S. Alex Kandel

Self-assembly of hydrogen-bonded two-dimensional quasicrystals

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.

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.

Through-Bond versus Through-Space Coupling in Mixed-Valence Molecules: Observation of Electron Localization at the Single-Molecule Scale

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.

Minimizing image-processing artifacts in scanning tunneling microscopy using linear-regression fitting

We present a method for removing noise from scanning tunneling microscopy images based on least-squares fitting of spatial data. Modeling the known structure of the surface, including isolated features and surface steps, allows for effective discrimination of signal from noise and produces minimal processing artifacts, even for very noisy images. This approach is effective for removing external noise due to vibrational or acoustic interference, and can also be applied to correct for tip-related height jumps as well as to flatten images warped by thermal effects or nonlinearity of the microscope scanner.

Scanning tunneling microscopy studies of pulse deposition of dinuclear organometallic molecules on Au(111)

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.

Synthesis of a Neutral Mixed‐Valence Diferrocenyl Carborane for Molecular Quantum‐Dot Cellular Automata Applications

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.

Note: Circuit design for direct current and alternating current electrochemical etching of scanning probe microscopy tips

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.

Structural changes of an octanethiol monolayer via hyperthermal rare-gas collisions

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.

Collision-induced annealing of octanethiol self-assembled monolayers by high-kinetic-energy xenon atoms

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.

Orientation as a probe of photodissociation dynamics

Molecular chlorine (Cl2) was photodissociated in the wavelength range 270–400 nm with linearly polarized light, and the orientation of the excited-state chlorine atom Cl*(2P1/2) was measured by 2+1 resonance enhanced multiphoton ionization (REMPI) using circularly polarized light. The degree of orientation of the Cl* photofragment is found to oscillate as a function of photolysis wavelength. The oscillation is a result of quantum mechanical coherence arising from electronic states of different symmetry that correlate to the same separated-atom asymptote. A simple curve-crossing model using abinitio potential energy curves reproduces the general shape of the oscillation but fails to give a quantitative fit.