Normal Incidence X-ray Standing Wave Research Articles

Probing the role of surface termination in the adsorption of azupyrene on copper.

The role of the inorganic substrate termination, within the organic-inorganic interface, has been well studied for systems that contain strong localised bonding. However, how varying the substrate termination affects coordination to delocalised electronic states, like that found in aromatic molecules, is an open question. Azupyrene, a non-alternant polycyclic aromatic hydrocarbon, is known to bind strongly to metal surfaces through its delocalised π orbitals, thus yielding an ideal probe into delocalised surface-adsorbate interactions. Normal incidence X-ray standing wave (NIXSW) measurements and density functional theory calculations are reported for the adsorption of azupyrene on the (111), (110) and (100) surface facets of copper to investigate the dependence of the adsorption structure on the substrate termination. Structural models based on hybrid density functional theory calculations with non-local many-body dispersion yield excellent agreement with the experimental NIXSW results. No statistically significant difference in the azupyrene adsorption height was observed between the (111) and (100) surfaces. On the Cu(110) surface, the molecule was found to adsorb 0.06 ± 0.04 Å closer to the substrate than on the other surface facets. The most energetically favoured adsorption site on each surface, as determined by DFT, is subtly different, but in each case involved a configuration where the aromatic rings were centred above a hollow site, consistent with previous reports for the adsorption of small aromatic molecules on metal surfaces.

Self-metalation of tetraphenyl porphyrin on Au(111): Structural characterisation via X-ray standing wave analysis

The study of surface-confined reactions provides a route towards characterising the mechanistic processes which underpin heterogeneous catalysis. On-surface reactions provide alternative pathways to solution phase synthesis, and can be studied by a range of techniques which can provide chemical and structural information. Importantly, these kinds of studies give us the insight required to potentially control the selectivity and efficiency of these reactions, as well as allowing for the design of molecular systems with specific functionalities. Porphyrin molecules are frequently selected as participants in these systems as they offer significant customisability, with respect to the reactivity of pendant groups and metal atoms which can be incorporated within the porphyrin macrocycle. Utilising the normal incidence X-ray standing wave (NIXSW) technique in conjunction with scanning probe methods and X-ray photoelectron spectroscopy (XPS) enables the generation of detailed models of on-surface systems, including the adsorption geometries of individual molecules. Here the NIXSW technique has been used to perform structural characterisation of three distinct phases of an on-surface reaction of tetraphenyl porphyrin (TPP) on Au(111); close-packed, diffuse and metalated. Using the chemical specificity of XPS and NIXSW we gain insight into chemical and structural changes exhibited by nitrogen atoms within the porphyrin macrocycle at several stages within the reaction process.

Adsorption structure of iron phthalocyanine and titanyl phthalocyanine on Cu(1 1 1)

The adsorption structure of iron phthalocyanine (FePc) and titanyl phthalocyanine (TiOPc) was studied by a combination of near edge X-ray absorption fine structure (NEXAFS) spectroscopy and normal incidence X-ray standing waves (NIXSW) technique. The FePc results demonstrate that the molecule adsorbs with the Fe metal centre at an adsorption height of 2.44 ± 0.09 Å, its macrocycle plane mostly parallel with the underlying surface and a single adsorption configuration. However, a small distortion of the isoindole groups, with respect to one another, is required to rationalise the results. The TiOPc results similarly indicate that the macrocycle plane is mostly parallel with the underlying surface up to thick multilayer films, yet, in the monolayer regime, the molecule must adsorb in multiple configurations. These configurations are nominally assigned to a mixture of adsorption configurations with some Ti=O bonds pointing towards the surface, and some pointing away. We determine that, in both configurations, the Ti metal centre sits at a similar adsorption height above the surface of 3.00 ± 0.20 Å.

