One of the largest problems in current medicine is the shortage of organs for transplant due to technological limitations in the storage of organs for any length of time. A possible solution to this problem would involve cryopreservation. However, current cryopreservatives such as sucrose or DMSO have concerning cytotoxic issues that limit their possible applications. A major cause of cryoinjury is the uncontrolled recrystallization of inter and intra-cellular ice crystals that occurs during the thawing process leading to mechanical damage and dehydration. The Ben lab has thus been interested in the design of compounds that are capable of inhibiting this process but do not possess other undesirable properties found in the native compounds. These synthetic analogues have been shown to increase cellular viability post-thaw. A series of mixed α/β glycopeptides are prepared and analyzed for antifreeze properties. The results of this study imply that it is not the gross conformation of the glycopeptide that is responsible for activity, but rather that intramolecular relationships may be responsible for disrupting the reorganization of ice. A technique was devised for the incorporation of triazoles into the analogues to investigate the importance of the linker and to greatly simplify the synthesis of a library of glycoconjugates. It was found that the IRI activity of glycopeptides is very sensitive to the distance between carbohydrate and peptide backbone. The electron density at the anomeric oxygen is an important parameter with respect to intramolecular networks. A series of substituted galactosides is presented that modify the electronics of the anomeric oxygen. The results demonstrate that decreasing electron density at this position appears to improve IRI activity in a predictable manner. To better understand the remarkable IRI activity of a key analogue, it was systematically truncated. This study led to the serendipitous discovery of a series of very highly IRI active analogues that do not contain a peptide backbone. These compounds represent the first non-glycopeptides that can show very significant IRI activity even at very low concentrations. The final portion of the thesis reports the efforts towards the preparation of a carbasugar analogue of AFGP-8.

The work presented here has a multidisciplinary character, having as a common factor the characterization of self-assembled nanostructures through force spectroscopy. Exploring AFM as a tool for characterizing self-assembly and interaction forces in soft matter nanostructures, three different Bio and nonbiological systems where investigated, all of them share the common characteristic of being soft matter molecular structures at the nanoscale. The studied systems in question are: a) Polyelectrolyte – lipid nanocomposites. Single polyelectrolyte adsorption-desorption from supported lipid bilayers, b) Polyelectrolyte brushes and c) Virus-Like particles (VLPs). The scientific interest and industrial applications for each of these different nanostructures is broad, and their potential uses in the near future ranges from smart nanocontainers for drug and gene delivery, surface platforms for molecular recognition to the development of new nanodevices with ultrasensitive external stimuli responsiveness. These nano-structures are constructed following assembly of smaller subunits and belong to representative examples of soft matter in modern nanotechnology. The stability, behavior, properties and long term durability of these self-organized structures depends strongly on the environmental conditions to which they are exposed since their building mechanism is a balance between attractive noncovalent interactions and momentum transmitted collisions due Brownian motion of the solvent molecules. For example a set of long chain molecules firmly attached to one end to a surface will alter their conformation as the space between them is reduced or the environmental conditions are modified (i.e. ionic strength, pH or temperature). For a highly packed condition, this fuzzy surface known as a polyelectrolyte brush will then behave as a responsive material with tunable responsiveness. Thus the objective in the present case was to investigate the change in morphology and the mechanical response of a polyelectrolyte brush to external forces by application of AFM nanoindentations under different ionic strength conditions. The degree of penetration of the AFM tip through the brush will provide insights into the forces exerted by the brush against the tip. Compressions on the brush should aid to characterize its changes in compressibility for different salt concentrations. For the second chosen system, the interaction between two assembled interfaces was investigated at the single molecular level. A multilayered film formed by the consecutive assembly of oppositely charged polyelectrolytes and subsequently coated with a lipid membrane represents a fascinating soft composite material resembling more than a few structural components emerging in living organisms. The fluid bilayer, thus provide a biocompatible interface where additional functionalities can further be integrated (fusion peptides for instance). The smooth polymer cushion confers not only structural flexibility but also adaptability of the chosen substrate properties to be coated. This type of interface could be useful in the development of novel molecular biosensors with single molecule recognition capacities or in the fabrication of assays against pathogenic agents. The aim of this project was to study the molecular binding mechanism between the last polyelectrolyte layer and the lipid head group of the lower lipid leaflet. Understanding this adsorption mechanism between both interfaces, should likewise contribute to improve the fabrication of lipid coated polymeric nano/micro capsules with targeting properties. For example this could be critical in the field of nonviral gene therapy, where the improvement in the design of condensates of nucleic acids and other polymers with lipids (lipoplexes) are of main interest for its posterior use as delivery vectors. Finally, viral capsids were investigated. These naturally occurring assembled nanocontainers within living organisms stand for a remarkable example of nature’s morphological designs. These structures self-assemble from a small number of different proteins occurring in identical copies. The capsid as a self-assembled structure carries multiple functions: compaction of the genome, protection against external chemical threats, target recognition, structural support and finally facilitating the release of the genome into the host cell. It is highly interesting how these different functions are organized within the capsid which consists, for example, in the case of the norovirus of 180 identical copies of one single protein. Therefore, the mechanical stability and elastic properties of virus-like particles of Rubella and Norovirus were investigated by external application of loading forces with an AFM tip. The measurements were performed under conditions relevant for the virus infection mechanism. The applied compressions on these protein shells at pH values mimicking the virus life cycle will aid to learn about possible internal transitions among proteins which may be important for switching between the various functions of the capsid. The choice of two unrelated viral systems with different entry pathways into the cell and with different morphological architectures is expected to reveal crucial information about the stability and mechanical resistance to deformation of these empty membrane-coated and bare viral capsids. This last might provide clues on the stage of particle disassembly and cargo release during the final step of the infection process.

