Surface X-ray Diffraction Data Research Articles

HAT: a high-energy surface X-ray diffraction analysis toolkit.

This work introduces the high-energy surface X-ray diffraction analysis toolkit (HAT), an open-source cross-platform software package written in Python to allow the extraction and processing of high-energy surface X-ray diffraction (HESXRD) data sets. Thousands of large-area detector images are collected in a single HESXRD scan, corresponding to billions of pixels and hence reciprocal space positions. HAT is an optimized reciprocal space binner that implements a graphical user interface to allow the easy and interactive exploration of HESXRD data sets. Regions of reciprocal space can be selected with movable and resizable masks in multiple views and are projected onto different axes to allow the creation of reciprocal space maps and the extraction of crystal truncation rods. Current and future versions of HAT can be downloaded and used free of charge.

Electrooxidation of Platinum

Platinum is an important catalyst widely used in energy conversion and storage, especially in the hydrogen-oxygen polymer electrolyte membrane fuel cell, where it is used at the anode and cathode1. However, potential excursions can lead to surface oxidation and reduction, which restructures the surface and can lower the efficiency of the catalyst and lead to dissolution2. Platinum atoms leave their original lattice sites during oxidation. Surface X-ray diffraction (SXRD) has determined that on Pt(111) the initial stage of Pt extraction is in a place-exchange process, in which the Pt atom moves directly above its original site, which is now occupied by an oxygen atom3. However, on Pt(100) recent work by our team has shown that the initial oxidation gives a “stripe” structure comprising 1D chains of raised Pt and oxygen atoms4.Presented here is an analysis of combined simultaneous SXRD and electrochemistry data for Pt(111) and Pt(100) oxidation in HClO4 and H2SO4. The correlation between the charge transfer and Pt extraction processes is investigated by in-situ cyclic voltammetry, potential step, and potential sweep-hold measurements.The prior structural analysis from a complete set of crystal truncation rods is used find calibration curves for the X-ray intensity of selected anti-Bragg reflections as a function of the coverages θPE of different types of extracted Pt atoms. Integration of charge during electrochemical measurements was converted to electrons passed per surface Pt atoms, to give a notional “electron coverage” θe. In this way, simultaneous measurement of intensity with current during the selected potential program can be converted to θe vs θPE curves. The slopes of these curves are compared with suggested stoichiometric reactions, based on the known SXRD-determined structures. There is some uncertainty insofar as SXRD cannot distinguish O from OH, but we are able to estimate Pt oxidation states. On Pt(111), the electron-transfer and Pt extraction coverage ratios vary with sweep rate, indicating that the rates of adsorption and extraction are kinetically determined and changing during the first oxidation peak. On Pt(100), the stripe structure and stoichiometry suggest a Pt(II) oxide component in the initial stages.We thank other team members involved in various phases of this work: Natalie Stubb (University of Victoria), Valentin Briega-Martos, Daniel Sandbeck (Forschungszentrum Jülich GmbH), Martin Ruge, Ole Fehrs (Kiel University), Federico Calle-Vallejo (Universistat de Barcelona), and the ID31 beamline staff at ESRF. Financial support from NSERC and DFG is appreciated.Reference R. Stamenkovic, D. Strmcnik, P. P. Lopes, N. M. Markovic, Energy and fuels from electrochemical interfaces, Nature materials, 16 (2017) 57-69.J. Sandbeck, O. Brummel, K. J. Mayrhofer, J. Libuda, I. Katsounaros, S. Cherevko, Dissolution of platinum single crystals in acidic medium, ChemPhysChem, 20 (2019) 2997.Drnec, M. Ruge, F. Reikowski, B. Rahn, F. Carlà, R. Felici, J. Stettner, O.M. Magnussen, D.A. Harrington, Initial stages of Pt(111) Electrooxidation: Dynamic and Structural Studies by Surface X-ray Diffraction, Electrochim. Acta, 224 (2017) 220-227.Fuchs, J. Drnec, F. Calle-Vallejo, N. Stubb, D. J. Sandbeck, M. Ruge, S. Cherevko, D. A. Harrington, O. M. Magnussen, Structure dependency of the atomic-scale mechanisms of platinum electro-oxidation and dissolution, Nature Catalysis, 3 (2020) 754-761.

