Surface Structure Determination Research Articles

Surface structure determination by exhaustive search of asymmetric unit

Surface structure determination by exhaustive search of asymmetric unit

Thin sheets of bean curd treated by cold plasma: Changes in surface structure and physicochemical properties

Thin sheets of bean curd (TSBC), a favorite food in China, is mostly vacuum packed to maintain the shelf life. However, the vacuum packing processing will cause adhesion between sheets, which is difficult to peel. To solve this problem, a rapid dehydration technique for the TSBC using cold plasma was developed. The surface structure and physicochemical properties of the TSBC treated by cold plasma were evaluated. The results indicated that water contact angle increased from 0° to 66.37° and 66.94°, and adhesion between sheets decreased from 2.81 g.sec to 0.01 g.sec. It was due to the removal of the bulk-phase water from the TSBC. And scanning electron microscopy showed the formation of a dense structure on the TSBC surface. Moreover, surface structure determination revealed that the cold plasma etching led to the depolymerization of protein and the exposure of hydrophobic points without any effect on the primary structure.

Surface reconstructions on Mn3O4(001) films

The structural complexity of surfaces of spinel-like oxides together with the existence of competing phases of different or mixed valencies have limited surface structure determinations so far. Only recently, the concept of subsurface cation vacancies (SCVs) could be demonstrated for an ${\mathrm{Fe}}_{3}{\mathrm{O}}_{4}$ single crystal surface. Here, we present the appearance of SCVs for ultrathin and thin films of ${\mathrm{Mn}}_{3}{\mathrm{O}}_{4}$(001) depending on film thickness. The structures of films grown by molecular beam epitaxy have been investigated using scanning tunneling microscopy (STM), low-energy electron diffraction (LEED), and near-edge x-ray absorption fine structure spectroscopy (NEXAFS). For coverage up to 4 (Mn ions)/(Ag atom) of ${\mathrm{Mn}}_{3}{\mathrm{O}}_{4}$ and an annealing temperature of 640 K, a $p(2\ifmmode\times\else\texttimes\fi{}1)$ reconstruction has been observed in STM and LEED. Using NEXAFS, the identity of the manganese oxide has been narrowed down to the spinel ${\mathrm{Mn}}_{3}{\mathrm{O}}_{4}$ and its related vacancy compound $\ensuremath{\gamma}\text{\ensuremath{-}}{\mathrm{Mn}}_{2}{\mathrm{O}}_{3}$. Thus the $p(2\ifmmode\times\else\texttimes\fi{}1)$ reconstruction corresponds to an ${\mathrm{Mn}}_{3}{\mathrm{O}}_{4}$(001) surface with $\mathrm{Mn}{\mathrm{O}}_{2}$ termination. For a lower annealing temperature of 450 K or thicker films [5 and 10 (Mn ions)/(Ag atom) ], additional $p(4\ifmmode\times\else\texttimes\fi{}2)$ and $c(4\ifmmode\times\else\texttimes\fi{}4)$ reconstructions have been observed. These extra reconstructions stem from lateral shifts of top-sublayer ions induced by SCVs.

Sim-trhepd-rheed – Open-source simulator of total-reflection high-energy positron diffraction (TRHEPD) and reflection high-energy electron diffraction (RHEED)

The present paper reports sim-trhepd-rheed (STR), an open-source simulator of total-reflection high-energy positron diffraction (TRHEPD) and reflection high-energy electron diffraction (RHEED) experiments which are used for atom-scale surface structure determination of a material. Diffraction data obtained by these experiments are analyzed by comparison with numerical simulations. The STR simulator is used for the analysis of experimental diffraction data by simulating the rocking curve from a given trial surface structure by solving the partial differential equation of the dynamical quantum diffraction theory for positron or electron wavefunctions. Using the obtained surface structure, electronic structure, and other physical quantities can be evaluated through first-principles calculations. For this purpose, a utility software was also developed in order to realize a first principles calculation with the Quantum ESPRESSO suite. Program summaryProgram title: sim-trhepd-rheedCPC Library link to program files:https://doi.org/10.17632/89vpfvp84k.1Developer's repository link:https://github.com/sim-trhepd-rheed/sim-trhepd-rheed/Code Ocean capsule:https://codeocean.com/capsule/2323181Licensing provisions: GNU General Public License v3.0Programming language: Fortran 90, Python 3External routines/libraries: BLAS library, LAPACK libraryNature of problem: Partial differential equation in dynamical quantum diffraction theory.Solution method: Numerical solution by the multi-slice method for the partial differential equation.

