Normal Incidence X-ray Standing Wave Data Research Articles

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.

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.

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.

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.

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.

The structure of the Au(111)/methylthiolate interface: New insights from near-edge x-ray absorption spectroscopy and x-ray standing waves

The local structure of the Au(111)(square root(3) x square root(3))R30 degrees-methylthiolate surface phase has been investigated by S K-edge near-edge s-ray absorption fine structure (NEXAFS) both experimentally and theoretically and by experimental normal-incidence x-ray standing waves (NIXSW) at both the C and S atomic sites. NEXAFS shows not only excitation into the intramolecular sigma(*) S-C resonance but also into a sigma(*) S-Au orbital perpendicular to the surface, clearly identifying the local S headgroup site as atop a Au atom. Simulations show that it is not possible, however, to distinguish between the two possible adatom reconstruction models; a single thiolate species atop a hollow-site Au adatom or a dithiolate moiety comprising two thiolate species bonded to a bridge-bonded Au adatom. Within this dithiolate moiety a second sigma(*) S-Au orbital that lies near parallel to the surface has a higher energy that overlaps that of the sigma(*) S-C resonance. The new NIXSW data show the S-C bond to be tilted by 61 degrees relative to the surface normal, with a preferred azimuthal orientation in <211>, corresponding to the intermolecular nearest-neighbor directions. This azimuthal orientation is consistent with the thiolate being atop a hollow-site Au adatom, but not consistent with the originally proposed Au-adatom-dithiolate moiety. However, internal conformational changes within this species could, perhaps, render this model also consistent with the experimental data.

Structure determination of PF 3 adsorption on Cu(1 0 0) using X-ray standing waves

The local structure of the Cu(1 0 0) c(4 × 2)–PF 3 adsorption phase has been investigated through the use of normal-incidence X-ray standing waves (NIXSW), monitored by P 1s and F 1s photoemission, together with P K-edge near-edge X-ray absorption fine structure (NEXAFS). NEXAFS shows the molecule to be oriented with its C 3v symmetry axis essentially perpendicular to the surface, while the P NIXSW data show the molecule to be adsorbed in atop sites 2.37 ± 0.04 Å above the surface, this distance corresponding to the Cu–P nearest-neighbour distance in the absence of any surface relaxation. F NIXSW indicates a surprisingly small height difference of the P and F atoms above the surface 0.44 ± 0.06 Å, compared with the value expected for an undistorted gas-phase geometry of 0.77 Å, implying significant increases in the F–P–F bond angles. In addition, however, the F NIXSW data indicate that the molecules have a well-defined azimuthal orientation with a molecular mirror plane aligned in a 〈0 1 1〉 substrate mirror plane, and with a small (5–10°) tilt of the molecule in this plane such that the two symmetrically-equivalent F atoms in each molecule are tilted down towards the surface.

Structure of the Pentylthiolate Self-Assembled Monolayer on Ag(111)

A combination of scanning tunneling microscopy (STM), low-energy electron diffraction (LEED), and normal incidence X-ray standing waves (NIXSW) has been used to investigate the structure of the self-assembled monolayer (SAM) formed by pentylthiolate on Ag(111) in ultrahigh vacuum through interaction with pentanethiol. NIXSW data are closely similar to those for methythiolate on Ag(111) in the commensurate (root 7x root 7)R19 degrees phase and consistent with a similar adsorbate-induced reconstruction of the outermost Ag layer comprising only 3/7 ML of Ag atoms. However, both STM and LEED show that the local lateral periodicity is similar to 5% larger in the pentylthiolate phase and that the resulting SAM is not commensurate with the substrate. The results are discussed in the context of previously published results for other alkylthiolate SAMs on Ag(111).

Solving surface structures from normal incidence X-ray standing wave data

A program is provided to determine structural parameters of atoms in or adsorbed on surfaces by refinement of atomistic models towards experimentally determined data generated by the normal incidence X-ray standing wave (NIXSW) technique. The method employs a combination of Differential Evolution Genetic Algorithms and Steepest Descent Line Minimisations to provide a fast, reliable and user friendly tool for experimentalists to interpret complex multidimensional NIXSW data sets.

