Scanned-energy Mode Photoelectron Diffraction Research Articles

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.

A structural investigation of the interaction of oxalic acid with Cu(110)

The interaction of oxalic acid with the Cu(110) surface has been investigated by a combination of scanning tunnelling microscopy (STM), low energy electron diffraction (LEED), soft X-ray photoelectron spectroscopy (SXPS), near-edge X-ray absorption fine structure (NEXAFS) and scanned-energy mode photoelectron diffraction (PhD), and density functional theory (DFT). O 1s SXPS and O K-edge NEXAFS show that at high coverages a singly deprotonated monooxalate is formed with its molecular plane perpendicular to the surface and lying in the [11¯0] azimuth, while at low coverage a doubly-deprotonated dioxalate is formed with its molecular plane parallel to the surface. STM, LEED and SXPS show the dioxalate to form a (3 × 2) ordered phase with a coverage of 1/6 ML. O 1s PhD modulation spectra for the monooxalate phase are found to be simulated by a geometry in which the carboxylate O atoms occupy near-atop sites on nearest-neighbour surface Cu atoms in [11¯0] rows, with a CuO bondlength of 2.00 ± 0.04 Å. STM images of the (3 × 2) phase show some centred molecules attributed to adsorption on second-layer Cu atoms below missing [001] rows of surface Cu atoms, while DFT calculations show adsorption on a (3 × 2) missing row surface (with every third [001] Cu surface row removed) is favoured over adsorption on the unreconstructed surface. O 1s PhD data from dioxalate is best fitted by a structure similar to that found by DFT to have the lowest energy, although there are some significant differences in intramolecular bondlengths.

Structure of a Model Dye/Titania Interface: Geometry of Benzoate on Rutile-TiO2 (110)(1 × 1)

Scanned-energy mode photoelectron diffraction (PhD) and ab initio density functional theory calculations have been employed to investigate the adsorption geometry of benzoate ([C6H5COO]−) on rutile-TiO2(110)(1 × 1). PhD data indicate that the benzoate moiety binds to the surface through both of its oxygen atoms to two adjacent fivefold surface titanium atoms in an essentially upright geometry. Moreover, its phenyl (C6H5−) and carboxylate ([−COO]−) groups are determined to be coplanar, being aligned along the [001] azimuth. This experimental result is consistent with the benzoate geometry emerging from DFT calculations conducted for laterally rather well-separated adsorbates. At shorter interadsorbate distances, the theoretical modeling predicts a more tilted and twisted adsorption geometry, where the phenyl and carboxylate groups are no longer coplanar; i.e., interadsorbate interactions influence the configuration of adsorbed benzoate.

The local structure of the azobenzene/aniline reaction intermediate on TiO2(110)

Scanned-energy mode photoelectron diffraction (PhD) and near-edge X-ray absorption fine structure (NEXAFS) have been used to study the surface species, previously proposed to be phenyl imide, C6H5N–, on rutile TiO2(110) following exposure to either azobenzene or aniline. All measurements are consistent with the two reactants forming a common surface species in the same local adsorption site. N K-edge NEXAFS confirms the scission of the NN bond in azobenzene, while C K-edge NEXAFS shows the phenyl ring to be intact with the molecular plane tilted relative to the surface normal and not aligned in either principle azimuth of the surface. N 1s PhD data indicate that the N atom bonds atop a surface five-fold-coordinated Ti atom, most probably at a TiN bondlength of 1.77±0.05Å, and not bridging two such atoms, as had been suggested. This atop geometry is favoured by recent density functional theory (DFT) calculations, but more quantitative aspects of the DFT result are not in agreement with the conclusions of our experimental study.