Data-efficient iterative training of Gaussian approximation potentials: Application to surface structure determination of rutile IrO2 and RuO2.

Machine-learning interatomic potentials, such as Gaussian Approximation Potentials (GAPs), constitute a powerful class of surrogate models to computationally involved first-principles calculations. At a similar predictive quality but significantly reduced cost, they could leverage otherwise barely tractable extensive sampling as in global surface structure determination (SSD). This efficiency is jeopardized though, if an a priori unknown structural and chemical search space as in SSD requires an excessive number of first-principles data for the GAP training. To this end, we present a general and data-efficient iterative training protocol that blends the creation of new training data with the actual surface exploration process. Demonstrating this protocol with the SSD of low-index facets of rutile IrO2 and RuO2, the involved simulated annealing on the basis of the refining GAP identifies a number of unknown terminations even in the restricted sub-space of (1 × 1) surface unit cells. Particularly in an O-poor environment, some of these, then metal-rich terminations, are thermodynamically most stable and are reminiscent of complexions as discussed for complex ceramic materials.

Complete three-dimensional structure of Bi-adsorbed Si(110) surface: Discovery of heavily reconstructed Si(110) substrate

Silicon is one of the most well-studied crystals in terms of surface structure. In particular, the three low Miller index surfaces---(100), (110), and (111)---which are located at the three apexes of the triangle of the irreducible orientation of the cubic crystal, are the most fundamental and have been extensively studied. However, the surface structure on Si(110) substrates is not as well understood as on other substrates. Here, we have investigated a surface structure induced by submonolayer Bi deposition on Si(110). The complete atomic arrangement from the surface to the fifth layer was directly determined by solving the Patterson function, which was obtained using a very large number of electron diffraction patterns. In contrast to the case of the Si(111) substrate, the Si(110) substrate showed significant reconstructions under a Bi overlayer. The obtained structure shows how dangling bonds can be reduced at the Si(110) substrate. The present result proves the high capability of the surface structure determination of the present method.

Data-driven sensitivity analysis in surface structure determination using total-reflection high-energy positron diffraction (TRHEPD)

The present article proposes a data analysis method for experimentally-derived measurements, which consists of an auto-optimization procedure and a sensitivity analysis. The method was applied to the results of a total-reflection high-energy positron diffraction (TRHEPD) experiment, a novel technique of determining surface structures or the position of the atoms near the material surface. This method solves numerically the partial differential equation in the fully-dynamical quantum diffraction theory with many trial surface structures. In the sensitivity analysis, we focused on the experimental uncertainties and the variation over individual fitting parameters, which was analyzed by solving the eigenvalue problem of the variance-covariance matrix. A modern massively parallel supercomputer was used to complete the analysis within a moderate computational time. The sensitivity analysis provides a basis for the choice of variables in the data analysis for practical reliability. The effectiveness of the present analysis method was demonstrated in the structure determination of a Si4O5N3 / 6H-SiC(0001)-(3×3) R30∘ surface. Furthermore, this analysis method is applicable to many experiments other than TRHEPD.

