Recent technological advances such as the transition from non-renewable to renewable energy have been intimately related to the development of new nanostructured materials. A rational thinking is required for the development of nanomaterials with functional properties by targeting the combination of two or more nanocomponents with different properties, and preparation methodologies ensuring the utilisation of cheaper and abundant materials such as non-precious metals. Therefore, the main motivation of this work is to expand the frontiers of knowledge for the preparation of functional nanomaterials by designing hybrid carbon nanostructures suitable for energy storage applications containing a range of electrochemically active nanocomponents including molecules, nanoparticles and metal coordination polymers. The first chapter describes a general overview of the current approaches within the energy area to prepare uncoupled carbon nanostructures as well as the strategies to combine them with several active components (i.e. molecular metal clusters, nanoparticles and metal coordination polymers). Relevant concepts for this thesis such as electrochemical storage mechanisms, differences between hybrid and composite nanomaterials, synergetic effects and the distinction between ex situ and in situ synthetic approaches are discussed in the introductory chapter. For the sake of clarity, only the most relevant examples of hybrid carbon nanostructures from the literature will be highlighted and discussed. Before describing the hybridisation of carbon with molecules, nanoparticles and metal-coordination polymers, different carbon nanostructures will be analysed on their own due to their outstanding electrochemical properties. After the introductory chapter (Chapter 1), the thesis is followed by two parts: Part A and B. Part A, which is divided in two chapters (Chapter 2 and 3), gathers only carbon nanostructure investigations. In Chapter 2, a facile and solvent-free method is proposed for the development of few-layer graphene nanostructure from carbon tubular nanofibers. In Chapter 3, the synthesis of hollow carbon cages on the surface of carbon nanostructures is thoroughly investigated to elucidate their novel mechanism of formation. The preparation and electrochemical characterization of metal-carbon nanostructures by combining carbon nanostructure with a molecular metal cluster, metal oxide nanoparticles and metal coordination polymers are discussed in Part B. In Chapter 4 the extreme confinement inside hollow tubular carbon nanotubes is investigated to overcome the intrinsic low stability of molecular Mn12 cluster during the electrochemical process. In Chapter 5, the synthesis of metal oxide nanoparticles is carried out in the presence of hollow tubular carbon nanofibers (what we called “in situ synthesis”) where special attention is paid to the carbon surface functionalization. Only the metal oxide-carbon hybrids of interest produced in previous chapter are extensively characterized by electrochemical means to elucidate the effect of confinement with respect to their electrochemical stability. In Chapter 6, a correlation between the structure and chemical composition of a coordinated metal polymer and its electrochemical performance is established in order to gain a better understanding of the alkali intercalation/deintercalation process. One of the key findings in this thesis has been the encapsulation of electrochemically active species, shows promising results not only due to the electron transfer between the guest specie and the host carbon nanostructure, but also to the improvement in the stability during electrochemical cycling. In addition, it has been observed that the electrochemical performance of metal-carbon nanohybrids depends dramatically on the synthetic process that determines the interaction between the nanocomponents and, therefore, the synergetic effect. To sum up, the work developed in this thesis contributes to the area of hybrid metal-carbon nanostructures for energy-storage applications, including new synthetic protocols and strategies, novel hybrid materials with confined electrochemical components, advanced understanding on the electrochemical-structure relationships and important concepts related to durability/recyclability.

No description available.

