L-cysteine adsorption structures on Au(111) investigated by scanning tunneling microscopy under ultrahigh vacuum conditions

Adsorption structures formed upon vapor deposition of the natural amino acid L-cysteine onto the (111) surface of gold have been investigated by scanning tunneling microscopy under ultrahigh vacuum conditions. Following deposition at room temperature and at cysteine coverages well below saturation of the first monolayer, we found coexistence of unordered molecular islands and extended domains of a highly ordered molecular overlayer of quadratic symmetry. As the coverage was increased, a number of other structures with local hexagonal order emerged and became dominant. Neither of the room temperature, as-deposited, ordered structures showed any fixed rotational relationship to the underlying gold substrate, suggesting a comparatively weak and nonspecific molecule-substrate interaction. Annealing of the cysteine-covered substrate to 380 K lead to marked changes in the observed adsorption structures. At low coverages, the unordered islands developed internal order and their presence started to perturb the appearance of the surrounding Au(111) herringbone reconstruction. At coverages beyond saturation of the first monolayer, annealing led to development of a ( radical3 x radical3)R30 degrees superstructure accompanied by the formation of characteristic monatomically deep etch pits, i.e., the behavior typically observed for alkanethiol self-assembled monolayers on Au(111). The data thus show that as-deposited and thermally annealed cysteine adsorption structures are quite different and suggest that thermal activation is required before vacuum deposited cysteine becomes covalently bound to single crystalline Au(111).     

Characterizing and Manipulating Individual Molecules by Scanning Tunneling Microscopy

Scanning tunneling microscopy (STM) can provide us the special means to characterize the locally physical and chemical properties of individual molecules, and even help us to manipulate the individual molecules for constructing new molecule-scale devices. Here we have adopted two new types of STM techniques to characterize the encapsulated metal atom inside a fullerene cage, and to construct a molecule-device with strong Kondo effect, respectively. The spatially dI/dV mapping spectra were used to unveil the energy-resolved metal-cage hybrid states of individual Dy@C82 molecule, and the important information about the spatial position of Dy atom inside the cage and the Dy-cage interaction was revealed. The high-voltage pulse by STM tip is controlled to induce the dehydrogenation of Co phthalocyanine molecule and change its adsorption configuration on Au(111) surface, so as to recover Kondo effect that disappears in the case of intact adsorbed molecule.     

Two-dimensional Molecular Phase Transition of Alkylated-TDPB on Au(111) and Cu(111) Surfaces

The derivatives of aromatic cores bearing alkyl chains with different lengths are of potential interest in on-surface chemistry, and thus have been widely investigated both at liquid-solid interfaces and in vacuum. Here, we report on the structural evaluation of self-assembled 1,3,5-tri(4-dodecylphenyl)benzene(TDPB) molecules with increased molecular coverages on both Au(111) and Cu(111) surfaces. As observed on Au(111), rhombic and herringbone structures emerge successively depending on surface coverage. In the case of Cu(111), the same process of phase conversion is also observed, but with two distinct structures. In comparison, the self-assembled structures on Au(111) surface are packed more densely than that on Cu(111) surface under the same preparation conditions. This may fundamentally result from the higher adsorption energy of TDPB molecules on Cu(111), restricting their adjustment to optimize a thermodynamically favorable molecular packing.     

Coverage effects and the nature of the metal-sulfur bond in S/Au(111): high-resolution photoemission and density-functional studies

The bonding of sulfur to surfaces of gold is an important subject in several areas of chemistry, physics, and materials science. Synchrotron-based high-resolution photoemission and first-principles density-functional (DF) slab calculations were used to study the interaction of sulfur with a well-defined Au(111) surface and polycrystalline gold. Our experimental and theoretical results show a complex behavior for the sulfur/Au(111) interface as a function of coverage and temperature. At small sulfur coverages, the adsorption of S on fcc hollow sites of the gold substrate is energetically more favorable than adsorption on bridge or a-top sites. Under these conditions, S behaves as a weak electron acceptor but substantially reduces the density-of-states that gold exhibits near the Fermi edge. As the sulfur coverage increases, there is a weakening of the Au-S bonds (with a simultaneous reduction in the Au --> S charge transfer and a modification in the S sp hybridization) that facilitates changes in adsorption site and eventually leads to S-S bonding. At sulfur coverages above 0.4 ML, S(2) and not atomic S is the more stable species on the gold surface. Formation of S(n)(n > 2) species occurs at sulfur coverages higher than a monolayer. Very similar trends were observed for the adsorption of sulfur on polycrystalline surfaces of gold. The S atoms bonded to Au(111) display a unique mobility/reactivity not seen on surfaces of early or late transition metals.     