Molecular distortion of NTCDA upon adsorption on Ag(111): a normal incidence x-ray standing wave study

We investigated the adsorption geometry of the model system NTCDA (1,4,5,8-naphthalin-tetracarboxylicacid-dianhydride) on Ag(111) using the normal incidence x-ray standing wave (NIXSW) technique. For the relaxed monolayer structure a significant vertical distortion of the molecule is found upon adsorption. The carboxylic oxygen atoms at the corners of the molecule are located 0.25(3) Å closer to the topmost Ag atoms than the naphthalene core at 2.997(16) Å. This distortion effect is similar to that of the larger mole- cule (3,4,9,10-perylene tetracarboxylicacid-dianhydride) (PTCDA)/Ag(111) (Hauschild A et al 2005 Phys. Rev. Lett. 95 209602), but the chemisorptive bonding is weaker. Our structural investigation is based on photoelectron and Auger emission NIXSW data, the independent measurement of which allows us to correct in a self-consistent way for non-dipolar contributions to the photoelectron yield as well as for electron induced Auger processes, two effects which may significantly influence the structural results if not considered.

Structural Investigation of the Interaction of Molecular Sulfur with Ag(111)

Scanning tunneling microscopy (STM) and normal-incidence X-ray standing wave (NIXSW) analysis, together with low-energy electron diffraction (LEED) and X-ray photoelectron spectroscopy (XPS), have been used to investigate the structure of surface phases formed by the dissociation of molecular sulfur (S2) on Ag(111) under ultrahigh vacuum conditions. Both a complex low coverage phase and the well-known Ag(111)(√7×√7)R19°-S surface have been investigated. In the case of the low coverage phase, the long-range periodicity seen in STM and the LEED pattern have been reconciled, while NIXSW data indicate a significant local coherence of the S atoms on the substrate. However, the complexity of this phase, with a minimum estimate of 11 S atoms per unit mesh, is too great for complete structural interpretation. A model for the (√7×√7)R19°-S phase, based on epitaxial growth of the high-temperature fcc phase of Ag2S(111), is found to be consistent with all the experimental data, while NIXSW provides information on th...

Structural characterisation of ultra-thin VO x films on TiO 2(1 1 0)

The normal incidence X-ray standing wave (NIXSW) technique has been applied to investigate the structure of ultra-thin VO x films grown on TiO 2(1 1 0) and pre-characterised by core level photoemission. For a film composed of a sub-monolayer coverage of V deposited in ultra-high vacuum the local structure of two coexistent species, labelled ‘oxidic’ and ‘metallic’, has been investigated independently through the use of chemical-shift-NIXSW. The ‘oxidic’ state is shown to be consistent with a mixture of epitaxial or substitutional sites and chemisorption into sites coordinated to three surface O atoms. The metallic V atoms also involve a mixture of chemisorption and second-layer sites above the substrate surface consistent with the formation of small V clusters. VO x films up to ∼6 atomic layers were also grown by post-oxidation (sequential V deposition and annealing in oxygen) and by reactive evaporation in a partial pressure of oxygen. While films of around one monolayer or less are consistent with epitaxial VO 2 growth, the film quality deteriorates rapidly with increasing thickness and is worse for reactive evaporation. A possible interpretation of the NIXSW data is increasing contributions of V 2O 3 crystallites. The inferior quality of the reactively evaporated films may be due to an insufficient supply of oxygen.

The local structure of SO 2 and SO 3 on Ni(1 1 1)

The normal incidence X-ray standing wave (NIXSW) technique, supported by X-ray photoelectron spectroscopy and near-edge X-ray absorption fine structure (NEXAFS), has been used to determine the local adsorption geometry of SO 2 and SO 3 on Ni(1 1 1). Chemical-state specific NIXSW data for coadsorbed SO 3 and S, formed by the disproportionation of adsorbed SO 2 after heating from 140 K to 270 K, were obtained using S 1s photoemission detection. For adsorbed SO 2 at 140 K the new results confirm those of an earlier study [Jackson et al., Surf. Sci. 389 (1997) 223] that the molecule is located above hollow sites with its molecular plane parallel to the surface and the S and O atoms in off-atop sites; corrections to account for the non-dipole effects in the interpretation of the NIXSW monitored by S 1s and O 1s photoemission, not included in the earlier work, remove the need for any significant adsorption-induced distortion of the SO 2 in this structure. SO 3, not previously investigated, is found to occupy an off-bridge site with the C 3v axis slightly tilted relative to the surface normal and with one O atom in an off-atop site and the other two O atoms roughly between bridge and hollow sites. The O atoms are approximately 0.87 Å closer to the surface than the S atom. This general bonding orientation for SO 3 is similar to that found on Cu(1 1 1) and Cu(1 0 0) both experimentally and theoretically, although the detailed adsorption sites differ.