Ionic Liquids (ILs) have drawn a great deal of attention as carbon capture agents, and in order to understand them studies must be performed probing the CO2–IL interaction. Many studies have focused upon measuring the solubility of CO2 within ILs, with fewer studies directly probing the CO2 adsorption environments within the IL. Understanding of the adsorption environments is of fundamental for the use of ILs industrially, if they are to be successfully applied within carbon capture and storage devices. Temperature programmed desorption (TPD) has been used to study the CO2–IL interaction within two ionic liquids; 1-octyl-3-methylimidazolium tetrafluoroborate ([C8C1Im][BF4]) and 1-octyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide ([C8C1Im][Tf2N]). Experiments were performed utilising low temperature line of sight mass spectrometry (LTLOS MS), ensuring that only species desorbing from the surface are observed. Surfaces were formed through a coadsorption method, where IL was deposited by chemical vapour deposition at a rate of ≈ 1 layer per minute while CO2 was simultaneously leaked into the chamber at pressures between 2×10−8 and 2×10−6 mbar. This study finds that CO2 does not form a monolayer on a gold surface at ≈ 90 K, with no CO2 TPD peak seen for those experiments, showing Edes,CO2 (the activation energy of desorption of CO2) < 24.5 kJ mol−1. When IL and CO2 are coadsorbed the IL is seen to stabilise the CO2, such that a TPD peak for CO2 is seen, with the amount of stabilisation depending upon the IL used. Comparison of experimental TPD curves with calculated TPD profiles, using CO2 states with a range of binding energies, shows that there are multiple CO2 environments within the ILs. The use of TPD allowed the relative populations of these CO2 adsorption environments to be measured, which is not possible using solubility measurements and Henry’s constants, providing insights into the IL–CO2 interaction. CO2 was observed to desorb from sites within the bulk IL, which have activation energies of desorption in the range 24.5 to 43 kJ mol−1. The CO2 was seen to be stabilised most within the [C8C1Im][BF4], giving a stabilisation in Edes of up to 18.5 kJ mol−1. The [C8C1Im][Tf2N] was typically seen to stabilise twice as much CO2 as [C8C1Im][BF4], which is consistent with the experimental Henry’s constants. Further to this a new experimental technique for determining surface structure, utilising high energy X-rays in the total reflection regime, to generate an X-ray standing wave (XSW) and detect the resulting photoelectrons from layered surfaces has been demonstrated. The variable period X-ray standing wave (VPXSW) technique relies on the fact that at low incident angles (typically < 2°) total external reflection of X-rays is observed. The incident and reflected X-rays interact to generate an XSW along the surface normal, with nodes and antinodes at different heights, z, above a reflector for different angles of incidence. By scanning the incident angle of the X-ray from 0° upwards the periodicity of the XSW decreases, resulting in the nodes and antinodes sweeping towards the surface. As this sweeping occurs the nodes and antinodes pass through material adsorbed on the surface of the reflector, and the photoelectron signal fluctuates. Comparing the fluctuations in the measured photoelectron signal to a theoretical model allows surface layering to be detected at larger depths and with a higher information content than with other surface science techniques. This allows distance information, relative to the interfaces between different materials, to be obtained for different chemical species. Data is presented from a surface consisting of the ionic liquid [C8C1Im][BF4] on a Si(001) reflector, held at ≈ 90 K, with a thick IL layer adsorbed on the reflector and a CHCl3 marker layer on top of the IL. Results from the frozen surface indicate a 12 Å layer of CHCl3 and background water had been dosed on top of a 211 Å IL layer. These values agree well with what was expected for this model IL system with a thin marker layer, designed to test the technique. It is therefore shown that VPXSW with photoelectron emission can be used to successfully characterise thin films with thicknesses between 15 Å and ≈ 300 Å with chemical shift specificity, something not possible with current experimental techniques.

Various high molecular weight dialkylnitrosamines were prepared including, for the first time, methyl-n-octadecylnitrosamine and di-n-dodecylnitrosamine. The infrared, ultraviolet and mass spectra of a selection of these compounds were recorded and studied. Gel permeation chromatography was used for the isolation of individual nitrosamines in standard nitrosamine mixtures, while ion-exchange chromatography effected complete clean-up of amine-contaminated nitrosamine solutions. Thin-layer and gas-liquid chromatographic methods were developed for the detection, separation and analysis of nanogram quantities of these lipophilic nitrosamines. In addition the above chromatographic systems were used for the analysis of distillates of spiked wheat flour samples. High recoveries of dicyclopentylnitrosamine, di-n-heptylnitrosamine and di-n-octylnitrosamine, from the spiked wheat flour samples, were achieved using a specially developed freeze-drying/vacuum distillation technique, the distillates obtained being relatively free from major contaminants. / KMBT_363 / Adobe Acrobat 9.54 Paper Capture Plug-in

