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Molecular self-assembly is driven by intermolecular interactions between the functional groups on the component molecules. Small changes in molecular structure can make large differences in extended structure, and understanding this connection will lead to predictive power and control of the self-assembly process. Scanning tunneling microscopy is used to study self-assembly in two-dimensional clusters and monolayers, and the experimental approach is to study "families" of molecules where one or more functional groups is varied in a methodical way. Studied families include indole carboxylic acids, isatin derivatives (which have the indole backbone), quinaldic acid, thioethers, and fluorenone derivatives. In these systems, a variety of intermolecular interactions drive the assembly of the molecular monolayer, including hydrogen bonds, van der Waals forces, zwitterionic interactions, surface interactions, and halogen interactions.

Traditionally, the goal of self-assembly and supramolecular chemistry is to engineer an equilibrium structure with a desired geometry and functionality; this is achieved through careful choice of molecular monomers, growth conditions, and substrate. Supramolecular assemblies produced under nonequilibrium conditions, in contrast, can form metastable structures with conformations quite different from those accessible in equilibrium self-assembly. The study of nonequilibrium growth of clusters potentially impacts the study of nucleation in atmospheric aerosols, nucleation in organic crystallization, and mesoscale organization for systems ranging from biological molecules to molecular electronics. In our experiments, we prepare surface monolayers of small organic and organometallic molecules through direct injection of a solution onto a substrate in high vacuum. During this process, the rapid evaporation of small solution droplets in high vacuum can lead to nonequilibrium growth conditions. The resulting structures are then characterized by scanning tunneling microscopy. Among the features observed in these experiments are cyclic, hydrogen-bonded pentamers. For carboxylic acids, the two-molecule ring dimer is the common binding motif. Large, cyclic hydrogen-bonded systems are uncommon, especially so for rings with five members. Despite this, pentagonal clusters appear to be a general phenomenon for systems containing adjacent strong and weak hydrogen-bonding elements on five-member aromatic rings. Regular pentamers have been observed as metastable structures for ferrocenecarboxylic acid, indole-2-carboxylic acid, and isatin (1-H-indole-2,3-dione). Electronic structure calculations confirm the relative stability of these structures with respect to the dimer or catemer conformations which are observed in the solid-state crystal structures. For ferrocenecarboxylic acid, cyclic pentamers undergo further self-assembly, resulting in long-range order in conjunction with local 5-fold rotational symmetry. This system is the first reported self-assembled molecular quasicrystal, and it remains the only example of a hydrogen-bonded quasicrystal. This supramolecular structure forms as a result of the cocrystallization of hydrogen-bonded cyclic pentamers with intercalated molecular dimers. The shared bonding to a single dimer is responsible for locking the adjacent pentamers in specific distances and orientations, which produces the quasicrystal. Careful analysis of experimental data provides evidence that, in some cases, metastable clusters are formed in solution and then subsequently adsorb on the surface. This is a unusual mechanism for supramolecular assembly, and it has important implications for understanding questions in crystal growth, namely: what the initial stages of crystal growth are as molecules are first precipitating from solution; what role the solvent plays in determining crystal structure; and whether solvent-mediated clustering is important in the broader phenomenon of solid-state polymorphism.

The direct injection of a 9,10-phenanthrenequinone in tetrahydrofuran solution on a Au(111) substrate in high vacuum results in the formation of metastable clusters with a non-intuitive structure. Metastable, rectangular tetramers of this molecule form in which the net molecular dipoles all orient toward the center of the cluster. This structure does not allow for additional hydrogen bonding and thus the origin of its metastability is not clear. We compare this feature to other structures observed on this surface, as well as those formed during the deposition of 9-fluorenone, which does not exhibit this anomalous clustering behavior.

The preparation of 7-Fc(+) -8-Fc-7,8-nido-[C2 B9 H10 ](-) (Fc(+) FcC2 B9 (-) ) demonstrates the successful incorporation of a carborane cage as an internal counteranion bridging between ferrocene and ferrocenium units. This neutral mixed-valence Fe(II) /Fe(III) complex overcomes the proximal electronic bias imposed by external counterions, a practical limitation in the use of molecular switches. A combination of UV/Vis-NIR spectroscopic and TD-DFT computational studies indicate that electron transfer within Fc(+) FcC2 B9 (-) is achieved through a bridge-mediated mechanism. This electronic framework therefore provides the possibility of an all-neutral null state, a key requirement for the implementation of quantum-dot cellular automata (QCA) molecular computing. The adhesion, ordering, and characterization of Fc(+) FcC2 B9 (-) on Au(111) has been observed by scanning tunneling microscopy., (© 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.)