Charge density wave in single-layer Pb/Ge(111) driven by Pb-substrate exchange interaction

Single layer Pb on top of (111) surfaces of group IV semiconductors hosts charge density wave and superconductivity depending on the coverage and on the substrate. These systems are normally considered to be experimental realizations of single band Hubbard models and their properties are mostly investigated using lattice models with frozen structural degrees of freedom, although the reliability of this approximation is unclear. Here, we consider the case of Pb/Ge(111) at $1/3$ coverage, for which surface x-ray diffraction and angle-resolved photoemission spectroscopy data are available. By performing first-principles calculations, we demonstrate that the nonlocal exchange between Pb and the substrate drives the system into a $3\ifmmode\times\else\texttimes\fi{}3$ charge density wave. The electronic structure of this charge ordered phase is mainly determined by two effects: The magnitude of the Pb distortion and the large spin-orbit coupling. Finally, we show that the effect applies also to the $3\ifmmode\times\else\texttimes\fi{}3$ phase of Pb/Si(111) where the Pb-substrate exchange interaction increases the bandwidth by more than a factor $1.5$ with respect to density functional theory $+\mathrm{U}$, in better agreement with scanning tunneling spectroscopy data. The delicate interplay between substrate, structural, and electronic degrees of freedom invalidates the widespread interpretation available in literature considering these compounds as physical realizations of single band Hubbard models.

Clay Mineral Alteration in Oil and Gas Fields: Integrated Analyses of Surface Expression, Soil Spectra, and X-Ray Diffraction Data

Subsurface hydrocarbon occurrences can be detected by clay mineral (CM) alteration at the surface as a consequence of hydrocarbon migration. This study analyzed CM alteration in an oil and gas (O&G) field in the West Tugu field, located in the northwest Java Basin of Indonesia. Landsat 8 OLI data acquired on 25 September 2015 and soil spectral reflectance (SSR) data recorded using analytical spectral devices (ASD) in March 2017 were processed using clay indices to analyze CM alteration. Soil samples from a field survey of the same area were also analyzed using X-ray diffraction (XRD) to identify their CM compositions. CM distribution was empirically modeled by integrating the SSR bands re-sampled to Landsat 8 OLI (SSRL) bands and the CM composition using the best subset regression method and regression analyses. The resulting model was applied to Landsat 8 OLI images to map the surface CM alteration. The results show that CM alteration observed in the O&G field is an indicator of hydrocarbon microseepage at the surface. These results can be used as a technique to identify prospective regions that contain hydrocarbons and differentiate from those that are barren, and could be useful for increasing the rate of drilling success.

Structure determination of the Si(111)−7×3−In atomic-layer superconductor

The atomic structure of a superconducting atomic sheet of indium grown on Si(111) surface, i.e., $\mathrm{In}/\mathrm{Si}(111)\text{\ensuremath{-}}\sqrt{7}\ifmmode\times\else\texttimes\fi{}\sqrt{3}$, is determined by using surface x-ray diffraction (SXRD) and low-energy electron diffraction (LEED). The structure consists of double layers of In atoms with a rectangular arrangement, verifying a theoretical prediction [J. W. Park and M. H. Kang, Phys. Rev. Lett. 109, 166102 (2012)]. For the so-called hexagonal phase, which has been considered to be a different $\sqrt{7}\ifmmode\times\else\texttimes\fi{}\sqrt{3}$ structure and to undergo a transition to the $\sqrt{7}\ifmmode\times\else\texttimes\fi{}\sqrt{7}$ structure below 265 K, LEED data indicate that the structural basis is $\sqrt{7}\ifmmode\times\else\texttimes\fi{}\sqrt{7}$ even at room temperature. The SXRD data are well reproduced by single-layer In with the In coverage of 10/7 In atoms per Si surface atom, proposed by a theory [J. W. Park and M. H. Kang, Phys. Rev. Lett. 117, 116102 (2016)].