Direct Experimental Determination of Ag Adatom Locations in TCNQ-Ag 2D Metal–Organic Framework on Ag(111)

A previous investigation of the structure of TCNQ adsorbed on Ag(111) using normal-incidence X-ray standing waves (NIXSW) and density functional theory (DFT) provided indirect evidence that Ag adatoms must be incorporated into the molecular overlayer. New surface X-ray diffraction (SXRD) results, presented here, provide direct evidence for the presence and location of these Ag adatoms and clearly distinguishes between two alternative models of the adatom registry favored by two different DFT studies.

Donor-Acceptor Co-Adsorption Ratio Controls the Structure and Electronic Properties of Two-Dimensional Alkali-Organic Networks on Ag(100).

The results are presented of a detailed combined experimental and theoretical investigation of the influence of coadsorbed electron-donating alkali atoms and the prototypical electron acceptor molecule 7,7,8,8-tetracyanoquinodimethane (TCNQ) on the Ag(100) surface. Several coadsorption phases were characterized by scanning tunneling microscopy, low-energy electron diffraction, and soft X-ray photoelectron spectroscopy. Quantitative structural data were obtained using normal-incidence X-ray standing wave (NIXSW) measurements and compared with the results of density functional theory (DFT) calculations using several different methods of dispersion correction. Generally, good agreement between theory and experiment was achieved for the quantitative structures, albeit with the prediction of the alkali atom heights being challenging for some methods. The adsorption structures depend sensitively on the interplay of molecule-metal charge transfer and long-range dispersion forces, which are controlled by the composition ratio between alkali atoms and TCNQ. The large difference in atomic size between K and Cs has negligible effects on stability, whereas increasing the ratio of K/TCNQ from 1:4 to 1:1 leads to a weakening of molecule-metal interaction strength in favor of stronger ionic bonds within the two-dimensional alkali-organic network. A strong dependence of the work function on the alkali donor-TCNQ acceptor coadsorption ratio is predicted.

Direct Experimental Evidence for Substrate Adatom Incorporation into a Molecular Overlayer.

While the phenomenon of metal substrate adatom incorporation into molecular overlayers is generally believed to occur in several systems, the experimental evidence for this relies on the interpretation of scanning tunneling microscopy (STM) images, which can be ambiguous and provides no quantitative structural information. We show that surface X-ray diffraction (SXRD) uniquely provides unambiguous identification of these metal adatoms. We present the results of a detailed structural study of the Au(111)-F4TCNQ system, combining surface characterization by STM, low-energy electron diffraction, and soft X-ray photoelectron spectroscopy with quantitative experimental structural information from normal incidence X-ray standing wave (NIXSW) and SXRD, together with dispersion-corrected density functional theory (DFT) calculations. Excellent agreement is found between the NIXSW data and the DFT calculations regarding the height and conformation of the adsorbed molecule, which has a twisted geometry rather than the previously supposed inverted bowl shape. SXRD measurements provide unequivocal evidence for the presence and location of Au adatoms, while the DFT calculations show this reconstruction to be strongly energetically favored.

Evolution of adsorption heights in the on-surface synthesis and decoupling of covalent organic networks on Ag(111) by normal-incidence X-ray standing wave.

