Zachary J. Donhauser

Control and placement of molecules via self-assembly

We use self- and directed assembly to pattern organic monolayers on the nanometre scale. The ability of the scanning tunnelling microscope to obtain both nanometre-scale structural and electronic information is used to characterize patterning techniques, to elucidate the intermolecular interactions that drive them and to probe the structures formed. We illustrate three successful approaches: (1) phase separation of self-assembled monolayers by terminal and internal functionalization, (2) phase separation of self-assembled monolayers induced by post-adsorption processing and (3) control of molecular placement by insertion into a self-assembled monolayer. These methods demonstrate the possibilities of patterning films by exploiting the intrinsic properties of the molecules. We employ these methods to prepare matrix-isolated samples to probe molecular electronic properties of single and bundled molecules.

Matrix-Mediated Control of Stochastic Single Molecule Conductance Switching

We have analyzed the conductance switching of single phenylene ethynylene oligomers embedded in matrices of alkanethiolates. When the molecules are studied using scanning tunneling microscopy, they switch reversibly between discrete states that differ in their apparent height by ~ 3 A. The persistence times for molecules in either state ranges from seconds to tens of hours. We demonstrate several methods to control the defect density and quality of the host alkanethiolate matrix, which in turn affects the rate at which the inserted molecules switch. A vapor annealing procedure is described that increases order in the matrix film and reduces the switching rate. Decreased matrix deposition time results in a less-ordered film that increases the switching rate. Because the molecular switching depends on matrix order, we conclude that the switching is a result of motions of the molecules or bundles, rather than electrostatic effects of charge transfer.

Cross-correlation image tracking for drift correction and adsorbate analysis

A digital image tracking algorithm based on Fourier-transform cross-correlation has been developed to correct for instrumental drift in scanning tunneling microscope images. A technique was developed to eliminate cumulative tracking errors associated with fractional pixel drift. This tracking algorithm was used to monitor conductance changes associated with different conformations in conjugated molecular switch molecules and to trace the diffusion of individual benzene molecules on Ag{110}. Molecular motions have been tracked for up to 25 h (400 images) of acquisition time.

Exploiting intermolecular interactions and self-assembly for ultrahigh resolution nanolithography

The combination of self-, directed, and positional assembly techniques, i.e., “bottom up” fabrication, will be essential for patterning and connecting future nanodevices. Systematic exploration of local intermolecular interactions on surfaces will permit their exploitation for the rational design of molecular-scale surface structures. We use the scanning tunneling microscope to probe the local behavior of self-assembled films at the nanometer scale. The ability to control the molecular placement within and by self-assembled monolayers is a means of patterning surfaces. A monolayer with customized features can be produced by manipulating the dynamics of film formation, which are heavily affected by the selectable intermolecular interactions of adsorbates and the structural components naturally occurring within the films. Additionally, the controlled placement and thickness of self-assembled multilayers created from alternating strata of α,ω-mercaptoalkanoic acids and coordinated metal ions can be developed...

Measurements and Mechanisms of Single-Molecule Conductance Switching

We have engineered and analyzed oligo(phenylene-ethynylene) (OPE) derivatives to understand and to control the bistable conductance switching exhibited by these molecules when inserted into saturated alkanethiolate and amidecontaining alkanethiolate self-assembled monolayers (SAMs) on Au{111}. By engineering the structures of the OPE derivatives, we have shown conductance switching to depend on hybridization changes at the molecule–substrate interface. In addition, we have demonstrated bias-dependent switching controlled by interactions between the dipole of the OPEs and the electric field applied between the scanning tunneling microscope tip and the substrate. These interactions are stabilized via intermolecular hydrogen bonding between the OPEs and host amide-containing SAMs.

High resolution dopant profiling using a tunable AC scanning tunneling microscope

Nonlinear tunable high frequency AC scanning tunneling microscopy (ACSTM) and spectroscopy have been applied to profiling dopants at ultrahigh resolution in patterned semiconductors. With difference frequency measurements on uniformly doped Si, we have shown that ACSTM is sensitive to both dopant type and density. The difference frequency signal vs. applied bias voltage gives a spectral signature characteristic of dopant type and density. We are then able to use a spectroscopic imaging mode to map the dopant density at ultrahigh resolution. The difference frequency signal is advantageous in that while two (or more) frequencies are applied to the ACSTM probe tip, a much lower mixed frequency is recorded. The background at this lower frequency is greatly reduced and detection is simplified.