Selecting ‘convenient observers’ to probe the atomic structure of CVD graphene on Ir(111) via photoelectron diffraction

CVD graphene grown on metallic substrates presents, in several cases, a long-range periodic structure due to a lattice mismatch between the graphene and the substrate. For instance, graphene grown on Ir(111), displays a corrugated supercell with distinct adsorption sites due to a variation of its local electronic structure. This type of surface reconstruction represents a challenging problem for a detailed atomic surface structure determination for experimental and theoretical techniques. In this work, we revisited the surface structure determination of graphene on Ir(111) by using the unique advantage of surface and chemical selectivity of synchrotron-based photoelectron diffraction. We take advantage of the Ir 4f photoemission surface state and use its diffraction signal as a probe to investigate the atomic arrangement of the graphene topping layer. We determine the average height and the overall corrugation of the graphene layer, which are respectively equal to 3.40 ± 0.11 Å and 0.45 ± 0.03 Å. Furthermore, we explore the graphene topography in the vicinity of its high-symmetry adsorption sites and show that the experimental data can be described by three reduced systems simplifying the moiré supercell multiple scattering analysis.

Preparation and characterization of MnO2-based nanoparticles at different annealing temperatures and their application in dye removal from water

In this research, manganese oxides (MnO2) nanoparticles were prepared by hydrothermal method using KMnO4 as a precursor. The final brown–black precipitate MnO2 nanoparticles as prepared, and annealed at different temperatures (250, 450, and 750 °C) were characterized. The nanoparticles prepared were tested for removal of methylene blue (MB), used as a model dye from water. In order to determine the structure and the chemical nature of the MnO2 nanoparticles prepared, the characterization was carried out by X-ray diffraction. For the surface morphological studies of nanoparticles, field emission scanning electron microscopy was used. In order to study the surface roughness atomic force microscopy was used for determination of the imaging surface structures in the nm scale. Fourier transform infrared spectrometry was used to investigate the vibrations of functional groups in MnO2. The tests for dye removal from water using MnO2 nanoparticles have been carried out for MnO2 nanoparticles as prepared and annealed at different temperatures. The process parameters such as speed of shaking, reaction time, and MB concentration were studied at 25 °C temperature to determine the best removal efficiency of methylene blue from water. UV/Visible spectrophotometer was used to follow the MB removal. MnO2 annealed at 750 °C exhibited the highest MB removal efficiency, 89%, as compared with MnO2 nanoparticles as prepared and annealed at 250 and 450 °C.

Effective Enrichment and Quantitative Determination of Trace Hg2+ Ions Using CdS-Decorated Cellulose Nanofibrils.

Water pollution caused by metal contamination is of serious concern. Direct determination of trace metal ions in real water samples remains challenging. A sample preparation technique is a prerequisite before analysis. Herein, we report the facile water-based hydrothermal synthesis of cadmium sulfide nanoparticles on a cellulose nanofiber surface to prepare a new adsorbent material. Field emission scanning electron microscopy, high-resolution tunneling electron microscopy, elemental mapping and X-ray photoelectron microscopy were used to characterize the surface morphology, structural determination, elemental composition and nature of bonding. The nanoadsorbent (cadmium-sulfide-decorated cellulose nanofibrils (CNFs@CdS)) was employed for the solid-phase extraction and determination of trace Hg(II) from aqueous media. The experimental conditions were optimized systematically and the data show a good Hg(II) adsorption capacity of 126.0 mg g−1. The CNFs@CdS adsorbent shows the selective removal of Hg(II) accordingly to the hard and soft acid–base theory of metal–ligand interaction. A high preconcentration limit of 0.36 µg L−1 was obtained with a preconcentration factor of 580. The lowest level of trace Hg(II) concentration, which was quantitatively analyzed by the proposed method, was found to be 0.06 µg L−1. No significant interferences from the sample matrix were observed in the extraction of Hg(II). Analysis of the standard reference material (SRM 1641d) was carried out to validate the proposed methodology. Good agreement between the certified and observed values indicates the applicability of the developed methodology for the analysis of Hg(II) in tap water, river water and industrial wastewater samples.