[No abstract available] / Science, Faculty of / Chemistry, Department of / Graduate

The mechanisms of permanganate oxidation of two very different substrates have been examined. Firstly, in an attempt to elucidate the mechanism of permanganate oxidation of alcohols, a number of meta and para substituted 2,2,2-trifluoro-1-phenylethanols have been prepared and the kinetics of permanganate oxidation studied over a pH range of 1 to 13.3. Secondly, the reaction between permanganate and cyanide ion has been examined over the pH range 3 to 14.6. The reaction between permanganate and 2,2,2-trifluoro-1-phenylethanol in aqueous alkaline solution was shown to give manganate and trifluoroacetophenone (hydrated form) in almost quantitative yield under kinetic conditions and is therefore represented by the equation, 2MnO⁻₄ + C₆H₅CHOHCF₃ + 20H⁻→ 2Mn0⁼₄ + C₆H₅COCF₃ + 2H₂0 The trifluorophenylethanols are more acidic than the normal hydrogen containing secondary alcohols and their pKas as determined spectrophotometrically showed the following order of decreasing acidity for substitution into the phenyl ring m-NO₂> m-Br > H > p-CH₃ >p-MeO. The rate of reduction of permanganate was followed iodometrically and the rate expression which fits the kinetic data for the alkaline catalyzed oxidation is the following: [formula omitted]. The rate of oxidation of the p-CH₃, m-Br and unsubstituted trifluorophenylethanols-l-d by permanganate was found in each case to be 16 times slower than the rate of oxidation of the corresponding protio compounds in alkaline solution. This latter result, the kinetics, i.e., the close similarity between the ionization type rate curves and the calculated ionization curves for the alcohols, the thermodynamics and positive salt effect indicate a mechanism which involves a primary ionization step to give the anion of the alcohol and then a rate controlling bimolecular step where permanganate abstracts a hydride ion from the anion. This mechanism is somewhat invalidated in view of the observation that the rate constants obtained for oxidation of the various substituted alcohols in alkaline solution are relatively insensitive to nuclear substitution. A plot of Hammett σ values versus the log of the rate constants appears to give a smooth curve. A number of mechanisms involving termolecular steps are considered to account for this latter observation and the large deuterium isotope effect is discussed in the light of present theories. Kinetic and oxygen¹⁸ tracer experiments have been performed in an attempt to elucidate the mechanism(s) of permanganate oxidation of cyanide. A mechanistic interpretation is attempted using the data obtained in basic solution above pH 12 to 14.6 where the oxidation is represented by the equation, 2MnO₄⁻ + CN⁻ + 20H⁻→ 2MnO₄⁼ + NCO⁻ + H₂0 From pH 12 to 6 the reaction was found to be complex and unstoichiometric yielding cyanate, carbon dioxide, cyanide ion and finally cyanogen at pH 9 to 6. The rate of reduction of permanganate as followed iodometrically and spectrophotometrically, is found to be markedly dependent on the pH of the medium and reactant concentration. The observation that the rate is negligible in acid solution but rapid in basic media suggests cyanide ion and not hydrocyanic acid molecule to be the primary reactive species. At pH greater than 12 two parallel processes are indicated which have been designated as Reaction A and Reaction B. Reaction A appears at low reactant concentrations < 0.0004 M cyanide and higher hydroxyl ion concentrations > pH 13. The rate of Reaction A is represented by the kinetic expression [formula omitted] where k₂ is independent of hydroxyl ion concentration and is insensitive to the effect of manganate and barium ions. A positive salt effect is observed and labeling experiments using permanganate enriched in oxygen¹⁸ showed that the oxygen introduced into the product cyanate comes mainly from the oxidant (70%-80% oxygen transferred). These observations suggest a mechanism which involves a rate determining bimolecular reaction between permanganate and cyanide ions to yield a Mn V species and cyanate ion. The possibility that a second parallel process Reaction B was occurring was indicated by the changing kinetics at higher reactant concentrations and lower basicities, by the non-linear Arrhenius plots and the observation that only 15%-25% oxygen¹⁸ transfer from permanganate to substrate had occurred at pH 13. The rate of this latter process can be tentatively represented by the kinetic expression [formula omitted]. A mode of oxidation is suggested which appears to fit these results. Permanganate, cyanide ion and a hydrocyanic acid molecule are reacted to produce a reactive species which undergoes further oxidation by permanganate to yield cyanogen. Cyanogen hydrolysis results in cyanate where oxygen is derived from the solvent. / Science, Faculty of / Chemistry, Department of / Graduate

