In this thesis I am presenting a detailed study to optimize the deposition of magnetic molecules and gold nanoparticles in atomically flat surfaces by self-assembling them from solution. Epitaxially grown and atomically flat gold surface on mica is used as substrate for this study. These surfaces have roughness of the order one tenth of a nanometer and are perfect to image molecules and nanoparticles in the 1-10 nanometers range. The purpose of these studies is to find the suitable parameters and conditions necessary to deposit a monolayer of nano-substance on chips containing gold nanowires which will eventually be used to form single electron transistors by electromigration breaking of the nanowire. Maximization of the covered surface area is crucial to optimize the yield of finding a molecule/nanoparticle near the gap formed in the nanowire after electromigration breaking. Coverage of the surface by molecules/nanoparticles mainly depends on the deposition time and concentration of the solution used for the self-assembly. Deposition of the samples under study was done for different solution concentrations and deposition times until a self-assembly monolayer covering most of the surface area is obtained. Imaging of the surfaces after deposition was done by tapping-mode AFM. Analysis of the AFM images was performed and deposition parameters (i.e. coverage or molecule/particle size distribution) were obtained. The subjects of this investigation were a molecular polyoxometalate, a single-molecule magnet and functionalized gold nanoparticles. The obtained results agree with the structure of each of the studied systems. Using the optimized deposition parameters found in this investigation, single-electron transport measurements have been carried out. Preliminary results indicate the right choice of the deposition parameters.

Optical activity is the defining property of chiral materials that is essential for characterization in biology, chemistry, and physics. While a substantial body of research has provided a strong theoretical framework of the origin of optical activity, we still know very little by way of experiment about an individual molecule’s contribution to the bulk optical activity. The chiroptical response of a single molecule can depend on molecular orientation and local molecular environment, information which is lost in ensemble averaging. This thesis focuses on establishing methods for a priori determination of chiral molecule orientations and refining measurements to probe the chiroptical response of a single molecule using a generalization of well-known defocused emission pattern imaging. Recent experiments probing the chiroptical response of single helicene dimer molecules offer new insight into the relationship between local molecular environment and coupling between chiral moieties. New experiments, such as probing the chiroptical response of an achiral, non-centrosymmetric molecular systems and polarization resolved spectral measurements which probe the Davydov splitting of coupled chromophore systems offer promising new avenues for understanding the connection between the polarization properties of single molecules and the ensemble.

Hybrid quantum dot /organic semiconductor systems are of great interest in optoelectronic and photovoltaic applications, because they combine the robust and tunable optical properties of inorganic semiconductors with the processability of organic thin films. In particular, cadmium selenide (CdSe) quantum dots coordinated with oligo-(phenylene vinylene) ligands have displayed a number of hybrid optical properties that make them particularly well-suited to these applications. When probed on an individual particle level, these so-called CdSe-OPV nanostructures display a number of surprising photophysical characteristics, including strong quenching of fluorescence from coordinating ligands, enhanced emission from the CdSe quantum dot core, suppression of fluorescence intermittency, and photon antibunching, all of which make them attractive in the applications described above. By correlating fluorescence properties with atomic force microscopy, the effects of ligands on quantum dot luminescence are elucidated. In addition, recent studies on individual CdSe-OPV nanostructures have revealed a strong electronic coupling between the coordinating ligands and the nanocrystal core. These studies have shown that excitations in the organic ligands can strongly affect the electronic properties of the quantum dot, leading to linearly polarized optical transitions (both in absorption and emission) and polarization-modulated shifts in band edge emission frequency. These polarization effects suggest exciting new uses for these nanostructures in applications that demand the robust optical properties of quantum dots combined with polarization-switchable control of photon emission.

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In this dissertation, we study the most important microscopic aspects that grant molecules such as Single Molecule Magnets (SMMs) their preferential spin direction. We do so by proposing and solving a model that includes correlations between electrons occupying atomic orbitals. In addition, we study the relation between the non-equilibrium electronic transport signatures in a SMM model weakly coupled to a three-terminal single electron transistor device, and the interference features of the SMM model in the presence of a magnetic field. Finally, we investigate the equilibrium transport features in a giant-spin model of a SMM in the Kondo regime. We study how the magnetic field modulation of the energy in a highly anisotropic molecule can affect the conductance of the molecule in the Kondo regime.

