Site dependence of the apparent shape of a molecule in scanning tunneling micoscope images: Benzene on Pt{111}

Electron stimulated desorption from condensed benzene

The electron induced dissociation of condensed benzene (C6H6) in thin films deposited on a Pt substrate is investigated by electron stimulated desorption (ESD) of anions and cations. The desorbed yields are recorded as a function of incident electron energy in the range of 10 to 950 eV for a fixed film thickness of 2 monolayers (ML) and for a fixed energy of 950 eV, as well as a function of film thickness from 0.5 to 8 monolayers (ML) for anions, and from 0.5 to 12ML for cations. Both energy and thickness dependencies are discussed in terms of the three main mechanisms yielding positively and/or negatively charged fragments: dissociative electron attachment (DEA), dipolar dissociation (DD) and dissociative ionization (DI) processes. At the probed energies, DD is the major mechanism, while DEA is predominantly induced by secondary electrons from the Pt substrate. Desorption of the parent positive ion is strongly suppressed. Similar qualitative behaviours are observed for the energy dependence of both anion and cation ESD yields, while some discrepancies exist in the thickness dependence, including a very significant systematic magnitude difference found between such ions formation. An estimation of the effective DD cross-section including the desorption probability is obtained. Feasible mechanisms behind the observed energy and thickness dependences for anion and cation yields are proposed. These results highlight the need for further investigations to better understand the underlying processes of electron induced dissociation in condensed matter.

Porous Honeycomb Self-Assembled Monolayers: Tripodal Adsorption and Hidden Chirality of Carboxylate Anchored Triptycenes on Ag

Molecules with tripodal anchoring to substrates represent a versatile platform for the fabrication of robust self-assembled monolayers (SAMs), complementing the conventional monopodal approach. In this context, we studied the adsorption of 1,8,13-tricarboxytriptycene (Trip-CA) on Ag(111), mimicked by a bilayer of silver atoms underpotentially deposited on Au. While tripodal SAMs frequently suffer from poor structural quality and inhomogeneous bonding configurations, the triptycene scaffold featuring three carboxylic acid anchoring groups yields highly crystalline SAM structures. A pronounced polymorphism is observed, with the formation of distinctly different structures depending on preparation conditions. Besides hexagonal molecular arrangements, the occurrence of a honeycomb structure is particularly intriguing as such an open structure is unusual for SAMs consisting of upright-standing molecules. Advanced spectroscopic tools reveal an equivalent bonding of all carboxylic acid anchoring groups. Notably, density functional theory calculations predict a chiral arrangement of the molecules in the honeycomb network, which, surprisingly, is not apparent in experimental scanning tunneling microscopy (STM) images. This seeming discrepancy between theory and experiment can be resolved by considering the details of the actual electronic structure of the adsorbate layer. The presented results represent an exemplary showcase for the intricacy of interpreting STM images of complex molecular films. They are also further evidence for the potential of triptycenes as basic building blocks for generating well-defined layers with unusual structural motifs.

First-principles calculations of hybrid inorganic-organic interfaces: from state-of-the-art to best practice

The computational characterization of inorganic-organic hybrid interfaces is arguably one of the technically most challenging applications of density functional theory. Due to the fundamentally different electronic properties of the inorganic and the organic components of a hybrid interface, the proper choice of the electronic structure method, of the algorithms to solve these methods, and of the parameters that enter these algorithms is highly non-trivial. In fact, computational choices that work well for one of the components often perform poorly for the other. As a consequence, default settings for one materials class are typically inadequate for the hybrid system, which makes calculations employing such settings inefficient and sometimes even prone to erroneous results. To address this issue, we discuss how to choose appropriate atomistic representations for the system under investigation, we highlight the role of the exchange-correlation functional and the van der Waals correction employed in the calculation and we provide tips and tricks how to efficiently converge the self-consistent field cycle and to obtain accurate geometries. We particularly focus on potentially unexpected pitfalls and the errors they incur. As a summary, we provide a list of best practice rules for interface simulations that should especially serve as a useful starting point for less experienced users and newcomers to the field.