This work concerns the description of eigenvalue independent: partitioning theory, and its application to quantum mechanical calculations of interest in chemistry. The basic theory for an m-fold partitioning of a hermitian matrix H, (2 < m < n, the dimension of the matrix), is developed in detail, with particular emphasis on the 2x2 partitioning, which is the most' useful. It consists of the partitioning of the basis space into two subspaces — an n[sub A]-dimensional subspace (n[sub A] > 1), and the complementary n-n[sub A] = n[sub B]-dimensional subspace. Various n[sub A]-(or n[sub B]-) dimensional effective operators, and projections onto n[sub A]- (or n[sub B] dimensional eigenspaces of H, are defined in terms of a mapping, f, relating the parts of eigenvectors lying im each of the partitioned subspaces. This mapping is shown to be determined by a simple nonlinear operator equation, which can be solved by iterative methods exactly, or by using a pertur-bation expansion. Properties of approximate solutions, and various alternative formulas for effective operators, are examined. The theory is developed for use with both orthonormal and non-orthonormal bases. Being a generalization of well known one-dimensional partitioning formalisms, this eigenvalue independent partitioning theory has a number of important areas of application. New and efficient methods are developed for the simultaneous determination of several eigenvalues and eigenvectors of a large hermitian matrix, which are based on the construction and diagonalization of an appropriate effective operator. Perturbation formulas are developed both for effective operators defined in terms of f, and for projections onto whole eigen-spaces of H. The usefulness of these formulas, especially when the zero order states of interest are degenerate, is illustrated by a number of examples, including a formal uncoupling of the four component Dirac hamiltonian to obtain a two component hamiltonian for electrons only, the construction of an effective nuclear spim hamiltonian in esr theory, and the derivation of perturbation series for the one-particle density matrix in molecular orbital theory (in both Huckel-type and closed shell self-consistent field contexts). A procedure is developed for the direct minimization of the total electronic energy in closed shell self-consistent field theory in terms of the elements of f, which are unconstrained and contain no redundancies. This formalism is extended straightforwardly to the general multi-shell single determinant case. The resulting formulas, along with refinements of the basic conjugate gradient minimization algorithm* which involve the use of scaled variables and frequent basis modification, lead to efficient, rapidly convergent methods for the determination of stationary values of the electronic energy* This is illustrated by some numerical calculations in the closed shell and unrestricted Hartree-Fock cases. / Science, Faculty of / Chemistry, Department of / Graduate

The highly interdisciplinary study of molecular magnetism spans a wide array of topics, ranging from spintronics and quantum computing to enzyme function and MRI contrast agents. At the core of all these fields is the study of materials whose properties can be controlled through the rational design of molecules. The chemical tailoring of molecular magnetic properties can only be achieved by understanding the relationship between the physical and electronic structures. In this dissertation, the interplay between structure and physical properties is probed using a variety of magnetic resonance techniques. In Chapter 1, we give a succinct overview of the various methods utilized in this dissertation. We first describe the experimental methods including electron paramagnetic resonance (EPR), 57Fe nuclear gamma resonance (Mössbauer) spectroscopy, electron double resonance detected nuclear magnetic resonance (ELDOR-NMR), and Fourier transform far-infrared (FTIR) spectroscopy. In addition to the introduction of each technique, we describe how the data is analyzed and what quantities may be extracted from each method. We also introduce the quantum chemical methods used to rationalize the spectroscopic parameters. In Chapter 2, we investigate a recently reported Fe-V triply bonded species, [V(iPrNPPh2)3FeI], using high frequency EPR (HFEPR), field- and temperature-dependent 57Fe Mössbauer spectroscopy, and high-field ELDOR-NMR. From the use of this suite of physical methods, we probe the electron spin distribution as well as the effects of spin-orbit coupling on the electronic structure. This is accomplished by measuring the effective g – factors as well as the Fe/V electro – nuclear hyperfine interaction tensors of the spin S = ½ ground state. We have rationalized these tensors in the context of ligand field theory supported by quantum chemical calculations. This combined theoretical and experimental analysis suggests that the S = ½ ground state originates from a single unpaired electron predominately localized on the Fe site. Chapter 3 describes a combined HFEPR and variable-field Mössbauer spectroscopic investigation of a pair of bimetallic compounds with Fe-Fe bonds, [Fe(iPrNPPh2)3FeR] (R = ≡NtBu and PMe3). Both of these compounds have high spin ground states, where R= PMe3 (S = 7/2) and the R= ≡NtBu displays (S = 5/2). The ligand set employed in this work encapsulates each Fe site in a different coordination environment. This results in polarized bonding orbitals which engender each nuclear site with unique hyperfine tensors as revealed by Mössbauer spectroscopy. Absent the metal-metal bond, the tris-amide