An apparatus that combines single molecule fluorescence, optical trapping and bright-field microscopy is presented. Given the spread over orders of magnitude of the light intensities for the different techniques, special considerations in choosing the spectral regions for each were taken. Moreover, imaging single molecules in a background of intense light from the infra red laser used for the optical trap has been shown to result in enhanced photo-bleaching due to two-photon processes. A scheme for fast time-sharing was implemented in which the fluorescence excitation light and the trap light alternate in fast succession. This eliminates two-photon effects and enables stable manipulation using the optical trap. The simultaneous use of the bright-field imaging in differential interference contrast arrangement enables observation of refractile objects in the sample over large distances. The apparatus was designed for future use in studies of molecular motor regulation. However, to demonstrate the functionality of the system, the rotational diffusion of a micro-sphere fluorescently labelled at one spot was measured. / text

Single molecule wide-field polarization fluorescence imaging is an experimental method to determine the self-assembly of molecules dispersed in a thin film. Through a combination of wide-field imaging and confocal spectroscopy, the effect of synthetic structure of the oligomeric PPV-based materials was investigated to understand the effect of conjugation length, role of hydrogen bonding side chains, and influence of regioregularity on controlling chromophore folding. By studying alkoxy-linked and alkyl-linked bis(2-ethylhexyl)-p-phenylene vinylene (BEH-PPV) units of varying lengths (three, five, or seven), it was determined that conjugation length controlled the extent of molecular ordering and emission properties. Comparison of the experimental results to molecular dynamics simulations performed by collaborators confirmed that the materials became increasingly ordered as conjugation length increased. Further regulation of the assembly can be obtained through inclusion of hydrogen bonding side chains as seen in the altered amine and carboxylic acid alkoxy-linked trimer BEH-PPV in contrast to the bulky side chain tert-butyl trimer. The study of regio-regular (RR) and regio-random (RRa) alkoxy-linked pentamer poly(2-methoxy-5-(2’-ethylhexyloxy)-p-phenylenevinylene) (MEH-PPV) illustrates the limited effect of regioregularity of the side chains on self-assembly. Through synthetic structure, it is possible to design highly ordered materials through control of conjugation length and selection of side chains. / text

This work reports the development and spectroscopic studies of blinking-suppressed compact quantum dots. It is shown that a linearly graded alloy shell can be grown on a small CdSe core via a precisely controlled layer-by-layer process, and that this graded shell leads to a dramatic suppression of QD blinking both in organic solvents and in water. A substantial portion (over 25%) of the resulting QDs essentially does not blink (more than 99% of the time in the bright or “on” state). Theoretical modeling studies indicate that this type of linearly graded and relatively thin shells can not only minimize charge carrier access to surface traps, but also reduce accumulated lattice strains and defects at the core/shell interface, both of which are believed to be responsible for carrier trapping and QD blinking. Further, the biological utility of blinking-suppressed QDs by using both polyethylene glycol (PEG)-based and multidentate capping ligands is evaluated, and the results show that their optical properties are maintained regardless of surface coatings or solvating media, and that the blinking-suppressed QDs can provide continuous trajectories in live cell receptor tracking studies.