Thiol with an unusual adsorption-desorption behavior: 6-mercaptopurine on Au(111)

A multitechnique study of 6-mercaptopurine (6MP) adsorption on Au(111) is presented. The molecule adsorbs on Au(111), originating short-range ordered domains and irregular nanosized aggregates with a total surface coverage by chemisorbed species smaller than those found for alkanethiol SAMs, as derived from scanning tunneling microscopy (STM) and electrochemical results. X-ray photoelectron spectroscopy (XPS) results show the presence of a thiolate bond, whereas density functional theory (DFT) data indicate strong chemisorption via a S-Au bond and additional binding to the surface via a N-Au bond. From DFT data, the positive charge on the Au topmost surface atoms is markedly smaller than that found for Au atoms in alkanethiolate SAMs. The adsorption of 6MP originates Au atom removal from step edges but no vacancy island formation at (111) terraces. The small coverage of Au islands after 6MP desorption strongly suggests the presence of only a small population of Au adatom-thiolate complexes. We propose that the absence of the Au-S interface reconstruction results from the lack of significant repulsive forces acting at the Au surface atoms.     

Low-temperature mobility and structure formation of a prochiral aromatic thiol (2,5-dichlorothiophenol) on Cu(111)

We present a low-temperature scanning tunneling microscopy study of increasing coverages of 2,5-dichlorothiophenol, an asymmetrically halo-substituted aromatic thiol, on Cu(111). At low coverage, deprotonation of the thiol occurs spontaneously upon adsorption at 80 K. Albeit the low deposition temperature, we find the formation of adsorbate islands at low coverage, which coalesce into a well-ordered film of horizontally adsorbed molecules at increasing coverage. This behavior indicates (i) significant mobility of the thiols on Cu(111) even at low temperatures and (ii) attractive adsorbate-adsorbate interactions. At higher coverages intermolecular interactions prevent long-range diffusion of adsorbates and thermal activation of the S-H bond becomes necessary. A close analysis of the molecular films reveals chiral recognition between neighboring molecules, which leads to the formation of enantiopure areas on the surface. Upright orientation of individual molecules starts at the boundaries between such phases and can be induced by scanning tunneling microscopy.     

Assembly dynamics and detailed structure of 1-propanethiol monolayers on Au(111) surfaces observed real time by in situ STM

1-Propanethiol is chosen as a model alkanethiol to probe detailed mechanisms of the self-assembled monolayer (SAM) formation at aqueous/Au(111) interfaces. The assembly processes, including initial physi- and chemisorption, pit formation, and domain growth, were recorded into movies in real-time with high resolution by in situ scanning tunneling microscopy (STM) under potential control. Two major adsorption steps were disclosed in the propanethiol SAM formation. The first step involves weak interactions accompanied by the lift of the Au(111) surface reconstruction, which depends reversibly on the electrochemical potentials. The second step is chemisorption to form a dense monolayer, accompanied by formation of pits as well as structural changes in the terrace edges. Pits emerged at the stage of the reconstruction lift and increased to a maximum surface coverage of 4.0 +/- 0.4% at the completion of the SAM formation. Well-defined triangular pits in the SAM were found on the large terraces (more than 300 nm wide), whereas few and small pinholes appeared at the terrace edge areas. Smooth edges were converted into saw-like structural features during the SAM formation, primarily along the Au(111) atomic rows. These observations suggest that shrinking and rearrangement of gold atoms are responsible for both formation of the pits and the shape changes of the terrace edges. STM images disclose a (2 square root 3 x 3)R30 degrees periodic lattice within the ordered domains. Along with electrochemical measurements, each lattice unit is assigned to contain four propanethiol molecules exhibiting different electronic contrasts, which might originate in different surface orientations of the adsorbed molecules.     