Effect of anions on electrodeposition of structured platinum nanocrystallites

Pulsed (square–wave) electrodeposition of platinum nanocrystallites with a high concentration of (100) regions from a H2PtCl6 solution with different background anions is studied. The effect of the background electrolyte is shown, namely, a more perfect cubic faceting of crystallites obtained in the 0.1 M HClO4 solution as compared to 0.5 M H2SO4. A procedure for deposit formation (secondary growth) with intermediate pulsed treatment in acid is suggested that does not involve application of high negative/positive overpotentials (no additional increasing of the mobility of platinum atoms). This allows preserving the crystallite structure and improving the overall deposit structure. In addition to conventional methods of fine surface structure determination on the basis of the hydrogen UPD region in cyclic voltammograms in sulfuric acid and SEM, we propose analysis of the Pt(100) terrace concentration/width based on the characteristic peak of nitrate ion reduction in voltammograms in perchloric acid. Stepped Pt single crystals with (100) terraces of different width are used for comparison. The effect of solution temperature on formation of faceted crystallites is shown and the optimum deposition temperature is determined: the optimum temperature in perchloric acid solution is 40 °C, while an increase in the temperature in sulfuric acid solutions results under the chosen conditions in deposition acceleration and an increase in the amount of surface defects.

Machine learning analysis of perovskite oxides grown by molecular beam epitaxy

Reflection high-energy electron diffraction (RHEED) is a ubiquitous in situ molecular beam epitaxial (MBE) characterization tool. Although RHEED can be a powerful means for crystal surface structure determination, it is often used as a static qualitative surface characterization method at discrete intervals during a growth. A full analysis of RHEED data collected during the entirety of MBE growths is made possible using principle component analysis (PCA) and k-means clustering to examine significant boundaries that occur in the temporal clusters grouped from RHEED data and identify statistically significant patterns. This process is applied to data from homoepitaxial SrTiO$_{3}$ growths, heteroepitaxial SrTiO$_{3}$ grown on scandate substrates, BaSnO$_{3}$ films grown on SrTiO$_{3}$ substrates, and LaNiO$_{3}$ films grown on LaAlO$_{3}$ substrates. This analysis may provide additional insights into the surface evolution and transitions in growth modes at precise times and depths during growth, and that video archival of an entire RHEED image sequence may be able to provide more insight and control over growth processes and film quality.

Surface termination and stoichiometry of LaAlO3(001) surface studied by HRTEM

As an important topic of condensed matter physics, metal oxide surfaces often exhibit exotic properties such as high catalytic activity, enhanced ferroelectricity and electronic phase transition, originating from the different local symmetry with respect to the bulk. As the structure determination of oxide surfaces presents challenges to conventional surface science techniques like scanning tunneling microscopy, aberration-corrected transmission electron microscopy (TEM) has been increasingly used to solve structures of oxide surfaces. In this work, the (001) surface of LaAlO3, one of the most used components of oxide heterostructures, has been investigated. Our TEM experiments and extensive image simulations show that the La-O terminated LaAlO3(001) surface undergoes significant reconstructions, forming La vacancies on the surface layer. Energetically, the LaAlO3(001) surface is stable with the reconstructed La-O termination in a wide range of oxygen chemical potentials. Polarity compensation, reduced density of states at the Fermi level and bond enhancement of subsurface oxygen anions all contribute to the stabilization of the reconstructed surface.

Development of Data-Analysis Software for Total-Reflection High-Energy Positron Diffraction (TRHEPD)

The present paper reports on the recent activity of the data analysis software development for total-reflection high-energy positron diffraction (TRHEPD), a novel experimental technique for surface structure determination. Experiments using TRHEPD are being conducted intensively at the Slow Positron Facility, Institute of Materials Structure Science, High Energy Accelerator Research Organization, revealing surface structure of interest. The data analysis software provides a solution to the inverse problem in which the atomic positions of a surface structure are determined from the experimental diffraction data (rocking curve). The forward problem is solved by the numerical solution of the partial differential equation in the quantum scattering problem. A technical demonstration with a test problem was carried out to confirm the software functioned as expected. Since the analysis method has a general mathematical foundation, it is also applicable to other experiments, such as X-ray or electron diffraction experiments.

Surface structure determination by x-ray standing waves at a free-electron laser

We demonstrate the structural sensitivity and accuracy of the x-ray standing wave technique at a high repetition rate free-electron laser, FLASH at DESY in Hamburg, by measuring the photoelectron yield from the surface SiO2 of Mo/Si multilayers. These experiments open up the possibility to obtain unprecedented structural information of adsorbate and surface atoms with picometer spatial and femtosecond temporal resolution. This technique will substantially contribute to a fundamental understanding of chemical reactions at catalytic surfaces and the structural dynamics of superconductors.

