitude- and phase-modulated cross-polarization heteronuclear recoupling strategy aims at efficient and robust recoupling in the entire range of coupling constants both in rigid and highly dynamic molecules. In the present study, the properties of this recoupling technique are investigated by theoretical analysis, spin-dynamics simulation, and experimentally. The resonance conditions and the efficiency of suppressing the rf field errors are examined and compared to those for other recoupling sequences based on similar principles. The experimental data obtained in a variety of rigid and soft solids illustrate the scope of the method and corroborate the results of analytical and numerical calculations. The technique benefits from the dipolar resolution over a wider range of coupling constants compared to that in other state-of-the-art methods and thus is advantageous in studies of complex solids with a broad range of dynamic processes and molecular mobility degrees.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2026

Locating the atoms at the hard-soft interface of gold nanoparticles

Surface structure affects the growth, shape and properties of nanoparticles. In wet chemical syntheses, metal additives and surfactants are used to modify surfaces and guide nanocrystal growth. To understand this process, it is critical to understand how the surface structure, and hence its energy, is modified. However, measuring the type and arrangement of atoms at hard-soft interfaces on nanoscale surfaces, especially in the presence of surfactants, is extremely challenging. Here, we determine the atomic structure of the hard-soft interface in a metallic nanoparticle by developing low-dose imaging conditions in four-dimensional scanning transmission electron microscopy that are preferentially sensitive to surface adatoms. By revealing experimentally the copper additives and bromide surfactant counterion at the surface of a gold nanocuboid and quantifying their interatomic distances, our direct, low-dose imaging method provides atomic-level understanding of chemically sophisticated nanomaterial surface structures. These measurements of the atomic structure of the hard-soft interface provide the information necessary to understand and quantify surface chemistries and energies and their pivotal role in nanocrystal growth.

Li, Weilun [Monash University, Melbourne, VIC (Aus↗