Water does partially dissociate on the perfect TiO2(110) surface: A quantitative structure determination

There has been a long-standing controversy as to whether water can dissociate on perfect areas of a TiO${}_{2}$(110) surface; most early theoretical work indicated this dissociation was facile, while experiments indicated little or no dissociation. More recently the consensus of most theoretical calculations is that no dissociation occurs. New results presented here, based on analysis of scanned-energy mode photoelectron diffraction data from the OH component of O 1$s$ photoemission, show the coexistence of molecular water and OH species in both atop (OH${}_{\mathrm{t}}$) and bridging (OH${}_{\mathrm{br}}$) sites. OH${}_{\mathrm{br}}$ can arise from reaction with oxygen vacancy defect sites (O${}_{\mathrm{vac}}$), but OH${}_{\mathrm{t}}$ have only been predicted to arise from dissociation on the perfect areas of the surface. The relative concentrations of OH${}_{\mathrm{t}}$ and OH${}_{\mathrm{br}}$ sites arising from these two dissociation mechanisms are found to be fully consistent with the initial concentration O${}_{\mathrm{vac}}$ sites, while the associated Ti-O bond lengths of the OH${}_{\mathrm{t}}$ and OH${}_{\mathrm{br}}$ species are found to be 1.85 \ifmmode\pm\else\textpm\fi{} 0.08 and 1.94 \ifmmode\pm\else\textpm\fi{} 0.07 \AA{}, respectively.

Quantitative local structure determination of R,R-tartaric acid on Cu(110): Monotartrate and bitartrate phases

The local adsorption site of the monotartrate and bitartrate species of R,R-tartaric acid deposited on Cu(110) have been determined by scanned-energy mode photoelectron diffraction (PhD). In the monotartrate phase the molecule is found to adsorb upright through the O atoms of the single deprotonated carboxylic acid (carboxylate) group, which are located in different off-atop sites with associated Cu―O bond lengths of 1.92±0.08Å and 1.93±0.06Å; the plane of the carboxylate group is tilted by 17±6° off the surface normal. The bitartrate species adopts a ‘lying down’ orientation, bonding to the surface through all four O atoms of the two carboxylate groups, also in off-atop sites. Three slightly different models give comparably good fits to the PhD data, but only one of these is similar to that predicted by earlier density functional theory calculations. This model is found to have Cu―O bond lengths of 1.93±0.08Å and 1.95±0.08Å, while the planes of the carboxylate groups are tilted by 38±6° from the surface normal.

Global search algorithms in surface structure determination using photoelectron diffraction

Three different algorithms to effect global searches of the variable-parameter hyperspace are compared for application to the determination of surface structure using the technique of scanned-energy mode photoelectron diffraction (PhD). Specifically, a new method not previously used in any surface science methods, the swarm-intelligence-based particle swarm optimisation (PSO) method, is presented and its results compared with implementations of fast simulated annealing (FSA) and a genetic algorithm (GA). These three techniques have been applied to experimental data from three adsorption structures that had previously been solved by standard trial-and-error methods, namely H2O on TiO2(110), SO2 on Ni(111) and CN on Cu(111). The performance of the three algorithms is compared to the results of a purely random sampling of the structural parameter hyperspace. For all three adsorbate systems, the PSO out-performs the other techniques as a fitting routine, although for two of the three systems studied the advantage relative to the GA and random sampling approaches is modest. The implementation of FSA failed to achieve acceptable fits in these tests.

Local hydroxyl adsorption geometry on TiO2(110)

The local structure of the hydroxyl species on the rutile TiO${}_{2}$(110) surface has been determined both experimentally and computationally. The experimental study exploited chemical state--specific O 1s scanned-energy mode photoelectron diffraction from a surface exposed to atomic hydrogen, while density functional theory calculations were used to provide complementary information. As expected on the basis of previous studies, the bridging O atoms of the clean surface are hydroxylated, but this causes surprisingly small changes in the surrounding surface relaxation. Experiment and theory are in good agreement regarding the magnitude of these atomic movements. Specifically, the Ti-O${}_{\mathrm{OH}}$ surface bond is significantly longer (by 0.10--0.15 \AA{}) than that of Ti-O${}_{\mathrm{bridging}}$ bonds on the clean surface.