Controlling the Adsorption of Aromatic Compounds on Pt(111) with Oxygenate Substituents: From DFT to Simple Molecular Descriptors

Aromatic chemistry on metallic surfaces is involved in many processes within the contexts of biomass valorization, pollutant degradation, or corrosion protection. Albeit theoretically and experimentally challenging, knowing the structure and the stability of aromatic compounds on such surfaces is essential to understand their properties. To gain insights on this topic, we performed periodic ab initio calculations on Pt(111) to determine a set of simple molecular descriptors that predict both the stability and the structure of aromatic adsorbates substituted with alkyl and alkoxy (or hydroxy) groups. While the van der Waals (vdW) interaction is controlled by the molecular weight and the deformation energy by both the nature and the relative position of the substituents to the surface, the chemical bonding can be correlated to the Hard and Soft Acids and Bases (HSAB) interaction energy. This work gives general insights on the interaction of aromatic compounds with the Pt(111) surface.

Differentiating amino acid residues and side chain orientations in peptides using scanning tunneling microscopy

Single-molecule measurements of complex biological structures such as proteins are an attractive route for determining structures of the large number of important biomolecules that have proved refractory to analysis through standard techniques such as X-ray crystallography and nuclear magnetic resonance. We use a custom-built low-current scanning tunneling microscope to image peptide structures at the single-molecule scale in a model peptide that forms β sheets, a structural motif common in protein misfolding diseases. We successfully differentiate between histidine and alanine amino acid residues, and further differentiate side chain orientations in individual histidine residues, by correlating features in scanning tunneling microscope images with those in energy-optimized models. Beta sheets containing histidine residues are used as a model system due to the role histidine plays in transition metal binding associated with amyloid oligomerization in Alzheimer's and other diseases. Such measurements are a first step toward analyzing peptide and protein structures at the single-molecule level.

Adsorption geometry determination of single molecules by atomic force microscopy

We measured the adsorption geometry of single molecules with intramolecular resolution using noncontact atomic force microscopy with functionalized tips. The lateral adsorption position was determined with atomic resolution, adsorption height differences with a precision of 3 pm, and tilts of the molecular plane within 0.2°. The method was applied to five π-conjugated molecules, including three molecules from the olympicene family, adsorbed on Cu(111). For the olympicenes, we found that the substitution of a single atom leads to strong variations of the adsorption height, as predicted by state-of-the-art density-functional theory, including van der Waals interactions with collective substrate response effects.

Adsorption site determination of a molecular monolayer via inelastic tunneling

We have combined scanning tunneling microscopy with inelastic electron tunneling spectroscopy (IETS) and density functional theory (DFT) to study a tetracyanoethylene monolayer on Ag(100). Images show that the molecules arrange in locally ordered patterns with three nonequivalent, but undeterminable, adsorption sites. While scanning tunneling spectroscopy only shows subtle variations of the local electronic structure at the three different positions, we find that vibrational modes are very sensitive to the local atomic environment. IETS detects sizable mode frequency shifts of the molecules located at the three topographically detected sites, which permits us to determine the molecular adsorption sites through identification with DFT calculations.

Photoresponsive molecules in well-defined nanoscale environments

Stimuli-responsive molecules are key building blocks of functional molecular materials and devices. These molecules can operate in a range of environments. A molecule's local environment will dictate its conformation, reactivity, and function; by controlling the local environment we can ultimately develop interfaces of individual molecules with the macroscopic environment. By isolating molecules in well-defined environments, we are able to obtain both accurate measurements and precise control. We exploit defect sites in self-assembled monolayers (SAMs) to direct the functional molecules into precise locations, providing a basis for the measurements and engineering of functional molecular systems. The structure and functional moieties of the SAM can be tuned to control not only the intermolecular interactions but also molecule-substrate interactions, resulting in extraction or control of desired molecular functions. Herein, we report our progress toward the assembly and measurements of photoresponsive molecules and their precise assemblies in SAM matrices.