Low-temperature scanning tunneling microscopy is used to observe self-assembled structures of ferrocenedicarboxylic acid (Fc(COOH)2) on the Au(111) surface. The surface is prepared by pulse-deposition of Fc(COOH)2 dissolved in methanol, and the solvent is evaporated before imaging. While the rows of hydrogen-bonded dimers that are common for carboxylic acid species are observed, the majority of adsorbed Fc(COOH)2 is instead found in six-molecule clusters with a well-defined and chiral geometry. The coverage and distribution of these clusters are consistent with a random sequential adsorption model, showing that solution-phase species are determinative of adsorbate distribution for this system under these reaction conditions.

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.

The process of molecular self-assembly on solid surfaces is essentially one of crystallization in two dimensions, and the structures that result depend on the interplay between intermolecular forces and the interaction between adsorbates and the underlying substrate. Because a single hydrogen bond typically has an energy between 15 and 35 kilojoules per mole, hydrogen bonding can be a strong driver of molecular assembly; this is apparent from the dominant role of hydrogen bonding in nucleic-acid base pairing, as well as in the secondary structure of proteins. Carboxylic acid functional groups, which provide two hydrogen bonds, are particularly promising and reliable in creating and maintaining surface order, and self-assembled monolayers of benzoic acids produce structure that depends on the number and relative placement of carboxylic acid groups. Here we use scanning tunnelling microscopy to study self-assembled monolayers of ferrocenecarboxylic acid (FcCOOH), and find that, rather than producing dimeric or linear structures typical of carboxylic acids, FcCOOH forms highly unusual cyclic hydrogen-bonded pentamers, which combine with simultaneously formed FcCOOH dimers to form two-dimensional quasicrystallites that exhibit local five-fold symmetry and maintain translational and rotational order (without periodicity) for distances of more than 400 ångströms.

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.

The chemical reaction of atomic chlorine with mixed monolayers of alkanethiolates having different chain lengths was investigated. In situ scanning tunneling microscopy was used to acquire time-lapsed series of images, allowing the measurement of the effect of monolayer structure and composition on reactivity. The rate of chemical reaction is strongly site-dependent. In particular, the boundary between two different-length alkanethiolates greatly promotes the reactivity of nearby molecules, much more so than any other native defect typical of single-component alkanethiolate monolayers.

We have designed and built a scanning tunneling microscope with a compact inertial-approach mechanism that fits inside the piezoelectric scanner tube. Rigid construction allows the microscope to be operated without the use of external vibration isolators or acoustic enclosures. Thermoelectric cooling and a water-ice bath are used to increase temperature stability when scanning under ambient conditions.

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 was used to investigate the reaction of octanethiolate self-assembled monolayers (SAMs) with atomic chlorine. We have found that exposing a SAM to low fluxes of radical Cl results primarily in the formation of new defects in areas with close-packed alkanethiolates, but has little to no effect on the domain boundaries of the SAM. Dosing high quantities of atomic chlorine results in the near-complete loss of surface order at room temperature, but not the complete removal of the thiolate monolayer. These observations are in stark contrast to the results of previous measurements of the reaction of atomic hydrogen with alkanethiolate SAMs.

We describe a thermal gas cracker designed to produce low fluxes of gas-phase radicals for use in radical-surface reaction studies. A resistively heated thin piece of highly oriented pyrolytic graphite is used as the pyrolysis filament, with the major advantage that this material remains inert at high temperatures. The instrument is built within an existing titanium sublimation pump, which simplifies construction and allows for self-pumping of the radical source. Thermal generation of Cl atoms from Cl(2) was chosen to test the effectiveness of the instrument. (35)Cl and (37)Cl were generated with a concomitant decrease in parent (70)Cl(2) and (72)Cl(2) species, as monitored by a residual gas analyzer. The cracking fraction of Cl(2) as a function of cell temperature is reported, with nearly full conversion achieved at high temperature., (© 2012 American Institute of Physics)

We present control circuits designed for electrochemically etching, reproducibly sharp STM probes. The design uses an Arduino UNO microcontroller to allow for both ac and dc operation, as well as a comparator driven shut-off that allows for etching to be stopped in 0.5-1 μs. The Arduino allows the instrument to be customized to suit a wide variety of potential applications without significant changes to hardware. Data is presented for coarse chemical etching of 80:20 platinum-iridium, tungsten, and nickel tips.