Expanding the Capabilities of the Scanning Tunneling Microscope

Scanning probe microscopes allow unprecedented views of surfaces and the site-specific interactions and dynamics of adsorbates. Our efforts to identify and to characterize atoms and molecules on surfaces and how it is that the scanning tunneling microscope images these surfaces and adsorbates will be discussed. We have extended the capabilities of scanning probe microscopes in several ways; two in particular will be highlighted. In the first section, recent advances in tunable microwave frequency scanning tunneling microscopy (STM) allow dopant profiling at unprecedented resolution will be presented. We apply nonlinear tunable microwave frequency scanning tunneling microscopy and spectroscopy to profiling dopants at ultrahigh resolution in semiconductors that is sensitive to both dopant type and density. We are then able to use a spectroscopic imaging mode to map the dopant density at the atomic scale. In the second part of this chapter, advanced image processing techniques that extend the scientific capabilities of STM will be presented. A digital image tracking algorithm based on Fourier-transform crosscorrelation has been developed to correct for instrumental drift in scanning tunneling microscope images. This tracking algorithm was used to monitor conductance changes associated with different conformations in conjugated switching molecules and to trace the diffusion of individual benzene molecules on silver.

Dimerization and Long-Range Repulsion Established by Both Termini of the Microtubule-Associated Protein Tau

Tau is a microtubule-associated protein found in neuronal axons that has several well-known functions, such as promoting microtubule polymerization, stabilizing microtubules against depolymerization, and spatially organizing microtubules in axons. Two contrasting models have been previously described to explain taus ability to organize the spacing between microtubules: complementary dimerization of the projection domains of taus on adjacent microtubules or taus projection domain acting as a polyelectrolyte brush. In this study, atomic force microscopy was used to interrogate intermolecular interactions between layers of tau protein immobilized on mica substrates and on silicon nitride atomic force microscope tips. On these surfaces, tau adopts an orientation comparable to that when bound to microtubules, with the basic microtubule binding domain immobilized and the acidic domains extending into solution. Force-distance curves collected via atomic force microscopy reveal that full length human tau, when assembled into dense surface-bound layers, can participate in attractive electrostatic interactions consistent with the previously reported dimerization model. However, modulating the ionic strength of the surrounding solution can change the structure of these layers to produce purely repulsive interactions consistent with a polyelectrolyte brush structure, thus providing biophysical evidence to support both the zipper and brush models. In addition, a pair of projection domain deletion mutants were examined to investigate whether the projection domain of the protein is essential for the dimerization and brush models. Force-distance curves collected on layers of these proteins demonstrate that the C-terminus can play a role analogous to that of the projection domain.

Nanometer-Scale Electronics and Storage

The ability to control the placement of molecules is essential for the patterning and fabrication of nanoscale electronic devices. We apply selective chemistry and self-assembly in combination with conventional nanolithographic techniques to reach higher resolution, greater precision, and chemical versatility in the nanostructures that we create. We illustrate three successful approaches: (1) phase separation of self-assembled monolayers (SAMs) by terminal and internal functionalization, (2) phase separation of SAMs induced by post-adsorption processing and (3) control of molecular placement by insertion into a self-assembled monolayer. These methods demonstrate the possibilities of patterning films by exploiting the intrinsic properties of the molecules. We then employ these self-assembled monolayers as a means to isolate molecules with electronic function to determine the mechanisms of function, and the relationships between molecular structure, environment, connection, coupling, and function. Using self-assembly techniques in combination with scanning tunneling microscopy (STM) we are able to study candidate molecular switches individually and in small bundles. Alkanethiolate SAMs on gold are used as a host two-dimensional matrix to isolate and to insulate electrically the molecular switches. We then individually address and electronically probeeach moleculeusing STM. The conjugated molecules exhibit reversible conductance switching, manifested as a change in the topographic height in the STM images. The origins of switching and the relevant aspects of the molecular structure and environment required will be discussed.