Dispersion of metallofullerene Y@C82 on bare, C60-modified, and iodine-modified Au(111) surfaces investigated with ECSTM

Two-dimensional (2D) assembling behaviors of the endohedral metallofullerene Y@C(82) on bare, C(60)-modified, and iodine-modified Au(111) surfaces have been investigated in 0.1 M HClO(4) solution employing electrochemical scanning tunneling microscopy (ECSTM). The results show that Y@C(82) molecules are mobile and aggregate to the terrace edges on bare and C(60)-modified Au(111) surfaces, but monodispersion of the Y@C(82) molecules is achieved on the iodine-modified Au(111) surface. The improvement of Y@C(82) dispersion on an iodine-modified gold surface is due to the strong Y@C(82)-substrate interactions. The modified-substrate method provides an effective strategy to disperse endohedral metallofullerenes.     

Structure of mercaptobiphenyl monolayers on mercury

The molecular-scale structure and phase behavior of single-component Langmuir films of 4'-methyl-4-mercaptobiphenyl (MMB) and 4'-perfluoromethyl-4-mercaptobiphenyl (FMMB) on mercury were studied using surface tensiometry, grazing incidence X-ray diffraction, and X-ray reflectivity. At low coverages, a condensed but in-plane disordered single layer of surface-parallel molecules is found for both compounds. At high coverages, both compounds exhibit in-plane-ordered phases of standing-up molecules. For MMB, the biphenyl core dominates the structure, yielding a centered-rectangular unit cell with an area A(x) of 21.8 A(2)/molecule, with molecules tilted by approximately 14 degrees from the surface normal in the nearest-neighbor direction, and a coherence length xi of >1000 A for the crystalline domains. For FMMB, the perfluoromethyl group dominates the structure, yielding a hexagonal unit cell with untilted molecules, an area A(x) of 24.2 A(2)/molecule, and a much smaller xi of approximately 110 A. The structure is discussed in comparison with self-assembled monolayers of MMB on crystalline Au(111) and similar-length alkanethiolate SAMs on Au(111) and on mercury. The differences in the structure are discussed and traced to the differences in the substrate's surface structure, and in the molecular cross section and rigidity.     

Chlorine adsorption on Au(111): chlorine overlayer or surface chloride?

We report the first scanning tunneling microscope (STM) investigation, combined with density functional theory calculations, to resolve controversy regarding the bonding and structure of chlorine adsorbed on Au(111). STM experiments are carried out at 120 K to overcome instability caused by mobile species upon chlorine adsorption at room temperature. Chlorine adsorption initially lifts the herringbone reconstruction. At low coverages (<0.33 ML), chlorine binds to the top of Au(111)-(1 x 1) surface and leads to formation of an overlayer with (square root(3) x square root(3))R30 degree structure at 0.33 ML. At higher coverages, packing chlorine into an overlayer structure is no longer favored. Gold atoms incorporate into a complex superlattice of a Au-Cl surface compound.     

Molecular orientations and interfacial structure of C60 on Pt(111)

Molecular orientations and assembled structures of C(60) molecules on Pt(111) have been characterized by low-temperature scanning tunneling microscopy for coverage between 0.1 ML and 1.5 ML. At room temperature, C(60) molecules preferentially decorate the steps and nucleate into single layer islands (SLIs) with hexagonal close-packed structures upon increasing coverage. C(60) islands comprise two differently oriented C(60)∕Pt(111)-(√13?×?√13) R13.9° phases, in which five types of molecular orientation of C(60) carbon cage configurations are clearly identified by the high-resolution scanning tunneling microscopy image. Further annealing treatment leads to more uniform molecular orientation without apparent aggregation of C(60) SLIs. As coverage increases above 1 ML, domains corresponding to (2√3?×?2√3) R30° superstructure appear. To explain the above transformation, an interfacial reconstruction model is proposed according to the detailed study of the molecular adsorption structures in different domains.     

