Interface architecture determined electrocatalytic activity of Pt on vertically oriented TiO(2) nanotubes.

PubMed

Rettew, Robert E; Allam, Nageh K; Alamgir, Faisal M

2011-02-01

The surface atomic structure and chemical state of Pt is consequential in a variety of surface-intensive devices. Herein we present the direct interrelationship between the growth scheme of Pt films, the resulting atomic and electronic structure of Pt species, and the consequent activity for methanol electro-oxidation in Pt/TiO(2) nanotube hybrid electrodes. X-ray photoelectron spectroscopy (XPS) and X-ray absorption spectroscopy (XAS) measurements were performed to relate the observed electrocatalytic activity to the oxidation state and the atomic structure of the deposited Pt species. The atomic structure as well as the oxidation state of the deposited Pt was found to depend on the pretreatment of the TiO(2) nanotube surfaces with electrodeposited Cu. Pt growth through Cu replacement increases Pt dispersion, and a separation of surface Pt atoms beyond a threshold distance from the TiO(2) substrate renders them metallic, rather than cationic. The increased dispersion and the metallic character of Pt results in strongly enhanced electrocatalytic activity toward methanol oxidation. This study points to a general phenomenon whereby the growth scheme and the substrate-to-surface-Pt distance dictates the chemical state of the surface Pt atoms, and thereby, the performance of Pt-based surface-intensive devices.

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.

Improved protein surface comparison and application to low-resolution protein structure data.

PubMed

Sael, Lee; Kihara, Daisuke

2010-12-14

Recent advancements of experimental techniques for determining protein tertiary structures raise significant challenges for protein bioinformatics. With the number of known structures of unknown function expanding at a rapid pace, an urgent task is to provide reliable clues to their biological function on a large scale. Conventional approaches for structure comparison are not suitable for a real-time database search due to their slow speed. Moreover, a new challenge has arisen from recent techniques such as electron microscopy (EM), which provide low-resolution structure data. Previously, we have introduced a method for protein surface shape representation using the 3D Zernike descriptors (3DZDs). The 3DZD enables fast structure database searches, taking advantage of its rotation invariance and compact representation. The search results of protein surface represented with the 3DZD has showngood agreement with the existing structure classifications, but some discrepancies were also observed. The three new surface representations of backbone atoms, originally devised all-atom-surface representation, and the combination of all-atom surface with the backbone representation are examined. All representations are encoded with the 3DZD. Also, we have investigated the applicability of the 3DZD for searching protein EM density maps of varying resolutions. The surface representations are evaluated on structure retrieval using two existing classifications, SCOP and the CE-based classification. Overall, the 3DZDs representing backbone atoms show better retrieval performance than the original all-atom surface representation. The performance further improved when the two representations are combined. Moreover, we observed that the 3DZD is also powerful in comparing low-resolution structures obtained by electron microscopy.

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.

Direct observation for atomically flat and ordered vertical {111} side-surfaces on three-dimensionally figured Si(110) substrate using scanning tunneling microscopy

NASA Astrophysics Data System (ADS)

Yang, Haoyu; Hattori, Azusa N.; Ohata, Akinori; Takemoto, Shohei; Hattori, Ken; Daimon, Hiroshi; Tanaka, Hidekazu

2017-11-01

A three-dimensional Si{111} vertical side-surface structure on a Si(110) wafer was fabricated by reactive ion etching (RIE) followed by wet-etching and flash-annealing treatments. The side-surface was studied with scanning tunneling microscopy (STM) in atomic scale for the first time, in addition to atomic force microscopy (AFM), scanning electron microscopy (SEM), and low-energy electron diffraction (LEED). AFM and SEM showed flat and smooth vertical side-surfaces without scallops, and STM proved the realization of an atomically-flat 7 × 7-reconstructed structure, under optimized RIE and wet-etching conditions. STM also showed that a step-bunching occurred on the produced {111} side-surface corresponding to a reversely taped side-surface with a tilt angle of a few degrees, but did not show disordered structures. Characteristic LEED patterns from both side- and top-reconstructed surfaces were also demonstrated.

Atomic and electronic structures of Si(1 1 1)-\\left(\\sqrt{\\mathbf{3}}\\times\\sqrt{\\mathbf{3}}\\right)\\text{R}\\mathbf{3}{{\\mathbf{0}}^{\\circ}} -Au and (6 × 6)-Au surfaces

NASA Astrophysics Data System (ADS)

Patterson, C. H.

2015-12-01

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 \\sqrt{3} -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 \\sqrt{3} -Au surface induce a gapped surface through interaction with the non-bonding states. Adsorption of extra Au atoms in interstitial sites of the \\sqrt{3} -Au surface is stabilized by interaction with the non-bonding orbitals and leads to higher coverage ordered structures including the ≤ft(6× 6\\right) -Au phase. Extra Au atoms bound in interstitial sites of the \\sqrt{3} -Au surface result in top layer Si atoms with an SiAu4 butterfly wing configuration. The structure of a ≤ft(6× 6\\right) -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 ≤ft(6× 6\\right) -Au structure. The ≤ft(6× 6\\right) -Au phase is 2D chiral and this is evident in computed and actual STM images. ≤ft(6× 6\\right) -Au and domain wall structures contain the SiAu4 motif with a butterfly wing shape. Chemical bonding within the Si-Au top layers of the \\sqrt{3} -Au and ≤ft(6× 6\\right) -Au surfaces is analyzed and an explanation for the SiAu4 motif structure is given.

Surface structure and chemistry of Pt/Cu/Pt(1 1 1) near surface alloy model catalyst in CO

NASA Astrophysics Data System (ADS)

Zeng, Shibi; Nguyen, Luan; Cheng, Fang; Liu, Lacheng; Yu, Ying; Tao, Franklin (Feng)

2014-11-01

Near surface alloy (NSA) model catalyst Pt/Cu/Pt(1 1 1) was prepared on Pt(1 1 1) through a controlled vapor deposition of Cu atoms. Different coordination environments of Pt atoms of the topmost Pt layer with the underneath Cu atoms in the subsurface result in different local electronic structures of surface Pt atoms. Surface structure and chemistry of the NAS model catalyst in Torr pressure of CO were studied with high pressure scanning tunneling microscopy (HP-STM) and ambient pressure X-ray photoelectron spectroscopy (AP-XPS). In Torr pressure of CO, the topmost Pt layer of Pt/Cu/Pt(1 1 1) is restructured to thin nanoclusters with size of about 1 nm. Photoemission feature of O 1s of CO on Pt/Cu/Pt(1 1 1) suggests CO adsorbed on both edge and surface of these formed nanoclusters. This surface is active for CO oxidation. Atomic layers of carbon are formed on Pt/Cu/Pt(1 1 1) at 573 K in 2 Torr of CO.

Chemically directing d-block heterometallics to nanocrystal surfaces as molecular beacons of surface structure

DOE PAGES

Rosen, Evelyn L.; Gilmore, Keith; Sawvel, April M.; ...

2015-07-28

Our understanding of structure and bonding in nanoscale materials is incomplete without knowledge of their surface structure. Needed are better surveying capabilities responsive not only to different atoms at the surface, but also their respective coordination environments. We report here that d-block organometallics, when placed at nanocrystal surfaces through heterometallic bonds, serve as molecular beacons broadcasting local surface structure in atomic detail. This unique ability stems from their elemental specificity and the sensitivity of their d-orbital level alignment to local coordination environment, which can be assessed spectroscopically. Re-surfacing cadmium and lead chalcogenide nanocrystals with iron- or ruthenium-based molecular beacons ismore » readily accomplished with trimethylsilylated cyclopentadienyl metal carbonyls. For PbSe nanocrystals with iron-based beacons, we show how core-level X-ray spectroscopies and DFT calculations enrich our understanding of both charge and atomic reorganization at the surface when beacons are bound.« less

Improved protein surface comparison and application to low-resolution protein structure data

PubMed Central

2010-01-01

Background Recent advancements of experimental techniques for determining protein tertiary structures raise significant challenges for protein bioinformatics. With the number of known structures of unknown function expanding at a rapid pace, an urgent task is to provide reliable clues to their biological function on a large scale. Conventional approaches for structure comparison are not suitable for a real-time database search due to their slow speed. Moreover, a new challenge has arisen from recent techniques such as electron microscopy (EM), which provide low-resolution structure data. Previously, we have introduced a method for protein surface shape representation using the 3D Zernike descriptors (3DZDs). The 3DZD enables fast structure database searches, taking advantage of its rotation invariance and compact representation. The search results of protein surface represented with the 3DZD has showngood agreement with the existing structure classifications, but some discrepancies were also observed. Results The three new surface representations of backbone atoms, originally devised all-atom-surface representation, and the combination of all-atom surface with the backbone representation are examined. All representations are encoded with the 3DZD. Also, we have investigated the applicability of the 3DZD for searching protein EM density maps of varying resolutions. The surface representations are evaluated on structure retrieval using two existing classifications, SCOP and the CE-based classification. Conclusions Overall, the 3DZDs representing backbone atoms show better retrieval performance than the original all-atom surface representation. The performance further improved when the two representations are combined. Moreover, we observed that the 3DZD is also powerful in comparing low-resolution structures obtained by electron microscopy. PMID:21172052

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.

Quantitative characterization of the atomic-scale structure of oxyhydroxides in rusts formed on steel surfaces

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

Saito, M.; Suzuki, S.; Kimura, M.

Quantitative X-ray structural analysis coupled with anomalous X-ray scattering has been used for characterizing the atomic-scale structure of rust formed on steel surfaces. Samples were prepared from rust layers formed on the surfaces of two commercial steels. X-ray scattered intensity profiles of the two samples showed that the rusts consisted mainly of two types of ferric oxyhydroxide, {alpha}-FeOOH and {gamma}-FeOOH. The amounts of these rust components and the realistic atomic arrangements in the components were estimated by fitting both the ordinary and the environmental interference functions with a model structure calculated using the reverse Monte Carlo simulation technique. The twomore » rust components were found to be the network structure formed by FeO{sub 6} octahedral units, the network structure itself deviating from the ideal case. The present results also suggest that the structural analysis method using anomalous X-ray scattering and the reverse Monte Carlo technique is very successful in determining the atomic-scale structure of rusts formed on the steel surfaces.« less

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.

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.

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

NASA Astrophysics Data System (ADS)

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

2017-11-01

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

Density Functional Theory Study of Leaching Performance of Different Acids on Pyrochlore (100) Surface

NASA Astrophysics Data System (ADS)

Yang, Xiuli; Fang, Qing; Ouyang, Hui

2018-04-01

Pyrochlore leaching using hydrofluoric, sulfuric, and hydrochloric acids has been studied via experimental methods for years, but the interactions between niobium atoms on the pyrochlore surface and different acids have not been investigated. In this work, first-principles calculations based on density functional theory were used to elucidate the leaching performance of these three acids from the viewpoint of geometrical and electronic structures. The calculation results indicate that sulfate, chloride, and fluoride anions influence the geometric structure of pyrochlore (100) to different extents, decreasing in the order: sulfate, fluoride, chloride. Orbitals of O1 and O2 atoms of sulfate hybridized with those of surface niobium atom. Fluorine orbitals hybridized with those of surface niobium atoms. However, no obvious overlap exists between any orbitals of chlorine and surface niobium, revealing that chlorine does not interact chemically with surface niobium atoms.

Density Functional Theory Study of Leaching Performance of Different Acids on Pyrochlore (100) Surface

NASA Astrophysics Data System (ADS)

Yang, Xiuli; Fang, Qing; Ouyang, Hui

2018-06-01

Pyrochlore leaching using hydrofluoric, sulfuric, and hydrochloric acids has been studied via experimental methods for years, but the interactions between niobium atoms on the pyrochlore surface and different acids have not been investigated. In this work, first-principles calculations based on density functional theory were used to elucidate the leaching performance of these three acids from the viewpoint of geometrical and electronic structures. The calculation results indicate that sulfate, chloride, and fluoride anions influence the geometric structure of pyrochlore (100) to different extents, decreasing in the order: sulfate, fluoride, chloride. Orbitals of O1 and O2 atoms of sulfate hybridized with those of surface niobium atom. Fluorine orbitals hybridized with those of surface niobium atoms. However, no obvious overlap exists between any orbitals of chlorine and surface niobium, revealing that chlorine does not interact chemically with surface niobium atoms.

X-Ray photoelectron diffraction and photoelectron holography as methods for investigating the local atomic structure of the surface of solids

NASA Astrophysics Data System (ADS)

Kuznetsov, M. V.; Ogorodnikov, I. I.; Vorokh, A. S.

2014-01-01

The state-of-the-art theory and experimental applications of X-ray photoelectron diffraction (XPD) and photoelectron holography (PH) are discussed. These methods are rapidly progressing and serve to examine the surface atomic structure of solids, including nanostructures formed on surfaces during adsorption of gases, epitaxial film growth, etc. The depth of analysis by these methods is several nanometres, which makes it possible to characterize the positions of atoms localized both on and beneath the surface. A remarkable feature of the XPD and PH methods is their sensitivity to the type of examined atoms and, in the case of high energy resolution, to the particular chemical form of the element under study. The data on experimental applications of XPD and PH to studies of various surface structures are analyzed and generalized. The bibliography includes 121 references.

Atomically Visualizing Elemental Segregation-Induced Surface Alloying and Restructuring

DOE PAGES

Zou, Lianfeng; Li, Jonathan; Zakharov, Dmitri; ...

2017-12-01

Using in situ transmission electron microscopy that spatially and temporally resolves the evolution of the atomic structure in the surface and subsurface regions, we Find that the surface segregation of Au atoms in a Cu(Au) solid solution results in the nucleation and growth of a (2 × 1) missing-row reconstructed, half-unit-cell thick L1 2 Cu 3Au(110) surface alloy. Our in situ electron microscopy observations and atomistic simulations demonstrate that the (2 × 1) reconstruction of the Cu 3Au(110) surface alloy remains as a stable surface structure as a result of the favored Cu-Au diatom configuration.

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...

Atomic Step Formation on Sapphire Surface in Ultra-precision Manufacturing

PubMed Central

Wang, Rongrong; Guo, Dan; Xie, Guoxin; Pan, Guoshun

2016-01-01

Surfaces with controlled atomic step structures as substrates are highly relevant to desirable performances of materials grown on them, such as light emitting diode (LED) epitaxial layers, nanotubes and nanoribbons. However, very limited attention has been paid to the step formation in manufacturing process. In the present work, investigations have been conducted into this step formation mechanism on the sapphire c (0001) surface by using both experiments and simulations. The step evolutions at different stages in the polishing process were investigated with atomic force microscopy (AFM) and high resolution transmission electron microscopy (HRTEM). The simulation of idealized steps was constructed theoretically on the basis of experimental results. It was found that (1) the subtle atomic structures (e.g., steps with different sawteeth, as well as steps with straight and zigzag edges), (2) the periodicity and (3) the degree of order of the steps were all dependent on surface composition and miscut direction (step edge direction). A comparison between experimental results and idealized step models of different surface compositions has been made. It has been found that the structure on the polished surface was in accordance with some surface compositions (the model of single-atom steps: Al steps or O steps). PMID:27444267

Atomic Step Formation on Sapphire Surface in Ultra-precision Manufacturing

NASA Astrophysics Data System (ADS)

Wang, Rongrong; Guo, Dan; Xie, Guoxin; Pan, Guoshun

2016-07-01

Surfaces with controlled atomic step structures as substrates are highly relevant to desirable performances of materials grown on them, such as light emitting diode (LED) epitaxial layers, nanotubes and nanoribbons. However, very limited attention has been paid to the step formation in manufacturing process. In the present work, investigations have been conducted into this step formation mechanism on the sapphire c (0001) surface by using both experiments and simulations. The step evolutions at different stages in the polishing process were investigated with atomic force microscopy (AFM) and high resolution transmission electron microscopy (HRTEM). The simulation of idealized steps was constructed theoretically on the basis of experimental results. It was found that (1) the subtle atomic structures (e.g., steps with different sawteeth, as well as steps with straight and zigzag edges), (2) the periodicity and (3) the degree of order of the steps were all dependent on surface composition and miscut direction (step edge direction). A comparison between experimental results and idealized step models of different surface compositions has been made. It has been found that the structure on the polished surface was in accordance with some surface compositions (the model of single-atom steps: Al steps or O steps).

Study of solid/liquid and solid/gas interfaces in Cu-isoleucine complex by surface X-ray diffraction

NASA Astrophysics Data System (ADS)

Ferrer, Pilar; Rubio-Zuazo, Juan; Castro, German R.

2013-02-01

The enzymes could be understood like structures formed by amino acids bonded with metals, which act as active sites. The research on the coordination of metal-amino acid complexes will bring light on the behavior of metal enzymes, due to the close relation existing between the atomic structure and the functionality. The Cu-isoleucine bond is considered as a good model system to attain a better insight into the characteristics of naturally occurring copper metalloproteins. The surface structure of metal-amino acid complex could be considered as a more realistic model for real systems under biologic working conditions, since the molecular packing is decreased. In the surface, the structural constrains are reduced, keeping the structural capability of surface complex to change as a function of the surrounding environment. In this work, we present a surface X-ray diffraction study on Cu-isoleucine complex under different ambient conditions. Cu(Ile)2 crystals of about 5 mm × 5 mm × 1 mm have been growth, by seeding method in a supersaturated solution, presenting a surface of high quality. The sample for the surface diffraction study was mounted on a cell specially designed for solid/liquid or solid/gas interface analysis. The Cu-isoleucine crystal was measured under a protective dry N2 gas flow and in contact with a saturated metal amino acid solution. The bulk and the surface signals were compared, showing different atomic structures. In both cases, from surface diffraction data, it is observed that the atomic structure of the top layer undergoes a clear structural deformation. A non-uniform surface relaxation is observed producing an inhomogeneous displacement of the surface atoms towards the surface normal.

Surface determination through atomically resolved secondary-electron imaging

PubMed Central

Ciston, J.; Brown, H. G.; D'Alfonso, A. J.; Koirala, P.; Ophus, C.; Lin, Y.; Suzuki, Y.; Inada, H.; Zhu, Y.; Allen, L. J.; Marks, L. D.

2015-01-01

Unique determination of the atomic structure of technologically relevant surfaces is often limited by both a need for homogeneous crystals and ambiguity of registration between the surface and bulk. Atomically resolved secondary-electron imaging is extremely sensitive to this registration and is compatible with faceted nanomaterials, but has not been previously utilized for surface structure determination. Here we report a detailed experimental atomic-resolution secondary-electron microscopy analysis of the c(6 × 2) reconstruction on strontium titanate (001) coupled with careful simulation of secondary-electron images, density functional theory calculations and surface monolayer-sensitive aberration-corrected plan-view high-resolution transmission electron microscopy. Our work reveals several unexpected findings, including an amended registry of the surface on the bulk and strontium atoms with unusual seven-fold coordination within a typically high surface coverage of square pyramidal TiO5 units. Dielectric screening is found to play a critical role in attenuating secondary-electron generation processes from valence orbitals. PMID:26082275

Surface determination through atomically resolved secondary-electron imaging

DOE PAGES

Ciston, J.; Brown, H. G.; D’Alfonso, A. J.; ...

2015-06-17

We report that unique determination of the atomic structure of technologically relevant surfaces is often limited by both a need for homogeneous crystals and ambiguity of registration between the surface and bulk. Atomically resolved secondary-electron imaging is extremely sensitive to this registration and is compatible with faceted nanomaterials, but has not been previously utilized for surface structure determination. Here we show a detailed experimental atomic-resolution secondary-electron microscopy analysis of the c(6 x 2) reconstruction on strontium titanate (001) coupled with careful simulation of secondary-electron images, density functional theory calculations and surface monolayer-sensitive aberration-corrected plan-view high-resolution transmission electron microscopy. Our workmore » reveals several unexpected findings, including an amended registry of the surface on the bulk and strontium atoms with unusual seven-fold coordination within a typically high surface coverage of square pyramidal TiO 5 units. Lastly, dielectric screening is found to play a critical role in attenuating secondary-electron generation processes from valence orbitals.« less

Dynamic probe of ZnTe(110) surface by scanning tunneling microscopy

PubMed Central

Kanazawa, Ken; Yoshida, Shoji; Shigekawa, Hidemi; Kuroda, Shinji

2015-01-01

The reconstructed surface structure of the II–VI semiconductor ZnTe (110), which is a promising material in the research field of semiconductor spintronics, was studied by scanning tunneling microscopy/spectroscopy (STM/STS). First, the surface states formed by reconstruction by the charge transfer of dangling bond electrons from cationic Zn to anionic Te atoms, which are similar to those of IV and III–V semiconductors, were confirmed in real space. Secondly, oscillation in tunneling current between binary states, which is considered to reflect a conformational change in the topmost Zn–Te structure between the reconstructed and bulk-like ideal structures, was directly observed by STM. Third, using the technique of charge injection, a surface atomic structure was successfully fabricated, suggesting the possibility of atomic-scale manipulation of this widely applicable surface of ZnTe. PMID:27877752

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.

Temperature effects on the atomic structure and kinetics in single crystal electrochemistry

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

Gründer, Yvonne; Markovic, Nenad M.; Thompson, Paul

2015-01-01

The influence of temperature on the atomic structure at the electrochemical interface has been studied using in-situ surface x-ray scattering (SXS) during the formation of metal monolayers on a Au(111) electrode. For the surface reconstruction of Au(111), higher temperatures increase the mobility of surface atoms in the unreconstructed phase which then determines the surface ordering during the formation of the reconstruction. For the underpotential deposition (UPD) systems, the surface diffusion of the depositing metal adatoms is significantly reduced at low temperatures which results in the frustration of ordered structures in the case of Cu UPD, occurring on a Br-modified surface,more » and in the formation of a disordered Ag monolayer during Ag UPD. The results indicate that temperature changes affect the mass transport and diffusion of metal adatoms on the electrode surface. This demonstrates the importance of including temperature as a variable in studying surface structure and reactions at the electrochemical interface.« 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.

Surface atomic structure of alloyed Mn 5Ge 3(0 0 0 1) by scanning tunneling microscopy

NASA Astrophysics Data System (ADS)

Kim, Howon; Jung, Goo-Eun; Yoon, Jong Keon; Chung, Kyung Hoon; Kahng, Se-Jong

Surface atomic structure of Mn 5Ge 3(0 0 0 1) is studied by scanning tunneling microscopy. Hexagonal honeycomb ordering is observed at high energy levels, ∣ E - EF∣ ˜ 1.2 eV, on the flat regions of three-dimensional Mn 5Ge 3 islands. At low energy levels, ∣ E - EF∣ ˜ 0.5 eV, however, atomic images exhibit dot-array and ring-array structures, which show complete and partial contrast inversion, compared to the honeycomb ordering. Experimental observations are discussed on the basis of possible atomic models.

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.

The role of titanium nitride supports for single-atom platinum-based catalysts in fuel cell technology.

PubMed

Zhang, Ren-Qin; Lee, Tae-Hun; Yu, Byung-Deok; Stampfl, Catherine; Soon, Aloysius

2012-12-28

As a first step towards a microscopic understanding of single-Pt atom-dispersed catalysts on non-conventional TiN supports, we present density-functional theory (DFT) calculations to investigate the adsorption properties of Pt atoms on the pristine TiN(100) surface, as well as the dominant influence of surface defects on the thermodynamic stability of platinized TiN. Optimized atomic geometries, energetics, and analysis of the electronic structure of the Pt/TiN system are reported for various surface coverages of Pt. We find that atomic Pt does not bind preferably to the clean TiN surface, but under typical PEM fuel cell operating conditions, i.e. strongly oxidizing conditions, TiN surface vacancies play a crucial role in anchoring the Pt atom for its catalytic function. Whilst considering the energetic stability of the Pt/TiN structures under varying N conditions, embedding Pt at the surface N-vacancy site is found to be the most favorable under N-lean conditions. Thus, the system of embedding Pt at the surface N-vacancy sites on TiN(100) surfaces could be promising catalysts for PEM fuel cells.

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

Computational simulation of the effects of oxygen on the electronic states of hydrogenated 3C-porous SiC

PubMed Central

2012-01-01

A computational study of the dependence of the electronic band structure and density of states on the chemical surface passivation of cubic porous silicon carbide (pSiC) was performed using ab initio density functional theory and the supercell method. The effects of the porosity and the surface chemistry composition on the energetic stability of pSiC were also investigated. The porous structures were modeled by removing atoms in the [001] direction to produce two different surface chemistries: one fully composed of silicon atoms and one composed of only carbon atoms. The changes in the electronic states of the porous structures as a function of the oxygen (O) content at the surface were studied. Specifically, the oxygen content was increased by replacing pairs of hydrogen (H) atoms on the pore surface with O atoms attached to the surface via either a double bond (X = O) or a bridge bond (X-O-X, X = Si or C). The calculations show that for the fully H-passivated surfaces, the forbidden energy band is larger for the C-rich phase than for the Si-rich phase. For the partially oxygenated Si-rich surfaces, the band gap behavior depends on the O bond type. The energy gap increases as the number of O atoms increases in the supercell if the O atoms are bridge-bonded, whereas the band gap energy does not exhibit a clear trend if O is double-bonded to the surface. In all cases, the gradual oxygenation decreases the band gap of the C-rich surface due to the presence of trap-like states. PMID:22913486

Crystalline Structure and Vacancy Ordering across a Surface Phase Transition in Sn/Cu(001).

PubMed

Martínez-Blanco, J; Joco, V; Quirós, C; Segovia, P; Michel, E G

2018-01-18

We report a surface X-ray diffraction study of the crystalline structure changes and critical behavior across the (3√2 × √2)R45° → (√2 × √2)R45° surface phase transition at 360 K for 0.5 monolayers of Sn on Cu(100). The phase transition is of the order-disorder type and is due to the disordering of the Cu atomic vacancies present in the low temperature phase. Two different atomic sites for Sn atoms, characterized by two different heights, are maintained across the surface phase transition.

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

Atomic and electronic structure of the CdTe(111)B–(2√3 × 4) orthogonal surface

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

Bekenev, V. L., E-mail: bekenev@ipms.kiev.ua; Zubkova, S. M.

2017-01-15

The atomic and electronic structure of four variants of Te-terminated CdTe(111)B–(2√3 × 4) orthogonal polar surface (ideal, relaxed, reconstructed, and reconstructed with subsequent relaxation) are calculated ab initio for the first time. The surface is modeled by a film composed of 12 atomic layers with a vacuum gap of ~16 Å in the layered superlattice approximation. To close Cd dangling bonds on the opposite side of the film, 24 fictitious hydrogen atoms with a charge of 1.5 electrons each are added. Ab initio calculations are performed using the Quantum Espresso program based on density functional theory. It is demonstrated thatmore » relaxation leads to splitting of the four upper layers. The band energy structures and total and layer-by-layer densities of electronic states for the four surface variants are calculated and analyzed.« less

Structure of the orthorhombic Al13Co4(100) surface using LEED, STM, and ab initio studies

NASA Astrophysics Data System (ADS)

Shin, Heekeun; Pussi, K.; Gaudry, É.; Ledieu, J.; Fournée, V.; Alarcón Villaseca, S.; Dubois, J.-M.; Grin, Yu.; Gille, P.; Moritz, W.; Diehl, R. D.

2011-08-01

In a combined scanning tunneling microscopy (STM), low-energy electron diffraction (LEED), and density functional theory (DFT) study of the surface of Al13Co4(100), all techniques have found that after annealing to 1165 K, the surface structure is consistent with a dense Al-rich plane with surface Co atom depletion. Various structure models were considered, and in the LEED study, the best agreement was found with a model that consists of Al-rich terminating planes with no Co atoms, and otherwise a structure similar to the bulk puckered layers. This structure was also found to be stable in the DFT study. The best-fit structural parameters are presented for the two domains of this structure, which contain bipentagons that can be related to the pentagonal bipyramidal structures in the bulk, plus additional glue atoms between them. These domains are not strictly related to each other by symmetry, as they have different surface relaxations. The STM study found significant differences in the surfaces of samples grown by different methods and is able to explain a different interpretation made in an earlier study.

Shape-Controlled Synthesis of Colloidal Metal Nanocrystals by Replicating the Surface Atomic Structure on the Seed.

PubMed

Gilroy, Kyle D; Yang, Xuan; Xie, Shuifen; Zhao, Ming; Qin, Dong; Xia, Younan

2018-06-01

Controlling the surface structure of metal nanocrystals while maximizing the utilization efficiency of the atoms is a subject of great importance. An emerging strategy that has captured the attention of many research groups involves the conformal deposition of one metal as an ultrathin shell (typically 1-6 atomic layers) onto the surface of a seed made of another metal and covered by a set of well-defined facets. This approach forces the deposited metal to faithfully replicate the surface atomic structure of the seed while at the same time serving to minimize the usage of the deposited metal. Here, the recent progress in this area is discussed and analyzed by focusing on the synthetic and mechanistic requisites necessary for achieving surface atomic replication of precious metals. Other related methods are discussed, including the one-pot synthesis, electrochemical deposition, and skin-layer formation through thermal annealing. To close, some of the synergies that arise when the thickness of the deposited shell is decreased controllably down to a few atomic layers are highlighted, along with how the control of thickness can be used to uncover the optimal physicochemical properties necessary for boosting the performance toward a range of catalytic reactions. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Electronic structure studies of adsorbate-induced surface reconstructions: oxygen on Rh(1 0 0)

NASA Astrophysics Data System (ADS)

Kirsch, Janet E.; Harris, Suzanne

2004-03-01

Solid-state Fenske-Hall band structure calculations have been used to study the electronic structure and bonding that occur on an "asymmetric" clock reconstructed Rh(1 0 0) surface with a half-monolayer of O atom adsorbates. The displacement of the top-layer Rh atoms on reconstructed O/Rh(1 0 0) is similar to that observed when a half-monolayer of C or N atoms adsorb onto clean Ni(1 0 0). Unlike the five-coordinate C or N adsorbates that adsorb into effectively coplanar sites on the Ni(1 0 0) surface, however, O atoms sit well above the Rh surface plane and occupy three-coordinate adsorption sites. The results of these calculations show that the asymmetric clock reconstruction of O/Rh(1 0 0) increases the negative charge localized on the highly electronegative O atoms and strengthens the O-Rh bonding relative to an unreconstructed surface. This suggests that, in contrast to the C(N)/Ni(1 0 0) clock, which appears to be driven primarily by the restoration of metal-metal bonding, the asymmetric O/Rh(1 0 0) clock reconstruction is driven by the optimization of the O atom bonding environment. Comparisons of the O/Rh(1 0 0) and C(N, O)/Ni(1 0 0) surfaces further indicate that the electronegativity and electron count of the adsorbed species, as well as the electron count and physical size of the metal, all play a role in determining the preferred atomic geometries of these adsorbate-covered transition metal surfaces.

Composition and structure of surfaces by time-of-flight scattering and recoiling spectrometry (TOF-SARS)

NASA Astrophysics Data System (ADS)

Ahn, Jeongheon

1997-10-01

Time-of-flight scattering and recoiling spectrometry (TOF-SARS) was applied to characterize surface structures in order to understand the chemical and physical phenomena on various surfaces. The combination of TOF-SARS, LEED, and classical ion trajectory simulations has allowed characterization of the elemental composition in the outermost atomic layers, surface symmetry, and possible reconstruction or relaxation. The composition and structure of the CdS\\{0001\\}-(1 x 1) and CdS\\{000bar1\\}-(1 x 1) surfaces were investigated. The termination layer of each surface was determined by grazing incidence TOF-SARS. Both (1 x 1) surfaces are bulk-terminated without any reconstruction or relaxation detected by TOF-SARS. Each surface has two domains which are rotated by 60sp° from each other and there exist steps on both surfaces. The CdS\\{0001\\}-(1 x 1) surface is stabilized by O and H covering half a monolayer which are structurally ordered on the surface, while the O and H on the CdS\\{000bar1\\}-(1 x 1) stabilize the surface without ordering. The study of GaN\\{000bar1\\}-(1 x 1) shows the bulk-termination of the surface with no detectable reconstruction or relaxation. The surface is terminated in a N layer with Ga in the 2sp{nd}-layer. H atoms are bound to the outermost N atoms with a coverage of ˜3/4 monolayer and protrude outward from the surface. The surface termination, composition and structure of the Alsb2Osb3 (sapphire) were examined. The surface relaxation was studied quantitatively using classical ion trajectory simulations along with TOF-SARS. The surface undergoes 1sp{st}{-}2sp{nd}-layer relaxation as large as 0.5 A from the bulk value resulting in near coplanarity of Al and O atoms. The reconstruction of the Ni\\{100\\}-(2 x 2)-C surface was studied by TOF-SARS. The surface contained 80% of the (2 x 2)p4g phase and 20% of the unreconstructed (2 x 2) phase. The displacement of Ni atoms was determined by comparing the experimental and simulated results.

Lithium effects on the mechanical and electronic properties of germanium nanowires

NASA Astrophysics Data System (ADS)

González-Macías, A.; Salazar, F.; Miranda, A.; Trejo-Baños, A.; Pérez, L. A.; Carvajal, E.; Cruz-Irisson, M.

2018-04-01

Semiconductor nanowire arrays promise rapid development of a new generation of lithium (Li) batteries because they can store more Li atoms than conventional crystals due to their large surface areas. During the charge-discharge process, the electrodes experience internal stresses that fatigue the material and limit the useful life of the battery. The theoretical study of electronic and mechanical properties of lithiated nanowire arrays allows the designing of electrode materials that could improve battery performance. In this work, we present a density functional theory study of the electronic band structure, formation energy, binding energy, and Young’s modulus (Y) of hydrogen passivated germanium nanowires (H-GeNWs) grown along the [111] and [001] crystallographic directions with surface and interstitial Li atoms. The results show that the germanium nanowires (GeNWs) with surface Li atoms maintain their semiconducting behavior but their energy gap size decreases when the Li concentration grows. In contrast, the GeNWs can have semiconductor or metallic behavior depending on the concentration of the interstitial Li atoms. On the other hand, Y is an indicator of the structural changes that GeNWs suffer due to the concentration of Li atoms. For surface Li atoms, Y stays almost constant, whereas for interstitial Li atoms, the Y values indicate important structural changes in the GeNWs.

Core-Level Photoemission Investigations of the CADMIUM-TELLURIDE(100) and INDIUM-ANTIMONY(100) Surface and Interfacial Structures.

NASA Astrophysics Data System (ADS)

John, Peter James

1988-12-01

Photoemission techniques, utilizing a synchrotron light source, were used to analyze the clean (100) surfaces of the zinc-blende semiconductor materials CdTe and InSb. Several interfacial systems involving the surfaces of these materials were also studied, including the CdTe(100)-Ag interface, the CdTe(100)-Sb system, and the InSb(100)-Sn interface. High -energy electron diffraction was also employed to acquire information about of surface structure. A one-domain (2x1) structure was observed for the CdTe(100) surface. Analysis of photoemission spectra of the Cd 4d core level for this surface structure revealed two components resulting from Cd surface atoms. The total intensity of these components accounts for a full monolayer of Cd atoms on the surface. A structural model is discussed commensurate with these results. Photoemission spectra of the Cd and Te 4d core levels indicate that Ag or Sb deposited on the CdTe(100)-(2x1) surface at room temperature do not bound strongly to the surface Cd atoms. The room temperature growth characteristics for these two elements on the CdTe(100)-(2x1) are discussed. The growth at elevated substrate temperatures was also studied for Sb deposition. The InSb(100) surface differed from the CdTe(100) surface. Using molecular beam epitaxy, several structures could be generated for the InSb(100) surface, including a c(8x2), a c(4x4), an asymmetric (1x3), a symmetric (1x3), and a (1x1). Analysis of photoemission intensities and line shapes indicates that the c(4x4) surface is terminated with 1{3 over 4} monolayers of Sb atoms. The c(8x2) surface is found to be terminated with {3over 4} monolayer of In atoms. Structural models for both of these surfaces are proposed based upon the photoemission results and upon models of the similar GaAs(100) structures. The room temperature growth characteristics of grey Sn on the InSb(100)-c(4x4) and InSb(100)-c(8x2) surfaces were studied with photoemission. The discontinuity in the valence band maximum for this semiconductor heterojunction system is measured to be 0.40 eV, independent of the starting surface structure and stoichiometry. This result is reconciled with theoretical predictions for heterostructure behavior.

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.

Zinc-blende MnN bilayer formation on the GaN(111) surface

NASA Astrophysics Data System (ADS)

Gutierrez-Ojeda, S. J.; Guerrero-Sánchez, J.; Garcia-Diaz, R.; Ramirez-Torres, A.; Takeuchi, Noboru; H. Cocoletzi, Gregorio

2017-07-01

Atomic layers of manganese nitride, deposited on the cubic gallium nitride (111) surface, are investigated using spin polarized periodic density functional theory calculations. The adsorption of a manganese atom has been evaluated at different high symmetry sites. Incorporation into the GaN substrate by replacing gallium atoms drives the formation of a site in which the displaced Ga atom forms bonds with Ga atoms at the surface. This energetically favorable configuration shows a ferromagnetic alignment. Surface formation energy calculations demonstrate that when a full Mn ML is incorporated into the GaN structure, a Ga ML on top of a MnN bilayer may be formed for very Ga-rich conditions. On the other hand, when a full Mn ML is deposited on top of the nitrogen terminated surface, an epitaxial MnN bilayer is formed with antiferromagnetic characteristics. Density of states and partial density of states are reported to show the antiferromagnetic alignment in both structures. This behavior is mainly induced by the Mn-d orbitals.

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

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

Observation of Structure of Surfaces and Interfaces by Synchrotron X-ray Diffraction: Atomic-Scale Imaging and Time-Resolved Measurements

NASA Astrophysics Data System (ADS)

Wakabayashi, Yusuke; Shirasawa, Tetsuroh; Voegeli, Wolfgang; Takahashi, Toshio

2018-06-01

The recent developments in synchrotron optics, X-ray detectors, and data analysis algorithms have enhanced the capability of the surface X-ray diffraction technique. This technique has been used to clarify the atomic arrangement around surfaces in a non-contact and nondestructive manner. An overview of surface X-ray diffraction, from the historical development to recent topics, is presented. In the early stage of this technique, surface reconstructions of simple semiconductors or metals were studied. Currently, the surface or interface structures of complicated functional materials are examined with sub-Å resolution. As examples, the surface structure determination of organic semiconductors and of a one-dimensional structure on silicon are presented. A new frontier is time-resolved interfacial structure analysis. A recent observation of the structure and dynamics of the electric double layer of ionic liquids, and an investigation of the structural evolution in the wettability transition on a TiO2 surface that utilizes a newly designed time-resolved surface diffractometer, are presented.

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.

Atomic scale study of strain relaxation in Sn islands on Sn-induced Si(111)-(2√3 ×2√3 ) surface

NASA Astrophysics Data System (ADS)

Wang, L. L.; Ma, X. C.; Ning, Y. X.; Ji, S. H.; Fu, Y. S.; Jia, J. F.; Kelly, K. F.; Xue, Q. K.

2009-04-01

Surface structure of the Sn islands 5 ML high, prepared on Si(111)-(2√3 ×2√3 )-Sn substrate, is investigated by low temperature scanning tunneling microscopy/spectroscopy. Due to the elastic strain relaxation in the islands, the in-plane unit cell structure distorts and the apparent height of the surface atoms varies regularly to form an overall modulated strip structure. The quantum well states are observed to depend on the relative position within this structure, which implies the change of the surface chemical potential induced by the elastic strain relaxation as well.

Defect Effects on TiO2 Nanosheets: Stabilizing Single Atomic Site Au and Promoting Catalytic Properties.

PubMed

Wan, Jiawei; Chen, Wenxing; Jia, Chuanyi; Zheng, Lirong; Dong, Juncai; Zheng, Xusheng; Wang, Yu; Yan, Wensheng; Chen, Chen; Peng, Qing; Wang, Dingsheng; Li, Yadong

2018-03-01

Isolated single atomic site catalysts have attracted great interest due to their remarkable catalytic properties. Because of their high surface energy, single atoms are highly mobile and tend to form aggregate during synthetic and catalytic processes. Therefore, it is a significant challenge to fabricate isolated single atomic site catalysts with good stability. Herein, a gentle method to stabilize single atomic site metal by constructing defects on the surface of supports is presented. As a proof of concept, single atomic site Au supported on defective TiO 2 nanosheets is prepared and it is discovered that (1) the surface defects on TiO 2 nanosheets can effectively stabilize Au single atomic sites through forming the Ti-Au-Ti structure; and (2) the Ti-Au-Ti structure can also promote the catalytic properties through reducing the energy barrier and relieving the competitive adsorption on isolated Au atomic sites. It is believed that this work paves a way to design stable and active single atomic site catalysts on oxide supports. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Atomic and Molecular Beam Scattering: Characterizing Structure and Dynamics of Hybrid Organic-Semiconductor Interfaces and Introducing Novel Isotope Separation Techniques

NASA Astrophysics Data System (ADS)

Nihill, Kevin John

This thesis details a range of experiments and techniques that use the scattering of atomic beams from surfaces to both characterize a variety of interfaces and harness mass-specific scattering conditions to separate and enrich isotopic components in a mixture of gases. Helium atom scattering has been used to characterize the surface structure and vibrational dynamics of methyl-terminated Ge(111), thereby elucidating the effects of organic termination on a rigid semiconductor interface. Helium atom scattering was employed as a surface-sensitive, non-destructive probe of the surface. By means of elastic gas-surface diffraction, this technique is capable of providing measurements of atomic spacing, step height, average atomic displacement as a function of surface temperature, gas-surface potential well depth, and surface Debye temperature. Inelastic time-of-flight studies provide highly resolved energy exchange measurements between helium atoms and collective lattice vibrations, or phonons; a collection of these measurements across a range of incident kinematic parameters allowed for a thorough mapping of low-energy phonons (e.g., the Rayleigh wave) across the surface Brillouin zone and subsequent comparison with complementary theoretical calculations. The scattering of molecular beams - here, hydrogen and deuterium from methyl-terminated Si(111) - enables the measurement of the anisotropy of the gas-surface interaction potential through rotationally inelastic diffraction (RID), whereby incident atoms can exchange internal energy between translational and rotational modes and diffract into unique angular channels as a result. The probability of rotational excitations as a function of incident energy and angle were measured and compared with electronic structure and scattering calculations to provide insight into the gas-surface interaction potential and hence the surface charge density distribution, revealing important details regarding the interaction of H2 with an organic-functionalized semiconductor interface. Aside from their use as probes for surface structure and dynamics, atomic beam sources are also demonstrated to enable the efficient separation of gaseous mixtures of isotopes by means of diffraction and differential condensation. In the former method, the kinematic conditions for elastic diffraction result in an incident beam of natural abundance neon diffracting into isotopically distinct angles, resulting in the enrichment of a desired isotope; this purification can be improved by exploiting the difference in arrival times of the two isotopes at a given final angle. In the latter method, the identical incident velocities of coexpanded isotopes lead to minor but important differences in their incident kinetic energies, and thus their probability of adsorbing on a sufficiently cold surface, resulting in preferential condensation of a given isotope that depends on the energy of the incident beam. Both of these isotope separation techniques are made possible by the narrow velocity distribution and velocity seeding effect offered only by high-Mach number supersonic beam sources. These experiments underscore the utility of supersonically expanded atomic and molecular beam sources as both extraordinarily precise probes of surface structure and dynamics and as a means for high-throughput, non-dissociative isotopic enrichment methods.

The role of HH interactions in the formation of ordered structures on Ni and Pd single crystals

NASA Astrophysics Data System (ADS)

Muscat, J. P.

1981-09-01

The interaction between H adatoms on a surface is calculated within the embedded cluster model of chemisorption. The model is first applied to the case of two H atoms on a free electron surface. The interaction energy is found to be an oscillatory function of the H-H separation Rab. Application of the free electron model to the problem of chemisorption on transition metal surfaces leads to unphysical results with the prediction of formation of ordered H overlayers which are not observed in LEED experiments. We next include the l = 2 TM muffin tins. Results for H adsorption on the low index faces of Ni and Pd substrates are presented. Graphitic structures are predicted for the (111) faces of both Ni and Pd with the H atoms occupying both types of three-fold hollow sites on the surface. This agrees with the results of LEED experiments for H/Ni(111). Comparison with experiment is not possible in the case of H/Pd(111) owing to the lack of low temperature studies for that system. Zig-zag chains with the H atoms adsorbed in sites of three-fold coordination on alternate sides of the TM(110) rows are predicted for both Ni and Pd. This is in agreement with the results of He diffraction experiments for H/Ni(110). No structure determination has been done for H/Pd(110). Adsorption in the four-fold centre sites for H on the (100) faces of Ni and Pd is found to be unfavourable. The H atoms are expected to adsorb in sites of three-fold symmetry below the (100) surface for H on Pd with formation of a c(2 × 2) structure in agreement with the LEED observations. For H/Ni(100) the H atoms are believed to adsorb above the surface, away from the centre site and to bond to two surface Ni atoms. No short-range ordered structures are predicted in this case.

Atomic Beam Scattering Methods to Study Overlayer Structures and H-Surface Interaction Relevant to Astrophysics

NASA Astrophysics Data System (ADS)

Lin, Jingsu

In this thesis we present results of experimental methods for studying surface structures of ultra-thin films and describe a new apparatus to study the recombination of atomic hydrogen on well characterized low temperature surface using atomic and molecular beam methods. We have used atomic beam scattering (ABS) to characterize the growth of mercury and lead overlayers on Cu(001) surface. The structures of ordered phases have been identified using ABS and low-energy electron diffraction (LEED). A model to analyze diffraction data from these phases is presented. The new apparatus we are going to describe includes a high performance atomic hydrogen source using radio-frequency (RF) dissociation. The dissociation efficiency can be as high as 90% in the optimized pressure range. An atomic hydrogen beam line has been added to our ultra-high vacuum (UHV) scattering apparatus. We have also designed and constructed a low temperature sample manipulator for experiments at liquid helium temperatures. The manipulator has one degree of freedom of rotation and the capability of heating the sample to 700K and cooling down to 12K. The first sample studied was a single graphite surface. We have used a He beam to characterize the sample surface and to monitor deposition of H on the sample surface in real time. A series of "adsorption curves" have been obtained at different temperature and doses. We found that at temperatures below 16K, both H and H_2 have formed a partial layer on the surface. From adsorption curve, we deduce that the initial sticking coefficient for H is about 0.06 when surface at 16K. When the H beam is interrupted, the He specularly reflected beam recovers partially, indicating that hydrogen atoms desorb, while others remain on the surface. The residual coverage of H is estimated to be about 2% of a monolayer.

Chlorine adsorption on the InAs (001) surface

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

Bakulin, A. V.; Eremeev, S. V.; Tereshchenko, O. E.

2011-01-15

Chlorine adsorption on the In-stabilized InAs(001) surface with {zeta}-(4 Multiplication-Sign 2) and {beta}3 Prime -(4 Multiplication-Sign 2) reconstructions and on the Ga-stabilized GaAs (001)-{zeta}-(4 Multiplication-Sign 2) surface has been studied within the electron density functional theory. The equilibrium structural parameters of these reconstructions, surface atom positions, bond lengths in dimers, and their changes upon chlorine adsorption are determined. The electronic characteristics of the clean surface and the surface with adsorbed chlorine are calculated. It is shown that the most energetically favorable positions for chlorine adsorption are top positions over dimerized indium or gallium atoms. The mechanism of chlorine binding withmore » In(Ga)-stabilized surface is explained. The interaction of chlorine atoms with dimerized surface atoms weakens surface atom bonds and controls the initial stage of surface etching.« less

Relationships between Atomic Level Surface Structure and Stability/Activity of Platinum Surface Atoms in Aqueous Environments

DOE PAGES

Lopes, Pietro P.; Strmcnik, Dusan; Tripkovic, Dusan; ...

2016-03-07

The development of alternative energy systems for clean production, storage and conversion of energy is strongly dependent on our ability to understand, at atomic-molecular-levels, functional links between activity and stability of electrochemical interfaces. Whereas structure-activity relationships are rapidly evolving, the corresponding structure-stability relationships are still missing. Primarily, this is because there is no adequate experimental approach capable of monitoring in situ stability of well-defined single crystals. Here, by blending the power of Inductively Coupled Plasma-Mass Spectrometer (ICP-MS) connected to a stationary probe to measure in situ and real time dissolution rates of surface atoms (at above 0.4 pg cm-2s-1 levels)more » and a rotating disk electrode method for monitoring simultaneously the kinetic rates of electrochemical reactions in a single unite, it was possible to establish almost “atom-by-atom” the structure-stability-activity relationships for platinum single crystals in both acidic and alkaline environments. Furthermore, we found that the degree of stability is strongly dependent on the coordination of surface atoms (less coordinated yields less stable), the nature of covalent (adsorption of hydroxyl, oxygen atoms and halides species), and non-covalent interactions (interactions between hydrated Li cations and surface oxide), the thermodynamic driving force for Pt complexation (Pt ion speciation in solution) and the nature of the electrochemical reaction (the oxygen reduction/evolution and CO oxidation reactions). Consequently, these findings are opening new opportunities for elucidating key fundamental descriptors that govern both activity and stability trends, that ultimately, will assist to develop real energy conversion and storage systems.« less

Atomic Resolution of Calcium and Oxygen Sublattices of Calcite in Ambient Conditions by Atomic Force Microscopy Using qPlus Sensors with Sapphire Tips.

PubMed

Wastl, Daniel S; Judmann, Michael; Weymouth, Alfred J; Giessibl, Franz J

2015-01-01

Characterization and imaging at the atomic scale with atomic force microscopy in biocompatible environments is an ongoing challenge. We demonstrate atomically resolved imaging of the calcite (101̅4) surface plane using stiff quartz cantilevers ("qPlus sensors", stiffness k = 1280 N/m) equipped with sapphire tips in ambient conditions without any surface preparation. With 10 atoms in one surface unit cell, calcite has a highly complex surface structure comprising three different chemical elements (Ca, C, and O). We obtain true atomic resolution of calcite in air at relative humidity ranging from 20% to 40%, imaging atomic steps and single atomic defects. We observe a great durability of sapphire tips with their Mohs hardness of 9, only one step below diamond. Depending on the state of the sapphire tip, we resolve either the calcium or the oxygen sublattice. We determine the tip termination by comparing the experimental images with simulations and discuss the possibility of chemical tip identification in air. The main challenges for imaging arise from the presence of water layers, which form on almost all surfaces and have the potential to dissolve the crystal surface. Frequency shift versus distance spectra show the presence of at least three ordered hydration layers. The measured height of the first hydration layer corresponds well to X-ray diffraction data and molecular dynamic simulations, namely, ∼220 pm. For the following hydration layers we measure ∼380 pm for the second and third layer, ending up in a total hydration layer thickness of at least 1 nm. Understanding the influence of water layers and their structure is important for surface segregation, surface reactions including reconstructions, healing of defects, and corrosion.

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

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

Petkov, Valeri; Hessel, Colin M.; Ovtchinnikoff, Justine

High-energy synchrotron X-ray diffraction coupled to atomic pair distribution function analysis and computer simulations is used to determine the atomic-scale structure of silicon (Si) nanoparticles obtained by two different synthetic routes. Results show that Si nanoparticles may have significant structural differences depending on the synthesis route and surface chemistry. In this case, one method produced Si nanoparticles that are highly crystalline but surface oxidized, whereas a different method yields organic ligand-passivated nanoparticles without surface oxide but that are structurally distorted at the atomic scale. Particular structural features of the oxide-free Si nanoparticles such as average first coordination numbers, length ofmore » structural coherence, and degree of local distortions are compared to their optical properties such as photoluminescence emission energy, quantum yield, and Raman spectra. A clear structure–properties correlation is observed indicating that the former may need to be taken into account when considering the latter.« less

Surface structure. Subatomic resolution force microscopy reveals internal structure and adsorption sites of small iron clusters.

PubMed

Emmrich, Matthias; Huber, Ferdinand; Pielmeier, Florian; Welker, Joachim; Hofmann, Thomas; Schneiderbauer, Maximilian; Meuer, Daniel; Polesya, Svitlana; Mankovsky, Sergiy; Ködderitzsch, Diemo; Ebert, Hubert; Giessibl, Franz J

2015-04-17

Clusters built from individual iron atoms adsorbed on surfaces (adatoms) were investigated by atomic force microscopy (AFM) with subatomic resolution. Single copper and iron adatoms appeared as toroidal structures and multiatom clusters as connected structures, showing each individual atom as a torus. For single adatoms, the toroidal shape of the AFM image depends on the bonding symmetry of the adatom to the underlying structure [twofold for copper on copper(110) and threefold for iron on copper(111)]. Density functional theory calculations support the experimental data. The findings correct our previous work, in which multiple minima in the AFM signal were interpreted as a reflection of the orientation of a single front atom, and suggest that dual and triple minima in the force signal are caused by dimer and trimer tips, respectively. Copyright © 2015, American Association for the Advancement of Science.

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-Scale Observations of (010) LiFePO4 Surfaces Before and After Chemical Delithiation.

PubMed

Kobayashi, Shunsuke; Fisher, Craig A J; Kato, Takeharu; Ukyo, Yoshio; Hirayama, Tsukasa; Ikuhara, Yuichi

2016-09-14

The ability to view directly the surface structures of battery materials with atomic resolution promises to dramatically improve our understanding of lithium (de)intercalation and related processes. Here we report the use of state-of-the-art scanning transmission electron microscopy techniques to probe the (010) surface of commercially important material LiFePO4 and compare the results with theoretical models. The surface structure is noticeably different depending on whether Li ions are present in the topmost surface layer or not. Li ions are also found to migrate back to surface regions from within the crystal relatively quickly after partial delithiation, demonstrating the facile nature of Li transport in the [010] direction. The results are consistent with phase transformation models involving metastable phase formation and relaxation, providing atomic-level insights into these fundamental processes.

TED analysis of the Si(113) surface structure

NASA Astrophysics Data System (ADS)

Suzuki, T.; Minoda, H.; Tanishiro, Y.; Yagi, K.

1999-09-01

We carried out a TED (transmission electron diffraction) analysis of the Si(113) surface structure. The TED patterns taken at room temperature showed reflections due to the 3×2 reconstructed structure. The TED pattern indicated that a glide plane parallel to the <332> direction suggested in some models is excluded. We calculated the R-factors (reliability factors) for six surface structure models proposed previously. All structure models with energy-optimized atomic positions have large R-factors. After revision of the atomic positions, the R-factors of all the structure models decreased below 0.3, and the revised version of Dabrowski's 3×2 model has the smallest R-factor of 0.17.

Molecular dynamics simulation of temperature effects on low energy near-surface cascades and surface damage in Cu

NASA Astrophysics Data System (ADS)

Zhu, Guo; Sun, Jiangping; Guo, Xiongxiong; Zou, Xixi; Zhang, Libin; Gan, Zhiyin

2017-06-01

The temperature effects on near-surface cascades and surface damage in Cu(0 0 1) surface under 500 eV argon ion bombardment were studied using molecular dynamics (MD) method. In present MD model, substrate system was fully relaxed for 1 ns and a read-restart scheme was introduced to save total computation time. The temperature dependence of damage production was calculated. The evolution of near-surface cascades and spatial distribution of adatoms at varying temperature were analyzed and compared. It was found that near-surface vacancies increased with temperature, which was mainly due to the fact that more atoms initially located in top two layers became adatoms with the decrease of surface binding energy. Moreover, with the increase of temperature, displacement cascades altered from channeling-like structure to branching structure, and the length of collision sequence decreased gradually, because a larger portion of energy of primary knock-on atom (PKA) was scattered out of focused chain. Furthermore, increasing temperature reduced the anisotropy of distribution of adatoms, which can be ascribed to that regular registry of surface lattice atoms was changed with the increase of thermal vibration amplitude of surface atoms.

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.

Adsorption and dynamics of Si atoms at the monolayer Pb/Si(111) surface

NASA Astrophysics Data System (ADS)

Kumar, Rakesh; Fang, Chuang-Kai; Lee, Chih-Hao; Hwang, Ing-Shouh

2017-06-01

In this work, we studied the adsorption behavior of deposited Si atoms along with their diffusion and other dynamic processes on a Pb monolayer-covered Si(111) surface from 125 to 230 K using a variable-temperature scanning tunneling microscope. The Pb-covered Si(111) surface forms a low-symmetry rowlike (√{7 }×√{3 } ) structure in this temperature range and the Si atoms bind favorably to two specific on-top sites (T1 A and T1 B) on the trimer row after deposition at the sample temperature of ˜125 K . The Si atoms were immobile at low temperatures and started to switch between the two neighboring T1 A and T1 B sites within the same trimer when the temperature was raised to ˜150 K . When the temperature was raised above ˜160 K , the adsorbed Si atoms could hop to other trimers along the same trimer row. Below ˜170 K , short hops to adjacent trimers dominated, but long hops dominated at temperatures above ˜170 K . The activation energy and prefactor for the Si atoms diffusion were derived through analysis of continuous-time imaging at temperatures from 160 to 174 K. In addition, irreversible aggregation of single Si atoms into Si clusters started to occur at the phase boundaries or defective sites at temperatures above ˜170 K . At temperature above ˜180 K , nearly all Si atoms aggregated into clusters, which may have important implications for the atomic mechanism of epitaxial growth of Si on the Pb-covered Si(111) surface. In addition, our study provides strong evidence for breaking in the mirror symmetry in the (√{7 }×√{3 } )-Pb structure, which has implications for the atomic model of this controversial structure.

Structure of high-index GaAs surfaces - the discovery of the stable GaAs(2511) surface

NASA Astrophysics Data System (ADS)

Jacobi, K.; Geelhaar, L.; Márquez, J.

We present a brief overview of surface structures of high-index GaAs surfaces, putting emphasis on recent progress in our own laboratory. By adapting a commercial scanning tunneling microscope (STM) to our molecular beam epitaxy and ultra high vacuum analysis chamber system, we have been able to atomically resolve the GaAs( {1} {1} {3})B(8 ×1), (114)Aα2(2×1), (137), (3715), and (2511) surface structures. In cooperation with P. Kratzer and M. Scheffler from the Theory Department of the Fritz-Haber Institute we determined the structure of some of these surfaces by comparing total-energy calculations and STM image simulations with the atomically resolved STM images. We present the results for the {112}, {113}, and {114} surfaces. Then we describe what led us to proceed into the inner parts of the stereographic triangle and to discover the hitherto unknown stable GaAs(2511) surface.

High-resolution imaging of silicene on an Ag(111) surface by atomic force microscopy

NASA Astrophysics Data System (ADS)

Onoda, Jo; Yabuoshi, Keisuke; Miyazaki, Hiroki; Sugimoto, Yoshiaki

2017-12-01

Silicene, a two-dimensional (2D) honeycomb arrangement of Si atoms, is expected to have better electronic properties than graphene and has been mostly synthesized on Ag surfaces. Although scanning tunneling microscopy (STM) has been used for visualizing its atomic structure in real space, the interpretation of STM contrast is not straightforward and only the topmost Si atoms were observed on the (4 ×4 ) silicene/Ag(111) surface. Here, we demonstrate that high-resolution atomic force microscopy (AFM) can resolve all constituent Si atoms in the buckled honeycomb arrangement of the (4 ×4 ) silicene. Site-specific force spectroscopy attributes the origin of the high-resolution AFM images to chemical bonds between the AFM probe apex and the individual Si atoms on the (4 ×4 ) silicene. A detailed analysis of the geometric parameters suggests that the pulling up of lower-buckled Si atoms by the AFM tip could be a key for high-resolution AFM, implying a weakening of the Si-Ag interactions at the interface. We expect that high-resolution AFM will also unveil atomic structures of edges and defects of silicene, or other emerging 2D materials.

Mapping of Proteomic Composition on the Surfaces of Bacillus spores by Atomic Force Microscopy-based Immunolabeling

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

Plomp, M; Malkin, A J

2008-06-02

Atomic force microscopy provides a unique capability to image high-resolution architecture and structural dynamics of pathogens (e.g. viruses, bacteria and bacterial spores) at near molecular resolution in native conditions. Further development of atomic force microscopy in order to enable the correlation of pathogen protein surface structures with specific gene products is essential to understand the mechanisms of the pathogen life cycle. We have applied an AFM-based immunolabeling technique for the proteomic mapping of macromolecular structures through the visualization of the binding of antibodies, conjugated with nanogold particles, to specific epitopes on Bacillus spore surfaces. This information is generated while simultaneouslymore » acquiring the surface morphology of the pathogen. The immunospecificity of this labeling method was established through the utilization of specific polyclonal and monoclonal antibodies that target spore coat and exosporium epitopes of Bacillus atrophaeus and Bacillus anthracis spores.« less

Probing the atomic structure of metallic nanoclusters with the tip of a scanning tunneling microscope.

PubMed

Schouteden, Koen; Lauwaet, Koen; Janssens, Ewald; Barcaro, Giovanni; Fortunelli, Alessandro; Van Haesendonck, Chris; Lievens, Peter

2014-02-21

Preformed Co clusters with an average diameter of 2.5 nm are produced in the gas phase and are deposited under controlled ultra-high vacuum conditions onto a thin insulating NaCl film on Au(111). Relying on a combined experimental and theoretical investigation, we demonstrate visualization of the three-dimensional atomic structure of the Co clusters by high-resolution scanning tunneling microscopy (STM) using a Cl functionalized STM tip that can be obtained on the NaCl surface. More generally, use of a functionalized STM tip may allow for systematic atomic structure determination with STM of nanoparticles that are deposited on metal surfaces.

Atomic Scale Structure-Chemistry Relationships at Oxide Catalyst Surfaces and Interfaces

NASA Astrophysics Data System (ADS)

McBriarty, Martin E.

Oxide catalysts are integral to chemical production, fuel refining, and the removal of environmental pollutants. However, the atomic-scale phenomena which lead to the useful reactive properties of catalyst materials are not sufficiently understood. In this work, the tools of surface and interface science and electronic structure theory are applied to investigate the structure and chemical properties of catalytically active particles and ultrathin films supported on oxide single crystals. These studies focus on structure-property relationships in vanadium oxide, tungsten oxide, and mixed V-W oxides on the surfaces of alpha-Al2O3 and alpha-Fe2O 3 (0001)-oriented single crystal substrates, two materials with nearly identical crystal structures but drastically different chemical properties. In situ synchrotron X-ray standing wave (XSW) measurements are sensitive to changes in the atomic-scale geometry of single crystal model catalyst surfaces through chemical reaction cycles, while X-ray photoelectron spectroscopy (XPS) reveals corresponding chemical changes. Experimental results agree with theoretical calculations of surface structures, allowing for detailed electronic structure investigations and predictions of surface chemical phenomena. The surface configurations and oxidation states of V and W are found to depend on the coverage of each, and reversible structural shifts accompany chemical state changes through reduction-oxidation cycles. Substrate-dependent effects suggest how the choice of oxide support material may affect catalytic behavior. Additionally, the structure and chemistry of W deposited on alpha-Fe 2O3 nanopowders is studied using X-ray absorption fine structure (XAFS) measurements in an attempt to bridge single crystal surface studies with real catalysts. These investigations of catalytically active material surfaces can inform the rational design of new catalysts for more efficient and sustainable chemistry.

Atomic Scale Analysis of the Enhanced Electro- and Photo-Catalytic Activity in High-Index Faceted Porous NiO Nanowires

NASA Astrophysics Data System (ADS)

Shen, Meng; Han, Ali; Wang, Xijun; Ro, Yun Goo; Kargar, Alireza; Lin, Yue; Guo, Hua; Du, Pingwu; Jiang, Jun; Zhang, Jingyu; Dayeh, Shadi A.; Xiang, Bin

2015-02-01

Catalysts play a significant role in clean renewable hydrogen fuel generation through water splitting reaction as the surface of most semiconductors proper for water splitting has poor performance for hydrogen gas evolution. The catalytic performance strongly depends on the atomic arrangement at the surface, which necessitates the correlation of the surface structure to the catalytic activity in well-controlled catalyst surfaces. Herein, we report a novel catalytic performance of simple-synthesized porous NiO nanowires (NWs) as catalyst/co-catalyst for the hydrogen evolution reaction (HER). The correlation of catalytic activity and atomic/surface structure is investigated by detailed high resolution transmission electron microscopy (HRTEM) exhibiting a strong dependence of NiO NW photo- and electrocatalytic HER performance on the density of exposed high-index-facet (HIF) atoms, which corroborates with theoretical calculations. Significantly, the optimized porous NiO NWs offer long-term electrocatalytic stability of over one day and 45 times higher photocatalytic hydrogen production compared to commercial NiO nanoparticles. Our results open new perspectives in the search for the development of structurally stable and chemically active semiconductor-based catalysts for cost-effective and efficient hydrogen fuel production at large scale.

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

Zou, Lianfeng; Li, Jonathan; Zakharov, Dmitri

Using in situ transmission electron microscopy that spatially and temporally resolves the evolution of the atomic structure in the surface and subsurface regions, we Find that the surface segregation of Au atoms in a Cu(Au) solid solution results in the nucleation and growth of a (2 × 1) missing-row reconstructed, half-unit-cell thick L1 2 Cu 3Au(110) surface alloy. Our in situ electron microscopy observations and atomistic simulations demonstrate that the (2 × 1) reconstruction of the Cu 3Au(110) surface alloy remains as a stable surface structure as a result of the favored Cu-Au diatom configuration.

Photoelectron Holographic Atomic Arrangement Imaging of Cleaved Bimetal-intercalated Graphite Superconductor Surface

PubMed Central

Matsui, Fumihiko; Eguchi, Ritsuko; Nishiyama, Saki; Izumi, Masanari; Uesugi, Eri; Goto, Hidenori; Matsushita, Tomohiro; Sugita, Kenji; Daimon, Hiroshi; Hamamoto, Yuji; Hamada, Ikutaro; Morikawa, Yoshitada; Kubozono, Yoshihiro

2016-01-01

From the C 1s and K 2p photoelectron holograms, we directly reconstructed atomic images of the cleaved surface of a bimetal-intercalated graphite superconductor, (Ca, K)C8, which differed substantially from the expected bulk crystal structure based on x-ray diffraction (XRD) measurements. Graphene atomic images were collected in the in-plane cross sections of the layers 3.3 Å and 5.7 Å above the photoelectron emitter C atom and the stacking structures were determined as AB- and AA-type, respectively. The intercalant metal atom layer was found between two AA-stacked graphenes. The K atomic image revealing 2 × 2 periodicity, occupying every second centre site of C hexagonal columns, was reconstructed, and the Ca 2p peak intensity in the photoelectron spectra of (Ca, K)C8 from the cleaved surface was less than a few hundredths of the K 2p peak intensity. These observations indicated that cleavage preferentially occurs at the KC8 layers containing no Ca atoms. PMID:27811975

STM study on the surface structures and defects of SnSe

NASA Astrophysics Data System (ADS)

Kim, Jungdae; Duvjir, Ganbat; Ly, Trinh Thi; Min, Taewon; Kim, Taehoon; Kim, Sang Hwa; Duong, Anh-Tuan; Rhim, S. H.; Cho, Sunglae; Lee, Jaekwang

Tin selenide (SnSe) is a IV-VI semiconductor with a band gap of 1.0 eV, and also one of layered chalcogenide materials (LCMs) where each layer is coupled by weak van der Waals interactions. 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. The atomic and electronic structures of SnSe surfaces are studied by a home-built low temperature scanning tunneling microscope (STM). 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 density functional theory (DFT) calculations, indicating that the bright extrusions of both filled and empty state images are mostly located at the positions of Sn atoms. We also report the origin of p-type behavior in SnSe by investigating three dominant intrinsic defects (Sn, Se, and Se-Sn-Se vacancies) using STM and DFT calculations. This work was supported by the National Research Foundation of Korea (NRF-2015R1D1A1A01057271, NRF-2009-0093818, and NRF-2014R1A4A1071686).