Gene regulation mediated by transcription factors (TFs) is essential for all organisms. The functionality of TFs can largely be described by the fraction of time they occupy their regulatory binding sites on the chromosome. DNA-binding proteins have been shown to find their targets through facilitated diffusion in vitro. In its simplest form this means that the protein combines a random 3D search in the cytoplasm with 1D sliding along DNA. This has been proposed to speed up target location. It is difficult to mimic the in vivo conditions for gene regulation in biochemistry experiments; i.e. the ionic strength, chromosomal structure, and the presence of other DNA-binding macromolecules.    In this thesis single molecule imaging assays for live cell measurements were developed to study the kinetics of the Escherichia coli transcription factor LacI. The low copy number LacI, in fusion with a fluorescent protein (Venus) is detected as a localized near-diffraction limited spot when being DNA-bound for longer than the exposure time. An allosteric inducer is used to control binding and release. Using this method we can measure the time it takes for LacI to bind to different operator sequences. We then extend the assay and show that LacI slides in to and out from the operator site, and that it is obstructed by another DNA-binding protein positioned next to its target. We present a new model where LacI redundantly passes over the operator many times before binding.    By combining experiments with molecular dynamics simulations we can characterize the details of non-specific DNA-binding. In particular, we validate long-standing assumptions that the non-specific association is diffusion-controlled. In addition it is seen that the non-specifically bound protein diffuses along DNA in a helical path.    Using microfluidics we design a chase assay to measure in vivo dissociation rates for the LacI-Venus dimer. Based on the comparison of these rates with association rates and equilibrium binding data we suggest that there might be a short time following TF dissociation when transcription initiation is silenced. This implies that the fraction of time the operator is occupied is not enough to describe the regulatory range of the promoter.

Common to molecular electronics studies, nanoscale break junctions created through electromigration also naturally produce electroluminescent arrays of individual gold nanoclusters spanning the electrodes. Due to inelastic electron tunneling into cluster electronic energy levels, these several-atom nanoclusters (Au~18-22) exhibit bright, field-dependent, antibunched emission in the near infrared (650800 nm), acting as room-temperature electrically driven single-photon sources. AC electrical excitation with time-stamping of photon arrival times enables fast and local tracking of electrode-nanocluster coupling dynamics demonstrating that charge injection to the clusters is directly modulated by dynamic coupling to individual electrodes. The electrode-nanocluster coupling rate fluctuates by nearly an order of magnitude and, due to the asymmetry of the electromigration process, exhibits preferential charge injection from the anode. Directly reporting on (and often facilitating) nanoscale charge transport, time-tagged single-molecule electroluminescence reveals a significant mechanism for nanoscale charge transport in nanoscale gold break junctions, and offers direct readout of the electrode-molecule interactions that can be correlated with current flow. Single-molecule electroluminescence techniques for characterization of electrode heterogeneity and dynamics as well as implications for future research are discussed.