Dynamic double lattice of 1-adamantaneselenolate self-assembled monolayers on Au{111}

We report a complex, dynamic double lattice for 1-adamantaneselenolate monolayers on Au{111}. Two lattices coexist, revealing two different binding modes for selenols on gold: molecules at bridge sites have lower conductance than molecules at three-fold hollow sites. The monolayer is dynamic, with molecules switching reversibly between the two site-dependent conductance states. Monolayer dynamics enable adsorbed molecules to reorganize according to the underlying gold electronic structure over long distances, which facilitates emergence of the self-organized rows of dimers. The low-conductance molecules assume a (7 × 7) all-bridge configuration, similar to the analogous 1-adamantanethiolate monolayers on Au{111}. The high-conductance molecules self-organize upon mild annealing into distinctive rows of dimers with long-range order, described by a (6√5 × 6√5)R15° unit cell.

Creating favorable geometries for directing organic photoreactions in alkanethiolate monolayers

The products of photoreactions of conjugated organic molecules may be allowed by selection rules but not observed in solution reactions because of unfavorable reaction geometries. We have used defect sites in self-assembled alkanethiolate monolayers on gold surfaces to direct geometrically unfavorable photochemical reactions between individual organic molecules. High conductivity and stochastic switching of anthracene-terminated phenylethynylthiolates within alkanethiolate monolayers, as well as in situ photochemical transformations, have been observed and distinguished with the scanning tunneling microscope (STM). Ultraviolet light absorbed during imaging increases the apparent heights of excited molecules in STM images, a direct manifestation of probing electronically excited states.

Electrons, photons, and force: quantitative single-molecule measurements from physics to biology

Single-molecule measurement techniques have illuminated unprecedented details of chemical behavior, including observations of the motion of a single molecule on a surface, and even the vibration of a single bond within a molecule. Such measurements are critical to our understanding of entities ranging from single atoms to the most complex protein assemblies. We provide an overview of the strikingly diverse classes of measurements that can be used to quantify single-molecule properties, including those of single macromolecules and single molecular assemblies, and discuss the quantitative insights they provide. Examples are drawn from across the single-molecule literature, ranging from ultrahigh vacuum scanning tunneling microscopy studies of adsorbate diffusion on surfaces to fluorescence studies of protein conformational changes in solution.

Furan hydrogenation over Pt(111) and Pt(100) single-crystal surfaces and Pt nanoparticles from 1 to 7 nm: a kinetic and sum frequency generation vibrational spectroscopy study

Sum frequency generation surface vibrational spectroscopy and kinetic measurements using gas chromatography have been used to systematically study the adsorption and hydrogenation of furan over Pt(111) and Pt(100) single-crystal surfaces and size-controlled 1.0-nm, 3.5-nm and 7.0-nm Pt nanoparticles at Torr pressures (10 Torr of furan, 100 Torr of H(2)) to form dihydrofuran, tetrahydrofuran, and the ring-cracking products butanol and propylene. As determined by SFG, the furan ring lies parallel to all Pt surfaces studied under hydrogenation conditions. Upright THF and the oxametallacycle intermediate are observed over the nanoparticle catalysts under reaction conditions. Butoxy increases in surface concentration over Pt(111) with increasing temperature in agreement with selectivity trends.

Manipulating double-decker molecules at the liquid-solid interface

We have used a scanning tunneling microscope (STM) to manipulate heteroleptic phthalocyaninato, naphthalocyaninato, and porphyrinato double-decker (DD) molecules at the liquid-solid interface between 1-phenyloctane solvent and graphite. We employed nanografting of phthalocyanines with eight octyl chains to place these molecules into a matrix of heteroleptic DD molecules; the overlayer structure is epitaxial on graphite. We have also used nanografting to place DD molecules in matrices of single-layer phthalocyanines with octyl chains. Rectangular scans with a STM at low bias voltage resulted in the removal of the adsorbed DD molecular layer and substituted the DD molecules with bilayer-stacked phthalocyanines from phenyloctane solution. Single heteroleptic DD molecules with lutetium sandwiched between naphthalocyanine and octaethylporphyrin were decomposed with voltage pulses from the probe tip; the top octaethylporphyrin ligand was removed, and the bottom naphthalocyanine ligand remained on the surface. A domain of decomposed molecules was formed within the DD molecular domain, and the boundary of the decomposed molecular domain self-cured to become rectangular. We demonstrated a molecular "sliding block puzzle" with cascades of DD molecules on the graphite surface.