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This thesis addresses development of a new force spectroscopy tool, correlation force spectroscopy (CFS), for the measurement of the mechanical properties of very small volumes of material (molecular to µm³) at kHz-MHz time-scales. CFS is based on atomic force microscopy (AFM) and the principles of CFS resemble those of dual-trap optical tweezers. CFS consists of two closely-spaced micro-cantilevers that undergo thermal fluctuations. Measurement of the correlation in thermal fluctuations of the two cantilevers can be used to determine the mechanical properties of the soft matter, e.g. a polymeric molecule, that connects the gap between the two cantilevers. Modeling of the correlations yields the effective stiffness and damping of the molecule. The resolution in stiffness is limited by the stiffness of the cantilever and the frequency by the natural frequency of the cantilevers, but, importantly, the damping resolution is not limited by the damping of the cantilever, which has enabled high-resolution measurements of the internal friction of a polymer. The concept of CFS was originally presented by Roukes' group in Caltech [Arlett et al., Lecture Notes in Physics, 2007]; I developed the first practical versions of CFS for experimentation, and have used it in two applications (1) microrheology of Newtonian fluids and (2) single molecule force spectroscopy. To understand the correlation in thermal fluctuations of two cantilevers I initially validated the theoretical approach for analyzing correlation in terms of deterministic model using the fluctuation-dissipation theorem [Paul and Cross, PRL, 2004]. I have shown that the main advantages of such correlation measurements are a large improvement in the ability to resolve stiffness and damping. Use of CFS as a rheometer was validated by comparison between experimental data and finite element modeling of the deterministic vibrations of the cantilevers using the known viscosity and density of fluids. Work in this thesis shows that the data can also be accurately fitted using a simple harmonic oscillator model, which can be used for rapid rheometric measurements, after calibration. The mechanical properties of biomolecules such as dextran and single stranded DNA (ssDNA) are also described. CFS measurements of single molecule properties of ssDNA reveal the internal friction of the molecule in solution. / Ph. D.

Doctor of Philosophy / Department of Chemical Engineering / Keith L. Hohn / Amorphous silica-alumina is widely used as a solid acid catalyst for various reactions in oil refining and the petrochemical industry. The strength and the number of the acid sites in the material are most often believed to arise from the alumina atoms inserted into the silica lattice. The existence of the acidity distribution across the framework is a result of the local composition or the short-range interactions on the silica-alumina surface. Conventional techniques used to characterize silica-alumina provide effective information on the average acidity, but may not reflect the heterogeneity of surface acidity within the material. Recently, it is possible to study individual catalytic sites on solid catalysts by single molecule fluorescence microscopy with high time and space resolution. Fluorophores can be chosen that emit at different wavelengths depending on the properties of the local environment. By doping these fluorophores into a solid matrix at nanomolar concentrations, individual probe molecules can be imaged. Valuable information can be extracted by analyzing changes in the fluorescence spectrum of the guest molecules within a host matrix. In this research, silica-alumina thin films were studied with single molecule fluorescence microscopy. The samples were prepared by a sol-gel method and a wide-field fluorescence microscope was used to locate and characterize the fluorescent behaviors of pH sensitive probes. In mesoporous thin films, the ratio of the dye emission at two wavelengths provides an effective means to sense the effective pH of the microenvironment in which each molecule resides. The goal of this work was to develop methods to quantify the acidity of individual micro-environments in heterogeneous networks. Pure silica films treated with external phosphate solutions of different pH values were used to provide references of the fluorescence signals from individual dye molecules. SM emission data were obtained from mesoporous Al-Si films as a function of Al content in films ranging from 0% to 20% alumina. Histograms of the emission ratio revealed that films became more acidic with increasing Al content. The acidity on interior surfaces in zeolite pores was also of interest in this work. A microfluidic device was built to isolate the interior surface from the exterior surface. Some preliminary results showed the potential of using SM fluorescence method to study the acidic properties inside the pores of zeolite crystals.