Si Nanoribbons on Ag(110) Studied by Grazing-Incidence X-Ray Diffraction, Scanning Tunneling Microscopy, and Density-Functional Theory: Evidence of a Pentamer Chain Structure.

PubMed

Prévot, Geoffroy; Hogan, Conor; Leoni, Thomas; Bernard, Romain; Moyen, Eric; Masson, Laurence

2016-12-30

We report a combined grazing incidence x-ray diffraction (GIXD), scanning tunneling microscopy (STM), and density-functional theory (DFT) study which clearly elucidates the atomic structure of the Si nanoribbons grown on the missing-row reconstructed Ag(110) surface. Our study allows us to discriminate between the theoretical models published in the literature, including the most stable atomic configurations and those based on a missing-row reconstructed Ag(110) surface. GIXD measurements unambiguously validate the pentamer model grown on the reconstructed surface, obtained from DFT. This pentamer atomistic model accurately matches the high-resolution STM images of the Si nanoribbons adsorbed on Ag(110). Our study closes the long-debated atomic structure of the Si nanoribbons grown on Ag(110) and definitively excludes a honeycomb structure similar to that of freestanding silicene.

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

Interaction of scandium and titanium atoms with a carbon surface containing five- and seven-membered rings

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

Krasnov, P. O., E-mail: kpo1980@gmail.com; Eliseeva, N. S.; Kuzubov, A. A., E-mail: alex_xx@rambler.ru

2012-01-15

The use of carbon nanotubes coated by atoms of transition metals to store molecular hydrogen is associated with the problem of the aggregation of these atoms, which leads to the formation of metal clusters. The quantum-chemical simulation of cluster models of the carbon surface of a graphene type with scandium and titanium atoms has been performed. It has been shown that the presence of five- and seven-membered rings, in addition to six-membered rings, in these structures makes it possible to strongly suppress the processes of the migration of metal atoms over the surface, preventing their clustering.

Growth and structural evolution of Sn on Ag(001): Epitaxial monolayer to thick alloy film

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

Chakraborty, Suvankar; Menon, Krishnakumar S. R., E-mail: krishna.menon@saha.ac.in

The growth and structure of Sn on Ag(001), from submonolayer to thick film coverages at room temperature, are studied using low energy electron diffraction, x-ray photoemission spectroscopy and angle-resolved photoemission spectroscopy (ARPES) techniques. The authors observe different growth modes for submonolayer Sn coverages and for higher Sn coverages. Systematic surface structural evolution, consistent with the substitution of surface Ag atoms by Sn atoms, is observed for submonolayer Sn coverages while an ordered Ag-Sn bulk alloy film is formed for higher Sn coverages with an Ag overlayer. For monolayer coverage of Sn, a pseudomorphic growth of a Sn layer without alloyingmore » is determined. ARPES results also confirm the presence of an ordered Ag overlayer on the bulk Ag-Sn alloy film, suggesting the formation of an Ag/Ag{sub 3}Sn/Ag(001) sandwich structure at the surface for higher Sn coverages. The present results illustrate the complex interplay of atomic mobilities, surface free-energies, and alloy formation energies in determining the growth and structural properties of the system.« less

Atomic Mechanism of Hybridization-Dependent Surface Reconstruction with Tailored Functionality in Hexagonal Multiferroics.

PubMed

Deng, Shiqing; Cheng, Shaobo; Xu, Changsong; Ge, Binghui; Sun, Xuefeng; Yu, Rong; Duan, Wenhui; Zhu, Jing

2017-08-16

The broken symmetry along with anomalous defect structures and charging conditions at multiferroics surface can alter both crystal structures and electronic configurations, bringing in emergent physical properties. Extraordinary surface states are induced into original mutually coupled order parameters in such strongly correlated oxides, which flourish in diverse properties but remain less explored. Here, we report the peculiar surface ferroelectric states and reconfigurable functionalities driven by the relaxation of surface and consequent changes in O 2p and Y 4d orbital (p-d) hybridization within a representative hexagonal multiferroics, YMnO 3 . An unprecedented surface reconstruction is achieved by tailored p-d hybridization coupling with in-plane oxygen vacancies, which is atomically revealed on the basis of the advantages of state-of-the-art aberration-corrected (scanning) transmission electron microscopy. Further ab initio density functional theory calculations verify the key roles of in-plane oxygen vacancies in modulating polarization properties and electronic structure, which should be regarded as the atomic multiferroic element. This surface configuration is found to induce tunable functionalities, such as surface ferromagnetism and conductivity. Meanwhile, the controversial origin of improper ferroelectricity that is unexpectedly free from critical size has also been atomically unraveled. Our findings provide new insights into the design and implementation of surface chemistry devices by simply controlling the oxygen stoichiometry, greatly advance our understandings of surface science in strongly correlated oxides, and enable exciting innovations and new technological functionality paradigms.

Study of α-Cu 0.82Al 0.18(100) using low energy ion scattering

NASA Astrophysics Data System (ADS)

Zhu, L.; Muhlen, E. Zur; O'Connor, D. J.; King, B. V.; MacDonald, R. J.

1996-07-01

The clean α-Cu 0.82Al 0.18(100) surface has been investigated using low energy ion scattering. The surface structure was found to be similar to the structure of the Cu(100) surface. By measuring the first layer concentration of Al using He + and Ne + beams and standard calibration procedure, the α-Cu 0.82Al 0.18(100) surface was found to be slightly Al-rich. Analysis of multiple scattering of ions suggests that Al atoms do not form islands. It was also found that Al atoms sit higher than the Cu atoms on the surface. By comparison with computer simulations (SABRE and FAN2D), the buckling of Al was found to be 0.16 ± 0.07 Å. No reconstructions were observed on the surface by low energy ion scattering which is in agreement with previous LEED studies.

Charge-Dependent Atomic-Scale Structures of High-Index and (110) Gold Electrode Surfaces as Revealed by Scanning Tunneling Microscopy

DTIC Science & Technology

1994-02-01

known gold atomic diameter of 2.89 A. Within a given domain, featuring adjacent terrace strings separated by monoatomic steps, the measured unit-cell...to utilize high-index gold faces in exploring the influence of monoatomic steps and related structural features on surface electrochemical phenomena...110) Gold Electrode Surfaces D1 T IC as Revealed by Scanning Tunneling Microscopy FLECTE MAR 10 19941 by E Xiaoping Gao, Gregory J. Edens, Antoinette

Metal/silicon Interfaces and Their Oxidation Behavior - Photoemission Spectroscopy Analysis.

NASA Astrophysics Data System (ADS)

Yeh, Jyh-Jye

Synchrotron radiation photoemission spectroscopy was used to study Ni/Si and Au/Si interface properties on the atomic scale at room temperature, after high temperature annealing and after oxygen exposures. Room temperature studies of metal/Si interfaces provide background for an understanding of the interface structure after elevated temperature annealing. Oxidation studies of Si surfaces covered with metal overlayers yield insight about the effect of metal atoms in the Si oxidation mechanisms and are useful in the identification of subtle differences in bonding relations between atoms at the metal/Si interfaces. Core level and valence band spectra with variable surface sensitivities were used to study the interactions between metal, Si, and oxygen for metal coverages and oxide thickness in the monolayer region. Interface morphology at the initial stage of metal/Si interface formation and after oxidation was modeled on the basis of the evolutions of metal and Si signals at different probing depths in the photoemission experiment. Both Ni/Si and Au/Si interfaces formed at room temperature have a diffusive region at the interface. This is composed of a layer of metal-Si alloy, formed by Si outdiffusion into the metal overlayer, above a layer of interstitial metal atoms in the Si substrate. Different atomic structures of these two regions at Ni/Si interface can account for the two different growth orientations of epitaxial Ni disilicides on the Si(111) surface after thermal annealing. Annealing the Au/Si interface at high temperature depletes all the Au atoms except for one monolayer of Au on the Si(111) surface. These phenomena are attributed to differences in the metal-Si chemical bonding relations associated with specific atomic structures. After oxygen exposures, both the Ni disilicide surface and Au covered Si surfaces (with different coverages and surface orderings) show silicon in higher oxidation states, in comparison to oxidized silicon on a clean surface. Preferential Si dioxide growth on the Au/Si surface is related to the strong distortion of the Si lattice when Au-Si bonds are formed. In comparison, a monolayer of Ni on a Si surface, with its weaker Ni-Si bond, does not enhance oxide formation.

A discriminatory function for prediction of protein-DNA interactions based on alpha shape modeling.

PubMed

Zhou, Weiqiang; Yan, Hong

2010-10-15

Protein-DNA interaction has significant importance in many biological processes. However, the underlying principle of the molecular recognition process is still largely unknown. As more high-resolution 3D structures of protein-DNA complex are becoming available, the surface characteristics of the complex become an important research topic. In our work, we apply an alpha shape model to represent the surface structure of the protein-DNA complex and developed an interface-atom curvature-dependent conditional probability discriminatory function for the prediction of protein-DNA interaction. The interface-atom curvature-dependent formalism captures atomic interaction details better than the atomic distance-based method. The proposed method provides good performance in discriminating the native structures from the docking decoy sets, and outperforms the distance-dependent formalism in terms of the z-score. Computer experiment results show that the curvature-dependent formalism with the optimal parameters can achieve a native z-score of -8.17 in discriminating the native structure from the highest surface-complementarity scored decoy set and a native z-score of -7.38 in discriminating the native structure from the lowest RMSD decoy set. The interface-atom curvature-dependent formalism can also be used to predict apo version of DNA-binding proteins. These results suggest that the interface-atom curvature-dependent formalism has a good prediction capability for protein-DNA interactions. The code and data sets are available for download on http://www.hy8.com/bioinformatics.htm kenandzhou@hotmail.com.

Quasi-2D silicon structures based on ultrathin Me2Si (Me = Mg, Ca, Sr, Ba) films

NASA Astrophysics Data System (ADS)

Migas, D. B.; Bogorodz, V. O.; Filonov, A. B.; Borisenko, V. E.; Skorodumova, N. V.

2018-04-01

By means of ab initio calculations with hybrid functionals we show a possibility for quasi-2D silicon structures originated from semiconducting Mg2Si, Ca2Si, Sr2Si and Ba2Si silicides to exist. Such a 2D structure is similar to the one of transition metal chalcogenides where silicon atoms form a layer in between of metal atoms aligned in surface layers. These metal surface atoms act as pseudo passivation species stabilizing crystal structure and providing semiconducting properties. Considered 2D Mg2Si, Ca2Si, Sr2Si and Ba2Si have band gaps of 1.14 eV, 0.69 eV, 0.33 eV and 0.19 eV, respectively, while the former one is also characterized by a direct transition with appreciable oscillator strength. Electronic states of the surface atoms are found to suppress an influence of the quantum confinement on the band gaps. Additionally, we report Sr2Si bulk in the cubic structure to have a direct band gap of 0.85 eV as well as sizable oscillator strength of the first direct transition.

Oxide surfaces and metal/oxide interfaces studied by grazing incidence X-ray scattering

NASA Astrophysics Data System (ADS)

Renaud, Gilles

Experimental determinations of the atomic structure of insulating oxide surfaces and metal/oxide interfaces are scarce, because surface science techniques are often limited by the insulating character of the substrate. Grazing incidence X-ray scattering (GIXS), which is not subject to charge effects, can provide very precise information on the atomic structure of oxide surfaces: roughness, relaxation and reconstruction. It is also well adapted to analyze the atomic structure, the registry, the misfit relaxation, elastic or plastic, the growth mode and the morphology of metal/oxide interfaces during their growth, performed in situ. GIXS also allows the analysis of thin films and buried interfaces, in a non-destructive way, yielding the epitaxial relationships, and, by variation of the grazing incidence angle, the lattice parameter relaxation along the growth direction. On semi-coherent interfaces, the existence of an ordered network of interfacial misfit dislocations can be demonstrated, its Burger's vector determined, its ordering during in situ annealing cycles followed, and sometimes even its atomic structure can be addressed. Careful analysis during growth allows the modeling of the dislocation nucleation process. This review emphasizes the new information that GIXS can bring to oxide surfaces and metal/oxide interfaces by comparison with other surface science techniques. The principles of X-ray diffraction by surfaces and interfaces are recalled, together with the advantages and properties of grazing angles. The specific experimental requirements are discussed. Recent results are presented on the determination of the atomic structure of relaxed or reconstructed oxide surfaces. A description of results obtained during the in situ growth of metal on oxide surfaces is also given, as well as investigations of thick metal films on oxide surfaces, with lattice parameter misfit relaxed by an array of dislocations. Recent work performed on oxide thin films having important physical properties such as superconductivity or magnetism is also briefly reviewed. The strengths and limitations of the technique, such as the need for single crystals and surfaces of high crystalline quality are discussed. Finally, an outlook of future prospects in the field is given, such as the study of more complex oxide surfaces, vicinal surfaces, reactive metal/oxide interfaces, metal oxidation processes, the use of surfactants to promote wetting of a metal deposited on an oxide surface or the study of oxide/liquid interfaces in a non-UHV environment.

Growth of two-dimensional Ge crystal by annealing of heteroepitaxial Ag/Ge(111) under N2 ambient

NASA Astrophysics Data System (ADS)

Ito, Koichi; Ohta, Akio; Kurosawa, Masashi; Araidai, Masaaki; Ikeda, Mitsuhisa; Makihara, Katsunori; Miyazaki, Seiichi

2018-06-01

The growth of a two-dimensional crystal of Ge atoms on an atomically flat Ag(111) surface has been demonstrated by the thermal annealing of a heteroepitaxial Ag/Ge structure in N2 ambient at atmospheric pressure. The surface morphology and chemical bonding features of heteroepitaxial Ag(111) grown on wet-cleaned Ge(111) after annealing at different temperatures and for various times have been systematically investigated to control the surface segregation of Ge atoms and the planarization of the heteroepitaxial Ag(111) surface.

Automated extraction of single H atoms with STM: tip state dependency

NASA Astrophysics Data System (ADS)

Møller, Morten; Jarvis, Samuel P.; Guérinet, Laurent; Sharp, Peter; Woolley, Richard; Rahe, Philipp; Moriarty, Philip

2017-02-01

The atomistic structure of the tip apex plays a crucial role in performing reliable atomic-scale surface and adsorbate manipulation using scanning probe techniques. We have developed an automated extraction routine for controlled removal of single hydrogen atoms from the H:Si(100) surface. The set of atomic extraction protocols detect a variety of desorption events during scanning tunneling microscope (STM)-induced modification of the hydrogen-passivated surface. The influence of the tip state on the probability for hydrogen removal was examined by comparing the desorption efficiency for various classifications of STM topographs (rows, dimers, atoms, etc). We find that dimer-row-resolving tip apices extract hydrogen atoms most readily and reliably (and with least spurious desorption), while tip states which provide atomic resolution counter-intuitively have a lower probability for single H atom removal.

Large-angle illumination STEM: Toward three-dimensional atom-by-atom imaging

DOE PAGES

Ishikawa, Ryo; Lupini, Andrew R.; Hinuma, Yoyo; ...

2014-11-26

To completely understand and control materials and their properties, it is of critical importance to determine their atomic structures in all three dimensions. Recent revolutionary advances in electron optics – the inventions of geometric and chromatic aberration correctors as well as electron source monochromators – have provided fertile ground for performing optical depth sectioning at atomic-scale dimensions. In this study we theoretically demonstrate the imaging of top/sub-surface atomic structures and identify the depth of single dopants, single vacancies and the other point defects within materials by large-angle illumination scanning transmission electron microscopy (LAI-STEM). The proposed method also allows us tomore » measure specimen properties such as thickness or three-dimensional surface morphology using observations from a single crystallographic orientation.« less

University of Maryland MRSEC - Research: IRG1

Science.gov Websites

structure based on fundamental interactions, to device preparation and characterization. Materials systems figure: Electrical current in nanoscale structure perturbed by scattering at atomic scale features on its surfaces. An electrical current in a nanoscale structure is perturbed by scattering at atomic scale

Chemical contrast in STM imaging of transition metal aluminides

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

Duguet, T.; Thiel, Patricia A.

2012-08-01

The present manuscript reviews recent scanning tunnelling microscopy (STM) studies of transition metal (TM) aluminide surfaces. It provides a general perspective on the contrast between Al atoms and TM atoms in STM imaging. A general trend is the much stronger bias dependence of TM atoms, or TM-rich regions of the surface. This dependence can be attenuated by the local chemical arrangements and environments. Al atoms can show a stronger bias dependence when their chemical environment, such as their immediate subsurface, is populated with TM. All this is well explained in light of combined results of STM and both theoretical andmore » experimental electronic and crystallographic structure determinations. Since STM probes the Fermi surface, the electronic structure in the vicinity of the Fermi level (EF) is essential for understanding contrast and bias dependence. Hence, partial density of states provides information about the TM d band position and width, s–p–d hybridization or interactions, or charge transfer between constituent elements. In addition, recent developments in STM image simulations are very interesting for elucidating chemical contrast at Al–TM alloy surfaces, and allow direct atomic identification, when the surface does not show too much disorder. Overall, we show that chemically-specific imaging is often possible at these surfaces.« less

3D-SURFER 2.0: web platform for real-time search and characterization of protein surfaces.

PubMed

Xiong, Yi; Esquivel-Rodriguez, Juan; Sael, Lee; Kihara, Daisuke

2014-01-01

The increasing number of uncharacterized protein structures necessitates the development of computational approaches for function annotation using the protein tertiary structures. Protein structure database search is the basis of any structure-based functional elucidation of proteins. 3D-SURFER is a web platform for real-time protein surface comparison of a given protein structure against the entire PDB using 3D Zernike descriptors. It can smoothly navigate the protein structure space in real-time from one query structure to another. A major new feature of Release 2.0 is the ability to compare the protein surface of a single chain, a single domain, or a single complex against databases of protein chains, domains, complexes, or a combination of all three in the latest PDB. Additionally, two types of protein structures can now be compared: all-atom-surface and backbone-atom-surface. The server can also accept a batch job for a large number of database searches. Pockets in protein surfaces can be identified by VisGrid and LIGSITE (csc) . The server is available at http://kiharalab.org/3d-surfer/.

Effects of temperature and surface orientation on migration behaviours of helium atoms near tungsten surfaces

NASA Astrophysics Data System (ADS)

Wang, Xiaoshuang; Wu, Zhangwen; Hou, Qing

2015-10-01

Molecular dynamics simulations were performed to study the dependence of migration behaviours of single helium atoms near tungsten surfaces on the surface orientation and temperature. For W{100} and W{110} surfaces, He atoms can quickly escape out near the surface without accumulation even at a temperature of 400 K. The behaviours of helium atoms can be well-described by the theory of continuous diffusion of particles in a semi-infinite medium. For a W{111} surface, the situation is complex. Different types of trap mutations occur within the neighbouring region of the W{111} surface. The trap mutations hinder the escape of He atoms, resulting in their accumulation. The probability of a He atom escaping into vacuum from a trap mutation depends on the type of the trap mutation, and the occurrence probabilities of the different types of trap mutations are dependent on the temperature. This finding suggests that the escape rate of He atoms on the W{111} surface does not show a monotonic dependence on temperature. For instance, the escape rate at T = 1500 K is lower than the rate at T = 1100 K. Our results are useful for understanding the structural evolution and He release on tungsten surfaces and for designing models in other simulation methods beyond molecular dynamics.

Sulfur Adsorption on the Goethite (110) Surface

NASA Astrophysics Data System (ADS)

Simonetti, S.; Damiani, D.; Brizuela, G.; Juan, A.

The electronic structure of S adsorption on goethite (110) surface has been studied by ASED-MO cluster calculations. For S location, the most exposed surface atoms of goethite surface were selected. The calculations show that the surface offers several places for S adsorption. The most energetically stable system corresponds to S location above H atom. We studied in detail the configurations that correspond to the higher OP values. For these configurations, the H-S and Fe-S computed distances are 2.1 and 3.7 Å, respectively. The H-S and Fe-S are mainly bonding interaction with OP values of 0.156 and 0.034, respectively. The Fe-S interaction mainly involves Fe 3dx2-y2 atomic orbitals with lesser participation of Fe 4py and Fe 3dyz atomic orbitals. The O-S interaction shows the same bonding and antibonding contributions giving a small OP value. The O-S interaction involves O 2p orbitals. There is an electron transfer to the Fe atom from the S atom. On the other hand, there is an electron transfer to S atom from the H and O atoms, respectively.

Atomic force microscope studies of fullerene films - Highly stable C60 fcc (311) free surfaces

NASA Technical Reports Server (NTRS)

Snyder, Eric J.; Tong, William M.; Williams, R. S.; Anz, Samir J.; Anderson, Mark S.

1991-01-01

Atomic force microscopy and X-ray diffractometry were used to study 1500 A-thick films of pure C60 grown by sublimation in ultrahigh vacuum onto a CaF2 (111) substrte. Topographs of the films did not reveal the expected close-packed structures, but they showed instead large regions that correspond to a face-centered cubic (311) surface and distortions of this surface. The open (311) structure may have a relatively low free energy because the low packing density contributes to a high entropy of the exposed surface.

Surface control of epitaxial manganite films via oxygen pressure

DOE PAGES

Tselev, Alexander; Vasudevan, Rama K.; Gianfrancesco, Anthony G.; ...

2015-03-11

The trend to reduce device dimensions demands increasing attention to atomic-scale details of structure of thin films as well as to pathways to control it. We found that this is of special importance in the systems with multiple competing interactions. We have used in situ scanning tunneling microscopy to image surfaces of La 5/8Ca 3/8MnO 3 films grown by pulsed laser deposition. The atomically resolved imaging was combined with in situ angle-resolved X-ray photoelectron spectroscopy. We find a strong effect of the background oxygen pressure during deposition on structural and chemical features of the film surface. Deposition at 50 mTorrmore » of O 2 leads to mixed-terminated film surfaces, with B-site (MnO 2) termination being structurally imperfect at the atomic scale. Moreover, a relatively small reduction of the oxygen pressure to 20 mTorr results in a dramatic change of the surface structure leading to a nearly perfectly ordered B-site terminated surface with only a small fraction of A-site (La,Ca)O termination. This is accompanied, however, by surface roughening at a mesoscopic length scale. The results suggest that oxygen has a strong link to the adatom mobility during growth. The effect of the oxygen pressure on dopant surface segregation is also pronounced: Ca surface segregation is decreased with oxygen pressure reduction.« less

Imaging and manipulation of adatoms on an alumina surface by noncontact atomic force microscopy

NASA Astrophysics Data System (ADS)

Simon, G. H.; Heyde, M.; Freund, H.-J.

2012-02-01

Noncontact atomic force microscopy (NC-AFM) has been performed on an aluminum oxide film grown on NiAl(110) in ultrahigh vacuum (UHV) at low temperature (5 K). Results reproduce the topography of the structural model, unlike scanning tunnelling microscopy (STM) images. Equipped with this extraordinary contrast the network of extended defects, which stems from domain boundaries intersecting the film surface, can be analysed in atomic detail. The knowledge of occurring surface structures opens up the opportunity to determine adsorption sites of individual adsorbates on the alumina film. The level of difficulty for such imaging depends on the imaging characteristics of the substrate and the interaction which can be maintained above the adsorbate. Positions of single adsorbed gold atoms within the unit cell have been determined despite their easy removal at slightly higher interaction strength. Preliminary manipulation experiments indicate a pick-up process for the vanishing of the gold adatoms from the film surface.

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

Interaction transfer of silicon atoms forming Co silicide for Co/√(3)×√(3)R30°-Ag/Si(111) and related magnetic properties

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

Chang, Cheng-Hsun-Tony; Fu, Tsu-Yi; Tsay, Jyh-Shen, E-mail: jstsay@phy.ntnu.edu.tw

Combined scanning tunneling microscopy, Auger electron spectroscopy, and surface magneto-optic Kerr effect studies were employed to study the microscopic structures and magnetic properties for ultrathin Co/√(3)×√(3)R30°-Ag/Si(111). As the annealing temperature increases, the upward diffusion of Si atoms and formation of Co silicides occurs at temperature above 400 K. Below 600 K, the √(3)×√(3)R30°-Ag/Si(111) surface structure persists. We propose an interaction transferring mechanism of Si atoms across the √(3)×√(3)R30°-Ag layer. The upward transferred Si atoms react with Co atoms to form Co silicide. The step height across the edge of the island, a separation of 0.75 nm from the analysis of the 2 × 2 structure,more » and the calculations of the normalized Auger signal serve as strong evidences for the formation of CoSi{sub 2} at the interface. The interaction transferring mechanism for Si atoms enhances the possibility of interactions between Co and Si atoms. The smoothness of the surface is advantage for that the easy axis of magnetization for Co/√(3)×√(3)R30°-Ag/Si(111) is in the surface plane. This provides a possible way of growing flat magnetic layers on silicon substrate with controllable silicide formation and shows potential applications in spintronics devices.« less

Oxygen adsorption on the Al₉Co₂(001) surface: first-principles and STM study.

PubMed

Villaseca, S Alarcón; Loli, L N Serkovic; Ledieu, J; Fournée, V; Gille, P; Dubois, J-M; Gaudry, E

2013-09-04

Atomic oxygen adsorption on a pure aluminum terminated Al9Co2(001) surface is studied by first-principle calculations coupled with STM measurements. Relative adsorption energies of oxygen atoms have been calculated on different surface sites along with the associated STM images. The local electronic structure of the most favourable adsorption site is described. The preferential adsorption site is identified as a 'bridge' type site between the cluster entities exposed at the (001) surface termination. The Al-O bonding between the adsorbate and the substrate presents a covalent character, with s-p hybridization occurring between the states of the adsorbed oxygen atom and the aluminum atoms of the surface. The simulated STM image of the preferential adsorption site is in agreement with experimental observations. This work shows that oxygen adsorption generates important atomic relaxations of the topmost surface layer and that sub-surface cobalt atoms strongly influence the values of the adsorption energies. The calculated Al-O distances are in agreement with those reported in Al2O and Al2O3 oxides and for oxygen adsorption on Al(111).

Thermal treatment induced modification of structural, surface and bulk magnetic properties of Fe61.5Co5Ni8Si13.5B9Nb3 metallic glass

NASA Astrophysics Data System (ADS)

Shah, M.; Satalkar, M.; Kane, S. N.; Ghodke, N. L.; Sinha, A. K.; Varga, L. K.; Teixeira, J. M.; Araujo, J. P.

2018-05-01

Effect of thermal annealing induced modification of structural, surface and bulk magnetic properties of Fe61.5Co5Ni8Si13.5B9Nb3 alloy is presented. The changes in properties were observed using synchrotron x-ray diffraction technique (SXRD), atomic force microscopy (AFM), magneto-optical kerr effect (MOKE) and bulk magnetic measurements. Significant variations on the both side of surface occur for the annealing temperature upto 500 °C promotes the surface crystallization. Surface roughness appears due to presence of nanocrystallization plays an important role in determining magnetic properties. Observed lower value of bulk coercivity Hc of 6.2 A/m annealed temperature at 450 °C/1 h ascribed to reduction of disorder as compared to the surface (both shiny and wheel side observed by MOKE measurement) whereas improvement of bulk saturation magnetization with annealing temperature indicates first near neighbor shell of Fe atoms are surrounded by Fe atoms. Evolution of coercivity of surface and bulk with annealing temperature has been presented in conjunction with the structural observations.

Atomic-Scale Structure of the Hematite α-Fe2O3(11̅02) “R-Cut” Surface

PubMed Central

2017-01-01

The α-Fe2O3(11̅02) surface (also known as the hematite r-cut or (012) surface) was studied using low-energy electron diffraction (LEED), X-ray photoelectron spectroscopy (XPS), ultraviolet photoelectron spectroscopy (UPS), scanning tunneling microscopy (STM), noncontact atomic force microscopy (nc-AFM), and ab initio density functional theory (DFT)+U calculations. Two surface structures are stable under ultrahigh vacuum (UHV) conditions; a stoichiometric (1 × 1) surface can be prepared by annealing at 450 °C in ≈10–6 mbar O2, and a reduced (2 × 1) reconstruction is formed by UHV annealing at 540 °C. The (1 × 1) surface is close to an ideal bulk termination, and the undercoordinated surface Fe atoms reduce the surface bandgap by ≈0.2 eV with respect to the bulk. The work function is measured to be 5.7 ± 0.2 eV, and the VBM is located 1.5 ± 0.1 eV below EF. The images obtained from the (2 × 1) reconstruction cannot be reconciled with previously proposed models, and a new “alternating trench” structure is proposed based on an ordered removal of lattice oxygen atoms. DFT+U calculations show that this surface is favored in reducing conditions and that 4-fold-coordinated Fe2+ cations at the surface introduce gap states approximately 1 eV below EF. The work function on the (2 × 1) termination is 5.4 ± 0.2 eV. PMID:29492182

Tailoring Dirac Fermions in Molecular Graphene

NASA Astrophysics Data System (ADS)

Gomes, Kenjiro K.; Mar, Warren; Ko, Wonhee; Camp, Charlie D.; Rastawicki, Dominik K.; Guinea, Francisco; Manoharan, Hari C.

2012-02-01

The dynamics of electrons in solids is tied to the band structure created by a periodic atomic potential. The design of artificial lattices, assembled through atomic manipulation, opens the door to engineer electronic band structure and to create novel quantum states. We present scanning tunneling spectroscopic measurements of a nanoassembled honeycomb lattice displaying a Dirac fermion band structure. The artificial lattice is created by atomic manipulation of single CO molecules with the scanning tunneling microscope on the surface of Cu(111). The periodic potential generated by the assembled CO molecules reshapes the band structure of the two-dimensional electron gas, present as a surface state of Cu(111), into a ``molecular graphene'' system. We create local defects in the lattice to observe the quasiparticle interference patterns that unveil the underlying band structure. We present direct comparison between the tunneling data, first-principles calculations of the band structure, and tight-binding models.

A Gaussian Approximation Potential for Silicon

NASA Astrophysics Data System (ADS)

Bernstein, Noam; Bartók, Albert; Kermode, James; Csányi, Gábor

We present an interatomic potential for silicon using the Gaussian Approximation Potential (GAP) approach, which uses the Gaussian process regression method to approximate the reference potential energy surface as a sum of atomic energies. Each atomic energy is approximated as a function of the local environment around the atom, which is described with the smooth overlap of atomic environments (SOAP) descriptor. The potential is fit to a database of energies, forces, and stresses calculated using density functional theory (DFT) on a wide range of configurations from zero and finite temperature simulations. These include crystalline phases, liquid, amorphous, and low coordination structures, and diamond-structure point defects, dislocations, surfaces, and cracks. We compare the results of the potential to DFT calculations, as well as to previously published models including Stillinger-Weber, Tersoff, modified embedded atom method (MEAM), and ReaxFF. We show that it is very accurate as compared to the DFT reference results for a wide range of properties, including low energy bulk phases, liquid structure, as well as point, line, and plane defects in the diamond structure.

A first principle study for the adsorption and absorption of carbon atom and the CO dissociation on Ir(100) surface

NASA Astrophysics Data System (ADS)

Erikat, I. A.; Hamad, B. A.

2013-11-01

We employ density functional theory to examine the adsorption and absorption of carbon atom as well as the dissociation of carbon monoxide on Ir(100) surface. We find that carbon atoms bind strongly with Ir(100) surface and prefer the high coordination hollow site for all coverages. In the case of 0.75 ML coverage of carbon, we obtain a bridging metal structure due to the balance between Ir-C and Ir-Ir interactions. In the subsurface region, the carbon atom prefers the octahedral site of Ir(100) surface. We find large diffusion barrier for carbon atom into Ir(100) surface (2.70 eV) due to the strong bonding between carbon atom and Ir(100) surface, whereas we find a very small segregation barrier (0.22 eV) from subsurface to the surface. The minimum energy path and energy barrier for the dissociation of CO on Ir(100) surface are obtained by using climbing image nudge elastic band. The energy barrier of CO dissociation on Ir(100) surface is found to be 3.01 eV, which is appreciably larger than the association energy (1.61 eV) of this molecule.

A first principle study for the adsorption and absorption of carbon atom and the CO dissociation on Ir(100) surface.

PubMed

Erikat, I A; Hamad, B A

2013-11-07

We employ density functional theory to examine the adsorption and absorption of carbon atom as well as the dissociation of carbon monoxide on Ir(100) surface. We find that carbon atoms bind strongly with Ir(100) surface and prefer the high coordination hollow site for all coverages. In the case of 0.75 ML coverage of carbon, we obtain a bridging metal structure due to the balance between Ir-C and Ir-Ir interactions. In the subsurface region, the carbon atom prefers the octahedral site of Ir(100) surface. We find large diffusion barrier for carbon atom into Ir(100) surface (2.70 eV) due to the strong bonding between carbon atom and Ir(100) surface, whereas we find a very small segregation barrier (0.22 eV) from subsurface to the surface. The minimum energy path and energy barrier for the dissociation of CO on Ir(100) surface are obtained by using climbing image nudge elastic band. The energy barrier of CO dissociation on Ir(100) surface is found to be 3.01 eV, which is appreciably larger than the association energy (1.61 eV) of this molecule.

The Tunneling Microscope: A New Look at the Atomic World.

ERIC Educational Resources Information Center

Golovchenko, J. A.

1986-01-01

A new instrument called the tunneling microscope has recently been developed that is capable of generating real-space images of surfaces showing atomic structure. Discusses current capabilities, limitations, and the physics involved in the technique. Includes results from a study of silicon crystal surfaces. (JN)

Experimental evidence and structural modeling of nonstoichiometric (010) surfaces coexisting in hydroxyapatite nano-crystals.

PubMed

Ospina, C A; Terra, J; Ramirez, A J; Farina, M; Ellis, D E; Rossi, A M

2012-01-01

High-resolution transmission electron microscopy (HRTEM) and ab initio quantum-mechanical calculations of electronic structure were combined to investigate the structure of the hydroxyapatite (HA) (010) surface, which plays an important role in HA interactions with biological media. HA was synthesized by in vitro precipitation at 37°C. HRTEM images revealed thin elongated rod nanoparticles with preferential growth along the [001] direction and terminations parallel to the (010) plane. The focal series reconstruction (FSR) technique was applied to develop an atomic-scale structural model of the high-resolution images. The HRTEM simulations identified the coexistence of two structurally distinct terminations for (010) surfaces: a rather flat Ca(II)-terminated surface and a zig-zag structure with open OH channels. Density functional theory (DFT) was applied in a periodic slab plane-wave pseudopotential approach to refine details of atomic coordination and bond lengths of Ca(I) and Ca(II) sites in hydrated HA (010) surfaces, starting from the HRTEM model. Copyright © 2011 Elsevier B.V. All rights reserved.

REVIEWS OF TOPICAL PROBLEMS: Properties of matter in ultrahigh magnetic fields and the structure of the surface of neutron stars

NASA Astrophysics Data System (ADS)

Liberman, Mikhail A.; Johansson, B.

1995-02-01

The physical properties of atoms, molecules, and solids in ultrahigh magnetic fields B gg 109 G that are believed to exist on the surface of neutron stars are discussed. In these fields, atoms are strongly deformed and elongated along the magnetic field lines; the binding energy and ionizing energy of the atoms are substantially increased and the interatomic interaction is dramatically changed. This strongly modifies the properties of matter at the surface of magnetic neutron stars which are crucial for modelling the pulsar magnetosphere. A scenario for magnetosphere evolution is proposed which suggests free emission for a young pulsar and strong binding of the matter to the surface at a later stage. This later stage is due to strongly bound chains of alternate heavy atoms and light atoms accreted on the surface of the star.

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.

The use of analytical surface tools in the fundamental study of wear. [atomic nature of wear

NASA Technical Reports Server (NTRS)

Buckley, D. H.

1977-01-01

Various techniques and surface tools available for the study of the atomic nature of the wear of materials are reviewed These include chemical etching, x-ray diffraction, electron diffraction, scanning electron microscopy, low-energy electron diffraction, Auger emission spectroscopy analysis, electron spectroscopy for chemical analysis, field ion microscopy, and the atom probe. Properties of the surface and wear surface regions which affect wear, such as surface energy, crystal structure, crystallographic orientation, mode of dislocation behavior, and cohesive binding, are discussed. A number of mechanisms involved in the generation of wear particles are identified with the aid of the aforementioned tools.

Atomic clusters and atomic surfaces in icosahedral quasicrystals.

PubMed

Quiquandon, Marianne; Portier, Richard; Gratias, Denis

2014-05-01

This paper presents the basic tools commonly used to describe the atomic structures of quasicrystals with a specific focus on the icosahedral phases. After a brief recall of the main properties of quasiperiodic objects, two simple physical rules are discussed that lead one to eventually obtain a surprisingly small number of atomic structures as ideal quasiperiodic models for real quasicrystals. This is due to the fact that the atomic surfaces (ASs) used to describe all known icosahedral phases are located on high-symmetry special points in six-dimensional space. The first rule is maximizing the density using simple polyhedral ASs that leads to two possible sets of ASs according to the value of the six-dimensional lattice parameter A between 0.63 and 0.79 nm. The second rule is maximizing the number of complete orbits of high symmetry to construct as large as possible atomic clusters similar to those observed in complex intermetallic structures and approximant phases. The practical use of these two rules together is demonstrated on two typical examples of icosahedral phases, i-AlMnSi and i-CdRE (RE = Gd, Ho, Tm).

Thermodynamic Stability of Molybdenum Oxycarbides Formed from Orthorhombic Mo 2 C in Oxygen-Rich Environments

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

Likith, S. R. J.; Farberow, C. A.; Manna, S.

Molybdenum carbide (Mo 2C) nanoparticles and thin films are particularly suitable catalysts for catalytic fast pyrolysis (CFP) as they are effective for deoxygenation and can catalyze certain reactions that typically occur on noble metals. Oxygen deposited during deoxygenation reactions may alter the carbide structure, leading to the formation of oxycarbides, which can determine changes in catalytic activity or selectivity. Despite emerging spectroscopic evidence of bulk oxycarbides, so far there have been no reports of their precise atomic structure or their relative stability with respect to orthorhombic Mo 2C. This knowledge is essential for assessing the catalytic properties of molybdenum (oxy)carbidesmore » for CFP. In this article, we use density functional theory (DFT) calculations to (a) describe the thermodynamic stability of surface and subsurface configurations of oxygen and carbon atoms for a commonly studied Mo-terminated surface of orthorhombic Mo 2C and (b) determine atomic structures for oxycarbides with a Mo:C ratio of 2:1. The surface calculations suggest that oxygen atoms are not stable under the top Mo layer of the Mo 2C(100) surface. Coupling DFT calculations with a polymorph sampling method, we determine (Mo 2C) xO y oxycarbide structures for a wide range of oxygen compositions. Oxycarbides with lower oxygen content (y/x = 2) adopt layered structures reminiscent of the parent carbide phase, with flat Mo layers separated by layers of oxygen and carbon; for higher oxygen content, our results suggest the formation of amorphous phases, as the atomic layers lose their planarity with increasing oxygen content. We characterize the oxidation states of Mo in the oxycarbide structures determined computationally, and simulate their X-ray diffraction (XRD) patterns in order to facilitate comparisons with experiments. Our study may provide a platform for large-scale investigations of the catalytic properties of oxycarbides and their surfaces and for tailoring the catalytic properties for different desired reactions.« less

Thermodynamic Stability of Molybdenum Oxycarbides Formed from Orthorhombic Mo 2 C in Oxygen-Rich Environments

DOE PAGES

Likith, S. R. J.; Farberow, C. A.; Manna, S.; ...

2017-12-20

Molybdenum carbide (Mo 2C) nanoparticles and thin films are particularly suitable catalysts for catalytic fast pyrolysis (CFP) as they are effective for deoxygenation and can catalyze certain reactions that typically occur on noble metals. Oxygen deposited during deoxygenation reactions may alter the carbide structure, leading to the formation of oxycarbides, which can determine changes in catalytic activity or selectivity. Despite emerging spectroscopic evidence of bulk oxycarbides, so far there have been no reports of their precise atomic structure or their relative stability with respect to orthorhombic Mo 2C. This knowledge is essential for assessing the catalytic properties of molybdenum (oxy)carbidesmore » for CFP. In this article, we use density functional theory (DFT) calculations to (a) describe the thermodynamic stability of surface and subsurface configurations of oxygen and carbon atoms for a commonly studied Mo-terminated surface of orthorhombic Mo 2C and (b) determine atomic structures for oxycarbides with a Mo:C ratio of 2:1. The surface calculations suggest that oxygen atoms are not stable under the top Mo layer of the Mo 2C(100) surface. Coupling DFT calculations with a polymorph sampling method, we determine (Mo 2C) xO y oxycarbide structures for a wide range of oxygen compositions. Oxycarbides with lower oxygen content (y/x = 2) adopt layered structures reminiscent of the parent carbide phase, with flat Mo layers separated by layers of oxygen and carbon; for higher oxygen content, our results suggest the formation of amorphous phases, as the atomic layers lose their planarity with increasing oxygen content. We characterize the oxidation states of Mo in the oxycarbide structures determined computationally, and simulate their X-ray diffraction (XRD) patterns in order to facilitate comparisons with experiments. Our study may provide a platform for large-scale investigations of the catalytic properties of oxycarbides and their surfaces and for tailoring the catalytic properties for different desired reactions.« less

Identification of the Structure Model of the Si(111)-(5×2)-Au Surface

NASA Astrophysics Data System (ADS)

Shirasawa, Tetsuroh; Voegeli, Wolfgang; Nojima, Takehiro; Iwasawa, Yusaku; Yamaguchi, Yudai; Takahashi, Toshio

2014-10-01

The atomic structure of the Si(111)-(5×2)-Au surface, a periodic gold chain on the silicon surface, has been a long-debated issue in surface science. The recent three candidates, the so-called Erwin-Barke-Himpsel (EBH) model [S. C. Erwin, I. Barke, and F. J. Himpsel, Phys. Rev. B 80, 155409 (2009)], the Abukawa-Nishigaya (AN) model [T. Abukawa and Y. Nishigaya, Phys. Rev. Lett. 110, 036102 (2013)], and the Kwon-Kang (KK) model [S. G. Kwon and M. H. Kang, Phys. Rev. Lett. 113, 086101 (2014)] that has one additional Au atom than the EBH model are tested by surface x-ray diffraction data. A two-dimensional Patterson map constructed from the in-plane diffraction intensities rejects the AN model and prefers the KK model over the EBH model. On the basis of the arrangement of Au obtained from the Patterson map, all the reconstructed Si atoms, such as the so-called honeycomb chain structure, are directly imaged out by utilizing a holographic method. The KK model reproduces out-of-plane diffraction data as well.

Interfaces in Heterogeneous Catalysts: Advancing Mechanistic Understanding through Atomic-Scale Measurements.

PubMed

Gao, Wenpei; Hood, Zachary D; Chi, Miaofang

2017-04-18

Developing novel catalysts with high efficiency and selectivity is critical for enabling future clean energy conversion technologies. Interfaces in catalyst systems have long been considered the most critical factor in controlling catalytic reaction mechanisms. Interfaces include not only the catalyst surface but also interfaces within catalyst particles and those formed by constructing heterogeneous catalysts. The atomic and electronic structures of catalytic surfaces govern the kinetics of binding and release of reactant molecules from surface atoms. Interfaces within catalysts are introduced to enhance the intrinsic activity and stability of the catalyst by tuning the surface atomic and chemical structures. Examples include interfaces between the core and shell, twin or domain boundaries, or phase boundaries within single catalyst particles. In supported catalyst nanoparticles (NPs), the interface between the metallic NP and support serves as a critical tuning factor for enhancing catalytic activity. Surface electronic structure can be indirectly tuned and catalytically active sites can be increased through the use of supporting oxides. Tuning interfaces in catalyst systems has been identified as an important strategy in the design of novel catalysts. However, the governing principle of how interfaces contribute to catalyst behavior, especially in terms of interactions with intermediates and their stability during electrochemical operation, are largely unknown. This is mainly due to the evolving nature of such interfaces. Small changes in the structural and chemical configuration of these interfaces may result in altering the catalytic performance. These interfacial arrangements evolve continuously during synthesis, processing, use, and even static operation. A technique that can probe the local atomic and electronic interfacial structures with high precision while monitoring the dynamic interfacial behavior in situ is essential for elucidating the role of interfaces and providing deeper insight for fine-tuning and optimizing catalyst properties. Scanning transmission electron microscopy (STEM) has long been a primary characterization technique used for studying nanomaterials because of its exceptional imaging resolution and simultaneous chemical analysis. Over the past decade, advances in STEM, that is, the commercialization of both aberration correctors and monochromators, have significantly improved the spatial and energy resolution. Imaging atomic structures with subangstrom resolution and identifying chemical species with single-atom sensitivity are now routine for STEM. These advancements have greatly benefitted catalytic research. For example, the roles of lattice strain and surface elemental distribution and their effect on catalytic stability and reactivity have been well documented in bimetallic catalysts. In addition, three-dimensional atomic structures revealed by STEM tomography have been integrated in theoretical modeling for predictive catalyst NP design. Recent developments in stable electronic and mechanical devices have opened opportunities to monitor the evolution of catalysts in operando under synthesis and reaction conditions; high-speed direct electron detectors have achieved sub-millisecond time resolutions and allow for rapid structural and chemical changes to be captured. Investigations of catalysts using these latest microscopy techniques have provided new insights into atomic-level catalytic mechanisms. Further integration of new microscopy methods is expected to provide multidimensional descriptions of interfaces under relevant synthesis and reaction conditions. In this Account, we discuss recent insights on understanding catalyst activity, selectivity, and stability using advanced STEM techniques, with an emphasis on how critical interfaces dictate the performance of precious metal-based heterogeneous catalysts. The role of extended interfacial structures, including those between core and shell, between separate phases and twinned grains, between the catalyst surface and gas, and between metal and support are discussed. We also provide an outlook on how emerging electron microscopy techniques, such as vibrational spectroscopy and electron ptychography, will impact future catalysis research.

Ferromagnetic Coupling of Mononuclear Fe Centers in a Self-Assembled Metal-Organic Network on Au(111)

NASA Astrophysics Data System (ADS)

Umbach, T. R.; Bernien, M.; Hermanns, C. F.; Krüger, A.; Sessi, V.; Fernandez-Torrente, I.; Stoll, P.; Pascual, J. I.; Franke, K. J.; Kuch, W.

2012-12-01

The magnetic state and magnetic coupling of individual atoms in nanoscale structures relies on a delicate balance between different interactions with the atomic-scale surroundings. Using scanning tunneling microscopy, we resolve the self-assembled formation of highly ordered bilayer structures of Fe atoms and organic linker molecules (T4PT) when deposited on a Au(111) surface. The Fe atoms are encaged in a three-dimensional coordination motif by three T4PT molecules in the surface plane and an additional T4PT unit on top. Within this crystal field, the Fe atoms retain a magnetic ground state with easy-axis anisotropy, as evidenced by x-ray absorption spectroscopy and x-ray magnetic circular dichroism. The magnetization curves reveal the existence of ferromagnetic coupling between the Fe centers.

Electronic structure and optical properties of N vacancy and O filling on n-GaN (0001) surface

NASA Astrophysics Data System (ADS)

Lu, Feifei; Liu, Lei; Xia, Sihao; Diao, Yu; Feng, Shu

2018-06-01

In the X-ray photoelectron spectroscopy experiment, we observed that the valence band spectrum of the n-GaN (0001) surface appeared a bump near 1.9 eV after Ar etching and the N/Ga ratio became smaller, while the bump disappeared upon exposure to air. In order to analyze this phenomenon theoretically, we mainly study the electronic structure and optical properties of n-GaN (0001) surface with N vacancy and filled with O atom based on the first principles of density functional theory. The results suggest that the n-GaN (0001) surface exhibits semi-metallic property. The introduction of N vacancy reduces the n-type conductivity, whereas the filling of O atom enhances conductivity. The density of state near -1.9eV shows a good agreement between the clean n-type surface and the O-atom-filled surface, while the N vacancy surface has a higher density of states, which is similar to the experimentally observed phenomenon. It is also found that the existence of N vacancy reduces the photoemission properties of the n-GaN (0001) surface and the filling of O atom alleviates the defect caused by vacancy. This study shows that N vacancy increases the doping difficulty of n-type GaN films, however, the filling of O atom may compensate for the diminished photoelectric properties induced by N vacancy and be conducive to prepare high-performance optoelectronic devices with the contact of n-GaN and metal.

Immobilization of single argon atoms in nano-cages of two-dimensional zeolite model systems.

PubMed

Zhong, Jian-Qiang; Wang, Mengen; Akter, Nusnin; Kestell, John D; Boscoboinik, Alejandro M; Kim, Taejin; Stacchiola, Dario J; Lu, Deyu; Boscoboinik, J Anibal

2017-07-17

The confinement of noble gases on nanostructured surfaces, in contrast to bulk materials, at non-cryogenic temperatures represents a formidable challenge. In this work, individual Ar atoms are trapped at 300 K in nano-cages consisting of (alumino)silicate hexagonal prisms forming a two-dimensional array on a planar surface. The trapping of Ar atoms is detected in situ using synchrotron-based ambient pressure X-ray photoelectron spectroscopy. The atoms remain in the cages upon heating to 400 K. The trapping and release of Ar is studied combining surface science methods and density functional theory calculations. While the frameworks stay intact with the inclusion of Ar atoms, the permeability of gasses (for example, CO) through them is significantly affected, making these structures also interesting candidates for tunable atomic and molecular sieves. These findings enable the study of individually confined noble gas atoms using surface science methods, opening up new opportunities for fundamental research.

Immobilization of single argon atoms in nano-cages of two-dimensional zeolite model systems

DOE PAGES

Zhong, Jian-Qiang; Wang, Mengen; Akter, Nusnin; ...

2017-07-17

The confinement of noble gases on nanostructured surfaces, in contrast to bulk materials, at non-cryogenic temperatures represents a formidable challenge. Here, individual Ar atoms are trapped at 300 K in nano-cages consisting of (alumino)silicate hexagonal prisms forming a two-dimensional array on a planar surface. The trapping of Ar atoms is detected in situ using synchrotron-based ambient pressure X-ray photoelectron spectroscopy. The atoms remain in the cages upon heating to 400 K. The trapping and release of Ar is studied combining surface science methods and density functional theory calculations. While the frameworks stay intact with the inclusion of Ar atoms, themore » permeability of gasses (for example, CO) through them is significantly affected, making these structures also interesting candidates for tunable atomic and molecular sieves. Our findings enable the study of individually confined noble gas atoms using surface science methods, opening up new opportunities for fundamental research.« less

Immobilization of single argon atoms in nano-cages of two-dimensional zeolite model systems

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

Zhong, Jian-Qiang; Wang, Mengen; Akter, Nusnin

The confinement of noble gases on nanostructured surfaces, in contrast to bulk materials, at non-cryogenic temperatures represents a formidable challenge. Here, individual Ar atoms are trapped at 300 K in nano-cages consisting of (alumino)silicate hexagonal prisms forming a two-dimensional array on a planar surface. The trapping of Ar atoms is detected in situ using synchrotron-based ambient pressure X-ray photoelectron spectroscopy. The atoms remain in the cages upon heating to 400 K. The trapping and release of Ar is studied combining surface science methods and density functional theory calculations. While the frameworks stay intact with the inclusion of Ar atoms, themore » permeability of gasses (for example, CO) through them is significantly affected, making these structures also interesting candidates for tunable atomic and molecular sieves. Our findings enable the study of individually confined noble gas atoms using surface science methods, opening up new opportunities for fundamental research.« less

FI-STM study of hydrogen adsorption on Si(100) surface

NASA Astrophysics Data System (ADS)

Hua, Lu; Xiang-dong, Wang; Motai, K.; Hashizume, T.; Sakurai, T.

1992-11-01

Chemisorption of atomic hydrogen on the Si(100)2 × 1 surface has been investigated in detail by using a field ion-scanning tunneling microscope (FI-STM). The results showed that the adsorption geometry changed from the 2 × 1 monohydride phase to the 1 × 1 dihydride phase with increasing exposure of hydrogen. The data of desorption of the hydrogen-saturated Si surface showed that on annealing at 670 K the surface becomes highly disordered: the 1 × 1 dihydride structure is eliminated and the 2 × 1 reconstructed monohydride is also hardly to identify. When the temperature rises to as high as 730 K, the surface is dominated by the 2 × 1 structure with missing dimer rows, and some adatom chains occur on the Si substrate terraces. We attribute the formation of these atomic chains to an epitaxial growth of Si atoms which are formed by the dissociation of SiHx (x = 1, 2, 3 or 4) compounds on the Si surface.

Adsorption of pentacene on (100) vicinal surfaces: role of coordination, surface chemistry and vdWs effects

NASA Astrophysics Data System (ADS)

Matos, Jeronimo; Kara, Abdelkader

2015-03-01

In contrast to low miller index surfaces, vicinal surfaces are characterized by steps and step edges that not only present an interesting atomic landscape for the adsorption organic molecules, but also a unique electronic structure resulting in part from the low coordinated atoms at the step edges. The adsorption of pentacene on the stepped (511), (711), (911) surfaces (respectively 3, 4 and 5-atom wide terraces) of Cu and Ag (coinage transition metals); Pt (reactive transition metal); and Ni (reactive, magnetic transition metal) are studied using density functional theory, in order to investigate the support effects arising from differing surface chemistry. We compare the adsorption energy, adsorption geometry and electronic structure predicted by the PBE functional with those obtained from one of the optimized vdW-DF methods: optB88-vdW. Work supported by the U.S. Department of Energy Basic Energy Science under Contract No. DE-FG02-11ER16243.

Optimal packing size of non-ligated CdSe nanoclusters for microstructure synthesis

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

Tefera, Anteneh G.; Mochena, Mogus D.; Johnson, Elijah

2014-09-14

Structural and electrostatic properties of nanoclusters of CdSe of diameter 1–2 nm are studied with first principle calculations to determine the optimal size for synthesizing microstructures. Based on robustness of the core structure, i.e., the retention of tetrahedral geometry, hexagonal ring structure, and overall wu{sup ¨}rtzite structure to surface relaxations, we conclude that nanoclusters of ~2 nm diameter are the best candidates to form a dense microstructure with minimal interstitial space. Se-terminated surfaces retain a zigzag structure as Se atoms are pulled out and Cd atoms are pulled in due to relaxation, therefore, are best suited for inter-nanocluster formations.

Do Ag{sub n} (up to n = 8) clusters retain their identity on graphite? Insights from first-principles calculations including dispersion interactions

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

Singh, Akansha; Sen, Prasenjit, E-mail: prasen@hri.res.in; Majumder, Chiranjib

Adsorption of pre-formed Ag{sub n} clusters for n = 1 − 8 on a graphite substrate is studied within the density functional theory employing the vdW-DF2 functional to treat dispersion interactions. Top sites above surface layer carbon atoms turn out to be most favorable for a Ag adatom, in agreement with experimental observations. The same feature is observed for clusters of almost all sizes which have the lowest energies when the Ag atoms are positioned over top sites. Most gas phase isomers retain their structures over the substrate, though a couple of them undergo significant distortions. Energetics of the adsorptionmore » can be understood in terms of a competition between energy cost of disturbing Ag–Ag bonds in the cluster and energy gain from Ag–C interactions at the surface. Ag{sub 3} turns out to be an exceptional candidate in this regard that undergoes significant structural distortion and has only two of the Ag atoms close to surface C atoms in its lowest energy structure.« less

Enhanced Stability of Pt-Cu Single-Atom Alloy Catalysts: In Situ Characterization of the Pt/Cu(111) Surface in an Ambient Pressure of CO

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

Simonovis, Juan Pablo; Hunt, Adrian; Palomino, Robert M.

The interaction between a catalyst and reactants often induce changes in the surface structure and composition of the catalyst, which, in turn, affect its reactivity. Therefore, it is important to study such changes using in situ techniques under well-controlled conditions. We have used ambient pressure X-ray photoelectron spectroscopy (AP-XPS) to study the surface stability of a Pt/Cu(111) single atom alloy (SAA) in an ambient pressure of CO. By directly probing the Pt atoms, we found that CO causes a slight surface segregation of Pt atoms at room temperature. In addition, while the Pt/Cu(111) surface demonstrates poor thermal stability in UHV,more » where surface Pt starts to diffuse to the subsurface layer above 400 K, the presence of adsorbed CO enhances the thermal stability of surface Pt atoms. Furthermore, we also found that temperatures above 450 K cause a restructuring of the subsurface layer, which consequently strengthens the CO binding to the surface Pt sites, likely due to the presence of neighboring subsurface Pt atoms.« less

Enhanced Stability of Pt-Cu Single-Atom Alloy Catalysts: In Situ Characterization of the Pt/Cu(111) Surface in an Ambient Pressure of CO

DOE PAGES

Simonovis, Juan Pablo; Hunt, Adrian; Palomino, Robert M.; ...

2018-02-05

The interaction between a catalyst and reactants often induce changes in the surface structure and composition of the catalyst, which, in turn, affect its reactivity. Therefore, it is important to study such changes using in situ techniques under well-controlled conditions. We have used ambient pressure X-ray photoelectron spectroscopy (AP-XPS) to study the surface stability of a Pt/Cu(111) single atom alloy (SAA) in an ambient pressure of CO. By directly probing the Pt atoms, we found that CO causes a slight surface segregation of Pt atoms at room temperature. In addition, while the Pt/Cu(111) surface demonstrates poor thermal stability in UHV,more » where surface Pt starts to diffuse to the subsurface layer above 400 K, the presence of adsorbed CO enhances the thermal stability of surface Pt atoms. Furthermore, we also found that temperatures above 450 K cause a restructuring of the subsurface layer, which consequently strengthens the CO binding to the surface Pt sites, likely due to the presence of neighboring subsurface Pt atoms.« less

Au-induced deep groove nanowire structure on the Ge(001) surface: DFT calculations

NASA Astrophysics Data System (ADS)

Tsay, Shiow-Fon

2016-09-01

The atomic geometry, stability, and electronic properties of self-organized Au induced nanowires on the Ge(001) surface are investigated based on the density-functional theory in GGA and the stoichiometry of Au. A giant Ge zigzag chain structure is suggested for 0.75 ML Au coverage, which displays c(8 × 2) deep groove zigzag nanowire structure simulated STM images. The top layer Ge and Au atomic disorder introduces the chevron units into the zigzag nanowire structure STM image as per the experimental observations. The zigzag Ge nanowire exhibits a semi-metallic characteristic, and the electric transport occurs in between the Ge zigzag nanowire and the subsurface. The system exhibits obvious electronic correlations among the Ge nanowire, the nano-facet Au trimers and the deeper layer Ge atoms, that play an important role in the electronic structure. At surface Brillouin zone boundaries, an anisotropic two-dimensional upward parabolic surface-state band is consistent with the ARPES spectra reported by Nakatsuji et al. [Phys. Rev. B 80, 081406(R) (2009); Phys. Rev. B 84, 115411 (2011)]; this electronic structure is different from the quasi-one-dimensional energy trough reported by Schäfer et al. [Phys. Rev. Lett. 101, 236802 (2008); Phys. Rev. B 83, 121411(R) (2011)].

Tailoring optical metamaterials to tune the atom-surface Casimir-Polder interaction.

PubMed

Chan, Eng Aik; Aljunid, Syed Abdullah; Adamo, Giorgio; Laliotis, Athanasios; Ducloy, Martial; Wilkowski, David

2018-02-01

Metamaterials are fascinating tools that can structure not only surface plasmons and electromagnetic waves but also electromagnetic vacuum fluctuations. The possibility of shaping the quantum vacuum is a powerful concept that ultimately allows engineering the interaction between macroscopic surfaces and quantum emitters such as atoms, molecules, or quantum dots. The long-range atom-surface interaction, known as Casimir-Polder interaction, is of fundamental importance in quantum electrodynamics but also attracts a significant interest for platforms that interface atoms with nanophotonic devices. We perform a spectroscopic selective reflection measurement of the Casimir-Polder interaction between a Cs(6P 3/2 ) atom and a nanostructured metallic planar metamaterial. We show that by engineering the near-field plasmonic resonances of the metamaterial, we can successfully tune the Casimir-Polder interaction, demonstrating both a strong enhancement and reduction with respect to its nonresonant value. We also show an enhancement of the atomic spontaneous emission rate due to its coupling with the evanescent modes of the nanostructure. Probing excited-state atoms next to nontrivial tailored surfaces is a rigorous test of quantum electrodynamics. Engineering Casimir-Polder interactions represents a significant step toward atom trapping in the extreme near field, possibly without the use of external fields.

Controlled electron doping into metallic atomic wires: Si(111)4×1-In

NASA Astrophysics Data System (ADS)

Morikawa, Harumo; Hwang, C. C.; Yeom, Han Woong

2010-02-01

We demonstrate the controllable electron doping into metallic atomic wires, indium wires self-assembled on the Si(111) surface, which feature one-dimensional (1D) band structure and temperature-driven metal-insulator transition. The electron filling of 1D metallic bands is systematically increased by alkali-metal adsorption, which, in turn, tunes the macroscopic property, that is, suppresses the metal-insulator transition. On the other hand, the dopant atoms induce a local lattice distortion without a band-gap opening, leading to a microscopic phase separation on the surface. The distinct bifunctional, electronic and structural, roles of dopants in different length scales are thus disclosed.

The interaction of hydrogen with the {010} surfaces of Mg and Fe olivine as models for interstellar dust grains: a density functional theory study

PubMed Central

Downing, C. A.; Ahmady, B.; Catlow, C. R. A.; de Leeuw, N. H.

2013-01-01

There is no consensus as yet to account for the significant presence of water on the terrestrial planets, but suggested sources include direct hydrogen adsorption from the parent molecular cloud after the planets’ formation, and delivery of hydrous material via comets or asteroids external to the zone of the terrestrial planets. Alternatively, a more recent idea is that water may have directly adsorbed onto the interstellar dust grains involved in planetary formation. In this work, we use electronic structure calculations based on the density functional theory to investigate and compare the bulk and {010} surface structures of the magnesium and iron end-members of the silicate mineral olivine, namely forsterite and fayalite, respectively. We also report our results on the adsorption of atomic hydrogen at the mineral surfaces, where our calculations show that there is no activation barrier to the adsorption of atomic hydrogen at these surfaces. Furthermore, different surface sites activate the atom to form either adsorbed hydride or proton species in the form of hydroxy groups on the same surface, which indicates that these mineral surfaces may have acted as catalytic sites in the immobilization and reaction of hydrogen atoms to form dihydrogen gas or water molecules. PMID:23734054

Structure Determination of Au on Pt(111) Surface: LEED, STM and DFT Study

PubMed Central

Krupski, Katarzyna; Moors, Marco; Jóźwik, Paweł; Kobiela, Tomasz; Krupski, Aleksander

2015-01-01

Low-energy electron diffraction (LEED), scanning tunneling microscopy (STM) and density functional theory (DFT) calculations have been used to investigate the atomic and electronic structure of gold deposited (between 0.8 and 1.0 monolayer) on the Pt(111) face in ultrahigh vacuum at room temperature. The analysis of LEED and STM measurements indicates two-dimensional growth of the first Au monolayer. Change of the measured surface lattice constant equal to 2.80 Å after Au adsorption was not observed. Based on DFT, the distance between the nearest atoms in the case of bare Pt(111) and Au/Pt(111) surface is equal to 2.83 Å, which gives 1% difference in comparison with STM values. The first and second interlayer spacing of the clean Pt(111) surface are expanded by +0.87% and contracted by −0.43%, respectively. The adsorption energy of the Au atom on the Pt(111) surface is dependent on the adsorption position, and there is a preference for a hollow fcc site. For the Au/Pt(111) surface, the top interlayer spacing is expanded by +2.16% with respect to the ideal bulk value. Changes in the electronic properties of the Au/Pt(111) system below the Fermi level connected to the interaction of Au atoms with Pt(111) surface are observed.

77 FR 52683 - UChicago Argonne, LLC, Notice of Decision on Applications for Duty-Free Entry of Scientific...

Federal Register 2010, 2011, 2012, 2013, 2014

2012-08-30

... science. This instrument is specialized for 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...

Molecular dynamics simulation of sodium aluminosilicate glass structures and glass surface-water reactions using the reactive force field (ReaxFF)

NASA Astrophysics Data System (ADS)

Dongol, R.; Wang, L.; Cormack, A. N.; Sundaram, S. K.

2018-05-01

Reactive potentials are increasingly used to study the properties of glasses and glass water reactions in a reactive molecular dynamics (MD) framework. In this study, we have simulated a ternary sodium aluminosilicate glass and investigated the initial stages of the glass surface-water reactions at 300 K using reactive force field (ReaxFF). On comparison of the simulated glass structures generated using ReaxFF and classical Buckingham potentials, our results show that the atomic density profiles calculated for the surface glass structures indicate a bond-angle distribution dependency. The atomic density profiles also show higher concentrations of non-bridging oxygens (NBOs) and sodium ions at the glass surface. Additionally, we present our results of formation of silanol species and the diffusion of water molecules at the glass surface using ReaxFF.

Intermetallic structures with atomic precision for selective hydrogenation of nitroarenes

DOE PAGES

Pei, Yuchen; Qi, Zhiyuan; Goh, Tian Wei; ...

2017-11-14

It is essential to bridge the structure-properties relationship of bimetallic catalysts for the rational design of heterogeneous catalysts. Different from random alloys, intermetallic compounds (IMCs) present atomically-ordered structures, which is advantageous for catalytic mechanism studies. Here, we used Pt-based intermetallic nanoparticles (iNPs), individually encapsulated in mesoporous silica shells, as catalysts for the hydrogenation of nitroarenes to functionalized anilines. With the capping-free nature and ordered atomic structure, PtSn iNPs show >99% selectivity to hydrogenate the nitro group of 3-nitrostyrene albeit with a lower activity, in contrast to Pt 3Sn iNPs and Pt NPs. The geometric structure of PtSn iNPs in eliminatingmore » Pt threefold sites hampers the adsorption/dissociation of molecular H 2 and leads to a non-Horiuti-Polanyi hydrogenation pathway, while Pt 3Sn and Pt surfaces are saturated by atomic H. Calculations using density functional theory (DFT) suggest a preferential adsorption of the nitro group on the intermetallic PtSn surface contributing to its high selectivity.« less

Density functional theory study the effects of oxygen-containing functional groups on oxygen molecules and oxygen atoms adsorbed on carbonaceous materials.