Potassium-benzene interactions on Pt(111) studied by metastable atom electron spectroscopy

Electron emission spectra obtained by thermal collisions of He(∗)(2(3)S) metastable atoms with C(6)H(6)/Pt(111), C(6)H(6)/K/Pt(111), and K/C(6)H(6)/Pt(111) were measured in the temperature range of 50-200 K to elucidate the adsorption/aggregation states, thermal stabilities of pure and binary films, and local electronic properties at the organic-metal interface. For C(6)H(6)/Pt(111), the He(∗)(2(3)S) atoms de-excite on the chemisorbed overlayer predominantly via resonance ionization followed by Auger neutralization and partly via Penning ionization (PI) yielding weak emission just below the Fermi level (E(F)). We assigned this emission to the C(6)H(6) π-derived states delocalized over the Pt 5d bands on the basis of recent density functional calculations. During the layer-by-layer growth, the C(6)H(6)-derived bands via PI reveal a characteristic shift caused by the final-state effect (hole response at the topmost layer). C(6)H(6) molecules chemisorb weakly on the bimetallic Pt(111) (θ(K)=0.1) and physisorb on the K multilayer. In both cases, the sum rule was found to be valid between the K 4s and C(6)H(6)-derived bands. The band intensity versus exposure plot indicates that the C(6)H(6) film grows on the K multilayer by the Volmer-Weber mechanism (island growth), reflecting the weak K-C(6)H(6) interactions. In case of K/C(6)H(6)/Pt(111), the K atoms are trapped on the topmost C(6)H(6) layer at 65 K, forming particlelike clusters. The surface plasmon satellite was identified for the first time and the loss energy increases with increasing cluster size. The K clusters are unstable above ∼100 K due to thermal migration into the C(6)H(6) film. When the cluster coverage is low, the K 4s band extends below and above E(F) of the Pt substrate and the anomaly is discussed in terms of vacuum level bending around the cluster.

Dynamics of molecular adsorption and rotation on nonequilibrium sites

It is generally accepted that important events on surfaces such as diffusion and reactions can be adsorption site dependent. However, due to their short lifetime and low concentration in most systems, adsorbates on nonequilibrium adsorption sites remain largely understudied. Using low-temperature scanning tunneling microscopy, site-dependent adsorption is shown for the molecule butyl methyl sulfide, which is trapped in multiple metastable adsorption sites upon deposition onto a Au(111) surface at 5 K. As this molecule does not have enough energy to diffuse to its preferred adsorption site on the surface, it is possible to study the behavior of individual molecules in a variety of nonequilibrium sites. Here we present atomic-scale data of the same chemical species in three independent, metastable adsorption sites and equilibration to a single equilibrium site as a function of either electrical or thermal excitation. Butyl methyl sulfide exhibits distinctly different physical properties at all four adsorption sites, including rotational dynamics and appearance in scanning tunneling microscopy (STM) images. An energy profile is proposed for the adsorption and equilibration of these species, and a correlation is drawn between rotational barrier and adsorption energy.

Molecular Dynamics in Two-Dimensional Supramolecular Systems Observed by STM

Since the invention of scanning tunneling microscopy (STM), 2D supramolecular architectures have been observed under various experimental conditions. The construction of these architectures arises from the balance between interactions at the medium-solid interface. This review summarizes molecular motion observed in 2D-supramolecular structures on surfaces using nanospace resolution STM. The observation of molecular motion on surfaces provides a visual understanding of intermolecular interactions, which are the major driving force behind supramolecular arrangement.

Structure analysis of thiouracil on Ag(111) and graphite (0001) by x-ray diffraction and scanning tunneling microscopy

The geometric structures of ordered monolayers of large organic molecules (thiouracil) adsorbed to the surface of Ag(111) and graphite (0001) were analyzed using surface x-ray diffraction and scanning tunneling microscopy (STM), respectively. Although the substrates are different, in both cases the molecules are found to be arranged in parallel zig-zag rows. On graphite (0001) the molecules form a unit cell similar to the ([unk]1[unk])plane of the bulk crystal whereas on Ag(111) the detailed x-ray analysis gives evidence that, in contrast to the bulk structure, all but one of the intermolecular hydrogen bonds present in the bulk are broken. The intact pyrimidine rings are tilted by about 30° with respect to the Ag surface in comparison to flat lying molecules on graphite. An elongation of the C=S bond distance by 0.16(7) Å and an increase of the intra-pyrimidine-ring distances by about 0.11(10) Å relative to the bulk is observed which can be attributed to the covalent interaction of the molecule with the substrate. We conclude that for an inert surface like graphite, where the molecules merely interact by van der Waals forces, the molecules build a unit cell mainly determined by intermolecular hydrogen bridge bonds and therefore almost unchanged with respect to the bulk, whereas even in the case of a weakly interacting surface like Ag(111) the crystal structure can considerably be altered with respect to the bulk.