Structural characterization in on-surface synthesis is primarily carried out by Scanning Probe Microscopy (SPM) which provides high lateral resolution. Yet, important fresh perspectives on surface interactions and molecular conformations are gained from adsorption heights that remain largely inaccessible to SPM, but can be precisely measured with both elemental and chemical sensitivity by Normal-Incidence X-ray Standing Wave (NIXSW) analysis. Here, we study the evolution of adsorption heights in the on-surface synthesis and post-synthetic decoupling of porous covalent triazine-phenylene networks obtained from 2,4,6-tris(4-bromophenyl)-1,3,5-triazine (TBPT) precursors on Ag(111). Room temperature deposition of TBPT and mild annealing to ∼150 °C result in full debromination and formation of organometallic intermediates, where the monomers are linked into reticulated networks by C-Ag-C bonds. Topologically identical covalent networks comprised of triazine vertices that are interconnected by biphenyl units are obtained by a thermally activated chemical transformation of the organometallic intermediates. Exposure to iodine vapor facilitates decoupling by intercalation of an iodine monolayer between the covalent networks and the Ag(111) surface. Accordingly, Scanning Tunneling Microscopy (STM), X-ray Photoelectron Spectroscopy (XPS) and NIXSW experiments are carried out for three successive sample stages: organometallic intermediates, covalent networks directly on Ag(111) and after decoupling. NIXSW analysis facilitates the determination of adsorption heights of chemically distinct carbon species, i.e. in the phenyl and triazine rings, and also for the organometallic carbon atoms. Thereby, molecular conformations are assessed for each sample stage. The interpretation of experimental results is informed by Density Functional Theory (DFT) calculations, providing a consistent picture of adsorption heights and molecular deformations in the networks that result from the interplay between steric hindrance and surface interactions. Quantitative adsorption heights, i.e. vertical distances between adsorbates and surface, provide detailed insight into surface interactions, but are underexplored in on-surface synthesis. In particular, the direct comparison with an in situ prepared decoupled state unveils the surface influence on the network structure, and shows that iodine intercalation is a powerful decoupling strategy.

Chemical shielding of H2O and HF encapsulated inside a C60 cage

Molecular surgery provides the opportunity to study relatively large molecules encapsulated within a fullerene cage. Here we determine the location of an H2O molecule isolated within an adsorbed buckminsterfullerene cage, and compare this to the intrafullerene position of HF. Using normal incidence X-ray standing wave (NIXSW) analysis, coupled with density functional theory and molecular dynamics simulations, we show that both H2O and HF are located at an off-centre position within the fullerene cage, caused by substantial intra-cage electrostatic fields generated by surface adsorption of the fullerene. The atomistic and electronic structure simulations also reveal significant internal rotational motion consistent with the NIXSW data. Despite this substantial intra-cage interaction, we find that neither HF or H2O contribute to the endofullerene frontier orbitals, confirming the chemical isolation of the encapsulated molecules. We also show that our experimental NIXSW measurements and theoretical data are best described by a mixed adsorption site model.

Vertical position of Sr dopants in the SrxBi2Se3 superconductor

The discovery of topological superconductivity in doped ${\mathrm{Bi}}_{2}{\mathrm{Se}}_{3}$ made this class of materials highly important for the field of condensed matter physics. However, the structural origin of the superconducting state remained elusive, despite being investigated intensively in recent years. We use scanning tunneling microscopy and the normal incidence x-ray standing wave (NIXSW) technique in order to determine the vertical position of the dopants---one of the key parameters for understanding topological superconductivity in this material--- for the case of ${\mathrm{Sr}}_{x}{\mathrm{Bi}}_{2}{\mathrm{Se}}_{3}$. In particular, we analyze the NIXSW data in consideration of the inelastic mean free path of the photoemitted electrons, which allows us to distinguish between symmetry-equivalent sites. We find that Sr atoms are not situated inside the van der Waals gap between the ${\mathrm{Bi}}_{2}{\mathrm{Se}}_{3}$ quintuple layers but rather in the quintuple layer close to the outer Se planes.

X-ray standing wave studies of molecular adsorption: why coherent fractions matter

The normal incidence x-ray standing wave (NIXSW) technique is the primary source of quantitative experimental information on the adsorption height of many near-planar molecules on metal surfaces, of relevance to organic electronics. The technique yields two structural parameters, the coherent position and the coherent fraction. For high values of the coherent fraction the coherent position can be related directly to the adsorption height, but because the coherent fraction is effectively an order parameter, low values of this parameter are often attributed to partial disorder. It is certainly true that in depositing these large molecules on a surface it is very challenging to produce a perfectly ordered surface. However, is the type of disorder that is likely to occur able to account for no other effect on measured NIXSW data than a lowering of the coherent fraction? Here we show, by considering a wide range of possible types of ‘disorder’, that in almost all such situations it is improbable that the coherent positions associated with very low coherent fractions actually provide a reliable measure of the adsorption height of the ordered component, as is often assumed to be the case. As such, presentations of NIXSW data that only consider coherent position values are likely to be extremely misleading, and provide an unreliable benchmark for detailed understanding of these interfaces.