PubMed

Qi, Xuejun; Song, Wenwu; Shi, Jianwei

2017-01-01

Density functional theory was used to study the effects of different types of oxygen-containing functional groups on the adsorption of oxygen molecules and single active oxygen atoms on carbonaceous materials. During gasification or combustion reactions of carbonaceous materials, oxygen-containing functional groups such as hydroxyl(-OH), carbonyl(-CO), quinone(-O), and carboxyl(-COOH) are often present on the edge of graphite and can affect graphite's chemical properties. When oxygen-containing functional groups appear on a graphite surface, the oxygen molecules are strongly adsorbed onto the surface to form a four-member ring structure. At the same time, the O-O bond is greatly weakened and easily broken. The adsorption energy value indicates that the adsorption of oxygen molecules changes from physisorption to chemisorption for oxygen-containing functional groups on the edge of a graphite surface. In addition, our results indicate that the adsorption energy depends on the type of oxygen-containing functional group. When a single active oxygen atom is adsorbed on the bridge site of graphite, it gives rise to a stable epoxy structure. Epoxy can cause deformation of the graphite lattice due to the transition of graphite from sp2 to sp3 after the addition of an oxygen atom. For quinone group on the edge of graphite, oxygen atoms react with carbon atoms to form the precursor of CO2. Similarly, the single active oxygen atoms of carbonyl groups can interact with edge carbon atoms to form the precursor of CO2. The results show that oxygen-containing functional groups on graphite surfaces enhance the activity of graphite, which promotes adsorption on the graphite surface.

Density functional theory study the effects of oxygen-containing functional groups on oxygen molecules and oxygen atoms adsorbed on carbonaceous materials

PubMed Central

Song, Wenwu; Shi, Jianwei

2017-01-01

Density functional theory was used to study the effects of different types of oxygen-containing functional groups on the adsorption of oxygen molecules and single active oxygen atoms on carbonaceous materials. During gasification or combustion reactions of carbonaceous materials, oxygen-containing functional groups such as hydroxyl(-OH), carbonyl(-CO), quinone(-O), and carboxyl(-COOH) are often present on the edge of graphite and can affect graphite’s chemical properties. When oxygen-containing functional groups appear on a graphite surface, the oxygen molecules are strongly adsorbed onto the surface to form a four-member ring structure. At the same time, the O-O bond is greatly weakened and easily broken. The adsorption energy value indicates that the adsorption of oxygen molecules changes from physisorption to chemisorption for oxygen-containing functional groups on the edge of a graphite surface. In addition, our results indicate that the adsorption energy depends on the type of oxygen-containing functional group. When a single active oxygen atom is adsorbed on the bridge site of graphite, it gives rise to a stable epoxy structure. Epoxy can cause deformation of the graphite lattice due to the transition of graphite from sp2 to sp3 after the addition of an oxygen atom. For quinone group on the edge of graphite, oxygen atoms react with carbon atoms to form the precursor of CO2. Similarly, the single active oxygen atoms of carbonyl groups can interact with edge carbon atoms to form the precursor of CO2. The results show that oxygen-containing functional groups on graphite surfaces enhance the activity of graphite, which promotes adsorption on the graphite surface. PMID:28301544

Investigation on nanoscale processes on the BaF{sub 2}(111) surface in various solutions by frequency modulation atomic force microscopy

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

Kobayashi, Naritaka, E-mail: naritaka@mail.saitama-u.ac.jp; Kawamura, Ryuzo; Yoshikawa, Hiroshi Y.

2016-06-07

In this study, we have directly observed nanoscale processes that occur on BaF{sub 2}(111) surfaces in various solutions using liquid-environment frequency modulation atomic force microscopy (FM-AFM) with a true atomic resolution. In addition, to investigate atomic-scale mechanisms of crystal growth process of BaF{sub 2}, we determined a suitable solution for atomic-resolution FM-AFM imaging of the BaF{sub 2}(111) surface. For undersaturated solutions, the surface is roughened by barium hydroxo complexes in the case of high pH, whereas by dissolution and proton or water molecule adsorption throughout the surface in the case of low pH. On the other hand, for supersaturated solutions,more » the surface shows two-dimensional nucleation and growth (σ = 0.1) and three-dimensional crystal growth with tetrahedral structures (σ = 1), where σ is the degree of supersaturation. The atomic-resolution imaging of the BaF{sub 2}(111) surface has been demonstrated in potassium fluoride (KF) and the supersaturated (σ = 0.1 and 1) solutions, wherein atomically flat terraces are shown at least for about 30 min.« less

Atomic structure of (111) SrTiO3/Pt interfaces

NASA Astrophysics Data System (ADS)

Schmidt, Steffen; Klenov, Dmitri O.; Keane, Sean P.; Lu, Jiwei; Mates, Thomas E.; Stemmer, Susanne

2006-03-01

Atomic resolution high-angle annular dark field (HAADF) imaging in scanning transmission electron microscopy was used to investigate the interface atomic structure of epitaxial, (111) oriented SrTiO3 films on epitaxial Pt electrodes grown on (0001) sapphire. The cube-on-cube orientation relationship of SrTiO3 on Pt was promoted by the use of a Ti adhesion layer underneath the Pt electrode. While a Ti-rich Pt surface was observed before SrTiO3 growth, HAADF images showed an atomically abrupt SrTiO3/Pt interface with no interfacial layers. The SrTiO3 films contained two twin variants that were related by a 180° rotation about the ⟨111⟩ surface normal. HAADF images showed two different interface atomic arrangements for the two twins. The role of Ti in promoting (111) epitaxy and the implications for the dielectric properties are discussed.

Low energy electron diffraction and low energy electron microscopy microspot I/V analysis of the (4 x 4)O structure on Ag(111): surface oxide or reconstruction?

PubMed

Reichelt, R; Günther, S; Wintterlin, J; Moritz, W; Aballe, L; Mentes, T O

2007-10-07

A low energy electron diffraction (LEED) I/V analysis was performed of the (4 x 4) oxygen structure on Ag(111). Two data sets were used, one recorded with a conventional LEED system and a second with a low energy electron microscope (LEEM). The data sets agree well with each other, demonstrating that I/V structure analyses can be performed with the same quality with LEEM as with conventional LEED. The structure obtained confirms the recently proposed model that involves a reconstruction of the Ag(111) surface. Previous models based on a thin layer of Ag(2)O that had been accepted for more than 30 years are disproved. The reconstruction model contains two units of six triangularly arranged Ag atoms and a stacking fault in one half of the unit cell. The six O atoms per unit cell occupy sites in the trenches between the Ag(6) triangles. Small lateral displacements of the Ag atoms lift the mirror symmetry of the structure, leading to two nonequivalent groups of O atoms. The atoms of both groups are located approximately 0.5 Angstrom below the top Ag layer, on fourfold positions with respect to the top layer Ag atoms. Ag-O distances between 2.05 and 2.3 Angstrom are found. The oxygen atoms exhibit large static or dynamic displacements of up to 0.3 Angstrom at 300 K.

Atomic structure of the GaAs(001)-c(4x4) surface: first-principles evidence for diversity of heterodimer motifs.

PubMed

Penev, E; Kratzer, P; Scheffler, M

2004-10-01

The GaAs(001)-c(4x4) surface was studied using ab initio atomistic thermodynamics based on density-functional theory calculations. We demonstrate that in a range of stoichiometries, between those of the conventional three As-dimer and the new three Ga-As-dimer models, there exists a diversity of atomic structures featuring Ga-As heterodimers. These results fully explain the experimental scanning tunneling microscopy images and are likely to be relevant also to the c(4x4)-reconstructed (001) surfaces of other III-V semiconductors.

Atomic-scale planarization of 4H-SiC (0001) by combination of thermal oxidation and abrasive polishing

NASA Astrophysics Data System (ADS)

Deng, Hui; Endo, Katsuyoshi; Yamamura, Kazuya

2013-09-01

Thermal oxidation (TO) and abrasive polishing were combined for atomic-scale planarization of 4H-SiC. It was found that the oxide/SiC interface was atomically flat regardless of the thickness of the oxide. The specimen prepared by TO was dipped in HF solution to remove the oxide. However, owing to the residual silicon oxycarbide (Si-C-O), the step/terrace structure of 4H-SiC could not be observed. Nanoindentation tests revealed that the hardness of Si-C-O was much lower than that of SiC. A thermally oxidized SiC surface was polished using CeO2 abrasives, which resulted in an atomically flat surface with a well-ordered two-bilayer step/terrace structure.

Surface sensitization mechanism on negative electron affinity p-GaN nanowires

NASA Astrophysics Data System (ADS)

Diao, Yu; Liu, Lei; Xia, Sihao; Feng, Shu; Lu, Feifei

2018-03-01

The surface sensitization is the key to prepare negative electron affinity photocathode. The thesis emphasizes on the study of surface sensitization mechanism of p-type doping GaN nanowires utilizing first principles based on density function theory. The adsorption energy, work function, dipole moment, geometry structure, electronic structure and optical properties of Mg-doped GaN nanowires surfaces with various coverages of Cs atoms are investigated. The GaN nanowire with Mg doped in core position is taken as the sensitization base. At the initial stage of sensitization, the best adsorption site for Cs atom on GaN nanowire surface is BN, the bridge site of two adjacent N atoms. Surface sensitization generates a p-type internal surface with an n-type surface state, introducing a band bending region which can help reduce surface barrier and work function. With increasing Cs coverage, work functions decrease monotonously and the "Cs-kill" phenomenon disappears. For Cs coverage of 0.75 ML and 1 ML, the corresponding sensitization systems reach negative electron affinity state. Through surface sensitization, the absorption curves are red shifted and the absorption coefficient is cut down. All theoretical calculations can guide the design of negative electron affinity Mg doped GaN nanowires photocathode.

Defects in oxide surfaces studied by atomic force and scanning tunneling microscopy

PubMed Central

König, Thomas; Simon, Georg H; Heinke, Lars; Lichtenstein, Leonid

2011-01-01

Summary Surfaces of thin oxide films were investigated by means of a dual mode NC-AFM/STM. Apart from imaging the surface termination by NC-AFM with atomic resolution, point defects in magnesium oxide on Ag(001) and line defects in aluminum oxide on NiAl(110), respectively, were thoroughly studied. The contact potential was determined by Kelvin probe force microscopy (KPFM) and the electronic structure by scanning tunneling spectroscopy (STS). On magnesium oxide, different color centers, i.e., F0, F+, F2+ and divacancies, have different effects on the contact potential. These differences enabled classification and unambiguous differentiation by KPFM. True atomic resolution shows the topography at line defects in aluminum oxide. At these domain boundaries, STS and KPFM verify F2+-like centers, which have been predicted by density functional theory calculations. Thus, by determining the contact potential and the electronic structure with a spatial resolution in the nanometer range, NC-AFM and STM can be successfully applied on thin oxide films beyond imaging the topography of the surface atoms. PMID:21977410

In and Si adatoms on Si(111)5×2-Au : Scanning tunneling microscopy and first-principles density functional calculations

NASA Astrophysics Data System (ADS)

Stępniak, A.; Nita, P.; Krawiec, M.; Jałochowski, M.

2009-09-01

Structural properties of monatomic indium chains on Si(111)5×2-Au surface are investigated by scanning tunneling microscopy (STM) and first-principles density functional calculations (DFT). The STM topography data show that submonolayer coverage of indium leads to a well-ordered chain structure with the same periodicity as the Si adatoms form on Si(111)5×2-Au surface. Bias-dependent STM topography and spectroscopy reveal two different mechanisms of In-atoms adsorption on the surface: bonding to Si adatoms and substitution for Si atoms in the adatom positions. Those mechanisms are further corroborated by DFT calculations. The obtained structural model of In-modified Si(111)5×2-Au surface remains in good agreement with the experimental data.

Density functional investigation of the adsorption effects of PH3 and SH2 on the structure stability of the Au55 and Pt55 nanoclusters

NASA Astrophysics Data System (ADS)

Guedes-Sobrinho, Diego; Chaves, Anderson S.; Piotrowski, Maurício J.; Da Silva, Juarez L. F.

2017-04-01

Although several studies have been reported for Pt55 and Au55 nanoclusters, our atomistic understanding of the interplay between the adsorbate-surface interactions and the mechanisms that lead to the formation of the distorted reduced core (DRC) structures, instead of the icosahedron (ICO) structure in gas phase, is still far from satisfactory. Here, we report a density functional theory (DFT) investigation of the role of the adsorption effects of PH3 (one lone pair of electrons) and SH2 (two lone pairs) on the relative stability of the Pt55 and Au55 nanoclusters. In gas phase, we found that the DRC structures with 7 and 9 atoms in the core region are about 5.34 eV (Pt55) and 2.20 eV (Au55) lower in energy than the ICO model with Ih symmetry and 13 atoms in the core region. However, the stability of the ICO structure increases by increasing the number of adsorbed molecules from 1 to 18, in which both DRC and ICO structures are nearly degenerate in energy at the limit of 18 ligands, which can be explained as follows. In gas phase, there is a strong compression of the cationic core region by the anionic surface atoms induced by the attractive Coulomb interactions (core+-surface-), and hence, the strain release is obtained by reducing the number of atoms in the cationic core region, which leads to the 55 atoms distorted reduced core structures. Thus, the Coulomb interactions between the core+ and surface- contribute to break the symmetry in the ICO55 structure. On the other hand, the addition of ligands on the anionic surface reduces the charge transfer between the core and surface, which contributes to decrease the Coulomb interactions and the strain on the core region of the ICO structure, and hence, it stabilizes a compact ICO structure. The same conclusion is obtained by adding van der Waals corrections to the plain DFT calculations. Similar results are obtained by the addition of steric effects, which are considered through the adsorption of triphenylphosphine (PPh3) molecules on Au55, in which the relative stability between ICO and DRC is the same as for PH3 and SH2. However, for Pt55, we found an inversion of stability due to the PPh3 ligand effects, where ICO has higher stability than DRC by 2.40 eV. Our insights are supported by several structural, electronic, and energetic analyses.

Density functional investigation of the adsorption effects of PH3 and SH2 on the structure stability of the Au55 and Pt55 nanoclusters.

PubMed

Guedes-Sobrinho, Diego; Chaves, Anderson S; Piotrowski, Maurício J; Da Silva, Juarez L F

2017-04-28

Although several studies have been reported for Pt 55 and Au 55 nanoclusters, our atomistic understanding of the interplay between the adsorbate-surface interactions and the mechanisms that lead to the formation of the distorted reduced core (DRC) structures, instead of the icosahedron (ICO) structure in gas phase, is still far from satisfactory. Here, we report a density functional theory (DFT) investigation of the role of the adsorption effects of PH 3 (one lone pair of electrons) and SH 2 (two lone pairs) on the relative stability of the Pt 55 and Au 55 nanoclusters. In gas phase, we found that the DRC structures with 7 and 9 atoms in the core region are about 5.34 eV (Pt 55 ) and 2.20 eV (Au 55 ) lower in energy than the ICO model with I h symmetry and 13 atoms in the core region. However, the stability of the ICO structure increases by increasing the number of adsorbed molecules from 1 to 18, in which both DRC and ICO structures are nearly degenerate in energy at the limit of 18 ligands, which can be explained as follows. In gas phase, there is a strong compression of the cationic core region by the anionic surface atoms induced by the attractive Coulomb interactions (core + -surface - ), and hence, the strain release is obtained by reducing the number of atoms in the cationic core region, which leads to the 55 atoms distorted reduced core structures. Thus, the Coulomb interactions between the core + and surface - contribute to break the symmetry in the ICO 55 structure. On the other hand, the addition of ligands on the anionic surface reduces the charge transfer between the core and surface, which contributes to decrease the Coulomb interactions and the strain on the core region of the ICO structure, and hence, it stabilizes a compact ICO structure. The same conclusion is obtained by adding van der Waals corrections to the plain DFT calculations. Similar results are obtained by the addition of steric effects, which are considered through the adsorption of triphenylphosphine (PPh 3 ) molecules on Au 55 , in which the relative stability between ICO and DRC is the same as for PH 3 and SH 2 . However, for Pt 55 , we found an inversion of stability due to the PPh 3 ligand effects, where ICO has higher stability than DRC by 2.40 eV. Our insights are supported by several structural, electronic, and energetic analyses.

Single crystalline thin films as a novel class of electrocatalysts

DOE PAGES

Snyder, Joshua; Markovic, Nenad; Stamenkovic, Vojislav

2013-01-01

The ubiquitous use of single crystal metal electrodes has garnered invaluable insight into the relationship between surface atomic structure and functional electrochemical properties. But, the sensitivity of their electrochemical response to surface orientation and the amount of precious metal required can limit their use. We present here a generally applicable procedure for producing thin metal films with a large proportion of atomically flat (111) terraces without the use of an epitaxial template. Thermal annealing in a controlled atmosphere induces long-range ordering of magnetron sputtered thin metal films deposited on an amorphous substrate. The ordering transition in these thin metal filmsmore » yields characteristic (111) electrochemical signatures with minimal amount of material and provides an adequate replacement for oriented bulk single crystals. Our procedure can be generalized towards a novel class of practical multimetallic thin film based electrocatalysts with tunable near-surface compositional profile and morphology. Annealing of atomically corrugated sputtered thin film Pt-alloy catalysts yields an atomically smooth structure with highly crystalline, (111)-like ordered and Pt segregated surface that displays superior functional properties, bridging the gap between extended/bulk surfaces and nanoscale systems.« less

Disentangling atomic-layer-specific x-ray absorption spectra by Auger electron diffraction spectroscopy

NASA Astrophysics Data System (ADS)

Matsui, Fumihiko; Matsushita, Tomohiro; Kato, Yukako; Hashimoto, Mie; Daimon, Hiroshi

2009-11-01

In order to investigate the electronic and magnetic structures of each atomic layer at subsurface, we have proposed a new method, Auger electron diffraction spectroscopy, which is the combination of x-ray absorption spectroscopy (XAS) and Auger electron diffraction (AED) techniques. We have measured a series of Ni LMM AED patterns of the Ni film grown on Cu(001) surface for various thicknesses. Then we deduced a set of atomic-layer-specific AED patterns in a numerical way. Furthermore, we developed an algorithm to disentangle XANES spectra from different atomic layers using these atomic-layer-specific AED patterns. Surface and subsurface core level shift were determined for each atomic layer.

Dimer formation and surface alloying: a STM study of lead on Cu(211)

NASA Astrophysics Data System (ADS)

Bartels, L.; Zöphel, S.; Meyer, G.; Henze, E.; Rieder, K.-H.

1997-02-01

We present a STM investigation of Pb adsorption on the Cu(211) surface in the temperature range between 30 K and room temperature. We observe three different kinds of ordered 1D Pb and PbCu chains (nanowires) located at the intrinsic step edges of the Cu(211) surface. On room temperature prepared samples, Pb is found to be incorporated into the step edges of the (211) surface. The first ordered structure consists of CuPb chains at the step edges (p(2 × disorder)) and is followed with increasing coverage by a close packed row of Pb-atoms (p(4 × disorder)). Preparation at low temperature yields Pb-dimers, and the first ordered structure is a row of Pb-dimers at the step edge (p(3 × disorder)) followed with increased coverage by a structure as described above. By systematic manipulation with the tunneling tip, we could get additional insight into the structural elements of the PbCu layer on the atomic scale. Furthermore, by measuring the threshold resistance to detach atoms from different ad-sites, we can approximately determine the binding energy and gain some insight into the thermodynamical parameters involved.

Mn induced 1 × 2 reconstruction in the τ-MnAl(0 0 1) surface

NASA Astrophysics Data System (ADS)

Guerrero-Sánchez, J.; Takeuchi, Noboru

2018-05-01

We report on first principles total energy calculations to describe the structural, electronic and magnetic properties of MnAl(0 0 1) surfaces. We have concentrated in structural models having 1 × 1 and 1 × 2 periodicities, since recent experiments of the similar MnGa(0 0 1) surface have found 1 × 1 and 1 × 2 reconstructions. Our calculations show the existence of two stable structures for different ranges of chemical potential. A 1 × 1 surface is stable for Al-rich conditions, whereas a Mn-induced 1 × 2 reconstruction appears after increasing the Mn chemical potential up to Mn-rich conditions. It is important to notice that experimentally, Mn rich conditions are important for improved magnetic properties. The Mn layers in both structures have ferromagnetic arrangements, but they are aligned antiferromagnetically with the almost no magnetic Al atoms. Moreover, the on top Mn atoms, which produce the 1 × 2 reconstruction, align antiferromagnetically with the second layer Mn atoms. These findings are similar to those obtained experimentally in MnGa thin films grown by molecular beam epitaxy. Therefore, this method could also be used to grow the proposed MnAl films.

Metallic Properties of the Si(111) - 5 × 2 - Au Surface from Infrared Plasmon Polaritons and Ab Initio Theory.

PubMed

Hötzel, Fabian; Seino, Kaori; Huck, Christian; Skibbe, Olaf; Bechstedt, Friedhelm; Pucci, Annemarie

2015-06-10

The metal-atom chains on the Si(111) - 5 × 2 - Au surface represent an exceedingly interesting system for the understanding of one-dimensional electrical interconnects. While other metal-atom chain structures on silicon suffer from metal-to-insulator transitions, Si(111) - 5 × 2 - Au stays metallic at least down to 20 K as we have proven by the anisotropic absorption from localized plasmon polaritons in the infrared. A quantitative analysis of the infrared plasmonic signal done here for the first time yields valuable band structure information in agreement with the theoretically derived data. The experimental and theoretical results are consistently explained in the framework of the atomic geometry, electronic structure, and IR spectra of the recent Kwon-Kang model.

Atomic mechanism for the growth of wafer-scale single-crystal graphene: theoretical perspective and scanning tunneling microscopy investigations

NASA Astrophysics Data System (ADS)

Niu, Tianchao; Zhang, Jialin; Chen, Wei

2017-12-01

Chemical vapor deposition (CVD) is the most promising approach for producing low-cost, high-quality, and large area graphene. Revealing the graphene growth mechanism at the atomic-scale is of great importance for realizing single crystal graphene (SCG) over wafer scale. Density functional theoretical (DFT) calculations are playing an increasingly important role in revealing the structure of the most stable carbon species, understanding the evolution processes, and disclosing the active sites. Scanning tunneling microscopy (STM) is a powerful surface characterization tool to illustrate the real space distribution and atomic structures of growth intermediates during the CVD process. Combining them together can provide valuable information to improve the atomically controlled growth of SCG. Starting from a basic concept of the substrate effect on realizing SCG, this review covers the progress made in theoretical investigations on various carbon species during graphene growth on different transition metal substrates, in the STM study of the structural intermediates on transition metal surfaces, and in synthesizing graphene nanoribbons with atomic-precise width and edge structure, ending with a perspective on the future development of 2D materials beyond graphene.

Theoretical characterization on the size-dependent electron and hole trapping activity of chloride-passivated CdSe nanoclusters

NASA Astrophysics Data System (ADS)

Cui, Yingqi; Cui, Xianhui; Zhang, Li; Xie, Yujuan; Yang, Mingli

2018-04-01

Ligand passivation is often used to suppress the surface trap states of semiconductor quantum dots (QDs) for their continuous photoluminescence output. The suppression process is related to the electrophilic/nucleophilic activity of surface atoms that varies with the structure and size of QD and the electron donating/accepting nature of ligand. Based on first-principles-based descriptors and cluster models, the electrophilic/nucleophilic activities of bare and chloride-coated CdSe clusters were studied to reveal the suppression mechanism of Cl-passivated QDs and compared to experimental observations. The surface atoms of bare clusters have higher activity than inner atoms and their activity decreases with cluster size. In the ligand-coated clusters, the Cd atom remains as the electrophilic site, while the nucleophilic site of Se atoms is replaced by Cl atoms. The activities of Cd and Cl atoms in the coated clusters are, however, remarkably weaker than those in bare clusters. Cluster size, dangling atoms, ligand coverage, electronegativity of ligand atoms, and solvent (water) were found to have considerable influence on the activity of surface atoms. The suppression of surface trap states in Cl-passivated QDs was attributed to the reduction of electrophilic/nucleophilic activity of Cd/Se/Cl atoms. Both saturation to under-coordinated surface atoms and proper selection for the electron donating/accepting strength of ligands are crucial for eliminating the charge carrier traps. Our calculations predicted a similar suppressing effect of chloride ligands with experiments and provided a simple but effective approach to assess the charge carrier trapping behaviors of semiconductor QDs.

Simulation studies for surfaces and materials strength

NASA Technical Reports Server (NTRS)

Halicioglu, T.

1986-01-01

During this reporting period three investigations were carried out. The first area of research concerned the analysis of the structure-energy relationship in small clusters. This study is very closely related to the improvement of the potential energy functions which are suitable and simple enough to be used in atomistic simulation studies. Parameters obtained from ab initio calculations for dimers and trimers of Al were used to estimate energetics and global minimum energy structures of clusters continuing up to 15 Al atoms. The second research topic addressed modeling of the collision process for atoms impinging on surfaces. In this simulation study qualitative aspects of the O atom collision with a graphite surface were analyzed. Four different O/graphite systems were considered and the aftermath of the impact was analyzed. The final area of investigation was related to the simulation of thin amorphous Si films on crystalline Si substrates. Parameters obtained in an earlier study were used to model an exposed amorphous Si surface and an a-Si/c-Si interface. Structural details for various film thicknesses were investigated at an atomistic level.

Detecting structural variances of Co 3O 4 catalysts by controlling beam-induced sample alterations in the vacuum of a transmission electron microscope

DOE PAGES

Kisielowski, C.; Frei, H.; Specht, P.; ...

2016-11-02

This article summarizes core aspects of beam-sample interactions in research that aims at exploiting the ability to detect single atoms at atomic resolution by mid-voltage transmission electron microscopy. Investigating the atomic structure of catalytic Co 3O 4 nanocrystals underscores how indispensable it is to rigorously control electron dose rates and total doses to understand native material properties on this scale. We apply in-line holography with variable dose rates to achieve this goal. Genuine object structures can be maintained if dose rates below ~100 e/Å 2s are used and the contrast required for detection of single atoms is generated by capturing largemore » image series. Threshold doses for the detection of single atoms are estimated. An increase of electron dose rates and total doses to common values for high resolution imaging of solids stimulates object excitations that restructure surfaces, interfaces, and defects and cause grain reorientation or growth. We observe a variety of previously unknown atom configurations in surface proximity of the Co 3O 4 spinel structure. These are hidden behind broadened diffraction patterns in reciprocal space but become visible in real space by solving the phase problem. Finallly, an exposure of the Co 3O 4 spinel structure to water vapor or other gases induces drastic structure alterations that can be captured in this manner.« less

Design of a new reactor-like high temperature near ambient pressure scanning tunneling microscope for catalysis studies.

PubMed

Tao, Franklin Feng; Nguyen, Luan; Zhang, Shiran

2013-03-01

Here, we present the design of a new reactor-like high-temperature near ambient pressure scanning tunneling microscope (HT-NAP-STM) for catalysis studies. This HT-NAP-STM was designed for exploration of structures of catalyst surfaces at atomic scale during catalysis or under reaction conditions. In this HT-NAP-STM, the minimized reactor with a volume of reactant gases of ∼10 ml is thermally isolated from the STM room through a shielding dome installed between the reactor and STM room. An aperture on the dome was made to allow tip to approach to or retract from a catalyst surface in the reactor. This dome minimizes thermal diffusion from hot gas of the reactor to the STM room and thus remains STM head at a constant temperature near to room temperature, allowing observation of surface structures at atomic scale under reaction conditions or during catalysis with minimized thermal drift. The integrated quadrupole mass spectrometer can simultaneously measure products during visualization of surface structure of a catalyst. This synergy allows building an intrinsic correlation between surface structure and its catalytic performance. This correlation offers important insights for understanding of catalysis. Tests were done on graphite in ambient environment, Pt(111) in CO, graphene on Ru(0001) in UHV at high temperature and gaseous environment at high temperature. Atom-resolved surface structure of graphene on Ru(0001) at 500 K in a gaseous environment of 25 Torr was identified.

Imaging and three-dimensional reconstruction of chemical groups inside a protein complex using atomic force microscopy

NASA Astrophysics Data System (ADS)

Kim, Duckhoe; Sahin, Ozgur

2015-03-01

Scanning probe microscopes can be used to image and chemically characterize surfaces down to the atomic scale. However, the localized tip-sample interactions in scanning probe microscopes limit high-resolution images to the topmost atomic layer of surfaces, and characterizing the inner structures of materials and biomolecules is a challenge for such instruments. Here, we show that an atomic force microscope can be used to image and three-dimensionally reconstruct chemical groups inside a protein complex. We use short single-stranded DNAs as imaging labels that are linked to target regions inside a protein complex, and T-shaped atomic force microscope cantilevers functionalized with complementary probe DNAs allow the labels to be located with sequence specificity and subnanometre resolution. After measuring pairwise distances between labels, we reconstruct the three-dimensional structure formed by the target chemical groups within the protein complex using simple geometric calculations. Experiments with the biotin-streptavidin complex show that the predicted three-dimensional loci of the carboxylic acid groups of biotins are within 2 Å of their respective loci in the corresponding crystal structure, suggesting that scanning probe microscopes could complement existing structural biological techniques in solving structures that are difficult to study due to their size and complexity.

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

Atomic-scale visualization of surface-assisted orbital order

PubMed Central

Kim, Howon; Yoshida, Yasuo; Lee, Chi-Cheng; Chang, Tay-Rong; Jeng, Horng-Tay; Lin, Hsin; Haga, Yoshinori; Fisk, Zachary; Hasegawa, Yukio

2017-01-01

Orbital-related physics attracts growing interest in condensed matter research, but direct real-space access of the orbital degree of freedom is challenging. We report a first, real-space, imaging of a surface-assisted orbital ordered structure on a cobalt-terminated surface of the well-studied heavy fermion compound CeCoIn5. Within small tip-sample distances, the cobalt atoms on a cleaved (001) surface take on dumbbell shapes alternatingly aligned in the [100] and [010] directions in scanning tunneling microscopy topographies. First-principles calculations reveal that this structure is a consequence of the staggered dxz-dyz orbital order triggered by enhanced on-site Coulomb interaction at the surface. This so far overlooked surface-assisted orbital ordering may prevail in transition metal oxides, heavy fermion superconductors, and other materials. PMID:28948229

Direct quantitative identification of the “surface trans-effect”

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

Deimel, Peter S.; Bababrik, Reda M.; Wang, Bin

The strong parallels between coordination chemistry and adsorption on metal surfaces, with molecules and ligands forming local bonds to individual atoms within a metal surface, have been established over many years of study. The recently proposed “surface trans-effect” (STE) appears to be a further manifestation of this analogous behaviour, but so far the true nature of the modified molecule–metal surface bonding has been unclear. The STE could play an important role in determining the reactivities of surface-supported metal–organic complexes, influencing the design of systems for future applications. However, the current understanding of this effect is incomplete and lacks reliable structuralmore » parameters with which to benchmark theoretical calculations. Using X-ray standing waves, we demonstrate that ligation of ammonia and water to iron phthalocyanine (FePc) on Ag(111) increases the adsorption height of the central Fe atom; dispersion corrected density functional theory calculations accurately model this structural effect. The calculated charge redistribution in the FePc/H 2O electronic structure induced by adsorption shows an accumulation of charge along the σ-bonding direction between the surface, the Fe atom and the water molecule, similar to the redistribution caused by ammonia. Finally, this apparent σ-donor nature of the observed STE on Ag(111) is shown to involve bonding to the delocalised metal surface electrons rather than local bonding to one or more surface atoms, thus indicating that this is a true surface trans-effect.« less

Direct quantitative identification of the “surface trans-effect”

DOE PAGES

Deimel, Peter S.; Bababrik, Reda M.; Wang, Bin; ...

2016-06-09

The strong parallels between coordination chemistry and adsorption on metal surfaces, with molecules and ligands forming local bonds to individual atoms within a metal surface, have been established over many years of study. The recently proposed “surface trans-effect” (STE) appears to be a further manifestation of this analogous behaviour, but so far the true nature of the modified molecule–metal surface bonding has been unclear. The STE could play an important role in determining the reactivities of surface-supported metal–organic complexes, influencing the design of systems for future applications. However, the current understanding of this effect is incomplete and lacks reliable structuralmore » parameters with which to benchmark theoretical calculations. Using X-ray standing waves, we demonstrate that ligation of ammonia and water to iron phthalocyanine (FePc) on Ag(111) increases the adsorption height of the central Fe atom; dispersion corrected density functional theory calculations accurately model this structural effect. The calculated charge redistribution in the FePc/H 2O electronic structure induced by adsorption shows an accumulation of charge along the σ-bonding direction between the surface, the Fe atom and the water molecule, similar to the redistribution caused by ammonia. Finally, this apparent σ-donor nature of the observed STE on Ag(111) is shown to involve bonding to the delocalised metal surface electrons rather than local bonding to one or more surface atoms, thus indicating that this is a true surface trans-effect.« less

Atomically thin transition metal layers: Atomic layer stabilization and metal-semiconductor transition

NASA Astrophysics Data System (ADS)

Hwang, Jeongwoon; Oh, Young Jun; Kim, Jiyoung; Sung, Myung Mo; Cho, Kyeongjae

2018-04-01

We have performed first-principle calculations to explore the possibility of synthesizing atomically thin transition metal (TM) layers. Buckled structures as well as planar structures of elemental 2D TM layers result in significantly higher formation energies compared with sp-bonded elemental 2D materials with similar structures, such as silicene and phosphorene. It is shown that the TM layers can be stabilized by surface passivation with HS, C6H5S2, or O, and O passivation is most effective. The surface oxygen passivation can improve stability leading to thermodynamically stable TM monolayers except Au, which is the most non-reactive metal element. Such stabilized TM monolayers also show an electronic structure transition from metallic state of free-standing TM layer to semiconducting O-passivated Mo and W monolayers with band gaps of 0.20-1.38 eV.

The role of charge transfer in the oxidation state change of Ce atoms in the TM13-CeO2(111) systems (TM = Pd, Ag, Pt, Au): a DFT + U investigation.

PubMed

Tereshchuk, Polina; Freire, Rafael L H; Ungureanu, Crina G; Seminovski, Yohanna; Kiejna, Adam; Da Silva, Juarez L F

2015-05-28

Despite extensive studies of transition metal (TM) clusters supported on ceria (CeO2), fundamental issues such as the role of the TM atoms in the change in the oxidation state of Ce atoms are still not well understood. In this work, we report a theoretical investigation based on static and ab initio molecular dynamics density functional theory calculations of the interaction of 13-atom TM clusters (TM = Pd, Ag, Pt, Au) with the unreduced CeO2(111) surface represented by a large surface unit cell and employing Hubbard corrections for the strong on-site Coulomb correlation in the Ce f-electrons. We found that the TM13 clusters form pyramidal-like structures on CeO2(111) in the lowest energy configurations with the following stacking sequence, TM/TM4/TM8/CeO2(111), while TM13 adopts two-dimensional structures at high energy structures. TM13 induces a change in the oxidation state of few Ce atoms (3 of 16) located in the topmost Ce layer from Ce(IV) (itinerant Ce f-states) to Ce(III) (localized Ce f-states). There is a charge flow from the TM atoms to the CeO2(111) surface, which can be explained by the electronegativity difference between the TM (Pd, Ag, Pt, Au) and O atoms, however, the charge is not uniformly distributed on the topmost O layer due to the pressure induced by the TM13 clusters on the underlying O ions, which yields a decrease in the ionic charge of the O ions located below the cluster and an increase in the remaining O ions. Due to the charge flow mainly from the TM8-layer to the topmost O-layer, the charge cannot flow from the Ce(IV) atoms to the O atoms with the same magnitude as in the clean CeO2(111) surface. Consequently, the effective cationic charge decreases mainly for the Ce atoms that have a bond with the O atoms not located below the cluster, and hence, those Ce atoms change their oxidation state from IV to III. This increases the size of the Ce(III) compared with the Ce(IV) cations, which builds-in a strain within the topmost Ce layer, and hence, also affecting the location of the Ce(III) cations and the structure of the TM13 clusters.

Sulfur-induced structural motifs on copper and gold surfaces

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

Walen, Holly

The interaction of sulfur with copper and gold surfaces plays a fundamental role in important phenomena that include coarsening of surface nanostructures, and self-assembly of alkanethiols. Here, we identify and analyze unique sulfur-induced structural motifs observed on the low-index surfaces of these two metals. We seek out these structures in an effort to better understand the fundamental interactions between these metals and sulfur that lends to the stability and favorability of metal-sulfur complexes vs. chemisorbed atomic sulfur. The experimental observations presented here—made under identical conditions—together with extensive DFT analyses, allow comparisons and insights into factors that favor the existence ofmore » metal-sulfur complexes, vs. chemisorbed atomic sulfur, on metal terraces. We believe this data will be instrumental in better understanding the complex phenomena occurring between the surfaces of coinage metals and sulfur.« less

Structural, electronic and optical properties of CO adsorbed on the defective anatase TiO2 (101) surface; a DFT study

NASA Astrophysics Data System (ADS)

Rafique, Muhammad; Shuai, Yong; Hassan, Muhammad

2017-08-01

This paper illustrates the study of stable structural, electronic and optical properties of carbon mono oxide (CO) molecule adsorbed on pure anatase TiO2 (101) surface and CO molecule adsorbed on defective anatase TiO2 (101) surface containing oxygen (O) atom subsurface vacancy using first-principles study calculations based on density functional theory (DFT) method. A foreign molecule CO was added in the interstitial space of anatase TiO2 (101) surface. It was observed that, adsorption of CO molecule is not favorable on pure anatase TiO2 (101) surface, however adsorption process is improved when subsurface contains O atom vacancy defect. In case of anatase TiO2 (101) surface containing subsurface vacancy, adsorption process is exothermic, resulting in stable structures. The adsorption energies calculated for CO molecules adsorbed at O2c site, at defect site and at Ti5c site of anatase surface containing subsurface O vacancy are 0.16 eV (at O2c), 0.32 eV (at defect site) and 0.43 eV (at Ti5c) site. DOS and PDOS plots are calculated for all the structures. Results indicated that CO molecule adsorption introduces surface states at the Fermi energy level (EF) as shown in partial density of states (PDOS) plots. The dielectric matrix and absorption coefficient (α) for defective anatase TiO2 (101) surface, CO adsorbed at O2c site, at defect site and at Ti5C site of anatase TiO2 (101) surface containing O atom subsurface vacancy has been calculated within the random phase approximation (RPA) using VASP (Vienna ab-initio simulation package) code. It was observed that upon CO adsorption at defective anatase surface, real and imaginary dielectric function peaks were shifted towards lower energy level and a small absorption peak was observed at 1.1 eV energy level which is not present in case of defective anatase (101) surface. CO adsorption produces a red shift in the absorption spectrum of anatase TiO2 (101) surface containing subsurface O atom vacancy.

Photoemission studies of CdTe(100) and the Ag-CdTe(100) interface: Surface structure, growth behavior, Schottky barrier, and surface photovoltage

NASA Astrophysics Data System (ADS)

John, P.; Miller, T.; Hsieh, T. C.; Shapiro, A. P.; Wachs, A. L.; Chiang, T.-C.

1986-11-01

The clean CdTe(100) surface prepared by sputtering and annealing was studied with high-energy electron diffraction (HEED) and photoemission. HEED showed the surface to be a one-domain, (2×1) reconstruction. Photoemission spectra showed two surface-shifted components for the Cd 4d core level, with an intensity ratio of about 1:3, accounting for nearly an entire atomic layer. No surface-induced shifts for the Te 4d core level were detected. A model is proposed for the surface structure in which the surface layer is free of Te, and Cd atoms form dimers resulting in a (2×1) reconstruction; in addition, about (1/4) of the surface area is covered by excess loosely attached Cd atoms. Ag was evaporated on the surface at room temperature and found to grow three dimensionally in the [111] direction. The Ag was found to interact only weakly with the substrate, although the Cd atoms originally loosely bound on top of the surface were found to float on the evaporated Ag islands. A small coverage-dependent surface photovoltage, induced by the synchrotron radiation used for photoemission, was observed; with this effect taken into account, band bending was monitored, the final Fermi-level position being near 0.96 eV above the valence-band maximum. This corresponds to a Schottky-barrier height of about 0.60 eV for the n-type sample used in this experiment. The mechanism for generation of the surface photovoltage will be discussed.

Evidence for a novel chemisorption bond: Formate (HCO/sub 2/) on Cu(100)

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

Stoehr, J.; Outka, D.A.; Madix, R.J.

1985-03-25

Surface extended-x-ray-absorption fine-structure measurements reveal that formate (HCO/sub 2/) groups on Cu(100) chemisorb via the two oxygen atoms in adjacent fourfold hollow sites with an average O-Cu nearest-neighbor bond length of 2.38 +- 0.03 A. This distance is sig- nificantly (approx.0.4 A) longer than typical O-Cu bonds in bulk compounds and all known surface complexes. The unusually large O-Cu distance is attributed to a steric effect involving the C atom in HCO/sub 2/ and the nearest-neighbor Cu surface atoms.

Molecular dynamics simulation studies of ionic liquid electrolytes for electric double layer capacitors

NASA Astrophysics Data System (ADS)

Hu, Zongzhi

Molecular Dynamics (MD) simulation has been performed on various Electric Double Layer Capacitors (EDLCs) systems with different Room Temperature Ionic Liquids (RTILs) as well as different structures and materials of electrodes using a computationally efficient, low cost, united atom (UA)/explicit atom (EA) force filed. MD simulation studies on two 1-butyl-3-methylimidazolium (BMIM) based RTILs, i.e., [BMIM][BF4] and [BMIM][PF6], have been conducted on both atomic flat and corrugated graphite as well as (001) and (011) gold electrode surfaces to understand the correlations between the Electric Double Layer (EDL) structure and their corresponding differential capacitance (DC). Our MD simulations have strong agreement with some experimental data. The structures of electrodes also have a strong effect on the capacitance of EDLCs. MD simulations have been conducted on RTILs of N-methyl-N- propylpyrrolidinium [pyr13] and bis(fluorosulfonyl)imide (FSI) as well as [BMIM][PF6] on both curvature electrodes (fullerenes, nanotube, nanowire) and atomic flat electrode surfaces. It turns out that the nanowire electrode systems have the largest capacitance, following by fullerene systems. Nanotube electrode systems have the smallest capacitance, but they are still larger than that of atomically flat electrode system. Also, RTILs with slightly different chemical structure such as [Cnmim], n = 2, 4, 6, and 8, FSI and bis(trifluoromethylsulfonyl)imide (TFSI), have been examined by MD simulation on both flat and nonflat graphite electrode surfaces to study the effect of cation and anion's chemical structures on EDL structure and DC. With prismatic (nonflat) graphite electrodes, a transition from a bell-shape to a camel-shape DC dependence on electrode potential was observed with increase of the cation alkyl tail length for FSI systems. In contrast, the [Cnmim][TFSI] ionic liquids generated only a camel-shape DC on the rough surface regardless of the length of alkyl tail.

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.

Controlled Synthesis of Pd/Pt Core Shell Nanoparticles Using Area-selective Atomic Layer Deposition

PubMed Central

Cao, Kun; Zhu, Qianqian; Shan, Bin; Chen, Rong

2015-01-01

We report an atomic scale controllable synthesis of Pd/Pt core shell nanoparticles (NPs) via area-selective atomic layer deposition (ALD) on a modified surface. The method involves utilizing octadecyltrichlorosilane (ODTS) self-assembled monolayers (SAMs) to modify the surface. Take the usage of pinholes on SAMs as active sites for the initial core nucleation, and subsequent selective deposition of the second metal as the shell layer. Since new nucleation sites can be effectively blocked by surface ODTS SAMs in the second deposition stage, we demonstrate the successful growth of Pd/Pt and Pt/Pd NPs with uniform core shell structures and narrow size distribution. The size, shell thickness and composition of the NPs can be controlled precisely by varying the ALD cycles. Such core shell structures can be realized by using regular ALD recipes without special adjustment. This SAMs assisted area-selective ALD method of core shell structure fabrication greatly expands the applicability of ALD in fabricating novel structures and can be readily applied to the growth of NPs with other compositions. PMID:25683469

Electronic structure, bonding, charge distribution, and x-ray absorption spectra of the (001) surfaces of fluorapatite and hydroxyapatite from first principles

NASA Astrophysics Data System (ADS)

Rulis, Paul; Yao, Hongzhi; Ouyang, Lizhi; Ching, W. Y.

2007-12-01

Fluorapatite (FAP) and hydroxyapatite (HAP) are two very important bioceramic crystals. The (001) surfaces of FAP and HAP crystals are studied by ab initio density functional calculations using a supercell slab geometry. It is shown that in both crystals, the O-terminated (001) surface is more stable with calculated surface energies of 0.865 and 0.871J/m2 for FAP and HAP, respectively. In FAP, the two surfaces are symmetric. In HAP, the orientation of the OH group along the c axis reduces the symmetry such that the top and bottom surfaces are no longer symmetric. It is revealed that the atoms near the surface and subsurface are significantly relaxed especially in the case of HAP. The largest relaxations occurred via the lateral movements of the O ions at the subsurface level. The electronic structures of the surface models in the form of layer-by-layer resolved partial density of states for all the atoms show systematic variation from the surface region toward the bulk region. The calculated Mulliken effective charge on each type of atom and the bond order values between cations (Ca, P) and anions (O, F) show different charge transfers and bond strength variations from the bulk crystal values. Electron charge density calculations show that the surfaces of both FAP and HAP crystals are mostly positively charged due to the presence of Ca ions at the surface. The positively charged surfaces have implications for the absorption on apatite surfaces of water and other organic molecules in an aqueous environment which are an important part of its bioactivity. The x-ray absorption near-edge structure (XANES) spectra ( Ca-K , O-K , F-K , P-K , and P-L3 edges) of both the surface models and the bulk crystals are calculated and compared. The calculations use a supercell approach which takes into account the electron-core-hole interaction. It is shown that the site-specific XANES spectra show significant differences between atoms near the surface and in the bulk and are very sensitive to the local atomic environment of each atom. This information will be very valuable for characterizing the apatite materials and in the interpretation of experimental data. Comparisons of several sets of experimental data with the weighted sums of the calculated spectra at different sites for the same element show very good agreement.

Clustering on Magnesium Surfaces - Formation and Diffusion Energies.

PubMed

Chu, Haijian; Huang, Hanchen; Wang, Jian

2017-07-12

The formation and diffusion energies of atomic clusters on Mg surfaces determine the surface roughness and formation of faulted structure, which in turn affect the mechanical deformation of Mg. This paper reports first principles density function theory (DFT) based quantum mechanics calculation results of atomic clustering on the low energy surfaces {0001} and [Formula: see text]. In parallel, molecular statics calculations serve to test the validity of two interatomic potentials and to extend the scope of the DFT studies. On a {0001} surface, a compact cluster consisting of few than three atoms energetically prefers a face-centered-cubic stacking, to serve as a nucleus of stacking fault. On a [Formula: see text], clusters of any size always prefer hexagonal-close-packed stacking. Adatom diffusion on surface [Formula: see text] is high anisotropic while isotropic on surface (0001). Three-dimensional Ehrlich-Schwoebel barriers converge as the step height is three atomic layers or thicker. Adatom diffusion along steps is via hopping mechanism, and that down steps is via exchange mechanism.

Hydration water and bulk water in proteins have distinct properties in radial distributions calculated from 105 atomic resolution crystal structures.

PubMed

Chen, Xianfeng; Weber, Irene; Harrison, Robert W

2008-09-25

Water plays a critical role in the structure and function of proteins, although the experimental properties of water around protein structures are not well understood. The water can be classified by the separation from the protein surface into bulk water and hydration water. Hydration water interacts closely with the protein and contributes to protein folding, stability, and dynamics, as well as interacting with the bulk water. Water potential functions are often parametrized to fit bulk water properties because of the limited experimental data for hydration water. Therefore, the structural and energetic properties of the hydration water were assessed for 105 atomic resolution (

Degradation of Perfluorinated Ether Lubricants on Pure Aluminum Surfaces: Semiempirical Quantum Chemical Modeling

NASA Technical Reports Server (NTRS)

Slaby, Scott M.; Ewing, David W.; Zehe, Michael J.

1997-01-01

The AM1 semiempirical quantum chemical method was used to model the interaction of perfluoroethers with aluminum surfaces. Perfluorodimethoxymethane and perfluorodimethyl ether were studied interacting with aluminum surfaces, which were modeled by a five-atom cluster and a nine-atom cluster. Interactions were studied for edge (high index) sites and top (low index) sites of the clusters. Both dissociative binding and nondissociative binding were found, with dissociative binding being stronger. The two different ethers bound and dissociated on the clusters in different ways: perfluorodimethoxymethane through its oxygen atoms, but perfluorodimethyl ether through its fluorine atoms. The acetal linkage of perfluorodimeth-oxymethane was the key structural feature of this molecule in its binding and dissociation on the aluminum surface models. The high-index sites of the clusters caused the dissociation of both ethers. These results are consistent with the experimental observation that perfluorinated ethers decompose in contact with sputtered aluminum surfaces.

Resolving the Structure of a Well-Ordered Hydroxyl Overlayer on In 2O 3 (111): Nanomanipulation and Theory

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

Wagner, Margareta; Lackner, Peter; Seiler, Steffen

Changes in chemical and physical properties resulting from water adsorption play an important role in the characterization and performance of device-relevant materials. Studies of model oxides with well-characterized surfaces can provide detailed information that is vital for a general understanding of water–oxide interactions. In this work, we study single crystals of indium oxide, the prototypical transparent contact material that is heavily used in a wide range of applications and most prominently in optoelectronic technologies. Water adsorbs dissociatively already at temperatures as low as 100 K, as confirmed by scanning tunneling microscopy (STM), photoelectron spectroscopy, and density functional theory. This dissociationmore » takes place on lattice sites of the defect-free surface. While the In 2O 3(111)-(1 × 1) surface offers four types of surface oxygen atoms (12 atoms per unit cell in total), water dissociation happens exclusively at one of them together with a neighboring pair of 5-fold coordinated In atoms. These O–In groups are symmetrically arranged around the 6-fold coordinated In atoms at the surface. At room temperature, the In 2O 3(111) surface thus saturates at three dissociated water molecules per unit cell, leading to a well-ordered hydroxylated surface with (1 × 1) symmetry, where the three water OWH groups plus the surface OSH groups are imaged together as one bright triangle in STM. Manipulations with the STM tip by means of voltage pulses preferentially remove the H atom of one surface OSH group per triangle. The change in contrast due to strong local band bending provides insights into the internal structure of these bright triangles. The experimental results are further confirmed by quantitative simulations of the STM image corrugation.« less

Resolving the Structure of a Well-Ordered Hydroxyl Overlayer on In 2O 3 (111): Nanomanipulation and Theory

DOE PAGES

Wagner, Margareta; Lackner, Peter; Seiler, Steffen; ...

2017-11-01

Changes in chemical and physical properties resulting from water adsorption play an important role in the characterization and performance of device-relevant materials. Studies of model oxides with well-characterized surfaces can provide detailed information that is vital for a general understanding of water–oxide interactions. In this work, we study single crystals of indium oxide, the prototypical transparent contact material that is heavily used in a wide range of applications and most prominently in optoelectronic technologies. Water adsorbs dissociatively already at temperatures as low as 100 K, as confirmed by scanning tunneling microscopy (STM), photoelectron spectroscopy, and density functional theory. This dissociationmore » takes place on lattice sites of the defect-free surface. While the In 2O 3(111)-(1 × 1) surface offers four types of surface oxygen atoms (12 atoms per unit cell in total), water dissociation happens exclusively at one of them together with a neighboring pair of 5-fold coordinated In atoms. These O–In groups are symmetrically arranged around the 6-fold coordinated In atoms at the surface. At room temperature, the In 2O 3(111) surface thus saturates at three dissociated water molecules per unit cell, leading to a well-ordered hydroxylated surface with (1 × 1) symmetry, where the three water OWH groups plus the surface OSH groups are imaged together as one bright triangle in STM. Manipulations with the STM tip by means of voltage pulses preferentially remove the H atom of one surface OSH group per triangle. The change in contrast due to strong local band bending provides insights into the internal structure of these bright triangles. The experimental results are further confirmed by quantitative simulations of the STM image corrugation.« less

Interface and Electronic Characterization of Thin Epitaxial Co3O4 Films

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

Vaz, C.A.; Zhu, Y.; Wang, H.-Q.

2009-01-15

The interface and electronic structure of thin ({approx} 20-74 nm) Co{sub 3}O{sub 4}(1 1 0) epitaxial films grown by oxygen-assisted molecular beam epitaxy on MgAl{sub 2}O{sub 4}(1 1 0) single crystal substrates have been investigated by means of real and reciprocal space techniques. As-grown film surfaces are found to be relatively disordered and exhibit an oblique low energy electron diffraction (LEED) pattern associated with the O-rich CoO{sub 2} bulk termination of the (1 1 0) surface. Interface and bulk film structure are found to improve significantly with post-growth annealing at 820 K in air and display sharp rectangular LEED patterns,more » suggesting a surface stoichiometry of the alternative Co{sub 2}O{sub 2} bulk termination of the (1 1 0) surface. Non-contact atomic force microscopy demonstrates the presence of wide terraces separated by atomic steps in the annealed films that are not present in the as-grown structures; the step height of {approx}2.7 {angstrom} corresponds to two atomic layers and confirms a single termination for the annealed films, consistent with the LEED results. A model of the (1 x 1) surfaces that allows for compensation of the polar surfaces is presented.« less

Additive Mixing and Conformal Coating of Noniridescent Structural Colors with Robust Mechanical Properties Fabricated by Atomization Deposition.

PubMed

Li, Qingsong; Zhang, Yafeng; Shi, Lei; Qiu, Huihui; Zhang, Suming; Qi, Ning; Hu, Jianchen; Yuan, Wei; Zhang, Xiaohua; Zhang, Ke-Qin

2018-04-24

Artificial structural colors based on short-range-ordered amorphous photonic structures (APSs) have attracted great scientific and industrial interest in recent years. However, the previously reported methods of self-assembling colloidal nanoparticles lack fine control of the APS coating and fixation on substrates and poorly realize three-dimensional (3D) conformal coatings for objects with irregular or highly curved surfaces. In this paper, atomization deposition of silica colloidal nanoparticles with poly(vinyl alcohol) as the additive is proposed to solve the above problems. By finely controlling the thicknesses of APS coatings, additive mixing of noniridescent structural colors is easily realized. Based on the intrinsic omnidirectional feature of atomization, a one-step 3D homogeneous conformal coating is also readily realized on various irregular or highly curved surfaces, including papers, resins, metal plates, ceramics, and flexible silk fabrics. The vivid coatings on silk fabrics by atomization deposition possess robust mechanical properties, which are confirmed by rubbing and laundering tests, showing great potential in developing an environmentally friendly coloring technique in the textile industry.

Surface atomic structure characterization of SnSe and black phosphorus using selected area uLEED-IV via LEEM

NASA Astrophysics Data System (ADS)

Dai, Zhongwei; Grady, Maxwell; Yu, Jiexiang; Zang, Jiadong; Pohl, Karsten; Jin, Wencan; Kim, Young Duck; Hone, James; Dadap, Jerry; Osgood, Richard; Sadowski, Jerzy; Vishwanath, Suresh; Xing, Huili

Selected area diffraction intensity-voltage (μLEED-IV) analysis via low energy electron microscopy (LEEM) has the combined functionality of atomic surface structure determination and μm area selectivity, making it ideal for structural investigations of 2-D materials. SnSe thin films have been predicted and observed to be topological crystalline insulators. Previous studies suggested that SnSe has a preferred Se-terminated surface configuration. Using μLEED-IV, we determined that SnSe has, on the contrary, a stable Sn termination. This surface is stabilized through an oscillatory interlayer relaxation, which agrees with previous DFT predictions. Black phosphorus (BP) has an intrinsic layer-dependent bandgap ranging from 0.3 eV to 2 eV. Previous STM and DFT studies suggested BP surfaces have a buckling of 0.02 Å to 0.06 Å. We experimentally determined that the surface buckling of BP to be near 0.2 Å. We further propose, using DFT calculations, that this large surface buckling is induced by the presence of surface defects. The influence of this surface buckling on the electronic structures of BP is under investigation.

Electrochemical oxygen reduction behavior of selectively deposited platinum atoms on gold nanoparticles.

PubMed

Sarkar, A; Kerr, J B; Cairns, E J

2013-07-22

Carbon-supported Pt@Au "core-shell" nanoparticles with varying surface concentration of platinum atoms have been synthesized using a novel redox-mediated synthesis approach. The synthesis technique allows for a selective deposition of platinum atoms on the surface of prefabricated gold nanoparticles. Energy dispersive spectroscopic analyses in a scanning electron microscope reveal that the platinum to gold atomic ratios are close to the nominal values, validating the synthesis scheme. X-ray diffraction data indicate an un-alloyed structure. The platinum to gold surface atomic ratio determined from cyclic voltammetry and copper under-potential deposition experiments reveal good agreement with the calculated values at low platinum concentration. However, there is an increase in non-uniformity in the deposition process upon increasing the platinum concentration. Koutecky-Levich analysis of the samples indicates a transition of the total number of electrons transferred (n) in the electrochemical oxygen reduction reaction from two to four electrons upon increasing the surface concentration of platinum atoms. Furthermore, the data indicate that isolated platinum atoms can reduce molecular oxygen but via a two-electron route. Moreover, successful four-electron reduction of molecular oxygen requires clusters of platinum atoms. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

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

Doping of the step-edge Si chain: Ag on a Si(557)-Au surface

NASA Astrophysics Data System (ADS)

Krawiec, M.; Jałochowski, M.

2010-11-01

Structural and electronic properties of monatomic Ag chains on the Au-induced, highly ordered Si(557) surface are investigated by scanning tunneling microscopy (STM)/spectroscopy and first-principles density functional theory (DFT) calculations. The STM topography data show that a small amount of Ag (0.25 ML) very weakly modifies the one-dimensional structure induced by Au atoms. However, the bias-dependent STM topography and spectroscopy point to the importance of the electronic effects in this system, which are further corroborated by the DFT calculations. The obtained results suggest that Ag atoms act as electron donors leaving the geometry of the surface almost unchanged.

Surface properties of atomically flat poly-crystalline SrTiO3

PubMed Central

Woo, Sungmin; Jeong, Hoidong; Lee, Sang A.; Seo, Hosung; Lacotte, Morgane; David, Adrian; Kim, Hyun You; Prellier, Wilfrid; Kim, Yunseok; Choi, Woo Seok

2015-01-01

Comparison between single- and the poly-crystalline structures provides essential information on the role of long-range translational symmetry and grain boundaries. In particular, by comparing single- and poly-crystalline transition metal oxides (TMOs), one can study intriguing physical phenomena such as electronic and ionic conduction at the grain boundaries, phonon propagation, and various domain properties. In order to make an accurate comparison, however, both single- and poly-crystalline samples should have the same quality, e.g., stoichiometry, crystallinity, thickness, etc. Here, by studying the surface properties of atomically flat poly-crystalline SrTiO3 (STO), we propose an approach to simultaneously fabricate both single- and poly-crystalline epitaxial TMO thin films on STO substrates. In order to grow TMOs epitaxially with atomic precision, an atomically flat, single-terminated surface of the substrate is a prerequisite. We first examined (100), (110), and (111) oriented single-crystalline STO surfaces, which required different annealing conditions to achieve atomically flat surfaces, depending on the surface energy. A poly-crystalline STO surface was then prepared at the optimum condition for which all the domains with different crystallographic orientations could be successfully flattened. Based on our atomically flat poly-crystalline STO substrates, we envision expansion of the studies regarding the TMO domains and grain boundaries. PMID:25744275

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.

Fabricating Large-Area Sheets of Single-Layer Graphene by CVD

NASA Technical Reports Server (NTRS)

Bronikowski, Michael; Manohara, Harish

2008-01-01

This innovation consists of a set of methodologies for preparing large area (greater than 1 cm(exp 2)) domains of single-atomic-layer graphite, also called graphene, in single (two-dimensional) crystal form. To fabricate a single graphene layer using chemical vapor deposition (CVD), the process begins with an atomically flat surface of an appropriate substrate and an appropriate precursor molecule containing carbon atoms attached to substituent atoms or groups. These molecules will be brought into contact with the substrate surface by being flowed over, or sprayed onto, the substrate, under CVD conditions of low pressure and elevated temperature. Upon contact with the surface, the precursor molecules will decompose. The substituent groups detach from the carbon atoms and form gas-phase species, leaving the unfunctionalized carbon atoms attached to the substrate surface. These carbon atoms will diffuse upon this surface and encounter and bond to other carbon atoms. If conditions are chosen carefully, the surface carbon atoms will arrange to form the lowest energy single-layer structure available, which is the graphene lattice that is sought. Another method for creating the graphene lattice includes metal-catalyzed CVD, in which the decomposition of the precursor molecules is initiated by the catalytic action of a catalytic metal upon the substrate surface. Another type of metal-catalyzed CVD has the entire substrate composed of catalytic metal, or other material, either as a bulk crystal or as a think layer of catalyst deposited upon another surface. In this case, the precursor molecules decompose directly upon contact with the substrate, releasing their atoms and forming the graphene sheet. Atomic layer deposition (ALD) can also be used. In this method, a substrate surface at low temperature is covered with exactly one monolayer of precursor molecules (which may be of more than one type). This is heated up so that the precursor molecules decompose and form one monolayer of the target material.

The structural and electronic properties of metal atoms adsorbed on graphene

NASA Astrophysics Data System (ADS)

Liu, Wenjiang; Zhang, Cheng; Deng, Mingsen; Cai, Shaohong

2017-09-01

Based on density functional theory (DFT), we studied the structural and electronic properties of seven different metal atoms adsorbed on graphene (M + graphene). The geometries, adsorption energies, density of states (DOS), band structures, electronic dipole moment, magnetic moment and work function (WF) of M + graphene were calculated. The adsorption energies ΔE indicated that Li, Na, K, Ca and Fe adsorbed on graphene were tending to form stable structures. However, diffusion would occur on Cu and Ag adsorbed on graphene. In addition, the electronic structure near the Fermi level of graphene was significantly affected by Fe (Cu and Ag), compared with Li (Na, K and Ca). The electronic dipole moment and magnetic moment of M + graphene were sensitive to the adsorbed metal atoms. Moreover, we found electropositive (electronegative) adsorption can decrease (increase) the WF of the surface. Specially, the WF of Ag + graphene and Fe + graphene would increase because surface dipole moment make a contribution to electron.

Nanomanufacturing of silicon surface with a single atomic layer precision via mechanochemical reactions.

PubMed

Chen, Lei; Wen, Jialin; Zhang, Peng; Yu, Bingjun; Chen, Cheng; Ma, Tianbao; Lu, Xinchun; Kim, Seong H; Qian, Linmao

2018-04-18

Topographic nanomanufacturing with a depth precision down to atomic dimension is of importance for advancement of nanoelectronics with new functionalities. Here we demonstrate a mask-less and chemical-free nanolithography process for regio-specific removal of atomic layers on a single crystalline silicon surface via shear-induced mechanochemical reactions. Since chemical reactions involve only the topmost atomic layer exposed at the interface, the removal of a single atomic layer is possible and the crystalline lattice beneath the processed area remains intact without subsurface structural damages. Molecular dynamics simulations depict the atom-by-atom removal process, where the first atomic layer is removed preferentially through the formation and dissociation of interfacial bridge bonds. Based on the parametric thresholds needed for single atomic layer removal, the critical energy barrier for water-assisted mechanochemical dissociation of Si-Si bonds was determined. The mechanochemical nanolithography method demonstrated here could be extended to nanofabrication of other crystalline materials.

Atomically manufactured nickel-silicon quantum dots displaying robust resonant tunneling and negative differential resistance

NASA Astrophysics Data System (ADS)

Cheng, Jian-Yih; Fisher, Brandon L.; Guisinger, Nathan P.; Lilley, Carmen M.

2017-12-01

Providing a spin-free host material in the development of quantum information technology has made silicon a very interesting and desirable material for qubit design. Much of the work and experimental progress has focused on isolated phosphorous atoms. In this article, we report on the exploration of Ni-Si clusters that are atomically manufactured via self-assembly from the bottom-up and behave as isolated quantum dots. These small quantum dot structures are probed at the atomic-scale with scanning tunneling microscopy and spectroscopy, revealing robust resonance through discrete quantized energy levels within the Ni-Si clusters. The resonance energy is reproducible and the peak spacing of the quantum dot structures increases as the number of atoms in the cluster decrease. Probing these quantum dot structures on degenerately doped silicon results in the observation of negative differential resistance in both I-V and dI/dV spectra. At higher surface coverage of nickel, a well-known √19 surface modification is observed and is essentially a tightly packed array of the clusters. Spatial conductance maps reveal variations in the local density of states that suggest the clusters are influencing the electronic properties of their neighbors. All of these results are extremely encouraging towards the utilization of metal modified silicon surfaces to advance or complement existing quantum information technology.

Atomically manufactured nickel–silicon quantum dots displaying robust resonant tunneling and negative differential resistance

DOE PAGES

Cheng, Jian -Yih; Fisher, Brandon L.; Guisinger, Nathan P.; ...

2017-05-22

Providing a spin-free host material in the development of quantum information technology has made silicon a very interesting and desirable material for qubit design. Much of the work and experimental progress has focused on isolated phosphorous atoms. In this article, we report on the exploration of Ni–Si clusters that are atomically manufactured via self-assembly from the bottom-up and behave as isolated quantum dots. These small quantum dot structures are probed at the atomic-scale with scanning tunneling microscopy and spectroscopy, revealing robust resonance through discrete quantized energy levels within the Ni–Si clusters. The resonance energy is reproducible and the peak spacingmore » of the quantum dot structures increases as the number of atoms in the cluster decrease. Probing these quantum dot structures on degenerately doped silicon results in the observation of negative differential resistance in both I–V and dI/dV spectra. At higher surface coverage of nickel, a well-known √19 surface modification is observed and is essentially a tightly packed array of the clusters. Spatial conductance maps reveal variations in the local density of states that suggest the clusters are influencing the electronic properties of their neighbors. Furthermore, all of these results are extremely encouraging towards the utilization of metal modified silicon surfaces to advance or complement existing quantum information technology.« less

Atomically manufactured nickel–silicon quantum dots displaying robust resonant tunneling and negative differential resistance

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

Cheng, Jian -Yih; Fisher, Brandon L.; Guisinger, Nathan P.

Providing a spin-free host material in the development of quantum information technology has made silicon a very interesting and desirable material for qubit design. Much of the work and experimental progress has focused on isolated phosphorous atoms. In this article, we report on the exploration of Ni–Si clusters that are atomically manufactured via self-assembly from the bottom-up and behave as isolated quantum dots. These small quantum dot structures are probed at the atomic-scale with scanning tunneling microscopy and spectroscopy, revealing robust resonance through discrete quantized energy levels within the Ni–Si clusters. The resonance energy is reproducible and the peak spacingmore » of the quantum dot structures increases as the number of atoms in the cluster decrease. Probing these quantum dot structures on degenerately doped silicon results in the observation of negative differential resistance in both I–V and dI/dV spectra. At higher surface coverage of nickel, a well-known √19 surface modification is observed and is essentially a tightly packed array of the clusters. Spatial conductance maps reveal variations in the local density of states that suggest the clusters are influencing the electronic properties of their neighbors. Furthermore, all of these results are extremely encouraging towards the utilization of metal modified silicon surfaces to advance or complement existing quantum information technology.« less

First-principles study of native defects in bulk Sm2CuO4 and its (001) surface structure

NASA Astrophysics Data System (ADS)

Zheng, Fubao; Zhang, Qinfang; Meng, Qiangqiang; Wang, Baolin; Song, Fengqi; Yunoki, Seiji; Wang, Guanghou

2018-04-01

Using the first-principles calculations based on the density functional theory, we have studied the bulk defect formation and surface structures of Sm2CuO4. To ensure the accuracy of calculations, the spin order of Cu atoms is rechecked and it is the well-known nearest-neighbor antiferromagnetic ground state, which can be attributed to the hole-mediated superexchange through the strong pdσ hybridization interaction between Cu dx2-y2 electron and the neighboring oxygen px (or py) electron. Under each present experimental condition, the Sm vacancy has a very high formation energy and is unlikely to be stable. The Cu vacancy is a shallow acceptor, which is preferred under O-rich conditions, whereas the O vacancy is a donor and energetically favorable under O-poor conditions. To construct its (001) surface structure, CuOO, CuO, and Cu terminated surfaces are found to be most favorable under different experimental conditions. The stable surface structures are always accompanied by significant surface atomic reconstructions and electron charge redistribution, which are intimately correlated to each other.