Combined low-temperature scanning tunneling/atomic force microscope for atomic resolution imaging and site-specific force spectroscopy

We present the design and first results of a low-temperature, ultrahigh vacuum scanning probe microscope enabling atomic resolution imaging in both scanning tunneling microscopy (STM) and noncontact atomic force microscopy (NC-AFM) modes. A tuning-fork-based sensor provides flexibility in selecting probe tip materials, which can be either metallic or nonmetallic. When choosing a conducting tip and sample, simultaneous STM/NC-AFM data acquisition is possible. Noticeable characteristics that distinguish this setup from similar systems providing simultaneous STM/NC-AFM capabilities are its combination of relative compactness (on-top bath cryostat needs no pit), in situ exchange of tip and sample at low temperatures, short turnaround times, modest helium consumption, and unrestricted access from dedicated flanges. The latter permits not only the optical surveillance of the tip during approach but also the direct deposition of molecules or atoms on either tip or sample while they remain cold. Atomic corrugations as low as 1 pm could successfully be resolved. In addition, lateral drifts rates of below 15 pm/h allow long-term data acquisition series and the recording of site-specific spectroscopy maps. Results obtained on Cu(111) and graphite illustrate the microscope's performance.

Functional and spectroscopic measurements with scanning tunneling microscopy

Invented as a surface analytical technique capable of imaging individual atoms and molecules in real space, scanning tunneling microscopy (STM) has developed and advanced into a technique able to measure a variety of structural, functional, and spectroscopic properties and relationships at the single-molecule level. Here, we review basic STM operation and image interpretation, techniques developed to manipulate single atoms and molecules with the STM to measure functional properties of surfaces, local spectroscopies used to characterize atoms and molecules at the single-molecule level, and surface perturbations affecting surface coverage and surface reactions. Each section focuses on determining the identity and function of chemical species so as to elucidate information beyond topography with STM.

Dimethyl sulfide on Cu{111}: molecular self-assembly and submolecular resolution imaging

The literature contains many studies of thiol-based, self-assembled monolayers (RSH); however, thioethers (RSR) have barely begun to be explored, despite having the potential advantages of being more resistant to oxidation and allowing for the control of self-assembly parallel to the surface. This paper describes a low-temperature scanning tunneling microscopy investigation of dimethyl sulfide on Cu{111}. Previous work on the adsorption of dibutyl sulfide on Cu{111} revealed that intermolecular van der Waals interactions directed the parallel ordering of dibutyl sulfide molecules in linear rows. Upon annealing to 120 K, small dibutyl sulfide domains reordered into very large, ordered domains free of defects. The current study reveals the effect of the shorter alkyl chain length of dimethyl sulfide on both the rate of diffusion and the packing structure of the molecule. At a medium surface coverage and at 78 K, it was found that dimethyl sulfide is mobile and forms large, ordered islands without the 120 K annealing that was required for dibutyl sulfide to arrange. Also, the molecular packing structure evolves from quadrupole-quadrupole interactions and results in a perpendicular arrangement of neighboring molecules instead of the parallel arrangement observed for dibutyl sulfide. We show high-resolution images of the dimethyl sulfide islands in which submolecular features are revealed. These high-resolution data allow us to propose a structural model for the adsorption site of each dimethyl sulfide molecule within the ordered structures. These results demonstrate that the length of the alkyl side chain is an important factor in determining how thioethers self-assemble on metal surfaces.

