A series of experiments and electronic structure calculations were performed to identify metastable 1,1′-ferrocenedicarboxylic acid supramolecular structures formed during solution deposition in a vacuum on a Au(111) substrate, as well as to observe their evolution into more stable species under mild annealing conditions. Electrospray ionization mass spectrometry measurments were performed to determine which species are likely to be present in the rapidly evaporating droplet, and these experiments found that a hexamer can exist in solution during deposition, albeit as a metastable species. The molecular clusters present after solution deposition were observed and analyzed using ultrahigh-vacuum scanning tunneling microscopy, and the initial monolayer contains four basic classes of structures: ordered dimer domains, tilted dimer rows, square tetramers, and rectangular chiral hexamers. Electronic structure calculations indicate that the chiral hexamers consist of a central dimer surrounded by four molecules oriented to form birfurcated hydrogen bonds with other carboxylic acid groups and weaker hydrogen bonds with hydrogens from the aromatic rings. The calculations also indicated that the tetramers are clusters held together by carboxylic acid dimer bonds on each ring oriented perpendicular to each other, and that this conformation is slightly more stable than two dimers for a cluster of four molecules. Annealing this surface at 50 °C for 1 h results in the formation of both isolated tetramers and ordered tetramer rows at the expense of the end-to-end dimer domains, with few chiral hexamers remaining. Further annealing at 50 °C, as well as annealing at 65 °C drives the system to form chiral dimer domains, as well as several other minor structures. Annealing at 75 °C resulted in a dramatic decrease in apparent surface coverage, and most ordered structures existed as large tilted dimer rows, whether isolated or in ordered domains. This drop in surface coverage is likely due to some combination of decomposition of the molecule, desorption, or the growth of three-dimensional crystal structures. The observed coexistence of many forms of ordered dimer structures after annealing indicates that the equilbrium conformation of 1,1′-ferrocenedicarboxylic acid is some array of ordered dimers, and the variety of supramolecular structures present after annealing is an indicator that this system evolves under kinetically controlled growth conditions.

Monolayers of indole-2-carboxylic acid and indole-3-carboxylic acid on gold are studied using ultrahigh-vacuum scanning tunneling microscopy. Both molecules form symmetric, cyclic, hydrogen-bonded pentamers, a structure that is stabilized by the presence of a weak hydrogen-bond donor (NH or CH) adjacent to the carboxylic acid on the five-membered ring. In addition to pentamers, indole-2-carboxylic acid forms hexamers and catemer chains, while indole-3-carboxylic acid monolayers are generally disordered. Density functional theory calculations show that pentamers and hexamers have stability comparable to dimers or short catemers. The coexistence of all of these structures likely arises from the nonequilibrium conditions present in solution during pulse deposition of the monolayer.

Self-assembled monolayers of ferrocenecarboxylic acid (FcCOOH) contain two fundamental units, both stabilized by intermolecular hydrogen bonding: dimers and cyclic five-membered catemers. At surface coverages below a full monolayer, however, there is a significantly more varied structure that includes double-row clusters containing two to twelve FcCOOH molecules. Statistical analysis shows a distribution of cluster sizes that is sharply peaked compared to a binomial distribution. This rules out simple nucleation-and-growth mechanisms of cluster formation, and strongly suggests that clusters are formed in solution and collapse into rows when deposited on the Au(111) surface.

A model scanning probe microscope, designed using similar principles of operation to research instruments, is described. Proximity sensing is done using a capacitance probe, and a mechanical linkage is used to scan this probe across surfaces. The signal is transduced as an audio tone using a heterodyne detection circuit analogous to that used in the theremin (one of the first electronic musical instruments, invented in the early 20th century). The instrument is useful for demonstrations and hands-on activities that introduce fundamentals of scanning probe microscopy and, by extension, nanoscience and nanotechnology. The details of instrument construction are provided, along with instructions for assembly and troubleshooting.Keywords: Demonstrations; Elementary/Middle School Science; General Public; Hands-On Learning/Manipulatives; High School/Introductory Chemistry; Laboratory Equipment/Apparatus; Nanotechnology; Physical Chemistry; Surface Science;

Scanning tunneling microscopy images of diferrocenylacetylene (DFA) coadsorbed with benzene on Au(111) show individual and close-packed DFA molecules, either adsorbed alongside benzene or on top of a benzene monolayer. Images acquired over a range of positive and negative tip–sample bias voltages show a shift in contrast, with the acetylene linker appearing brighter than the ferrocenes at positive sample bias (where unoccupied states primarily contribute) and the reverse contrast at negative bias. Density functional theory was used to calculate the electronic structure of the gas-phase DFA molecule, and simulated images produced through two-dimensional projections of these calculations approximate the experimental images. The symmetry of both experimental and calculated molecular features for DFA rules out a cis adsorption geometry, and comparison of experiment to simulation indicates torsion around the inter-ferrocene axis between 90° and 180° (trans); the cyclopentadienyl rings are thus angled with respect to the surface.