Role of oxygen functional groups for structure and dynamics of interfacial water on low rank coal surface: a molecular dynamics simulation

NASA Astrophysics Data System (ADS)

You, Xiaofang; Wei, Hengbin; Zhu, Xianchang; Lyu, Xianjun; Li, Lin

2018-07-01

Molecular dynamics simulations were employed to study the effects of oxygen functional groups for structure and dynamics properties of interfacial water molecules on the subbituminous coal surface. Because of complex composition and structure, the graphite surface modified by hydroxyl, carboxyl and carbonyl groups was used to represent the surface model of subbituminous coal according to XPS results, and the composing proportion for hydroxyl, carbonyl and carboxyl is 25:3:5. The hydration energy with -386.28 kJ/mol means that the adsorption process between water and coal surface is spontaneous. Density profiles for oxygen atoms and hydrogen atoms indicate that the coal surface properties affect the structural and dynamic characteristics of the interfacial water molecules. The interfacial water exhibits much more ordering than bulk water. The results of radial distribution functions, mean square displacement and local self-diffusion coefficient for water molecule related to three oxygen moieties confirmed that the water molecules prefer to absorb with carboxylic groups, and adsorption of water molecules at the hydroxyl and carbonyl is similar.

Monoatomic and dimer Mn adsorption on the Au(111) surface from first principles

NASA Astrophysics Data System (ADS)

Muñoz, Francisco; Romero, Aldo H.; Mejía-López, Jose; Morán-López, J. L.

2011-05-01

A theoretical study based on the density functional theory of the adsorption of Mn monomers and dimers on a Au-(111) surface is presented. As necessary preliminary steps, the bulk and clean surface electronic structure are calculated, which agree well with previous reports. Then, the electronic structure of the Mn adatom, chemisorbed on four different surface geometries, is analyzed. It is found that the most stable geometry is when the Mn atom is chemisorbed on threefold coordinated sites. Using this geometry for a single adatom a second Mn atom is chemisorbed and the most stable dimer geometrical structure is calculated. The lowest-energy configuration corresponds to the molecule lying parallel to the surface, adsorbed on two topological equivalent threefold coordinated sites. It is also found that the lowest-energy magnetic configuration corresponds to the antiferromagnetic arrangement with individual magnetic moments of 4.64μB. Finally, it is concluded that the dimer is not stable and should fragment at the surface.

Prediction of Carbohydrate Binding Sites on Protein Surfaces with 3-Dimensional Probability Density Distributions of Interacting Atoms

PubMed Central

Tsai, Keng-Chang; Jian, Jhih-Wei; Yang, Ei-Wen; Hsu, Po-Chiang; Peng, Hung-Pin; Chen, Ching-Tai; Chen, Jun-Bo; Chang, Jeng-Yih; Hsu, Wen-Lian; Yang, An-Suei

2012-01-01

Non-covalent protein-carbohydrate interactions mediate molecular targeting in many biological processes. Prediction of non-covalent carbohydrate binding sites on protein surfaces not only provides insights into the functions of the query proteins; information on key carbohydrate-binding residues could suggest site-directed mutagenesis experiments, design therapeutics targeting carbohydrate-binding proteins, and provide guidance in engineering protein-carbohydrate interactions. In this work, we show that non-covalent carbohydrate binding sites on protein surfaces can be predicted with relatively high accuracy when the query protein structures are known. The prediction capabilities were based on a novel encoding scheme of the three-dimensional probability density maps describing the distributions of 36 non-covalent interacting atom types around protein surfaces. One machine learning model was trained for each of the 30 protein atom types. The machine learning algorithms predicted tentative carbohydrate binding sites on query proteins by recognizing the characteristic interacting atom distribution patterns specific for carbohydrate binding sites from known protein structures. The prediction results for all protein atom types were integrated into surface patches as tentative carbohydrate binding sites based on normalized prediction confidence level. The prediction capabilities of the predictors were benchmarked by a 10-fold cross validation on 497 non-redundant proteins with known carbohydrate binding sites. The predictors were further tested on an independent test set with 108 proteins. The residue-based Matthews correlation coefficient (MCC) for the independent test was 0.45, with prediction precision and sensitivity (or recall) of 0.45 and 0.49 respectively. In addition, 111 unbound carbohydrate-binding protein structures for which the structures were determined in the absence of the carbohydrate ligands were predicted with the trained predictors. The overall prediction MCC was 0.49. Independent tests on anti-carbohydrate antibodies showed that the carbohydrate antigen binding sites were predicted with comparable accuracy. These results demonstrate that the predictors are among the best in carbohydrate binding site predictions to date. PMID:22848404

Tutorial on Atomic Oxygen Effects and Contamination

NASA Technical Reports Server (NTRS)

Miller, Sharon K.

2017-01-01

Atomic oxygen is the most predominant specie in low Earth orbit (LEO) and is contained in the upper atmosphere of many other planetary bodies. Formed by photo-dissociation of molecular oxygen, it is highly reactive and energetic enough to break chemical bonds on the surface of many materials and react with them to form either stable or volatile oxides. The extent of the damage for spacecraft depends a lot on how much atomic oxygen arrives at the surface, the energy of the atoms, and the reactivity of the material that is exposed to it. Oxide formation can result in shrinkage, cracking, or erosion which can also result in changes in optical, thermal, or mechanical properties of the materials exposed. The extent of the reaction can be affected by mechanical loading, temperature, and other environmental components such as ultraviolet radiation or charged particles. Atomic oxygen generally causes a surface reaction, but it can scatter under coatings and into crevices causing oxidation much farther into a spacecraft surface or structure than would be expected. Contamination can also affect system performance. Contamination is generally caused by arrival of volatile species that condense on spacecraft surfaces. The volatiles are typically a result of outgassing of materials that are on the spacecraft. Once the volatiles are condensed on a surface, they can then be fixed on the surface by ultraviolet radiation andor atomic oxygen reaction to form stable surface contaminants that can change optical and thermal properties of materials in power systems, thermal systems, and sensors. This tutorial discusses atomic oxygen erosion and contaminate formation, and the effect they have on typical spacecraft materials. Scattering of atomic oxygen, some effects of combined environments and examples of effects of atomic oxygen and contamination on spacecraft systems and components will also be presented.

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

Atomic scale morphology, growth behaviour and electronic properties of semipolar {101[overline]3} GaN surfaces.

PubMed

Kioseoglou, J; Kalesaki, E; Lymperakis, L; Karakostas, Th; Komninou, Ph

2013-01-30

First-principles calculations relating to the atomic structure and electronic properties of {101[overline]3} GaN surfaces reveal significant differentiations between the two polarity orientations. The (101[overline]3) surface exhibits a remarkable morphological stability, stabilizing a metallic structure (Ga adlayer) over the entire range of the Ga chemical potential. In contrast, the semiconducting, cleaved surface is favoured on (101[overline]3[overline]) under extremely and moderately N-rich conditions, a Ga bilayer is stabilized under corresponding Ga-rich conditions and various transitions between metallic reconstructions take place in intermediate growth stoichiometries. Efficient growth schemes for smooth, two-dimensional GaN layers and the isolation of {101[overline]3} material from parasitic orientations are identified.

Investigation of laser-fired point contacts on KOH structured laser-crystallized silicon by conductive atomic force microscopy

NASA Astrophysics Data System (ADS)

Gref, Orman; Weizman, Moshe; Rhein, Holger; Gabriel, Onno; Gernert, Ulrich; Schlatmann, Rutger; Boit, Christian; Friedrich, Felice

2016-06-01

A conductive atomic force microscope is used to study the local topography and conductivity of laser-fired aluminum contacts on KOH-structured multicrystalline silicon surfaces. A significant increase in conductivity is observed in the laser-affected area. The area size and spatial uniformity of this enhanced conductivity depends on the laser energy fluence. The laser-affected area shows three ring-shaped regimes of different conductance depending on the local aluminum and oxygen concentration. Finally, it was found that the topographic surface structure determined by the silicon grain orientation does not significantly affect the laser-firing process.

Si(111) strained layers on Ge(111): Evidence for c (2 ×4 ) domains

NASA Astrophysics Data System (ADS)

Zhachuk, R.; Coutinho, J.; Dolbak, A.; Cherepanov, V.; Voigtländer, B.

2017-08-01

The tensile-strained Si (111 ) layers grown on top of Ge (111 ) substrates are studied by combining scanning tunneling microscopy, low-energy electron diffraction, and first-principles calculations. It is shown that the layers exhibit c (2 ×4 ) domains, which are separated by domain walls along <1 ¯10 > directions. A model structure for the c (2 ×4 ) domains is proposed, which shows low formation energy and good agreement with the experimental data. The results of our calculations suggest that Ge atoms are likely to replace Si atoms with dangling bonds on the surface (rest-atoms and adatoms), thus significantly lowering the surface energy and inducing the formation of domain walls. The experiments and calculations demonstrate that when surface strain changes from compressive to tensile, the (111) reconstruction converts from dimer-adatom-stacking fault-based to adatom-based structures.

Formation of Micro- and Nanostructures on the Nanotitanium Surface by Chemical Etching and Deposition of Titania Films by Atomic Layer Deposition (ALD)

PubMed Central

Nazarov, Denis V.; Zemtsova, Elena G.; Valiev, Ruslan Z.; Smirnov, Vladimir M.

2015-01-01

In this study, an integrated approach was used for the preparation of a nanotitanium-based bioactive material. The integrated approach included three methods: severe plastic deformation (SPD), chemical etching and atomic layer deposition (ALD). For the first time, it was experimentally shown that the nature of the etching medium (acidic or basic Piranha solutions) and the etching time have a significant qualitative impact on the nanotitanium surface structure both at the nano- and microscale. The etched samples were coated with crystalline biocompatible TiO2 films with a thickness of 20 nm by Atomic Layer Deposition (ALD). Comparative study of the adhesive and spreading properties of human osteoblasts MG-63 has demonstrated that presence of nano- and microscale structures and crystalline titanium oxide on the surface of nanotitanium improve bioactive properties of the material. PMID:28793716

Self-organization of S adatoms on Au(111): √3R30° rows at low coverage

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

Walen, Holly, E-mail: hwalen@iastate.edu; Liu, Da-Jiang; Oh, Junepyo

Using scanning tunneling microscopy, we observe an adlayer structure that is dominated by short rows of S atoms, on unreconstructed regions of a Au(111) surface. This structure forms upon adsorption of low S coverage (less than 0.1 monolayer) on a fully reconstructed clean surface at 300 K, then cooling to 5 K for observation. The rows adopt one of three orientations that are rotated by 30° from the close-packed directions of the Au(111) substrate, and adjacent S atoms in the rows are separated by √3 times the surface lattice constant, a. Monte Carlo simulations are performed on lattice-gas models, derivedmore » using a limited cluster expansion based on density functional theory energetics. Models which include long-range pairwise interactions (extending to 5a), plus selected trio interactions, successfully reproduce the linear rows of S atoms at reasonable temperatures.« less

Self-organization of S adatoms on Au(111): √3R30° rows at low coverage.

PubMed

Walen, Holly; Liu, Da-Jiang; Oh, Junepyo; Lim, Hyunseob; Evans, J W; Kim, Yousoo; Thiel, P A

2015-07-07

Using scanning tunneling microscopy, we observe an adlayer structure that is dominated by short rows of S atoms, on unreconstructed regions of a Au(111) surface. This structure forms upon adsorption of low S coverage (less than 0.1 monolayer) on a fully reconstructed clean surface at 300 K, then cooling to 5 K for observation. The rows adopt one of three orientations that are rotated by 30° from the close-packed directions of the Au(111) substrate, and adjacent S atoms in the rows are separated by √3 times the surface lattice constant, a. Monte Carlo simulations are performed on lattice-gas models, derived using a limited cluster expansion based on density functional theory energetics. Models which include long-range pairwise interactions (extending to 5a), plus selected trio interactions, successfully reproduce the linear rows of S atoms at reasonable temperatures.

Confinement properties of 2D porous molecular networks on metal surfaces

NASA Astrophysics Data System (ADS)

Müller, Kathrin; Enache, Mihaela; Stöhr, Meike

2016-04-01

Quantum effects that arise from confinement of electronic states have been extensively studied for the surface states of noble metals. Utilizing small artificial structures for confinement allows tailoring of the surface properties and offers unique opportunities for applications. So far, examples of surface state confinement include thin films, artificial nanoscale structures, vacancy and adatom islands, self-assembled 1D chains, vicinal surfaces, quantum dots and quantum corrals. In this review we summarize recent achievements in changing the electronic structure of surfaces by adsorption of nanoporous networks whose design principles are based on the concepts of supramolecular chemistry. Already in 1993, it was shown that quantum corrals made from Fe atoms on a Cu(1 1 1) surface using single atom manipulation with a scanning tunnelling microscope confine the Shockley surface state. However, since the atom manipulation technique for the construction of corral structures is a relatively time consuming process, the fabrication of periodic two-dimensional (2D) corral structures is practically impossible. On the other side, by using molecular self-assembly extended 2D porous structures can be achieved in a parallel process, i.e. all pores are formed at the same time. The molecular building blocks are usually held together by non-covalent interactions like hydrogen bonding, metal coordination or dipolar coupling. Due to the reversibility of the bond formation defect-free and long-range ordered networks can be achieved. However, recently also examples of porous networks formed by covalent coupling on the surface have been reported. By the choice of the molecular building blocks, the dimensions of the network (pore size and pore to pore distance) can be controlled. In this way, the confinement properties of the individual pores can be tuned. In addition, the effect of the confined state on the hosting properties of the pores will be discussed in this review article.

Confinement properties of 2D porous molecular networks on metal surfaces.

PubMed

Müller, Kathrin; Enache, Mihaela; Stöhr, Meike

2016-04-20

Quantum effects that arise from confinement of electronic states have been extensively studied for the surface states of noble metals. Utilizing small artificial structures for confinement allows tailoring of the surface properties and offers unique opportunities for applications. So far, examples of surface state confinement include thin films, artificial nanoscale structures, vacancy and adatom islands, self-assembled 1D chains, vicinal surfaces, quantum dots and quantum corrals. In this review we summarize recent achievements in changing the electronic structure of surfaces by adsorption of nanoporous networks whose design principles are based on the concepts of supramolecular chemistry. Already in 1993, it was shown that quantum corrals made from Fe atoms on a Cu(1 1 1) surface using single atom manipulation with a scanning tunnelling microscope confine the Shockley surface state. However, since the atom manipulation technique for the construction of corral structures is a relatively time consuming process, the fabrication of periodic two-dimensional (2D) corral structures is practically impossible. On the other side, by using molecular self-assembly extended 2D porous structures can be achieved in a parallel process, i.e. all pores are formed at the same time. The molecular building blocks are usually held together by non-covalent interactions like hydrogen bonding, metal coordination or dipolar coupling. Due to the reversibility of the bond formation defect-free and long-range ordered networks can be achieved. However, recently also examples of porous networks formed by covalent coupling on the surface have been reported. By the choice of the molecular building blocks, the dimensions of the network (pore size and pore to pore distance) can be controlled. In this way, the confinement properties of the individual pores can be tuned. In addition, the effect of the confined state on the hosting properties of the pores will be discussed in this review article.

First-principles molecular dynamics study of water dissociation on the γ-U(1 0 0) surface

NASA Astrophysics Data System (ADS)

Yang, Yu; Zhang, Ping

2015-05-01

Based on first-principles molecular dynamics simulations at finite temperatures, we systematically study the adsorption and dissociation of water molecules on the γ-U(1 0 0) surface. We predict that water molecules spontaneously dissociate upon approaching the native γ-U(1 0 0) surface. The dissociation results from electronic interactions between surface uranium 6d states and 1b2, 3a1, and 1b1 molecular orbitals of water. With segregated Nb atoms existing on the surface, adsorbing water molecules also dissociate spontaneously because Nb 3d electronic states can also interact with the molecular orbitals similarly. After dissociation, the isolated hydrogen atoms are found to diffuse fast on both the γ-U surface and that with a surface substitutional Nb atom, which is very similar to the ‘Hot-Atom’ dissociation of oxygen molecules on the Al(1 1 1) surface. From a series of consecutive molecular dynamics simulations, we further reveal that on both the γ-U surface and that with a surface substitutional Nb atom, one surface U atom will be pulled out to form the U-O-U structure after dissociative adsorption of 0.44 ML water molecules. This result indicates that oxide nucleus can form at low coverage of water adsorption on the two surfaces.

First-principles calculations of the thermal stability of Ti 3SiC 2(0001) surfaces

NASA Astrophysics Data System (ADS)

Orellana, Walter; Gutiérrez, Gonzalo

2011-12-01

The energetic, thermal stability and dynamical properties of the ternary layered ceramic Ti3SiC2(0001) surface are addressed by density-functional theory calculations and molecular dynamic (MD) simulations. The equilibrium surface energy at 0 K of all terminations is contrasted with thermal stability at high temperatures, which are investigated by ab initio MD simulations in the range of 800 to 1400 °C. We find that the toplayer (sublayer) surface configurations: Si(Ti2) and Ti2(Si) show the lowest surface energies with reconstruction features for Si(Ti2). However, at high temperatures they are unstable, forming disordered structures. On the contrary, Ti1(C) and Ti2(C) despite their higher surface energies, show a remarkable thermal stability at high temperatures preserving the crystalline structures up to 1400 °C. The less stable surfaces are those terminated in C atoms, C(Ti1) and C(Ti2), which at high temperatures show surface dissociation forming amorphous TiCx structures. Two possible atomic scale mechanisms involved in the thermal stability of Ti3SiC2(0001) are discussed.

Spectroscopic Study of the Thermal Degradation of PVP-capped Rh and Pt Nanoparticles in H2 and O2 Environments

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

Borodko, Yuri; Lee, Hyun Sook; Joo, Sang Hoon

2009-09-15

Poly(N-vinylpyrrolidone) (PVP) capped platinum and rhodium nanoparticles (7-12 nm) have been studied with UV-VIS, FTIR and Raman spectroscopy. The absorption bands in the region 190-900 nm are shown to be sensitive to the electronic structure of surface Rh and Pt atoms as well as to the aggregation of the nanoparticles. In-situ FTIR-DRIFT spectroscopy of the thermal decay of PVP stabilized Rh and Pt nanoparticles in H{sub 2} and O{sub 2} atmospheres in temperatures ranging from 30 C-350 C reveal that decomposition of PVP above 200 C, PVP transforms into a 'polyamidpolyene' - like material that is in turn converted intomore » a thin layer of amorphous carbon above 300 C. Adsorbed carbon monoxide was used as a probing molecule to monitor changes of electronic structure of surface Rh and Pt atoms and accessible surface area. The behavior of surface Rh and Pt atoms with ligated CO and amide groups of pyrrolidones resemble that of surface coordination compounds.« less

Theoretical aspects of studies of oxide and semiconductor surfaces using low energy positrons

NASA Astrophysics Data System (ADS)

Fazleev, N. G.; Maddox, W. B.; Weiss, A. H.

2011-01-01

This paper presents the results of a theoretical study of positron surface and bulk states and annihilation characteristics of surface trapped positrons at the oxidized Cu(100) single crystal and at both As- and Ga-rich reconstructed GaAs(100) surfaces. The variations in atomic structure and chemical composition of the topmost layers of the surfaces associated with oxidation and reconstructions and the charge redistribution at the surfaces are found to affect localization and spatial extent of the positron surface-state wave functions. The computed positron binding energy, work function, and annihilation characteristics reveal their sensitivity to charge transfer effects, atomic structure and chemical composition of the topmost layers of the surfaces. Theoretical positron annihilation probabilities with relevant core electrons computed for the oxidized Cu(100) surface and the As- and Ga-rich reconstructed GaAs(100) surfaces are compared with experimental ones estimated from the positron annihilation induced Auger peak intensities measured from these surfaces.

Low temperature scanning tunneling microscopy of metallic and organic nanostructures

NASA Astrophysics Data System (ADS)

Fölsch, Stefan

2006-03-01

Low temperature scanning tunneling microscopy (LT-STM) is capable of both characterizing and manipulating atomic-scale structures at surfaces. It thus provides a powerful experimental tool to gain fundamental insight into how electronic properties evolve when controlling size, geometry, and composition of nanometric model systems at the level of single atoms and molecules. The experiments discussed in this talk employ a Cu(111) surface onto which perfect nanostructures are assembled from native adatoms and organic molecules. Using single Cu adatoms as building blocks, we obtain zero-, one-, and two-dimensional quantum objects (corresponding to the discrete adatom, monatomic adatom chains, and compact adatom assemblies) with intriguing electronic properties. Depending on the structure shape and the number of incorporated atoms we observe the formation of characteristic quantum levels which merge into the sp-derived Shockley surface state in the limit of extended 2D islands; this state exists on many surfaces, such as Cu(111). Our results reveal the natural linkage between this traditional surface property, the quantum confinement in compact adatom structures, and the quasi-atomic state associated with the single adatom. In a second step, we study the interaction of pentacene (C22H14) with Cu adatom chains serving as model quantum wires. We find that STM-based manipulation is capable of connecting single molecules to the chain ends in a defined way, and that the molecule-chain interaction shifts the chain-localized quantum states to higher binding energies. The present system provides an instructive model case to study single organic molecules interacting with metallic nanostructures. The microscopic nature of such composite structures is of importance for any future molecular-based device realization since it determines the contact conductance between the molecular unit and its metal ''contact pad''.

Structure of the Si(111)-(5×2)-Au Surface

NASA Astrophysics Data System (ADS)

Abukawa, Tadashi; Nishigaya, Yoshiki

2013-01-01

The structure of the Si(111)-(5×2)-Au surface, one of the long-standing problems in surface science, has been solved by means of Weissenberg reflection high-energy electron diffraction. The arrangement of the Au atoms and their positions with respect to the substrate were determined from a three-dimensional Patterson function with a lateral resolution of 0.3 Å based on a large amount of diffraction data. The new structural model consists of six Au atoms in a 5×2 unit, which agrees with the recently confirmed Au coverage of 0.6 ML [I. Barke , Phys. Rev. B 79, 155301 (2009).PRBMDO1098-0121]. The model has a distinct ×2 periodicity, and includes a Au dimer. The model is also compatible with previously obtained STM images.

Surface reconstruction switching induced by tensile stress of DB steps: From Ba/Si(0 0 1)- 2 × 3 to Ba/Si(0 0 1)-4° off- 3 × 2

NASA Astrophysics Data System (ADS)

Kim, Hidong; Lkhagvasuren, Altaibaatar; Zhang, Rui; Seo, Jae M.

2018-05-01

The alkaline-earth metal adsorption on Si(0 0 1) has attracted much interest for finding a proper template in the growth of high- κ and crystalline films. Up to now on the flat Si(0 0 1) surface with double domains and single-layer steps, the adsorbed Ba atoms are known to induce the 2 × 3 structure through removing two Si dimers and adding a Ba atom per unit cell in each domain. In the present investigation, the Si(0 0 1)-4° off surface with DB steps and single domains has been employed as a substrate and the reconstruction at the initial stage of Ba adsorption has been investigated by scanning tunneling microscopy and synchrotron photoemission spectroscopy. On this vicinal and single domain terrace, a novel 3 × 2 structure rotated by 90° from the 2 × 3 structure has been found. Such a 3 × 2 structure turns out to be formed by adding a Ba atom and a Si dimer per unit cell. This results from the fact that the adsorbed Ba2+ ions with a larger ionic radius relieve tensile stress on the original Si dimers exerted by the rebonded atoms at the DB step.

Effect of nitrogen plasma afterglow on the surface charge effect resulted during XPS surface analysis of amorphous carbon nitride thin films

NASA Astrophysics Data System (ADS)

Kayed, Kamal

2018-06-01

The aim of this paper is to investigate the relationship between the micro structure and the surface charge effect resulted during XPS surface analysis of amorphous carbon nitride thin films prepared by laser ablation method. The study results show that the charge effect coefficient (E) is not just a correction factor. We found that the changes in this coefficient value due to incorporation of nitrogen atoms into the carbon network are related to the spatial configurations of the sp2 bonded carbon atoms, order degree and sp2 clusters size. In addition, results show that the curve E vs. C(sp3)-N is a characteristic curve of the micro structure. This means that using this curve makes it easy to sorting the samples according to the micro structure (hexagonal rings or chains).

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

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

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

1990-04-01

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

Tomography of a Probe Potential Using Atomic Sensors on Graphene.

PubMed

Wyrick, Jonathan; Natterer, Fabian D; Zhao, Yue; Watanabe, Kenji; Taniguchi, Takashi; Cullen, William G; Zhitenev, Nikolai B; Stroscio, Joseph A

2016-12-27

Our ability to access and explore the quantum world has been greatly advanced by the power of atomic manipulation and local spectroscopy with scanning tunneling and atomic force microscopes, where the key technique is the use of atomically sharp probe tips to interact with an underlying substrate. Here we employ atomic manipulation to modify and quantify the interaction between the probe and the system under study that can strongly affect any measurement in low charge density systems, such as graphene. We transfer Co atoms from a graphene surface onto a probe tip to change and control the probe's physical structure, enabling us to modify the induced potential at a graphene surface. We utilize single Co atoms on a graphene field-effect device as atomic scale sensors to quantitatively map the modified potential exerted by the scanning probe over the whole relevant spatial and energy range.

Grain boundaries at the surface of consolidated MgO nanocrystals and acid-base functionality.

PubMed

Vingurt, Dima; Fuks, David; Landau, Miron V; Vidruk, Roxana; Herskowitz, Moti

2013-09-21

The increase of the surface basicity-acidity of MgO material by factors of 1.8-3.0 due to consolidation of its nanocrystals was demonstrated by the indicator titration. It was shown that the parallel increase of surface acidity and basicity is attributed to the formation of grain boundaries (GB) after MgO aerogel densification. A simple model predicting the increase of surface acidity-basicity of MgO that correlates with the results of direct measurements was proposed. The model is based on the study of the fine atomic structure at GB surface areas in consolidated MgO nanocrystals in the framework of Density Functional Theory. It is found that the displacements of coordinatively unsaturated surface ions near the GB are significant at the distances ~3-4 atomic layers from the geometrical contact plane between nanocrystals. The detailed analysis of atomic positions inside GB demonstrated the coordination deficiency of surface atoms at the GB areas leading to the formation of stretched bonds and to creation of low coordinated surface ions due to splitting of coordination numbers of surface atoms belonging to GB areas. Density of states for electrons shows the existence of additional states in the band gap close to the bottom of the conduction band. The adsorption energy of CO2 molecules atop oxygen atoms exposed at surface GB areas is of the same order of magnitude as that reported for oxygen atoms at crystallographic edges and corners of MgO crystals. It provides additional options for bonding of molecules at the surface of nanocrystalline MgO increasing the adsorption capacity and catalytic activity.

Effect of surface Fe-S hybrid structure on the activity of the perfect and reduced α-Fe2O3(001) for chemical looping combustion

NASA Astrophysics Data System (ADS)

Xiao, Xianbin; Qin, Wu; Wang, Jianye; Li, Junhao; Dong, Changqing

2018-05-01

Sulfurization of the gradually reduced Fe2O3 surfaces is inevitable while Fe2O3 is used as an oxygen carrier (OC) for coal chemical looping combustion (CLC), which will result in formation of Fe-S hybrid structure on the surfaces. The Fe-S hybrid structure will directly alter the reactivity of the surfaces. Therefore, detailed properties of Fe-S hybrid structure over the perfect and reduced Fe2O3(001) surfaces, and its effect on the interfacial interactions, including CO oxidization and decomposition on the surfaces, were investigated by using density functional theory (DFT) calculations. The S atom prefers to chemically bind to Fe site with electron transfer from the surfaces to the S atom, and a deeper reduction of Fe2O3(001) leads to an increasing interaction between S and Fe. The formation of Fe-S hybrid structure alters the electronic properties of the gradually reduced Fe2O3(001) surfaces, promoting CO oxidation on the surfaces ranging from Fe2O3 to FeO, but depressing carbon deposition on the surfaces ranging from FeO to Fe. The sulfurized FeO acts as a watershed to realize relatively high CO oxidation rate and low carbon deposition. Results provided a fundamental understanding for controlling and optimizing the CLC processes.

Cluster adsorption on amorphous and crystalline surfaces - A molecular dynamics study of model Pt on Cu and model Pd on Pt

NASA Technical Reports Server (NTRS)

Garofalini, S. H.; Halicioglu, T.; Pound, G. M.

1981-01-01

Molecular dynamics was used to study the structure, dispersion and short-time behavior of ten-atom clusters adsorbed onto amorphous and crystalline substrates, in which the cluster atoms differed from the substrate atoms. Two adatom-substrate model systems were chosen; one, in which the interaction energy between adatom pairs was greater than that between substrate pairs, and the other, in which the reverse was true. At relatively low temperature ranges, increased dispersion of cluster atoms occurred: (a) on the amorphous substrate as compared to the FCC(100) surface, (b) with increasing reduced temperature, and (c) with adatom-substrate interaction energy stronger than adatom-adatom interaction. Two-dimensional clusters (rafts) on the FCC(100) surface displayed migration of edge atoms only, indicating a mechanism for the cluster rotation and shape changes found in experimental studies.

Are X-rays the key to integrated computational materials engineering?

DOE PAGES

Ice, Gene E.

2015-11-01

The ultimate dream of materials science is to predict materials behavior from composition and processing history. Owing to the growing power of computers, this long-time dream has recently found expression through worldwide excitement in a number of computation-based thrusts: integrated computational materials engineering, materials by design, computational materials design, three-dimensional materials physics and mesoscale physics. However, real materials have important crystallographic structures at multiple length scales, which evolve during processing and in service. Moreover, real materials properties can depend on the extreme tails in their structural and chemical distributions. This makes it critical to map structural distributions with sufficient resolutionmore » to resolve small structures and with sufficient statistics to capture the tails of distributions. For two-dimensional materials, there are high-resolution nondestructive probes of surface and near-surface structures with atomic or near-atomic resolution that can provide detailed structural, chemical and functional distributions over important length scales. Furthermore, there are no nondestructive three-dimensional probes with atomic resolution over the multiple length scales needed to understand most materials.« less

Atomic force microscopy study of the structure function relationships of the biofilm-forming bacterium Streptococcus mutans

NASA Astrophysics Data System (ADS)

Cross, Sarah E.; Kreth, Jens; Zhu, Lin; Qi, Fengxia; Pelling, Andrew E.; Shi, Wenyuan; Gimzewski, James K.

2006-02-01

Atomic force microscopy (AFM) has garnered much interest in recent years for its ability to probe the structure, function and cellular nanomechanics inherent to specific biological cells. In particular, we have used AFM to probe the important structure-function relationships of the bacterium Streptococcus mutans. S. mutans is the primary aetiological agent in human dental caries (tooth decay), and is of medical importance due to the virulence properties of these cells in biofilm initiation and formation, leading to increased tolerance to antibiotics. We have used AFM to characterize the unique surface structures of distinct mutants of S. mutans. These mutations are located in specific genes that encode surface proteins, thus using AFM we have resolved characteristic surface features for mutant strains compared to the wild type. Ultimately, our characterization of surface morphology has shown distinct differences in the local properties displayed by various S. mutans strains on the nanoscale, which is imperative for understanding the collective properties of these cells in biofilm formation.

Critical assessment of Pt surface energy - An atomistic study

NASA Astrophysics Data System (ADS)

Kim, Jin-Soo; Seol, Donghyuk; Lee, Byeong-Joo

2018-04-01

Despite the fact that surface energy is a fundamental quantity in understanding surface structure of nanoparticle, the results of experimental measurements and theoretical calculations for the surface energy of pure Pt show a wide range of scattering. It is necessary to further ensure the surface energy of Pt to find the equilibrium shape and atomic configuration in Pt bimetallic nanoparticles accurately. In this article, we critically assess and optimize the Pt surface energy using a semi-empirical atomistic approach based on the second nearest-neighbor modified embedded-atom method interatomic potential. That is, the interatomic potential of pure Pt was adjusted in a way that the surface segregation tendency in a wide range of Pt binary alloys is reproduced in accordance with experimental information. The final optimized Pt surface energy (mJ/m2) is 2036 for (100) surface, 2106 for (110) surface, and 1502 for (111) surface. The potential can be utilized to find the equilibrium shape and atomic configuration of Pt bimetallic nanoparticles more accurately.

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.

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.

Surface Roughness of Various Diamond-Like Carbon Films

NASA Astrophysics Data System (ADS)

Liu, Dongping; Liu, Yanhong; Chen, Baoxiang

2006-11-01

Atomic force microscopy is used to estimate and compare the surface morphology of hydrogenated and hydrogen-free diamond-like carbon (DLC) films. The films were prepared by using DC magnetron sputtering of a graphite target, pulsed cathodic carbon arcs, electron cyclotron resonance (ECR), plasma source ion implantation and dielectric barrier discharge (DBD). The difference in the surface structure is presented for each method of deposition. The influences of various discharge parameters on the film surface properties are discussed based upon the experimental results. The coalescence process via the diffusion of adsorbed carbon species is responsible for the formation of hydrogen-free DLC films with rough surfaces. The films with surface roughness at an atomic level can be deposited by energetic ion impacts in a highly ionized carbon plasma. The dangling bonds created by atomic hydrogen lead to the uniform growth of hydrocarbon species at the a-C:H film surfaces of the ECR or DBD plasmas.

Spatio-temporal behaviour of atomic-scale tribo-ceramic films in adaptive surface engineered nano-materials.

PubMed

Fox-Rabinovich, G; Kovalev, A; Veldhuis, S; Yamamoto, K; Endrino, J L; Gershman, I S; Rashkovskiy, A; Aguirre, M H; Wainstein, D L

2015-03-05

Atomic-scale, tribo-ceramic films associated with dissipative structures formation are discovered under extreme frictional conditions which trigger self-organization. For the first time, we present an actual image of meta-stable protective tribo-ceramics within thicknesses of a few atomic layers. A mullite and sapphire structure predominates in these phases. They act as thermal barriers with an amazing energy soaking/dissipating capacity. Less protective tribo-films cannot sustain in these severe conditions and rapidly wear out. Therefore, a functional hierarchy is established. The created tribo-films act in synergy, striving to better adapt themselves to external stimuli. Under a highly complex structure and non-equilibrium state, the upcoming generation of adaptive surface engineered nano-multilayer materials behaves like intelligent systems - capable of generating, with unprecedented efficiency, the necessary tribo-films to endure an increasingly severe environment.

Structural and optical properties of GaAs(100) with a thin surface layer doped with chromium

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

Seredin, P. V., E-mail: paul@phys.vsu.ru; Fedyukin, A. V.; Arsentyev, I. N.

The aim of this study is to explore the structural and optical properties of single-crystal GaAs(100) doped with Cr atoms by burning them into the substrate at high temperatures. The diffusion of chromium into single-crystal GaAs(100) substrates brings about the formation of a thin (~20–40 μm) GaAs:Cr transition layer. In this case, chromium atoms are incorporated into the gallium-arsenide crystal lattice and occupy the regular atomic sites of the metal sublattice. As the chromium diffusion time is increased, such behavior of the dopant impurity yields changes in the energy structure of GaAs, a decrease in the absorption at free chargemore » carriers, and a lowering of the surface recombination rate. As a result, the photoluminescence signal from the sample is significantly enhanced.« less

Spatio-temporal behaviour of atomic-scale tribo-ceramic films in adaptive surface engineered nano-materials

PubMed Central

Fox-Rabinovich, G.; Kovalev, A.; Veldhuis, S.; Yamamoto, K.; Endrino, J. L.; Gershman, I. S.; Rashkovskiy, A.; Aguirre, M. H.; Wainstein, D. L.

2015-01-01

Atomic-scale, tribo-ceramic films associated with dissipative structures formation are discovered under extreme frictional conditions which trigger self-organization. For the first time, we present an actual image of meta-stable protective tribo-ceramics within thicknesses of a few atomic layers. A mullite and sapphire structure predominates in these phases. They act as thermal barriers with an amazing energy soaking/dissipating capacity. Less protective tribo-films cannot sustain in these severe conditions and rapidly wear out. Therefore, a functional hierarchy is established. The created tribo-films act in synergy, striving to better adapt themselves to external stimuli. Under a highly complex structure and non-equilibrium state, the upcoming generation of adaptive surface engineered nano-multilayer materials behaves like intelligent systems - capable of generating, with unprecedented efficiency, the necessary tribo-films to endure an increasingly severe environment. PMID:25740153

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)).

The atomic level structure of the TiO(2)-NiTi interface.

PubMed

Nolan, M; Tofail, S A M

2010-09-07

The biocompatibility of NiTi shape memory alloys (SMA) has made possible applications in invasive and minimally invasive biomedical devices. The NiTi intermetallic alloy spontaneously forms a thin passive layer of TiO(2), which provides its biocompatibility. The oxide layer is thought to form as Ti in the alloy reacts with oxygen. In this paper, we study the details of the oxide-alloy interface. The atomic model is the (110) NiTi surface interfaced with the (100) rutile TiO(2) surface; this combination provides the best lattice match of alloy and oxide. When the interface forms, static minimisations and molecular dynamics show that there is no migration of atoms between the alloy and the oxide. In the alloy there are some notable structural relaxations. We find that a columnar structure appears in which alternating long and short Ni-Ti bonds are present in each surface and subsurface plane into the fourth subsurface layer. The oxide undergoes some structural changes as a result of terminal oxygen coordinating to Ti in the NiTi surface. The electronic structure shows that Ti(3+) species are present at the interface, with Ti(4+) in the bulk of the oxide layer and that the metallic character of the alloy is unaffected by the interaction with oxygen, all of which is consistent with experiment. A thermodynamic analysis is used to examine the stability of different possible structures-a perfect interface and one with Ti and O vacancies. We find that under conditions typical of oxidation and shape memory treatments, the most stable interface structure is that with Ti vacancies in the alloy surface, leaving an Ni-rich layer, consistent with the experimental findings for this interface.

Computational Study on Atomic Structures, Electronic Properties, and Chemical Reactions at Surfaces and Interfaces and in Biomaterials

NASA Astrophysics Data System (ADS)

Takano, Yu; Kobayashi, Nobuhiko; Morikawa, Yoshitada

2018-06-01

Through computer simulations using atomistic models, it is becoming possible to calculate the atomic structures of localized defects or dopants in semiconductors, chemically active sites in heterogeneous catalysts, nanoscale structures, and active sites in biological systems precisely. Furthermore, it is also possible to clarify physical and chemical properties possessed by these nanoscale structures such as electronic states, electronic and atomic transport properties, optical properties, and chemical reactivity. It is sometimes quite difficult to clarify these nanoscale structure-function relations experimentally and, therefore, accurate computational studies are indispensable in materials science. In this paper, we review recent studies on the relation between local structures and functions for inorganic, organic, and biological systems by using atomistic computer simulations.

Friction and Wear on the Atomic Scale

NASA Astrophysics Data System (ADS)

Gnecco, Enrico; Bennewitz, Roland; Pfeiffer, Oliver; Socoliuc, Anisoara; Meyer, Ernst

Friction has long been the subject of research: the empirical da Vinci-Amontons friction laws have been common knowledge for centuries. Macroscopic experiments performed by the school of Bowden and Tabor revealed that macroscopic friction can be related to the collective action of small asperities. Over the last 15 years, experiments performed with the atomic force microscope have provided new insights into the physics of single asperities sliding over surfaces. This development, together with the results from complementary experiments using surface force apparatus and the quartz microbalance, have led to the new field of nanotribology. At the same time, increasing computing power has permitted the simulation of processes that occur during sliding contact involving several hundreds of atoms. It has become clear that atomic processes cannot be neglected when interpreting nanotribology experiments. Even on well-defined surfaces, experiments have revealed that atomic structure is directly linked to friction force. This chapter will describe friction force microscopy experiments that reveal, more or less directly, atomic processes during sliding contact.

Clustering on Magnesium Surfaces – Formation and Diffusion Energies

DOE PAGES

Chu, Haijian; Huang, Hanchen; Wang, Jian

2017-07-12

The formation and diffusion energies of atomic clusters on Mg surfaces determine the surface roughness and formation of faulted structure, which in turn affect the mechanical deformation of Mg. This paper reports first principles density function theory (DFT) based quantum mechanics calculation results of atomic clustering on the low energy surfaces {0001} and {more » $$\\bar{1}$$011} . In parallel, molecular statics calculations serve to test the validity of two interatomic potentials and to extend the scope of the DFT studies. On a {0001} surface, a compact cluster consisting of few than three atoms energetically prefers a face-centered-cubic stacking, to serve as a nucleus of stacking fault. On a {$$\\bar{1}$$011} , clusters of any size always prefer hexagonal-close-packed stacking. Adatom diffusion on surface {$$\\bar{1}$$011} is high anisotropic while isotropic on surface (0001). Three-dimensional Ehrlich–Schwoebel barriers converge as the step height is three atomic layers or thicker. FInally, adatom diffusion along steps is via hopping mechanism, and that down steps is via exchange mechanism.« less

Clustering on Magnesium Surfaces – Formation and Diffusion Energies

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

Chu, Haijian; Huang, Hanchen; Wang, Jian

The formation and diffusion energies of atomic clusters on Mg surfaces determine the surface roughness and formation of faulted structure, which in turn affect the mechanical deformation of Mg. This paper reports first principles density function theory (DFT) based quantum mechanics calculation results of atomic clustering on the low energy surfaces {0001} and {more » $$\\bar{1}$$011} . In parallel, molecular statics calculations serve to test the validity of two interatomic potentials and to extend the scope of the DFT studies. On a {0001} surface, a compact cluster consisting of few than three atoms energetically prefers a face-centered-cubic stacking, to serve as a nucleus of stacking fault. On a {$$\\bar{1}$$011} , clusters of any size always prefer hexagonal-close-packed stacking. Adatom diffusion on surface {$$\\bar{1}$$011} is high anisotropic while isotropic on surface (0001). Three-dimensional Ehrlich–Schwoebel barriers converge as the step height is three atomic layers or thicker. FInally, adatom diffusion along steps is via hopping mechanism, and that down steps is via exchange mechanism.« less

Theoretical evidence for unexpected O-rich phases at corners of MgO surfaces

NASA Astrophysics Data System (ADS)

Bhattacharya, Saswata; Berger, Daniel; Reuter, Karsten; Ghiringhelli, Luca M.; Levchenko, Sergey V.

2017-12-01

Realistic oxide materials are often semiconductors, in particular at elevated temperatures, and their surfaces contain undercoordinated atoms at structural defects such as steps and corners. Using hybrid density-functional theory and ab initio atomistic thermodynamics, we investigate the interplay of bond-making, bond-breaking, and charge-carrier trapping at the corner defects at the (100) surface of a p -doped MgO in thermodynamic equilibrium with an O2 atmosphere. We show that by manipulating the coordination of surface atoms, one can drastically change and even reverse the order of stability of reduced versus oxidized surface sites.

Ensemble modeling of very small ZnO nanoparticles.

PubMed

Niederdraenk, Franziska; Seufert, Knud; Stahl, Andreas; Bhalerao-Panajkar, Rohini S; Marathe, Sonali; Kulkarni, Sulabha K; Neder, Reinhard B; Kumpf, Christian

2011-01-14

The detailed structural characterization of nanoparticles is a very important issue since it enables a precise understanding of their electronic, optical and magnetic properties. Here we introduce a new method for modeling the structure of very small particles by means of powder X-ray diffraction. Using thioglycerol-capped ZnO nanoparticles with a diameter of less than 3 nm as an example we demonstrate that our ensemble modeling method is superior to standard XRD methods like, e.g., Rietveld refinement. Besides fundamental properties (size, anisotropic shape and atomic structure) more sophisticated properties like imperfections in the lattice, a size distribution as well as strain and relaxation effects in the particles and-in particular-at their surface (surface relaxation effects) can be obtained. Ensemble properties, i.e., distributions of the particle size and other properties, can also be investigated which makes this method superior to imaging techniques like (high resolution) transmission electron microscopy or atomic force microscopy, in particular for very small nanoparticles. For the particles under study an excellent agreement of calculated and experimental X-ray diffraction patterns could be obtained with an ensemble of anisotropic polyhedral particles of three dominant sizes, wurtzite structure and a significant relaxation of Zn atoms close to the surface.

Charge transfer in single and multiple scattering events at metal surfaces: a wavepacket study of the Na(+)/Cu(100) system.

PubMed

Sindona, A; Pisarra, M; Maletta, S; Riccardi, P; Falcone, G

2010-12-01

Resonant neutralization of hyperthermal energy Na(+) ions impinging on Cu(100) surfaces is studied, focusing on two specific collision events: one in which the projectile is reflected off the surface, the other in which the incident atom penetrates the outer surface layers initiating a series of scattering processes, within the target, and coming out together with a single surface atom. A semi-empirical model potential is adopted that embeds: (i) the electronic structure of the sample, (ii) the central field of the projectile, and (iii) the contribution of the Cu atom ejected in multiple scattering events. The evolution of the ionization orbital of the scattered atom is simulated, backwards in time, using a wavepacket propagation algorithm. The output of the approach is the neutralization probability, obtained by projecting the time-reversed valence wavefunction of the projectile onto the initially filled conduction band states. The results are in agreement with available data from the literature (Keller et al 1995 Phys. Rev. Lett. 75 1654) indicating that the motion of surface atoms, exiting the targets with kinetic energies of the order of a few electronvolts, plays a significant role in the final charge state of projectiles.

Ligand-protected gold clusters: the structure, synthesis and applications

NASA Astrophysics Data System (ADS)

Pichugina, D. A.; Kuz'menko, N. E.; Shestakov, A. F.

2015-11-01

Modern concepts of the structure and properties of atomic gold clusters protected by thiolate, selenolate, phosphine and phenylacetylene ligands are analyzed. Within the framework of the superatom theory, the 'divide and protect' approach and the structure rule, the stability and composition of a cluster are determined by the structure of the cluster core, the type of ligands and the total number of valence electrons. Methods of selective synthesis of gold clusters in solution and on the surface of inorganic composites based, in particular, on the reaction of Aun with RS, RSe, PhC≡C, Hal ligands or functional groups of proteins, on stabilization of clusters in cavities of the α-, β and γ-cyclodextrin molecules (Au15 and Au25) and on anchorage to a support surface (Au25/SiO2, Au20/C, Au10/FeOx) are reviewed. Problems in this field are also discussed. Among the methods for cluster structure prediction, particular attention is given to the theoretical approaches based on the density functional theory (DFT). The structures of a number of synthesized clusters are described using the results obtained by X-ray diffraction analysis and DFT calculations. A possible mechanism of formation of the SR(AuSR)n 'staple' units in the cluster shell is proposed. The structure and properties of bimetallic clusters MxAunLm (M=Pd, Pt, Ag, Cu) are discussed. The Pd or Pt atom is located at the centre of the cluster, whereas Ag and Cu atoms form bimetallic compounds in which the heteroatom is located on the surface of the cluster core or in the 'staple' units. The optical properties, fluorescence and luminescence of ligand-protected gold clusters originate from the quantum effects of the Au atoms in the cluster core and in the oligomeric SR(AuSR)x units in the cluster shell. Homogeneous and heterogeneous reactions catalyzed by atomic gold clusters are discussed in the context of the reaction mechanism and the nature of the active sites. The bibliography includes 345 references.

Shape Complementarity of Protein-Protein Complexes at Multiple Resolutions

PubMed Central

Zhang, Qing; Sanner, Michel; Olson, Arthur J.

2010-01-01

Biological complexes typically exhibit intermolecular interfaces of high shape complementarity. Many computational docking approaches use this surface complementarity as a guide in the search for predicting the structures of protein-protein complexes. Proteins often undergo conformational changes in order to create a highly complementary interface when associating. These conformational changes are a major cause of failure for automated docking procedures when predicting binding modes between proteins using their unbound conformations. Low resolution surfaces in which high frequency geometric details are omitted have been used to address this problem. These smoothed, or blurred, surfaces are expected to minimize the differences between free and bound structures, especially those that are due to side chain conformations or small backbone deviations. In spite of the fact that this approach has been used in many docking protocols, there has yet to be a systematic study of the effects of such surface smoothing on the shape complementarity of the resulting interfaces. Here we investigate this question by computing shape complementarity of a set of 66 protein-protein complexes represented by multi-resolution blurred surfaces. Complexed and unbound structures are available for these protein-protein complexes. They are a subset of complexes from a non-redundant docking benchmark selected for rigidity (i.e. the proteins undergo limited conformational changes between their bound and unbound states). In this work we construct the surfaces by isocontouring a density map obtained by accumulating the densities of Gaussian functions placed at all atom centers of the molecule. The smoothness or resolution is specified by a Gaussian fall-off coefficient, termed “blobbyness”. Shape complementarity is quantified using a histogram of the shortest distances between two proteins' surface mesh vertices for both the crystallographic complexes and the complexes built using the protein structures in their unbound conformation. The histograms calculated for the bound complex structures demonstrate that medium resolution smoothing (blobbyness=−0.9) can reproduce about 88% of the shape complementarity of atomic resolution surfaces. Complexes formed from the free component structures show a partial loss of shape complementarity (more overlaps and gaps) with the atomic resolution surfaces. For surfaces smoothed to low resolution (blobbyness=−0.3), we find more consistency of shape complementarity between the complexed and free cases. To further reduce bad contacts without significantly impacting the good contacts we introduce another blurred surface, in which the Gaussian densities of flexible atoms are reduced. From these results we discuss the use of shape complementarity in protein-protein docking. PMID:18837463

The impacts of surface polarity on the solubility of nanoparticle

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

Zhu, Jianzhuo; Su, Jiguo, E-mail: jiguosu@ysu.edu.cn; Ou, Xinwen

In order to study the dependence of water solubility and hydration behavior of nanoparticles on their surface polarity, we designed polar nanoparticles with varying surface polarity by assigning atomic partial charge to the surface of C60. The water solubility of the nanoparticle is enhanced by several orders of magnitude after the introduction of surface polarity. Nevertheless, when the atomic partial charge grows beyond a certain value (q{sub M}), the solubility continuously decreases to the level of nonpolar nanoparticle. It should be noted that such q{sub M} is comparable with atomic partial charge of a variety of functional groups. The hydrationmore » behaviors of nanoparticles were then studied to investigate the non-monotonic dependence of solubility on the surface polarity. The interaction between the polar nanoparticle and the hydration water is stronger than the nonpolar counterpart, which should facilitate the dissolution of the nanoparticles. On the other hand, the surface polarity also reduces the interaction of hydration water with the other water molecules and enhances the interaction between the nanoparticles which may hinder their dispersion. Besides, the introduction of surface polarity disturbs and even rearranges the hydration structure of nonpolar nanoparticle. Interestingly, the polar nanoparticle with less ordered hydration structure tends to have higher water solubility.« less

Atomic structure and composition of the yttria-stabilized zirconia (111) surface.

PubMed

Vonk, Vedran; Khorshidi, Navid; Stierle, Andreas; Dosch, Helmut

2013-06-01

Anomalous and nonanomalous surface X-ray diffraction is used to investigate the atomic structure and composition of the yttria-stabilized zirconia (YSZ)(111) surface. By simulation it is shown that the method is sensitive to Y surface segregation, but that the data must contain high enough Fourier components in order to distinguish between different models describing Y/Zr disorder. Data were collected at room temperature after two different annealing procedures. First by applying oxidative conditions at 10 - 5  mbar O 2 and 700 K to the as-received samples, where we find that about 30% of the surface is covered by oxide islands, which are depleted in Y as compared with the bulk. After annealing in ultrahigh vacuum at 1270 K the island morphology of the surface remains unchanged but the islands and the first near surface layer get significantly enriched in Y. Furthermore, the observation of Zr and oxygen vacancies implies the formation of a porous surface region. Our findings have important implications for the use of YSZ as solid oxide fuel cell electrode material where yttrium atoms and zirconium vacancies can act as reactive centers, as well as for the use of YSZ as substrate material for thin film and nanoparticle growth where defects control the nucleation process.

Features of structural changes in the near-surface aluminum layer under various schemes of ion implantation

NASA Astrophysics Data System (ADS)

Kryzhevich, Dmitrij S.; Zolnikov, Konstantin P.; Korchuganov, Aleksandr V.

2017-10-01

The molecular dynamics simulation of structural rearrangements in the surface layer of aluminum samples under ion implantation of various intensities was carried out. The features of the internal structure and the crystallographic orientation of the irradiated crystallite were taken into account. To describe the interatomic interaction many-body potentials obtained in the framework of the embedded atom method were used. Irradiation of the {100} surface results in much less number of formed defects than irradiation of the {110} and {111} ones. When irradiating surfaces with beams of relatively low energy grains remain unchanged in the surface region and the formation of stacking faults was not observed. At a high intensity of irradiation, the near-surface layer of the crystallite melts. In the absence of heat removal, the centers of crystallization become grains lying on the boundary of the solid and liquid phases. Those grains increase due to the adjustment of the atoms of the liquid phase to their lattice. As a result, the grain size in the near-surface region increases.

Quantum theory of atoms in molecules: results for the SR-ZORA Hamiltonian.

PubMed

Anderson, James S M; Ayers, Paul W

2011-11-17

The quantum theory of atoms in molecules (QTAIM) is generalized to include relativistic effects using the popular scalar-relativistic zeroth-order regular approximation (SR-ZORA). It is usually assumed that the definition of the atom as a volume bounded by a zero-flux surface of the electron density is closely linked to the form of the kinetic energy, so it is somewhat surprising that the atoms corresponding to the relativistic kinetic-energy operator in the SR-ZORA Hamiltonian are also bounded by zero-flux surfaces. The SR-ZORA Hamiltonian should be sufficient for qualitative descriptions of molecular electronic structure across the periodic table, which suggests that QTAIM-based analysis can be useful for molecules and solids containing heavy atoms.

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.

Structural transformation in monolayer materials: a 2D to 1D transformation.

PubMed

Momeni, Kasra; Attariani, Hamed; LeSar, Richard A

2016-07-20

Reducing the dimensions of materials to atomic scales results in a large portion of atoms being at or near the surface, with lower bond order and thus higher energy. At such scales, reduction of the surface energy and surface stresses can be the driving force for the formation of new low-dimensional nanostructures, and may be exhibited through surface relaxation and/or surface reconstruction, which can be utilized for tailoring the properties and phase transformation of nanomaterials without applying any external load. Here we used atomistic simulations and revealed an intrinsic structural transformation in monolayer materials that lowers their dimension from 2D nanosheets to 1D nanostructures to reduce their surface and elastic energies. Experimental evidence of such transformation has also been revealed for one of the predicted nanostructures. Such transformation plays an important role in bi-/multi-layer 2D materials.

Analysis of Surface and Bulk Behavior in Ni-Pd Alloys

NASA Technical Reports Server (NTRS)

Bozzolo, Guillermo; Noebe, Rondald D.

2003-01-01

The most salient features of the surface structure and bulk behavior of Ni-Pd alloys have been studied using the BFS method for alloys. Large-scale atomistic simulations were performed to investigate surface segregation profiles as a function of temperature, crystal face, and composition. Pd enrichment of the first layer was observed in (111) and (100) surfaces, and enrichment of the top two layers occurred for (110) surfaces. In all cases, the segregation profile shows alternate planes enriched and depleted in Pd. In addition, the phase structure of bulk Ni-Pd alloys as a function of temperature and composition was studied. A weak ordering tendency was observed at low temperatures, which helps explain the compositional oscillations in the segregation profiles. Finally, based on atom-by-atom static energy calculations, a comprehensive explanation for the observed surface and bulk features will be presented in terms of competing chemical and strain energy effects.

Low-temperature adsorption of H2S on Ni(001) studied by near-edge- and surface-extended-x-ray-absorption fine structure

NASA Astrophysics Data System (ADS)

McGrath, R.; MacDowell, A. A.; Hashizume, T.; Sette, F.; Citrin, P. H.

1989-11-01

The adsorption of H2S on Ni(001) has been studied with surface-extended x-ray-absorption fine structure and near-edge x-ray-absorption fine structure (NEXAFS) using the AT&T Bell Laboratories X15B beamline at the National Synchrotron Light Source. At 95 K and full saturation coverage, ~0.45 monolayer (ML) of S atoms in fourfold-hollow sites are produced, characteristic of room-temperature adsorption, accompanied by ~0.05 ML of oriented molecular H2S. Both these atomic and molecular chemisorbed species are buried under ~0.9 ML of disordered physisorbed H2S. No evidence for HS is found. Above 190 K the two molecular H2S phases desorb, leaving only dissociated S. These findings differ from previously reported interpretations of data obtained with high-resolution electron-energy-loss spectroscopy. They also exemplify the utility of NEXAFS for identifying and quantifying atomic and molecular surface species even when their difference involves only H and the two species coexist.

Analysis of Helium Segregation on Surfaces of Plasma-Exposed Tungsten

NASA Astrophysics Data System (ADS)

Maroudas, Dimitrios; Hu, Lin; Hammond, Karl; Wirth, Brian

2015-11-01

We report a systematic theoretical and atomic-scale computational study of implanted helium segregation on surfaces of tungsten, which is considered as a plasma facing component in nuclear fusion reactors. We employ a hierarchy of atomic-scale simulations, including molecular statics to understand the origin of helium surface segregation, targeted molecular-dynamics (MD) simulations of near-surface cluster reactions, and large-scale MD simulations of implanted helium evolution in plasma-exposed tungsten. We find that small, mobile helium clusters (of 1-7 He atoms) in the near-surface region are attracted to the surface due to an elastic interaction force. This thermodynamic driving force induces drift fluxes of these mobile clusters toward the surface, facilitating helium segregation. Moreover, the clusters' drift toward the surface enables cluster reactions, most importantly trap mutation, at rates much higher than in the bulk material. This cluster dynamics has significant effects on the surface morphology, near-surface defect structures, and the amount of helium retained in the material upon plasma exposure.

Substrate Vibrations as Promoters of Chemical Reactivity on Metal Surfaces.

PubMed

Campbell, Victoria L; Chen, Nan; Guo, Han; Jackson, Bret; Utz, Arthur L

2015-12-17

Studies exploring how vibrational energy (Evib) promotes chemical reactivity most often focus on molecular reagents, leaving the role of substrate atom motion in heterogeneous interfacial chemistry underexplored. This combined theoretical and experimental study of methane dissociation on Ni(111) shows that lattice atom motion modulates the reaction barrier height during each surface atom's vibrational period, which leads to a strong variation in the reaction probability (S0) with surface temperature (Tsurf). State-resolved beam-surface scattering studies at Tsurf = 90 K show a sharp threshold in S0 at translational energy (Etrans) = 42 kJ/mol. When Etrans decreases from 42 kJ/mol to 34 kJ/mol, S0 decreases 1000-fold at Tsurf = 90 K, but only 2-fold at Tsurf = 475 K. Results highlight the mechanism for this effect, provide benchmarks for DFT calculations, and suggest the potential importance of surface atom induced barrier height modulation in heterogeneously catalyzed reactions, particularly on structurally labile nanoscale particles and defect sites.

Interatomic scattering in energy dependent photoelectron spectra of Ar clusters

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

Patanen, M.; Benkoula, S.; Nicolas, C.

2015-09-28

Soft X-ray photoelectron spectra of Ar 2p levels of atomic argon and argon clusters are recorded over an extended range of photon energies. The Ar 2p intensity ratios between atomic argon and clusters’ surface and bulk components reveal oscillations similar to photoelectron extended X-ray absorption fine structure signal (PEXAFS). We demonstrate here that this technique allows us to analyze separately the PEXAFS signals from surface and bulk sites of free-standing, neutral clusters, revealing a bond contraction at the surface.

Experimental and Theoretical Structural Investigation of AuPt Nanoparticles Synthesized using a Direct Electrochemical Method

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

Lapp, Aliya S.; Duan, Zhiyao; Marcella, Nicholas

In this report we examine the structure of bimetallic nanomaterials prepared by an electrochemical approach known as hydride-terminated (HT) electrodeposition. It has been shown previously that this method can lead to deposition of a single Pt monolayer on bulk-phase Au surfaces. Specifically, under appropriate electrochemical conditions and using a solution containing PtCl 4 2-, a monolayer of Pt atoms electrodeposits onto bulk-phase Au immediately followed by a monolayer of H atoms. The H-atom capping layer prevents deposition of Pt multilayers. We applied this method to ~1.6 nm Au nanoparticles (AuNPs) immobilized on an inert electrode surface. In contrast to themore » well-defined, segregated Au/Pt structure of the bulk-phase surface, we observe that HT electrodeposition leads to the formation of AuPt quasi-random alloy NPs rather than the core@shell structure anticipated from earlier reports relating to deposition onto bulk phases. The results provide a good example of how the phase behavior of macro materials does not always translate to the nano world. A key component of this study was the structure determination of the AuPt NPs, which required a combination of electrochemical methods, electron microscopy, X-ray absorption spectroscopy, and theory (DFT and MD).« less

Experimental and Theoretical Structural Investigation of AuPt Nanoparticles Synthesized using a Direct Electrochemical Method

DOE PAGES

Lapp, Aliya S.; Duan, Zhiyao; Marcella, Nicholas; ...

2018-06-01

In this report we examine the structure of bimetallic nanomaterials prepared by an electrochemical approach known as hydride-terminated (HT) electrodeposition. It has been shown previously that this method can lead to deposition of a single Pt monolayer on bulk-phase Au surfaces. Specifically, under appropriate electrochemical conditions and using a solution containing PtCl 4 2-, a monolayer of Pt atoms electrodeposits onto bulk-phase Au immediately followed by a monolayer of H atoms. The H-atom capping layer prevents deposition of Pt multilayers. We applied this method to ~1.6 nm Au nanoparticles (AuNPs) immobilized on an inert electrode surface. In contrast to themore » well-defined, segregated Au/Pt structure of the bulk-phase surface, we observe that HT electrodeposition leads to the formation of AuPt quasi-random alloy NPs rather than the core@shell structure anticipated from earlier reports relating to deposition onto bulk phases. The results provide a good example of how the phase behavior of macro materials does not always translate to the nano world. A key component of this study was the structure determination of the AuPt NPs, which required a combination of electrochemical methods, electron microscopy, X-ray absorption spectroscopy, and theory (DFT and MD).« less

Experimental and Theoretical Structural Investigation of AuPt Nanoparticles Synthesized Using a Direct Electrochemical Method.

PubMed

Lapp, Aliya S; Duan, Zhiyao; Marcella, Nicholas; Luo, Long; Genc, Arda; Ringnalda, Jan; Frenkel, Anatoly I; Henkelman, Graeme; Crooks, Richard M

2018-05-11

In this report, we examine the structure of bimetallic nanomaterials prepared by an electrochemical approach known as hydride-terminated (HT) electrodeposition. It has been shown previously that this method can lead to deposition of a single Pt monolayer on bulk-phase Au surfaces. Specifically, under appropriate electrochemical conditions and using a solution containing PtCl 4 2- , a monolayer of Pt atoms electrodeposits onto bulk-phase Au immediately followed by a monolayer of H atoms. The H atom capping layer prevents deposition of Pt multilayers. We applied this method to ∼1.6 nm Au nanoparticles (AuNPs) immobilized on an inert electrode surface. In contrast to the well-defined, segregated Au/Pt structure of the bulk-phase surface, we observe that HT electrodeposition leads to the formation of AuPt quasi-random alloy NPs rather than the core@shell structure anticipated from earlier reports relating to deposition onto bulk phases. The results provide a good example of how the phase behavior of macro materials does not always translate to the nano world. A key component of this study was the structure determination of the AuPt NPs, which required a combination of electrochemical methods, electron microscopy, X-ray absorption spectroscopy, and theory (DFT and MD).

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

Predicting Ligand Binding Sites on Protein Surfaces by 3-Dimensional Probability Density Distributions of Interacting Atoms

PubMed Central

Jian, Jhih-Wei; Elumalai, Pavadai; Pitti, Thejkiran; Wu, Chih Yuan; Tsai, Keng-Chang; Chang, Jeng-Yih; Peng, Hung-Pin; Yang, An-Suei

2016-01-01

Predicting ligand binding sites (LBSs) on protein structures, which are obtained either from experimental or computational methods, is a useful first step in functional annotation or structure-based drug design for the protein structures. In this work, the structure-based machine learning algorithm ISMBLab-LIG was developed to predict LBSs on protein surfaces with input attributes derived from the three-dimensional probability density maps of interacting atoms, which were reconstructed on the query protein surfaces and were relatively insensitive to local conformational variations of the tentative ligand binding sites. The prediction accuracy of the ISMBLab-LIG predictors is comparable to that of the best LBS predictors benchmarked on several well-established testing datasets. More importantly, the ISMBLab-LIG algorithm has substantial tolerance to the prediction uncertainties of computationally derived protein structure models. As such, the method is particularly useful for predicting LBSs not only on experimental protein structures without known LBS templates in the database but also on computationally predicted model protein structures with structural uncertainties in the tentative ligand binding sites. PMID:27513851

Atomic-scale recognition of surface structure and intercalation mechanism of Ti3C2X.

PubMed

Wang, Xuefeng; Shen, Xi; Gao, Yurui; Wang, Zhaoxiang; Yu, Richeng; Chen, Liquan

2015-02-25

MXenes represent a large family of functionalized two-dimensional (2D) transition-metal carbides and carbonitrides. However, most of the understanding on their unique structures and applications stops at the theoretical suggestion and lack of experimental support. Herein, the surface structure and intercalation chemistry of Ti3C2X are clarified at the atomic scale by aberration-corrected scanning transmission electron microscope (STEM) and density functional theory (DFT) calculations. The STEM studies show that the functional groups (e.g., OH(-), F(-), O(-)) and the intercalated sodium (Na) ions prefer to stay on the top sites of the centro-Ti atoms and the C atoms of the Ti3C2 monolayer, respectively. Double Na-atomic layers are found within the Ti3C2X interlayer upon extensive Na intercalation via two-phase transition and solid-solution reactions. In addition, aluminum (Al)-ion intercalation leads to horizontal sliding of the Ti3C2X monolayer. On the basis of these observations, the previous monolayer surface model of Ti3C2X is modified. DFT calculations using the new modeling help to understand more about their physical and chemical properties. These findings enrich the understanding of the MXenes and shed light on future material design and applications. Moreover, the Ti3C2X exhibits prominent rate performance and long-term cycling stability as an anode material for Na-ion batteries.

Modelling of Surfaces. Part 2: Metallic Alloy Surfaces Using the BFS Method

NASA Technical Reports Server (NTRS)

Bozzolo, Guillermo; Ferrante, John; Kobistek, Robert J.

1994-01-01

Using BFS, a new semiempirical method for alloys, we study the surface structure of fcc ordered binary alloys. We concentrate on the calculation of surface energies and surface relaxations for the L1(sub 0) and L1(sub 2) ordered structures. Different terminations of the low-index faces are studied. Also, we present results for the interlayer relaxations for planes close to the surface, revealing different relaxations for atoms of different species producing a rippled surface layer.