Single molecule magnets (SMMs) are molecules of mesoscopic scale which exhibit quantum properties such as quantum tunneling of magnetization, quantum interference, spin filtering effects, strong spin-phonon coupling and strong hyperfine Stark effects. These effects allow applications of SMMs to high-density information storage, molecular spintronics, and quantum information science. Therefore, SMMs are of interest to physicists, chemists, and engineers. Recently, experimental fabrication of individual SMMs within transistor set-ups have been achieved, offering a new method to examine magnetic properties of individual SMMs. In this thesis, two types of SMMs, specifically Eu2(C8H8)3 and Ni9Te6(PEt3)8, are theoretically investigated by simulating their electron transport properties within three-terminal transistor set-ups. An extended metal atom chain (EMAC) consists of a string of metallic atoms with organic ligands surrounding the string. EMACs are an important research field for nanoelectronics. Homometallic iron-based EMACs are especially attractive due to the high spin and large magnetic anisotropy of iron(II). We explore the exchange coupling of iron atoms in two EMACs: [Fe2(mes)2(dpa)2] and [Fe4(tpda)3Cl2]. Chapter 1 provides an introduction to SMMs, electron transport experiments via SMMs and an introduction to density functional theory (DFT). Chapter 2 presents a theoretical study of electron transport via Eu2(C8H8)3. This type of molecule is interesting since its magnetic anisotropy type changes with oxidation state. The unique magnetic properties lead to spin blockade effects at zero and low bias. In other words, the current through this molecule is completely suppressed until the bias voltage exceeds a certain value. Chapter 3 discusses a theoretical study of electron transport via Ni9Te6(PEt3)8. The magnetic anisotropy of this magnetic cluster has cubic symmetry, which is higher than most SMMs. With appropriate magnetic anisotropy parameters, in the presence of an external magnetic field, uncommon phenomena such as low-bias blockade effects, negative conductance and discontinuous conductance lines, are observed. In Chapter 2 and 3 DFT-calculated magnetic anisotropy parameters are used and electron transport properties are calculated by solving master equations at low temperature. Chapter 4 examines the exchange coupling between iron ions in EMACs [Fe2(mes)2(dpa)2] and [Fe4(tpda)3Cl2]. The exchange coupling constants are calculated by using the least-squares fitting method, based on the DFT-calculated energies from different spin configurations. / Ph. D. / Single molecule magnets (SMMs) are molecules of mesoscopic scale which exhibit quantum properties. Its quantum effects are used to describe the behavior of SMMs at the smallest scales. These quantum properties could also be used to reveal possible applications of SMMs to high-density information storage, molecular spintronics, and quantum information science. Thus SMMs are of interest to physicists, chemists, and engineers. Recently, electron transport via individual SMMs was achieved in experiments. Electron transport is obviously affected by the magnetic properties of the SMM, thus one can examine magnetic properties of an SMM indirectly by measuring electron transport via the SMM. In this thesis, two types of SMMs, Eu2(C8H8)3 and Ni9Te6(PEt3)8, are investigated theoretically by simulating their electron transport properties. An extended metal atom chain (EMAC) consists of a string of metallic atoms with organic ligands surrounding the string. EMACs are an important research field for nanoelectronics. Homometallic iron-based EMACs are especially attractive due to the high spin and large magnetic anisotropy of iron(II). If a molecule has magnetic anisotropy, its magnetic properties change with the direction of its magnetic moment. We explore how iron atoms interact with each other in the EMACs [Fe2(mes)2(dpa)2] and [Fe4(tpda)3Cl2]. Chapter 1 provides an introduction to SMMs, electron transport experiments via SMMs and an approximation method, density functional theory (DFT). DFT is a method to approximate electronic structure and magnetic properties of various many-body systems. Chapter 2 investigates theoretical electron transport via Eu2(C8H8)3. Eu2(C8H8)3 changes its type of magnetic anisotropy when it obtains an extra electron, which is different from most SMMs. If the Eu2(C8H8)3 is short of an extra electron, its magnetization direction is in-plane, that is, its magnetic energy is lowest when its magnetic moment is along any direction in a specific plane. If an extra electron is captured by Eu2(C8H8)3, its magnetization direction becomes out-of-plane, and its lowest energy is obtained when its magnetic moment is along the direction normal to the specific plane. The unique magnetic properties lead to blockade effects at low bias: the current through this molecule is completely suppressed until the bias voltage exceeds a certain value. The bias voltage on a molecule equals the electrical potential difference between two ends of the molecule. Chapter 3 investigates theoretical electron transport via Ni9Te6(PEt3)8. Magnetic anisotropy of Ni9Te6(PEt3)8 is cubic symmetric, and its symmetry is higher than most SMMs. With appropriate magnetic anisotropy parameters, in the presence of an external magnetic field, uncommon phenomena are observed. These phenomena include (1) current is completely suppressed when bias is low; (2) current via SMM decreases while bias on SMM increases; (3) there are discontinuous lines in the figures that describe electrical conductance of current. Chapter 4 examines the iron atoms’ interaction strength in both [Fe2(mes)2(dpa)2] and [Fe4(tpda)3Cl2]. Reasonable spin Hamiltonians are used to describe the energy of EMACs. Considering all possible directions of the spins of iron atoms in two EMACs, we calculate the energy of every possible spin configuration using DFT. The energy of each spin configuration can be expressed as an equation containing one or more coupling constants. We apply the least-squares fitting method to obtain the values of the coupling constants in the spin Hamiltonians.

Recent experiments have shown that junctions consisting of individual single-molecule magnets (SMMs) bridged between two electrodes can be fabricated in three-terminal devices, and that the characteristic magnetic anisotropy of the SMMs can be affected by electrons tunneling through the molecule. Vibrational modes of the SMM can couple to electronic charge and spin degrees of freedom, and this coupling also influences the magnetic and transport properties of the SMM. The effect of electron-vibron coupling on transport has been extensively studied in small molecules, but not yet for junctions of SMMs. The goals of this thesis will be two-fold: to present a novel approach for studying the effects of this electron-vibron coupling on transport through SMMs that utilizes both density functional theory calculations and model Hamiltonian construction and analysis, and to present a software framework based on this hybrid approach for the simulation of transport across user-defined SMMs. The results of these simulations will indicate a characteristic suppression of the current at low energies that is strongly dependent on the overall electron-vibron coupling strength and number of molecular vibrational modes considered. / Master of Science

No description available.

