Local Adsorption Structure Research Articles

Local adsorption structure and bonding of porphine on Cu(111) before and after self-metalation.

We have experimentally determined the lateral registry and geometric structure of free-base porphine (2H-P) and copper-metalated porphine (Cu-P) adsorbed on Cu(111), by means of energy-scanned photoelectron diffraction (PhD), and compared the experimental results to density functional theory (DFT) calculations that included van der Waals corrections within the Tkatchenko-Scheffler approach. Both 2H-P and Cu-P adsorb with their center above a surface bridge site. Consistency is obtained between the experimental and DFT-predicted structural models, with a characteristic change in the corrugation of the four N atoms of the molecule's macrocycle following metalation. Interestingly, comparison with previously published data for cobalt porphine adsorbed on the same surface evidences a distinct increase in the average height of the N atoms above the surface through the series 2H-P, Cu-P, and cobalt porphine. Such an increase strikingly anti-correlates the DFT-predicted adsorption strength, with 2H-P having the smallest adsorption height despite the weakest calculated adsorption energy. In addition, our findings suggest that for these macrocyclic compounds, substrate-to-molecule charge transfer and adsorption strength may not be univocally correlated.

Capturing the Local Adsorption Structures of Carbon Dioxide in Polyamine-Impregnated Mesoporous Silica Adsorbents.

Interactions between amines and carbon dioxide (CO2) are essential to amine-functionalized solid adsorbents for carbon capture, and an in-depth knowledge of these interactions is crucial to adsorbent design and fabrication as well as adsorption/desorption processes. The local structures of CO2 adsorbed on a tetraethylenepentamine-impregnated mesoporous silica SBA-15 were investigated by solid-state (13)C{(14)N} S-RESPDOR MAS NMR technique and theoretical DFT calculations. Two types of adsorption species, namely, secondary and tertiary carbamates as well as distant ammonium groups were identified together with their relative concentrations and relevant (14)N quadrupolar parameters. Moreover, a dipolar coupling of 716 Hz was derived, corresponding to a (13)C-(14)N internuclear distance of 1.45 Å. These experimental data are in excellent agreement with results obtained from DFT calculations, revealing that the distribution of surface primary and secondary amines readily dictates the CO2 adsorption/desorption properties of the adsorbent.

C60on the Pt(111) surface: Structural tuning of electronic properties

The structure and electronic properties of the $(\sqrt{13}\ifmmode\times\else\texttimes\fi{}\sqrt{13})R13.{9}^{\ensuremath{\circ}}$ and $(2\sqrt{3}\ifmmode\times\else\texttimes\fi{}2\sqrt{3})R{30}^{\ensuremath{\circ}}$ ordered phases of C${}_{60}$ on the Pt(111) surface are investigated using combined dynamic low-energy electron diffraction and density functional theory (DFT) calculations. The two phases have the same local adsorption structure, while they are predicted by DFT calculations to exhibit very different electronic structures due to their different inter-C${}_{60}$ orientations and distances. This result demonstrates the structural tuning of electronic properties for molecular films or junctions composed of the same materials.

Reactive rearrangements of step atoms by adsorption and asymmetric electronic states of tetrafluoro-tetracyanoquinodimethane on Cu(100)

We investigated the local adsorption structure and electronic states of 2,3,5,6-tetrafluoro-7,7,8,8-tetracyanoquinodimethane (F4-TCNQ) on Cu(100) at low coverage using scanning tunneling microscopy (STM) and scanning tunneling spectroscopy (STS). F4-TCNQ molecules, which are preferentially adsorbed at a lower step edge, induce the reactive rearrangements of Cu atoms, including the formation of periodic kinks and step etching. The cyano groups of F4-TCNQ adsorbed at the step edge interact with not only the Cu(100) terrace but also Cu atoms at an upper step edge. This extra interaction results in the asymmetric electronic states in F4-TCNQ species, which are evidenced by STM and STS.

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 ...