In-situ atomic force microscopy observation revealing gel-like plasticity on a metallic glass surface

NASA Astrophysics Data System (ADS)

Lu, Y. M.; Zeng, J. F.; Huang, J. C.; Kuan, S. Y.; Nieh, T. G.; Wang, W. H.; Pan, M. X.; Liu, C. T.; Yang, Y.

2017-03-01

It has been decade-long and enduring efforts to decipher the structural mechanism of plasticity in metallic glasses; however, it still remains a challenge to directly reveal the structural change, if any, that precedes; and dominant plastics flow in them. Here, by using the dynamic atomic force microscope as an "imaging" as well as a "forcing" tool, we unfold a real-time sequence of structural evolution occurring on the surface of an Au-Si thin film metallic glass. In sharp contrast to the common notion that plasticity comes along with mechanical softening in bulk metallic glasses, our experimental results directly reveal three types of nano-sized surface regions, which undergo plasticity but exhibit different characters of structural evolution following the local plasticity events, including stochastic structural rearrangement, unusual local relaxation and rejuvenation. As such, yielding on the metallic-glass surface manifests as a dynamic equilibrium between local relaxation and rejuvenation as opposed to shear instability in bulk metallic-glasses. Our finding demonstrates that plasticity on the metallic glass surface of Au-Si metallic glass bears much resemblance to that of the colloidal gels, of which nonlinear rheology rather than shear instability governs the constitutive behavior of plasticity.

Building Complex Kondo Impurities by Manipulating Entangled Spin Chains.

PubMed

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

2017-10-11

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

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.

Self-Assembly of Parallel Atomic Wires and Periodic Clusters of Silicon on a Vicinal Si(111) Surface

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

Sekiguchi, Takeharu; Yoshida, Shunji; Itoh, Kohei M.

2005-09-02

Silicon self-assembly at step edges in the initial stage of homoepitaxial growth on a vicinal Si(111) surface is studied by scanning tunneling microscopy. The resulting atomic structures change dramatically from a parallel array of 0.7 nm wide wires to one-dimensionally aligned periodic clusters of diameter {approx}2 nm and periodicity 2.7 nm in the very narrow range of growth temperatures between 400 and 300 deg. C. These nanostructures are expected to play important roles in future developments of silicon quantum computers. Mechanisms leading to such distinct structures are discussed.

Crystallographic perturbations to valence charge density and hydrogen-surface interactions

NASA Astrophysics Data System (ADS)

Ciston, James W.

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

Quantum Chemical Study of Water Adsorption on the Surfaces of SrTiO3 Nanotubes.

PubMed

Bandura, Andrei V; Kuruch, Dmitry D; Evarestov, Robert A

2015-07-20

We have studied the adsorption of water molecules on the inner and outer surfaces of nanotubes generated by rolling (001) layers of SrTiO3 cubic crystals. The stability and the atomic and electronic structures of the adsorbed layers are determined by using hybrid density functional theory. The absorption energy and the preferred adsorbate structure are essentially governed by the nature of the surface of the nanotube. Dissociative adsorption prevails on the outer nanotube surfaces. The stability of the adsorbed layers on the inner surfaces is related to the possibility of the formation of hydrogen bonds between water molecules and surface oxygen atoms, and depends on the surface curvature. The presence of water molecules on the inner surface of the nanotubes leads to an increase of the electronic band gap. Externally TiO2 -terminated nanotubes could be used for the photocatalytic decomposition of water by ultraviolet radiation. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Quantitative structure-property relationships for octanol-water partition coefficients of polybrominated diphenyl ethers.

PubMed

Li, Linnan; Xie, Shaodong; Cai, Hao; Bai, Xuetao; Xue, Zhao

2008-08-01

Theoretical molecular descriptors were tested against logK(OW) values for polybrominated diphenyl ethers (PBDEs) using the Partial Least-Squares Regression method which can be used to analyze data with many variables and few observations. A quantitative structure-property relationship (QSPR) model was successfully developed with a high cross-validated value (Q(cum)(2)) of 0.961, indicating a good predictive ability and stability of the model. The predictive power of the QSPR model was further cross-validated. The values of logK(OW) for PBDEs are mainly governed by molecular surface area, energy of the lowest unoccupied molecular orbital and the net atomic charges on the oxygen atom. All these descriptors have been discussed to interpret the partitioning mechanism of PBDE chemicals. The bulk property of the molecules represented by molecular surface area is the leading factor, and K(OW) values increase with the increase of molecular surface area. Higher energy of the lowest unoccupied molecular orbital and higher net atomic charge on the oxygen atom of PBDEs result in smaller K(OW). The energy of the lowest unoccupied molecular orbital and the net atomic charge on PBDEs oxygen also play important roles in affecting the partition of PBDEs between octanol and water by influencing the interactions between PBDEs and solvent molecules.

An intermetallic Au24Ag20 superatom nanocluster stabilized by labile ligands.

PubMed

Wang, Yu; Su, Haifeng; Xu, Chaofa; Li, Gang; Gell, Lars; Lin, Shuichao; Tang, Zichao; Häkkinen, Hannu; Zheng, Nanfeng

2015-04-08

An intermetallic nanocluster containing 44 metal atoms, Au24Ag20(2-SPy)4(PhC≡C)20Cl2, was successfully synthesized and structurally characterized by single-crystal analysis and density funtional theory computations. The 44 metal atoms in the cluster are arranged as a concentric three-shell Au12@Ag20@Au12 Keplerate structure having a high symmetry. For the first time, the co-presence of three different types of anionic ligands (i.e., phenylalkynyl, 2-pyridylthiolate, and chloride) was revealed on the surface of metal nanoclusters. Similar to thiolates, alkynyls bind linearly to surface Au atoms using their σ-bonds, leading to the formation of two types of surface staple units (PhC≡C-Au-L, L = PhC≡C(-) or 2-pyridylthiolate) on the cluster. The co-presence of three different surface ligands allows the site-specific surface and functional modification of the cluster. The lability of PhC≡C(-) ligands on the cluster was demonstrated, making it possible to keep the metal core intact while removing partial surface capping. Moreover, it was found that ligand exchange on the cluster occurs easily to offer various derivatives with the same metal core but different surface functionality and thus different solubility.

Theoretical study of Ag doping-induced vacancies defects in armchair graphene

NASA Astrophysics Data System (ADS)

Benchallal, L.; Haffad, S.; Lamiri, L.; Boubenider, F.; Zitoune, H.; Kahouadji, B.; Samah, M.

2018-06-01

We have performed a density functional theory (DFT) study of the absorption of silver atoms (Ag,Ag2 and Ag3) in graphene using SIESTA code, in the generalized gradient approximation (GGA). The absorption energy, geometry, magnetic moments and charge transfer of Ag clusters-graphene system are calculated. The minimum energy configuration demonstrates that all structures remain planar and silver atoms fit into this plane. The charge transfer between the silver clusters and carbon atoms constituting the graphene surface is an indicative of a strong bond. The structure doped with a single silver atom has a magnetic moment and the two other are nonmagnetic.

I Situ Structural Study of Underpotential Deposition and Electrocatalysis on GOLD(111) Electrodes

NASA Astrophysics Data System (ADS)

Chen, Chun-Hsien

This thesis work has studied systems of Bi, Pb, Ag, and Hg underpotential deposition (UPD) on Au(111) electrodes. The application of the atomic force microscope (AFM), the scanning tunneling microscope (STM), and the surface x-ray scattering (SXS) to these UPD studies has provided in situ measurements from which we investigate factors that determine UPD surface structures and correlate these structures with surface reactivity. For all the UPD systems in this thesis work, atomic level features of the electrode surface have been revealed. In the case of Pb UPD, Pb starts to deposit by forming islands which exhibit a hexagonal close packed structure of Pb adatoms, while, in the other systems, the UPD adatoms form open lattices. In the Bi and Pb studies, we correlate the activities of the modified surface toward electroreduction of H_2O_2 with the adlattice structures. A heterobimetallic bridge model for H_2O_2 on the surface could explain the enhanced reactivity. The full monolayers of Bi and Hg, rhombohedral metals, form rectangular lattice structures on the hexagonal Au(111) surfaces. The partial charge retention on the Bi and Hg adatom opens the adlayer structure when the coverage is less than a full monolayer. The structure of the first submonolayers of Ag UPD is electrolyte-dependent. The electrode surface exhibits 3 x 3 and 4 x 4 overlayer structures in solutions containing sulfate and nitrate, respectively. In perchloric acid another open structure is observed and a close-packed monolayer is formed in acetic acid. The different monolayer structures give rise to packing densities which correlate with electrolyte size. This implies that the anions participate in reducing metal ions.

Raman-atomic force microscopy of the ommatidial surfaces of Dipteran compound eyes.

PubMed

Anderson, Mark S; Gaimari, Stephen D

2003-06-01

The ommatidial lens surfaces of the compound eyes in several species of files (Insecta: Diptera) and a related order (Mecoptera) were analyzed using a recently developed Raman-atomic force microscope. We demonstrate in this work that the atomic force microscope (AFM) is a potentially useful instrument for gathering phylogenetic data and that the newly developed Raman-AFM may extend this application by revealing nanometer-scale surface chemistry. This is the first demonstration of apertureless near-field Raman spectroscopy on an intact biological surface. For Chrysopilus testaceipes Bigot (Rhagionidae), this reveals unique cerebral cortex-like surface ridges with periodic variation in height and surface chemistry. Most other Brachyceran flies, and the "Nematoceran" Sylvicola fenestralis (Scopoli) (Anisopodidae), displayed the same morphology, while other taxa displayed various other characteristics, such as a nodule-like (Tipula (Triplicitipula) sp. (Tipulidae)) or coalescing nodule-like (Tabanus punctifer Osten Sacken (Tabanidae)) morphology, a smooth morphology with distinct pits and grooves (Dilophus orbatus (Say) (Bibionidae)), or an entirely smooth surface (Bittacus chlorostigma MacLachlan (Mecoptera: Bittacidae)). The variation in submicrometer structure and surface chemistry provides a new information source of potential phylogenetic importance, suggesting the Raman-atomic force microscope could provide a new tool useful to systematic and evolutionary inquiry.

Raman-atomic force microscopy of the ommatidial surfaces of Dipteran compound eyes

NASA Technical Reports Server (NTRS)

Anderson, Mark S.; Gaimari, Stephen D.

2003-01-01

The ommatidial lens surfaces of the compound eyes in several species of files (Insecta: Diptera) and a related order (Mecoptera) were analyzed using a recently developed Raman-atomic force microscope. We demonstrate in this work that the atomic force microscope (AFM) is a potentially useful instrument for gathering phylogenetic data and that the newly developed Raman-AFM may extend this application by revealing nanometer-scale surface chemistry. This is the first demonstration of apertureless near-field Raman spectroscopy on an intact biological surface. For Chrysopilus testaceipes Bigot (Rhagionidae), this reveals unique cerebral cortex-like surface ridges with periodic variation in height and surface chemistry. Most other Brachyceran flies, and the "Nematoceran" Sylvicola fenestralis (Scopoli) (Anisopodidae), displayed the same morphology, while other taxa displayed various other characteristics, such as a nodule-like (Tipula (Triplicitipula) sp. (Tipulidae)) or coalescing nodule-like (Tabanus punctifer Osten Sacken (Tabanidae)) morphology, a smooth morphology with distinct pits and grooves (Dilophus orbatus (Say) (Bibionidae)), or an entirely smooth surface (Bittacus chlorostigma MacLachlan (Mecoptera: Bittacidae)). The variation in submicrometer structure and surface chemistry provides a new information source of potential phylogenetic importance, suggesting the Raman-atomic force microscope could provide a new tool useful to systematic and evolutionary inquiry.

Surface states and annihilation characteristics of positrons trapped at the oxidized Cu(100) surface

NASA Astrophysics Data System (ADS)

Fazleev, N. G.; Weiss, A. H.

2013-06-01

In this work we present the results of theoretical studies of positron surface and bulk states and annihilation probabilities of surface-trapped positrons with relevant core electrons at the oxidized Cu(100) surface under conditions of high oxygen coverage. Oxidation of the Cu(100) surface has been studied by performing an ab-initio investigation of the stability and electronic structure of the Cu(100) missing row reconstructed surface at various on-surface and subsurface oxygen coverages ranging from 0.5 to 1.5 monolayers using density functional theory (DFT). All studied structures have been found to be energetically more favorable as compared to structures formed by purely on-surface oxygen adsorption. The observed decrease in the positron work function when oxygen atoms occupy on-surface and subsurface sites has been attributed to a significant charge redistribution within the first two layers, buckling effects within each layer and an interlayer expansion. The computed positron binding energy, positron surface state wave function, and annihilation probabilities of the surface trapped positrons with relevant core electrons demonstrate their sensitivity to oxygen coverage, atomic structure of the topmost layers of surfaces, and charge transfer effects. Theoretical results are compared with experimental data obtained from studies of oxidation of the Cu(100) surface using positron annihilation induced Auger electron spectroscopy (PAES). The results presented provide an explanation for the changes observed in the probability of annihilation of surface trapped positrons with Cu 3p core-level electrons as a function of annealing temperature.

An equilibrium ab initio atomistic thermodynamics study of chlorine adsorption on the Cu(001) surface.

PubMed

Suleiman, Ibrahim A; Radny, Marian W; Gladys, Michael J; Smith, Phillip V; Mackie, John C; Kennedy, Eric M; Dlugogorski, Bogdan Z

2011-06-07

The effect of chlorine (Cl) chemisorption on the energetics and atomic structure of the Cu(001) surface over a wide range of chlorine pressures and temperatures has been studied using equilibrium ab initio atomistic thermodynamics to elucidate the formation of cuprous chloride (CuCl) as part of the Deacon reaction on copper metal. The calculated surface free energies show that the 1/2 monolayer (ML) c(2 × 2)-Cl phase with chlorine atoms adsorbed at the hollow sites is the most stable structure for a wide range of Cl chemical potential, in agreement with experimental observations. It is also found that at very low pressure and exposure, but elevated temperature, the 1/9 ML and 1/4 ML phases become the most stable. By contrast, a high coverage of Cl does not lead to thermodynamically stable geometries. The subsurface adsorption of Cl atoms, however, dramatically increases the stability of the 1 ML and 2 ML adsorption configurations providing a possible pathway for the formation of the bulk-chloride surface phases in the kinetic regime.

Properties of model atomic free-standing thin films.

PubMed

Shi, Zane; Debenedetti, Pablo G; Stillinger, Frank H

2011-03-21

We present a computational study of the thermodynamic, dynamic, and structural properties of free-standing thin films, investigated via molecular dynamics simulation of a glass-forming binary Lennard-Jones mixture. An energy landscape analysis is also performed to study glassy states. At equilibrium, species segregation occurs, with the smaller minority component preferentially excluded from the surface. The film's interior density and interface width depend solely on temperature and not the initialization density. The atoms at the surface of the film have a higher lateral diffusivity when compared to the interior. The average difference between the equilibrium and inherent structure energies assigned to individual particles, as a function of the distance from the center of the film, increases near the surface. A minimum of this difference occurs in the region just under the liquid-vapor interface. This suggests that the surface atoms are able to sample the underlying energy landscape more effectively than those in the interior, and we suggest a possible relationship of this observation to the recently reported formation of stable glasses by vapor phase deposition.

Effect of lattice-gas atoms on the adsorption behaviour of thioether molecules.

PubMed

Pan, Yi; Yang, Bing; Hulot, Catherine; Blechert, Siegfried; Nilius, Niklas; Freund, Hans-Joachim

2012-08-21

Using STM topographic imaging and spectroscopy, we have investigated the adsorption of two thioether molecules, 1,2-bis(phenylthio)benzene and (bis(3-phenylthio)-phenyl)sulfane, on noble and transition metal surfaces. The two substrates show nearly antipodal behaviour. Whereas complexes with one or two protruding centres are observed on Au(111), only flat and uniform ad-structures are found on NiAl(110). The difference is ascribed to the possibility of the thioethers to form metal-organic complexes by coordinating lattice-gas atoms on the Au(111), while only the pristine molecules adsorb on the alloy surface. The metal coordination in the first case is driven by the formation of strong Au-S bonds and enables the formation of characteristic monomer, dimer and chain-like structures of the thioethers, using the Au atoms as linkers. A similar mechanism is not available on the NiAl, because no lattice gas develops at this surface at room temperature. Our work demonstrates how surface properties, i.e. the availability of mobile ad-species, determine the interaction of organic molecules with metallic substrates.

Direct observation of X-ray induced atomic motion using scanning tunneling microscope combined with synchrotron radiation.

PubMed

Saito, Akira; Tanaka, Takehiro; Takagi, Yasumasa; Hosokawa, Hiromasa; Notsu, Hiroshi; Ohzeki, Gozo; Tanaka, Yoshihito; Kohmura, Yoshiki; Akai-Kasaya, Megumi; Ishikawa, Tetsuya; Kuwahara, Yuji; Kikuta, Seishi; Aono, Masakazu

2011-04-01

X-ray induced atomic motion on a Ge(111)-c(2 x 8) clean surface at room temperature was directly observed with atomic resolution using a synchrotron radiation (SR)-based scanning tunneling microscope (STM) system under ultra high vacuum condition. The atomic motion was visualized as a tracking image by developing a method to merge the STM images before and after X-ray irradiation. Using the tracking image, the atomic mobility was found to be strongly affected by defects on the surface, but was not dependent on the incident X-ray energy, although it was clearly dependent on the photon density. The atomic motion can be attributed to surface diffusion, which might not be due to core-excitation accompanied with electronic transition, but a thermal effect by X-ray irradiation. The crystal surface structure was possible to break even at a lower photon density than the conventionally known barrier. These results can alert X-ray studies in the near future about sample damage during measurements, while suggesting the possibility of new applications. Also the obtained results show a new availability of the in-situ SR-STM system.

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

Tao, Franklin

Two main categories of heterogeneous catalysts are metal and metal oxide which catalyze 80% chemical reactions at solid-gas and solid-liquid interfaces. Metal oxide catalysts are much more complicated than metal catalysts. The reason is that the cations of the metal atoms could exhibit a few different oxidation states on surface of the same catalyst particle such as Co 3O 4 or change of their oxidation states under different reactive environments. For a metal catalyst, there is only one oxidation state typically. In addition, surface of a metal oxide can be terminated with multiple surface functionalities including O atoms with differentmore » binding configurations and OH group. For metal, only metal atoms are exposed typically. Obviously, the complication of surface chemistry and structure of a metal oxide makes studies of surface of an oxide catalyst very challenging. Due to the complication of surface of a meal oxide, the electronic and geometric structures of surface of a metal oxide and the exposed species have received enormous attention since oxide catalysts catalyze at least 1/3 chemical reactions in chemical and energy industries. Understanding of catalytic reactions on early transition metal oxide-based catalysts is fundamentally intriguing and of great practical interest in energy- and environment-related catalysis. Exploration of surface chemistry of oxide-based catalysts at molecular level during catalysis has remained challenging though it is critical in deeply understanding catalysis on oxide-based catalysts and developing oxide-based catalysts with high activity and selectivity. Thus, the overall objective of this project is to explore surface chemistry and structure of early transition metal oxide-based catalysts through in-situ characterization of surface of catalysts, measurements of catalytic performances, and then build an intrinsic correlation of surface chemistry and structure with their catalytic performances in a few important catalytic reactions, and essentially fundamentally understand catalytic mechanism. Furthermore, this correlation will guide the design of catalysts with high activity and selectivity.« less

Learning surface molecular structures via machine vision

NASA Astrophysics Data System (ADS)

Ziatdinov, Maxim; Maksov, Artem; Kalinin, Sergei V.

2017-08-01

Recent advances in high resolution scanning transmission electron and scanning probe microscopies have allowed researchers to perform measurements of materials structural parameters and functional properties in real space with a picometre precision. In many technologically relevant atomic and/or molecular systems, however, the information of interest is distributed spatially in a non-uniform manner and may have a complex multi-dimensional nature. One of the critical issues, therefore, lies in being able to accurately identify (`read out') all the individual building blocks in different atomic/molecular architectures, as well as more complex patterns that these blocks may form, on a scale of hundreds and thousands of individual atomic/molecular units. Here we employ machine vision to read and recognize complex molecular assemblies on surfaces. Specifically, we combine Markov random field model and convolutional neural networks to classify structural and rotational states of all individual building blocks in molecular assembly on the metallic surface visualized in high-resolution scanning tunneling microscopy measurements. We show how the obtained full decoding of the system allows us to directly construct a pair density function—a centerpiece in analysis of disorder-property relationship paradigm—as well as to analyze spatial correlations between multiple order parameters at the nanoscale, and elucidate reaction pathway involving molecular conformation changes. The method represents a significant shift in our way of analyzing atomic and/or molecular resolved microscopic images and can be applied to variety of other microscopic measurements of structural, electronic, and magnetic orders in different condensed matter systems.

Anatase (101)-like Structural Model Revealed for Metastable Rutile TiO2(011) Surface.

PubMed

Xu, Meiling; Shao, Sen; Gao, Bo; Lv, Jian; Li, Quan; Wang, Yanchao; Wang, Hui; Zhang, Lijun; Ma, Yanming

2017-03-08

Titanium dioxide has been widely used as an efficient transition metal oxide photocatalyst. However, its photocatalytic activity is limited to the ultraviolet spectrum range due to the large bandgap beyond 3 eV. Efforts to reduce the bandgap to achieve a broader spectrum range of light absorption have been successfully attempted via the experimental synthesis of dopant-free metastable surface structures of rutile-type TiO 2 (011) 2 × 1. This new surface phase possesses a reduced bandgap of ∼2.1 eV, showing great potential for an excellent photocatalyst covering a wide range of visible light. There is a need to establish the atomistic structure of this metastable surface to understand the physical cause for the bandgap reduction and to improve the future design of photocatalysts. Here, we report computational investigations in an effort to unravel this surface structure via swarm structure-searching simulations. The established structure adopts the anatase (101)-like structure model, where the topmost 2-fold O atoms form a quasi-hexagonal surface pattern and bond with the unsaturated 5-fold and 4-fold Ti atoms in the next layer. The predicted anatase (101)-like surface model can naturally explain the experimental observation of the STM images, the electronic bandgap, and the oxidation state of Ti 4+ . Dangling bonds on the anatase (101)-like surface are abundant making it a superior photocatalyst. First-principles molecular dynamics simulations have supported the high photocatalytic activity by showing that water and formic acid molecules dissociate spontaneously on the anatase (101)-like surface.

Reference system for scanning probe tip fingerprinting

NASA Astrophysics Data System (ADS)

Turansky, Robert; Bamidele, Joseph; Sugawara, Yasuhiro; Kantorovitch, Lev; Stich, Ivan

2012-02-01

Knowledge of the chemical structure of the tip asperity in Non-Contact Atomic Force Microscopy (NC-AFM) is crucial as controlled manipulation of atoms and/or molecules on surfaces can only be performed if this information is available. However, a simple and robust protocol for ensuring a specific tip termination has not yet been developed. We propose a procedure for chemical tip finger printing and an example of a reference system, the oxygen-terminated Cu(110) surface, that enables one to ensure a specific tip termination with Si, Cu, or O atoms. To follow this up and unambiguously determine tip types, we performed a theoretical DFT study of the line scans with the tip models in question and found that the tip characterization made based on experimental results (Cu/O-terminated tip imaging Cu/O atoms) is in fact incorrect and the opposite is true (Cu/O-terminated tip imaging O/Cu atoms). This protocol allows the tip asperity's chemical structure to be verified and established both before as well as at any stage of the manipulation experiment when numerous tip changes may take place.

ADSORPTION AND DISSOCIATION OF O2 ON Ti3Al (0001) STUDIED BY FIRST-PRINCIPLES

NASA Astrophysics Data System (ADS)

Wei, Li-Jing; Guo, Jian-Xin; Dai, Xiu-Hong; Wang, Ying-Long; Liu, Bao-Ting

2015-05-01

The adsorption and dissociation of oxygen molecule on Ti3Al (0001) surface have been investigated by density functional theory (DFT) with the generalized gradient approximation (GGA). All possible adsorption sites including nine vertical and fifteen parallel sites of O2 are considered on Ti3Al (0001) surface. It is found that all oxygen molecules dissociate except for three vertical adsorption sites after structure optimization. This indicates that oxygen molecules prefer to dissociate on the junction site between Ti and Al atoms. Oxygen atoms coming from dissociation of oxygen molecule tend to occupy the most stable adsorption sites of the Ti3Al (0001) surface. The distance of O-O is related to the surface dissociation distance of Ti3Al (0001) surface. The valence electron localization function (ELF) and projected density of states (DOS) show that the bonds of O-O are breakaway at parallel adsorption end structures.

The possibility of using platinum foils with a rippled surface as diffraction gratings

NASA Astrophysics Data System (ADS)

Korsukov, V. E.; Ankudinov, A. V.; Butenko, P. N.; Knyazev, S. A.; Korsukova, M. M.; Obidov, B. A.; Shcherbakov, I. P.

2014-09-01

The atomic structure and surface relief of thin cold-rolled platinum foils upon recrystallization annealing and loading under ultrahigh vacuum conditions have been studied by low energy electron diffraction (LEED), atomic force microscopy (AFM), and scanning tunneling microscopy (STM). The surface of samples upon high-temperature annealing and subsequent uniaxial extension of recrystallized Pt foils represents a fractal structure of unidirectional ripples on various spatial scales. The total fractal dimension of this surface is D GW = 2.3, while the fractal dimensions along and across ripples are D ‖ ≈ 1 and D ⊥ ≈ 1.3, respectively. The optical spectra of a halogen lamp and a PRK-2 mercury lamp were recorded using these rippled Pt foils as reflection diffraction gratings. It is shown that Pt foils with this surface relief can be used as reflection diffraction gratings for electromagnetic radiation in a broad spectral range.

Atomic level characterization in corrosion studies

NASA Astrophysics Data System (ADS)

Marcus, Philippe; Maurice, Vincent

2017-06-01

Atomic level characterization brings fundamental insight into the mechanisms of self-protection against corrosion of metals and alloys by oxide passive films and into how localized corrosion is initiated on passivated metal surfaces. This is illustrated in this overview with selected data obtained at the subnanometre, i.e. atomic or molecular, scale and also at the nanometre scale on single-crystal copper, nickel, chromium and stainless steel surfaces passivated in well-controlled conditions and analysed in situ and/or ex situ by scanning tunnelling microscopy/spectroscopy and atomic force microscopy. A selected example of corrosion modelling by ab initio density functional theory is also presented. The discussed aspects include the surface reconstruction induced by hydroxide adsorption and formation of two-dimensional (hydr)oxide precursors, the atomic structure, orientation and surface hydroxylation of three-dimensional ultrathin oxide passive films, the effect of grain boundaries in polycrystalline passive films acting as preferential sites of passivity breakdown, the differences in local electronic properties measured at grain boundaries of passive films and the role of step edges at the exposed surface of oxide grains on the dissolution of the passive film. This article is part of the themed issue 'The challenges of hydrogen and metals'.

Molecular-orbital models for the catalytic activity and selectivity of coordinatively unsaturated platinum surfaces and complexes

NASA Astrophysics Data System (ADS)

Balazs, A. C.; Johnson, K. H.

1982-01-01

Electronic structures have been calculated for 5-, 6-, and 10-atom Pt clusters, as well as for a Pt(PH 3) 4 coordination complex, using the self-consistent-field X-alpha scattered-wave (SCF-Xα-SW) molecular-orbital technique. The 10-atom cluster models the local geometry of a flat, unreconstructed Pt(100) surface, while the 5- and 6-atom clusters show features of a stepped Pt surface. Pt(PH 3) 4 resembles the chemically similar homogeneous catalyst Pt(PPh 3) 4. Common to all these coordinatively unsaturated complexes are orbitals lying near or coinciding with the highest occupied molecular orbital ("Fermi level") which show pronounced d lobes pointing directly into the vacuum. Under the hypothesis that these molecular orbitals are mainly responsible for the chemical activities of the above species, one can account for the relative similarities and differences in catalytic activity and selectivity displayed by unreconstructed Pt(100) surfaces, stepped Pt surfaces or particles, and isolated Pt(PPh 3) 4 coordination complexes. The relevance of these findings to catalyst-support interactions is also discussed. Finally, relativistic corrections to the electronic structures are calculated and their implications on catalytic properties discussed.

Origin of dislocation luminescence centers and their reorganization in p-type silicon crystal subjected to plastic deformation and high temperature annealing.

PubMed

Pavlyk, Bohdan; Kushlyk, Markiyan; Slobodzyan, Dmytro

2017-12-01

Changes of the defect structure of silicon p-type crystal surface layer under the influence of plastic deformation and high temperature annealing in oxygen atmosphere were investigated by deep-level capacitance-modulation spectroscopy (DLCMS) and IR spectroscopy of molecules and atom vibrational levels. Special role of dislocations in the surface layer of silicon during the formation of its energy spectrum and rebuilding the defective structure was established. It is shown that the concentration of linear defects (N ≥ 10 4  cm -2 ) enriches surface layer with electrically active complexes (dislocation-oxygen, dislocation-vacancy, and dislocation-interstitial atoms of silicon) which are an effective radiative recombination centers.

Inherent structures of crystalline pentacene

NASA Astrophysics Data System (ADS)

Della Valle, Raffaele Guido; Venuti, Elisabetta; Brillante, Aldo; Girlando, Alberto

2003-01-01

Using a quasi-Monte Carlo scheme, we search the potential energy surface of crystalline pentacene to sample its local minima, which represent the "inherent" structures, i.e., the possible configurations of mechanical equilibrium. The system is described in terms of rigid molecules interacting through a standard atom-atom potential model. Several hundreds of distinct minima are encountered, with a surprising variety of structural arrangements. We find that deep minima are easily accessible because they exhibit a favorable energy distribution and their attraction basins tend to be wide. Thanks to these features of the potential surface, the localization the global minimum becomes entirely feasible, allowing reliable a priori predictions of the crystallographic structures. The results for pentacene are very satisfactory. In fact, the two deepest minima correspond to the structures of the two known experimental polymorphs, which are described correctly. Further polymorphs are also likely to exist.

Surface atoms in Sc-O/W(1 0 0) system as Schottky emitter at high temperature

NASA Astrophysics Data System (ADS)

Tsujita, T.; Iida, S.; Nagatomi, T.; Takai, Y.

2003-12-01

The chemical bonding state of surface atoms in the Sc-O/W(1 0 0) system as a Schottky emitter was investigated at high temperature using a profile of Auger electron peaks to elucidate the mechanism of the marked reduction of the work function of the Sc-O/W(1 0 0) Schottky emitter. For this, Sc-deposited W(1 0 0), oxygen-exposed W(1 0 0) and Sc surfaces were prepared as reference surfaces. A comparison of the profiles of the Auger electron peaks from the Sc-O/W(1 0 0) surface with those from the reference surfaces has revealed that oxygen and Sc atoms on the Sc-O/W(1 0 0) surface form the Sc-O complexes at the operating temperature of the Sc-O/W(1 0 0) emitter of 1400 K. In addition, the ratio of the number of Sc atoms to that of oxygen atoms is estimated as 1:1 by the quantitative analysis of the AES peaks. The present results strongly suggest that the work function of the Sc-O/W(1 0 0) emitter is caused by the formation of Sc-O electric dipoles aligning into the p(2 × 1)-p(1 × 2) double-domain structure [Surf. Sci. 523 (2003) L37] on the Sc-O/W(1 0 0) surface at the operating temperature.

Archetypal structure of ultrathin alumina films: Grazing-incidence x-ray diffraction on Ni(111)

NASA Astrophysics Data System (ADS)

Prévot, G.; Le Moal, S.; Bernard, R.; Croset, B.; Lazzari, R.; Schmaus, D.

2012-05-01

We have studied by grazing-incidence x-ray diffraction the atomic structure of an ultrathin alumina film grown on Ni(111). We show that, since there is neither registry between the film and the substrate nor induced Ni relaxations, this system appears to be a prototypical freestanding oxide layer. We have been able to unambiguously determine the three-dimensional structure of the film, which consists of a substrate/Al16/O24/Al24/O28 stacking within a (18.23 × 10.53 Å) R0° unit cell. From the different Al coordinations (3/4/5) in the layer and from the precise determination of the Al-O interatomic distances, we conclude that the film structure presents some similarities with the η phase of bulk alumina, which also has a high surface/bulk ratio. The precise comparison between these two structures allows us to explain that the perfect 3 ratio between the two sides of the mesh of the film is governed by the stacking of the two central planes, combining oxygen close-packed atoms below Al atoms in tetrahedral or pyramidal positions. Moreover, Al atoms at the interface plane of the ultrathin film adopt a quasitrihedral configuration, which confirms that, in the alumina η phase, Al atoms with such a coordination are located near the surface of the nanocrystals. The atomic structure is also very close to the one first proposed by Kresse [G. Kresse, M. Schmid, E. Napetschnig, M. Shishkin, L. Köhler, and P. Varga, ScienceSCIEAS0036-807510.1126/science.1107783 308, 1440 (2005)] for alumina films on NiAl(110). This strongly suggests that this atomic model, within small variations, can be extended to ultrathin alumina film on numerous other metal substrates and may be quasi-intrinsic to a freestanding layer rather than governed by the interactions between the film and the substrate.

PREFACE: Vibrations at surfaces Vibrations at surfaces

NASA Astrophysics Data System (ADS)

Rahman, Talat S.

2011-12-01

This special issue is dedicated to the phenomenon of vibrations at surfaces—a topic that was indispensible a couple of decades ago, since it was one of the few phenomena capable of revealing the nature of binding at solid surfaces. For clean surfaces, the frequencies of modes with characteristic displacement patterns revealed how surface geometry, as well as the nature of binding between atoms in the surface layers, could be different from that in the bulk solid. Dispersion of the surface phonons provided further measures of interatomic interactions. For chemisorbed molecules on surfaces, frequencies and dispersion of the vibrational modes were also critical for determining adsorption sites. In other words, vibrations at surfaces served as a reliable means of extracting information about surface structure, chemisorption and overlayer formation. Experimental techniques, such as electron energy loss spectroscopy and helium-atom-surface scattering, coupled with infra-red spectroscopy, were continually refined and their resolutions enhanced to capture subtleties in the dynamics of atoms and molecules at surfaces. Theoretical methods, whether based on empirical and semi-empirical interatomic potential or on ab initio electronic structure calculations, helped decipher experimental observations and provide deeper insights into the nature of the bond between atoms and molecules in regions of reduced symmetry, as encountered on solid surfaces. Vibrations at surfaces were thus an integral part of the set of phenomena that characterized surface science. Dedicated workshops and conferences were held to explore the variety of interesting and puzzling features revealed in experimental and theoretical investigations of surface vibrational modes and their dispersion. One such conference, Vibrations at Surfaces, first organized by Harald Ibach in Juelich in 1980, continues to this day. The 13th International Conference on Vibrations at Surfaces was held at the University of Central Florida, Orlando, in March 2010. Several speakers at this meeting were invited to contribute to the special section in this issue. As is clear from the articles in this special section, the phenomenon of vibrations at surfaces continues to be a dynamic field of investigation. In fact, there is a resurgence of effort because the insights provided by surface dynamics are still fundamental to the development of an understanding of the microscopic factors that control surface structure formation, diffusion, reaction and structural stability. Examination of dynamics at surfaces thus complements and supplements the wealth of information that is obtained from real-space techniques such as scanning tunneling microscopy. Vibrational dynamics is, of course, not limited to surfaces. Surfaces are important since they provide immediate deviation from the bulk. They display how lack of symmetry can lead to new structures, new local atomic environments and new types of dynamical modes. Nanoparticles, large molecules and nanostructures of all types, in all kinds of local environments, provide further examples of regions of reduced symmetry and coordination, and hence display characteristic vibrational modes. Given the tremendous advance in the synthesis of a variety of nanostructures whose functionalization would pave the way for nanotechnology, there is even greater need to engage in experimental and theoretical techniques that help extract their vibrational dynamics. Such knowledge would enable a more complete understanding and characterization of these nanoscale systems than would otherwise be the case. The papers presented here provide excellent examples of the kind of information that is revealed by vibrations at surfaces. Vibrations at surface contents Poisoning and non-poisoning oxygen on Cu(410)L Vattuone, V Venugopal, T Kravchuk, M Smerieri, L Savio and M Rocca Modifying protein adsorption by layers of glutathione pre-adsorbed on Au(111)Anne Vallée, Vincent Humblot, Christophe Méthivier, Paul Dumas and Claire-Marie Pradier Relating temperature dependence of atom scattering spectra to surface corrugationW W Hayes and J R Manson Effects of the commensurability and disorder on friction for the system Xe/CuA Franchini, V Bortolani, G Santoro and K Xheka Switching ability of nitro-spiropyran on Au(111): electronic structure changes as a sensitive probe during a ring-opening reactionChristopher Bronner, Gunnar Schulze, Katharina J Franke, José Ignacio Pascual and Petra Tegeder High-resolution phonon study of the Ag(100) surfaceK L Kostov, S Polzin and W Widdra On the interpretation of IETS spectra of a small organic molecule Karina Morgenstern

Sequence-Dependent Structure/Function Relationships of Catalytic Peptide-Enabled Gold Nanoparticles Generated under Ambient Synthetic Conditions.

PubMed

Bedford, Nicholas M; Hughes, Zak E; Tang, Zhenghua; Li, Yue; Briggs, Beverly D; Ren, Yang; Swihart, Mark T; Petkov, Valeri G; Naik, Rajesh R; Knecht, Marc R; Walsh, Tiffany R

2016-01-20

Peptide-enabled nanoparticle (NP) synthesis routes can create and/or assemble functional nanomaterials under environmentally friendly conditions, with properties dictated by complex interactions at the biotic/abiotic interface. Manipulation of this interface through sequence modification can provide the capability for material properties to be tailored to create enhanced materials for energy, catalysis, and sensing applications. Fully realizing the potential of these materials requires a comprehensive understanding of sequence-dependent structure/function relationships that is presently lacking. In this work, the atomic-scale structures of a series of peptide-capped Au NPs are determined using a combination of atomic pair distribution function analysis of high-energy X-ray diffraction data and advanced molecular dynamics (MD) simulations. The Au NPs produced with different peptide sequences exhibit varying degrees of catalytic activity for the exemplar reaction 4-nitrophenol reduction. The experimentally derived atomic-scale NP configurations reveal sequence-dependent differences in structural order at the NP surface. Replica exchange with solute-tempering MD simulations are then used to predict the morphology of the peptide overlayer on these Au NPs and identify factors determining the structure/catalytic properties relationship. We show that the amount of exposed Au surface, the underlying surface structural disorder, and the interaction strength of the peptide with the Au surface all influence catalytic performance. A simplified computational prediction of catalytic performance is developed that can potentially serve as a screening tool for future studies. Our approach provides a platform for broadening the analysis of catalytic peptide-enabled metallic NP systems, potentially allowing for the development of rational design rules for property enhancement.

Surface Composition of NiPd Alloys

NASA Technical Reports Server (NTRS)

Noebe, Ronald D.; Khalil, Joe; Bozzolo, Guillermo; Gray, Hugh R. (Technical Monitor)

2002-01-01

Surface segregation in Ni-Pd alloys has been studied using the BFS method for alloys. Not only does the method predict an oscillatory segregation profile but it also indicates that the number of Pd-enriched surface planes can vary as a function of orientation. The segregation profiles were computed as a function of temperature, crystal face, and composition. Pd enrichment of the first layer is observed in (111) and (100) surfaces, and enrichment of the top two layers occurs for (110) surfaces. In all cases, the segregation profile shows oscillations that are actually related to weak ordering tendencies in the bulk. An atom-by-atom analysis was performed to identify the competing mechanisms leading to the observed surface behaviors. Large-scale atomistic simulations were also performed to investigate the temperature dependence of the segregation profiles as well as for analysis of the bulk structures. Finally, the observed surface behaviors are discussed in relation to the bulk phase structure of Ni-Pd alloys, which exhibit a tendency to weakly order.

Frictional Behavior of Micro/nanotextured Surfaces Investigated by Atomic Force Microscope: a Review

NASA Astrophysics Data System (ADS)

Zhang, Xiaoliang; Jia, Junhong

2015-08-01

Tribological issues between friction pair are fundamental problems for minimized devices because of their higher surface-to-volume ratio. Micro/nanotexturing is an effective technique to reduce actual contact area between contact pair at the nanoscale. Micro/nanotexture made a great impact on the frictional behavior of textured surfaces. This paper summarizes the recent advancements in the field of frictional behavior of micro/nanotextured surfaces, which are based on solid surface contact in atmosphere environment, especially focusing on the factors influencing the frictional behavior: Surface property, texturing density, texturing height, texturing structure and size of contact pair (atomic force microscope (AFM) tip) and texturing structures. Summarizing the effects of these factors on the frictional behavior is helpful for the understanding and designing of the surfaces in sliding micro/nanoelectromechanical systems (MEMS/NEMS). Controlling and reducing the friction force in moving mechanical systems is very important for the performance and reliability of nanosystems, which contribute to a sustainable future.

Ultrastructural investigation of intact orbital implant surfaces using atomic force microscopy.

PubMed

Choi, Samjin; Lee, Seung Jun; Shin, Jae-Ho; Cheong, Youjin; Lee, Hui-Jae; Paek, Joo Hee; Kim, Jae Sik; Jin, Kyung-Hyun; Park, Hun-Kuk

2011-01-01

This study examined the surface nanostructures of three orbital implants: nonporous poly(methyl methacrylate) (PMMA), porous aluminum oxide and porous polyethylene. The morphological characteristics of the orbital implants surfaces were observed by atomic force microscopy (AFM). The AFM topography, phase shift and deflection images of the intact implant samples were obtained. The surface of the nonporous PMMA implant showed severe scratches and debris. The surface of the aluminum oxide implant showed a porous structure with varying densities and sizes. The PMMA implant showed nodule nanostructures, 215.56 ± 52.34 nm in size, and the aluminum oxide implant showed crystal structures, 730.22 ± 341.02 nm in size. The nonporous PMMA implant showed the lowest roughness compared with other implant biomaterials, followed by the porous aluminum oxide implant. The porous polyethylene implant showed the highest roughness and severe surface irregularities. Overall, the surface roughness of orbital implants might be associated with the rate of complications and cell adhesion. Copyright © 2011 Wiley Periodicals, Inc.

On-Surface Synthesis and Characterization of 9-Atom Wide Armchair Graphene Nanoribbons

DOE PAGES

Talirz, Leopold; Söde, Hajo; Dumslaff, Tim; ...

2017-01-27

The bottom-up approach to synthesize graphene nanoribbons strives not only to introduce a band gap into the electronic structure of graphene but also to accurately tune its value by designing both the width and edge structure of the ribbons with atomic precision. Within this paper, we report the synthesis of an armchair graphene nanoribbon with a width of nine carbon atoms on Au(111) through surface-assisted aryl–aryl coupling and subsequent cyclodehydrogenation of a properly chosen molecular precursor. By combining high-resolution atomic force microscopy, scanning tunneling microscopy, and Raman spectroscopy, we demonstrate that the atomic structure of the fabricated ribbons is exactlymore » as designed. Angle-resolved photoemission spectroscopy and Fourier-transformed scanning tunneling spectroscopy reveal an electronic band gap of 1.4 eV and effective masses of ≈0.1 m e for both electrons and holes, constituting a substantial improvement over previous efforts toward the development of transistor applications. We use ab initio calculations to gain insight into the dependence of the Raman spectra on excitation wavelength as well as to rationalize the symmetry-dependent contribution of the ribbons’ electronic states to the tunneling current. Lastly, we propose a simple rule for the visibility of frontier electronic bands of armchair graphene nanoribbons in scanning tunneling spectroscopy.« less

On-surface synthesis on a bulk insulator surface

NASA Astrophysics Data System (ADS)

Richter, Antje; Floris, Andrea; Bechstein, Ralf; Kantorovich, Lev; Kühnle, Angelika

2018-04-01

On-surface synthesis has rapidly emerged as a most promising approach to prepare functional molecular structures directly on a support surface. Compared to solution synthesis, performing chemical reactions on a surface offers several exciting new options: due to the absence of a solvent, reactions can be envisioned that are otherwise not feasible due to the insolubility of the reaction product. Perhaps even more important, the confinement to a two-dimensional surface might enable reaction pathways that are not accessible otherwise. Consequently, on-surface synthesis has attracted great attention in the last decade, with an impressive number of classical reactions transferred to a surface as well as new reactions demonstrated that have no classical analogue. So far, the majority of the work has been carried out on conducting surfaces. However, when aiming for electronic decoupling of the resulting structures, e.g. for the use in future molecular electronic devices, non-conducting surfaces are highly desired. Here, we review the current status of on-surface reactions demonstrated on the (10.4) surface of the bulk insulator calcite. Besides thermally induced C-C coupling of halogen-substituted aryls, photochemically induced [2  +  2] cycloaddition has been proven possible on this surface. Moreover, experimental evidence exists for coupling of terminal alkynes as well as diacetylene polymerization. While imaging of the resulting structures with dynamic atomic force microscopy provides a direct means of reaction verification, the detailed reaction pathway often remains unclear. Especially in cases where the presence of metal atoms is known to catalyze the corresponding solution chemistry reaction (e.g. in the case of the Ullmann reaction), disclosing the precise reaction pathway is of importance to understand and generalize on-surface reactivity on a bulk insulator surface. To this end, density-functional theory calculations have proven to provide atomic-scale insights that have greatly contributed to unravelling the details of on-surface synthesis on a bulk insulator surface.

Oxygen adsorption onto pure and doped Al surfaces--the role of surface dopants.

PubMed

Lousada, Cláudio M; Korzhavyi, Pavel A

2015-01-21

Using density functional theory (DFT) with the PBE0 density functional we investigated the role of surface dopants in the molecular and dissociative adsorption of O2 onto Al clusters of types Al50, Al50Alad, Al50X and Al49X, where X represents a dopant atom of the following elements Si, Mg, Cu, Sc, Zr, and Ti. Each dopant atom was placed on the Al(111) surface as an adatom or as a substitutional atom, in the last case replacing a surface Al atom. We found that for the same dopant geometry, the closer is the ionization energy of the dopant element to that of elemental Al, the more exothermic is the dissociative adsorption of O2 and the stronger are the bonds between the resulting O atoms and the surface. Additionally we show that the Mulliken concept of electronegativity can be applied in the prediction of the dissociative adsorption energy of O2 on the doped surfaces. The Mulliken modified second-stage electronegativity of the dopant atom is proportional to the exothermicity of the dissociative adsorption of O2. For the same dopant element in an adatom position the dissociation of O2 is more exothermic when compared to the case where the dopant occupies a substitutional position. These observations are discussed in view of the overlap population densities of states (OPDOS) computed as the overlap between the electronic states of the adsorbate O atoms and the clusters. It is shown that a more covalent character in the bonding between the Al surface and the dopant atom causes a more exothermic dissociation of O2 and stronger bonding with the O atoms when compared to a more ionic character in the bonding between the dopant and the Al surface. The extent of the adsorption site reconstruction is dopant atom dependent and is an important parameter for determining the mode of adsorption, adsorption energy and electronic structure of the product of O2 adsorption. The PBE0 functional could predict the existence of the O2 molecular adsorption product for many of the cases investigated here.

Atomic structure of water/Au, Ag, Cu and Pt atomic junctions.

PubMed

Li, Yu; Kaneko, Satoshi; Fujii, Shintaro; Nishino, Tomoaki; Kiguchi, Manabu

2017-02-08

Much progress has been made in understanding the transport properties of atomic-scale conductors. We prepared atomic-scale metal contacts of Cu, Ag, Au and Pt using a mechanically controllable break junction method at 10 K in a cryogenic vacuum. Water molecules were exposed to the metal atomic contacts and the effect of molecular adsorption was investigated by electronic conductance measurements. Statistical analysis of the electronic conductance showed that the water molecule(s) interacted with the surface of the inert Au contact and the reactive Cu ant Pt contacts, where molecular adsorption decreased the electronic conductance. A clear conductance signature of water adsorption was not apparent at the Ag contact. Detailed analysis of the conductance behaviour during a contact-stretching process indicated that metal atomic wires were formed for the Au and Pt contacts. The formation of an Au atomic wire consisting of low coordination number atoms leads to increased reactivity of the inert Au surface towards the adsorption of water.

Identification of a Catalytically Highly Active Surface Phase for CO Oxidation over PtRh Nanoparticles under Operando Reaction Conditions

NASA Astrophysics Data System (ADS)

Hejral, U.; Franz, D.; Volkov, S.; Francoual, S.; Strempfer, J.; Stierle, A.

2018-03-01

Pt-Rh alloy nanoparticles on oxide supports are widely employed in heterogeneous catalysis with applications ranging from automotive exhaust control to energy conversion. To improve catalyst performance, an atomic-scale correlation of the nanoparticle surface structure with its catalytic activity under industrially relevant operando conditions is essential. Here, we present x-ray diffraction data sensitive to the nanoparticle surface structure combined with in situ mass spectrometry during near ambient pressure CO oxidation. We identify the formation of ultrathin surface oxides by detecting x-ray diffraction signals from particular nanoparticle facets and correlate their evolution with the sample's enhanced catalytic activity. Our approach opens the door for an in-depth characterization of well-defined, oxide-supported nanoparticle based catalysts under operando conditions with unprecedented atomic-scale resolution.

Reaction paths of alane dissociation on the Si(0 0 1) surface

NASA Astrophysics Data System (ADS)

Smith, Richard; Bowler, David R.

2018-03-01

Building on our earlier study, we examine the kinetic barriers to decomposition of alane, AlH3, on the Si(0 0 1) surface, using the nudged elastic band approach within density functional theory. We find that the initial decomposition to AlH with two H atoms on the surface proceeds without a significant barrier. There are several pathways available to lose the final hydrogen, though these present barriers of up to 1 eV. Incorporation is more challenging, with the initial structures less stable in several cases than the starting structures, just as was found for phosphorus. We identify a stable route for Al incorporation following selective surface hydrogen desorption (e.g. by scanning tunneling microscope tip). The overall process parallels PH3, and indicates that atomically precise acceptor doping should be possible.

Atom probe trajectory mapping using experimental tip shape measurements.

PubMed

Haley, D; Petersen, T; Ringer, S P; Smith, G D W

2011-11-01

Atom probe tomography is an accurate analytical and imaging technique which can reconstruct the complex structure and composition of a specimen in three dimensions. Despite providing locally high spatial resolution, atom probe tomography suffers from global distortions due to a complex projection function between the specimen and detector which is different for each experiment and can change during a single run. To aid characterization of this projection function, this work demonstrates a method for the reverse projection of ions from an arbitrary projection surface in 3D space back to an atom probe tomography specimen surface. Experimental data from transmission electron microscopy tilt tomography are combined with point cloud surface reconstruction algorithms and finite element modelling to generate a mapping back to the original tip surface in a physically and experimentally motivated manner. As a case study, aluminium tips are imaged using transmission electron microscopy before and after atom probe tomography, and the specimen profiles used as input in surface reconstruction methods. This reconstruction method is a general procedure that can be used to generate mappings between a selected surface and a known tip shape using numerical solutions to the electrostatic equation, with quantitative solutions to the projection problem readily achievable in tens of minutes on a contemporary workstation. © 2011 The Authors Journal of Microscopy © 2011 Royal Microscopical Society.

Ab initio study of novel carbon nanofoam structure as an anode material for Li secondary battery

NASA Astrophysics Data System (ADS)

Park, Hanjin; Park, Sora; Kang, Seoung-Hun; Kwon, Young-Kyun

2014-03-01

Using ab inito density functional theory, we investigate the adsorption and diffusion properties of Li atoms on a new carbon nanostructure, which may be used as an anode of Li secondary battery. We focus on a special carbon nanofoam structure consisting of Schwarzite structures with negative Gaussian curvature as core parts, which are interconnected through (4,4) CNT segments. Considering the symmetry of the nanofoam structure, we find various Li adsorption sites exhibiting relatively large binding energies (>= 2 . 00 eV). Based on these adsorption sites, we identify several diffusion paths on the outside or inside surface of the nanofoam structure and examine the diffusion barriers along the paths. Our results show that Li atom can diffuse almost freely due to its low energy barriers on both outside and inside surfaces. Finally, we also evaluate the energy gain tendency and the volume expansion as well as the average binding energy while adding Li atoms to estimate the Li-capacity and recyclability of the system, which are important characterisitics for anode materials. We conclude that the carbon nanofoam structure would be better as an anode material than graphite in Li capacity and volume expansion.

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.

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.

Polar catastrophe and the structure of KT a 1 - x N b x O 3 surfaces: Results from elastic and inelastic helium atom scattering

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

Flaherty, F. A.; Trelenberg, T. W.; Li, Jiefang A.

2015-07-13

In this paper, the structure and dynamics of cleaved (001) surfaces of potassium tantalates doped with niobium, KTa 1-xNb xO 3 (KTN), with x ranging from 0% to 30%, were measured by helium atom scattering (HAS). Through HAS time-of-flight (TOF) experiments, a dispersionless branch (Einstein phonon branch) with energy of 13-14meV was observed across the surface Brillouin zone in all samples. When this observation is combined with the results from earlier experimental and theoretical studies on these materials, a consistent picture of the stable surface structure emerges: After cleaving the single-crystal sample, the surface should be composed of equal areasmore » of KO and TaO 2/NbO 2 terraces. The data, however, suggest that K + and O 2- ions migrate from the bulk to the surface, forming a charged KO lattice that is neutralized primarily by additional K + ions bridging pairs of surface oxygens. This structural and dynamic modification at the (001) surface of KTN appears due to its formally charged KO(-1) and TaO 2/NbO 2(+1) layers and avoids a “polar catastrophe.” Finally, this behavior is contrasted with the (001) surface behavior of the fluoride perovskite KMnF 3 with its electrically neutral KF and MnF 2 layers.« less

Polar catastrophe and the structure of KTa 1-xNb xO₃ surfaces: Results from elastic and inelastic helium atom scattering

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

Flaherty, F. A.; Trelenberg, T. W.; Li, J. A.

2015-07-13

The structure and dynamics of cleaved (001) surfaces of potassium tantalates doped with niobium, KTa 1-xNb xO₃ (KTN), with x ranging from 0% to 30%, were measured by helium atom scattering (HAS). Through HAS time-of-flight (TOF) experiments, a dispersionless branch (Einstein phonon branch) with energy of 13-14 meV was observed across the surface Brillouin zone in all samples. When this observation is combined with the results from earlier experimental and theoretical studies on these materials, a consistent picture of the stable surface structure emerges: After cleaving the single-crystal sample, the surface should be composed of equal areas of KO andmore » TaO₂/NbO₂ terraces. The data, however, suggest that K⁺ and O²⁻ ions migrate from the bulk to the surface, forming a charged KO lattice that is neutralized primarily by additional K⁺ ions bridging pairs of surface oxygens. This structural and dynamic modification at the (001) surface of KTN appears due to its formally charged KO(-1) and TaO₂/NbO₂(+1) layers and avoids a “polar catastrophe.” This behavior is contrasted with the (001) surface behavior of the fluoride perovskite KMnF₃ with its electrically neutral KF and MnF₂ layers.« less

Predicting Catalytic Activity of Nanoparticles by a DFT-Aided Machine-Learning Algorithm.

PubMed

Jinnouchi, Ryosuke; Asahi, Ryoji

2017-09-07

Catalytic activities are often dominated by a few specific surface sites, and designing active sites is the key to realize high-performance heterogeneous catalysts. The great triumphs of modern surface science lead to reproduce catalytic reaction rates by modeling the arrangement of surface atoms with well-defined single-crystal surfaces. However, this method has limitations in the case for highly inhomogeneous atomic configurations such as on alloy nanoparticles with atomic-scale defects, where the arrangement cannot be decomposed into single crystals. Here, we propose a universal machine-learning scheme using a local similarity kernel, which allows interrogation of catalytic activities based on local atomic configurations. We then apply it to direct NO decomposition on RhAu alloy nanoparticles. The proposed method can efficiently predict energetics of catalytic reactions on nanoparticles using DFT data on single crystals, and its combination with kinetic analysis can provide detailed information on structures of active sites and size- and composition-dependent catalytic activities.

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

Yadav, Praveen Kumar, E-mail: praveenyadav@rrcat.gov.in; Nayak, Maheswar; Rai, Sanjay Kumar

The authors report the effect of argon ion to molybdenum atom ratio (r) on the microstructure of low energy (70 eV) argon ion assisted electron beam evaporated Mo thin films. Surface roughness, morphology, and crystallinity of Mo films are found to strongly depend on “r.” Increase of “r” from 0 to 100 induces gradual loss in crystallinity, reduction in surface roughness and systematic increase in density of the film. For “r” ∼ 100, average atomic density of the film approaches the bulk value (97%) with lowest surface roughness. Further, increasing “r” up to 170 reduces the atomic density, increases roughness, and increase inmore » crystallinity induced by low energy Ar ion beam. The observed surface roughness and grain size determined by x-ray reflectivity and glancing incidence x-ray diffraction correlate well with atomic force microscopy measurements. This study demonstrates that for r = 100 one gets lowest roughness Mo film with highest density and nearly amorphous microstructure. The growth model is discussed by structural zone model.« less

Gold–promoted structurally ordered intermetallic palladium cobalt nanoparticles for the oxygen reduction reaction

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

Kuttiyiel, Kurian A.; Sasaki, Kotaro; Su, Dong

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 via addition of gold atoms PdCo nanoparticles undergo at elevated temperatures an atomic structural transition from core-shell to a rare intermetallic ordered structure with twin boundaries forming stable {111}, {110} and {100} facets. The superior stability of this catalyst compared to platinum after 10,000 potential cycles in alkaline media is attributedmore » 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 matters.« less

Plasmonic trapping potentials for cold atoms

NASA Astrophysics Data System (ADS)

Mildner, Matthias; Horrer, Andreas; Fleischer, Monika; Zimmermann, Claus; Slama, Sebastian

2018-07-01

This paper reports on conceptual and experimental work towards the realization of plasmonic surface traps for cold atoms. The trapping mechanism is based on the combination of a repulsive and an attractive potential generated by evanescent light waves that are plasmonically enhanced. The strength of enhancement can be locally manipulated via the thickness of a metal nanolayer deposited on top of a dielectric substrate. Thus, in principle the trapping geometry can be predefined by the metal layer design. We present simulations of a plasmonic lattice potential using a gold grating with sinusoidally modulated thickness. Experimentally, a first plasmonic test structure is presented and characterized. Furthermore, the surface potential landscape is detected by reflecting ultracold atom clouds from the test structure revealing the influence of both evanescent waves. A parameter range is identified where stable traps can be expected.

Analysis and modification of defective surface aggregates on PCDTBT:PCBM solar cell blends using combined Kelvin probe, conductive and bimodal atomic force microscopy

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

Noh, Hanaul; Diaz, Alfredo J.; Solares, Santiago D.

Organic photovoltaic systems comprising donor polymers and acceptor fullerene derivatives are attractive for inexpensive energy harvesting. Extensive research on polymer solar cells has provided insight into the factors governing device-level efficiency and stability. However, the detailed investigation of nanoscale structures is still challenging. Here we demonstrate the analysis and modification of unidentified surface aggregates. The aggregates are characterized electrically by Kelvin probe force microscopy and conductive atomic force microscopy (C-AFM), whereby the correlation between local electrical potential and current confirms a defective charge transport. Bimodal AFM modification confirms that the aggregates exist on top of the solar cell structure, andmore » is used to remove them and to reveal the underlying active layer. The systematic analysis of the surface aggregates suggests that the structure consists of PCBM molecules.« less

Analysis and modification of defective surface aggregates on PCDTBT:PCBM solar cell blends using combined Kelvin probe, conductive and bimodal atomic force microscopy

DOE PAGES

Noh, Hanaul; Diaz, Alfredo J.; Solares, Santiago D.

2017-03-08

Organic photovoltaic systems comprising donor polymers and acceptor fullerene derivatives are attractive for inexpensive energy harvesting. Extensive research on polymer solar cells has provided insight into the factors governing device-level efficiency and stability. However, the detailed investigation of nanoscale structures is still challenging. Here we demonstrate the analysis and modification of unidentified surface aggregates. The aggregates are characterized electrically by Kelvin probe force microscopy and conductive atomic force microscopy (C-AFM), whereby the correlation between local electrical potential and current confirms a defective charge transport. Bimodal AFM modification confirms that the aggregates exist on top of the solar cell structure, andmore » is used to remove them and to reveal the underlying active layer. The systematic analysis of the surface aggregates suggests that the structure consists of PCBM molecules.« less

Analysis and modification of defective surface aggregates on PCDTBT:PCBM solar cell blends using combined Kelvin probe, conductive and bimodal atomic force microscopy

PubMed Central

Noh, Hanaul; Diaz, Alfredo J

2017-01-01

Organic photovoltaic systems comprising donor polymers and acceptor fullerene derivatives are attractive for inexpensive energy harvesting. Extensive research on polymer solar cells has provided insight into the factors governing device-level efficiency and stability. However, the detailed investigation of nanoscale structures is still challenging. Here we demonstrate the analysis and modification of unidentified surface aggregates. The aggregates are characterized electrically by Kelvin probe force microscopy and conductive atomic force microscopy (C-AFM), whereby the correlation between local electrical potential and current confirms a defective charge transport. Bimodal AFM modification confirms that the aggregates exist on top of the solar cell structure, and is used to remove them and to reveal the underlying active layer. The systematic analysis of the surface aggregates suggests that the structure consists of PCBM molecules. PMID:28382247

Effects of surface structural disorder and surface coverage on isotopic fractionation during Zn(II) adsorption onto quartz and amorphous silica surfaces

DOE PAGES

Nelson, Joey; Wasylenki, Laura; Bargar, John R.; ...

2017-08-05

Metal ion-mineral surface interactions and the attendant isotopic fractionation depend on the properties of the mineral surface and the local atomic-level chemical environment. Furthermore, these factors have not been systematically examined for phases of the same composition with different levels of surface disorder.

Effects of surface structural disorder and surface coverage on isotopic fractionation during Zn(II) adsorption onto quartz and amorphous silica surfaces

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

Nelson, Joey; Wasylenki, Laura; Bargar, John R.

Metal ion-mineral surface interactions and the attendant isotopic fractionation depend on the properties of the mineral surface and the local atomic-level chemical environment. Furthermore, these factors have not been systematically examined for phases of the same composition with different levels of surface disorder.

CO adsorption on small Au{sub n} (n = 1–4) structures supported on hematite. I. Adsorption on iron terminated α-Fe{sub 2}O{sub 3} (0001) surface

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

Pabisiak, Tomasz; Kiejna, Adam, E-mail: kiejna@ifd.uni.wroc.pl; Winiarski, Maciej J.

2016-01-28

This is the first of two papers dealing with the adsorption of Au and formation of Au{sub n} nanostructures (n = 1–4) on hematite (0001) surface and adsorption of CO thereon. The stoichiometric Fe-terminated (0001) surface of hematite was investigated using density functional theory in the generalized gradient approximation of Perdew-Burke-Ernzerhof (PBE) form with Hubbard correction U, accounting for strong electron correlations (PBE+U). The structural, energetic, and electronic properties of the systems studied were examined for vertical and flattened configurations of Au{sub n} nanostructures adsorbed on the hematite surfaces. The flattened ones, which can be viewed as bilayer-like structures, weremore » found energetically more favored than vertical ones. For both classes of structures the adsorption binding energy increases with the number of Au atoms in a structure. The adsorption of Au{sub n} induces charge rearrangement at the Au{sub n}/oxide contact which is reflected in work function changes. In most considered cases Au{sub n} adsorption increases the work function. A detailed analysis of the bonding electron charge is presented and the corresponding electron charge rearrangements at the contacts were quantified by a Bader charge analyses. The interaction of a CO molecule with the Au{sub n} nanostructures supported on α-Fe{sub 2}O{sub 3} (0001) and the oxide support was studied. It is found that the CO adsorption binding to the hematite supported Au{sub n} structures is more than twice as strong as to the bare hematite surface. Analysis of the Bader charges on the atoms showed that in each case CO binds to the most positively charged (cationic) atom of the Au{sub n} structure. Changes in the electronic structure of the Au{sub n} species and of the oxide support, and their consequences for the interactions with CO, are discussed.« less

Communication: Hot-atom abstraction dynamics of hydrogen from tungsten surfaces: The role of surface structure

NASA Astrophysics Data System (ADS)

Galparsoro, Oihana; Busnengo, Heriberto Fabio; Juaristi, Joseba Iñaki; Crespos, Cédric; Alducin, Maite; Larregaray, Pascal

2017-09-01

Adiabatic and non-adiabatic quasiclassical molecular dynamics simulations are performed to investigate the role of the crystal face on hot-atom abstraction of H adsorbates by H scattering from covered W(100) and W(110). On both cases, hyperthermal diffusion is strongly affected by the energy dissipated into electron-hole pair excitations. As a result, the hot-atom abstraction is highly reduced in favor of adsorption at low incidence energy and low coverages, i.e., when the mean free path of the hyperthermal H is typically larger. Qualitatively, this reduction is rather similar on both surfaces, despite at such initial conditions, the abstraction process involves more subsurface penetration on W(100) than on W(110).

Spinel-structured metal oxide on a substrate and method of making same by molecular beam epitaxy

DOEpatents

Chambers, Scott A.

2006-02-21

A method of making a spinel-structured metal oxide on a substrate by molecular beam epitaxy, comprising the step of supplying activated oxygen, a first metal atom flux, and at least one other metal atom flux to the surface of the substrate, wherein the metal atom fluxes are individually controlled at the substrate so as to grow the spinel-structured metal oxide on the substrate and the metal oxide is substantially in a thermodynamically stable state during the growth of the metal oxide. A particular embodiment of the present invention encompasses a method of making a spinel-structured binary ferrite, including Co ferrite, without the need of a post-growth anneal to obtain the desired equilibrium state.

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.

Structural Analysis of MoS2 and other 2D layered materials using LEEM/LEED-I(V) and STM

NASA Astrophysics Data System (ADS)

Grady, Maxwell; Dai, Zhongwei; Jin, Wencan; Dadap, Jerry; Osgood, Richard; Sadowski, Jerzy; Pohl, Karsten

Layered two-dimensional materials, such as molybdenum disulfide, MoS2, are of interest for the development of many types of novel electronic devices. To fully understand the interfaces between these new materials, the atomic reconstructions at their surfaces must be understood. Low Energy Electron Microscopy and Diffraction, LEEM/ μLEED, present a unique method for rapid material characterization in real space and reciprocal space with high resolution. Here we present a study of the surface structure of 2H-MoS2 using μLEED intensity-voltage analysis. To aid this analysis, software is under development to automate the procedure of extracting I(V) curves from LEEM and LEED data. When matched with computational modeling, this data provides information with angstrom level resolution concerning the three dimensional atomic positions. We demonstrate that the surface structure of bulk MoS2 is distinct from the bulk crystal structure and exhibits a smaller surface relaxation at 320K compared to previous results at 95K. Furthermore, suspended monolayer samples exhibit large interlayer relaxations compared to the bulk surface termination. Further techniques for refining layer thickness determination are under development.