The structure of furan reaction products on Pd(111)

Previous experimental studies of the interaction of molecular furan, C(4)H(4)O, with Pd(111) have led to the conclusion that partial dissociation leads to two coadsorbed reaction products, CO and a C(3)H(3) species. Using density functional theory (DFT), a range of possible molecular conformation and adsorption sites of the C(3)H(3) species have been explored and the lowest energy structures, and associated C 1s photoelectron core-level binding energy shifts (CLSs), have been determined. Comparison of these CLS values with published experimental measurements allows one possible conformation to be rejected. New simulations of the C 1s scanned-energy mode photoelectron diffraction (PhD) spectra for several of lowest-energy structures found in DFT are compared with the results of an earlier experimental study. The lowest energy structure found in DFT is not consistent with the PhD data, suggesting that energy barriers to achieve the associated conformation cannot be overcome in the dissociation process. Through consideration of the results of both methods, the most probable surface structures are discussed.

The structure of methoxy species on Cu(110): A combined photoelectron diffraction and density functional theory determination

The local structure of the methoxy species on Cu(110) has been investigated experimentally using chemical-state specific O 1s scanned-energy mode photoelectron diffraction (PhD), and also by density functional theory (DFT) calculations. The PhD data show a clear preference for adsorption with the O bonding atoms in short-bridge sites, though the best fit of multiple-scattering simulations to the experimental data is achieved with two slightly different short-bridge geometries. The DFT calculations also show that not only are the short-bridge sites energetically favoured in isolation, but that coordination to pairs of Cu adatoms has a similar energy. A structure consistent with both the PhD data and the DFT calculations is proposed for the previously-observed (5 × 2)pg ordered phase, based on methoxy species in short-bridge sites on pairs of Cu adatoms and on the underlying surface. Simulated scanning tunnelling microscopy images agree well with those observed experimentally, while the model is also shown to be consistent with the qualitative behaviour seen in early X-ray photoelectron diffraction (XPD) forward-scattering experiments.

Structure of Cytosine on Cu(110): a Scanned-Energy Mode Photoelectron Diffraction Study

The local adsorption structure formed by the interaction of cytosine with a Cu(110) surface, following adsorption at ∼300 K and annealing to ∼420 K, has been investigated by O 1s and N 1s scanned-energy mode photoelectron diffraction (PhD). Initial characterization by soft-X-ray photoelectron spectroscopy and O K-edge near-edge X-ray absorption fine structure (NEXAFS) indicates that chemisorption leads to dehydrogenation of the NH species in the molecular ring and indicates that the molecular plane is perpendicular to the surface and close to the [110] azimuth. The PhD results confirm this orientation and show that the molecule bonds to the surface through the deprotonated N atom and the O atom, both of which occupy off-atop sites. The associated Cu−N and Cu−O bondlengths are 1.94(+0.07/−0.03) A and 1.94(+0.06/−0.04) A, respectively. Density functional theory calculations provide further support for this local structure and provide information on the possible role of intermolecular interaction. Possible ...

Methoxy Species on Cu(110): Understanding the Local Structure of a Key Catalytic Reaction Intermediate

Partial oxidation of methanol to formaldehyde over Cu(110) is one of the most studied catalytic reactions in surface science, yet the local site of the reaction intermediate, methoxy, remains unknown. Using a combination of experimental scanned-energy mode photoelectron diffraction, and density functional theory, a consistent structural solution is presented in which all methoxy species occupy twofold coordinated "short-bridge" adsorption sites. The results are consistent with previously-published scanning tunnelling microscopy images and theoretical calculations of the reaction mechanism.