Benzene on Au[111] at 4 K: monolayer growth and tip-induced molecular cascades

Low-temperature scanning tunneling microscopy has been used to characterize the various structures of submonolayer and near-monolayer coverages of benzene (C6H6) on Au[111] at 4 K. At low coverage, benzene is found to adsorb preferentially at the top of the Au monatomic steps and is weakly adsorbed on the terraces. At near-monolayer coverage, benzene was found to form several long-range commensurate overlayer structures that depend on the regions of the reconstructed Au[111] surface, namely a (radical 52 x radical 52)R13.9 degrees structure over the hcp regions and a (radical 133 x radical 133)R17.5 degrees "pinwheel" structure over the fcc regions. Time-lapse imaging revealed concerted cascade motion of the benzene molecules in the (radical 133 x radical 133)R17.5 degrees pinwheel overlayer. We demonstrate that the observed cascade motion is a result of concerted molecular motion and not independent random motion.     

Small Au and Pt clusters at the anatase TiO2(101) surface: behavior at terraces, steps, and surface oxygen vacancies

The adsorption properties of Au and Pt metal nanoclusters on TiO2 anatase (101) were calculated using density functional theory. Structures and energetics of adsorbed Au and Pt monomers, dimers, and trimers at clean anatase TiO2(101) terraces and two major step edges, as well as O-vacancies, were systematically determined. The theoretical predictions were tested by vapor-depositing small coverages of Au and Pt on anatase (101) and investigating the resulting clusters with Scanning Tunneling Microscopy. On the clean surface, Au shows a strong tendency to form large clusters that nucleate on step edges. A preference for adsorption at type D-(112) steps is observed, which is probably a result of kinetic effects. For Pt, clusters as small as monomers are observed on the terraces, in agreement with the predicted large binding energy of 2.2 eV. Step edges play a less important role than in the case of Au. Oxygen vacancies, produced by electron irradiation, dramatically influence the growth of Au, while the nucleation behavior of Pt was found to be less affected.     

Alkanethiol/Au(111) self-assembled monolayers contain gold adatoms: scanning tunneling microscopy before and after reaction with atomic hydrogen

Alkanethiol self-assembled monolayers on Au(111) are widely studied, yet the exact nature of the sulfur-gold bond is still debated. Recent studies suggest that Au(111) is significantly reconstructed, with alkanethiol molecules binding to gold adatoms on the surface. These adatoms are observed using scanning tunneling microscopy before and after removing the organic monolayer with an atomic hydrogen beam. Upon monolayer removal, changes in the gold substrate are seen in the formation of bright, triangularly shaped islands, decreasing size of surface vacancy islands, and faceting of terrace edges. A 0.143 +/- 0.033 increase in gold coverage after monolayer removal shows that there is one additional gold adatom for every two octanethiol molecules on the surface.     

Configuration-dependent interface charge transfer at a molecule-metal junction

The role of the molecule-metal interface is a key issue in molecular electronics. Interface charge transfer processes for 4-fluorobenzenethiol monolayers with different molecular orientations on Au(111) were studied by resonant photoemission spectroscopy. The electrons excited into the LUMO or LUMO+1 are strongly localized for the molecules standing up on Au(111). In contrast, an ultrafast charge transfer process was observed for the molecules lying down on Au(111). This configuration-dependent ultrafast electron transfer is dominated by an adiabatic mechanism and directly reflects the delocalization of the molecular orbitals for molecules lying down on Au(111). Theoretical calculations confirm that the molecular orbitals indeed experience a localization-delocalization transition resulting from hybridization between the molecular orbitals and metal surface. Such an orientation-dependent transition could be harnessed in molecular devices that switch via charge transfer when the molecular orientation is made to change.     

Nanografting versus solution self-assembly of alpha,omega-alkanedithiols on Au(111) investigated by AFM

The solution self-assembly of alpha,omega-alkanedithiols onto Au(111) was investigated using atomic force microscopy (AFM). A heterogeneous surface morphology is apparent for 1,8-octanedithiol and for 1,9-nonanedithiol self-assembled monolayers (SAMs) prepared by solution immersion as compared to methyl-terminated n-alkanethiols. Local views from AFM images reveal a layer of mixed molecular orientations for alpha,omega-alkanedithiols, which evidence surface structures with heights corresponding to both lying-down and standing-up orientations. For dithiol SAMs prepared by solution self-assembly, the majority of alpha,omega-alkanedithiol molecules chemisorb with both thiol end groups bound to the Au(111) surface with the backbone of the alkane chain aligned parallel to the surface. However, AFM images disclose that there are also islands of standing molecules scattered throughout the surface. To measure the thickness of alpha,omega-alkanedithiol SAMs with angstrom sensitivity, methyl-terminated n-alkanethiols with known dimensions were used as molecular rulers. Under conditions of spatially constrained self-assembly, nanopatterns of alpha,omega-alkanedithiols written by nanografting formed monolayers with heights corresponding to an upright configuration.     