Prediction of a new graphenelike Si2BN solid

NASA Astrophysics Data System (ADS)

Andriotis, Antonis N.; Richter, Ernst; Menon, Madhu

2016-02-01

While the possibility to create a single-atom-thick two-dimensional layer from any material remains, only a few such structures have been obtained other than graphene and a monolayer of boron nitride. Here, based upon ab initio theoretical simulations, we propose a new stable graphenelike single-atomic-layer Si2BN structure that has all of its atoms with s p2 bonding with no out-of-plane buckling. The structure is found to be metallic with a finite density of states at the Fermi level. This structure can be rolled into nanotubes in a manner similar to graphene. Combining first- and second-row elements in the Periodic Table to form a one-atom-thick material that is also flat opens up the possibility for studying new physics beyond graphene. The presence of Si will make the surface more reactive and therefore a promising candidate for hydrogen storage.

Cleaning of Fire Damaged Watercolor and Textiles Using Atomic Oxygen

NASA Technical Reports Server (NTRS)

Rutledge, Sharon K.; Banks, Bruce A.; Chichernea, Virgil A.; Haytas, Christy A.

2000-01-01

A noncontact technique is described that uses atomic oxygen generated under low pressure in the presence of nitrogen to remove soot from the surface of a test watercolor panel and strips of cotton, wool and silk. The process, which involves surface oxidation, permits control of the amount of surface material removed. The effectiveness of soot removal from test panels of six basic watercolors (alizarin crimson, burnt sienna, lemon yellow, yellow ochre, cerulean blue and ultramarine blue) and strips of colored cotton, wool and silk was measured using reflectance spectroscopy. The atomic oxygen removed soot effectively from the treated areas and enabled partial recovery of charred watercolors. However, overexposure can result in removal of sizing, bleaching, and weakening of the structure. With the proper precautions, atomic oxygen treatment appears to have great potential to salvage heavily smoke damaged artworks which were previously considered unrestorable.

Clarification of the interaction between Au atoms and the anatase TiO2 (112) surface using density functional theory

NASA Astrophysics Data System (ADS)

Tada, Kohei; Koga, Hiroaki; Okumura, Mitsutaka; Tanaka, Shingo

2018-04-01

A model (112) surface slab of anatase TiO2 (112) was optimized, and the adsorption of Au atoms onto the (112) surface was investigated by first-principles calculations based on DFT (density functional theory) with the generalized gradient approximation (GGA). Furthermore, the results were compared with those of Au/anatase TiO2 (101) system. The (112) surface has a ridge and a groove (zig-zag structure). The Au atoms were strongly adsorbed in the grooves but became unstable as they climbed toward the ridges, and the promotion of electrons in the 5d orbitals to the 6s and 6p orbitals in the absorbed Au atom occurred. At the Au/anatase TiO2 interface, the Au-Ti4+ coordinate bond in the (112) system is stronger than that in the (101) system because the promotion of electrons is greater in the former interaction than the latter. The results suggest that Au/anatase TiO2 catalysts with a higher dispersion of Au nanoparticles could be prepared when the (112) surface is preferentially exposed.

A theoretical investigation of the structural and electronic properties of 55-atom nanoclusters: The examples of Y-Tc and Pt.

PubMed

Batista, Krys E A; Piotrowski, Maurício J; Chaves, Anderson S; Da Silva, Juarez L F

2016-02-07

Several studies have found that the Pt55 nanocluster adopts a distorted reduced core structure, DRC55, in which there are 8-11 atoms in the core and 47-44 atoms in the surface, instead of the compact and high-symmetry icosahedron structure, ICO55, with 13 and 42 atoms in the core and surface, respectively. The DRC structure has also been obtained as the putative global minimum configuration (GMC) for the Zn55 (3d), Cd55 (4d), and Au55 (5d) systems. Thus, the DRC55 structure has been reported only for systems with a large occupation of the d-states, where the effects of the occupation of the valence anti-bonding d-states might play an important role. Can we observe the DRC structure for 55-atom transition-metal systems with non-occupation of the anti-bonding d-states? To address this question, we performed a theoretical investigation of the Y 55, Zr55, Nb55, Mo55, Tc55, and Pt55 nanoclusters, employing density functional theory calculations. For the putative GMCs, we found that the Y 55 adopts the ICO55 structure, while Nb55 and Mo55 adopt a bulk-like fragment based on the hexagonal close-packed structure and Tc55 adopts a face-centered cubic fragment; however, Zr55 adopts a DRC55 structure, like Zn55, Cd55, Pt55, and Au55. Thus we can conclude that the preference for DRC55 structure is not related to the occupation of the anti-bonding d-states, but to a different effect, in fact, a combination of structural and electronic effects. Furthermore, we obtained that the binding energy per atom follows the occupation of the bonding and anti-bonding model, i.e., the stability of the studied systems increases from Y to Tc with a small oscillation for Mo, which also explains the equilibrium bond lengths. We obtained a larger magnetic moment for Y 55 (31 μB) which can be explained by the localization of the d-states in Y at nanoscale, which is not observed for the remaining systems (0-1 μB).

CO adsorption on small Au{sub n} (n = 1–4) structures supported on hematite. II. Adsorption on the O-rich termination of α-Fe{sub 2}O{sub 3}(0001) surface

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

Pabisiak, Tomasz; Kiejna, Adam, E-mail: kiejna@ifd.uni.wroc.pl; Winiarski, Maciej J.

2016-01-28

The adsorption of small Au{sub n} (n = 1–4) nanostructures on oxygen terminated α-Fe{sub 2}O{sub 3}(0001) surface was investigated using density functional theory in the generalized gradient approximation of Perdew-Burke-Ernzerhof (PBE) form with Hubbard correction U, accounting for strong electron correlations (PBE+U). The structural, energetic, and electronic properties were examined for two classes of the adsorbed Au{sub n} nanostructures with vertical and flattened configurations. Similarly to the Fe-terminated α-Fe{sub 2}O{sub 3}(0001) surface considered in Part I, the flattened configurations were found energetically more favored than vertical ones. The binding of Au{sub n} to the O-terminated surface is much stronger thanmore » to the Fe-termination. The adsorption bonding energy of Au{sub n} and the work function of the Au{sub n}/α-Fe{sub 2}O{sub 3}(0001) systems decrease with the increased number of Au atoms in a structure. All of the adsorbed Au{sub n} structures are positively charged. The bonding of CO molecules to the Au{sub n} structures is distinctly stronger than on the Fe-terminated surface; however, it is weaker than the binding to the bare O-terminated surface. The CO molecule binds to the Au{sub n}/α-Fe{sub 2}O{sub 3}(0001) system through a peripheral Au atom partly detached from the Au{sub n} structure. The results of this work indicate that the most energetically favored sites for adsorption of a CO molecule on the Au{sub n}/α-Fe{sub 2}O{sub 3}(0001) systems are atoms in the Au{sup 0.5+} oxidation state.« less

Self-assembling layers created by membrane proteins on gold.

PubMed

Shah, D S; Thomas, M B; Phillips, S; Cisneros, D A; Le Brun, A P; Holt, S A; Lakey, J H

2007-06-01

Membrane systems are based on several types of organization. First, amphiphilic lipids are able to create monolayer and bilayer structures which may be flat, vesicular or micellar. Into these structures membrane proteins can be inserted which use the membrane to provide signals for lateral and orientational organization. Furthermore, the proteins are the product of highly specific self-assembly otherwise known as folding, which mostly places individual atoms at precise places in three dimensions. These structures all have dimensions in the nanoscale, except for the size of membrane planes which may extend for millimetres in large liposomes or centimetres on planar surfaces such as monolayers at the air/water interface. Membrane systems can be assembled on to surfaces to create supported bilayers and these have uses in biosensors and in electrical measurements using modified ion channels. The supported systems also allow for measurements using spectroscopy, surface plasmon resonance and atomic force microscopy. By combining the roles of lipids and proteins, highly ordered and specific structures can be self-assembled in aqueous solution at the nanoscale.

Structural Rearrangement of Au-Pd Nanoparticles under Reaction Conditions: An ab Initio Molecular Dynamics Study.

PubMed

Xu, Cong-Qiao; Lee, Mal-Soon; Wang, Yang-Gang; Cantu, David C; Li, Jun; Glezakou, Vassiliki-Alexandra; Rousseau, Roger

2017-02-28

The structure, composition, and atomic distribution of nanoalloys under operating conditions are of significant importance for their catalytic activity. In the present work, we use ab initio molecular dynamics simulations to understand the structural behavior of Au-Pd nanoalloys supported on rutile TiO 2 under different conditions. We find that the Au-Pd structure is strongly dependent on the redox properties of the support, originating from strong metal-support interactions. Under reducing conditions, Pd atoms are inclined to move toward the metal/oxide interface, as indicated by a significant increase of Pd-Ti bonds. This could be attributed to the charge localization at the interface that leads to Coulomb attractions to positively charged Pd atoms. In contrast, under oxidizing conditions, Pd atoms would rather stay inside or on the exterior of the nanoparticle. Moreover, Pd atoms on the alloy surface can be stabilized by hydrogen adsorption, forming Pd-H bonds, which are stronger than Au-H bonds. Our work offers critical insights into the structure and redox properties of Au-Pd nanoalloy catalysts under working conditions.

The hydrophilic-to-hydrophobic transition in glassy silica is driven by the atomic topology of its surface

NASA Astrophysics Data System (ADS)

Yu, Yingtian; Krishnan, N. M. Anoop; Smedskjaer, Morten M.; Sant, Gaurav; Bauchy, Mathieu

2018-02-01

The surface reactivity and hydrophilicity of silicate materials are key properties for various industrial applications. However, the structural origin of their affinity for water remains unclear. Here, based on reactive molecular dynamics simulations of a series of artificial glassy silica surfaces annealed at various temperatures and subsequently exposed to water, we show that silica exhibits a hydrophilic-to-hydrophobic transition driven by its silanol surface density. By applying topological constraint theory, we show that the surface reactivity and hydrophilic/hydrophobic character of silica are controlled by the atomic topology of its surface. This suggests that novel silicate materials with tailored reactivity and hydrophilicity could be developed through the topological nanoengineering of their surface.

Study on the structural transition of CoNi nanoclusters using molecular dynamics simulations

NASA Astrophysics Data System (ADS)

Xia, J. H.; Gao, Xue-Mei

2018-04-01

In this work, the segregation and structural transitions of CoNi clusters, between 1500 and 300 K, have been investigated using molecular dynamics simulations with the embedded atom method potential. The radial distribution function was used to analyze the segregation during the cooling processes. It is found that Co atoms segregate to the inside and Ni atoms preferably to the surface during the cooling processes, the Co147Ni414 cluster becomes a core-shell structure. We discuss the structural transition according to the pair-correction function and pair-analysis technique, and finally the liquid Co147Ni414 crystallizes into the coexistence of hcp and fcc structure at 300 K. At the same time, it is found that the frozen structure of CoNi cluster is strongly related to the Co concentration.

The surface sulfur doping induced enhanced performance of cobalt catalysts in oxygen evolution reactions.

PubMed

Al-Mamun, Mohammad; Zhu, Zhengju; Yin, Huajie; Su, Xintai; Zhang, Haimin; Liu, Porun; Yang, Huagui; Wang, Dan; Tang, Zhiyong; Wang, Yun; Zhao, Huijun

2016-08-04

A novel surface sulfur (S) doped cobalt (Co) catalyst for the oxygen evolution reaction (OER) is theoretically designed through the optimisation of the electronic structure of highly reactive surface atoms which is also validated by electrocatalytic OER experiments.

Theoretical study of adsorption of organic phosphines on transition metal surfaces

NASA Astrophysics Data System (ADS)

Lou, Shujie; Jiang, Hong

2018-04-01

The adsorption properties of organic phosphines on transition metal (TM) surfaces (Fe, Co, Ni, Cu, Ru, Rh, Pd, Ag, Ir, Pt, and Au) have been studied to explore the possibility of building novel heterogeneous chiral catalytic systems based on organic phosphines. Preferred adsorption sites, adsorption energies and surface electronic structures of a selected set of typical organic phosphines adsorbed on TM surfaces are calculated with density-functional theory to obtain a systematic understanding on the nature of adsorption interactions. All organic phosphines considered are found to chemically adsorb on these TM surfaces with the atop site as the most preferred one, and the TM-P bond is formed via the lone-pair electrons of the P atom and the directly contacted TM atom. These findings imply that it is indeed possible to build heterogeneous chiral catalytic systems based on organic phosphines adsorbed on TM surfaces, which, however, requires a careful design of molecular structure of organic phosphines.

In situ growth, structure, and real-time chemical reactivity of well-defined CeO x-Ru(0001) model surfaces

DOE PAGES

Grinter, David C.; Senanayake, Sanjaya D.; Flege, Jan Ingo

2016-11-15

Ceria is an important material for chemical conversion processes in catalysis. Its intrinsic properties as a reducible oxide can be exploited to achieve catalytic selectivity and activity. However, numerous phenomenological characteristics of ceria remain unknown and its active nature is ever slowly being unraveled. Well defined models of ceria (111) are an important way to systematically study these properties and take advantage of new in situ methods that require pristine materials that allow for the interrogation of the most fundamental traits of this material. The ceria-Ru(0001) model is now the most well studied model surface with numerous aspects of itsmore » preparation, atomic structure and reactivity studied by several groups. The preparation of CeO x structures oriented with a (111) surface termination can be achieved through molecular beam deposition, facilitating the growth of well-defined nanostructures, microparticles, and films on the Ru(0001) surface. The growth mechanism exploits the epitaxial relationship between CeOx and Ru to form a carpet mode of well oriented layers of Osingle bondCesingle bondO. These models can be studied to unravel the atomic structure and the oxidation state (Ce 4+ and Ce 3+), as prepared and under redox conditions (reduction/oxidation) or with reaction using reactants (e.g., H 2, methanol). Here, we present a discussion of these most recent observations pertaining to the growth mode, arrangement of atoms on the surface, characteristic chemical state, and redox chemistry of the CeO x-Ru surface. As a result, with insights from these studies we propose new strategies to further unravel the chemistry of ceria.« less

Atomic scale study of nanocontacts

NASA Astrophysics Data System (ADS)

Buldum, A.; Ciraci, S.; Batra, Inder P.; Fong, C. Y.

1998-03-01

Nanocontact and subsequent pulling off a sharp Ni(111) tip on a Cu(110) surface are investigated by using molecular dynamics method with embedded atom model. As the contact is formed, the sharp tip experiences multiple jump to contact in the attractive force range. The contact interface develops discontinuously mainly due to disorder-order transformations which lead to disappearance of a layer and hence abrupt changes in the normal force variation. Atom exchange occurs in the repulsive range. The connective neck is reduced also discontinuously by pulling off the tip. The novel atomic structure of the neck under the tensile force is analyzed. We also presented a comperative study for the contact by a Si(111) tip on Si(111)-(2x1) surface.

Theoretical study for heterojunction surface of NEA GaN photocathode dispensed with Cs activation

NASA Astrophysics Data System (ADS)

Xia, Sihao; Liu, Lei; Wang, Honggang; Wang, Meishan; Kong, Yike

2016-09-01

For the disadvantages of conventional negative electron affinity (NEA) GaN photocathodes activated by Cs or Cs/O, new-type NEA GaN photocathodes with heterojunction surface dispensed with Cs activation are investigated based on first-principle study with density functional theory. Through the growth of an ultrathin n-type GaN cap layer on p-type GaN emission layer, a p-n heterojunction is formed on the surface. According to the calculation results, it is found that Si atoms tend to replace Ga atoms to result in an n-type doped cap layer which contributes to the decreasing of work function. After the growth of n-type GaN cap layer, the atom structure near the p-type emission layer is changed while that away from the surface has no obvious variations. By analyzing the E-Mulliken charge distribution of emission surface with and without cap layer, it is found that the positive charge of Ga and Mg atoms in the emission layer decrease caused by the cap layer, while the negative charge of N atom increases. The conduction band moves downwards after the growth of cap layer. Si atom produces donor levels around the valence band maximum. The absorption coefficient of GaN emission layer decreases and the reflectivity increases caused by n-type GaN cap layer.

Super-reduced polyoxometalates: excellent molecular cluster battery components and semipermeable molecular capacitors.

PubMed

Nishimoto, Yoshio; Yokogawa, Daisuke; Yoshikawa, Hirofumi; Awaga, Kunio; Irle, Stephan

2014-06-25

Theoretical investigations are presented on the molecular and electronic structure changes that occur as α-Keggin-type polyoxometalate (POM(3-)) clusters [PM12O40](3-) (M = Mo, W) are converted toward their super-reduced POM(27-) state during the discharging process in lithium-based molecular cluster batteries. Density functional theory was employed in geometry optimization, and first-principles molecular dynamics simulations were used to explore local minima on the potential energy surface of neutral POM clusters adorned with randomly placed Li atoms as electron donors around the cluster surface. On the basis of structural, electron density, and molecular orbital studies, we present evidence that the super-reduction is accompanied by metal-metal bond formation, beginning from the 12th to 14th excess electron transferred to the cluster. Afterward, the number of metal-metal bonds increases nearly linearly with the number of additionally transferred excess electrons. In α-Keggin-type POMs, metal triangles are a prominently emerging structural feature. The origin of the metal triangle formation during super-reduction stems from the formation of characteristic three-center two-electron bonds in triangular metal atom sites, created under preservation of the POM skeleton via "squeezing out" of oxygen atoms bridging two metal atoms when the underlying metal atoms form covalent bonds. The driving force for this unusual geometrical and electronic structure change is a local Jahn-Teller distortion at individual transition-metal octahedral sites, where the triply degenerate t2 d orbitals become partially filled during reduction and gain energy by distortion of the octahedron in such a way that metal-metal bonds are formed. The bonding orbitals show strong contributions from mixing with metal-oxygen antibonding orbitals, thereby "shuffling away" excess electrons from the cluster center to the outside of the cage. The high density of negatively charged yet largely separated oxygen atoms on the surface of the super-reduced POM(27-) polyanion allows the huge Coulombic repulsion due to the presence of the excess electrons to be counterbalanced by the presence of Li countercations, which partially penetrate into the outer oxygen shell. This "semiporous molecular capacitor" structure is likely the reason for the effective electron uptake in POMs.

Remote Sensing of Icy Galilean Moon Surface and Atmospheric Composition Using Low Energy (1 eV-4 keV) Neutral Atom Imaging

NASA Technical Reports Server (NTRS)

Collier, M. R.; Sittler, E.; Chornay, D.; Cooper, J. F.; Coplan, M.; Johnson, R. E.

2004-01-01

We describe a low energy neutral atom imager suitable for composition measurements Europa and other icy Galilean moons in the Jovian magnetosphere. This instrument employs conversion surface technology and is sensitive to either neutrals converted to negative ions, neutrals converted to positive ions and the positive ions themselves depending on the power supply. On a mission such as the Jupiter Icy Moons Orbiter (JIMO), two back-to-back sensors would be flown with separate power supplies fitted to the neutral atom and iodneutral atom sides. This will allow both remote imaging of 1 eV < E < 4 keV neutrals from icy moon surfaces and atmospheres, and in situ measurements of ions at similar energies in the moon ionospheres and Jovian magnetospheric plasma. The instrument provides composition measurements of the neutrals and ions that enter the spectrometer with a mass resolution dependent on the time-of-flight subsystem and capable of resolving molecules. The lower energy neutrals, up to tens of eV, arise from atoms and molecules sputtered off the moon surfaces and out of the moon atmospheres by impacts of more energetic (keV to MeV) ions from the magnetosphere. Direct Simulation Monte Carlo (DSMC) models are used to convert measured neutral abundances to compositional distributions of primary and trace species in the sputtered surfaces and atmospheres. The escaping neutrals can also be detected as ions after photo- or plasma-ionization and pickup. Higher energy, keV neutrals come from charge exchange of magnetospheric ions in the moon atmospheres and provide information on atmospheric structure. At the jovicentric orbits of the icy moons the presence of toroidal gas clouds, as detected at Europa's orbit, provide M e r opportunities to analyze both the composition of neutrals and ions originating from the moon surfaces, and the characteristics of magnetospheric ions interacting with neutral cloud material. Charge exchange of low energy ions near the moons, and directional distributions of the resultant neutrals, allow indirect global mapping of magnetic field structures around the moons. Temporal variation of the magnetic structures can be linked to induced magnetic fields associated with subsurface oceans.

Annihilation of positronium atoms confined in mesoporous and macroporous SiO2 films

NASA Astrophysics Data System (ADS)

Cooper, B. S.; Boilot, J.-P.; Corbel, C.; Guillemot, F.; Gurung, L.; Liszkay, L.; Cassidy, D. B.

2018-05-01

We report experiments in which positronium (Ps) atoms were created in thin, porous silica films containing isolated voids with diameters ranging from 5 to 75 nm. Ps lifetimes in the pore structures were measured directly via time-delayed laser excitation of 13S1→23PJ transitions. In a film containing 5-nm pores Ps was predominantly emitted into vacuum, with a small component of confined Ps with a lifetime of 75 ns also observed. In films with larger pores Ps atoms were not emitted into vacuum except from the film surface, and confined Ps lifetimes of ≈90 ns were measured with no dependence on the pore size. However, for such large pores, extended Tao-Eldrup (ETE)-type models predict Ps lifetimes close to the 142-ns vacuum value. Moreover, 13S1→23PJ excitation of Ps atoms inside the pores was found to result in annihilation and exhibited an extremely broad (≈10 THz) linewidth. We attribute these observations to a process in which nonthermal Ps atoms in the isolated voids become temporarily trapped in a series of surface states that dissociate following excitation. The occurrence of this mechanism is not necessarily apparent from ground-state Ps decay rates without some prior knowledge of the sample structure, and it precludes the application of ETE-type models as they do not take into account surface interactions other than pickoff annihilation.

Modeling of the Structure of Disordered Metallic Alloys and Its Transformation Under Thermal Forcing

NASA Astrophysics Data System (ADS)

Cress, Ryan Paul

The morphology of disordered binary metallic alloys is investigated. The structure of disordered binary metallic alloys is modeled as a randomly close packed (RCP) assembly of atoms. It was observed through a 2-D binary hard sphere experiment that RCP structure can be modeled as a mixture of nano-crystallites and glassy matter. We define the degree of crystallinity as the fraction of atoms contained in nano-crystallites in an RCP medium. Nano-crystallites by size in a crystallite size distribution were determined experimentally to define the morphology of the RCP medium. Both the degree of crystallinity and the crystallite size distribution have been found to be determined by the composition of a given binary mixture. A 2-D Monte Carlo simulation was developed in order to replicate the RCP structure observed in the experiment which is then extended to cases of arbitrary composition. Crystallites were assumed to be spherical with isotropic cross sections. The number of atoms in an individual crystallite in 2-D is simply transformed into the number of atoms in 3-D; we then obtain the crystallite size distribution in 3-D. This experiment accounts for the contribution from the repulsive core of the inter-atomic potential. The attractive part of the potential is recovered by constructing spherical nano-crystallites of a given radius from a crystalline specimen of each given alloy. A structural model of a disordered alloy is thus obtained. With the basic structure of the RCP medium defined, the response to heating would be in the form of changes to the crystallite size distribution. This was first investigated in a hard sphere mechanical oven experiment. The experimental setup consists of a 2-D cell which is driven by two independent stepper motors. The motors drive a binary RCP bed of spheres on a slightly tilted plane according to a chaotic algorithmm. The motors are driven at four different speed settings. The RCP medium was analyzed using a sequence of digital images taken of the beds. The bursts of images provide a Gaussian distribution of particle speeds in x and y directions thus giving rise to the notion of "temperature." This temperature scales with the motor speed settings. The measured average degree of crystallinity is found to decrease as the effective temperature was raised suggesting that nano-crystallites dissociate under thermal forcing. The evolution of a specimen's structure is calculated rigorously by means of the law of mass action formalism. A system of thermal dissociation reaction equations is written out for the set of nano-crystallites according to the 3-D crystallite size distribution. The equilibrium treatment is justified because the energy differences between metastable RCP structures fall within kT. Thermal dissociation of one surface atom at a time is assumed because the energy cost in dissociation of a surface atom on a nano-crystallite is significantly less than that of a multi atom cluster. The full set of reaction equations cover all possible dissociation steps, which may amount to several thousand for a disordered alloy specimen. The primary determining factor in each of these dissociation equations is the dissociation potential or the amount of attractive energy needed to remove a surface atom on a nano-crystallite of a given size. The attractive potential between atoms is calculated using a Lennard-Jones potential between a pair of atoms for which quantum chemistry calculations exist in the literature. All interactions impinged on the surface atom by all other atoms in a crystallite are summed. As the nano-crystallites dissociate due to heating, the structure of the alloy changes, and this leads to modifications of alloy's transport properties. The model is found to predict the melting temperature of various disordered binary alloys as well as refractory metals in good agreement with known data. The structure model for disordered binary alloys gives an excellent characterization of the alloy morphology. It therefore provides fruitful avenues for making predictions about how thermophysical properties of disordered binary alloys change as the alloy temperature is raised by heating.

First-principles theoretical investigation of monoatomic and dimer Mn adsorption on noble metal (111) surfaces

NASA Astrophysics Data System (ADS)

Muñoz, Francisco; Romero, Aldo H.; Mejía-López, Jose; Morán-López, J. L.

2012-03-01

A theoretical investigation of the adsorption of Mn single atoms and dimers on the (111) surface of Cu, Ag, and Au, within the framework of the density functional theory, is presented. First, the bulk and the clean (111) surface electronic structures are calculated, with results that agree well with previous reports. To understand the adatom-substrate interaction, also the electronic characteristics of the free Mn dimer are determined. Then, the electronic structure of the Mn adatom, chemisorbed on four different surface geometries, is analyzed for the three noble metals. It is found that the most stable geometry, in all three cases, Cu, Ag, and Au, occurs when the Mn atom is chemisorbed on threefold coordinated sites. For the dimer, the lowest-energy configuration corresponds to the molecule lying parallel to the surface. In the three noble metals, the geometry corresponds to both atoms chemisorbed in threefold coordinated sites, but with different local symmetry. It is also found that the magnetic configuration with the lowest energy corresponds to the antiferromagnetic arrangement of Mn atoms, with individual magnetic moments close to 5μB. The ferromagnetic and antiferromagnetic solutions, in the case of a Ag substrate, are close in energy. It is also found that in this case the Mn2 molecule is chemisorbed with very similar energy on various geometries. To study the dynamical motion of the dimer components, we calculated the potential energy barriers for the Mn motion in the various surfaces. In contrast to Cu and Au, this leads to the conclusion that on Ag the Mn dimer moves relatively freely.

Spin texture induced by oxygen vacancies in strontium perovskite (001) surfaces: A theoretical comparison between SrTiO3 and SrHfO3

NASA Astrophysics Data System (ADS)

Garcia-Castro, A. C.; Vergniory, M. G.; Bousquet, E.; Romero, A. H.

2016-01-01

The electronic structure of SrTiO3 and SrHfO3 (001) surfaces with oxygen vacancies is studied by means of first-principles calculations. We reveal how oxygen vacancies within the first atomic layer of the SrTiO3 surface (i) induce a large antiferrodistortive motion of the oxygen octahedra at the surface, (ii) drive localized magnetic moments on the Ti 3 d orbitals close to the vacancies, and (iii) form a two-dimensional electron gas localized within the first layers. The analysis of the spin texture of this system exhibits a splitting of the energy bands according to the Zeeman interaction, lowering of the Ti 3 dx y level in comparison with dx z and dy z, and also an in-plane precession of the spins. No Rashba-like splitting for the ground state or for the ab initio molecular dynamics trajectory at 400 K is recognized as suggested recently by A. F. Santander-Syro et al. [Nat. Mater. 13, 1085 (2014), 10.1038/nmat4107]. Instead, a sizable Rashba-like splitting is observed when the Ti atom is replaced by a heavier Hf atom with a much larger spin-orbit interaction. However, we observe the disappearance of the magnetism and the surface two-dimensional electron gas when full structural optimization of the SrHfO3 surface is performed. Our results uncover the sensitive interplay of spin-orbit coupling, atomic relaxations, and magnetism when tuning these Sr-based perovskites.

The (2×2) reconstructions on the surface of cobalt silicides: Atomic configuration at the annealed Co/Si(111) interface

NASA Astrophysics Data System (ADS)

Kotlyar, V. G.; Alekseev, A. A.; Olyanich, D. A.; Utas, T. V.; Zotov, A. V.; Saranin, A. A.

2017-08-01

We have used scanning tunneling microscopy (STM) and ab initio total-energy calculations to characterize surface and interfacial structure of Co-Si(111) system. It has been found experimentally that two different types of the (2×2) surface structures occur. The coexistence of two phases is demonstrated by the example of STM image of the surface formed at the early stages of cobalt silicide formation under moderate annealing temperatures (500 °C). The measured height difference between the adjacent (2×2) reconstructed patches equal to about 1.0 Å (as determined from the filled-state STM images). In addition, the shift of the atomic rows by half of the row spacing is observed. Two adatom models of the (2×2) surface structures are developed. According to our data, these structures are assigned to CaF2-type CoSi2 and CsCl-type CoSi with a (2×2) array of Si adatoms on their surfaces. If the latter is the case, it has а coherent double interface CoSi/CoSi2/Si(111) with a two-layer CoSi2. Both of these interfaces are characterized by the eightfold cobalt coordination and incorporate a grown-in stacking fault.

Water structuring and collagen adsorption at hydrophilic and hydrophobic silicon surfaces.

PubMed

Cole, Daniel J; Payne, Mike C; Ciacchi, Lucio Colombi

2009-12-28

The adsorption of a collagen fragment on both a hydrophobic, hydrogen-terminated and a hydrophilic, natively oxidised Si surface is investigated using all-atom molecular dynamics. While favourable direct protein-surface interactions via localised contact points characterise adhesion to the hydrophilic surface, evenly spread surface/molecule contacts and stabilisation of the helical structure occurs upon adsorption on the hydrophobic surface. In the latter case, we find that adhesion is accompanied by a mutual fit between the hydrophilic/hydrophobic pattern within the protein and the layered water structure at the solid/liquid interface, which may provide an additional driving force to the classic hydrophobic effect.

Glassy nature and glass-to-crystal transition in the binary metallic glass CuZr

NASA Astrophysics Data System (ADS)

Wei, Zi-Yang; Shang, Cheng; Zhang, Xiao-Jie; Liu, Zhi-Pan

2017-06-01

The prediction for the stability of glassy material is a key challenge in physical science. Here, we report a theoretical framework to predict the glass stability based on stochastic surface walking global optimization and reaction pathway sampling. This is demonstrated by revealing for the first time the global potential energy surface (PES) of two systems, CuZr binary metallic glass and nonglassy pure Cu systems, and establishing the lowest energy pathways linking glassy/amorphous structures with crystalline structures. The CuZr system has a significant number of glassy structures on PES that are ˜0.045 eV /atom above the crystal structure. Two clear trends are identified from global PES in the glass-to-crystal transition of the CuZr system: (i) the local Zr-Cu coordination (nearest neighbor) increases, and (ii) the local Zr bonding environment becomes homogeneous. This allows us to introduce quantitative structural and energetics conditions to distinguish the glassy structures from the crystalline structures. Because of the local Zr-Cu exchange in the glass-to-crystal transition, a high reaction barrier (>0.048 eV /atom ) is present to separate the glassy structures and the crystals in CuZr. By contrast, the Cu system, although it does possess amorphous structures that appear at much higher energy (˜0.075 eV /atom ) with respect to the crystal structure, has very low reaction barriers for the crystallization of amorphous structures, i.e. <0.011 eV /atom . The quantitative data on PES now available from global optimization techniques deepens our understanding on the microscopic nature of glassy material and might eventually facilitate the design of stable glassy materials.

Atomic force microscope characterization of self-assembly behaviors of cyclo[8] pyrrole on solid substrates

NASA Astrophysics Data System (ADS)

Xu, Hai; Zhao, Siqi; Xiong, Xiang; Jiang, Jinzhi; Xu, Wei; Zhu, Daoben; Zhang, Yi; Liang, Wenjie; Cai, Jianfeng

2017-04-01

Cyclo [8] pyrrole (CP) is a porphyrin analogue containing eight α-conjugated pyrrole units which are arranged in a nearly coplanar conformation. The π-π interactions between CP molecules lead to regular aggregations through a solution casting process. Using tapping mode atomic force microscope (AFM), we investigated the morphology of self-assembled aggregates formed by deposition of different CP solutions on different substrates. We found that in the n-butanol solution, nanofibrous structures could be formed on the silicon or mica surface. Interestingly, on the highly oriented pyrolytic graphite (HOPG) surface, or silicon and mica surface with a toluene solution, only irregular spherical structures were identified. The difference in the nanomorphology may be attributed to distinct interactions between molecule-molecule, molecule-solvent and molecule-substrate.

Learning surface molecular structures via machine vision

DOE PAGES

Ziatdinov, Maxim; Maksov, Artem; Kalinin, Sergei V.

2017-08-10

Recent advances in high resolution scanning transmission electron and scanning probe microscopies have allowed researchers to perform measurements of materials structural parameters and functional properties in real space with a picometre precision. In many technologically relevant atomic and/or molecular systems, however, the information of interest is distributed spatially in a non-uniform manner and may have a complex multi-dimensional nature. One of the critical issues, therefore, lies in being able to accurately identify (‘read out’) all the individual building blocks in different atomic/molecular architectures, as well as more complex patterns that these blocks may form, on a scale of hundreds andmore » thousands of individual atomic/molecular units. Here we employ machine vision to read and recognize complex molecular assemblies on surfaces. Specifically, we combine Markov random field model and convolutional neural networks to classify structural and rotational states of all individual building blocks in molecular assembly on the metallic surface visualized in high-resolution scanning tunneling microscopy measurements. We show how the obtained full decoding of the system allows us to directly construct a pair density function—a centerpiece in analysis of disorder-property relationship paradigm—as well as to analyze spatial correlations between multiple order parameters at the nanoscale, and elucidate reaction pathway involving molecular conformation changes. Here, the method represents a significant shift in our way of analyzing atomic and/or molecular resolved microscopic images and can be applied to variety of other microscopic measurements of structural, electronic, and magnetic orders in different condensed matter systems.« less

Learning surface molecular structures via machine vision

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

Ziatdinov, Maxim; Maksov, Artem; Kalinin, Sergei V.

Recent advances in high resolution scanning transmission electron and scanning probe microscopies have allowed researchers to perform measurements of materials structural parameters and functional properties in real space with a picometre precision. In many technologically relevant atomic and/or molecular systems, however, the information of interest is distributed spatially in a non-uniform manner and may have a complex multi-dimensional nature. One of the critical issues, therefore, lies in being able to accurately identify (‘read out’) all the individual building blocks in different atomic/molecular architectures, as well as more complex patterns that these blocks may form, on a scale of hundreds andmore » thousands of individual atomic/molecular units. Here we employ machine vision to read and recognize complex molecular assemblies on surfaces. Specifically, we combine Markov random field model and convolutional neural networks to classify structural and rotational states of all individual building blocks in molecular assembly on the metallic surface visualized in high-resolution scanning tunneling microscopy measurements. We show how the obtained full decoding of the system allows us to directly construct a pair density function—a centerpiece in analysis of disorder-property relationship paradigm—as well as to analyze spatial correlations between multiple order parameters at the nanoscale, and elucidate reaction pathway involving molecular conformation changes. Here, the method represents a significant shift in our way of analyzing atomic and/or molecular resolved microscopic images and can be applied to variety of other microscopic measurements of structural, electronic, and magnetic orders in different condensed matter systems.« less

Direct evidence of atomic-scale structural fluctuations in catalyst nanoparticles.

PubMed

Lin, Pin Ann; Gomez-Ballesteros, Jose L; Burgos, Juan C; Balbuena, Perla B; Natarajan, Bharath; Sharma, Renu

2017-05-01

Rational catalyst design requires an atomic scale mechanistic understanding of the chemical pathways involved in the catalytic process. A heterogeneous catalyst typically works by adsorbing reactants onto its surface, where the energies for specific bonds to dissociate and/or combine with other species (to form desired intermediate or final products) are lower. Here, using the catalytic growth of single-walled carbon nanotubes (SWCNTs) as a prototype reaction, we show that the chemical pathway may in-fact involve the entire catalyst particle, and can proceed via the fluctuations in the formation and decomposition of metastable phases in the particle interior. We record in situ and at atomic resolution, the dynamic phase transformations occurring in a Cobalt catalyst nanoparticle during SWCNT growth, using a state-of-the-art environmental transmission electron microscope (ETEM). The fluctuations in catalyst carbon content are quantified by the automated, atomic-scale structural analysis of the time-resolved ETEM images and correlated with the SWCNT growth rate. We find the fluctuations in the carbon concentration in the catalyst nanoparticle and the fluctuations in nanotube growth rates to be of complementary character. These findings are successfully explained by reactive molecular dynamics (RMD) simulations that track the spatial and temporal evolution of the distribution of carbon atoms within and on the surface of the catalyst particle. We anticipate that our approach combining real-time, atomic-resolution image analysis and molecular dynamics simulations will facilitate catalyst design, improving reaction efficiencies and selectivity towards the growth of desired structure.

Optimization of Neutral Atom Imagers

NASA Technical Reports Server (NTRS)

Shappirio, M.; Coplan, M.; Balsamo, E.; Chornay, D.; Collier, M.; Hughes, P.; Keller, J.; Ogilvie, K.; Williams, E.

2008-01-01

The interactions between plasma structures and neutral atom populations in interplanetary space can be effectively studied with energetic neutral atom imagers. For neutral atoms with energies less than 1 keV, the most efficient detection method that preserves direction and energy information is conversion to negative ions on surfaces. We have examined a variety of surface materials and conversion geometries in order to identify the factors that determine conversion efficiency. For chemically and physically stable surfaces smoothness is of primary importance while properties such as work function have no obvious correlation to conversion efficiency. For the noble metals, tungsten, silicon, and graphite with comparable smoothness, conversion efficiency varies by a factor of two to three. We have also examined the way in which surface conversion efficiency varies with the angle of incidence of the neutral atom and have found that the highest efficiencies are obtained at angles of incidence greater then 80deg. The conversion efficiency of silicon, tungsten and graphite were examined most closely and the energy dependent variation of conversion efficiency measured over a range of incident angles. We have also developed methods for micromachining silicon in order to reduce the volume to surface area over that of a single flat surface and have been able to reduce volume to surface area ratios by up to a factor of 60. With smooth micro-machined surfaces of the optimum geometry, conversion efficiencies can be increased by an order of magnitude over instruments like LENA on the IMAGE spacecraft without increase the instruments mass or volume.

Molecular dynamics studies of interfacial water at the alumina surface.

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

Argyris, Dr. Dimitrios; Ho, Thomas; Cole, David

2011-01-01

Interfacial water properties at the alumina surface were investigated via all-atom equilibrium molecular dynamics simulations at ambient temperature. Al-terminated and OH-terminated alumina surfaces were considered to assess the structural and dynamic behavior of the first few hydration layers in contact with the substrates. Density profiles suggest water layering up to {approx}10 {angstrom} from the solid substrate. Planar density distribution data indicate that water molecules in the first interfacial layer are organized in well-defined patterns dictated by the atomic terminations of the alumina surface. Interfacial water exhibits preferential orientation and delayed dynamics compared to bulk water. Water exhibits bulk-like behavior atmore » distances greater than {approx}10 {angstrom} from the substrate. The formation of an extended hydrogen bond network within the first few hydration layers illustrates the significance of water?water interactions on the structural properties at the interface.« less

Sequence-Dependent Structure/Function Relationships of Catalytic Peptide-Enabled Gold Nanoparticles Generated under Ambient Synthetic Conditions

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

Bedford, Nicholas M.; Hughes, Zak E.; Tang, Zhenghua

Peptide-enabled nanoparticle (NP) synthesis routes can create and/or assemble functional nanomaterials under environmentally friendly conditions, with properties dictated by complex interactions at the biotic/abiotic interface. Manipulation of this interface through sequence modification can provide the capability for material properties to be tailored to create enhanced materials for energy, catalysis, and sensing applications. Fully realizing the potential of these materials requires a comprehensive understanding of sequence-dependent structure/function relationships that is presently lacking. In this work, the atomic-scale structures of a series of peptide-capped Au NPs are determined using a combination of atomic pair distribution function analysis of high-energy X-ray diffraction datamore » and advanced molecular dynamics (MD) simulations. The Au NPs produced with different peptide sequences exhibit varying degrees of catalytic activity for the exemplar reaction 4-nitrophenol reduction. The experimentally derived atomic-scale NP configurations reveal sequence-dependent differences in structural order at the NP surface. Replica exchange with solute-tempering MD simulations are then used to predict the morphology of the peptide overlayer on these Au NPs and identify factors determining the structure/catalytic properties relationship. We show that the amount of exposed Au surface, the underlying surface structural disorder, and the interaction strength of the peptide with the Au surface all influence catalytic performance. A simplified computational prediction of catalytic performance is developed that can potentially serve as a screening tool for future studies. Our approach provides a platform for broadening the analysis of catalytic peptide-enabled metallic NP systems, potentially allowing for the development of rational design rules for property enhancement.« less

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….

On the surface trapping parameters of polytetrafluoroethylene block

NASA Astrophysics Data System (ADS)

Zhang, Guan-Jun; Yang, Kai; Zhao, Wen-Bin; Yan, Zhang

2006-12-01

Surface flashover phenomena under high electric field are closely related to the surface characteristics of a solid insulating material between energized electrodes. Based on measuring the surface potential decaying curve of polytetrafluoroethylene (PTFE) block charged by a needle-plane corona discharge, its surface trapping parameters are calculated with the isothermal current theory, and the correlative curve between the surface trap density and its energy level is obtained. The maximum density of electron traps and hole traps in the surface layer of PTFE presents a similar value of ∼2.7 × 1017 eV-1 m-3, and the energy level of its electron and hole traps is of about 0.85-1.0 eV and 0.80-0.90 eV, respectively. Via the X-ray photoelectron spectroscopy (XPS) technique, the F, C, K and O elements are detected on the surface of PTFE samples, and F shows a remarkable atom proportion of ∼73.3%, quite different from the intrinsic distribution corresponding to its chemical formula. The electron traps are attributed to quantities of F atoms existing on the surface of PTFE due to its molecular chain with C atoms surrounded by F atoms spirally. It is considered that the distortions of chemical and electronic structure on solid surface are responsible for the flashover phenomena occurring at a low applied voltage.

Bulk-surface relationship of an electronic structure for high-throughput screening of metal oxide catalysts

NASA Astrophysics Data System (ADS)

Kweun, Joshua Minwoo; Li, Chenzhe; Zheng, Yongping; Cho, Maenghyo; Kim, Yoon Young; Cho, Kyeongjae

2016-05-01

Designing metal-oxides consisting of earth-abundant elements has been a crucial issue to replace precious metal catalysts. To achieve efficient screening of metal-oxide catalysts via bulk descriptors rather than surface descriptors, we investigated the relationship between the electronic structure of bulk and that of the surface for lanthanum-based perovskite oxides, LaMO3 (M = Ti, V, Cr, Mn, Fe, Co, Ni, Cu). Through density functional theory calculations, we examined the d-band occupancy of the bulk and surface transition-metal atoms (nBulk and nSurf) and the adsorption energy of an oxygen atom (Eads) on (001), (110), and (111) surfaces. For the (001) surface, we observed strong correlation between the nBulk and nSurf with an R-squared value over 94%, and the result was interpreted in terms of ligand field splitting and antibonding/bonding level splitting. Moreover, the Eads on the surfaces was highly correlated with the nBulk with an R-squared value of more than 94%, and different surface relaxations could be explained by the bulk electronic structure (e.g., LaMnO3 vs. LaTiO3). These results suggest that a bulk-derived descriptor such as nBulk can be used to screen metal-oxide catalysts.

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

PubMed

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

2015-05-01

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

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

NASA Astrophysics Data System (ADS)

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

2018-06-01

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

Self-organization of S adatoms on Au(111): √3R30° rows at low coverage

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

Walen, Holly; Liu, Da -Jiang; Oh, Junepyo

Using scanning tunneling microscopy, we observe an adlayer structure that is dominated by short rows of S atoms, on unreconstructed regions of a Au(111) surface. This structure forms upon adsorption of low S coverage (less than 0.1 monolayer) on a fully reconstructed cleansurface at 300 K, then cooling to 5 K for observation. The rows adopt one of three orientations that are rotated by 30° from the close-packed directions of the Au(111) substrate, and adjacent S atoms in the rows are separated by √3 times the surface lattice constant, a. Monte Carlo simulations are performed on lattice-gas models, we derivedmore » using a limited cluster expansion based on density functional theory energetics. Furthermore, models which include long-range pairwise interactions (extending to 5a), plus selected trio interactions, successfully reproduce the linear rows of S atoms at reasonable temperatures.« less

Self-organization of S adatoms on Au(111): √3R30° rows at low coverage

DOE PAGES

Walen, Holly; Liu, Da -Jiang; Oh, Junepyo; ...

2015-07-06

Using scanning tunneling microscopy, we observe an adlayer structure that is dominated by short rows of S atoms, on unreconstructed regions of a Au(111) surface. This structure forms upon adsorption of low S coverage (less than 0.1 monolayer) on a fully reconstructed cleansurface at 300 K, then cooling to 5 K for observation. The rows adopt one of three orientations that are rotated by 30° from the close-packed directions of the Au(111) substrate, and adjacent S atoms in the rows are separated by √3 times the surface lattice constant, a. Monte Carlo simulations are performed on lattice-gas models, we derivedmore » using a limited cluster expansion based on density functional theory energetics. Furthermore, models which include long-range pairwise interactions (extending to 5a), plus selected trio interactions, successfully reproduce the linear rows of S atoms at reasonable temperatures.« less

Chiral Asymmetric Structures in Aspartic Acid and Valine Crystals Assessed by Atomic Force Microscopy.

PubMed

Teschke, Omar; Soares, David Mendez

2016-03-29

Structures of crystallized deposits formed by the molecular self-assembly of aspartic acid and valine on silicon substrates were imaged by atomic force microscopy. Images of d- and l-aspartic acid crystal surfaces showing extended molecularly flat sheets or regions separated by single molecule thick steps are presented. Distinct orientation surfaces were imaged, which, combined with the single molecule step size, defines the geometry of the crystal. However, single molecule step growth also reveals the crystal chirality, i.e., growth orientations. The imaged ordered lattice of aspartic acid (asp) and valine (val) mostly revealed periodicities corresponding to bulk terminations, but a previously unreported molecular hexagonal lattice configuration was observed for both l-asp and l-val but not for d-asp or d-val. Atomic force microscopy can then be used to identify the different chiral forms of aspartic acid and valine crystals.

Oxide surfaces in practical and model catalytic systems

NASA Astrophysics Data System (ADS)

Lanier, Courtney H.

Oxide surface structures play a key role in many technological processes, including catalysis, thin film growth, and layered structures, and a thorough understanding of surface structures and surface structure dynamics is required in order to better engineer materials systems for these processes. This research works towards understanding these fundamental principles through an investigation of practical and model catalytic systems. In this work, the surface structures and dynamics of Mg3(VO4)2, LaAlO3, SrTiO3, and alpha-Fe2O3/Fe3O 4 are investigated under a variety of conditions and by a range of experimental and computational techniques. The structure and morphology of LaAlO3 has been investigated over a range of annealing temperatures, and the ( 5x5 )R26.6° reconstruction of LaAlO3 (001) has been determined using transmission electron diffraction combined with direct methods. The structure is relatively simple, consisting of a lanthanum oxide termination with one lanthanum cation vacancy per surface unit cell. The electronic structure is unusual since a fractional number of holes or atomic occupancies per surface unit cell are required to achieve charge neutrality. The reconstruction can be understood in terms of expulsion of the more electropositive cation from the surface followed by an increased covalency between the remaining surface lanthanum atoms and adjacent oxygen atoms. The c(6x2) is a reconstruction of the SrTiO3 (001) surface that is formed between 1050-1100°C in oxidizing annealing conditions. This work proposes a model for the atomic structure for the c(6x2) obtained through a combination of results from transmission electron diffraction, surface x-ray diffraction, direct methods analysis, computational combinational screening, and density functional theory. As it is formed at high temperatures, the surface is complex and can be described as a short-range ordered phase featuring microscopic domains composed of four main structural motifs. Additionally, non-periodic TiO2 units are present on the surface. The surface and bulk of oriented single crystal Mg3(VO 4)2 have been characterized after treatment in a reducing environment. Annealing in a flow of 7% H2 in N2 causes the reduction of Mg3(VO4)2 to Mg3V 2O6, which is shown to be single-crystal to single-crystal and occurs in such a way that the oxygen framework of the crystal is preserved. Transmission electron microscopy images of crystals at the early stages of reduction show low angle grain boundaries and the formation of channels approximately 50nm in diameter. A model for reduction of Mg3(VO4) 2 to Mg3V2O6 based on the experimental observations and derived from classic nucleation theory is proposed. The so-called Biphase structure on alpha-Fe2O3 has been previously reported and described as islands of Fe1-xO and alpha-Fe2O3 arranged in a 40A periodic unit cell. Based on thermodynamic arguments and experimental evidence, including transmission electron diffraction, we find that the previous structure model was incorrect. Rather, it is found that the Biphase structure is, in fact, related to the reduction of alpha-Fe2O3 to Fe 3O4, is a layered structure, and does not contain islands of Fe1-xO. A model for the Biphase termination consisting of bulk alpha-Fe 2O3 with an Fe3O4 -derived overlayer is developed and is consistent with all current and previously reported experimental findings.

Atomistic Method Applied to Computational Modeling of Surface Alloys

NASA Technical Reports Server (NTRS)

Bozzolo, Guillermo H.; Abel, Phillip B.

2000-01-01

The formation of surface alloys is a growing research field that, in terms of the surface structure of multicomponent systems, defines the frontier both for experimental and theoretical techniques. Because of the impact that the formation of surface alloys has on surface properties, researchers need reliable methods to predict new surface alloys and to help interpret unknown structures. The structure of surface alloys and when, and even if, they form are largely unpredictable from the known properties of the participating elements. No unified theory or model to date can infer surface alloy structures from the constituents properties or their bulk alloy characteristics. In spite of these severe limitations, a growing catalogue of such systems has been developed during the last decade, and only recently are global theories being advanced to fully understand the phenomenon. None of the methods used in other areas of surface science can properly model even the already known cases. Aware of these limitations, the Computational Materials Group at the NASA Glenn Research Center at Lewis Field has developed a useful, computationally economical, and physically sound methodology to enable the systematic study of surface alloy formation in metals. This tool has been tested successfully on several known systems for which hard experimental evidence exists and has been used to predict ternary surface alloy formation (results to be published: Garces, J.E.; Bozzolo, G.; and Mosca, H.: Atomistic Modeling of Pd/Cu(100) Surface Alloy Formation. Surf. Sci., 2000 (in press); Mosca, H.; Garces J.E.; and Bozzolo, G.: Surface Ternary Alloys of (Cu,Au)/Ni(110). (Accepted for publication in Surf. Sci., 2000.); and Garces, J.E.; Bozzolo, G.; Mosca, H.; and Abel, P.: A New Approach for Atomistic Modeling of Pd/Cu(110) Surface Alloy Formation. (Submitted to Appl. Surf. Sci.)). Ternary alloy formation is a field yet to be fully explored experimentally. The computational tool, which is based on the BFS (Bozzolo, Ferrante, and Smith) method for the calculation of the energetics, consists of a small number of simple PCbased computer codes that deal with the different aspects of surface alloy formation. Two analysis modes are available within this package. The first mode provides an atom-by-atom description of real and virtual stages 1. during the process of surface alloying, based on the construction of catalogues of configurations where each configuration describes one possible atomic distribution. BFS analysis of this catalogue provides information on accessible states, possible ordering patterns, and details of island formation or film growth. More importantly, it provides insight into the evolution of the system. Software developed by the Computational Materials Group allows for the study of an arbitrary number of elements forming surface alloys, including an arbitrary number of surface atomic layers. The second mode involves large-scale temperature-dependent computer 2. simulations that use the BFS method for the energetics and provide information on the dynamic processes during surface alloying. These simulations require the implementation of Monte-Carlo-based codes with high efficiency within current workstation environments. This methodology capitalizes on the advantages of the BFS method: there are no restrictions on the number or type of elements or on the type of crystallographic structure considered. This removes any restrictions in the definition of the configuration catalogues used in the analytical calculations, thus allowing for the study of arbitrary ordering patterns, ultimately leading to the actual surface alloy structure. Moreover, the Monte Carlo numerical technique used for the large-scale simulations allows for a detailed visualization of the simulated process, the main advantage of this type of analysis being the ability to understand the underlying features that drive these processes. Because of the simplicity of the BFS method for e energetics used in these calculations, a detailed atom-by-atom analysis can be performed at any point in the simulation, providing necessary insight on the details of the process. The main objective of this research program is to develop a tool to guide experimenters in understanding and interpreting often unexpected results in alloy formation experiments. By reducing the computational effort without losing physical accuracy, we expect that powerful simulation tools will be developed in the immediate future, which will allow material scientists to easily visualize and analyze processes at a level not achievable experimentally.

Growth and characterization of epitaxial silver indium diselenide

NASA Astrophysics Data System (ADS)

Pena Martin, Pamela

Photovoltaics (solar cells) are a key player in the renewable energy frontier, and will become increasingly important as their cost per watt continues to drop, especially if fossil fuel costs increase. One particularly promising photovoltaic technology is based on chalcopyrite-structure semiconductors. Within the chalcopyrite compounds the highest efficiency thin film solar cell absorber material to date is Cu(In,Ga)Se2 (CIGS). While current efficiency records are over 21% for single-junction cells, there is still room for improvement. Replacing some of the Cu with Ag has been shown to be beneficial in CIGS devices. However, the Ag- containing chalcopyrites are still relatively unknown in terms of their growth mechanism, energetics, and surface atomic and electronic properties. These are best inferred through study of epitaxial films, yet they have little mention in literature and have not been the subject of a detailed study. This work describes the growth of epitaxial AgInSe2 (AIS) on GaAs substrates, studying the morphology, structure, and surface properties to understand how growth takes place. It also seeks to experimentally determine the surface electronic and atomic structure at the atomic scale to gain insight into the part of the material that forms the heterojunction that collects photon energy in the device. Finally, this work seeks to compare and contrast these findings with what is known about CIGS to determine where similarities and, more importantly, the differences may lie. This study has found that single phase tetragonal AIS can be epitaxially grown on GaAs, as illustrated by x-ray diffraction (XRD), transmission electron microscope (TEM), and surface morphology data. Like CIGS, the close packed polar (112) planes have the lowest energy. The morphology points to a difference in step dynamics, leading to less faceted, straight edged island shapes compared to CIGS. Epitaxial temperature as a function of growth direction shows a different trend in AIS than in CIGS. Interdiffusion of the group III elements across the substrate interface was found to result in an epitaxial intermixed layer between the film and substrate in some cases, which may help mediate the lattice mismatch. At the atomic scale, scanning tunneling microscopy (STM) was used to observe details of the surface morphology, which indicated growth of the (112)A orientation of AIS by a screw dislocation mechanism (other surfaces were not examined by STM but are expected to show similar results). The surface atomic structure was directly imaged for the first time, revealing an arrangement similar to that expected from a bulk terminated surface. The electronic structure shows a gap in surface electronic states with a width comparable to bulk AIS, n-type conduction, and a tail of states near the valence band edge that decay well into the gap. The conduction and valence bands show fluctuations as a function of position on the surface, with greater magnitude in the valence band. The fluctuations in both bands are less than those observed on the surface of CIS by STM. It seems to indicate a reduction in band tails, both in magnitude and spacial extent, in AIS compared to CIS, likely tied to a reduction in point defect concentration at the surface.

Prenucleation Induced by Crystalline Substrates

NASA Astrophysics Data System (ADS)

Men, H.; Fan, Z.

2018-04-01

Prenucleation refers to the phenomenon of atomic ordering in the liquid adjacent to the substrate/liquid interface at temperatures above the liquidus. In this paper, we have systematically investigated and holistically quantified the prenucleation phenomenon as a function of temperature and the lattice misfit between the substrate and the solid, using molecular dynamics (MD) simulations. Our results have confirmed that at temperatures above the liquidus, the atoms in the liquid at the interface may exhibit pronounced atomic ordering, manifested by atomic layering normal to the interface, in-plane atomic ordering parallel to the interface, and the formation of a 2-dimensional (2D) ordered structure (a few atomic layers in thickness) on the substrate surface. Holistic quantification of such atomic ordering at the interface has revealed that the atomic layering is independent of lattice misfit and is only slightly enhanced by reducing temperature while both in-plane atomic ordering and the formation of the 2D ordered structure are significantly enhanced by reducing the lattice misfit and/or temperature. This substrate-induced atomic ordering in the liquid may have a significant influence on the subsequent heterogeneous nucleation process.

The birth and evolution of surface science: child of the union of science and technology.

PubMed

Duke, C B

2003-04-01

This article is an account of the birth and evolution of surface science as an interdisciplinary research area. Surface science emanated from the confluence of concepts and tools in physics and chemistry with technological innovations that made it possible to determine the structure and properties of surfaces and interfaces and the dynamics of chemical reactions at surfaces. The combination in the 1960s and 1970s of ultra-high-vacuum (i.e., P < 10(-7) Pascal or 10(-9) Torr) technology with the recognition that electrons in the energy range from 50 to 500 eV exhibited inelastic collision mean free paths of the order of a few angstroms fostered an explosion of activity. The results were a reformulation of the theory of electron solid scattering, the nearly universal use of electron spectroscopies for surface characterization, the rise of surface science as an independent interdisciplinary research area, and the emergence of the American Vacuum Society (AVS) as a major international scientific society. The rise of microelectronics in the 1970s and 1980s resulted in huge increases in computational power. These increases enabled more complex experiments and the utilization of density functional theory for the quantitative prediction of surface structure and dynamics. Development of scanning-probe microscopies in the 1990s led to atomic-resolution images of macroscopic surfaces and interfaces as well as videos of atoms moving about on surfaces during growth and diffusion. Scanning probes have since brought solid-liquid interfaces into the realm of atomic-level surface science, expanding its scope to more complex systems, including fragile biological materials and processes.

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.

Stability and band offsets between c-plane ZnO semiconductor and LaAlO3 gate dielectric

NASA Astrophysics Data System (ADS)

Wang, Jianli; Chen, Xinfeng; Wu, Shuyin; Tang, Gang; Zhang, Junting; Stampfl, C.

2018-03-01

Wurtzite-perovskite heterostructures composed of a high dielectric constant oxide and a wide bandgap semiconductor envision promising applications in field-effect transistors. In the present paper, the structural and electronic properties of LaAlO3/ZnO heterojunctions are investigated by first-principles calculations. We study the initial adsorption of La, Al, and oxygen atoms on ZnO (0001) and (000 1 ¯ ) surfaces and find that La atoms may occupy interstitial sites during the growth of stoichiometric ZnO (0001). The band gap of the stoichiometric ZnO (0001) surface is smaller than that of the stoichiometric ZnO (000 1 ¯ ) surface. The surface formation energy indicates that La or Al atoms may substitute Zn atoms at the nonstoichiometric ZnO (0001) surface. The atomic charges, electronic density of states, and band offsets are analyzed for the optimized LaAlO3/ZnO heterojunctions. There is a band gap for the LaAlO3/ZnO (000 1 ¯ ) heterostructures, and the largest variation in charge occurs at the surface or interface. Our results suggest that the Al-terminated LaAlO3/ZnO (000 1 ¯ ) interfaces are suitable for the design of metal oxide semiconductor devices because the valence and conduction band offsets are both larger than 1 eV and the interface does not produce any in-gap states.

A Hybrid Density Functional Study of Atomic Hydrogen and Oxygen Adsorptions on the (0001) Surface of Non-Magnetic DHCP Americium

NASA Astrophysics Data System (ADS)

Amdani-Moten, Shafaq; Atta-Fynn, Raymond; Ray, Asok

2010-03-01

As our group have recently shown^+, hybrid density functional theory (HDFT) which replaces a fraction (40%) of approximate DFT exchange with exact Hartree-Fock exchange yield structural, magnetic, and electronic properties for Americium-I that are in excellent agreement with experimental data. As a natural progression, ab initio calculations for atomic adsorptions on the (0001) surface of non-magnetic americium have been performed using HDFT. The americium surface is modeled by a seven-layer slab using inversion symmetry consisting of one atom per layer and non-magnetic ABAC stacking arrangement of these layers. Top, bridge, hcp and fcc chemisorption sites have been investigated with energies optimized with respect to the adatom distance from the surface. Details of the chemisorptions processes as well as comparisons of different sites will be presented. ^+ R. Atta-Fynn and A. K. Ray, Chemical Physics Letters, 482, 223-227 (2009).

Probing the Surface Charge on the Basal Planes of Kaolinite Particles with High-Resolution Atomic Force Microscopy

PubMed Central

2017-01-01

High-resolution atomic force microscopy is used to map the surface charge on the basal planes of kaolinite nanoparticles in an ambient solution of variable pH and NaCl or CaCl2 concentration. Using DLVO theory with charge regulation, we determine from the measured force–distance curves the surface charge distribution on both the silica-like and the gibbsite-like basal plane of the kaolinite particles. We observe that both basal planes do carry charge that varies with pH and salt concentration. The silica facet was found to be negatively charged at pH 4 and above, whereas the gibbsite facet is positively charged at pH below 7 and negatively charged at pH above 7. Investigations in CaCl2 at pH 6 show that the surface charge on the gibbsite facet increases for concentration up to 10 mM CaCl2 and starts to decrease upon further increasing the salt concentration to 50 mM. The increase of surface charge at low concentration is explained by Ca2+ ion adsorption, while Cl– adsorption at higher CaCl2 concentrations partially neutralizes the surface charge. Atomic resolution imaging and density functional theory calculations corroborate these observations. They show that hydrated Ca2+ ions can spontaneously adsorb on the gibbsite facet of the kaolinite particle and form ordered surface structures, while at higher concentrations Cl– ions will co-adsorb, thereby changing the observed ordered surface structure. PMID:29140711

Probing the Surface Charge on the Basal Planes of Kaolinite Particles with High-Resolution Atomic Force Microscopy.

PubMed

Kumar, N; Andersson, M P; van den Ende, D; Mugele, F; Siretanu, I

2017-12-19

High-resolution atomic force microscopy is used to map the surface charge on the basal planes of kaolinite nanoparticles in an ambient solution of variable pH and NaCl or CaCl 2 concentration. Using DLVO theory with charge regulation, we determine from the measured force-distance curves the surface charge distribution on both the silica-like and the gibbsite-like basal plane of the kaolinite particles. We observe that both basal planes do carry charge that varies with pH and salt concentration. The silica facet was found to be negatively charged at pH 4 and above, whereas the gibbsite facet is positively charged at pH below 7 and negatively charged at pH above 7. Investigations in CaCl 2 at pH 6 show that the surface charge on the gibbsite facet increases for concentration up to 10 mM CaCl 2 and starts to decrease upon further increasing the salt concentration to 50 mM. The increase of surface charge at low concentration is explained by Ca 2+ ion adsorption, while Cl - adsorption at higher CaCl 2 concentrations partially neutralizes the surface charge. Atomic resolution imaging and density functional theory calculations corroborate these observations. They show that hydrated Ca 2+ ions can spontaneously adsorb on the gibbsite facet of the kaolinite particle and form ordered surface structures, while at higher concentrations Cl - ions will co-adsorb, thereby changing the observed ordered surface structure.

Multi-walled carbon nanotube structural instability with/without metal nanoparticles under electron beam irradiation

NASA Astrophysics Data System (ADS)

Khan, Imran; Huang, Shengli; Wu, Chenxu

2017-12-01

The structural transformation of multi-walled carbon nanotubes (MWCNT) under electron beam (e-beam) irradiation at room temperature is studied, with respect to a novel passivation effect due to gold nanoparticles (Au NPs). MWCNT structural evolution induced by energetic e-beam irradiation leads to faster shrinkage, as revealed via in situ transmission electron microscopy, while MWCNT surface modification with Au NPs (Au-MWCNT) slows down the shrinkage by impeding the structural evolution process for a prolonged time under the same irradiation conditions. The new relationship between MWCNT and Au-MWCNT shrinking radii and irradiation time illustrates that the MWCNT shrinkage rate is faster than either theoretical predictions or the same process in Au-MWCNTs. As compared with the outer surface energy (positive curvature), the inner surface energy (negative curvature) of the MWCNT contributes more to the athermal evaporation of tube wall atoms, leading to structural instability and shrinkage under e-beam irradiation. Conversely, Au NPs possess only outer surface energy (positive curvature) compared with the MWCNT. Their presence on MWCNT surfaces retards the dynamics of MWCNT structural evolution by slowing down the evaporation process of carbon atoms, thus restricting Au-MWCNT shrinkage. Au NP interaction and growth evolves athermally on MWCNT surfaces, exhibits increase in their size, and indicates the association of this mechanism with the coalescence induced by e-beam activated electronic excitations. Despite their growth, Au NPs show extreme structural stability, and remain crystalline under prolonged irradiation. It is proposed that the surface energy of MWCNTs and Au NPs, together with e-beam activated soft modes or lattice instability effects, predominantly govern all the above varieties of structural evolution.

Microstructure, tribological and strength properties of the surface layer in metal-ceramic composite nano-structured by electron irradiation

NASA Astrophysics Data System (ADS)

Ovcharenko, V. E.; Ivanov, K. V.; Mokhovikov, A. A.

2017-12-01

Exemplified by metal-ceramic composite TiC-(Ni-Cr) with the ratio of components 50:50, the paper presents findings of the study on patterns of nanoscale structural-phase state formation in the surface layer of the composite under pulsed electron irradiation in inert gas plasmas with different ionization energies and atomic weights and their influence on tribological and strength properties of the surface layer.

In Situ Structural Studies of the Underpotential Deposition of Copper onto an Iodine Covered Platinum Surface Using X-Ray Standing Waves

DTIC Science & Technology

1991-01-01

electrocrystallization, catalysis, and surface chemistry. In this process, submonolayer to monolayer(s) amounts of a metal can be electrodeposited on a foreign...mechanisms involving nucleation and growth processes. Although electrochemical methods are invaluable in controlling and measuring thermodynamic...obtain direct atomic structural information about metal deposits on an iodine covered Pt(IIl) surface . They found that electrodeposition occurred in a

Electronic and mechanical properties of graphene-germanium interfaces grown by chemical vapor deposition

DOE PAGES

Kiraly, Brian T.; Jacobberger, Robert M.; Mannix, Andrew J.; ...

2015-10-27

Epitaxially oriented wafer-scale graphene grown directly on semiconducting Ge substrates is of high interest for both fundamental science and electronic device applications. To date, however, this material system remains relatively unexplored structurally and electronically, particularly at the atomic scale. To further understand the nature of the interface between graphene and Ge, we utilize ultrahigh vacuum scanning tunneling microscopy (STM) and scanning tunneling spectroscopy (STS) along with Raman and X-ray photoelectron spectroscopy to probe interfacial atomic structure and chemistry. STS reveals significant differences in electronic interactions between graphene and Ge(110)/Ge(111), which is consistent with a model of stronger interaction on Ge(110)more » leading to epitaxial growth. Raman spectra indicate that the graphene is considerably strained after growth, with more point-to-point variation on Ge(111). Furthermore, this native strain influences the atomic structure of the interface by inducing metastable and previously unobserved Ge surface reconstructions following annealing. These nonequilibrium reconstructions cover >90% of the surface and, in turn, modify both the electronic and mechanical properties of the graphene overlayer. Finally, graphene on Ge(001) represents the extreme strain case, where graphene drives the reorganization of the Ge surface into [107] facets. From this study, it is clear that the interaction between graphene and the underlying Ge is not only dependent on the substrate crystallographic orientation, but is also tunable and strongly related to the atomic reconfiguration of the graphene–Ge interface.« less

Application of Powder Diffraction Methods to the Analysis of Short- and Long-Range Atomic Order in Nanocrystalline Diamond and SiC: The Concept of the Apparent Lattice Parameter (alp)

NASA Technical Reports Server (NTRS)

Palosz, B.; Grzanka, E.; Gierlotka, S.; Stelmakh, S.; Pielaszek, R.; Bismayer, U.; Weber, H.-P.; Palosz, W.