The local adsorption structure of methylthiolate and butylthiolate on Au(1 1 1): A photoemission core-level shift investigation

Measurements of the core-level shifts in Au 4f photoemission spectra from Au(1 1 1) at different coverages of methylthiolate and butylthiolate are reported. Adsorption leads to two components in addition to that from the bulk, one at lower photoelectron binding energy attributed to surface atoms not bonded to thiolate species, while the second component has a higher binding energy and is attributed to Au atoms bonded to the surface thiolate. The relative intensities of these surface components for the saturation coverage (mainly (√3 × √3)R30°) phases are discussed in terms of different local adsorption sites in a well-ordered surface, and favour adsorption of the thiolate species atop Au adatoms. Alternative interpretations that might be consistent with an Au-adatom-dithiolate model are discussed, particularly in the context of the possible influence of reduced coverage associated with a disordered surface. Marked differences from previously-reported results for longer-chain alkylthiolate layers are highlighted.

Local Methylthiolate Adsorption Geometry on Au(111) from Photoemission Core-Level Shifts

The local adsorption structure of methylthiolate in the ordered Au(111)-(sqrt[3]xsqrt[3])R30 degrees phase has been investigated using core-level-shift measurements of the surface and bulk components of the Au 4f(7/2) photoelectron binding energy. The amplitude ratio of the core-level-shift components associated with surface Au atoms that are, and are not, bonded to the thiolate is found to be compatible only with the previously proposed Au-adatom-monothiolate moiety in which the thiolate is bonded atop Au adatoms in hollow sites, and not on an unreconstructed surface, or in Au-adatom-dithiolate species.

The local adsorption structure of benzene onSi(001)-(2 × 1): a photoelectron diffraction investigation

Scanned-energy mode C 1s photoelectron diffraction has been used to investigate the localadsorption geometry of benzene on Si(001) at saturation coverage and room temperature.The results show that two different local bonding geometries coexist, namely the‘standard butterfly’ (SB) and ‘tilted bridge’ (TB) forms, with a composition of58 ± 29% of the SB species. Detailed structural parameter values are presented for both speciesincluding Si–C bond lengths. On the basis of published measurements of the rateof conversion of the SB to the TB form on this surface, we estimate that thetimescale of our experiment is sufficient for achieving equilibrium, and in this caseour results indicate that the difference in the Gibbs free energy of adsorption,ΔG(TB)−ΔG(SB), is inthe range −0.023 to +0.049 eV. We suggest, however, that the relative concentration of the two species may also beinfluenced by a combination of steric effects influencing the kinetics, and a sensitivity of theadsorption energies of the adsorbed SB and TB forms to the nature of the surroundingbenzene molecules.

Quantitative determination of the local structure of thymine on Cu(1 1 0) using scanned-energy mode photoelectron diffraction

The local adsorption structures of the surface species formed by interaction of thymine with a Cu(1 1 0) surface at room temperature, and after heating to ∼530 K, have been investigated. Initial characterisation by soft-X-ray photoelectron spectroscopy and O K-edge near-edge X-ray absorption fine structure (NEXAFS) indicates the effect of sequential dehydrogenation of the NH species and provides information on the molecular orientation. O 1s and N 1s scanned-energy mode photoelectron diffraction shows the species at both temperatures bond to the surface through both carbonyl O atoms and the deprotonated N atom between them, each bonding atom adopting near-atop sites on the outermost Cu surface layer. The associated bondlengths are 1.96 ± 0.03 Å for Cu–N and 1.91 ± 0.03 Å and 2.03 ± 0.03 Å for the two inequivalent Cu--O bonds. The molecular plane lies almost exactly in the close-packed [ 1 1 ¯ 0 ] azimuth, but with a tilt relative to the surface normal of approximately 20°. Heating to ∼530 K, or deposition at this temperature, appears to lead to dehydrogenation of the second N atom in the ring, but no significant change in the adsorption geometry.