Water Structure, Dynamics and Ion Adsorption at the Aqueous {010} Brushite Surface

Understanding the growth processes of calcium phosphate minerals in aqueous environments has implications for both health and geology. Brushite, in particular, is a component of certain kidney stones and is used as a bone implant coating. Understanding the water–brushite interface at the molecular scale will help inform the control of its growth. Liquid-ordering and the rates of water exchange at the brushite–solution interface have been examined through the use of molecular dynamics simulation and the results compared to surface X-ray diffraction data. This comparison highlights discrepancies between the two sets of results, regardless of whether force field or first principles methods are used in the simulations, or the extent of water coverage. In order to probe other possible reasons for this difference, the free energies for the adsorption of several ions on brushite were computed. Given the exothermic nature found in some cases, it is possible that the discrepancy in the surface electron density may be caused by adsorption of excess ions.

Surface atomic structure of epitaxialLaNiO3thin films studied byin situLEED-I(V)

We report in situ low-energy electron diffraction intensity versus voltage [LEED-$I$($V$)] studies of the surface atomic structure of epitaxially grown ${(001)}_{\text{pc}}$-oriented $(\text{pc}=\text{pseudocubic})$ thin films of the correlated $3d$ transition-metal oxide ${\mathrm{LaNiO}}_{3}$. Our analysis indicates the presence of large out-of-plane bucklings of the topmost LaO layers but only minor bucklings of the topmost ${\mathrm{NiO}}_{2}$ layers, in close agreement with earlier surface x-ray diffraction data. In view of materials design approaches that have suggested using atomic-scale polar structural distortions to produce designer electronic structures in artificial nickelate heterostructures, we propose that the broken inversion symmetry inherent to the surface of rare-earth nickelate thin films offers a similar opportunity to study the coupling between atomic structure and electronic properties in this family of materials.

Atomic structure of Pt nanoclusters supported by graphene/Ir(111) and reversible transformation under CO exposure

We have investigated the atomic structure of graphene/Ir(111) supported platinum clusters with on average fewer than 40 atoms by means of surface x-ray diffraction (SXRD), grazing incidence small angle x-ray scattering (GISAXS), and normal incidence x-ray standing waves (NIXSW) measurements, in comparison with density functional theory calculations (DFT). GISAXS revealed that the clusters with 1.3 nm diameter form a regular array with domain sizes of 90 nm. SXRD shows that the 1--2 monolayer high, (111) oriented Pt nanoparticles grow epitaxially on the graphene support. From the combined analysis of the SXRD and NIXSW data, a three-dimensional (3D) structural model of the clusters and the graphene support can be deduced which is in line with the DFT results. For the clusters grown in ultrahigh vacuum the lattice parameter is reduced by $(4.6\ifmmode\pm\else\textpm\fi{}0.1)%$ compared to bulk platinum. The graphene layer undergoes a strong Pt adsorption induced buckling, caused by a rehybridization of the carbon atoms below the cluster. In situ observation of the Pt clusters in CO and ${\mathrm{O}}_{2}$ environments revealed a reversible change of the clusters' strain state while successively dosing CO at room temperature and ${\mathrm{O}}_{2}$ at 575 K, pointing to a CO oxidation activity of the Pt clusters.

Dibenzo crown ether layer formation on muscovite mica.

Stable layers of crown ethers were grown on muscovite mica using the potassium-crown ether interaction. The multilayers were grown from solution and from the vapor phase and were analyzed with atomic force microscopy (AFM), matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry, and surface X-ray diffraction (SXRD). The results show that the first molecular layer of the three investigated dibenzo crown ethers is more rigid than the second because of the strong interaction of the first molecular layer with the potassium ions on the surface of muscovite mica. SXRD measurements revealed that for all of the investigated dibenzo crown ethers the first molecule lies relatively flat whereas the second lies more upright. The SXRD measurements further revealed that the molecules of the first layer of dibenzo-15-crown-5 are on top of a potassium atom, showing that the binding mechanism of this layer is indeed of the coordination complex form. The AFM and SXRD data are in good agreement, and the combination of these techniques is therefore a powerful way to determine the molecular orientation at surfaces.

Identification of the structure model of the Si(111)-(5 × 2)-Au surface.

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.