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., (© 2011 American Chemical Society)

{Cp*(dppe)Fe(C≡C-)}(2)(1,3-C(6)H(4)) 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.

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.

Ultrahigh-vacuum scanning tunneling microscopy (STM) was used to study trans-[Cl(dppe)2Ru(C Triple Bond C)6Ru(dppe)2Cl] [abbreviated as Ru2, diphenylphosphinoethane (dppe)] on Au(111). This large organometallic molecule was pulse deposited onto the Au(111) surface under ultrahigh-vacuum (UHV) conditions. UHV STM studies on the prepared sample were carried out at room temperature and 77 K in order to probe molecular adsorption and to characterize the surface produced by the pulse deposition process. Isolated Ru2 molecules were successfully imaged by STM at room temperature; however, STM images were degraded by mobile toluene solvent molecules that remain on the surface after the deposition. Cooling the sample to 77 K allows the solvent molecules to be observed directly using STM, and under these conditions, toluene forms organized striped domains with regular domain boundaries and a lattice characterized by 5.3 and 2.7 A intermolecular distances. When methylene chloride is used as the solvent, it forms analogous domains on the surface at 77 K. Mild annealing under vacuum causes most toluene molecules to desorb from the surface; however, this annealing process may lead to thermal degradation of Ru2 molecules. Although pulse deposition is an effective way to deposit molecules on surfaces, the presence of solvent on the surface after pulse deposition is unavoidable without thermal annealing, and this annealing may cause undesired chemical changes in the adsorbates under study. Preparation of samples using pulse deposition must take into account the characteristics of sample molecules, solvent, and surfaces.

Mixed monolayers of C70 and octanethiol are prepared on Au(111) by a sequential adsorption method. A partial C70 monolayer is first formed and characterized, followed by the vapor deposition of octanethiol. This results in a well-ordered alkanethiol film where single C70 molecules and small molecular clusters are located at domain boundaries and in disordered regions. Substrate step defects have a large influence on the spatial distribution of C70; adjacent to a substrate defect, C70 binds preferentially on the upper terrace and is depleted on the lower terrace. We explain these observations as resulting from the kinetics of alkanethiol monolayer formation, and we present a simple model for the evolution of surface structure in the C70/octanethiol system.

Collisions with high-energy xenon atoms (1.3 eV) induce structural changes in octanethiol self-assembled monolayers on Au(111). These changes are characterized at the molecular scale using an in situ scanning tunneling microscope. Gas-surface collisions induce three types of structural transformations: domain boundary annealing, vacancy island diffusion, and phase changes. Collision-induced changes that occur tend to increase order and create more stable structures on the surface. We propose a mechanism where monolayer transformations are driven by large amounts of vibrational energy localized in the alkanethiol molecules. Because we monitor incremental changes over small regions of the surface, we can obtain structural information about octanethiol monolayers that cannot be observed directly in scanning tunneling microscopy images.

We report a scanning tunneling microscopy (STM) investigation of a dinuclear organometallic molecule, trans-[Cl(dppe)2Ru(C[triple bond]C)6Ru(dppe)2Cl] (Ru2), absorbed on a Au(111) surface; this molecule is a potential candidate for use in molecular quantum-dot cellular automata (QCA) devices. Isolated Ru2 molecules were observed under ultra-high-vacuum conditions. Submolecular structure was clearly discernible in the STM images, with a bright feature corresponding to each of the two Ru-ligand complexes within the Ru2 molecule. Rotation and translation of the Ru2 molecules were observed to be induced by the STM tip under some tunneling conditions.

In situ scanning tunneling microscopy is used to measure the effect of hyperthermal rare-gas bombardment on octanethiol self-assembled monolayers. Close-packed monolayers remain largely unchanged, even after repeated collisions with 0.4 eV argon and 1.3 eV xenon atoms. In contrast, gas-surface collisions do induce structural changes in the octanethiol film near defects, domain boundaries, and disordered regions, with relatively larger changes observed for xenon-atom bombardment.

Adsorbate interactions and reactions on metal surfaces have been investigated using scanning tunneling microscopy. The manners in which adsorbates perturb the surface electronic structure in their vicinity are discussed. The effects these perturbations have on other molecules are shown to be important in overlayer growth. Interactions of molecules with surface steps are addressed, and each molecule's electron affinity is shown to dictate its adsorption sites at step edges. Standing waves emanating from steps are demonstrated to effect transient molecular adsorption up to 40 A away from the step edge. Halobenzene derivatives are used to demonstrate how the surface is important in aligning reactive intermediates.