Ions-free electrochemically synthetized in aqueous media flake-like CuO nanostructures as SERS reproducible substrates for the detection of neurotransmitters.

The process of catalytic destruction of tumor cells can be strengthened by introducing copper(II) oxide nanostructures (CuONSs) with receptor's agonists/antagonists immobilized on their surface. Here we show a simple and reliable electrochemical method for the fabrication ions-free flake-like CuO nanostructures in a surfactant/ions free aqueous environment. For the determination of the metal surface plasmon, size, rheology, and structure of the fabricated nanostructures ultraviolet-visible (UV-Vis), Fourier-transform infrared (FT-IR), Raman, and X-ray photoelectron (XPS) spectroscopies as well as scanning electron microscope (SEM), high-resolution transmission electron microscopy with energy dispersive X-ray (HDTEM-EDS), X-ray powder diffraction (XRD), and dynamic light scattering (DLS) analysis were used. The fabricated nanostructures were used as highly sensitive, uniform, and reproducible sensors of a natural ligand (bombesin) of some types of metabotropic seven transmembrane G protein-coupled superfamily receptors (GPCRs), which are over-express on the surface of many malignant tumors. Surface-enhanced Raman scattering (SERS) was used to monitor the geometry of adsorbate, separate, enrich, and detect various bombesin C-terminal fragments. It has been shown that the type of used substrate, surface development, and ions present in the solution have little effect on the mode of adsorption.

Global search optimization using the particle swarm algorithm applied to photoelectron diffraction

The photoelectron diffraction (PED) is an element and chemical selective technique, which have been used for surface structure determinations. Due the complexity phenomena of low-energy photoelectron diffraction, obtain the structure by holographic inversion method from the experimental data present difficulties which unfeasible the method. To perform a structure determination It s necessary use the comparative method between the experimental and theoretical data from a hypothetical structure in a try-and-error approach, which could spent high computational time. In this project we have developed a Particle Swarm Optimization (PSO) algorithm for structural determination using the PED technique.

Nature-Inspired Quasicrystal SRG Using Fibonacci Sequences in Photo-Reconfiguration on Azo Polymer Films

In this study, we present the fabrication route of quasicrystal surface relief grating (SRG) of azopolymer. Based on photo-reconfigurable azobenzene property, various morphologies of grating patterns were inscribed on azopolymer thin-films by two-beam coupling light interference lithography (LIL) process. Multiplexing the LIL with different rotation sequence on azopolymers resulted in unusual surface structures including quasicrystal-like SRGs with Fibonacci sequences in rotational LIL. We investigated the effect of rotation sequence on the grating patterns by atomic force microscope, revealing that rotation sequence is a critical parameter determining surface structures of azopolymer films.

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

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.

Thiol Treatment Creates Selective Palladium Catalysts for Semihydrogenation of Internal Alkynes

Summary Surface and interfacial engineering of heterogeneous metal catalysts is effective and critical for optimizing selective hydrogenation for fine chemicals. By using thiol-treated ultrathin Pd nanosheets as a model catalyst, we demonstrate the development of stable, efficient, and selective Pd catalysts for semihydrogenation of internal alkynes. In the hydrogenation of 1-phenyl-1-propyne, the thiol-treated Pd nanosheets exhibited excellent catalytic selectivity (>97%) toward the semihydrogenation product (1-phenyl-1-propene). The catalyst was highly stable and showed no obvious decay in either activity or selectivity for over ten cycles. Systematic studies demonstrated that a unique Pd-sulfide/thiolate interface created by the thiol treatment was crucial to the semihydrogenation. The high catalytic selectivity and activity benefited from the combined steric and electronic effects that inhibited the deeper hydrogenation of C=C bonds. More importantly, this thiol treatment strategy is applicable to creating highly active and selective practical catalysts from commercial Pd/C catalysts for semihydrogenation of internal alkynes.