Scanning tunneling microscopy (STM) in ultra-high-vacuum is used to investigate the reaction of gas-phase atomic chlorine with octanethiolate self-assembled-monolayers on Au(111). Exposure to Cl atoms results in the formation of a variety of surface defects, and eventually leads to a complete loss of order within the alkanethiolate monolayer. X-ray photoelectron spectroscopy and thermal desorption mass spectrometry show that these morphological changes are accompanied by significant chlorination of the monolayer as well as a ∼30% decrease in the amount of adsorbed sulfur. The rate of reaction is measured through the analysis of sequences of STM images, and coverage-vs.-exposure data shows that the average reactivity of any given molecule within the monolayer decreases as the reaction progresses. Working with the assumption that monolayer defects created by Cl-atom reaction will affect the reactivity of neighboring molecules, a kinetic Monte Carlo simulation shows the data are consistent with defect sites inhibiting reaction rate by a factor of 5 or more. This behavior is opposite to that found for hydrogen-atom reactions, where edge and defect sites were far more reactive. The dynamics of chlorine-atom reactivity are described primarily in terms of the formation and subsequent reaction of surface-adsorbed radicals, with surface defects providing sites where these radicals can be quenched.

In chemical reactions at the gas–surface interface, the heterogeneity in structure of reaction sites plays a critical role in determining surface reactivity. This Perspective describes reaction mechanisms in such systems and details the use of in situ scanning probe microscopy to investigate reactions of gas-phase radicals with self-assembled alkanethiolate monolayers on gold surfaces. For both atomic hydrogen and atomic chlorine reagents, the presence of defects in the alkanethiolate surface order has a substantial influence on what reactions can occur and the speed at which they do so. Data acquired from a series of images were modeled using kinetic Monte Carlo simulations, and a surface radical reaction model was developed to explain the observed evolution of surface structure as the reactions proceed.

We use scanning tunneling microscopy (STM) to study octanethiol self-assembled monolayers (SAMs) on Au(111) exposed to atomic hydrogen. While the overall net reaction is to remove octanethiol molecules from the underlying gold surface, the monolayer structure heavily influences the rate of this reaction and molecules located along surface defects are preferentially removed before those located in close-packed areas. Octanethiol molecules remaining on the gold surface can go through significant rearrangement: domain boundaries can change both size and structure, annealing into surrounding close-packed domains; film defects diffuse to the edge of close-packed areas; and molecules located along the edge of close-packed domains shift position, changing the size and shape of the remaining close-packed features. Monolayer reactivity increases with increasing hydrogen-atom exposure, and we compare the experimental results with kinetic Monte Carlo simulations. We find that the edges of defect sites are potentially over 500 times more reactive than close-packed monolayer areas.

The molecule {Cp*(dppe)Fe(C≡C−)}3(1,3,5-C6H3) (Fe3) was adsorbed on a single-crystal gold surface and studied using ultrahigh-vacuum scanning tunneling microscopy (STM). Both the singly oxidized Fe3+ and doubly oxidized Fe32+ are mixed-valence ions, and localization of the charge at specific metal centers was observed as the appearance of pronounced asymmetry in STM images. Switching the tip–sample bias voltage demonstrates that this asymmetry is electronic in nature. The nature of intramolecular structure and the degree of asymmetry produced in STM images varies according to the state of the scanning tip. Constrained density functional theory was used to simulate STM images for the neutral molecule and for both mixed-valence species, and simulated images agreed closely with observed results. In particular, changing the number of molecular electronic states contributing to contrast in the STM image produced a good match to the variation in structures measured experimentally.

Scanning tunneling microscopy (STM) is used to study two dinuclear organometallic molecules, meta-Fe2 and para-Fe2, which have identical molecular formulas but differ in the geometry in which the metal centers are linked through a central phenyl ring. Both molecules show symmetric electron density when imaged with STM under ultrahigh-vacuum conditions at 77 K. Chemical oxidation of these molecules results in mixed-valence species, and STM images of mixed-valence meta-Fe2 show pronounced asymmetry in electronic state density, despite the structural symmetry of the molecule. In contrast, images of mixed-valence para-Fe2 show that the electronic state density remains symmetric. Images are compared to constrained density functional (CDFT) calculations and are consistent with full localization of charge for meta-Fe2 on to a single metal center, as compared with charge delocalization over both metal centers for para-Fe2. The conclusion is that electronic coupling between the two metal centers occurs through the bonds of the organic linker, and through-space coupling is less important. In addition, the observation that mixed-valence para-Fe2 is delocalized shows that electron localization in meta-Fe2 is not determined by interactions with the Au(111) substrate or the position of neighboring solvent molecules or counterion species.