2003-01-01

Two methods of the analysis of powder diffraction patterns of diamond and SiC nanocrystals are presented: (a) examination of changes of the lattice parameters with diffraction vector Q ('apparent lattice parameter', alp) which refers to Bragg scattering, and (b), examination of changes of inter-atomic distances based on the analysis of the atomic Pair Distribution Function, PDF. Application of these methods was studied based on the theoretical diffraction patterns computed for models of nanocrystals having (i) a perfect crystal lattice, and (ii), a core-shell structure, i.e. constituting a two-phase system. The models are defined by the lattice parameter of the grain core, thickness of the surface shell, and the magnitude and distribution of the strain field in the shell. X-ray and neutron experimental diffraction data of nanocrystalline SiC and diamond powders of the grain diameter from 4 nm up to micrometers were used. The effects of the internal pressure and strain at the grain surface on the structure are discussed based on the experimentally determined dependence of the alp values on the Q-vector, and changes of the interatomic distances with the grain size determined experimentally by the atomic Pair Distribution Function (PDF) analysis. The experimental results lend a strong support to the concept of a two-phase, core and the surface shell structure of nanocrystalline diamond and SiC.

Atomic force microscopic imaging of Acanthamoeba castellanii and Balamuthia mandrillaris trophozoites and cysts.

PubMed

Aqeel, Yousuf; Siddiqui, Ruqaiyyah; Ateeq, Muhammad; Raza Shah, Muhammad; Kulsoom, Huma; Khan, Naveed Ahmed

2015-01-01

Light microscopy and electron microscopy have been successfully used in the study of microbes, as well as free-living protists. Unlike light microscopy, which enables us to observe living organisms or the electron microscope which provides a two-dimensional image, atomic force microscopy provides a three-dimensional surface profile. Here, we observed two free-living amoebae, Acanthamoeba castellanii and Balamuthia mandrillaris under the phase contrast inverted microscope, transmission electron microscope and atomic force microscope. Although light microscopy was of lower magnification, it revealed functional biology of live amoebae such as motility and osmoregulation using contractile vacuoles of the trophozoite stage, but it is of limited value in defining the cyst stage. In contrast, transmission electron microscopy showed significantly greater magnification and resolution to reveal the ultra-structural features of trophozoites and cysts including intracellular organelles and cyst wall characteristics but it only produced a snapshot in time of a dead amoeba cell. Atomic force microscopy produced three-dimensional images providing detailed topographic description of shape and surface, phase imaging measuring boundary stiffness, and amplitude measurements including width, height and length of A. castellanii and B. mandrillaris trophozoites and cysts. These results demonstrate the importance of the application of various microscopic methods in the biological and structural characterization of the whole cell, ultra-structural features, as well as surface components and cytoskeleton of protist pathogens. © 2014 The Author(s) Journal of Eukaryotic Microbiology © 2014 International Society of Protistologists.

Structure and Formation Mechanism of Black TiO 2 Nanoparticles

DOE PAGES

Tian, Mengkun; Mahjouri-Samani, Masoud; Eres, Gyula; ...

2015-10-27

The remarkable properties of black TiO 2 are due to its disordered surface shell surrounding a crystalline core. However, the chemical composition and the atomic and electronic structure of the disordered shell and its relationship to the core remain poorly understood. Using advanced transmission electron microscopy methods, we show that the outermost layer of black TiO 2 nanoparticles consists of a disordered Ti 2O 3 shell. The measurements show a transition region that connects the disordered Ti 2O 3 shell to the perfect rutile core consisting first of four to five monolayers of defective rutile, containing clearly visible Ti interstitialmore » atoms, followed by an ordered reconstruction layer of Ti interstitial atoms. Our data suggest that this reconstructed layer presents a template on which the disordered Ti 2O 3 layers form by interstitial diffusion of Ti ions. In contrast to recent reports that attribute TiO 2 band-gap narrowing to the synergistic action of oxygen vacancies and surface disorder of nonspecific origin, our results point to Ti 2O 3, which is a narrow-band-gap semiconductor. In conclusion, as a stoichiometric compound of the lower oxidation state Ti 3+ it is expected to be a more robust atomic structure than oxygen-deficient TiO 2 for preserving and stabilizing Ti 3+ surface species that are the key to the enhanced photocatalytic activity of black TiO 2.« less

Static friction between rigid fractal surfaces

NASA Astrophysics Data System (ADS)

Alonso-Marroquin, Fernando; Huang, Pengyu; Hanaor, Dorian A. H.; Flores-Johnson, E. A.; Proust, Gwénaëlle; Gan, Yixiang; Shen, Luming

2015-09-01

Using spheropolygon-based simulations and contact slope analysis, we investigate the effects of surface topography and atomic scale friction on the macroscopically observed friction between rigid blocks with fractal surface structures. From our mathematical derivation, the angle of macroscopic friction is the result of the sum of the angle of atomic friction and the slope angle between the contact surfaces. The latter is obtained from the determination of all possible contact slopes between the two surface profiles through an alternative signature function. Our theory is validated through numerical simulations of spheropolygons with fractal Koch surfaces and is applied to the description of frictional properties of Weierstrass-Mandelbrot surfaces. The agreement between simulations and theory suggests that for interpreting macroscopic frictional behavior, the descriptors of surface morphology should be defined from the signature function rather than from the slopes of the contacting surfaces.

X-ray reflectometry and simulation of the parameters of SiC epitaxial films on Si(111), grown by the atomic substitution method

NASA Astrophysics Data System (ADS)

Kukushkin, S. A.; Nussupov, K. Kh.; Osipov, A. V.; Beisenkhanov, N. B.; Bakranova, D. I.

2017-05-01

The structure and composition of SiC nanolayers are comprehensively studied by X-ray reflectometry, IR-spectroscopy, and atomic-force microscopy (AFM) methods for the first time. SiC films were synthesized by the new method of topochemical substitution of substrate atoms at various temperatures and pressure of CO active gas on the surface of high-resistivity low-dislocation single-crystal n-type silicon (111). Based on an analysis and generalization of experimental data obtained using X-ray reflectometry, IR spectroscopy, and AFM methods, a structural model of SiC films on Si was proposed. According to this model, silicon carbide film consists of a number of layers parallel to the substrate, reminiscent of a layer cake. The composition and thickness of each layer entering the film structure is experimentally determined. It was found that all samples contain superstoichiometric carbon; however, its structure is significantly different for the samples synthesized at temperatures of 1250 and 1330°C, respectively. In the former case, the film surface is saturated with silicon vacancies and carbon in the structurally loose form reminiscent of HOPG carbon. In the films grown at 1330°C, carbon is in a dense structure with a close-to-diamond density.

A topological screening heuristic for low-energy, high-index surfaces

NASA Astrophysics Data System (ADS)

Sun, Wenhao; Ceder, Gerbrand

2018-03-01

Robust ab initio investigations of nanoparticle surface properties require a method to identify candidate low-energy surface facets a priori. By assuming that low-energy surfaces are planes with high atomic density, we devise an efficient algorithm to screen for low-energy surface orientations, even if they have high (hkl) miller indices. We successfully predict the observed low-energy, high-index { 10 12 bar } and { 10 1 bar 4 } surfaces of hematite α-Fe2O3, the {311} surfaces of cuprite Cu2O, and the {112} surfaces of anatase TiO2. We further tabulate candidate low-energy surface orientations for nine of the most common binary oxide structures. Screened surfaces are found to be generally applicable across isostructural compounds with varying chemistries, although relative surface energies between facets may vary based on the preferred coordination of the surface atoms.

Transmission electron diffraction determination of the Ge(001)-(2 × 1) surface structure

NASA Astrophysics Data System (ADS)

Collazo-Davila, C.; Grozea, D.; Landree, E.; Marks, L. D.

1997-04-01

The lateral displacements in the Ge(001)-(2 × 1) surface reconstruction have been determined using transmission electron diffraction (TED). The best-fit model includes displacements extending six layers into the bulk. The atomic positions found agree with X-ray studies to within a few hundredths of an ångström. With the positions determined so precisely, it is suggested that the Ge(001)-(2 × 1) surface can now serve as a standard for comparison with theoretical surface structure calculations. The results from the currently available theoretical studies on the surface are compared with the experimentally determined structure.

Strong influence of coadsorbate interaction on CO desorption dynamics on Ru(0001) probed by ultrafast x-ray spectroscopy and ab initio simulations

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

Xin, H.; LaRue, J.; Oberg, H.

2015-04-16

We show that coadsorbed oxygen atoms have a dramatic influence on the CO desorption dynamics from Ru(0001). In contrast to the precursor-mediated desorption mechanism on Ru(0001), the presence of surface oxygen modifies the electronic structure of Ru atoms such that CO desorption occurs predominantly via the direct pathway. This phenomenon is directly observed in an ultrafast pump-probe experiment using a soft x-ray free-electron laser to monitor the dynamic evolution of the valence electronic structure of the surface species. This is supported with the potential of mean force along the CO desorption path obtained from density-functional theory calculations. Charge density distributionmore » and frozen-orbital analysis suggest that the oxygen-induced reduction of the Pauli repulsion, and consequent increase of the dative interaction between the CO 5σ and the charged Ru atom, is the electronic origin of the distinct desorption dynamics. Ab initio molecular dynamics simulations of CO desorption from Ru(0001) and oxygen-coadsorbed Ru(0001) provide further insights into the surface bond-breaking process.« less

Wettability and friction of water on a MoS{sub 2} nanosheet

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

Luan, Binquan, E-mail: bluan@us.ibm.com, E-mail: ruhongz@us.ibm.com; Zhou, Ruhong, E-mail: bluan@us.ibm.com, E-mail: ruhongz@us.ibm.com

2016-03-28

The molybdenum disulfide (MoS{sub 2}) nanosheet is a promising two-dimensional (2D) material and has recently been used in biological sensing. While the electronic structure of 2D MoS{sub 2} sheet has been actively studied, the role of its atomic structure and thus the interfacial interactions with bio-fluids are still elusive. Using Molecular dynamics simulations, we developed MoS{sub 2} force field parameters to reproduce the experimentally determined water contact angle of the MoS{sub 2} nanosheet and then predicted the slip-length of water that has not been measured in experiment yet. Simulation results suggest that the MoS{sub 2} nanosheet is a hydrophobic andmore » low-friction surface, despite its seemingly significant charges of surface atoms and relatively strong strength of van der Waals potentials. We expect that the developed force fields for depicting surface atoms of MoS{sub 2} will facilitate future research in understanding biomolecule-MoS{sub 2} interactions in MoS{sub 2}-based biosensors.« less

The Potential Role Played by the Fullerene-Like Structures of Interstellar Carbon Dust in the Formation of Molecular Hydrogen in Space

NASA Astrophysics Data System (ADS)

Cataldo, Franco; Iglesias-Groth, Susana

After a general introduction to the problem of formation of molecular hydrogen from atomic hydrogen in the interstellar medium and in the dense molecular clouds in particular, and after the explanation of the key role played by the surfaces on this process, it is proposed that the most suitable carbon surface for the formation of molecular hydrogen (from the radiative association process of atomic hydrogen) can be represented by carbon black rather than by graphite. Furthermore, it is proposed that the fullerene-like structures present in the carbon black graphene sheets are the reaction sites where molecular hydrogen may be formed.

Structure of Boron Nitride Nanotubes: Tube Closing Vs. Chirality

NASA Technical Reports Server (NTRS)

Srivastava, Deepak; Menon, Madhu

1998-01-01

The structure of boron nitride nanotubes is investigated using a generalized tight-binding molecular dynamics method. It is shown that dynamic relaxation results in a wavelike or "rippled" surface in which the B atoms rotate inward and the N atoms move outward, reminiscent of the surface relaxation of the III-V semiconductors. More importantly, the three different morphologies of the tube closing with flat, conical and amorphous ends, as observed in experiments, are shown to be directly related to the tube chiralities. The abundance of flat end tubes observed in experiments is, thus, shown to be an indication of the greater stability of "zig-zag" BN tubes over the "arm-chair" tubes under experimental conditions.

Surface effects on the mechanical elongation of AuCu nanowires: De-alloying and the formation of mixed suspended atomic chains

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

Lagos, M. J.; Laboratório Nacional de Nanotecnologia-LNNANO, 13083-970 Campinas-SP; Autreto, P. A. S.

2015-03-07

We report here an atomistic study of the mechanical deformation of Au{sub x}Cu{sub (1−x)} atomic-size wires (nanowires (NWs)) by means of high resolution transmission electron microscopy experiments. Molecular dynamics simulations were also carried out in order to obtain deeper insights on the dynamical properties of stretched NWs. The mechanical properties are significantly dependent on the chemical composition that evolves in time at the junction; some structures exhibit a remarkable de-alloying behavior. Also, our results represent the first experimental realization of mixed linear atomic chains (LACs) among transition and noble metals; in particular, surface energies induce chemical gradients on NW surfacesmore » that can be exploited to control the relative LAC compositions (different number of gold and copper atoms). The implications of these results for nanocatalysis and spin transport of one-atom-thick metal wires are addressed.« less

Nature of adsorption on TiC(111) investigated with density-functional calculations

NASA Astrophysics Data System (ADS)

Ruberto, Carlo; Lundqvist, Bengt I.

2007-06-01

Extensive density-functional calculations are performed for chemisorption of atoms in the three first periods (H, B, C, N, O, F, Al, Si, P, S, and Cl) on the polar TiC(111) surface. Calculations are also performed for O on TiC(001), for full O(1×1) monolayer on TiC(111), as well as for bulk TiC and for the clean TiC(111) and (001) surfaces. Detailed results concerning atomic structures, energetics, and electronic structures are presented. For the bulk and the clean surfaces, previous results are confirmed. In addition, detailed results are given on the presence of C-C bonds in the bulk and at the surface, as well as on the presence of a Ti-based surface resonance (TiSR) at the Fermi level and of C-based surface resonances (CSR’s) in the lower part of the surface upper valence band. For the adsorption, adsorption energies Eads and relaxed geometries are presented, showing great variations characterized by pyramid-shaped Eads trends within each period. An extraordinarily strong chemisorption is found for the O atom, 8.8eV /adatom. On the basis of the calculated electronic structures, a concerted-coupling model for the chemisorption is proposed, in which two different types of adatom-substrate interactions work together to provide the obtained strong chemisorption: (i) adatom-TiSR and (ii) adatom-CSR’s. This model is used to successfully describe the essential features of the calculated Eads trends. The fundamental nature of this model, based on the Newns-Anderson model, should make it apt for general application to transition-metal carbides and nitrides and for predictive purposes in technological applications, such as cutting-tool multilayer coatings and MAX phases.

Density-functional theory study of the initial oxygen incorporation in Pd(111)

NASA Astrophysics Data System (ADS)

Todorova, Mira; Reuter, Karsten; Scheffler, Matthias

2005-05-01

Pd(111) has recently been shown to exhibit a propensity to form a subnanometer thin surface oxide film already well before a full monolayer coverage of adsorbed O atoms is reached on the surface. Aiming at an atomic-scale understanding of this finding, we study the initial oxygen incorporation into the Pd(111) surface using density-functional theory. We find that oxygen incorporation into the sub-surface region starts at essentially the same coverage as formation of the surface oxide. This implies that the role of sub-surface oxygen should be considered as that of a metastable precursor in the oxidation process of the surface. The mechanisms found to play a role towards the ensuing stabilization of an ordered oxidic structure with a mixed on-surface/sub-surface site occupation follow a clear trend over the late 4d transition metal series, as seen by comparing our data to previously published studies concerned with oxide formation at the basal surface of Ru, Rh, and Ag. The formation of a linearly aligned O-TM-O trilayered structure (TM=Ru,Rh,Pd,Ag) , together with an efficient coupling to the underlying substrate seem to be key ingredients in this respect.

Biomolecular Chemistry of Isopropyl Fibrates

PubMed Central

Rath, Niharika; Kotheimer, Amenda; Miller, Chad; Zeller, Matthias; Rath, Nigam P.

2012-01-01

Isopropyl 2-[4-(4-chlorobenzoyl)-phenoxy]-2-methylpropanoic acid and isopropyl 2-(4-chlorophenoxy)-2-methylpropanoate, also known as fenofibrate and isopropyl clofibrate, are hypolipidemic agents of the fibrate family. In a previously reported triclinic structure of fenofibrate (polymorph I) the methyl groups of the isopropyl moiety (iPr) are located symmetrically about the carboxylate group. We report a new monoclinic form (polymorph II) of fenofibrate and a first structural description of isopropyl clofibrate, and in these the methyl groups are placed asymmetrically about the carboxylate group. In particular the dihedral (torsion) angle between the hydrogen atom on the secondary C and the C atom of the carboxyl group makes a 2.74° angle about the ester O-C bond in the symmetric fenofibrate structure of polymorph I, whereas the same dihedral angle is 45.94° in polymorph II and -30.9° in the crystal structure of isopropyl clofibrate. Gas phase DFT geometry minimizations of fenofibrate and isopropyl clofibrate result in lowest energy conformations for both molecules with a value of about ± 30° for this same angle between the O=C-O-C plane and the C-H bond of the iPr group. A survey of crystal structures containing an iPr ester group reveals that the asymmetric conformation is predominant. Although the hydrogen atom on the secondary C atom of the isopropyl group is located at a comparable distance from the carbonyl oxygen in the symmetric and asymmetric fenofibrate (2.52 and 2.28 Å) and the isopropyl clofibrate (2.36 Å) structures, this hydrogen atom participates in a puckered five membered ring arrangement in the latter two that is unlike the planar arrangement found in symmetric fenofibrate (polymorph I). Polar molecular surface area (PSA) values indicate fenofibrate and isopropyl clofibrate are less able to act as acceptors of hydrogen bonds than their corresponding acid derivatives. Surface area calculations show dynamic polar molecular surface area (PSAd) values of the iPr esters of the fibrates are lower than those of their acids, implying that the fibrates have better membrane permeability and a higher absorbability and hence are better prodrugs when these agents need to be orally administered. PMID:22246648

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

Li, Rong; Wu, Yongquan, E-mail: yqwu@shu.edu.cn; Xiao, Junjiang

We observed homogeneous nucleation process of supercooled liquid Fe by molecular dynamics simulations. Using bond-orientational order parameters together with Voronoi polyhedron method, we characterized local structure, calculated the volume of Voronoi polyhedra of atoms and identified the structure and density fluctuations. We monitored the formation of nucleus and analyzed its inner structure. The birth and growth of the pre-nucleus and nucleus are accompanied with aggregating and disaggregating processes in the time scale of femtosecond. Only the initial solid-like clusters (ISLC), ranging from 1 to 7 atoms, pop up directly from liquid. The relation between the logarithm of number of clustersmore » and the cluster size was found to be linear for ISLCs and was observed to be parabolic for all solid-like clusters (SLC) due to aggregating and disaggregating effects. The nucleus and pre-nuclei mainly consist of body centered cubic (BCC) and hexagonal close packed atoms, while the BCC atoms tend to be located at the surface. Medium-range structure fluctuations induce the birth of ISLCs, benefit the aggregation of embryos and remarkably promote the nucleation. But density fluctuations contribute little to nucleation. The lifetime of most icosahedral-like atoms (ICO) is shorter than 0.7 ps. No obvious relationship was found between structure/density fluctuations and the appearance of ICO atoms.« less

Three-dimensional atom probe tomography of oxide, anion, and alkanethiolate coatings on gold.

PubMed

Zhang, Yi; Hillier, Andrew C

2010-07-15

We have used three-dimensional atom probe tomography to analyze several nanometer-thick and monomolecular films on gold surfaces. High-purity gold wire was etched by electropolishing to create a sharp tip suitable for field evaporation with a radius of curvature of <100 nm. The near-surface region of a freshly etched gold tip was examined with the atom probe at subnanometer spatial resolution and with atom-level composition accuracy. A thin contaminant layer, primarily consisting of water and atmospheric gases, was observed on a fresh tip. This sample exhibited crystalline lattice spacings consistent with the interlayer spacing of {200} lattice planes of bulk gold. A thin oxide layer was created on the gold surface via plasma oxidation, and the thickness and composition of this layer was measured. Clear evidence of a nanometer-thick oxide layer was seen coating the gold tip, and the atomic composition of the oxide layer was consistent with the expected stoichiometry for gold oxide. Monomolecular anions layers of Br(-) and I(-) were created via adsorption from aqueous solutions onto the gold. Atom probe data verified the presence of the monomolecular anion layers on the gold surface, with ion density values consistent with literature values. A hexanethiolate monolayer was coated onto the gold tip, and atom probe analysis revealed a thin film whose ion fragments were consistent with the molecular composition of the monolayer and a surface coverage similar to that expected from literature. Details of the various coating compositions and structures are presented, along with discussion of the reconstruction issues associated with properly analyzing these thin-film systems.

Shape-dependent surface magnetism of Co-Pt and Fe-Pt nanoparticles from first principles

NASA Astrophysics Data System (ADS)

Liu, Zhenyu; Wang, Guofeng

2017-12-01

In this paper, we have performed the first-principles density functional theory calculations to predict the magnetic properties of the CoPt and FePt nanoparticles in cuboctahedral, decahedral, and icosahedral shapes. The modeled alloy nanoparticles have a diameter of 1.1 nm and consist of 31 5 d Pt atoms and 24 3 d Co (or Fe) atoms. For both CoPt and FePt, we found that the decahedral nanoparticles had appreciably lower surface magnetic moments than the cuboctahedral and icosahedral nanoparticles. Our analysis indicated that this reduction in the surface magnetism was related to a large contraction of atomic spacing and high local Co (or Fe) concentration in the surface of the decahedral nanoparticles. More interestingly, we predicted that the CoPt and FePt cuboctahedral nanoparticles exhibited dramatically different surface spin structures when noncollinear magnetism was taken into account. Our calculation results revealed that surface anisotropy energy decided the fashion of surface spin canting in the CoPt and FePt nanoparticles, confirming previous predictions from atomistic Monte Carlo simulations.

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

Not Available

This report contains viewgraphs on the following topics. The advanced light source U8 undulator beamline, 20--300 eV; gas-phase actinide studies with synchrotron radiation; atomic structure calculations for heavy atoms; flux growth of single crystal uranium intermetallics: Extension to transuranics; x-ray absorption near-edge structure studies of actinide compounds; surface as a new stage for studying actinides: Theoretical study of the surface electronic structure of uranium; magnetic x-ray scattering experiments at resonant energies; beamline instruments for radioactive materials; the search for x-ray absorption magnetic circular dichroism in actinide materials: preliminary experiments using UFe[sub 2] and U-S; the laser plasma laboratory light source:more » a source of preliminary transuranic data; electron spectroscopy of heavy fermion actinide materials; study of thin layers of actinides. Present status and future use of synchrotron radiation; electronic structure and correlated-electron theory for actinide materials; and heavy fermion and kondo phenomena in actinide materials.« less

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

Not Available

This report contains viewgraphs on the following topics. The advanced light source U8 undulator beamline, 20--300 eV; gas-phase actinide studies with synchrotron radiation; atomic structure calculations for heavy atoms; flux growth of single crystal uranium intermetallics: Extension to transuranics; x-ray absorption near-edge structure studies of actinide compounds; surface as a new stage for studying actinides: Theoretical study of the surface electronic structure of uranium; magnetic x-ray scattering experiments at resonant energies; beamline instruments for radioactive materials; the search for x-ray absorption magnetic circular dichroism in actinide materials: preliminary experiments using UFe{sub 2} and U-S; the laser plasma laboratory light source:more » a source of preliminary transuranic data; electron spectroscopy of heavy fermion actinide materials; study of thin layers of actinides. Present status and future use of synchrotron radiation; electronic structure and correlated-electron theory for actinide materials; and heavy fermion and kondo phenomena in actinide materials.« less

LEED STUDY OF Ag(111)-(√ 7×√ 7)R19.1^o-4Ar

NASA Astrophysics Data System (ADS)

Caragiu, Mellita; Diehl, Renee D.; Leatherman, Gerry S.

2000-03-01

Recent LEED studies of the adsorption geometries of Xe and Kr on metal surfaces have indicated that, contrary to expectations, the low-coordination adsorption sites are generally preferred, even on relatively corrugated surfaces such as Cu(1\\overline 1 0). This study extends the range of this phenomenon to include Ar. On Ag(111), Ar can form a commensurate structure, Ag(111)-(√ 7×√ 7)R19.1^o-4Ar, if the step sites are first blocked by preadsorbing another species such as CO. A dynamical LEED analysis of this structure at 33K indicates that the structure includes one atom per unit cell on a top site and the remaining three on bridge sites. This structure is clearly preferred over ones in which hollow sites are occupied, providing evidence that the preference of noble gases atoms for low-coordination sites on metals extends to Ar.

Atomic dynamics and the problem of the structural stability of free clusters of solidified inert gases

NASA Astrophysics Data System (ADS)

Verkhovtseva, É. T.; Gospodarev, I. A.; Grishaev, A. V.; Kovalenko, S. I.; Solnyshkin, D. D.; Syrkin, E. S.; Feodos'ev, S. B.

2003-05-01

The dependence of the rms amplitudes of atoms in free clusters of solidified inert gases on the cluster size is investigated theoretically and experimentally. Free clusters are produced by homogeneous nucleation in an adiabatically expanding supersonic stream. Electron diffraction is used to measure the rms amplitudes of the atoms; the Jacobi-matrix method is used for theoretical calculations. A series of distinguishing features of the atomic dynamics of microclusters was found. This was necessary to determine the character of the formation and the stability conditions of the crystal structure. It wass shown that for clusters consisting of less than N˜103 atoms, as the cluster size decreases, the rms amplitudes grow much more rapidly than expected from the increase in the specific contribution of the surface. It is also established that an fcc structure of a free cluster, as a rule, contains twinning defects (nuclei of an hcp phase). One reason for the appearance of such defects is the so-called vertex instability (anomalously large oscillation amplitudes) of the atoms in coordination spheres.

Prediction of octanol-water partition coefficients of organic compounds by multiple linear regression, partial least squares, and artificial neural network.

PubMed

Golmohammadi, Hassan

2009-11-30

A quantitative structure-property relationship (QSPR) study was performed to develop models those relate the structure of 141 organic compounds to their octanol-water partition coefficients (log P(o/w)). A genetic algorithm was applied as a variable selection tool. Modeling of log P(o/w) of these compounds as a function of theoretically derived descriptors was established by multiple linear regression (MLR), partial least squares (PLS), and artificial neural network (ANN). The best selected descriptors that appear in the models are: atomic charge weighted partial positively charged surface area (PPSA-3), fractional atomic charge weighted partial positive surface area (FPSA-3), minimum atomic partial charge (Qmin), molecular volume (MV), total dipole moment of molecule (mu), maximum antibonding contribution of a molecule orbital in the molecule (MAC), and maximum free valency of a C atom in the molecule (MFV). The result obtained showed the ability of developed artificial neural network to prediction of partition coefficients of organic compounds. Also, the results revealed the superiority of ANN over the MLR and PLS models. Copyright 2009 Wiley Periodicals, Inc.

Atomically thick bismuth selenide freestanding single layers achieving enhanced thermoelectric energy harvesting.

PubMed

Sun, Yongfu; Cheng, Hao; Gao, Shan; Liu, Qinghua; Sun, Zhihu; Xiao, Chong; Wu, Changzheng; Wei, Shiqiang; Xie, Yi

2012-12-19

Thermoelectric materials can realize significant energy savings by generating electricity from untapped waste heat. However, the coupling of the thermoelectric parameters unfortunately limits their efficiency and practical applications. Here, a single-layer-based (SLB) composite fabricated from atomically thick single layers was proposed to optimize the thermoelectric parameters fully. Freestanding five-atom-thick Bi(2)Se(3) single layers were first synthesized via a scalable interaction/exfoliation strategy. As revealed by X-ray absorption fine structure spectroscopy and first-principles calculations, surface distortion gives them excellent structural stability and a much increased density of states, resulting in a 2-fold higher electrical conductivity relative to the bulk material. Also, the surface disorder and numerous interfaces in the Bi(2)Se(3) SLB composite allow for effective phonon scattering and decreased thermal conductivity, while the 2D electron gas and energy filtering effect increase the Seebeck coefficient, resulting in an 8-fold higher figure of merit (ZT) relative to the bulk material. This work develops a facile strategy for synthesizing atomically thick single layers and demonstrates their superior ability to optimize the thermoelectric energy harvesting.

Influence of tool shape on lattice rearrangement under loading conditions reproducing friction stir welding

NASA Astrophysics Data System (ADS)

Konovalenko, Ivan S.; Konovalenko, Igor S.

2015-10-01

Metal behavior under loading conditions that reproduce friction stir welding was studied on the atomic scale. Calculations were conducted based on molecular dynamics simulation with potentials calculated within the embedded atom method. The loading of the interface between two crystallites, whose structure corresponded to aluminum alloy 2024, was simulated by the motion of a cone-shaped tool along the interface with constant angular and translational velocities. The motion of the rotating tool causes fracture of the workpiece crystal structure with subsequent mixing of surface atoms of the interfacing crystallites. It is shown that the resistance force acting on the moving tool from the workpiece and the process of structural defect formation in the workpiece depend on the tool shape.

Atomic-scale analysis of deposition and characterization of a-Si:H thin films grown from SiH radical precursor

NASA Astrophysics Data System (ADS)

Sriraman, Saravanapriyan; Aydil, Eray S.; Maroudas, Dimitrios

2002-07-01

Growth of hydrogenated amorphous silicon films (a-Si:H) on an initial H-terminated Si(001)(2 x1) substrate at T=500 K was studied through molecular-dynamics (MD) simulations of repeated impingement of SiH radicals to elucidate the effects of reactive minority species on the structural quality of the deposited films. The important reactions contributing to film growth were identified through detailed visualization of radical-surface interaction trajectories. These reactions include (i) insertion of SiH into Si-Si bonds, (ii) adsorption onto surface dangling bonds, (iii) surface H abstraction by impinging SiH radicals through an Eley-Rideal mechanism, (iv) surface adsorption by penetration into subsurface layers or dissociation leading to interstitial atomic hydrogen, (v) desorption of interstitial hydrogen into the gas phase, (vi) formation of higher surface hydrides through the exchange of hydrogen, and (vii) dangling-bond-mediated dissociation of surface hydrides into monohydrides. The MD simulations of a-Si:H film growth predict an overall surface reaction probability of 95% for the SiH radical that is in good agreement with experimental measurements. Structural and chemical characterization of the deposited films was based on the detailed analysis of evolution of the films' structure, surface morphology and roughness, surface reactivity, and surface composition. The analysis revealed that the deposited films exhibit high dangling bond densities and rough surface morphologies. In addition, the films are abundant in voids and columnar structures that are detrimental to producing device-quality a-Si:H thin films.

The Use of Atomic-Force Microscopy for Studying the Crystallization Process of Amorphous Alloys

NASA Astrophysics Data System (ADS)

Elmanov, G. N.; Ivanitskaya, E. A.; Dzhumaev, P. S.; Skrytniy, V. I.

The crystallization process of amorphous alloys is accompanied by the volume changes as a result of structural phase transitions. This leads to changes in the surface topography, which was studied by atomic force microscopy (AFM). The changes of the surface topography, structure and phase composition during multistage crystallization process of the metallic glasses with composition Ni71,5Cr6,8Fe2,7B11,9Si7,1 and Ni63,4Cr7,4Fe4,3Mn0,8B15,6Si8,5 (AWS BNi2) has been investigated. The obtained results on changing of the surface topography in crystallization process are in good agreement with the data of X-ray diffraction analysis (XRD). The nature of redistribution of some alloy components in the crystallization process has been suggested.

Atom-by-atom assembly

NASA Astrophysics Data System (ADS)

Hla, Saw Wai

2014-05-01

Atomic manipulation using a scanning tunneling microscope (STM) tip enables the construction of quantum structures on an atom-by-atom basis, as well as the investigation of the electronic and dynamical properties of individual atoms on a one-atom-at-a-time basis. An STM is not only an instrument that is used to ‘see’ individual atoms by means of imaging, but is also a tool that is used to ‘touch’ and ‘take’ the atoms, or to ‘hear’ their movements. Therefore, the STM can be considered as the ‘eyes’, ‘hands’ and ‘ears’ of the scientists, connecting our macroscopic world to the exciting atomic world. In this article, various STM atom manipulation schemes and their example applications are described. The future directions of atomic level assembly on surfaces using scanning probe tips are also discussed.

Surface study of irradiated sapphires from Phrae Province, Thailand using AFM

NASA Astrophysics Data System (ADS)

Monarumit, N.; Jivanantaka, P.; Mogmued, J.; Lhuaamporn, T.; Satitkune, S.

2017-09-01

The irradiation is one of the gemstone enhancements for improving the gem quality. Typically, there are many varieties of irradiated gemstones in the gem market such as diamond, topaz, and sapphire. However, it is hard to identify the gemstones before and after irradiation. The aim of this study is to analyze the surface morphology for classifying the pristine and irradiated sapphires using atomic force microscope (AFM). In this study, the sapphire samples were collected from Phrae Province, Thailand. The samples were irradiated by high energy electron beam for a dose of ionizing radiation at 40,000 kGy. As the results, the surface morphology of pristine sapphires shows regular atomic arrangement, whereas, the surface morphology of irradiated sapphires shows the nano-channel observed by the 2D and 3D AFM images. The atomic step height and root mean square roughness have changed after irradiation due to the micro-structural defect on the sapphire surface. Therefore, this study is a frontier application for sapphire identification before and after irradiation.

Fast interaction of atoms with crystal surfaces: coherent lighting

NASA Astrophysics Data System (ADS)

Gravielle, M. S.

2017-11-01

Quantum coherence of incident waves results essential for the observation of interference patterns in grazing incidence fast atom diffraction (FAD). In this work we investigate the influence of the impact energy and projectile mass on the transversal length of the surface area that is coherently illuminated by the atomic beam, after passing through a collimating aperture. Such a transversal coherence length controls the general features of the interference structures, being here derived by means of the Van Cittert-Zernike theorem. The coherence length is then used to build the initial coherent wave packet within the Surface Initial Value Representation (SIVR) approximation. The SIVR approach is applied to fast He and Ne atoms impinging grazingly on a LiF(001) surface along a low-indexed crystallographic direction. We found that with the same collimating setup, by varying the impact energy we would be able to control the interference mechanism that prevails in FAD patterns, switching between inter-cell and unit-cell interferences. These findings are relevant to use FAD spectra adequately as a surface analysis tool, as well as to choose the appropriate collimating scheme for the observation of interference effects in a given collision system.

Research Update: Spatially resolved mapping of electronic structure on atomic level by multivariate statistical analysis

NASA Astrophysics Data System (ADS)

Belianinov, Alex; Ganesh, Panchapakesan; Lin, Wenzhi; Sales, Brian C.; Sefat, Athena S.; Jesse, Stephen; Pan, Minghu; Kalinin, Sergei V.

2014-12-01

Atomic level spatial variability of electronic structure in Fe-based superconductor FeTe0.55Se0.45 (Tc = 15 K) is explored using current-imaging tunneling-spectroscopy. Multivariate statistical analysis of the data differentiates regions of dissimilar electronic behavior that can be identified with the segregation of chalcogen atoms, as well as boundaries between terminations and near neighbor interactions. Subsequent clustering analysis allows identification of the spatial localization of these dissimilar regions. Similar statistical analysis of modeled calculated density of states of chemically inhomogeneous FeTe1-xSex structures further confirms that the two types of chalcogens, i.e., Te and Se, can be identified by their electronic signature and differentiated by their local chemical environment. This approach allows detailed chemical discrimination of the scanning tunneling microscopy data including separation of atomic identities, proximity, and local configuration effects and can be universally applicable to chemically and electronically inhomogeneous surfaces.

Oxygen Displacement in Cuprates under Ionic Liquid Field-Effect Gating

PubMed Central

Dubuis, Guy; Yacoby, Yizhak; Zhou, Hua; He, Xi; Bollinger, Anthony T.; Pavuna, Davor; Pindak, Ron; Božović, Ivan

2016-01-01

We studied structural changes in a 5 unit cell thick La1.96Sr0.04CuO4 film, epitaxially grown on a LaSrAlO4 substrate with a single unit cell buffer layer, when ultra-high electric fields were induced in the film by applying a gate voltage between the film (ground) and an ionic liquid in contact with it. Measuring the diffraction intensity along the substrate-defined Bragg rods and analyzing the results using a phase retrieval method we obtained the three-dimensional electron density in the film, buffer layer, and topmost atomic layers of the substrate under different applied gate voltages. The main structural observations were: (i) there were no structural changes when the voltage was negative, holes were injected into the film making it more metallic and screening the electric field; (ii) when the voltage was positive, the film was depleted of holes becoming more insulating, the electric field extended throughout the film, the partial surface monolayer became disordered, and equatorial oxygen atoms were displaced towards the surface; (iii) the changes in surface disorder and the oxygen displacements were both reversed when a negative voltage was applied; and (iv) the c-axis lattice constant of the film did not change in spite of the displacement of equatorial oxygen atoms. PMID:27578237

Wet-chemical passivation of atomically flat and structured silicon substrates for solar cell application

NASA Astrophysics Data System (ADS)

Angermann, H.; Rappich, J.; Korte, L.; Sieber, I.; Conrad, E.; Schmidt, M.; Hübener, K.; Polte, J.; Hauschild, J.

2008-04-01

Special sequences of wet-chemical oxidation and etching steps were optimised with respect to the etching behaviour of differently oriented silicon to prepare very smooth silicon interfaces with excellent electronic properties on mono- and poly-crystalline substrates. Surface photovoltage (SPV) and photoluminescence (PL) measurements, atomic force microscopy (AFM) and scanning electron microscopy (SEM) investigations were utilised to develop wet-chemical smoothing procedures for atomically flat and structured surfaces, respectively. Hydrogen-termination as well as passivation by wet-chemical oxides were used to inhibit surface contamination and native oxidation during the technological processing. Compared to conventional pre-treatments, significantly lower micro-roughness and densities of surface states were achieved on mono-crystalline Si(100), on evenly distributed atomic steps, such as on vicinal Si(111), on silicon wafers with randomly distributed upside pyramids, and on poly-crystalline EFG ( Edge-defined Film-fed- Growth) silicon substrates. The recombination loss at a-Si:H/c-Si interfaces prepared on c-Si substrates with randomly distributed upside pyramids was markedly reduced by an optimised wet-chemical smoothing procedure, as determined by PL measurements. For amorphous-crystalline hetero-junction solar cells (ZnO/a-Si:H(n)/c-Si(p)/Al) with textured c-Si substrates the smoothening procedure results in a significant increase of short circuit current Isc, fill factor and efficiency η. The scatter in the cell parameters for measurements on different cells is much narrower, as compared to conventional pre-treatments, indicating more well-defined and reproducible surface conditions prior to a-Si:H emitter deposition and/or a higher stability of the c-Si surface against variations in the a-Si:H deposition conditions.

Structure and chemical reactivity of the polar three-fold surfaces of GaPd: A density-functional study

NASA Astrophysics Data System (ADS)

Krajčí, M.; Hafner, J.

2013-03-01

The polar threefold surfaces of the GaPd compound crystallizing in the B20 (FeSi-type) structure (space group P213) have been investigated using density-functional methods. Because of the lack of inversion symmetry the B20 structure exists in two enantiomorphic forms denoted as A and B. The threefold {111} surfaces have polar character. In both nonequivalent (111) and (bar{1}bar{1}bar{1}) directions several surface terminations differing in structure and chemical composition are possible. The formation of the threefold surfaces has been studied by simulated cleavage experiments and by calculations of the surface energies. Because of the polar character of the threefold surfaces calculations for stoichiometric slabs permit only the determination of the average energy of the surfaces exposed on both sides of the slab. Calculations for nonstoichiometric slabs performed in the grand canonical ensemble yield differences of the surface energies for the possible terminations as a function of the chemical potential in the reactive atmosphere above the surface and predict a transition between Ga- and Pd-terminated surfaces as a function of the chemical potential. The {100} surfaces are stoichiometric and uniquely defined. The calculated surface energies are identical to the average energies of the {100} surfaces of the pure metals. The {210} surfaces are also stoichiometric, with an energy very close to that of the {100} surfaces. Assuming that for the {111} surfaces the energies of different possible terminations are in a proportion equal to that of the concentration-weighted energies of the {111} surfaces of the pure metals, surface energies for all possible {111} terminations may be calculated. The preferable termination perpendicular to the A⟨111⟩ direction consists of a bilayer with three Ga atoms in the upper and three Pd atoms in the lower part. The surface energy of this termination further decreases if the Pd triplet is covered by additional Ga atom. Perpendicular to the A< bar{1}bar{1}bar{1} > direction the lowest energy has been found for a bilayer with three Ga atoms per surface cell in the upper layer and one Ga and one Pd in the lower part. The calculated surface energies are in agreement with a simulated cleavage experiment. However, cleavage does not result in the formation of the lowest-energy surfaces, because all possible {111} cleavage planes expose a low-energy surface on one, and a high-energy surface on the other side. The prediction of Ga-terminated surfaces has been tested against the available experimental information. The calculated surface electronic density of states is in very good agreement with photo-emission spectroscopy. Calculated STM images of the most stable surfaces agree with all details of the available experimental images. The chemical reactivity of the most stable surfaces has been studied by the adsorption of CO molecules. The adsorption energies and maximum coverages calculated for the Ga-terminated surfaces permit a reasonable interpretation of the observed thermal desorption spectra, whereas for the Pd-terminated surfaces the calculated adsorption energies are far too high.

Modifying the anti-wetting property of butterfly wings and water strider legs by atomic layer deposition coating: surface materials versus geometry.

PubMed

Ding, Yong; Xu, Sheng; Zhang, Yue; Wang, Aurelia C; Wang, Melissa H; Xiu, Yonghao; Wong, Ching Ping; Wang, Zhong Lin

2008-09-03

Although butterfly wings and water strider legs have an anti-wetting property, their working conditions are quite different. Water striders, for example, live in a wet environment and their legs need to support their weight and bear the high pressure during motion. In this work, we have focused on the importance of the surface geometrical structures in determining their performance. We have applied an atomic layer deposition technique to coat the surfaces of both butterfly wings and water strider legs with a uniform 30 nm thick hydrophilic Al(2)O(3) film. By keeping the surface material the same, we have studied the effect of different surface roughness/structure on their hydrophobic property. After the surface coating, the butterfly wings changed to become hydrophilic, while the water strider legs still remained super-hydrophobic. We suggest that the super-hydrophobic property of the water strider is due to the special shape of the long inclining spindly cone-shaped setae at the surface. The roughness in the surface can enhance the natural tendency to be hydrophobic or hydrophilic, while the roughness in the normal direction of the surface is favorable for forming a composite interface.

Ion induced millimetre-scale structures growth on metal surfaces

NASA Astrophysics Data System (ADS)

Girka, O.; Bizyukov, O.; Balkova, Y.; Myroshnyk, M.; Bizyukov, I.; Bogatyrenko, S.

2018-04-01

Polished polycrystalline Plansee tungsten (W) sample with purity 99.99 wt% and 0.75 mm thickness has been exposed to intense argon (Ar) ion beam with average energy of 2 keV and etched through in the centre. As a result, castle-like structures with strong asymmetry and with the height of >200 μm have been formed. Structures can be observed by naked eyes and with scanning-electron microscopy (SEM). It has been revealed, that the structures have been formed not immediately, but at the later stages of irradiation. Primary factors favouring the formation for the structures are relaxation of the surface stresses and activated surface mobility of atoms.

Role of Defects on Regioselectivity of Nano Pristine Graphene.

PubMed

Kudur Jayaprakash, Gururaj; Casillas, Norberto; Astudillo-Sánchez, Pablo D; Flores-Moreno, Roberto

2016-11-17

Here analytical Fukui functions based on density functional theory are applied to investigate the redox reactivity of pristine and defected graphene lattices. A carbon H-terminated graphene structure (with 96 carbon atoms) and a graphene defected surface with Stone-Wales rearrangement and double vacancy defects are used as models. Pristine sp 2 -hybridized, hexagonal arranged carbon atoms exhibit a symmetric reactivity. In contrast, common carbon atoms at reconstructed polygons in Stone-Wales and double vacancy graphene display large reactivity variations. The improved reactivity and the regioselectivity at defected graphene is correlated to structural changes that caused carbon-carbon bond length variations at defected zones.

Direct visualization of quasi-ordered oxygen chain structures on Au(110)-(1 × 2)

NASA Astrophysics Data System (ADS)

Hiebel, F.; Montemore, M. M.; Kaxiras, E.; Friend, C. M.

2016-08-01

The Au(110) surface offers unique advantages for atomically-resolved model studies of catalytic oxidation processes on gold. We investigate the adsorption of oxygen on Au(110) using a combination of scanning tunneling microscopy (STM) and density functional theory (DFT) methods. We identify the typical (empty-states) STM contrast resulting from adsorbed oxygen as atomic-sized dark features of electronic origin. DFT-based image simulations confirm that chemisorbed oxygen is generally detected indirectly, from the binding-induced electronic structure modification of gold. STM images show that adsorption occurs without affecting the general structure of the pristine Au(110) missing-row reconstruction. The tendency to form one-dimensional structures is observed already at low coverage (< 0.05 ML), with oxygen adsorbing on alternate sides of the reconstruction ridges. Consistently, calculations yield preferred adsorption on the (111) facets of the reconstruction, on a 3-fold coordination site, with increased stability when adsorbed in chains. Gold atoms with two oxygen neighbors exhibit enhanced electronic hybridization with the O states. Finally, the species observed are reactive to CO oxidation at 200 K and desorption of CO2 leaves a clean and ordered gold surface.

XAFS studies of surface structures of TiO{sub 2} nanoparticles and photocatalytic reduction of metal ions.

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

Chen, L. X.; Rajh, T.; Wang, Z.

1997-01-01

To probe the origin of the unique functions of titanium dioxide (TiO{sub 2}) nanoparticles observed in photocatalytic reactions, structures of Ti atom sites in titanium dioxide (TiO{sub 2}) nanoparticles with different sizes were studied by Ti K-edge XAFS (X-ray absorption fine structure). Compared to the bulk TiO{sub 2} structure, a shorter Ti-O distance from surface TiO{sub 2} resulting from Ti-OH bonding was observed. The XAFS spectra also revealed an increasing disorder of the lattice with decreasing sizes of the nanoparticles based on a coordination number decrease for the third-shell O atoms as well as changes in relative intensities of pre-edgemore » peaks A1, A2, and A3. However, the Ti sites largely remain octahedral even in the 30 Angstrom diameter particles. These results imply that the increasing number of surface Ti sites as well as possible corner defects in small nanoparticles may be the main cause of the unique surface chemistry exhibited by nanoparticles of TiO{sub 2}. XAFS was also used in monitoring the photoreduction reaction products of Cu{sup 2+} and Hg{sup 2+} on TiO{sub 2} nanoparticle surfaces, with or without surface adsorbers, alanine (Ala) and thiolactic acid (TLA). Ala dramatically enhanced photoreduction of Cu{sup 2+} on TiO{sub 2} nanoparticle surfaces, whereas thiolactic acid did not affect or even hindered Hg{sup 2+} photoreduction. Although both surface adsorbers chelated with the metal ions in the absence of TiO{sub 2} nanoparticles, this chelation was drastically changed in the Cu-Ala complex but was largely retained in the Hg-TLA complex when TiO{sub 2} was present. This may correlate with the different effects of the adsorbers on the photoreduction of the metal. Our experimental results suggest that a proper balance between the affinities of the adsorber to the metal ions and to the surface Ti atoms of TiO{sub 2} may be one of the keys in selecting a surface adsorber for enhanced photoreduction efficiency.« less

Pulse regime in formation of fractal fibers

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

Smirnov, B. M., E-mail: bmsmirnov@gmail.com

The pulse regime of vaporization of a bulk metal located in a buffer gas is analyzed as a method of generation of metal atoms under the action of a plasma torch or a laser beam. Subsequently these atoms are transformed into solid nanoclusters, fractal aggregates and then into fractal fibers if the growth process proceeds in an external electric field. We are guided by metals in which transitions between s and d-electrons of their atoms are possible, since these metals are used as catalysts and filters in interaction with gas flows. The resistance of metal fractal structures to a gasmore » flow is evaluated that allows one to find optimal parameters of a fractal structure for gas flow propagation through it. The thermal regime of interaction between a plasma pulse or a laser beam and a metal surface is analyzed. It is shown that the basic energy from an external source is consumed on a bulk metal heating, and the efficiency of atom evaporation from the metal surface, that is the ratio of energy fluxes for vaporization and heating, is 10{sup –3}–10{sup –4} for transient metals under consideration. A typical energy flux (~10{sup 6} W/cm{sup 2}), a typical surface temperature (~3000 K), and a typical pulse duration (~1 μs) provide a sufficient amount of evaporated atoms to generate fractal fibers such that each molecule of a gas flow collides with the skeleton of fractal fibers many times.« less

Structural properties and diffusion processes of the Cu 3Au (0 0 1) surface

NASA Astrophysics Data System (ADS)

Wang, Fang; Zhang, Jian-Min; Zhang, Yan; Ji, Vincent

2010-09-01

The surface relaxation and surface energy of both the mixed AuCu and pure Cu terminated Cu 3Au (0 0 1) surfaces are simulated and calculated by using the modified analytical embedded-atom method. We find that the mixed AuCu termination is energetically preferred over the pure Cu termination thereby the mono-vacancy diffusion is also investigated in the topmost few layers of the mixed AuCu terminated Cu 3Au (0 0 1) surface. In the mixed AuCu terminated surface the relaxed Au atoms are raised above Cu atoms for 0.13 Å in the topmost layer. All the surface atoms displace outwards, this effect occurs in the first three layers and changes the first two inter-layer spacing. For mono-vacancy migration in the first layer, the migration energies of Au and Cu mono-vacancy via two-type in-plane displace: the nearest neighbor jump (NNJ) and the second nearest neighbor jump (2NNJ), are calculated and the results show that the NNJ requires a much lower energy than 2NNJ. For the evolution of the energy requirements for successive nearest neighbor jumps (SNNJ) along three different paths: circularity, zigzag and beeline, we find that the circularity path is preferred over the other two paths due to its minimum energy barriers and final energies. In the second layer, the NN jumps in intra- and inter-layer of the Cu mono-vacancy are investigated. The calculated energy barriers and final energies show that the vacancy prefer jump up to a proximate Cu site. This replacement between the Cu vacancy in the second layer and Cu atom in the first layer is remunerative for the Au atoms enrichment in the topmost layer.

Study of zinc-induced changes in lymphocyte membranes using atomic force microscopy, luminescence, and light scattering methods

NASA Astrophysics Data System (ADS)

Filimonenko, D. S.; Khairullina, A. Ya.; Yasinskii, V. M.; Kozlova, N. M.; Zubritskaja, G. P.; Slobozhanina, E. I.

2011-07-01

Changes in the surface structure of lymphocyte membranes exposed to various concentrations of zinc ions are studied. It is found by atomic force microscopy that increasing the concentration of zinc ions leads to a reduction in the correlation length of the autocorrelation function of the roughness profile of a lymphocyte compared to control samples; this may indicate the existence of fine structure in the membrane surface. Fluorescence markers are used to observe a reduction in the microviscosity of the lipids in the outer monolayer of the lipid bilayer after lymphocytes are exposed to Zn ions, as well as the exposure of phosphatidylserine on the surface membrane, and the oxidation of HS-groups of membrane proteins. Calculations of the absorption coefficients of lymphocytes modified with zinc reveal the existence of absorption bands owing to the formation of metal-protein complexes and zinc oxide nanoparticles. These results indicate significant changes in the structural and functional state of lymphocyte membranes exposed to zinc ions.

In-situ probing of coupled atomic restructuring and metallicity of oxide heterointerfaces induced by polar adsorbates

NASA Astrophysics Data System (ADS)

Ryu, S.; Zhou, H.; Paudel, T. R.; Irwin, J.; Podkaminer, J. P.; Bark, C. W.; Lee, D.; Kim, T. H.; Fong, D. D.; Rzchowski, M. S.; Tsymbal, E. Y.; Eom, C. B.

2017-10-01

Microscopic understanding of the surface-controlled conductivity of the two dimensional electron gas at complex oxide interfaces is crucial for developing functional interfaces. We observe conductivity and structural modification using in-situ synchrotron surface x-ray diffraction as the surface of a model LaAlO3/SrTiO3 (001) heterostructure is changed by polar adsorbates. We find that polar adsorbate-induced interfacial metallicity reduces polar distortions in the LaAlO3 layer. First-principles density functional theory calculations show that surface dipoles introduced by polar adsorbates lead to additional charge transfer and the reduction of polar displacements in the LaAlO3 layer, consistent with the experimental observations. Our study supports that internal structural deformations controlling functionalities can be driven without the application of direct electrical or thermal bias and offers a route to tuning interfacial properties. These results also highlight the important role of in-situ x-ray scattering with atomic resolution in capturing and exploring structural distortions and charge density changes caused by external perturbations such as chemical adsorption, redox reaction, and generation and/or annihilation of surface defects.

In-situ probing of coupled atomic restructuring and metallicity of oxide heterointerfaces induced by polar adsorbates

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

Ryu, S.; Zhou, H.; Paudel, T. R.

Microscopic understanding of the surface-controlled conductivity of the two dimensional electron gas at complex oxide interfaces is crucial for developing functional interfaces. We observe conductivity and structural modification using in-situ synchrotron surface x-ray diffraction as the surface of a model LaAlO3/SrTiO3 (001) heterostructure is changed by polar adsorbates. We find that polar adsorbate-induced interfacial metallicity reduces polar distortions in the LaAlO3 layer. First-principles density functional theory calculations show that surface dipoles introduced by polar adsorbates lead to additional charge transfer and the reduction of polar displacements in the LaAlO3 layer, consistent with the experimental observations. Our study supports that internalmore » structural deformations controlling functionalities can be driven without the application of direct electrical or thermal bias and offers a route to tuning interfacial properties. These results also highlight the important role of in-situ x-ray scattering with atomic resolution in capturing and exploring structural distortions and charge density changes caused by external perturbations such as chemical adsorption, redox reaction, and generation and/or annihilation of surface defects.« less

Comments on the interaction of materials with atomic oxygen

NASA Technical Reports Server (NTRS)

Torre, Larry P.; Pippin, H. Gary

1987-01-01

An explanation of the relative resistance of various materials to attack by atomic oxygen is presented. Data from both ground based and on-orbit experiments is interpreted. The results indicate the importance of bond strengths, size and structure of pendant groups, and fluorination to the resistance of certain polymers to atomic oxygen. A theory which provides a partial explanation of the degradation of materials in low Earth orbit due to surface recombination of oxygen atoms is also included. Finally, a section commenting on mechanisms of material degradation is provided.

Theory and Application of Photoelectron Diffraction for Complex Oxide Systems

NASA Astrophysics Data System (ADS)

Chassé, Angelika; Chassé, Thomas

2018-06-01

X-ray photoelectron diffraction (XPD) has been used to investigate film structures and local sites of surface and dopant atoms in complex oxide materials. We have performed angular-resolved measurements of intensity distribution curves (ADCs) and patterns (ADPs) of elemental core level intensities from binary to quaternary mixed oxide samples and compared them to multiple-scattering cluster (MSC) calculations in order to derive information on structural models and related parameters. MSC calculations permitted to describe both bulk diffraction features of binary oxide MnO(001) and the thickness-dependence of the tetragonal distortion of epitaxial MnO films on Ag(001). XPD was further used to investigate the surface termination of perovskite SrTiO3 and BaTiO3 substrates in order to evaluate influence of different ex situ and in situ preparation procedures on the surface layers, which are crucial for quality of following film growth. Despite the similarity of local environments of Sr (Ba) and Ti atoms in the perovskite film structure an angular region in the ADCs was identified as a fingerprint with the help of MSC simulations which provided clear conclusions on the perovskite oxide surfaces. Dopant sites in quaternary perovskite manganites La1-xCaxMnO3, La1-xSrxMnO3, and La1-xCexMnO3 were studied with polar angle scans of the photoemission intensities of host and dopant atoms. Both direct comparison of experimental ADCs and to the simulations within MSC models confirm the occupation of A sites by the dopants and the structural quality of the complex oxide films.

Structural factors affecting 13C NMR chemical shifts of cellulose: a computational study

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

Yang, Hui; Wang, Tuo; Oehme, Daniel

Here, the doublet C4 peaks at ~ 85 and ~ 89 ppm in solid-state 13C NMR spectra of native cellulose have been attributed to signals of C4 atoms on the surface (solvent-exposed) and in the interior of microfibrils, designated as sC4 and iC4, respectively. The relative intensity ratios of sC4 and iC4 observed in NMR spectra of cellulose have been used to estimate the degree of crystallinity of cellulose and the number of glucan chains in cellulose microfibrils. However, the molecular structures of cellulose responsible for the specific surface and interior C4 peaks have not been positively confirmed. Using densitymore » functional theory (DFT) methods and structures produced from classical molecular dynamics simulations, we investigated how the following four factors affect 13C NMR chemical shifts in cellulose: conformations of exocyclic groups at C6 ( tg, gt and gg), H 2O molecules H-bonded on the surface of the microfibril, glycosidic bond angles (Φ, Ψ) and the distances between H4 and HO3 atoms. We focus on changes in the δ 13C4 value because it is the most significant observable for the same C atom within the cellulose structure. DFT results indicate that different conformations of the exocyclic groups at C6 have the greatest influence on δ 13C4 peak separation, while the other three factors have secondary effects that increase the spread of the calculated C4 interior and surface peaks.« less

Structural factors affecting 13C NMR chemical shifts of cellulose: a computational study

DOE PAGES

Yang, Hui; Wang, Tuo; Oehme, Daniel; ...

2017-11-02

Here, the doublet C4 peaks at ~ 85 and ~ 89 ppm in solid-state 13C NMR spectra of native cellulose have been attributed to signals of C4 atoms on the surface (solvent-exposed) and in the interior of microfibrils, designated as sC4 and iC4, respectively. The relative intensity ratios of sC4 and iC4 observed in NMR spectra of cellulose have been used to estimate the degree of crystallinity of cellulose and the number of glucan chains in cellulose microfibrils. However, the molecular structures of cellulose responsible for the specific surface and interior C4 peaks have not been positively confirmed. Using densitymore » functional theory (DFT) methods and structures produced from classical molecular dynamics simulations, we investigated how the following four factors affect 13C NMR chemical shifts in cellulose: conformations of exocyclic groups at C6 ( tg, gt and gg), H 2O molecules H-bonded on the surface of the microfibril, glycosidic bond angles (Φ, Ψ) and the distances between H4 and HO3 atoms. We focus on changes in the δ 13C4 value because it is the most significant observable for the same C atom within the cellulose structure. DFT results indicate that different conformations of the exocyclic groups at C6 have the greatest influence on δ 13C4 peak separation, while the other three factors have secondary effects that increase the spread of the calculated C4 interior and surface peaks.« less

Sodium-induced ordering of the benzoate species on Si(100)-2×1: a combined HREELS, XPS and NEXAFS study

NASA Astrophysics Data System (ADS)

Bitzer, T.; Richardson, N. V.; Reiss, S.; Wühn, M.; Wöll, Ch.

2000-06-01

The structure of benzoate on Na/Si(100)-2×1 has been studied by high resolution electron energy loss spectroscopy, X-ray photoelectron spectroscopy and near edge X-ray adsorption fine structure spectroscopy. At room temperature, benzoic acid (C 6H 5COOH) chemisorbs on Na/Si(100)-2×1 through a cleavage of the OH bond in the carboxylic group. The benzoate molecules formed are bonded exclusively to the sodium atoms in a bidentate coordination, in which the oxygen atoms are equivalent. At room temperature, benzoate saturation on Na/Si(100)-2×1 is reached at a coverage of one benzoate species for each Na atom or silicon dimer. At this coverage, the molecules are tilted in polar direction by 62°±4° to the surface plane and azimuthally rotated by 41°±4° with respect to the [01 1] surface azimuth. We propose an adsorbate structure, in which the benzoate molecules are oriented parallel to each other in densely packed rows.

Structural Study of GaAs(001):In 4×2 Surface

NASA Astrophysics Data System (ADS)

Lee, T.-L.; Zegenhagen, J.; Lyman, P. F.; Bedzyk, M. J.

1997-03-01

In a STM and LEED investigation (U. Resch-Esser et al., JVST B 13, 1672 (1995)), the indium-terminated GaAs(001) surface exhibited a (4×2) reconstruction. Based on this study, a dimer model, similar to that proposed by Biegelsen et al. (PRB 41, 5701(1990)) for the (4×2) clean surface, was proposed. However, the detailed local structure of the In ad-atoms was not resolvable from the STM image. In this work, we applied in situ x-ray standing wave (XSW) measurements to determine the surface structure of the GaAs(001) upon the adsorption of In at low coverages. The (4×2)/c(8×2) In-terminated GaAs(001) surface (Θ_In = 0.2 ML) was prepared by MBE. The (004) XSW measurement showed that the In ad-atoms were located 1.61 Åabove the (004) diffraction planes. At higher In coverages (up to 0.6 ML) the In (004) coherent fraction was small. This is consistent with the ladder-type pattern observed by STM at Θ_In > 0.5 ML, which indicated that there were two coexisting surface structures. For Θ_In = 0.2 ML, we found that our off-normal XSW measurements did not agree with the model proposed by Resch-Esser et al.. This work is sponsored by DOE-BES No. W-31-109-ENG-38 and by NSF No. DMR-9632472.

CO overlayers on Ru(0001) studied by helium atom scattering: Structure, dynamics, and the influence of coadsorbed H and O

NASA Astrophysics Data System (ADS)

Braun, J.; Kostov, K. L.; Witte, G.; Wöll, Ch.

1997-05-01

Ordered phases of CO on a Ru(0001) surface have been characterized with regard to structural and dynamical properties using high resolution helium atom scattering. In the energy regime below 10 meV a vibrational mode corresponding to a frustrated translation parallel to the surface (FTx) could be identified, the energy amounts to 5.9 meV for isolated CO molecules and to 5.75 meV for the (∛×∛)R30°CO structure. The formation of the more compressed (2∛×2∛)R30°CO and (5∛×5∛)R30°CO structures is accompanied by significant changes of the low energy external vibrations, in pronounced contrast to the gradual frequency increase of the CO internal ν1-vibration. Coadsorption of hydrogen or oxygen was found to result in substantially larger FTx energies. Implications of these findings on the character of the molecule-surface interaction will be discussed, as well as the connection between the FTx-dispersion and the strength and type of the adsorbate-adsorbate interaction.

Interactions of small platinum clusters with the TiC(001) surface

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

Mao, Jianjun; Li, Shasha; Chu, Xingli

2015-11-14

Density functional theory calculations are used to elucidate the interactions of small platinum clusters (Pt{sub n}, n = 1–5) with the TiC(001) surface. The results are analyzed in terms of geometric, energetic, and electronic properties. It is found that a single Pt atom prefers to be adsorbed at the C-top site, while a Pt{sub 2} cluster prefers dimerization and a Pt{sub 3} cluster forms a linear structure on the TiC(001). As for the Pt{sub 4} cluster, the three-dimensional distorted tetrahedral structure and the two-dimensional square structure almost have equal stability. In contrast with the two-dimensional isolated Pt{sub 5} cluster, the adsorbed Pt{submore » 5} cluster prefers a three-dimensional structure on TiC(001). Substantial charge transfer takes place from TiC(001) surface to the adsorbed Pt{sub n} clusters, resulting in the negatively charged Pt{sub n} clusters. At last, the d-band centers of the absorbed Pt atoms and their implications in the catalytic activity are discussed.« less

Mapping Hydrophobicity on the Protein Molecular Surface at Atom-Level Resolution

PubMed Central

Nicolau Jr., Dan V.; Paszek, Ewa; Fulga, Florin; Nicolau, Dan V.

2014-01-01

A precise representation of the spatial distribution of hydrophobicity, hydrophilicity and charges on the molecular surface of proteins is critical for the understanding of the interaction with small molecules and larger systems. The representation of hydrophobicity is rarely done at atom-level, as this property is generally assigned to residues. A new methodology for the derivation of atomic hydrophobicity from any amino acid-based hydrophobicity scale was used to derive 8 sets of atomic hydrophobicities, one of which was used to generate the molecular surfaces for 35 proteins with convex structures, 5 of which, i.e., lysozyme, ribonuclease, hemoglobin, albumin and IgG, have been analyzed in more detail. Sets of the molecular surfaces of the model proteins have been constructed using spherical probes with increasingly large radii, from 1.4 to 20 Å, followed by the quantification of (i) the surface hydrophobicity; (ii) their respective molecular surface areas, i.e., total, hydrophilic and hydrophobic area; and (iii) their relative densities, i.e., divided by the total molecular area; or specific densities, i.e., divided by property-specific area. Compared with the amino acid-based formalism, the atom-level description reveals molecular surfaces which (i) present an approximately two times more hydrophilic areas; with (ii) less extended, but between 2 to 5 times more intense hydrophilic patches; and (iii) 3 to 20 times more extended hydrophobic areas. The hydrophobic areas are also approximately 2 times more hydrophobicity-intense. This, more pronounced “leopard skin”-like, design of the protein molecular surface has been confirmed by comparing the results for a restricted set of homologous proteins, i.e., hemoglobins diverging by only one residue (Trp37). These results suggest that the representation of hydrophobicity on the protein molecular surfaces at atom-level resolution, coupled with the probing of the molecular surface at different geometric resolutions, can capture processes that are otherwise obscured to the amino acid-based formalism. PMID:25462574

Surface Structure and Surface Electronic States Related to Plasma Cleaning of Silicon and Germanium

NASA Astrophysics Data System (ADS)

Cho, Jaewon

This thesis discusses the surface structure and the surface electronic states of Si and Ge(100) surfaces as well as the effects of oxidation process on the silicon oxide/Si(100) interface structure. The H-plasma exposure was performed in situ at low temperatures. The active species, produced in the H-plasma by the rf-excitation of H_2 gas, not only remove microcontaminants such as oxygen and carbon from the surface, but also passivate the surface with atomic hydrogen by satisfying the dangling bonds of the surface atoms. The surfaces were characterized by Angle Resolved UV-Photoemission Spectroscopy (ARUPS) and Low Energy Electron Diffraction (LEED). In the case of Si(100), H-plasma exposure produced ordered H-terminated crystallographic structures with either a 2 x 1 or 1 x 1 LEED pattern. The hydride phases, found on the surfaces of the cleaned Si(100), were shown to depend on the temperature of the surface during H-plasma cleaning. The electronic states for the monohydride and dihydride phases were identified by ARUPS. When the plasma cleaned surface was annealed, the phase transition from the dihydride to monohydride was observed. The monohydride Si-H surface bond was stable up to 460^circC, and the dangling bond surface states were identified after annealing at 500^circC which was accompanied by the spectral shift. The H-terminated surface were characterized to have a flat band structure. For the Ge(100) surface, an ordered 2 x 1 monohydride phase was obtained from the surface cleaned at 180 ^circC. After plasma exposure at <=170^circC a 1 x 1 surface was observed, but the ARUPS indicated that the surface was predominantly composed of disordered monohydride structures. After annealing above the H-dissociation temperatures, the shift in the spectrum was shown to occur with the dangling bond surface states. The H-terminated surfaces were identified to be unpinned. The interface structure of silicon oxide/Si(100) was studied using ARUPS. Spectral shifts were observed, which were dependent on the processes of surface preparation and oxidation. The shift was characterized in association with the band bending. The origins of the spectral shifts were discussed, including defects at interface and H-passivation in Si. The interface structure is considered to be dependent on the surface preparation and oxidation process.