Synchrotron X-ray standing wave Characterization of atomic arrangement at interface between transferred graphene and α-Al2O3(0001)

Graphene is expected to be one of the most promising materials for nanoelectronics and spintronics. In most graphene-based devices, the graphene channel is placed on insulating substrates. Therefore, the study of interfacial interactions between graphene and the insulator surface is of critical importance. In this study, the vertical arrangement of graphene which is transferred on α-Al2O3(0001) has been studied by normal incidence X-ray standing wave (NIXSW) technique. The analysis of the NIXSW profile reveals that the graphene layer is located at 3.57 Å above the α-Al2O3(0001) surface, which is larger than the interlayer distance of graphite (3.356 Å). Micro-Raman spectroscopy shows that the transferred graphene has a limited spatial distribution of hole concentration. The present study shows that transferred graphene on the sapphire substrate followed by vacuum-annealing has an atomically flat surface free from residual contaminations such as organic compounds and there occurs the hole-doping in graphene.

The structure of 2D charge transfer salts formed by TCNQ/alkali metal coadsorption on Ag(111)

The structure of coadsorption phases formed on Ag(111) by TCNQ (7,7,8,8-tetracyanoquinodimethane) with Cs are compared with previously reported coadsorption phases formed with K, following investigation by scanning tunnelling microscopy (STM), low energy electron diffraction, soft X-ray photoelectrons spectroscopy and normal incidence X-ray standing waves (NIXSW). For each alkali we identify two ordered phases, one with an alkali: TCNQ stoichiometry of 1:1 and the other 2:1. STM images show the molecular organisation is the same for Cs and K, although only the K2TCNQ phase is commensurate with the substrate. A previously-published detailed structure determination of the K2TCNQ phase, complemented by density function theory calculations that identify bonding strengths, showed that the binding within the layer is much stronger than that of the layer to the substrate. Insensitivity to commensuration is thus to be expected. The situation for KTCNQ and CsTCNQ is less clear; these ordered incommensurate overlayers clearly have strong intralayer bonding, but the relative strength of the average overlayer-substrate bonding is unknown. NIXSW data show that the alkalis in these phases occupy adsorption sites far more distant from the substrate than the TCNQ molecules when compared to the near coplanar alkali-TCNQ geometry of K2TCNQ and Cs2TCNQ. Ultraviolet photoelectron spectra show increasing bonding shifts of TCNQ orbital states with alkali coverage.

Molecule–Metal Bond of Alternant versus Nonalternant Aromatic Systems on Coinage Metal Surfaces: Naphthalene versus Azulene on Ag(111) and Cu(111)

Interfaces between polycyclic π-electron systems and metals play prominent roles in organic or graphene-based (opto)electronic devices, in which performance-related parameters depend critically on the properties of metal/semiconductor contacts. Here, we explore how the topology of the π-electron system influences the bonding and the electronic properties of the interface. We use azulene as a model for nonalternant pentagon–heptagon (5–7) ring pairs and compare it to its isomer naphthalene, which represents the alternant 6–6 ring pair. Their coverage-dependent interaction with Ag(111) and Cu(111) surfaces was studied with the normal-incidence X-ray standing wave (NIXSW) technique, near-edge X-ray absorption fine structure (NEXAFS) spectroscopy, UV and X-ray photoelectron spectroscopies (UPS and XPS), and density functional theory (DFT). Coverage-dependent adsorption heights and spectroscopic data reveal that azulene forms shorter interfacial bonds than naphthalene and engages in stronger electronic interactions with both surfaces. These differences are more pronounced on Cu. Increasing coverages lead to larger adsorption heights, indicating bond weakening by intermolecular repulsion. The extensive DFT calculations include dispersive interactions using (1) the DFT-D3 scheme, (2) the vdWsurf correction based on DFT-TS, (3) a many-body dispersion (MBD) correction scheme, and (4) the D3surf scheme. All methods predict the adsorption heights reasonably well with an average error below 0.1 A. The stronger bond of azulene is attributed to its nonalternant topology, which results in a reduced highest occupied molecular orbital (HOMO)–lowest occupied molecular orbital (LUMO) gap and brings the LUMO energetically close to the Fermi energy of the metal, causing stronger hybridization with electronic states of the metal surfaces.