Structure and Bonding of Alkanethiols on Cu(111) and Cu(100)

The local structure of the sulfur atom of methanethiolate and ethanethiolate on the Cu(111) and Cu(100) surfaces was investigated from first principles employing the periodic supercell approach in the framework of density functional theory. On the 111 surface, we investigated the (square root 3 x square root 3)R30 degrees and (2 x 2) structures, whereas on the 100 surface, we investigated the p(2 x 2) and c(2 x 2) structures. The landscape of the potential energy surface on each metal surface presents distinctive features that explain the local adsorption structure of thiolates found experimentally. On the Cu(111) surface, the energy difference between the hollow and bridge sites is only 3 kcal/mol, and consequently, adsorption sites ranging from the hollow to the bridge site were observed for increasing surface coverages. On the Cu(100) surface, there is a large energy difference of 12 kcal/mol between the hollow and bridge sites, and therefore, only the 4-fold coordination was observed. The high stabilization of thiolates on the hollow site of Cu(100) may be the driving force for the pseudosquare reconstruction observed experimentally on Cu(111). Density of states analysis and density difference plots were employed to characterize the bonding on different surface sites. Upon interaction with the metal d bands, the pi* orbital of methanethiolate splits into several peaks. The two most prominent peaks are located on either edge of the metal d band. They correspond to bonding and antibonding S-Cu interactions. In the case of ethanethiolate, all the back-bonds are affected by the surface bonding, leading to alternating regions of depletion and accumulation of charge in the successive bonds.

Density functional theory investigation of the structure of SO 2 and SO 3 on Cu(1 1 1) and Ni(1 1 1)

Density functional theory (DFT) slab calculations, mainly using the generalised gradient approximation, have been used to investigate the minimum energy structures of molecular SO 2 and SO 3 on Cu(1 1 1) and Ni(1 1 1) surfaces. On Ni(1 1 1) the optimal local adsorption structures are in close agreement with experimental results for both molecular species obtained using the X-ray standing wavefield technique, although for adsorbed SO 2 the energetic difference between two alternative lateral positions of the lying-down molecule on the surface is marginally significant. On Cu(1 1 1) the results for adsorbed SO 2, in particular, were sensitive to the DFT functional used in the calculations, but in all cases failed to reproduce the experimentally-established preference for adsorption with the molecular plane perpendicular to the surface. This result is discussed in the context of previously published DFT results for these species adsorbed on Cu(1 0 0). The optimal geometry found for SO 3 on Cu(1 1 1) is similar to that on Ni(1 1 1), providing agreement with experiment regarding the molecular orientation but not the adsorption site.

Polymorphism in supramolecular chiral structures of R- and S-alanine on Cu(1 1 0)

A comprehensive study of the local and supramolecular adsorption structures created by the chiral R- and S-enantiomers of alanine on the Cu(1 1 0) surface has been conducted using a multi-technique approach, including reflection absorption infrared spectroscopy (RAIRS), X-ray photoelectron spectroscopy (XPS), low energy electron diffraction (LEED) and scanning tunnelling microscopy (STM). Over the entire 300–470 K temperature range studied, the amino acid is found to adsorb as an alaninate species with a local chiral adsorption motif. However, this singular preference of local chemical form contrasts sharply with the supramolecular organisation at the surface where polymorphism is exhibited. This polymorphic behaviour arises from subtle and dynamic changes in the bonding, orientation and adsorption footprints of individual molecules, leading to alterations in the molecule–metal, intermolecular and metal–metal interactions that dictate self-assembly. Thus, at low coverage, a single disordered phase is observed but at higher coverage, three other temperature dependent phases occur. At room temperature, a two-dimensional equivalent of a ‘nematic’ phase is constructed from short single- and double-chain chiral assemblies that possess a preferred chiral orientation but no long range periodicity. This ‘nematic’ phase acts as a precursor to a highly ordered chiral supramolecular assembly, created at 430 K, that consists of regular arrays of size- and shape-defined chiral clusters. This phase possesses global organisational chirality with only one chiral domain observed for each enantiomer. For both the ‘nematic’ and the highly ordered chiral phase, the organisation for the R-enantiomer is the mirror image of that seen for the S-enantiomer, i.e., there is chirality transfer from the nanoscale to the macroscale. By 470 K, both R- and S-alanine form an achirally organised (3 × 2) structure that appears to be the thermodynamically favoured phase for the alanine/Cu(1 1 0) system. The supramolecular organisation and chirality of the various structures are discussed in terms of the molecular chirality and footprint chirality of the alaninate, together with possible intermolecular interactions and reconstructions of the underlying metal surface atoms. A number of candidate models for the system are suggested, but it is clear that a full understanding of this complex adsorption system will only emerge from further careful, high level experimental and computational efforts that currently remain a challenge.