Structures and orientations of cobalt phthalocyanine adsorbed on Sb(111)

The structures and orientations of cobalt phthalocyanine (CoPc) adsorbed on Sb(111) were investigated by low-temperature scanning tunneling microscope. We found that at the initial coverage molecular domains formed both on the terraces and at the vicinity of step edges that were saturated by molecular chains in advance. With the increasing of molecular coverage, the alternately arranged molecular rows of CoPc adsorbed on the bridge sites of Sb(111) and the orientations of them were rotated by 14° ± 2° with respect to the [-101] direction. At the coverage above one monolayer, the molecules of the second layer were assembled along the directions of the underlying molecular rows and showed similar configurations. Consequently, the second-layer CoPc molecules interacted with neighboring molecules via π orbitals, resulting in the observation of overlapped molecular orbitals.     

Determination of different local potentials of zero charge of a Pd–Au(111) heterogeneous surface

Local values of potential of zero charge (pzc) and potential of zero total charge (pztc) have been determined for Au(111) surfaces partially covered with palladium at low coverages. The pztc of the palladium islands has been measured with the CO charge displacement procedure. The adsorption of CO only takes place on the palladium-covered domains allowing us to selectively displace the charge residing in this part of the surface. The resulting pztc values of the palladium islands are located around 0.25 V for the entire range of palladium coverages. The pzc of gold-uncovered areas has been determined by identifying the position of the differential capacity minimum (0.52 V). It appears that this pzc is only slightly affected by the presence of deposited palladium.     

Adsorption of fumaramide [2]rotaxane and its components on a solid substrate: a coverage-dependent study

The coverage-dependent adsorption on Au(111) of a fumaramide [2]rotaxane and its components, a benzylic amide macrocycle and a fumaramide thread, is studied using high-resolution electron energy loss spectroscopy (HREELS). Up to monolayer coverage, the relative intensity of out-of-plane to in-plane phenyl ring vibrational modes indicates that the macrocycle adopts an orientation with the phenyl rings largely parallel to the surface. The formation of a chemisorption bond is evidenced by the presence of a Au-O stretching vibration. In contrast, the thread shows no evidence of chemisorption or a preferential orientation. The introduction of the thread into the macrocycle partly disrupts the film order so that the resulting chemisorbed rotaxane shows intermediate behavior with a preferential orientation up to 0.5 ML coverage. A decrease in film order and the absence of a preferred molecular orientation is observed for all three molecules at multilayer coverages. The spectral differences are addressed by molecular dynamics simulations in terms of the mobility of the phenyls of the three molecules on Au(111).     

Interaction of cobalt with ceria thin films and its influence on supported Au nanoparticles

The interaction of Co with ceria thin films and its influence on the sintering behavior of Au were investigated by scanning tunneling microscopy(STM), synchrotron radiation photoemission spectroscopy(SRPES) and X-ray photoelectron spectroscopy(XPS). The strong interaction between Co and CeO_2(111) leads to oxidation of Co to Co~(2+) at 300 K, accompanied by partial reduction of ceria surface at low Co coverages. Subsequent Co deposition results in an increasing fraction of metallic Co. Annealing to high temperatures induces Co~(2+)ions diffuse into the CeO_2 film, while the small metallic Co islands agglomerate into larger ones. The bimetallic Co–Au particles were prepared by deposition of Au on the existing Co particles on ceria surfaces. The sintering behavior of Co–Au bimetallic surfaces is found to be highly determined by the stoichiometry of ceria supports. The addition of Co to the Au/CeO_2 surface suppresses the sintering of Au particles at high temperatures in comparison with that of pure Au particles. However, Au particles are less stable on the Co/CeO_(1.82) layer than on CeO_(1.82) surface.