Integration techniques for surface X-ray diffraction data obtained with a two-dimensional detector

This article proposes two integration methods to determine the structure factors along a surface diffraction rod measured with a two-dimensional detector. The first method applies the classic way of calculating integrated intensities in angular space. This is adapted to work efficiently with two-dimensional data. The second method is based on integration in reciprocal space. An intensity map is created by converting the detected intensity pixel by pixel to the reciprocal space. The integration is then performed directly on this map. A theoretical framework, as well as a comparison between the two integration methods, is provided.

Cluster method for analysing surface X-ray diffraction data sets using area detectors

An automated cluster algorithm is described, applicable to any image where a signal is to be analysed. The algorithm is employed in the context of surface X-ray diffraction data and extended to automate the data reduction process, which at present limits both the lead time to and the reliability of the retrieved structural information. A detailed evaluation of the constraints used to automate surface X-ray diffraction data analysis is provided. To overcome limitations of the algorithm and the experiment itself in certain geometries, the full field of view of area detectors is exploited to obtain orders of magnitude improvements in data collection. The method extends the surface X-ray diffraction technique to new systems and highlights the often archaic approach to the analysis of data collected with a two-dimensional detector.

Structural investigation of ZnO O-polar ([formula omitted]) surfaces and Schottky interfaces

We report on the atomic structures of bare and metal-coated ZnO O-polar (0001¯) surfaces as determined by model fitting of surface X-ray diffraction data. O-polar surfaces measured under typical device fabrication conditions are significantly rougher than Zn-polar (0001) surfaces, exhibiting Gaussian-shaped roughness profiles with a width of about 1.5 unit cells, regardless of the existence of a metal over-layer. All samples show a decreased layer distance between the topmost oxygen and zinc layers, consistent with theoretical predictions. Clear differences are observed in the occupations of the topmost oxygen layer in oxidized-metal-coated samples.

The Long-Time Low-Temperature Degradation (“LTD”) Kinetics in 3Y-TZP Bioceramics

This work follows a study on hydrothermal aged 3Y-TZP bioceramics, which showed that the surface X-ray diffraction data from moisture exposed samples give distorted results, reflecting a simple linear growth of a partially transformed layer from the surface into the interior. There is no indication for a leveling off or retardation of this growth at elevated temperatures (134°C) and here we present evidence that this is probably true at body temperatures as well. However, the rate constants at body temperature for the studied material are low and indicate a long lifetime. It should be noted that this statement is specific and other materials with minor changes to chemistry or microstructure may behave much better or much worse under those conditions. Furthermore slow crack growth and crack interactions are not yet investigated and may necessitate a minimum of low-temperature degradation susceptibility to ensure reliable long-time use.

Atomic imaging and direct phase retrieval using anomalous surface x-ray diffraction

The application of multi-wavelength anomalous diffraction to thin films, interfaces and surface structures is presented. The method directly determines the amplitudes and phases of the complex surface structure factors from surface x-ray diffraction data, measured at three different energies around the absorption edge of one of the elements present in the film. Thereby, one is able to directly Fourier transform the data, which immediately provides meaningful and unambiguous electron-density distributions. These serve as a starting point for subsequent structural refinement. The robustness of the algorithm was evaluated on simulated data as a proof of principle. The experimental limitations and their effect on the method will be discussed as well as stability tests for the algorithm, such as the positions of the anomalous scatterers and the interfacial roughness. It will be shown that the method can be applied to real structures. The algorithm was tested on real data from a thin film of SrTiO3 grown on NdGaO3(110).

Stress and structure at the NiO/Ag(001) interface

We present a combined stress and structural analysis of the growth of epitaxial NiO monolayers on Ag(001). Our experimental results indicate an unexpectedly complex interface formation, where a fraction of the first NiO monolayer (ML) is embedded into the Ag surface. This interface formation induces a tensile surface stress change. Subsequent deposition leads to a layer-by-layer growth of NiO up to 5 ML. Here, the average film stress is compressive $\ensuremath{-}5.8$ GPa, and it corresponds quantitatively to the misfit-induced stress. Our density functional calculations complement the experimental results by identifying the proper O-Ag bonding geometry in the ML regime from two indistinguishable options as provided by the analysis of surface x-ray diffraction data.