For polymers near the glass transition, the dynamics in some regions can be orders of magnitude different compared with the dynamics in other regions only a few nanometers away, so called spatial heterogeneity [1]. In this thesis, single molecule fluorescence microscopy as a powerful tool, was applied to study the spatially heterogeneous dynamics, both orientational and translational, within the polymer matrix near the glass transition temperature. With our total internal reflection fluorescence microscopy (TIRFM) methods, many individual fluorescent dye molecules embedded in the poly (isopropyl acrylate) (PIPA) thin films can be simultaneously excited. Their emission patterns are analyzed using our orientation determination methods [2] to give the true 3D orientational trajectories of the individual molecules. At Tg < T < 1.2 Tg, single molecule tracking was used to study the dye molecules translational diffusion. Results show that, below 1.1 Tg, the probe molecules are in the confined flow region [3]; at T > 1.1 Tg, the diffusion follows normal diffusion model; at T = 1.2 Tg, although the statistical results shows that normal random walk behavior is followed, the individual molecules still show different diffusion behaviors, clear evidence of the spatial heterogeneity that still exists at this temperature. The second part of this thesis is a development of the 3-detector method to determine the 3D orientation of single molecules [4]. This method is based on the work proposed by Fourkas [4] in 2001. Results utilizing this experimental setup are compared with our emission pattern fitting methods. The results show that, with a little bit higher error range (10º in θ, 20º in φ), the 3-detector method can give agreeable orientation fittings, further more, with higher time resolution of < 10 ms. This 3-detector method is useful and can be applied to study the fast orientation dynamics in different systems.

Abstract This study aims to measure the flow field distribution in a microchannel with different heights adjusted. Two different materials, PDMS and Coverglass, were used to observe the flow velocity distribution change resulting from the difference in Zeta potential. The velocity distribution data were also obtained. In the experiment, 1¡Ñ TBE buffer solution with viscosity of 1 cp was used with the electric field intensity controlled under 5, 7.5 and 10 kV/m, respectively. Micrometer resolution Particle Image Velocimetry (£gPIV) was used to measure partial velocity distribution in order to explore the hydrodynamic stretch effect on DNA molecules when the microchannel, where the solution was placed, was adjusted to different heights. This study also statistically analyzed the stretch length distribution of DNA molecules in the microchannel and calculated the time of DNA molecule deformation and stress relaxation time in order to understand the stretch condition under different heights as well as the stretch and deformation of DNA molecules in microchannels.

In this study, the structures of two ultrathin Pd nanowires were predicted by the simulated annealing basin-hopping method (SABH) with the tight-binding potential. The thermal stability of the Pd wires and adsorption, dissociation and diffusion behaviors were further examined by the density functional theory (DFT) calculation and DFT molecular dynamics (DFT-MD) simulation. In terms of thermal stability, these two Pd nanowires are still very stable at temperatures as high as 400 K. The configurations and adsorption energy have been calculated for H atom and H2 molecular adsorption on Pd nanowires. The minimum energy pathways and transition states of H2 molecular dissociation and H atom diffusion process on Pd nanowires were studied by the nudged elastic band (NEB) method. For the dissociation of hydrogen molecules, results show the dissociation is almost barrierless so the dissociation is easy to occur at very low temperatures, and their catalytic reactivity is very similar to the Pd bulk material. The thermal stability of the H atom within these Pd nanowires were also investigated by DFT-MD, with results showing that the H atom can only stay within Pd nanowires at temperatures much lower than room temperature (298 K). This phenomenon is very different from that of H atoms within Pd bulk material or other reported nanomaterials, leading to hydrogen embrittlement. Our results reveal that these two ultrathin Pd nanowires not only possess the same excellent catalytic activity for hydrogen molecules as the bulk Pd materials or other Pd nanomaterials do, but also avoid the hydrogen embrittlement occur.

In this study, molecular dynamics (MD) simulations was employed to investigate (5,5), (10,10) single-walled nanocoils and (5,5)@(10,10) double-walled carbon nanocoils. The study can be arranged into two parts¡G In part I: Investigate the mechanical properties of (5,5), (10,10) single-walled nanocoils and (5,5)@(10,10) double-walled carbon nanocoils. The second reactive empirical bond order (REBO) potential was employed to model the interaction between carbon atoms. The contours of atomic slip vector and sequential slip vector were used to investigate the structural variations at different strains during the tension process. The yielding stress, maximum tensile strength, and Young¡¦s modulus were determined from the tensile stress-strain profiles. The results show that the nanocoils have superelastic characteristics to the carbon nanotube in the same tube diameter. In part II: Investigate the diffusion behavior of water molecules confined inside narrow (5,5) and (10,10) carbon nanocoils under different tensile strains. The condensed-phase optimized molecular potentials for atomistic simulation studies (COMPASS) potential was employed to model the interaction between carbon-carbon atoms¡Acarbon atoms-water molecules and water-water molecules. To analysis the kinetic behavior of water molecules in two carbon nanocoils, the diffusion coefficients, square displacement (SD) and mean square displacement (MSD) of water molecules were calculated. The results show that diffusion coefficient of water will increase with the strains of carbon nanocoils. However, the diffusion coefficient has a significant decrease in a large strain due to the structural deformation of carbon nanocoils. The diffusion behaviors of water inside the (5,5) and (10,10) carbon nanotubes were also investigated to compare the results in (5,5) and (10,10) carbon nanotubes. Our results indicate that two carbon nanocoils have a lower diffusion coefficient of water than that of carbon nanotubes because the geometry of carbon nanocoil is easily to block up the diffusion of water molecules.