Direct Evidence of Arsenic(III)−Carbonate Complexes Obtained Using Electrochemical Scanning Tunneling Microscopy

Electrochemical scanning tunneling microscopy (ECSTM), ion chromatography (IC), and electrospray ionization-mass spectrometry/mass spectrometry were applied to investigate the interactions between arsenite [As(III)] and carbonate and arsenate [As(V)] and carbonate. The chemical species in the single and binary component solutions of As(III), As(V), and carbonate were attached to a Au(111) surface and then imaged in a 0.1 M NaClO4 solution at the molecular level by ECSTM. The molecules formed highly ordered adlayers on the Au(111) surface. High-resolution STM images revealed the orientation and packing arrangement of the molecular adlayers. Matching the STM images with the molecular models constructed using the Hyperchem software package indicated that As(III) formed two types of complexes with carbonate, including As(OH)2CO3- and As(OH)3(HCO3-)2. No complexes were formed between As(V) and carbonate. IC chromatograms of the solutions revealed the emergence of the new peak only in the aged As(III)-carbonate solution. MS spectra showed the presence of a new peak at m/z 187 in the aged As(III)-carbonate solution. The results obtained with the three independent methods confirmed the formation of As(OH)2CO3-. The results also indicated that As(OH)3 could be associated with HCO3- through a hydrogen bond. The knowledge of the formation of the As(III) and carbonate complexes will improve the understanding of As(III) mobility in the environment and removal of As(III) in water treatment systems.

Chiral recognition of PVBA on Pd(111) and Ag(111) surfaces

An asymmetric planar molecule, 4-trans-2-(pyrid-4-yl-vinyl) benzoic acid (PVBA), has been used to establish the organic chiral recognition on fcc(111) metal surfaces. The strong correlation between the orientation and chiral recognition of PVBA on both Ag(111) and Pd(111) guides the choice of a model potential, which determines the relative binding energy of PVBA on fcc(111). An angle-dependent calculation of relative binding energy reproduces the experimental observation of the chiral recognition of PVBA on Ag(111) but not on Pd(111).

Sum Frequency Generation Vibrational Spectroscopic and High-Pressure Scanning Tunneling Microscopic Studies of Benzene Hydrogenation on Pt(111)

Sum frequency generation (SFG) vibrational spectroscopy and high-pressure scanning tunneling microscopy (HP-STM) have been used in combination for the first time to study a catalytic reaction. These techniques have been able to identify surface intermediates in situ during benzene hydrogenation on a Pt(111) single-crystal surface at Torr pressures. In a background of 10 Torr of benzene, STM is able to image small ordered regions corresponding to the c(2 radical3 x 3)rect structure in which each molecule is chemisorbed at a bridge site. In addition, individual benzene molecules are also observed between the ordered regions. These individual molecules are assumed to be physisorbed benzene on the basis of the SFG results showing both chemisorbed and physisorbed molecules. The surface becomes too mobile to image upon addition of hydrogen but is determined to have physisorbed and chemisorbed benzene present by SFG. It was spectroscopically determined that heating the platinum surface after poisoning with CO displaces benzene molecules. The high-coverage pure CO structure of (radical19 x radical19)R23.4 degrees imaged with STM is a verification of spectroscopic measurements.

Structure Effects of Benzene Hydrogenation Studied with Sum Frequency Generation Vibrational Spectroscopy and Kinetics on Pt(111) and Pt(100) Single-Crystal Surfaces

Sum frequency generation (SFG) surface vibrational spectroscopy and kinetic measurements using gas chromatography have identified at least two reaction pathways for benzene hydrogenation on the Pt(100) and Pt(111) single-crystal surfaces at Torr pressures. Kinetic studies at low temperatures (310-370 K) show that benzene hydrogenation does not proceed through cyclohexene. A Langmuir-Hinshelwood-type rate law for the low-temperature reaction pathway is identified. The rate-determining step for this pathway is the addition of the first hydrogen atom to adsorbed benzene for both single-crystal surfaces, which is verified by the spectroscopic observation of adsorbed benzene at low temperatures on both the Pt(100) and Pt(111) crystal faces. Low-temperature SFG studies reveal chemisorbed and physisorbed benzene on both surfaces. At higher temperatures (370-440 K), hydrogenation of benzene to pi-allyl c-C(6)H(9) is observed only on the Pt(100) surface. Previous single-crystal studies have identified pi-allyl c-C(6)H(9) as the rate-determining step for cyclohexene hydrogenation to cyclohexane.