The Structure of VOPc on Cu(111): Does V=O Point Up, or Down, or Both?

The local structure of the nonplanar phthalocyanine, vanadyl phthalocyanine (VOPc), adsorbed on Cu(111) at a coverage of approximately one-half of a saturated molecular layer, has been investigated by a combination of normal-incidence X-ray standing waves (NIXSW), scanned-energy mode photoelectron diffraction (PhD), and density-functional theory (DFT), complemented by scanning tunnelling microscopy (STM). Qualitative assessment of the NIXSW data clearly shows that both “up” and “down” orientations of the molecule (with V=O pointing out of, and into, the surface) must coexist on the surface. O 1s PhD proves to be inconclusive regarding the molecular orientation. DFT calculations, using two different dispersion correction schemes, show good quantitative agreement with the NIXSW structural results for equal co-occupation of the two different molecular orientations and clearly favor the many body dispersion (MBD) method to deal with long-range dispersion forces. The calculated relative adsorption energies of the differently oriented molecules at the lowest coverage show a strong preference for the “up” orientation, but at higher local coverages, this energetic difference decreases, and mixed orientation phases are almost energetically equivalent to pure “up”-oriented phases. DFT-based Tersoff–Hamann simulations of STM topographs for the two orientations cast some light on the extent to which such images provide a reliable guide to molecular orientation.

Direct measurement of Ni incorporation into Fe3O4(001).

The normal incidence X-ray standing wave (NIXSW) technique has been used to follow the evolution of the adsorption geometry of Ni adatoms on the Fe3O4(001)-(√2 × √2)R45° surface as a function of temperature. Two primary surface region sites are identified: a bulk-continuation tetrahedral site and a sub-surface octahedral site, the latter site being preferred at higher annealing temperatures. The ease of incorporation is linked to the presence of subsurface cation vacancies in the (√2 × √2)R45° reconstruction and is consistent with the preference for octahedral coordination observed in the spinel compound NiFe2O4.

Determination of the adsorption geometry of PTCDA on the Cu(100) surface

The adsorption geometry, namely the height and the site, of 3,4,9,10-perylene tetracarboxylic dianhydride (PTCDA) on the Cu(100) surface was determined by the normal incidence x-ray standing wave (NIXSW) technique including triangulation. The two PTCDA molecules in the superstructure unit cell, which have perpendicular azimuthal orientation, are both located at bridge sites, the long molecular axis being parallel to the bridge. Carboxylic oxygen atoms and several atoms of the carbon backbone are located close to on-top positions. The vertical distortion motif of PTCDA on Cu(100) differs from that on the three low-index Ag surfaces, because significant downward displacement of the carboxylic oxygen atoms is lacking. In particular, the carbon backbone of PTCDA adsorbs closer to the surface than extrapolated from Ag data. This suggests a relative increase of the attractive interactions between the carbon backbone of PTCDA and the Cu(100) surface versus the attractive interactions on the carboxylic oxygen atoms.

Direct observation of site-selective hydrogenation and spin-polarization in hydrogenated hexagonal boron nitride on Ni(111).