The structure and bonding of furan on Pd(111)

The structure and bonding of molecular furan, C 4H 4O, on Pd(111) has been investigated using density functional theory (DFT) calculations and the results compared with those of a recent experimental investigation using scanned-energy mode photoelectron diffraction (PhD). The DFT results confirm the orientation of the molecular plane to be essentially parallel to the surface and show a clear energetic preference for one of the two possible structures identified in the PhD study, namely that with the molecule centred over the hollow sites of the surface. Two slightly different geometries at the hollow sites are found to be essentially energetically equivalent; in both cases, one Pd surface atom bonds to two C atoms, while two other Pd atoms each bond to one C atom. These structures differ in that in one case the pair of C atoms bonding to a single Pd atom are both β-C (C atoms not bonded to O in the furan molecule), whereas in the second case this pair of C atoms comprises one β-C and one α-C (adjacent to the O atom in furan). In both structures the C–Pd bonding is accompanied by displacements of the H and O atoms away from the surface and out of the molecular plane and local C–Pd coordination consistent with a rehybridisation of the C bonding to sp 3 character.

A photoelectron diffraction investigation of vanadyl phthalocyanine on Au(1 1 1)

Scanned-energy mode photoelectron diffraction using the O 1s and V 2p emission perpendicular to the surface has been used to investigate the orientation and internal conformation of vanadyl phthalocyanine (VOPc) adsorbed on Au(1 1 1). The results confirm earlier indications from scanning tunnelling microscopy that the V O vanadyl bond points out of, and not into, the surface. The V O bondlength is 1.60 ± 0.04 Å, not significantly different from its value in bulk crystalline VOPc. However, the V atom in the adsorbed molecule is almost coplanar with the surrounding N atoms and is thus pulled down into the approximately planar region defined by the N and C atoms by 0.52 (+0.14/−0.10) Å, relative to its location in crystalline VOPc. This change must be attributed to the bonding interaction between the molecule and the underlying metal surface.

Adsorption structure of glycine on TiO 2(1 1 0): A photoelectron diffraction determination

High-resolution core-level photoemission and scanned-energy mode photoelectron diffraction (PhD) of the O 1s and N 1s states have been used to investigate the interaction of glycine with the rutile TiO 2(1 1 0) surface. Whilst there is clear evidence for the presence of the zwitterion NH 3 + CH 2COO − with multilayer deposition, at low coverage only the deprotonated glycinate species, NH 2CH 2COO is present. Multiple-scattering simulations of the O 1s PhD data show the glycinate is bonded to the surface through the two carboxylate O atoms which occupy near-atop sites above the five-fold-coordinated surface Ti atoms, with a Ti–O bondlength of 2.12 ± 0.06 Å. Atomic hydrogen arising from the deprotonation is coadsorbed to form hydroxyl species at the bridging oxygen sites with an associated Ti–O bondlength of 2.01 ± 0.03 Å. Absence of any significant PhD modulations of the N 1s emission is consistent with the amino N atom not being involved in the surface bonding, unlike the case of glycinate on Cu(1 1 0) and Cu(1 0 0).

The local structure of SO 2 and SO 3 on Ni(1 1 1): A scanned-energy mode photoelectron diffraction study

O 1s and S 2p scanned-energy mode photoelectron diffraction (PhD) data, combined with multiple-scattering simulations, have been used to determine the local adsorption geometry of the SO 2 and SO 3 species on a Ni(1 1 1) surface. For SO 2, the application of reasonable constraints on the molecular conformation used in the simulations leads to the conclusion that the molecule is centred over hollow sites on the surface, with the molecular plane essentially parallel to the surface, and with both S and O atoms offset from atop sites by almost the same distance of 0.65 Å. For SO 3, the results are consistent with earlier work which concluded that surface bonding is through the O atoms, with the S atom higher above the surface and the molecular symmetry axis almost perpendicular to the surface. Based on the O 1s PhD data alone, three local adsorption geometries are comparably acceptable, but only one of these is consistent with the results of an earlier normal-incidence X-ray standing wave (NIXSW) study. This optimised structural model differs somewhat from that originally proposed in the NIXSW investigation.

The local adsorption site of methylthiolate on Au(1 1 1): Bridge or atop?