Observation of an anti-phase domain structure in the Cu{1 0 0}/Sn surface alloy system

Low energy electron diffraction (LEED), scanning tunneling microscopy (STM) and the normal incidence X-ray standing wave (NIXSW) technique have been used to determine the structure of the first surface phase formed on Cu{1 0 0} upon deposition of 0.21 monolayers (ML) of tin. At this coverage the LEED images exhibits a modified p(2 × 2) structure with split fractional order diffraction spots. A double scattering LEED pattern simulation consistent with both the Sn surface coverage and the complex split beam LEED pattern suggests an ordered phase based on a p(2 × 2) structure with light anti-phase domain walls. Possible adsorption sites are identified from NIXSW data by triangulation of the distances between the Sn atoms and the (2 0 0) and (1 1 1) planes. The results indicate that Sn atoms adsorb in a fourfold site but does not distinguish between overlayer and substitutional sites. The STM data reveal small domains of p(2 × 2) structure formed by the Sn atoms being adsorbed in substitutional sites. These domains typically contain 16 Sn atoms arranged in a square 4 × 4 array, however larger and smaller rectangular domains are also observed with sides containing three, five and six Sn atoms. The width of the domain wall is found to vary with rows of one, three or five copper atoms separating the domains in both the [0 1 1] and [ 0 1 1 ̄ ] directions. The STM images indicate that the Cu atoms in the domain walls are vertically displaced from their expected positions. This is attributed to elastic strain due to the large metallic diameter of Sn (0.162 nm) relative to Cu (0.127 nm).

A structural study of the interaction of methanethiol with Pt [formula omitted] using X-ray standing waves

In combination with surface characterisation by synchrotron radiation X-ray photoelectron spectroscopy, the normal incidence X-ray standing wave (NIXSW) technique has been applied to a determination of the structure of surface phases formed on Pt(1 1 1) by reaction with methanethiol. On surfaces heated to ⩾ ≈500 K, producing only coadsorbed atomic S and C, the S atoms are found to occupy fcc hollow sites (directly above Pt atoms in the third layer) in a geometry essentially identical to that of simple ordered S overlayer phases on Pt(1 1 1) with a S–Pt layer spacing of 1.67 Å, but with possible fractional co-occupation of a complex S phase. On a surface annealed to ≈223 K only a surface methanethiolate (CH 3S–) species is believed to be present, the favoured model involves a tilted off-atop bonding such that the S atoms are located offset from the fcc hollow sites, with frustrated rotational vibrations of large amplitude, although an alternative model based on co-occupation of atop and fcc hollow sites is also consistent with the NIXSW data.

X-ray Studies of Self-Assembled Monolayers on Coinage Metals. 2. Surface Adsorption Structures in 1-Octanethiol on Cu(111) and Ag(111) and Their Determination by the Normal Incidence X-ray Standing Wave Technique

The adsorption structures of self-assembled monolayers (SAMs) formed at saturation coverages of 1-octanethiol SAMs, prepared under ultrahigh vacuum (UHV) conditions on Cu(111) and Ag(111) substrates, were measured using a normal-incidence X-ray standing wave (NIXSW) technique. A thorough and pedagogical exposition of the relationship between the structural parameters determined in NIXSW and a number of simple adsorption structures is presented. In the two SAMs studied, the NIXSW data indicated the formation of monolayers which induced a reconstruction of the outermost layer of the substrate. SAMs on Cu and Ag were indistinguishable using the NIXSW technique, but given the different steric requirements imposed by each surface it is proposed that a different adsorption geometry is adopted in each case, which is either incommensurate with the underlying substrate or commensurate on a large mesh. In the case of Ag(111) the NIXSW data are consistent with the formation of a distorted (√7×√7)R19.1° structure, proposed by other workers. In the case of Cu(111), it is proposed that the adsorbate structure is most likely a significant distortion of the (√3×√3)R30° structure observed in SAMs of alkanethiols on Au(111) and we speculate on the existence of an overlayer of CH3−(CH2)7−S−Cu3 clusters.