Holographic diffuse LEED image reconstruction for simultaneous occupation of different oxygen adsorption sites on Ni(1 1 1)

We determined the local adsorption structure of disordered oxygen on the Ni(111) surface by means of diffuse holographic LEED. The measurements have been performed above the critical temperature (Tc=450 K) for the oxygen order–disorder phase transition at 500 K and at a coverage of Θ=0.25 ML. At this temperature we found, in agreement with a previous LEED-IV-analysis [Surf. Sci. 349 (1996) 185], that besides the fcc threefold sites also hcp sites are occupied. In addition, a small amount seems to be located also at top and bridge sites. Reconstructing the holographic wavefield information, the different oxygen adsorption geometries are superimposed in the real space image. Nevertheless, a spatial resolution of 0.5–1 Å was sufficient to clearly distinguish between them. The influence of algorithmic parameters on the image quality was tested.

Coverage-dependent diffuse spin-polarized electron diffraction analysis of CO on Pt( [formula omitted

The coverage dependence of the local adsorption structure of carbon monoxide on Pt(1 1 1) is investigated by means of diffuse spin-polarized electron diffraction (DSPLEED). We present the theoretical discussion of the scattering of spin-polarized electrons from the disordered CO layer adsorbed on the Pt(1 1 1) surface. The spin-dependent diffuse low-energy electron diffraction (LEED) intensity and the resulting diffuse scattering asymmetry parameter are calculated for different adsorption structures of CO connected with different coverages. We report the energy as well as the angular dependence of the diffuse relativistic intensity and of the spin–orbit asymmetry. We explore the information that may be extracted from the DSPLEED rotation curves which are calculated at a selected beam energy. The polar angle of incidence of a polarized beam is held fixed and the azimuthal angle is scanned. We are focusing on the sensitivity of features in the rotation curves to the coverage-dependent structure of the adlayer keeping other geometrical parameters of the CO/Pt(1 1 1) system fixed. We find the rotation curves to be very sensitive with respect to the correlation effects governing the adlayer formation while the energy-dependent DSPLEED spectra do not expose such strong dependency.

The local adsorption geometry of CO and NH3 on NiO([formula omitted]) determined by scanned-energy mode photoelectron diffraction

The local adsorption structures of CO and NH3 on NiO(100) have been determined by C 1s and N 1s scanned-energy mode photoelectron diffraction. CO adsorbs atop Ni surface atoms through the C atom in an essentially perpendicular geometry (tilt angle 12±12°) with a C–Ni nearest-neighbour distance of 2.07±0.02 Å. NH3 also adsorbs atop Ni surface atoms with a N–Ni distance of 2.06±0.02 Å. These bondlengths are only very slightly longer than the comparable values for adsorption on metallic Ni surfaces. By contrast theoretical values obtained from total energy calculations, which exist for CO adsorption on NiO(100) (2.46 Å and 2.86 Å) are very much longer than the experimental value. Similar discrepancies exist for the N–Ni nearest-neighbour bondlength for NO adsorbed on NiO(100). Combined with the published measurements of the desorption energies, which also exceed the calculated bonding energies, these results indicate a significant failure of current theoretical treatments to provide an effective description of molecular adsorbate bonding on NiO(100).

The determination of the local adsorption structure ofSO2/Ni(111): multiple-scattering cluster studies

The multiple-scattering cluster (MSC) method has been used to calculate thesulphur 1s near-edge x-ray absorption fine structure of SO2 adsorbed onNi(111). Our investigation confirms the flat-lying adsorption structure ofSO2/Ni(111) and shows for the first time that the fcc threefold hollow site isthe most preferable adsorption site. It has been shown that the O-Sintramolecular bond length is elongated by 0.07 Å, the ∠OSO bond angle is reduced by10° after adsorption and the adsorption height is 2.0±0.2 Å. Furthermore,R-factor analysis exhibits a local minimum in the vicinity of the fcc threefoldhollow site, which is partly in agreement with the experimental result.