Atomic structure and composition of the2×Nreconstruction of the Ge wetting layer on Si(001) investigated by surface x-ray diffraction

The 2 \ifmmode\times\else\texttimes\fi{} $N$ reconstruction of the Ge/Si(001) wetting layer has been investigated by surface x-ray diffraction. At a substrate temperature of $670 {}^{ˆ}\mathrm{C}$, the average $N$ periodicity decreases from $N$ $=$ 11.5 to 8 with an increasing Ge coverage from one to three monolayers (ML). The top layer consists of asymmetric dimers with a bond length in the range of 2.50--2.60 \AA{} and a buckling angle in the range of 9.4\ifmmode^\circ\else\textdegree\fi{}--15.6\ifmmode^\circ\else\textdegree\fi{}, depending on the Ge coverage. The obtained dimer bond lengths are similar to those calculated for alternating asymmetric mixed dimers. Intermixing of Ge with Si is found down to the sixth (eighth) layer for 2 (from 3 to 5) ML coverage. For 2 ML coverage, a quantitative surface x-ray diffraction data set has been measured. It is analyzed using a model describing the atomic structure and Ge occupation probability with a limited set of parameters to bypass the intrinsic lack of appreciable reflections of the 2 \ifmmode\times\else\texttimes\fi{} $N$ ($N$ $=$ 9) reconstruction. The Ge occupation probability varies periodically along the $N$ direction, having its minimum value below the dimer vacancy lines. In addition, a more direct calculation of the Lorentz and detector acceptance corrections is given for rocking and radial scans.

Geometric structure ofTiO2(110)(1×1): Confirming experimental conclusions

Low-energy electron-diffraction and surface x-ray diffraction data acquired from TiO2(110)(1X1) are re-analyzed to confirm the integrity of the previously reported optimized geometries. This work is performed in response to ab initio density-functional theory calculations that suggest that the atomic displacements determined from low-energy electron-diffraction measurements may be compromised by the limited number of optimized atom positions. Performing structural optimizations as a function of depth into the selvedge, this present study validates the previous experimental structure determinations.

Structure ofO/Fe(001)-p(1×1)studied by surface x-ray diffraction

The geometric structure of $\text{O}/\text{Fe}(001)\text{-p}(1\ifmmode\times\else\texttimes\fi{}1)$ is studied by surface x-ray diffraction (SXRD). After dosing of about 4 L $(1\text{ }\text{L}={10}^{\ensuremath{-}6}\text{ }\text{Torr}\text{ }\text{s})$ of oxygen at room temperature we find approximately one monolayer (ML) of oxygen in an FeO-like structure forming two layer thick islands covering about 40% of a roughened Fe(001) surface. Subsequent annealing up to $500\text{ }\ifmmode^\circ\else\textdegree\fi{}\text{C}$ results in surface flattening leading to a highly ordered structure. Very precise SXRD data reveal the presence of 1 ML of oxygen atoms located in fourfold hollow sites at ${d}_{(\text{O}\text{\ensuremath{-}}\text{Fe})}=0.48\ifmmode\pm\else\textpm\fi{}0.08\text{ }\text{\AA{}}$ above the first Fe layer. The first Fe--Fe-interlayer spacing is expanded to ${d}_{12}=1.66\ifmmode\pm\else\textpm\fi{}0.02\text{ }\text{\AA{}}$ corresponding to an increase of 16% relative to the bulk spacing $(1.43\text{ }\text{\AA{}})$. Density-functional calculations confirm our findings and indicate a strong dependence of the (local) layer expansion on the oxygen coverage. Our results are important for understanding the surface magnetic properties of the $\text{O}/\text{Fe}(001)\text{-p}(1\ifmmode\times\else\texttimes\fi{}1)$ surface in general.

Surface x-ray diffraction analysis using a genetic algorithm: the case of Sn/Cu(100)-

The application of genetic algorithms to the analysis of surface x-ray diffraction data isdiscussed and the implementation of a genetic algorithm of evolutionary type is describedin detail. The structure of Sn/Cu(100)- is determined on the basis of surface x-ray diffraction data analysed using thisalgorithm. The results are compared to previous findings using other techniques.