The effect of sputter temperature on vacancy island behavior on Ni(111) measured by photoemission of adsorbed xenon

NASA Astrophysics Data System (ADS)

Malafsky, Geoffrey P.

1994-04-01

The temperature dependence of vacancy coalescence on an ion bombarded Ni(111) surface is measured by photoemission of adsorbed xenon (PAX). The Ni(111) crystal is sputtered by a low fluence (0.06 ML incident ions) Ar + ion beam with incident kinetic energies of 500-3000 eV. The Xe coverage decreases rapidly with increasing temperature between 88 and 375 K with little additional change from 375 to 775 K. The PAX spectra are acquired with a Xe chamber pressure of 8 × 10 -10 Torr and at a temperature of 88 K. Under these conditions, the Xe is selectively adsorbed at defect sites which would make the Xe coverage proportional to the surface defect density on simple defect structures but the large size of the Xe atom relative to the Ni atom prevents the direct relationship of Xe coverage to the defect density when complex and varying defect structures are present. The decrease in Xe coverage is not attributed to the loss of defect sites by adatom-vacancy recombination but the changing vacancy island shape and size with temperature which alters the ratio of adsorbed Xe atoms to surface vacancy sites. This ratio decreases with increasing temperature as the vacancy islands progress from small and irregularly shaped islands to larger and hexagonally shaped islands. This transition is seen in Monte Carlo simulations of the kinetically driven atomic diffusion on the sputtered surface.

Imaging Dirac-mass disorder from magnetic dopant atoms in the ferromagnetic topological insulator Crx(Bi0.1Sb0.9)2-xTe3.

PubMed

Lee, Inhee; Kim, Chung Koo; Lee, Jinho; Billinge, Simon J L; Zhong, Ruidan; Schneeloch, John A; Liu, Tiansheng; Valla, Tonica; Tranquada, John M; Gu, Genda; Davis, J C Séamus

2015-02-03

To achieve and use the most exotic electronic phenomena predicted for the surface states of 3D topological insulators (TIs), it is necessary to open a "Dirac-mass gap" in their spectrum by breaking time-reversal symmetry. Use of magnetic dopant atoms to generate a ferromagnetic state is the most widely applied approach. However, it is unknown how the spatial arrangements of the magnetic dopant atoms influence the Dirac-mass gap at the atomic scale or, conversely, whether the ferromagnetic interactions between dopant atoms are influenced by the topological surface states. Here we image the locations of the magnetic (Cr) dopant atoms in the ferromagnetic TI Cr0.08(Bi0.1Sb0.9)1.92Te3. Simultaneous visualization of the Dirac-mass gap Δ(r) reveals its intense disorder, which we demonstrate is directly related to fluctuations in n(r), the Cr atom areal density in the termination layer. We find the relationship of surface-state Fermi wavevectors to the anisotropic structure of Δ(r) not inconsistent with predictions for surface ferromagnetism mediated by those states. Moreover, despite the intense Dirac-mass disorder, the anticipated relationship [Formula: see text] is confirmed throughout and exhibits an electron-dopant interaction energy J* = 145 meV·nm(2). These observations reveal how magnetic dopant atoms actually generate the TI mass gap locally and that, to achieve the novel physics expected of time-reversal symmetry breaking TI materials, control of the resulting Dirac-mass gap disorder will be essential.

Imaging Dirac-mass disorder from magnetic dopant atoms in the ferromagnetic topological insulator Crx(Bi0.1Sb0.9)2-xTe3

PubMed Central

Lee, Inhee; Kim, Chung Koo; Lee, Jinho; Billinge, Simon J. L.; Zhong, Ruidan; Schneeloch, John A.; Liu, Tiansheng; Valla, Tonica; Tranquada, John M.; Gu, Genda; Davis, J. C. Séamus

2015-01-01

To achieve and use the most exotic electronic phenomena predicted for the surface states of 3D topological insulators (TIs), it is necessary to open a “Dirac-mass gap” in their spectrum by breaking time-reversal symmetry. Use of magnetic dopant atoms to generate a ferromagnetic state is the most widely applied approach. However, it is unknown how the spatial arrangements of the magnetic dopant atoms influence the Dirac-mass gap at the atomic scale or, conversely, whether the ferromagnetic interactions between dopant atoms are influenced by the topological surface states. Here we image the locations of the magnetic (Cr) dopant atoms in the ferromagnetic TI Cr0.08(Bi0.1Sb0.9)1.92Te3. Simultaneous visualization of the Dirac-mass gap Δ(r) reveals its intense disorder, which we demonstrate is directly related to fluctuations in n(r), the Cr atom areal density in the termination layer. We find the relationship of surface-state Fermi wavevectors to the anisotropic structure of Δ(r) not inconsistent with predictions for surface ferromagnetism mediated by those states. Moreover, despite the intense Dirac-mass disorder, the anticipated relationship Δ(r)∝n(r) is confirmed throughout and exhibits an electron–dopant interaction energy J* = 145 meV·nm2. These observations reveal how magnetic dopant atoms actually generate the TI mass gap locally and that, to achieve the novel physics expected of time-reversal symmetry breaking TI materials, control of the resulting Dirac-mass gap disorder will be essential. PMID:25605947

Three-dimensional hydration layer mapping on the (10.4) surface of calcite using amplitude modulation atomic force microscopy.

PubMed

Marutschke, Christoph; Walters, Deron; Walters, Deron; Hermes, Ilka; Bechstein, Ralf; Kühnle, Angelika

2014-08-22

Calcite, the most stable modification of calcium carbonate, is a major mineral in nature. It is, therefore, highly relevant in a broad range of fields such as biomineralization, sea water desalination and oil production. Knowledge of the surface structure and reactivity of the most stable cleavage plane, calcite (10.4), is pivotal for understanding the role of calcite in these diverse areas. Given the fact that most biological processes and technical applications take place in an aqueous environment, perhaps the most basic - yet decisive - question addresses the interaction of water molecules with the calcite (10.4) surface. In this work, amplitude modulation atomic force microscopy is used for three-dimensional (3D) mapping of the surface structure and the hydration layers above the surface. An easy-to-use scanning protocol is implemented for collecting reliable 3D data. We carefully discuss a comprehensible criterion for identifying the solid-liquid interface within our data. In our data three hydration layers form a characteristic pattern that is commensurate with the underlying calcite surface.

Atomically precise lateral modulation of a two-dimensional electron liquid in anatase TiO 2 thin films

DOE PAGES

Wang, Zhiming; Zhong, Z.; Walker, S. McKeown; ...

2017-03-10

Engineering the electronic band structure of two-dimensional electron liquids (2DELs) confined at the surface or interface of transition metal oxides is key to unlocking their full potential. Here we describe a new approach to tailoring the electronic structure of an oxide surface 2DEL demonstrating the lateral modulation of electronic states with atomic scale precision on an unprecedented length scale comparable to the Fermi wavelength. To this end, we use pulsed laser deposition to grow anatase TiO 2 films terminated by a (1 x 4) in-plane surface reconstruction. Employing photo-stimulated chemical surface doping we induce 2DELs with tunable carrier densities thatmore » are confined within a few TiO 2 layers below the surface. Subsequent in situ angle resolved photoemission experiments demonstrate that the (1 x 4) surface reconstruction provides a periodic lateral perturbation of the electron liquid. Furthermore, this causes strong backfolding of the electronic bands, opening of unidirectional gaps and a saddle point singularity in the density of states near the chemical potential.« less

Imaging the molecular dimensions and oligomerization of protein molecules at the solid-liquid interface by surface oriented molecular sizing (SOMS) microscopy

NASA Astrophysics Data System (ADS)

Waner, Mark Joseph

The structure and behavior of proteins at the solid/liquid interface is of great scientific interest. It has application both to fundamental biochemical understanding, as well as to biotechnological purposes. Interfaces play a critical role in many physiological processes. The mechanism of protein adsorption to surfaces is not very well understood. The current model put forth in much of the literature assumes a two step model. In the first step of this model the protein collides with the surface and adsorbs if its energy is sufficient to overcome the free energy of desorption of surface adsorbed solvent. The second step is often assumed to involve significant conformational change of the secondary and tertiary structure of the protein or enzyme, akin to denaturation. This unfolding of the protein would tend to indicate that loss of function would occur concomitantly, but studies have found very little loss in activity upon adsorption for a number of different protein systems. The recent development of the atomic force microscope (AFM) offers another tool for the examination of protein structure at liquid/solid interfaces. For atomically flat crystals the AFM has been used to determine atomic positions to <1 A resolution. In the case of samples with topographic features larger than atoms, the probe tip of the AFM 'convolutes' with the size and shape of surface features. This has hindered the use of AFM for molecular level structural determination of proteins at the liquid/solid interface. The work presented in this dissertation covers the development of the surface oriented molecular sizing (SOMS) technique which makes use of the angstrom height resolution of the AFM and a physically based mathematical framework for the analysis of the height distribution of adsorbed protein molecules. The surface adsorption and orientation (SAO) model is developed using statistical thermodynamics to model the expected height distributions for molecules adsorbed on a surface. The SOMS technique will be shown to be viable through studies of ferritin and concanavalin A (Con A) at the water/mica interface. Using this technique we are able to determine both the three-dimensional size and the oligomerization state of the adsorbed molecules. This technique will then be utilized for the examination of denaturation of Con A at the interface, by a number of mechanisms. Further, the structural and orientational changes in Con A as a function of pH will also be presented. The final chapter of this dissertation will present an extension of these studies to the deposition and structure of Con A thin films on mica.

Modeling and optimization of atomic layer deposition processes on vertically aligned carbon nanotubes.

PubMed

Yazdani, Nuri; Chawla, Vipin; Edwards, Eve; Wood, Vanessa; Park, Hyung Gyu; Utke, Ivo

2014-01-01

Many energy conversion and storage devices exploit structured ceramics with large interfacial surface areas. Vertically aligned carbon nanotube (VACNT) arrays have emerged as possible scaffolds to support large surface area ceramic layers. However, obtaining conformal and uniform coatings of ceramics on structures with high aspect ratio morphologies is non-trivial, even with atomic layer deposition (ALD). Here we implement a diffusion model to investigate the effect of the ALD parameters on coating kinetics and use it to develop a guideline for achieving conformal and uniform thickness coatings throughout the depth of ultra-high aspect ratio structures. We validate the model predictions with experimental data from ALD coatings of VACNT arrays. However, the approach can be applied to predict film conformality as a function of depth for any porous topology, including nanopores and nanowire arrays.

Effects of growth rate on structural property and adatom migration behaviors for growth of GaInNAs/GaAs (001) by molecular beam epitaxy

NASA Astrophysics Data System (ADS)

Li, Jingling; Gao, Peng; Zhang, Shuguang; Wen, Lei; Gao, Fangliang; Li, Guoqiang

2018-03-01

We have investigated the structural properties and the growth mode of GaInNAs films prepared at different growth rates (Rg) by molecular beam epitaxy. The crystalline structure is studied by high resolution X-ray diffraction, and the evolution of GaInNAs film surface morphologies is studied by atomic force microscopy. It is found that both the crystallinity and the surface roughness are improved by increasing Rg, and the change in the growth mode is attributed to the adatom migration behaviors particularly for In atoms, which is verified by elemental analysis. In addition, we have presented some theoretical calculation results related to the N adsorption energy to show the unique N migration behavior, which is instructive to interpret the growth mechanism of GaInNAs films.

Detection of subsurface core-level shifts in Si 2p core-level photoemission from Si(111)-(1x1):As

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

Paggel, J.J.; Hasselblatt, M.; Horn, K.

1997-04-01

The (7 x 7) reconstruction of the Si(111) surface arises from a lowering energy through the reduction of the number of dangling bonds. This reconstruction can be removed by the adsorption of atoms such as hydrogen which saturate the dangling bonds, or by the incorporation of atoms, such as arsenic which, because of the additional electron it possesses, can form three bonds and a nonreactive lone pair orbital from the remaining two electrons. Core and valence level photoemission and ion scattering data have shown that the As atoms replace the top silicon atoms. Previous core level spectra were interpreted inmore » terms of a bulk and a single surface doublet. The authors present results demonstrate that the core level spectrum contains two more lines. The authors assign these to subsurface silicon layers which also experience changes in the charge distribution when a silicon atom is replaced by an arsenic atom. Subsurface core level shifts are not unexpected since the modifications of the electronic structure and/or of photohole screening are likely to decay into the bulk and not just to affect the top-most substrate atoms. The detection of subsurface components suggests that the adsorption of arsenic leads to charge flow also in the second double layer of the Si(111) surface. In view of the difference in atomic radius between As and Si, it was suggested that the (1 x 1): As surface is strained. The presence of charge rearrangement up to the second double layer implies that the atomic coordinates also exhibit deviations from their ideal Si(111) counterparts, which might be detected through a LEED I/V or photoelectron diffraction analysis.« less

The birth and evolution of surface science: Child of the union of science and technology

PubMed Central

Duke, C. B.

2003-01-01

This article is an account of the birth and evolution of surface science as an interdisciplinary research area. Surface science emanated from the confluence of concepts and tools in physics and chemistry with technological innovations that made it possible to determine the structure and properties of surfaces and interfaces and the dynamics of chemical reactions at surfaces. The combination in the 1960s and 1970s of ultra-high-vacuum (i.e., P < 10−7 Pascal or 10−9 Torr) technology with the recognition that electrons in the energy range from 50 to 500 eV exhibited inelastic collision mean free paths of the order of a few angstroms fostered an explosion of activity. The results were a reformulation of the theory of electron solid scattering, the nearly universal use of electron spectroscopies for surface characterization, the rise of surface science as an independent interdisciplinary research area, and the emergence of the American Vacuum Society (AVS) as a major international scientific society. The rise of microelectronics in the 1970s and 1980s resulted in huge increases in computational power. These increases enabled more complex experiments and the utilization of density functional theory for the quantitative prediction of surface structure and dynamics. Development of scanning-probe microscopies in the 1990s led to atomic-resolution images of macroscopic surfaces and interfaces as well as videos of atoms moving about on surfaces during growth and diffusion. Scanning probes have since brought solid–liquid interfaces into the realm of atomic-level surface science, expanding its scope to more complex systems, including fragile biological materials and processes. PMID:12651946

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

NASA Astrophysics Data System (ADS)

Yee, Dennis

1995-01-01

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

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

Grinter, David C.; Senanayake, Sanjaya D.; Flege, Jan Ingo

Ceria is an important material for chemical conversion processes in catalysis. Its intrinsic properties as a reducible oxide can be exploited to achieve catalytic selectivity and activity. However, numerous phenomenological characteristics of ceria remain unknown and its active nature is ever slowly being unraveled. Well defined models of ceria (111) are an important way to systematically study these properties and take advantage of new in situ methods that require pristine materials that allow for the interrogation of the most fundamental traits of this material. The ceria-Ru(0001) model is now the most well studied model surface with numerous aspects of itsmore » preparation, atomic structure and reactivity studied by several groups. The preparation of CeO x structures oriented with a (111) surface termination can be achieved through molecular beam deposition, facilitating the growth of well-defined nanostructures, microparticles, and films on the Ru(0001) surface. The growth mechanism exploits the epitaxial relationship between CeOx and Ru to form a carpet mode of well oriented layers of Osingle bondCesingle bondO. These models can be studied to unravel the atomic structure and the oxidation state (Ce 4+ and Ce 3+), as prepared and under redox conditions (reduction/oxidation) or with reaction using reactants (e.g., H 2, methanol). Here, we present a discussion of these most recent observations pertaining to the growth mode, arrangement of atoms on the surface, characteristic chemical state, and redox chemistry of the CeO x-Ru surface. As a result, with insights from these studies we propose new strategies to further unravel the chemistry of ceria.« less

Bridging Zirconia Nodes within a Metal–Organic Framework via Catalytic Ni-Hydroxo Clusters to Form Heterobimetallic Nanowires

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

Platero-Prats, Ana E.; League, Aaron B.; Bernales, Varinia

2017-07-24

Metal-organic frameworks (MOFs), with their well-ordered pore networks and tunable surface chemistries, offer a versatile platform for preparing well-defined nanostructures wherein functionality such as catalysis can be incorporated. We resolved the atomic structure of Ni-oxo species deposited in the MOF NU-1000 through atomic layer deposition using local and long-range structure probes, including X-ray absorption spectroscopy, pair distribution function analysis and difference envelope density analysis, with electron microscopy imaging and computational modeling.

The surface energy of water: functional implications of hexagonal/cuboidal transformations in the surface arrays.

PubMed

Widdas, W F

2006-10-30

Hyde's scientific book The Language of Shape has emphasized the importance of minimum surfaces in the structure of biological membranes. Minimum surfaces can be visualized as the property which brings many droplets of liquids to spherical bubbles, since a sphere has the minimum surface to volume ratio. Thus, a sphere with a surface of 4pir2 and volume of 4/3pir3 has a surface to volume ratio of 3/r, that is, the ratio is dependent upon the reciprocal of the radius. The chemistry of water as dihydrides of the electronegative element oxygen is fundamentally dependent upon its polar properties and particularly the delta positive charges on the hydrogen atoms and the double delta negative charge on the larger oxygen atom, which from its mass (16 Da) is regarded as the centre of the water molecules. The cohesion of water as a liquid or as semi-crystal like structures in the surface depends upon electrostatic forces that are comparable in strength to covalent bonds. This review discusses the functional implications of some unexpected properties which have been evinced by model building and illustrated as a Poster in the 4th World Congress of Cellular and Molecular Biology.

Xe adsorption site distributions on Pt(111), Pt(221) and Pt(531)

NASA Astrophysics Data System (ADS)

Gellman, Andrew J.; Baker, L.; Holsclaw, B. S.

2016-04-01

The ideal structures of the Pt(111), Pt(221) and Pt(531) surfaces expose adsorption sites that can be qualitatively described as terrace sites on Pt(111), both step and terrace sites on Pt(221), and kink sites on Pt(531). The real surface structures of these surfaces can be complicated by imperfections such as misorientation, reconstruction and thermal roughening, all of which will influence their distributions of adsorption sites. Xe adsorption sites on the Pt(111), Pt(221) and Pt(531) surfaces have been probed using both photoemission of adsorbed Xe (PAX) and temperature programmed desorption (TPD) of Xe. Both PAX and Xe TPD are sensitive to the adsorption sites of the Xe and serve as complementary means of assessing the distributions of adsorption sites on these three Pt surfaces. The adsorption of Xe is sufficiently sensitive to detect the presence of residual steps on the Pt(111) surface at a density of 1.5% step atoms per Pt atom. On the Pt(221) surface, PAX and Xe TPD reveal adsorption at both terrace and step sites simultaneously. Although the ideal structure of the Pt(531) surface has no well-defined steps or terraces, Xe adsorption indicates that its adsorption sites are best described as a distribution of both step and kink sites with roughly twice as many steps sites as kinks.

Effects of SiO 2 overlayer at initial growth stage of epitaxial Y 2O 3 film growth

NASA Astrophysics Data System (ADS)

Cho, M.-H.; Ko, D.-H.; Choi, Y. G.; Lyo, I. W.; Jeong, K.; Whang, C. N.

2000-12-01

We investigated the dependence of the Y 2O 3 film growth on Si surface at initial growth stage. The reflection high-energy electron diffraction, X-ray scattering, and atomic force microscopy showed that the film crystallinity and morphology strongly depended on whether Si surface contained O or not. In particular, the films grown on oxidized surfaces revealed significant improvement in crystallinity and surface smoothness. A well-ordered atomic structure of Y 2O 3 film was formed on 1.5 nm thick SiO 2 layer with the surface and interfacial roughness markedly enhanced, compared with the film grown on the clean Si surfaces. The epitaxial film on the oxidized Si surface exhibited extremely small mosaic structures at interface, while the film on the clean Si surface displayed an island-like growth with large mosaic structures. The nucleation sites for Y 2O 3 were provided by the reaction between SiO 2 and Y at the initial growth stage. The SiO 2 layer known to hinder crystal growth is found to enhance the nucleation of Y 2O 3, and provides a stable buffer layer against the silicide formation. Thus, the formation of the initial SiO 2 layer is the key to the high-quality epitaxial growth of Y 2O 3 on Si.

Viral capsomere structure, surface processes and growth kinetics in the crystallization of macromolecular crystals visualized by in situ atomic force microscopy

NASA Astrophysics Data System (ADS)

Malkin, A. J.; Kuznetsov, Yu. G.; McPherson, A.

2001-11-01

In situ atomic force microscopy (AFM) was used to investigate surface evolution during the growth of single crystals of turnip yellow mosaic virus (TYMV), cucumber mosaic virus (CMV) and glucose isomerase. Growth of these crystals proceeded by two-dimensional (2D) nucleation. For glucose isomerase, from supersaturation dependencies of tangential step rates and critical step length, the kinetic coefficients of the steps and the surface free energy of the step edge were calculated for different crystallographic directions. The molecular structure of the step edges, the adsorption of individual virus particles and their aggregates, and the initial stages of formation of 2D nuclei on the surfaces of TYMV and CMV crystals were recorded. The surfaces of individual TYMV virions within crystals were visualized, and hexameric and pentameric capsomers of the T=3 capsids were clearly resolved. This, so far as we are aware, is the first direct visualization of the capsomere structure of a virus by AFM. In the course of recording the in situ development of the TYMV crystals, a profound restructuring of the surface arrangement was observed. This transformation was highly cooperative in nature, but the transitions were unambiguous and readily explicable in terms of an organized loss of classes of virus particles from specific lattice positions.

Influence of surface phenomena in oxidative desulfurization with WOx/ZrO2 catalysts

NASA Astrophysics Data System (ADS)

Torres-García, E.; Canizal, G.; Velumani, S.; Ramírez-Verduzco, L. F.; Murrieta-Guevara, F.; Ascencio, J. A.

2004-12-01

Oil refinery related catalysis, particularly hydro desulfurization is viewed as a mature technology, but still we view that more efforts have to be made to boost the efficiency of the existing catalysts. So in this article we report the use of WOx/ZrO2 catalysts for the oxidation of dibenzothiophene (DBT) as a more effective material in nanometer scales. The WOx/ZrO2 samples were prepared by solid impregnation of ZrO2-x(OH)2x with ammonium metatungstate solution maintaining the pH at 10. Detailed structural and surface morphological analyses were carried out using Raman spectroscopy and Atomic force microscopy. In order to understand the catalytic activity which is largely influenced by the surface morphology, an interpretation based on the experimental results is given. The results showed an important correlation between the catalytic efficiency with the morphology of the surface which is identified as arrays of planes with steps of around 10 nm with the structures showing faceting with a preferential angle of 90°. It was established that when the number of W atoms in the surface increase the catalytic efficiency also increases. Thus we conclude that the material efficiency as a catalyst is directly related with the surface structure.

Potential-specific structure at the hematite-electrolyte interface

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

McBriarty, Martin E.; Stubbs, Joanne; Eng, Peter

The atomic-scale structure of interfaces between metal oxides and aqueous electrolytes controls their catalytic, geochemical, and corrosion behavior. Measurements that probe these interfaces in situ provide important details of ion and solvent arrangements, but atomically precise structural models do not exist for common oxide-electrolyte interfaces far from equilibrium. Using a novel cell, we measured the structure of the hematite (a-Fe 2O 3) (110more » $$\\bar{2}$$)-electrolyte interface under controlled electrochemical bias using synchrotron crystal truncation rod X ray scattering. At increasingly cathodic potentials, charge-compensating protonation of surface oxygen groups increases the coverage of specifically bound water while adjacent water layers displace outwardly and became disordered. Returning to open circuit potential leaves the surface in a persistent metastable protonation state. The flux of current and ions at applied potential is thus regulated by a unique interfacial electrolyte environment, suggesting that electrical double layer models should be adapted to the dynamically changing interfacial structure far from equilibrium.« less

Multi-scale predictive modeling of nano-material and realistic electron devices

NASA Astrophysics Data System (ADS)

Palaria, Amritanshu

Among the challenges faced in further miniaturization of electronic devices, heavy influence of the detailed atomic configuration of the material(s) involved, which often differs significantly from that of the bulk material(s), is prominent. Device design has therefore become highly interrelated with material engineering at the atomic level. This thesis aims at outlining, with examples, a multi-scale simulation procedure that allows one to integrate material and device aspects of nano-electronic design to predict behavior of novel devices with novel material. This is followed in four parts: (1) An approach that combines a higher time scale reactive force field analysis with density functional theory to predict structure of new material is demonstrated for the first time for nanowires. Novel stable structures for very small diameter silicon nanowires are predicted. (2) Density functional theory is used to show that the new nanowire structures derived in 1 above have properties different from diamond core wires even though the surface bonds in some may be similar to the surface of bulk silicon. (3) Electronic structure of relatively large-scale germanium sections of realistically strained Si/strained Ge/ strained Si nanowire heterostructures is computed using empirical tight binding and it is shown that the average non-homogeneous strain in these structures drives their interesting non-conventional electronic characteristics such as hole effective masses which decrease as the wire cross-section is reduced. (4) It is shown that tight binding, though empirical in nature, is not necessarily limited to the material and atomic structure for which the parameters have been empirically derived, but that simple changes may adapt the derived parameters to new bond environments. Si (100) surface electronic structure is obtained from bulk Si parameters.

Exploring the Structure of Nitrogen-Rich Ionic Liquids and Their Binding to the Surface of Oxide-Free Boron Nanoparticles

DTIC Science & Technology

2013-01-29

Shreeve et al . synthesized a number of highly energetic ionic liquids with multiple nitrogen atoms in their structures,18−23 in the hope of increasing...results have to be interpreted with caution. Lovelock et al .61 have shown that clean surfaces can be obtained by sputtering for the [CnC1Im][Tf2N] IL...flat on the gold surface while a long chain ether functional group is directed away from the surface, providing steric stabilization.74 Zhang et al

Nanoscale mass conveyors

DOEpatents

Regan, Brian C [Oakland, CA; Aloni, Shaul [Albany, CA; Zettl, Alexander K [Kensington, CA

2008-03-11

A mass transport method and device for individually delivering chargeable atoms or molecules from source particles is disclosed. It comprises a channel; at least one source particle of chargeable material fixed to the surface of the channel at a position along its length; a means of heating the channel; and a means for applying an controllable electric field along the channel, whereby the device transports the atoms or molecules along the channel in response to applied electric field. In a preferred embodiment, the mass transport device will comprise a multiwalled carbon nanotube (MWNT), although other one dimensional structures may also be used. The MWNT or other structure acts as a channel for individual or small collections of atoms due to the atomic smoothness of the material. Also preferred is a source particle of a metal such as indium. The particles move by dissociation into small units, in some cases, individual atoms. The particles are preferably less than 100 nm in size.

Substrate Effects for Atomic Chain Electronics

NASA Technical Reports Server (NTRS)

Yamada, Toshishige; Saini, Subhash (Technical Monitor)

1998-01-01

A substrate for future atomic chain electronics, where adatoms are placed at designated positions and form atomically precise device components, is studied theoretically. The substrate has to serve as a two-dimensional template for adatom mounting with a reasonable confinement barrier and also provide electronic isolation, preventing unwanted coupling between independent adatom structures. For excellent structural stability, we demand chemical bonding between the adatoms and substrate atoms, but then good electronic isolation may not be guaranteed. Conditions are clarified for good isolation. Because of the chemical bonding, fundamental adatom properties are strongly influenced: a chain with group IV adatoms having two chemical bonds, or a chain with group III adatoms having one chemical bond is semiconducting. Charge transfer from or to the substrate atoms brings about unintentional doping, and the electronic properties have to be considered for the entire combination of the adatom and substrate systems even if the adatom modes are well localized at the surface.

Electrode structure of a compact microwave driven capacitively coupled atomic beam source

NASA Astrophysics Data System (ADS)

Shimabukuro, Yuji; Takahashi, Hidenori; Wada, Motoi

2018-01-01

A compact magnetic field free atomic beam source was designed, assembled and tested the performance to produce hydrogen and nitrogen atoms. A forced air-cooled solid-state microwave power supply at 2.45 GHz frequency drives the source up to 100 W through a coaxial transmission cable coupled to a triple stub tuner for realizing a proper matching condition to the discharge load. The discharge structure of the source affected the range of operation pressure, and the pressure was reduced by four orders of magnitude through improving the electrode geometry to enhance the local electric field intensity. Optical emission spectra of the produced plasmas indicate production of hydrogen and nitrogen atoms, while the flux intensity of excited nitrogen atoms monitored by a surface ionization type detector showed the signal level close to a source developed for molecular beam epitaxy applications with 500 W RF power.

Atomic force microscopy of starch systems.

PubMed

Zhu, Fan

2017-09-22

Atomic force microscopy (AFM) generates information on topography, adhesion, and elasticity of sample surface by touching with a tip. Under suitable experimental settings, AFM can image biopolymers of few nanometers. Starch is a major food and industrial component. AFM has been used to probe the morphology, properties, modifications, and interactions of starches from diverse botanical origins at both micro- and nano-structural levels. The structural information obtained by AFM supports the blocklet structure of the granules, and provides qualitative and quantitative basis for some physicochemical properties of diverse starch systems. It becomes evident that AFM can complement other microscopic techniques to provide novel structural insights for starch systems.

Molecular-dynamics simulations of self-assembled monolayers (SAM) on parallel computers

NASA Astrophysics Data System (ADS)

Vemparala, Satyavani

The purpose of this dissertation is to investigate the properties of self-assembled monolayers, particularly alkanethiols and Poly (ethylene glycol) terminated alkanethiols. These simulations are based on realistic interatomic potentials and require scalable and portable multiresolution algorithms implemented on parallel computers. Large-scale molecular dynamics simulations of self-assembled alkanethiol monolayer systems have been carried out using an all-atom model involving a million atoms to investigate their structural properties as a function of temperature, lattice spacing and molecular chain-length. Results show that the alkanethiol chains tilt from the surface normal by a collective angle of 25° along next-nearest neighbor direction at 300K. At 350K the system transforms to a disordered phase characterized by small tilt angle, flexible tilt direction, and random distribution of backbone planes. With increasing lattice spacing, a, the tilt angle increases rapidly from a nearly zero value at a = 4.7A to as high as 34° at a = 5.3A at 300K. We also studied the effect of end groups on the tilt structure of SAM films. We characterized the system with respect to temperature, the alkane chain length, lattice spacing, and the length of the end group. We found that the gauche defects were predominant only in the tails, and the gauche defects increased with the temperature and number of EG units. Effect of electric field on the structure of poly (ethylene glycol) (PEG) terminated alkanethiol self assembled monolayer (SAM) on gold has been studied using parallel molecular dynamics method. An applied electric field triggers a conformational transition from all-trans to a mostly gauche conformation. The polarity of the electric field has a significant effect on the surface structure of PEG leading to a profound effect on the hydrophilicity of the surface. The electric field applied anti-parallel to the surface normal causes a reversible transition to an ordered state in which the oxygen atoms are exposed. On the other hand, an electric field applied in a direction parallel to the surface normal introduces considerable disorder in the system and the oxygen atoms are buried inside.

TED Study of Si(113) Surfaces

NASA Astrophysics Data System (ADS)

Suzuki, T.; Minoda, H.; Tanishiro, Y.; Yagi, K.

A TED study of Si(113) surfaces was carried out. Reflections from the 3 × 2 reconstruction were seen at room temperature, while half-order reflections were very faint. The surface showed the phase transition between the 3 × 1 and the disordered (rough) structures at about 930°C. The (113) surface structure at room temperature was analyzed using TED intensity. Four kinds of structure models proposed previously, including both the 3 × 1 and the 3 × 2 reconstructed structures, were examined. The R-factors calculated using the energy-optimized atomic coordinates are not sufficiently small. After minimization of the R-factors, Dabrowski's 3 × 2 structure model is most agreeable, while Ranke's 3 × 1 and 3 × 2 structure models are not to be excluded. STM observation showed that the surface is composed of small domains of the 3 × 2 structure.

Correlating structural dynamics and catalytic activity of AgAu nanoparticles with ultrafast spectroscopy and all-atom molecular dynamics simulations.

PubMed

Ferbonink, G F; Rodrigues, T S; Dos Santos, D P; Camargo, P H C; Albuquerque, R Q; Nome, R A

2018-05-29

In this study, we investigated hollow AgAu nanoparticles with the goal of improving our understanding of the composition-dependent catalytic activity of these nanoparticles. AgAu nanoparticles were synthesized via the galvanic replacement method with controlled size and nanoparticle compositions. We studied extinction spectra with UV-Vis spectroscopy and simulations based on Mie theory and the boundary element method, and ultrafast spectroscopy measurements to characterize decay constants and the overall energy transfer dynamics as a function of AgAu composition. Electron-phonon coupling times for each composition were obtained from pump-power dependent pump-probe transients. These spectroscopic studies showed how nanoscale surface segregation, hollow interiors and porosity affect the surface plasmon resonance wavelength and fundamental electron-phonon coupling times. Analysis of the spectroscopic data was used to correlate electron-phonon coupling times to AgAu composition, and thus to surface segregation and catalytic activity. We have performed all-atom molecular dynamics simulations of model hollow AgAu core-shell nanoparticles to characterize nanoparticle stability and equilibrium structures, besides providing atomic level views of nanoparticle surface segregation. Overall, the basic atomistic and electron-lattice dynamics of core-shell AgAu nanoparticles characterized here thus aid the mechanistic understanding and performance optimization of AgAu nanoparticle catalysts.

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.

Lubricants or lubricant additives composed of ionic liquids containing ammonium cations

DOEpatents

Qu, Jun [Knoxville, TN; Truhan, Jr; John, J [Cookeville, TN; Dai, Sheng [Knoxville, TN; Luo, Huimin [Knoxville, TN; Blau, Peter J [Knoxville, TN

2010-07-13

A lubricant or lubricant additive is an ionic liquid alkylammonium salt. The alkylammonium salt has the structure R.sub.xNH.sub.(4-x).sup.+,[F.sub.3C(CF.sub.2).sub.yS(O).sub.2].sub.2N.sup- .- where x is 1 to 3, R is independently C.sub.1 to C.sub.12 straight chain alkyl, branched chain alkyl, cycloalkyl, alkyl substituted cycloalkyl, cycloalkyl substituted alkyl, or, optionally, when x is greater than 1, two R groups comprise a cyclic structure including the nitrogen atom and 4 to 12 carbon atoms, and y is independently 0 to 11. The lubricant is effective for the lubrication of many surfaces including aluminum and ceramics surfaces.

Adsorption and Electronic Structure of Sr and Ag Atoms on Graphite Surfaces: a First-Principles Study

NASA Astrophysics Data System (ADS)

Luo, Xiao-Feng; Fang, Chao; Li, Xin; Lai, Wen-Sheng; Sun, Li-Feng; Liang, Tong-Xiang

2013-06-01

The adsorption behaviors of radioactive strontium and silver nuclides on the graphite surface in a high-temperature gas-cooled reactor are studied by first-principles theory using generalized gradient approximation (GGA) and local density approximation (LDA) pseudo-potentials. It turns out that Sr prefers to be absorbed at the hollow of the carbon hexagonal cell by 0.54 eV (GGA), while Ag likes to sit right above the carbon atom with an adsorption energy of almost zero (GGA) and 0.45 eV (LDA). Electronic structure analysis reveals that Sr donates its partial electrons of the 4p and 5s states to the graphite substrate, while Ag on graphite is a physical adsorption without any electron transfer.

Multibody correlations in the hydrophobic solvation of glycine peptides

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

Harris, Robert C.; Drake, Justin A.; Pettitt, B. Montgomery, E-mail: mpettitt@utmb.edu

2014-12-14

Protein collapse during folding is often assumed to be driven by a hydrophobic solvation energy (ΔG{sub vdw}) that scales linearly with solvent-accessible surface area (A). In a previous study, we argued that ΔG{sub vdw}, as well as its attractive (ΔG{sub att}) and repulsive (ΔG{sub rep}) components, was not simply a linear function of A. We found that the surface tensions, γ{sub rep}, γ{sub att}, and γ{sub vdw}, gotten from ΔG{sub rep}, ΔG{sub att}, and ΔG{sub vdw} against A for four configurations of deca-alanine differed from those obtained for a set of alkanes. In the present study, we extend our analysismore » to fifty decaglycine structures and atomic decompositions. We find that different configurations of decaglycine generate different estimates of γ{sub rep}. Additionally, we considered the reconstruction of the solvation free energy from scaling the free energy of solvation of each atom type, free in solution. The free energy of the isolated atoms, scaled by the inverse surface area the atom would expose in the molecule does not reproduce the γ{sub rep} for the intact decaglycines. Finally, γ{sub att} for the decaglycine conformations is much larger in magnitude than those for deca-alanine or the alkanes, leading to large negative values of γ{sub vdw} (−74 and −56 cal/mol/Å{sup 2} for CHARMM27 and AMBER ff12sb force fields, respectively). These findings imply that ΔG{sub vdw} favors extended rather than compact structures for decaglycine. We find that ΔG{sub rep} and ΔG{sub vdw} have complicated dependencies on multibody correlations between solute atoms, on the geometry of the molecular surface, and on the chemical identities of the atoms.« less

Hybrid quantum and molecular mechanics embedded cluster models for chemistry on silicon and silicon carbide surfaces

NASA Astrophysics Data System (ADS)

Shoemaker, James Richard

Fabrication of silicon carbide (SiC) semiconductor devices are of interest for aerospace applications because of their high-temperature tolerance. Growth of an insulating SiO2 layer on SiC by oxidation is a poorly understood process, and sometimes produces interface defects that degrade device performance. Accurate theoretical models of surface chemistry, using quantum mechanics (QM), do not exist because of the huge computational cost of solving Schrodinger's equation for a molecular cluster large enough to represent a surface. Molecular mechanics (MM), which describes a molecule as a collection of atoms interacting through classical potentials, is a fast computational method, good at predicting molecular structure, but cannot accurately model chemical reactions. A new hybrid QM/MM computational method for surface chemistry was developed and applied to silicon and SiC surfaces. The addition of MM steric constraints was shown to have a large effect on the energetics of O atom adsorption on SiC. Adsorption of O atoms on Si-terminated SiC(111) favors above surface sites, in contrast to Si(111), but favors subsurface adsorption sites on C- terminated SiC(111). This difference, and the energetics of C atom etching via CO2 desorption, can explain the observed poor performance of SiC devices in which insulating layers were grown on C-terminated surfaces.

Synthesis of borophenes: Anisotropic, two-dimensional boron polymorphs

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

Mannix, A. J.; Zhou, X. -F.; Kiraly, B.

At the atomic-cluster scale, pure boron is markedly similar to carbon, forming simple planar molecules and cage-like fullerenes. Theoretical studies predict that two-dimensional (2D) boron sheets will adopt an atomic configuration similar to that of boron atomic clusters. We synthesized atomically thin, crystalline 2D boron sheets (i.e., borophene) on silver surfaces under ultrahigh-vacuum conditions. Atomic-scale characterization, supported by theoretical calculations, revealed structures reminiscent of fused boron clusters with multiple scales of anisotropic, out-of-plane buckling. Unlike bulk boron allotropes, borophene shows metallic characteristics that are consistent with predictions of a highly anisotropic, 2D metal.

Application of atomic force microscopy to microbial surfaces: from reconstituted cell surface layers to living cells.

PubMed

Dufrêne, Y F

2001-02-01

The application of atomic force microscopy (AFM) to probe the ultrastructure and physical properties of microbial cell surfaces is reviewed. The unique capabilities of AFM can be summarized as follows: imaging surface topography with (sub)nanometer lateral resolution; examining biological specimens under physiological conditions; measuring local properties and interaction forces. AFM is being used increasingly for: (i) visualizing the surface ultrastructure of microbial cell surface layers, including bacterial S-layers, purple membranes, porin OmpF crystals and fungal rodlet layers; (ii) monitoring conformational changes of individual membrane proteins; (iii) examining the morphology of bacterial biofilms, (iv) revealing the nanoscale structure of living microbial cells, including fungi, yeasts and bacteria, (v) mapping interaction forces at microbial surfaces, such as van der Waals and electrostatic forces, solvation forces, and steric/bridging forces; and (vi) probing the local mechanical properties of cell surface layers and of single cells.

Relaxation of Actinide Surfaces: An All Electron Study

NASA Astrophysics Data System (ADS)

Atta-Fynn, Raymond; Dholabhai, Pratik; Ray, Asok

2006-10-01

Fully relativistic full potential density functional calculations with a linearized augmented plane wave plus local orbitals basis (LAPW + lo) have been performed to investigate the relaxations of heavy actinide surfaces, namely the (111) surface of fcc δ-Pu and the (0001) surface of dhcp Am using WIEN2k. This code uses the LAPW + lo method with the unit cell divided into non-overlapping atom-centered spheres and an interstitial region. The APW+lo basis is used to describe all s, p, d, and f states and LAPW basis to describe all higher angular momentum states. Each surface was modeled by a three-layer periodic slab separated by 60 Bohr vacuum with four atoms per surface unit cell. In general, we have found a contraction of the interlayer separations for both Pu and Am. We will report, in detail, the electronic and geometric structures of the relaxed surfaces and comparisons with the respective non-relaxed surfaces.

Influence of tool shape on lattice rearrangement under loading conditions reproducing friction stir welding

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

Konovalenko, Ivan S., E-mail: ivkon@ispms.tsc.ru; Konovalenko, Igor S., E-mail: igkon@ispms.tsc.ru; National Research Tomsk Polytechnic University, Tomsk, 634050

2015-10-27

Metal behavior under loading conditions that reproduce friction stir welding was studied on the atomic scale. Calculations were conducted based on molecular dynamics simulation with potentials calculated within the embedded atom method. The loading of the interface between two crystallites, whose structure corresponded to aluminum alloy 2024, was simulated by the motion of a cone-shaped tool along the interface with constant angular and translational velocities. The motion of the rotating tool causes fracture of the workpiece crystal structure with subsequent mixing of surface atoms of the interfacing crystallites. It is shown that the resistance force acting on the moving toolmore » from the workpiece and the process of structural defect formation in the workpiece depend on the tool shape.« less

Crystal faces of anhydrite (CaSO 4) and their preferential dissolution in aqueous solutions studied with AFM

NASA Astrophysics Data System (ADS)

Shindo, H.; Kaise, M.; Kondoh, H.; Nishihara, C.; Nozoye, H.

Structures of cleaved surfaces of anhydrite were studied with atomic force microscopy (AFM) before and after partial dissolution in aqueous solutions of NH 4Cl and NaHSO 4. Two crystal faces showed atom-resolved images just after cleavage, (100) and (010), of which the former was roughened by the dissolution, while step structures were developed on the latter. After dissolution, steplines ran along the a- and c-axes on the (010) face, while they ran in directions inclined to these axes before. It was revealed that the arrangement of dipoles is a key factor in determining stabilities of step structures on crystal faces. On the terraces, the arrangement of oxygen atoms of the sulfate groups and calcium ions were clearly observed.

Activity of N-coordinated multi-metal-atom active site structures for Pt-free oxygen reduction reaction catalysis: Role of *OH ligands

DOE PAGES

Holby, Edward F.; Taylor, Christopher D.

2015-03-19

We report calculated oxygen reduction reaction energy pathways on multi-metal-atom structures that have previously been shown to be thermodynamically favorable. We predict that such sites have the ability to spontaneously cleave the O₂ bond and then will proceed to over-bind reaction intermediates. In particular, the *OH bound state has lower energy than the final 2 H₂O state at positive potentials. Contrary to traditional surface catalysts, this *OH binding does not poison the multi-metal-atom site but acts as a modifying ligand that will spontaneously form in aqueous environments leading to new active sites that have higher catalytic activities. These *OH boundmore » structures have the highest calculated activity to date.« less

Decarboxylation of furfural on Pd(111): Ab initio molecular dynamics simulations

NASA Astrophysics Data System (ADS)

Xue, Wenhua; Dang, Hongli; Shields, Darwin; Liu, Yingdi; Jentoft, Friederike; Resasco, Daniel; Wang, Sanwu

2013-03-01

Furfural conversion over metal catalysts plays an important role in the studies of biomass-derived feedstocks. We report ab initio molecular dynamics simulations for the decarboxylation process of furfural on the palladium surface at finite temperatures. We observed and analyzed the atomic-scale dynamics of furfural on the Pd(111) surface and the fluctuations of the bondlengths between the atoms in furfural. We found that the dominant bonding structure is the parallel structure in which the furfural plane, while slightly distorted, is parallel to the Pd surface. Analysis of the bondlength fluctuations indicates that the C-H bond is the aldehyde group of a furfural molecule is likely to be broken first, while the C =O bond has a tendency to be isolated as CO. Our results show that the reaction of decarbonylation dominates, consistent with the experimental measurements. Supported by DOE (DE-SC0004600). Simulations and calculations were performed on XSEDE's and NERSC's supercomputers.

Interstitial copper defect induced reconstruction of a new ;CuO4; quadrilateral in CaCu3Ti4O12: A first-principles study

NASA Astrophysics Data System (ADS)

Xiao, Haibo; Xu, Linfang; Wang, Ruilong; Yang, Changping

2017-09-01

The geometric structure, electronic structure and formation energy of CaCu3Ti4O12 (CCTO) with interstitial copper atom have been studied using the density-functional method within the GGA approximation. Result of structural optimization shows that the interstitial Cu-atom (Cu7) prefers to occupy a special location which is symmetrical with an intrinsic copper atom (Cu13) deviated from the normal site. The mulliken analysis indicates the loss of electrons from interstitial atom (Cu7) and Cu13 are only half more of the losing in other copper atom, which reveals a characteristics of covalent bonding between Cu7/Cu13 and surrounding oxygen atoms respectively. Meanwhile, it is found from electron density difference (EDD) and orbital analysis that the introduction of interstitial Cu atom causes prominent structural reconstruction of a new ;CuO4; quadrilateral. Moreover, the new ;CuO4; planar leads to a corresponding electronic reconstruction in the hybridization between Cu7/Cu13 3d and O 2p at the vicinity of fermi surface, for which a new conductive filament channel comes into being. Besides, the formation energies of the interstitial defects in various charge states are corrected with the value of 2.18, -4.17 and -9.46 eV for charge of 0, 1+ and 2+, respectively.

Detailed low-energy electron diffraction analysis of the (4×4) surface structure of C60 on Cu(111): Seven-atom-vacancy reconstruction

NASA Astrophysics Data System (ADS)

Xu, Geng; Shi, Xing-Qiang; Zhang, R. Q.; Pai, Woei Wu; Jeng, H. T.; Van Hove, M. A.

2012-08-01

A detailed and exhaustive structural analysis by low-energy electron diffraction (LEED) is reported for the C60-induced reconstruction of Cu(111), in the system Cu(111) + (4 × 4)-C60. A wide LEED energy range allows enhanced sensitivity to the crucial C60-metal interface that is buried below the 7-Å-thick molecular layer. The analysis clearly favors a seven-Cu-atom vacancy model (with Pendry R-factor Rp = 0.376) over a one-Cu-atom vacancy model (Rp = 0.608) and over nonreconstructed models (Rp = 0.671 for atop site and Rp = 0.536 for hcp site). The seven-Cu-atom vacancy forms a (4 × 4) lattice of bowl-like holes. In each hole, a C60 molecule can nestle by forming strong bonds (shorter than 2.30 Å) between 15 C atoms of the molecule and 12 Cu atoms of the outermost and second Cu layers.

Resolving the Chemically Discrete Structure of Synthetic Borophene Polymorphs.

PubMed

Campbell, Gavin P; Mannix, Andrew J; Emery, Jonathan D; Lee, Tien-Lin; Guisinger, Nathan P; Hersam, Mark C; Bedzyk, Michael J

2018-05-09

Atomically thin two-dimensional (2D) materials exhibit superlative properties dictated by their intralayer atomic structure, which is typically derived from a limited number of thermodynamically stable bulk layered crystals (e.g., graphene from graphite). The growth of entirely synthetic 2D crystals, those with no corresponding bulk allotrope, would circumvent this dependence upon bulk thermodynamics and substantially expand the phase space available for structure-property engineering of 2D materials. However, it remains unclear if synthetic 2D materials can exist as structurally and chemically distinct layers anchored by van der Waals (vdW) forces, as opposed to strongly bound adlayers. Here, we show that atomically thin sheets of boron (i.e., borophene) grown on the Ag(111) surface exhibit a vdW-like structure without a corresponding bulk allotrope. Using X-ray standing wave-excited X-ray photoelectron spectroscopy, the positions of boron in multiple chemical states are resolved with sub-angström spatial resolution, revealing that the borophene forms a single planar layer that is 2.4 Å above the unreconstructed Ag surface. Moreover, our results reveal that multiple borophene phases exhibit these characteristics, denoting a unique form of polymorphism consistent with recent predictions. This observation of synthetic borophene as chemically discrete from the growth substrate suggests that it is possible to engineer a much wider variety of 2D materials than those accessible through bulk layered crystal structures.

Atomic and molecular oxygen adsorbed on (111) transition metal surfaces: Cu and Ni

NASA Astrophysics Data System (ADS)

López-Moreno, S.; Romero, A. H.

2015-04-01

Density functional theory is used to investigate the reaction of oxygen with clean copper and nickel [111]-surfaces. We study several alternative adsorption sites for atomic and molecular oxygen on both surfaces. The minimal energy geometries and adsorption energies are in good agreement with previous theoretical studies and experimental data. From all considered adsorption sites, we found a new O2 molecular precursor with two possible dissociation paths on the Cu(111) surface. Cross barrier energies for the molecular oxygen dissociation have been calculated by using the climbing image nudge elastic band method, and direct comparison with experimental results is performed. Finally, the structural changes and adsorption energies of oxygen adsorbed on surface when there is a vacancy nearby the adsorption site are also considered.

Self-assembly of acetate adsorbates drives atomic rearrangement on the Au(110) surface

DOE PAGES

Hiebel, Fanny; Shong, Bonggeun; Chen, Wei; ...

2016-10-12

Weak inter-adsorbate interactions are shown to play a crucial role in determining surface structure, with major implications for its catalytic reactivity. This is exemplified here in the case of acetate bound to Au(110), where the small extra energy of the van der Waals interactions among the surface-bound groups drives massive restructuring of the underlying Au. Acetate is a key intermediate in electro-oxidation of CO 2 and a poison in partial oxidation reactions. Metal atom migration originates at surface defects and is likely facilitated by weakened Au–Au interactions due to bonding with the acetate. Even though the acetate is a relativelymore » small molecule, weak intermolecular interaction provides the energy required for molecular self-assembly and reorganization of the metal surface.« less

Self-assembly of acetate adsorbates drives atomic rearrangement on the Au(110) surface

PubMed Central

Hiebel, Fanny; Shong, Bonggeun; Chen, Wei; Madix, Robert J.; Kaxiras, Efthimios; Friend, Cynthia M.

2016-01-01

Weak inter-adsorbate interactions are shown to play a crucial role in determining surface structure, with major implications for its catalytic reactivity. This is exemplified here in the case of acetate bound to Au(110), where the small extra energy of the van der Waals interactions among the surface-bound groups drives massive restructuring of the underlying Au. Acetate is a key intermediate in electro-oxidation of CO2 and a poison in partial oxidation reactions. Metal atom migration originates at surface defects and is likely facilitated by weakened Au–Au interactions due to bonding with the acetate. Even though the acetate is a relatively small molecule, weak intermolecular interaction provides the energy required for molecular self-assembly and reorganization of the metal surface. PMID:27731407

Atomic and molecular oxygen adsorbed on (111) transition metal surfaces: Cu and Ni.

PubMed

López-Moreno, S; Romero, A H

2015-04-21

Density functional theory is used to investigate the reaction of oxygen with clean copper and nickel [111]-surfaces. We study several alternative adsorption sites for atomic and molecular oxygen on both surfaces. The minimal energy geometries and adsorption energies are in good agreement with previous theoretical studies and experimental data. From all considered adsorption sites, we found a new O2 molecular precursor with two possible dissociation paths on the Cu(111) surface. Cross barrier energies for the molecular oxygen dissociation have been calculated by using the climbing image nudge elastic band method, and direct comparison with experimental results is performed. Finally, the structural changes and adsorption energies of oxygen adsorbed on surface when there is a vacancy nearby the adsorption site are also considered.

Modification of Structure and Tribological Properties of the Surface Layer of Metal-Ceramic Composite under Electron Irradiation in the Plasmas of Inert Gases

NASA Astrophysics Data System (ADS)

Ovcharenko, V. E.; Ivanov, K. V.; Mohovikov, A. A.; Yu, B.; Xu, Yu; Zhong, L.

2018-01-01

Metal-ceramic composites are the main materials for high-load parts in tribomechanical systems. Modern approaches to extend the operation life of tribomechanical systems are based on increasing the strength and tribological properties of the surface layer having 100 to 200 microns in depth. The essential improvement of the properties occurs when high dispersed structure is formed in the surface layer using high-energy processing. As a result of the dispersed structure formation the more uniform distribution of elastic stresses takes place under mechanical or thermal action, the energy of stress concentrators emergence significantly increases and the probability of internal defects formation reduces. The promising method to form the dispersed structure in the surface layer is pulse electron irradiation in the plasmas of inert gases combining electron irradiation and ion bombardment in one process. The present work reports upon the effect of pulse electron irradiation in plasmas of different inert gases with different atomic mass and ionization energy on the structure and tribological properties of the surface layer of TiC/(Ni-Cr) metal-ceramic composite with the volume ratio of the component being 50:50. It is experimentally shown that high-dispersed heterophase structure with a fraction of nanosized particles is formed during the irradiation. Electron microscopy study reveals that refining of the initial coarse TiC particles occurs via their dissolution in the molten metal binder followed by the precipitation of secondary fine particles in the interparticle layers of the binder. The depth of modified layer and the fraction of nanosized particles increase when the atomic number of the plasma gas increases and ionization energy decreases. The wear resistance of metal-ceramic composite improves in accordance to the formation of nanocrystalline structure in the surface layer.

Emergence of Metallic Properties at LiFePO4 Surfaces and LiFePO4/Li2S Interfaces: An Ab Initio Study.

PubMed

Timoshevskii, Vladimir; Feng, Zimin; Bevan, Kirk H; Zaghib, Karim

2015-08-26

The atomic and electronic structures of the LiFePO4 (LFP) surface, both bare and reconstructed upon possible oxygenation, are theoretically studied by ab initio methods. On the basis of total energy calculations, the atomic structure of the oxygenated surface is proposed, and the effect of surface reconstruction on the electronic properties of the surface is clarified. While bare LFP(010) surface is insulating, adsorption of oxygen leads to the emergence of semimetallic behavior by inducing the conducting states in the band gap of the system. The physical origin of these conducting states is investigated. We further demonstrate that deposition of Li2S layers on top of oxygenated LFP(010) surface leads to the formation of additional conducting hole states in the first layer of Li2S surface because of the charge transfer from sulfur p-states to the gap states of LFP surface. This demonstrates that oxygenated LFP surface not only provides conducting layers itself, but also induces conducting channels in the top layer of Li2S. These results help to achieve further understanding of potential role of LFP particles in improving the performance of Li-S batteries through emergent interface conductivity.

Theoretical Studies of the Structure and the Dynamics on Clean and Chemisorbed Metal Surfaces

NASA Astrophysics Data System (ADS)

Yang, Liqiu

Molecular dynamics (MD) and lattice dynamics (LD) techniques are employed to investigate several phenomena related to the structure and vibrations at metal surfaces. The MD simulations are performed with the many-body interaction potentials obtained using the Embedded-Atom Method (EAM). As specific examples, we present the results for Ag(100) at 300 K and Cu(100) at 150 K, 300 K, and 600 K. The calculated frequencies and polarizations of all surface modes and resonances at the high-symmetry points in the two-dimensional Brillouin zone are in good agreement with available data, as well as, existing lattice dynamics results with force constants obtained from first-principles calculations. Our calculated surface relaxation is also in reasonable agreement with the data. We also test a much simpler lattice dynamics model with nearest neighbor central force interactions, and conclude that it can reproduce the main features of the phonon modes, but only when adjustable surface parameters are used. Additionally, the temperature dependent studies of the phonon line-widths and the mean-square displacement (MSD) of surface atoms are indicative of enhanced surface anharmonicity. On several chemisorbed metal surfaces, for which force constants are not available from first-principles calculations or the EAM, we perform lattice dynamics studies of phonon dispersion curves using simple force-constant models. These studies provide reliable mean-square displacement of surface atoms and can distinguish between possible reconstruction patterns, the results being insensitive to the exact values of the surface parameters. On c(2 times 2)S-Ni(100), it is found that the parallel component of the mean-square displacement for sulfur is around 50% larger than the vertical component, but for the mean-square displacement of oxygen atoms in the system c(2 times 2)O-Ni(100), the opposite is the case. As regards surface reconstruction, for both p(2 times 1)O-Ag(110) and p(2 times 1)O-Ni(110) surfaces, it is concluded that a substrate missing-row type reconstruction is induced by the adsorbates, but the local symmetry is C_{2v} with oxygen atoms at the long-bridge sites for the former and C_{s} with (110) being the only symmetry axis for the latter. In the above theoretical analysis, close contacts are made to many available experimental results such as surface phonon dispersion curves, interlayer relaxations, and Debye -Waller factors and adsorbate-substrate bond lengths.

Atomic Structures of Silicene Layers Grown on Ag(111): Scanning Tunneling Microscopy and Noncontact Atomic Force Microscopy Observations

PubMed Central

Resta, Andrea; Leoni, Thomas; Barth, Clemens; Ranguis, Alain; Becker, Conrad; Bruhn, Thomas; Vogt, Patrick; Le Lay, Guy

2013-01-01

Silicene, the considered equivalent of graphene for silicon, has been recently synthesized on Ag(111) surfaces. Following the tremendous success of graphene, silicene might further widen the horizon of two-dimensional materials with new allotropes artificially created. Due to stronger spin-orbit coupling, lower group symmetry and different chemistry compared to graphene, silicene presents many new interesting features. Here, we focus on very important aspects of silicene layers on Ag(111): First, we present scanning tunneling microscopy (STM) and non-contact Atomic Force Microscopy (nc-AFM) observations of the major structures of single layer and bi-layer silicene in epitaxy with Ag(111). For the (3 × 3) reconstructed first silicene layer nc-AFM represents the same lateral arrangement of silicene atoms as STM and therefore provides a timely experimental confirmation of the current picture of the atomic silicene structure. Furthermore, both nc-AFM and STM give a unifying interpretation of the second layer (√3 × √3)R ± 30° structure. Finally, we give support to the conjectured possible existence of less stable, ~2% stressed, (√7 × √7)R ± 19.1° rotated silicene domains in the first layer. PMID:23928998

One-atom-layer 4×4 compound in (Tl, Pb)/Si(111) system

NASA Astrophysics Data System (ADS)

Mihalyuk, A. N.; Hsing, C. R.; Wei, C. M.; Gruznev, D. V.; Bondarenko, L. V.; Tupchaya, A. Y.; Zotov, A. V.; Saranin, A. A.

2017-03-01

An ordered 4×4-periodicity 2D compound has been found in the (Tl, Pb)/Si(111) system and its composition, structure and electronic properties have been characterized using low-energy electron diffraction, scanning tunneling microscopy observations and density-functional-theory calculations. The compound has been concluded to contain 9 Tl atoms and 12 Pb atoms per 4×4 unit cell, i.e., 0.56 ML of Tl and 0.75 ML of Pb. Structural model was proposed for the 4×4-(Tl, Pb) compound where building blocks are a hexagonal array of 12 Pb atoms, a triangular array of 6 Tl atoms and a Tl trimer. The proposed structure has a C3 symmetry and occurs in the two equivalent orientations. The electron band structure of the compound contains two metallic spin-split surface-state bands. Bearing in mind the advanced properties of the known √{ 3 } ×√{ 3 } 2D compound in the same (Tl, Pb)/Si(111) system (i.e., combination of giant Rashba effect and superconductivity), the found 4×4-(Tl, Pb) compound is believed to be a promising object for exploration of its superconductive properties.

Spectroscopic determination of surface geometry: Ti(0001)-H(1×1)

NASA Astrophysics Data System (ADS)

Feibelman, Peter J.; Hamann, D. R.

1980-02-01

The electronic structure of a Ti(0001) film covered by a monolayer of H is shown to depend strongly on the location of the H atom in the surface unit cell. Best agreement with experiment is found with the H's in three-fold sites, 0.8 a.u. outside the outer Ti layer. In this geometry the H atoms "heal" the surface-the clean Ti(0001) surface state near the Fermi level is removed and the outer layer d-like local density of states (LDOS) is quite similar to that of the interior. Additionally, the calculated work function is 4.0 eV and an H-derived peak in the calculated LDOS appears 5 eV below EF, in agreement with photoemission measurements.

Low temperature surface chemistry and nanostructures

NASA Astrophysics Data System (ADS)

Sergeev, G. B.; Shabatina, T. I.

2002-03-01

The new scientific field of low temperature surface chemistry, which combines the low temperature chemistry (cryochemistry) and surface chemistry approaches, is reviewed in this paper. One of the most exciting achievements in this field of science is the development of methods to create highly ordered hybrid nanosized structures on different organic and inorganic surfaces and to encapsulate nanosized metal particles in organic and polymer matrices. We consider physical and chemical behaviour for the systems obtained by co-condensation of the components vapours on the surfaces cooled down to 4-10 and 70-100 K. In particular the size effect of both types, the number of atoms in the reactive species structure and the thickness of growing co-condensate film, on the chemical activity of the system is analysed in detail. The effect of the internal mechanical stresses on the growing interfacial co-condensate film formation and on the generation of fast (explosive) spontaneous reactions at low temperatures is discussed. The examples of unusual chemical interactions of metal atoms, clusters and nanosized particles, obtained in co-condensate films on the cooled surfaces under different conditions, are presented. The examples of highly ordered surface and volume hybrid nanostructures formation are analysed.

Peierls instability as the insulating origin of the Na/Si(111)-(3 × 1) surface with a Na coverage of 2/3 monolayers

NASA Astrophysics Data System (ADS)

Kang, Myung Ho; Kwon, Se Gab; Jung, Sung Chul

2018-03-01

Density functional theory (DFT) calculations are used to investigate the insulating origin of the Na/Si(111)-(3 × 1) surface with a Na coverage of 2/3 monolayers. In the coverage definition, one monolayer refers to one Na atom per surface Si atom, so this surface contains an odd number of electrons (i.e., three Si dangling-bond electrons plus two Na electrons) per 3 × 1 unit cell. Interestingly, this odd-electron surface has been ascribed to a Mott-Hubbard insulator to account for the measured insulating band structure with a gap of about 0.8 eV. Here, we instead propose a Peierls instability as the origin of the experimental band gap. The concept of Peierls instability is fundamental in one-dimensional metal systems but has not been taken into account in previous studies of this surface. Our DFT calculations demonstrate that the linear chain structure of Si dangling bonds in this surface is energetically unstable with respect to a × 2 buckling modulation, and the buckling-induced band gap of 0.79 eV explains well the measured insulating nature.

Surface Characterization of Mechanochemically Modified Exfoliated Halloysite Nanoscrolls.

PubMed

Zsirka, Balázs; Táborosi, Attila; Szabó, Péter; Szilágyi, Róbert K; Horváth, Erzsébet; Juzsakova, Tatjána; Fertig, Dávid; Kristóf, János

2017-04-11

Surface modifications fundamentally influence the morphology of kaolinite nanostructures as a function of crystallinity and the presence of contaminants. Besides morphology, the catalytic properties of 1:1-type exfoliated aluminosilicates are also influenced by the presence of defect sites that can be generated in a controlled manner by mechanochemical activation. In this work, we investigated exfoliated halloysite nanoparticles with a quasi-homogeneous, scroll-type secondary structure toward developing structural/functional relationships for composition, atomic structure, and morphology. The surface properties of thin-walled nanoscrolls were studied as a function of mechanochemical activation expressed by the duration of dry-grinding. The surface characterizations were carried out using N 2 , NH 3 , and CO 2 adsorption measurements. The effects of grinding on the nanohalloysite structure were followed using thermoanalytical thermogravimetric/derivative thermogravimetric (TG/DTG) and infrared spectroscopic [Fourier transform infrared/attenuated total reflection (FTIR/ATR)] techniques. Grinding results in partial dehydroxylation with similar changes as those observed for heat treatment above 300 °C. Mechanochemical activation shows a decrease in the dehydroxylation mass loss and the DTG peak temperature, a decrease in the specific surface area and the number of mesopores, an increase in the surface acidity, blue shift of surface hydroxide bands, and a decrease in the intensity of FTIR/ATR bands as a function of the grinding time. The experimental observations were used to guide atomic-scale structural and energetic simulations using realistic molecular cluster models for a nanohalloysite particle. A full potential energy surface description was developed for the mechanochemical activation and/or heating toward nanometahalloysite formation that aids the interpretation of experimental results. The calculated differences upon dehydroxylation show a remarkable agreement with the mass loss values from DTG measurements.

Water's Interfacial Hydrogen Bonding Structure Reveals the Effective Strength of Surface-Water Interactions.

PubMed

Shin, Sucheol; Willard, Adam P

2018-06-05

We combine all-atom molecular dynamics simulations with a mean field model of interfacial hydrogen bonding to analyze the effect of surface-water interactions on the structural and energetic properties of the liquid water interface. We show that the molecular structure of water at a weakly interacting ( i.e., hydrophobic) surface is resistant to change unless the strength of surface-water interactions are above a certain threshold. We find that below this threshold water's interfacial structure is homogeneous and insensitive to the details of the disordered surface, however, above this threshold water's interfacial structure is heterogeneous. Despite this heterogeneity, we demonstrate that the equilibrium distribution of molecular orientations can be used to quantify the energetic component of the surface-water interactions that contribute specifically to modifying the interfacial hydrogen bonding network. We identify this specific energetic component as a new measure of hydrophilicity, which we refer to as the intrinsic hydropathy.

Chevron Defect at the Intersection of Grain Boundaries with Free Surfaces in Au

NASA Astrophysics Data System (ADS)

Radetic, T.; Lançon, F.; Dahmen, U.

2002-08-01

We have identified a new defect at the intersection between grain boundaries and surfaces in Au using atomic resolution transmission electron microscopy. At the junction line of 90° <110> tilt grain boundaries of (110)-(001) orientation with the free surface, a small segment of the grain boundary, about 1nm in length, dissociates into a triangular region with a chevronlike stacking disorder and a distorted hcp structure. The structure and stability of these defects are confirmed by atomistic simulations, and we point out the relationship with the one-dimensional incommensurate structure of the grain boundary.