Doctor of Philosophy / Department of Chemistry / Daniel A. Higgins / In this dissertation, state-of-the-art fluorescence microscopy techniques are employed to probe unique nanoscale phenomena in poly(dimethylsiloxane) (PDMS) films and on single carbon nanofibers. In one study, the mobility and physical entrapment of single dye molecules in dry and solvent-loaded PDMS films is explored. Experiments are performed under dry nitrogen and at various levels of isopropyl alcohol (IPA) loading from the vapor phase, as monitored by a PDMS-coated quartz-crystal microbalance. Single molecules are shown to be predominantly immobile under dry conditions and mostly mobile under IPA-saturated conditions. FCS is used to measure the apparent diffusion coefficient, yielding a mean that is virtually independent of IPA loading and sample class. An increase in the population of mobile molecules under high IPA conditions is attributed to the filling of film micropores with solvent, rather than by incorporation of molecularly dispersed solvent into the PDMS. In a second study, the molecular mobility of both neutral and cationic molecules in cured PDMS films is studied as a function of oligomer extraction. Cross correlation and Bayesian burst analysis methods were used to quantify the populations of fixed and total molecules, respectively. The results show that the total concentration of dye increases with increased oligomer extraction, while the relative populations of fixed and mobile molecules decrease and increase, respectively. These results are relevant to the use of PDMS in microfluidics, nanofiltration and pervaporation membranes and solid phase microextraction fibers. In a final study, molecular beacons (MBs) were immobilized onto the ends of single, sol-gel encapsulated vertically-alligned carbon nanofibers (VACNFs) attached to a silicon electrode. MB fluorescence was monitored as a function of the potential applied to the VACNF in a three-electrode electrochemical cell. Application of positive potentials attracts the negatively charged backbone of the MB, causing hybridization of the stem and a reduction in beacon fluorescence. Negative potentials cause dehybridization of the stem, and an increase in MB fluorescence. This study presents the first measurement of potential-dependent dehybridization/rehybridization of MBs attached directly to the end of a single VACNF. These studies will help to characterize the mechanism by which future lab-on-a-chip devices will detect harmful bio-organisms.

This thesis will present the synthesis, characterization and magnetic measurements of lanthanide complexes with varying nuclearities (Ln, Ln2, Ln3 and Ln4). EuIII, GdIII, TbIII, DyIII, HoIII and YbIII have been selected as the metal centers. Eight polydentate Schiff-base ligands have been synthesized with N- and mostly O-based coordination environments which chelate 7-, 8- or 9-coordinate lanthanide ions. The molecular structures were characterized by single crystal X-ray crystallography and the magnetic properties were measured using a SQUID magnetometer. Each chapter consists of crystal structures and magnetic measurements for complexes with the same nuclearity. There are eight DyIII SMMs in this thesis which are discrete molecules that act as magnets below a certain temperature called their blocking temperature. This phenomenon results from an appreciable spin ground state (S) as well as negative uni-axial anisotropy (D), both present in lanthanide ions owing to their f electron shell, generating an effective energy barrier for the reversal of the magnetization (Ueff). The ab initio calculations are also included for the SMMs with high anisotropic energy barriers to understand the mechanisms of slow magnetic relaxation in these systems.

Several key flexure sites exist in the muscle crossbridge including the actomyosin binding site which play important roles in the actomyosin crossbridge cycle. To distinguish between these sources of flexibility, a new single molecule assay was developed to observe the swiveling of rod about a single myosin. Myosins attached through a single crossbridge displayed mostly similar torsional characteristics compared to myosins attached through two crossbridges, which indicates that most of the torsional flexibility resides in the myosin subfragment-2, and thus the hinge between subfragment-2 and light meromyosin should contribute the most to this flexibility. The comparison of torsional characteristics in the absence and presence of ADP demonstrated a small but significant increase in twist rates for the double-headed myosins but no increase for single-headed myosins, which indicates that the ADP-induced increase in flexibility arises due to changes in the myosin head and verifies that most flexibility resides in myosin subfragment-2.

In this work a system-level approach was taken to the single-molecule fluorescence microscopy of living cells. This primarily involved the unification of relevant information within appropriately structured artefacts that were used to inform and enhance experimentation. Initially the diversity of emerging single-molecule techniques was reviewed and presented with a novel article structure to suit the purpose of designing an experiment (Harriman and Leake 2011). Techniques were grouped by the type of information they could access, rather than the standard organisation centred on the techniques themselves. A bespoke microscope was conceived and built with reference to knowledge and tools from the fields of Architecture and Systems-Engineering. The microscope layout would enable multiple experiment types through independent control of multiple illumination beams. A technique was developed enabling the prescription of evanescent field penetration depth for each incident beam. The various empirical and theoretical results that are used to understand and modify a microscopy experiment were integrated into an internally consistent simulation model (Harriman and Leake. 2013). This was used to inform the selection of experimental components and parameters and ultimately acquire higher data quality as measured by functions such as signal-to-noise ratio (SNR). The combined experimental system of microscope and simulation model was applied in two live-cell investigations. In Escherichia coli, the spatial distribution of membrane bound proteins was investigated and a novel technique was applied to the analysis of colocalisation. Results indicate that NADH dehydrogenase and ATP synthase follow uncorrelated trajectories. This supports the hypothesis of spatial decoupling of molecules that energise the membrane and molecules that use membrane energy. In human carcinoma cells, the mechanism of ligand-receptor binding was investigated. Data was collected prior to and periodically after the addition of ligands, and fluorescence images were acquired of both ligands and receptors. Analyses based on single particle tracking are currently being carried out by a collaborator to extract information on stoichiometry and dynamics at the single-molecule level.