Two-component octanethiolate-dialkyldithiocarbamate (DTC) monolayers were formed on Au(111) surfaces and studied using scanning tunneling microscopy (STM). Octanethiolate monolayers exposed to DTC in solution results in the erosion of octanethiolate domain boundaries and areas along terrace step edges and the insertion of DTC into these areas; this is consistent with the broad literature of substitution in alkanethiolate monolayers. Conversely, a DTC monolayer exposed to octanethiol results in displacement of DTC and the eventual formation of ordered octanethiolate domains. The effects of temperature, solution concentration, and deposition time are investigated.

Scanning tunneling microscopy is used to study monolayers of 1-adamantanethiolate as they are exposed to gas-phase atomic hydrogen. H-atom reaction results in complete removal of the organic monolayer. The relaxation of the reconstruction present at the gold–sulfur interface results in the formation of gold-atom islands, as well as the addition of gold atoms to extant surface defects such as steps and pits. Characterization of these changes shows that for 1-adamantanethiolate monolayers, 0.18 ± 0.033 monolayers of gold adatoms participate in bonding with thiolate sulfur atoms. This results in a 1:1 Au:S ratio, in contrast to the 1:2 Au:S ratio reported for n-alkanethiolate monolayers. The difference in adatom density implies a qualitative difference in binding between n-alkanethiols and 1-adamantanethiols.

{Cp*(dppe)Fe(C≡C−)}2(1,3-C6H4) is studied both as a neutral molecule, Fe(II)−Fe(II), and as a mixed-valence complex, Fe(II)−Fe(III). Scanning tunneling microscopy (STM) is used to image these species at 77 K under ultrahigh-vacuum conditions. The neutral molecule Fe(II)−Fe(II) has a symmetric, “dumbbell” appearance in STM images, while the mixed-valence complex Fe(II)−Fe(III) demonstrates an asymmetric, bright-dim double-dot structure. This asymmetry results from localization of the electron to one of the iron-ligand centers, a result which is confirmed through comparison to theoretical STM images calculated using constrained density-functional theory (CDFT). The observation of charge localization in mixed-valence complexes outside of the solution environment opens up new avenues for the control and patterning of charge on surfaces, with potential applications in smart materials and molecular electronic devices.

Single-molecule electronic components are potential building blocks for next-generation electronic devices. One architecture for such devices is quantum dot cellular automata (QCA), in which binary information is encoded in the charge configuration of a single cell and transferred by electric coupling between neighboring cells. A single mixed-valence molecule with two oxidation−reduction centers can serve as a QCA cell, and ensemble measurements have shown that such molecules may have the desired electronic properties. Scanning tunneling microscopy (STM) is used to image dinuclear metal complexes, trans-[Cl(dppe)2Ru(C≡C)6Ru(dppe)2Cl] (Ru2) on Au(111) at 77 K. Oxidation to Ru2+[PF6]− creates an unbalanced charge that localizes on one end group of the otherwise symmetric Ru2 molecule. This electronic asymmetry appears in STM images, which also resolve the associated [PF6]− counterions. Comparison of Ru2 and Ru2+ monolayers show that Coulomb interactions create long-range ordering of Ru2+ electronic charge. This is a requirement for functionality in a QCA device.Keywords (keywords): low-temperature scanning tunneling microscopy; molecular line; pulse deposition; quantum dot cellular automata (QCA); ultrahigh vacuum (UHV);

The nature of the sulfur−gold bond in alkanethiol films self-assembled on Au(111) surfaces is widely contested, despite significant interest in these systems over the last 25 years. Recent theoretical and experimental studies have suggested gold adatoms are incorporated into the alkanethiol−gold interface. We have exposed alkanethiol self-assembled monolayers (SAMs) to gas-phase hydrogen atoms to remove the monolayer; the gold adatoms remain on the surface and form features that we observe using scanning tunneling microscopy (STM). The features include the formation of single-atom-thick gold islands, decreasing size of surface vacancy pits, and faceting of terrace step edges; compared to the alkanethiol-terminated surface, these features indicate a net increase in the amount of gold present on the surface, compared to the alkanethiol-terminated bulk structure. Varying the length of the alkane chain does not affect the total adatom coverage, as the adatom coverages for ethanethiol (0.172 ± 0.039), octanethiol (0.143 ± 0.033), and dodecanethiol (0.154 ± 0.024) SAMs are within experimental error of one another. This corresponds to one gold adatom for every six atoms in the bulk-terminated surface, and thus one gold adatom for every two alkanethiol molecules.