We report the structural analysis and spin-dependent band structure of hydrogenated boron nitride adsorbed on Ni(111). The atomic displacement studied by using the normal incidence X-ray standing wave (NIXSW) technique supports the H-B(fcc):N(top) model, in which hydrogen atoms are site-selectively chemisorbed on boron atoms and N atoms remain on top of Ni atoms. The distance between the Ni plane and nitrogen plane did not change after hydrogenation, which implies that the interaction between Ni and N is 3d-π orbital mixing (donation and back-donation) even after hydrogenation of boron. The remaining π* peaks in near-edge X-ray absorption fine structure (NEXAFS) spectra are a manifestation of the rehybridization of sp2 into sp3 states, which is consistent with the N-B-N bonding angle derived from NIXSW measurement. The SPMDS measurement revealed the spin asymmetry appearing on hydrogenated h-BN, which was originated from a π related orbital with back donation from the Ni 3d state. Even though the atomic displacement is reproduced by the density functional theory (DFT) calculation with the H-B(fcc):N(top) model, the experimental spin-dependent band structure was not reproduced by DFT possibly due to the self-interaction error (SIE). These results reinforce the site-selective hydrogenation of boron and pave the way for efficient design of BN nanomaterials for hydrogen storage.

Au enrichment and vertical relaxation of theCu3Au(111)surface studied by normal-incidence x-ray standing waves

We have investigated the ${\mathrm{Cu}}_{3}\mathrm{Au}(111)$ surface, prepared under ultrahigh vacuum conditions by sputtering and annealing, by low energy electron diffraction (LEED), scanning tunneling microscopy (STM), x-ray photoelectron spectroscopy, and normal incidence x-ray standing waves (NIXSW). We find the surface to be depleted with Cu and enriched with Au at the same time, yielding a nominal Cu:Au ratio of 0.61:0.39 in the topmost layer. The STM images reveal that the first layer is nearly closely filled with atoms and contains a small amount of vacancies with an area concentration of about $5%$. Together with the Au enrichment, these cause local short-range disorder of the Au $p(2\ifmmode\times\else\texttimes\fi{}2)$ reconstruction. From this data, the average stoichiometry of the $p(2\ifmmode\times\else\texttimes\fi{}2)$ surface unit cell is estimated at $\mathrm{C}{\mathrm{u}}_{2.22}\mathrm{A}{\mathrm{u}}_{1.44}{\ensuremath{\square}}_{0.20}$ (instead of $\mathrm{C}{\mathrm{u}}_{3.00}\mathrm{A}{\mathrm{u}}_{1.00}{\ensuremath{\square}}_{0.00}$ of the ideal surface; \ensuremath{\square} denotes an atomic vacancy site). From NIXSW we find a significant outward relaxation of both the Cu and Au atoms of the topmost layer by 0.28 \AA{} and 0.33 \AA{}, which corresponds to $13%$ and $15%$ of the (111) bulk layer spacing of $\mathrm{C}{\mathrm{u}}_{3}\mathrm{Au}$. We suggest that this originates from a widening of the first/second layer spacing, by $6.8%$ and $8.8%$ for the Cu and Au atoms, respectively, plus an additional rigid increase in the second/third layer spacing by $6.2%$. We explain this by steric repulsions between Au atoms of the topmost layer, replacing smaller Cu atoms, and Au atoms in the second layer in combination with disorder. Finally, a lateral reconstruction, similar to that on the Au(111) surface, but with a much larger periodicity of 290 \AA{}, is identified from LEED.

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.

X-ray standing wave simulations based on Fourier vector analysis as a method to retrieve complex molecular adsorption geometries

We present an analysis method of normal incidence x-ray standing wave (NIXSW) data that allows detailed adsorption geometries of complex molecules to be retrieved. This method (Fourier vector analysis) is based on the comparison of both the coherence and phase of NIXSW data to NIXSW simulations of different molecular geometries as the relevant internal degrees of freedom are tuned. We introduce this analysis method using the prototypical molecular switch azobenzene (AB) adsorbed on the Ag(111) surface as a model system. The application of the Fourier vector analysis to AB/Ag(111) provides, on the one hand, detailed adsorption geometries including dihedral angles, and on the other hand, insights into the dynamics of molecules and their bonding to the metal substrate. This analysis scheme is generally applicable to any adsorbate, it is necessary for molecules with potentially large distortions, and will be particularly valuable for molecules whose distortion on adsorption can be mapped on a limited number of internal degrees of freedom.