Measurements of the local adsorption geometry of the S head-group atom in the Au(1 1 1)(√3 × √3) R30°–CH 3S surface have been made using normal incidence X-ray standing waves (NIXSW) and S 1s scanned-energy mode photoelectron diffraction on the same surface preparations. The results confirm that the local adsorption site is atop an Au atom in a bulk-continuation site with a S–Au bondlength of 2.42 ± 0.02 Å, and that there can be no significant fraction of coadsorbed bridging species as recently proposed in a combined molecular dynamics/experimental study by Mazzarello et al. [R. Mazzarello, A. Cossaro, A. Verdini, R. Rousseau, L. Casalis, M.F. Danisman, L. Floreano, S. Scandolo, A. Morgante, G. Scoles, Phys. Rev. Lett. 98 (2007) 016102]. The results do not, however, clearly distinguish the different local reconstruction (adatom) models proposed for this surface.

A structural study of a C 3H 3 species coadsorbed with CO on Pd(1 1 1)

The combination of chemical-state-specific C 1s scanned-energy mode photoelectron diffraction (PhD) and O K-edge near-edge X-ray absorption fine structure (NEXAFS) has been used to determine the local adsorption geometry of the coadsorbed C 3H 3 and CO species formed on Pd(1 1 1) by dissociation of molecular furan. CO is found to adopt the same geometry as in the Pd(1 1 1)c(4 × 2)-CO phase, occupying the two inequivalent three-fold coordinated hollow sites with the C–O axis perpendicular to the surface. C 3H 3 is found to lie with its molecular plane almost parallel to the surface, most probably with the two ‘outer’ C atoms in equivalent off-atop sites, although the PhD analysis formally fails to distinguish between two distinct local adsorption sites.

The adsorption structure of furan on Pd(1 1 1)

The structure of molecular furan, C 4H 4O, on Pd(1 1 1) has been investigated by O K-edge near-edge X-ray absorption fine structure (NEXAFS) and C 1s scanned-energy mode photoelectron diffraction (PhD). NEXAFS shows the molecule to be adsorbed with the molecular plane close to parallel to the surface, a conclusion confirmed by the PhD analysis. Chemical-state specific C 1s PhD data were obtained for the two inequivalent C atoms in the furan, the α-C atoms adjacent to the O atom, and the β-C atoms bonded only to C atoms, but only the PhD modulations for the α-C emitters were of sufficiently large amplitude for detailed evaluation using multiple scattering calculations. This analysis shows the α-C atoms to be located approximately 0.6 Å off-atop surface Pd atoms with an associated C–Pd bondlength of 2.13 ± 0.03 Å. Two alternative local geometries consistent with the data place the O atom in off-atop or near-hollow locations, and for each of these local structures there are two equally-possible registries relative to the fcc and hcp hollow sites. The results are in good agreement with earlier density functional theory calculations which indicate that the fcc and hcp registries are equally probable, but the PhD results fail to distinguish the two distinct local bonding geometries.

The local adsorption geometry of benzenethiolate on Cu(1 0 0)

The local adsorption geometry of benzenethiolate in the ordered c(2 × 6) phase on Cu(1 0 0) has been investigated by a combination of S K-edge near-edge X-ray absorption fine structure (NEXAFS), normal incidence X-ray standing waves (NIXSW) and S 1s scanned-energy mode photoelectron diffraction (PhD). NEXAFS and PhD show that the molecular plane is tilted from the surface normal by 20 ± 15°, while NIXSW clearly identifies the S head-group as occupying the four-fold coordinated hollow sites. PhD shows the S atoms lies 1.34 ± 0.04 Å above the outermost Cu atomic layer, leading to a Cu–S bondlength of 2.25 ± 0.02 Å. The combination of the PhD and NIXSW results shows the Cu surface layer has an outward relaxation of 0.15 ± 0.06 Å. Possible origins for this large adsorbate-induced relaxation are discussed.