Octanethiol self-assembled monolayers were exposed to gas-phase hydrogen atoms, and the resulting changes in the order and chemical structure of the surface were monitored using scanning tunneling microscopy (STM). Extensive damage to the monolayer was observed in the form of both dark and bright features in STM images. These changes began along domain boundaries and moved into close-packed regions of the monolayer as hydrogen-atom exposure time increased. Increasing exposure also results in an accelerated rate of observed surface changes, indicating that the reactivity of the surface increases as a result of initial gas-surface reactions. Complex restructuring of the alkanethiol monolayer is observed, including defect formation and the disordering of the alkanethiol monolayer. However, in some cases the monolayer demonstrates the capability of self-healing, with local annealing and reordering of close-packed domains. This annealing and reordering likely results from increased mobility of surface-bound alkanethiolates in the vicinity of monolayer defects, or from diffusion and readsorption of transiently formed alkanethiol molecules.

Scanning tunneling microscopy (STM) is used to characterize partial monolayers of C60, C70, and C84 adsorbed on the Au(1 1 1) surface at room temperature and under ambient conditions. A high degree of structural polymorphism is observed for monolayers of each of these fullerenes. For C60, three lattice packings are observed, including a previously unreported 7 × 7 R21.8° structure that is stabilized by adjacent surface step defects. For C70, two lattice packings are observed, and analysis of molecular features in STM images allows molecular binding geometry to be determined. In one of the two observed lattice structures, C70 molecules align their long axis along the surface normal, while in the other, molecules align parallel to the surface and along a gold lattice direction. The parallel geometry is also preferred for isolated and loosely packed molecules on the surface. C84 exhibits a large number of lattice orientations and no long-range order, and likely binds incommensurately on Au(1 1 1). Time series of images of partial C70 monolayers show progressive surface modification as a result of perturbation by the STM tip; this is in contrast to the behavior of C60, where alterations in surface structure at room temperature are thermally driven.

Scanning tunneling microscopy (STM) in ultra-high-vacuum is used to investigate the reaction of gas-phase atomic chlorine with octanethiolate self-assembled-monolayers on Au(111). Exposure to Cl atoms results in the formation of a variety of surface defects, and eventually leads to a complete loss of order within the alkanethiolate monolayer. X-ray photoelectron spectroscopy and thermal desorption mass spectrometry show that these morphological changes are accompanied by significant chlorination of the monolayer as well as a ∼30% decrease in the amount of adsorbed sulfur. The rate of reaction is measured through the analysis of sequences of STM images, and coverage-vs.-exposure data shows that the average reactivity of any given molecule within the monolayer decreases as the reaction progresses. Working with the assumption that monolayer defects created by Cl-atom reaction will affect the reactivity of neighboring molecules, a kinetic Monte Carlo simulation shows the data are consistent with defect sites inhibiting reaction rate by a factor of 5 or more. This behavior is opposite to that found for hydrogen-atom reactions, where edge and defect sites were far more reactive. The dynamics of chlorine-atom reactivity are described primarily in terms of the formation and subsequent reaction of surface-adsorbed radicals, with surface defects providing sites where these radicals can be quenched.

Self-assembled monolayers of ferrocenecarboxylic acid (FcCOOH) contain two fundamental units, both stabilized by intermolecular hydrogen bonding: dimers and cyclic five-membered catemers. At surface coverages below a full monolayer, however, there is a significantly more varied structure that includes double-row clusters containing two to twelve FcCOOH molecules. Statistical analysis shows a distribution of cluster sizes that is sharply peaked compared to a binomial distribution. This rules out simple nucleation-and-growth mechanisms of cluster formation, and strongly suggests that clusters are formed in solution and collapse into rows when deposited on the Au(111) surface.

Scanning tunneling microscopy images of diferrocenylacetylene (DFA) coadsorbed with benzene on Au(111) show individual and close-packed DFA molecules, either adsorbed alongside benzene or on top of a benzene monolayer. Images acquired over a range of positive and negative tip–sample bias voltages show a shift in contrast, with the acetylene linker appearing brighter than the ferrocenes at positive sample bias (where unoccupied states primarily contribute) and the reverse contrast at negative bias. Density functional theory was used to calculate the electronic structure of the gas-phase DFA molecule, and simulated images produced through two-dimensional projections of these calculations approximate the experimental images. The symmetry of both experimental and calculated molecular features for DFA rules out a cis adsorption geometry, and comparison of experiment to simulation indicates torsion around the inter-ferrocene axis between 90° and 180° (trans); the cyclopentadienyl rings are thus angled with respect to the surface.