This dissertation focuses on three separate studies. First, magnetization of the Mn12- acetate was studied by low temperature hysteresis loops and DC magnetization data on magnetically aligned Mn12-acetate micro-crystals. Secondly, Mn12-acetate thin films were fabricated and characterized by AFM and STM. Finally, magnetization of the film material was also studied. Enhanced alignment of Mn12-acetate micro-crystals as compared to prior studies was verified by observation of several sharp steps in low temperature hysteresis loops. It was found that ~ 0.5 T is sufficient to orient the micro-crystals in an organic solvent to a degree comparable to a single crystal. The degree of the alignment was controlled by varying the magnetic field at room temperature and during the cooling process. Subsequently, low temperature hysteresis loops and DC magnetizations were measured for each prepared orientation state of a sample. The high temperature magnetic anisotropy responsible for the alignment could not be measured, possibly due to its small magnitude. Mn12-acetate was deposited onto Si/SiO2 by a solution evaporation method. Atomic force microscopy studies revealed that 2 nm thick films of molecular level smoothness were formed. Mn12-acetate was also deposited onto a Highly Ordered Pyrolytic Graphite (HOPG) surface for scanning tunneling microscopy (STM) studies. A self-assembled triangular lattice was observed in the Mn12-acetate thin films by STM at room temperature under ambient conditions. These STM images show typical center to center intermolecular separations of about 6.3 nm and height corrugation of less than 0.5 nm. Magnetization measurements were not successful in Mn12-acetate thin films due to the small amount of material in the film and the large background signal from the substrate. Therefore, a sample for the magnetization measurements, called “film material”, was made by evaporating a dilute solution of Mn12-acetate powder in acetonitrile. Significant changes in magnetic properties of the film material were observed from magnetization measurements. The blocking temperature of the film material was found to increase to TB > 10 K at low magnetic fields.

The cyanide ligand has frequently been used to prepare clusters with novel magnetic properties due to its ability to provide an efficient pathway for superexchange between metal centers that are bound in an end-to-end fashion. One of the common synthetic approaches in this chemistry is to design suitable cyanide containing precursors and then to react such building blocks with metal complexes consisting of accessible sites. The triphos ligand (triphos: 1,1,1-tris(diphenylphosphinomethyl)ethane) has been employed in this vein to prepare metal complexes, one of which is a five coordinate paramagnetic complex (S = 1/2) with a square pyramidal metal center, [CoII(triphos)(CN)2]. A family of molecular squares, [{MIICl2}2{CoII(triphos)(CN)2}2] (M= Mn (2), Fe (3), Co (4), Ni (5), and Zn (6)), has been synthesized by the reaction of CoII(triphos)(CN)2 and MCl2 (M= Mn, Co, Ni, Zn) or Fe4Cl8(THF)6 in CH2Cl2/EtOH mixture. A series of cyanide-bridged trinuclear complexes, {[Co(triphos)(CN)2]2 [M(MeOH)4]}(ClO4)2 ( M = Mn (7), Fe (8), Co (9), and Ni (10)) and tetranuclear complexes, {[Co(triphos)(CN)2]2[M(MeOH)4]2}(ClO4)4 ([Co2M2] M = Mn (11) and Ni (12)) have been synthesized in a similar fashion by the reaction of CoII(triphos)(CN)2 and M(ClO4)2.6H2O (M= Mn, Fe, Co, Ni) in methanol. The trinuclear compounds (7-9), and tetranuclear complexes (2-6, 11, 12), are characterized by antiferromagnetic coupling between metal centers while magnetic behavior of 10 indicates the presence of ferromagnetic interactions between the paramagnetic metal centers. Interactions between magnetic orbitals of Co(II) and M(II) ions were also investigated by means of the density functional theoretical (DFT) calculations. Another triphos containing building block, [(triphos)Re(CN)3] anion (13), has been employed to prepare derivatives of a cubic SMM cluster with four octahedral Re(II) ions and four tetrahedral Mn(II) sites bridging through cyanide ligand. The reactions of Re(II) precursor with MnI2 and solvated Mn(II) ions resulting in derivatives of Re4Mn4 cube with different ligands attached to the Mn center other than the chloride atom were reported. Our efforts on linking these cubes using organo cyanide ligands such as dicyanamide (dca) and 7,7,8,8-tetracyanoquinodimethane (TCNQ) to form extended networks were also discussed.