LEED investigations on Co(0001): The(2×2)−(K+2CO)overlayer

The local adsorption structure of the coadsorption phase of K and CO on Co(0001) has been determined at 160 K using dynamical low-energy electron diffraction. The K atoms in the $(2\ifmmode\times\else\texttimes\fi{}2)$ overlayer adopt the on-top sites as in the $(2\ifmmode\times\else\texttimes\fi{}2)$-K structure, but the bond length to the nearest Co atom increases by 0.2 \AA{} to $3.14\ifmmode\pm\else\textpm\fi{}0.05 \mathrm{\AA{}}.$ The CO molecules are shifted from the on-top sites of the $(\sqrt{3}\ifmmode\times\else\texttimes\fi{}\sqrt{3})R30\ifmmode^\circ\else\textdegree\fi{}$-CO structure to the fcc and hcp three-fold hollow sites. The axis of the CO molecule is perpendicular to the surface. The adsorption induce buckling in the top Co layer, pushing the Co atom beneath the K by $0.27\ifmmode\pm\else\textpm\fi{}0.03 \mathrm{\AA{}}\mathrm{}$ towards the bulk. The optimum length for the C-O bond is $1.22\ifmmode\pm\else\textpm\fi{}0.1 \mathrm{\AA{}}\mathrm{}$ and that for the C-Co bond $2.0\ifmmode\pm\else\textpm\fi{}0.1 \mathrm{\AA{}}.$ The obtained structure is compared to other known CO+K coadsorption structures on transition metals, as well as to the $(\sqrt{3}\ifmmode\times\else\texttimes\fi{}\sqrt{3})R30\ifmmode^\circ\else\textdegree\fi{}$-CO and $(2\ifmmode\times\else\texttimes\fi{}2)$-K structures on Co(0001).

THE LOCAL ADSORPTION STRUCTURE OF SO2/Ni(111):THEMULTIPLE-SCATTERING CLUSTER STUDIES

The multiple-scattering cluster (MSC) method has been used to calculate the sulphur 1s near edge X-ray absorption fine structure of SO2 adsorbed on the Ni(111). The local adsorption structure of SO2/Ni(111) was determined by a direct comparison between MSC calculation and the experimental NEXAFS spectra. This study confirms the flat-lying structure and shows that the fcc three-fold hollow site is the most preferable adsorption site.It has been shown that the O—S intramolecular bond length is elongated by (0.007±0.002)nm,∠OSO bond angle is reduced by 10° after adsorption,and the adsorption heihgt is (0.20±0.02)nm.

The structure of oxygen on Cu(1 0 0) at low and high coverages

The local adsorption structure of oxygen on Cu(1 0 0) has been studied using O 1s scanned-energy mode photoelectron diffraction. A detailed quantitative determination of the structure of the 0.5 ML (√2×2√2) R45°-O ordered phase confirms the missing-row character of this reconstruction and agrees well with earlier structural determinations of this phase by other methods, the adsorbed O atoms lying only approximately 0.1 Å above the outermost Cu layer. At much lower coverages, the results indicate that the O atoms adopt unreconstructed hollow sites at a significantly larger O–Cu layer spacing, but with some form of local disorder. The best fit to these data is achieved with a two-site model involving O atoms at Cu–O layer spacings of 0.41 and 0.70 Å in hollow sites; these two sites (also implied by an earlier electron-energy-loss study) are proposed to be associated with edge and centre positions in very small c(2×2) domains as seen in a recent scanning tunnelling microscopy investigation.

LEED investigations on Co(0001): the [formula omitted] overlayer

The local adsorption structure of CO on Co(0001) has been determined at 160 K using dynamical low-energy electron diffraction (LEED). The CO molecules in the ( 3 × 3 ) R30°- CO overlayer adopt the on-top site with the CO axis perpendicular to the surface and induce buckling in the top Co layer pulling the Co atom beneath the CO by 0.04±0.04 Å outwards. The optimum length for the CO bond is 1.17±0.06 Å and that for the CCo distance 1.78±0.06 Å. The first-layer CoCo distance is 2.04 Å and thus only slightly expanded from the bulk value. The structure obtained is compared with other known CO structures on transition metals.