bound site in both compounds is expected to be Fe(II). To gain insight into the local site electronic structure, we have concurrently studied a compound containing a single Fe(II) in a tris-amide site. Our spectroscopic studies have allowed us to assess the electronic structure via the determination of the zero field splitting parameters and 57Fe electronuclear-hyperfine tensors for the entire series. Through the insight gained in this study, we propose some strategies for the design of polymetallic single molecule magnets where the metal-metal interactions are mediated by the formation of covalent bonds between metal centers. Recently, a great deal of the work in molecular magnetism has moved away from polymetallic compounds and towards molecules containing only a single magnetic ion. A critical challenge in this endeavor is to ensure the preservation of orbital angular momentum in the groundstate. The stabilization of the ground state orbital moment generates the strong magnetic anisotropy which is often required for the design of magnetic materials. The presence of unquenched orbital angular momentum can be identified by significant shifts in the g-value away from the free ion value. In an initial report of a Ni(I) coordination complex, which was found to exhibit field-induced slow magnetic relaxation, no EPR signal was observed. Given the expectation that orbital angular momentum can shift the g-values beyond the range expected for a typical S= ½ system, we have reexamined this compound using multi-frequency EPR and field-dependent FTIR spectroscopy. Through a combined spectroscopic and theoretical effort, we have characterized the effect of first order spin-orbit coupling on the electronic structure. The final report, Chapter 5, examines an exciting new class of photomagnetic materials based on bisdithiazolyl radicals. These materials, and others with magnetic properties that can be modulated via optical excitation, offer enticing opportunities for the development of next generation technologies. The dimorphic system in this study crystallizes in two phases, one composed of diamagnetic dimers and the other of paramagnetic radicals. Here we report on the use of high-field electron paramagnetic resonance spectroscopy to characterize both the thermally- and light-induced transitions in the dimer phase. During the course of this study we show that signals originating from residual radical defects in the dimer phase can be differentiated from those arising from the radical phase. / A Dissertation submitted to the Department of Chemistry and Biochemistry in partial fulfillment of the requirements for the degree of Doctor of Philosophy. / Fall Semester 2018. / October 15, 2018. / Includes bibliographical references. / Stephen Hill, Professor Co-Directing Dissertation; Michael Shatruk, Professor Co-Directing Dissertation; Peng Xiong, University Representative; A. Eugene DePrince, III, Committee Member; Oliver Steinbock, Committee Member.

This dissertation presents structure-specific descriptions of optical properties and electronic energy relaxation dynamics of structure precise monolayer-protected gold clusters (MPCs) and narrow size distributed semiconductor nanocrystals (NCs). Femtosecond pump-probe transient extinction spectroscopy has been conducted on MPCs to determine the size at which the transition from non-metallic to metallic electronic behavior occurs. Excitation-pulse-energy-dependent measurements confirmed Au144(pMBA)60 (1.8 nm) as the smallest MPC to exhibit metallic behavior, with a quantifiable electron-phonon coupling constant of (1.63 ± 0.25) × 1016 W m-3 K-1 after a series of gold monolayer protected clusters (MPCs) whose sizes ranged from 1.5 nm to 2.4 nm were studied. Smaller, non-metallic MPCs exhibited nanocluster-specific transient extinction spectra characteristic of transitions between discrete quantum-confined electronic states. Volume-dependent electronic relaxation dynamics for < 1.8 nm MPCs were attributed to an electron-phonon bottleneck, which arose from a combination of large energy differences between electronic states and phonon frequencies and spatial separation of photo-excited electrons and holes. Then, electronic energy relaxation of Au144(SR)60q ligand-protected nanoclusters, where SR = SC6H13 and q = -1, 0, +1 and +2, was examined using femtosecond time-resolved transient extinction spectroscopy. The observed differential transient spectra contained three distinct components: 1) transient bleaches at 525 nm and 600 nm, 2) broad visible excited-state absorption (ESA), and 3) stimulated emission (SE) at 670 nm. The bleach recovery kinetics depended upon the excitation pulse energy and were thus attributed to electron-phonon coupling typical of metallic nanostructures. The prominent bleach at 525 nm was assigned to a core-localized plasmon resonance (CLPR). ESA decay kinetics were oxidation-state dependent and could be described using a metal-sphere charging model. The dynamics, emission energy, and intensity of the SE peak exhibited dielectric-dependent responses indicative of Superatom charge transfer states. Based on these data, the Au144(SR)60 system is one of the smallest-known nanocluster to exhibit quantifiable electron dynamics and optical properties characteristic of metals. To understand the origin of near infrared (NIR) photoluminescence (PL) of Superatomic nanoclusters, electronic energy relaxation dynamics of Au25(SR)18-1 were studied. The transient spectra were composed of three distinct components: 1) spectrally broad excited-state absorption (ESA); 2) stimulated emission and 3) ground-state bleaching. Strong solvent dielectric dependencies of the component 2 relaxation rates and photoluminescence emission implicated metal-to-ligand charge transfer mechanisms in mediating electronic energy relaxation dynamics of MPCs. A full picture of electronic relaxation pathways in Au25(SR)18 has been proposed. After initial excitation from ligand bands into high-energy excited states, rapid internal conversion is followed by non-radiative relaxation into charge transfer states localized on MPC protecting ligands. NIR photoluminescence is attributed to the radiative transition from charge transfer states to ground states. All these data suggested that protecting ligand structure and the surrounding environment could modify nanoclusters-to-ligand charge transfer in MPCs. Finally, charge carrier relaxation dynamics of electronically excited CdSe and CdSe/CdS core/shell nanocrystals (NCs) were studied using femtosecond time-resolved transient absorption spectroscopy, employing both visible and NIR probe laser pulses. Following 400-nm excitation, the combination of visible and NIR laser probe pulses were used to determine the influence of surface passivation on electronic relaxation dynamics for nanocrystals overcoated with either organic ligands or inorganic semiconductors. In particular, low-energy NIR photons were used to isolate transient absorption signals due to either electron and hole intraband transitions. Four relaxation components were detected for CdSe NCs passivated by organic molecules: 1) picosecond hole relaxation; 2) electron deep trapping; 3) electron surface trapping; and 4) exciton radiative recombination. Based on TA data collected over a broad energy range, electron deep trapping at Se2- sites was suppressed for CdSe NCs passivated by inorganic (CdS) semiconducting materials. By comparing the time-dependent transient absorption data of a series of CdSe/CdS NCs with different shell thicknesses, evidence for the transition from Type-I to quasi Type-II NCs was obtained. These data illustrate the sensitivity of femtosecond time-resolved transient absorption measurements carried out over visible and near infrared probe energies for determining the influence of nanocrystal structure on electronic relaxation dynamics. / A Dissertation submitted to the Department of Chemistry and Biochemistry in partial fulfillment of the requirements for the degree of Doctor of Philosophy. / Spring Semester, 2015. / April 9, 2015. / electron-phonon coupling, nanoclusters, plasmon, quantum dots, ultrafast spectroscopy / Includes bibliographical references. / Kenneth L. Knappenberger, Jr., Professor Directing Dissertation; Peter G. Fajer, University Representative; Hedi Mattoussi, Committee Member; Wei Yang, Committee Member.

Monoclonal antibody (mAb) A20 is the best characterized AAV2 neutralizing mAb [18, 116, 165]. Large quantities of the mAb A20 were obtained from hybridomas cell culture, and A20 Fab fragments were produced and purified by standard methods [289]. Following optimization of the AAV2-A20 Fab ratio, low resolution preliminary images of AAV2-A20 Fab have been obtained. Data from cryo-electron microscopy and X-ray crystallography have been combined to study the interactions of AAV2 with A20. The structure of the AAV2-A20 Fab complex was determined to 28Å resolution using cryo-electron microscopy and image analysis. The known structure of AAV2 [31] and Fab 1CL7 [168] were fitted to the cryo-electron microscope density map. Preliminary results are plausible. Part of the identified A20 footprint is well matched with peptide scanning results (532-541) [116] and mutations at 548, 708 [171]. It is known that A20 is neutralizing, post-attachment, and therefore unlikely to be bound at the primary receptor site. The reconstruction shows mAb A20 binding to the surface off the shoulder of the threefold spike along the twofold axes side, and this region is away from the putative primary receptor binding sites. The reconstruction continues to be improved through addition of EM images, and through improved processing. The crystal structure of heparin-derived hexasaccharides complexed with AAV2 was determined at a resolution of 5.5Å. Here we identify the specific amino acids on the surface of the capsid that facilitate binding to the cell surface receptor heparin sulfate proteoglycan (HSPG). Our data indicate that residues R585 and R588, are primarily responsible for HSPG binding, and therefore for infectivity. They are the minimal necessary and sufficient requirements for HSPG binding. The heparin hexasaccharide also interacts with an additional binding site formed by K-507. No significant conformational change in AAV2 occurred upon heparin oligosaccharide binding, which suggests that heparin primarily serves to juxtapose components of the AAV2 signal transduction pathway. HS might function as an accessory molecule, enhancing the efficiency of a second, internalization receptor. / A Dissertation submitted to the Institute of Molecular Biophysics in partial fulfillment of the requirements for the degree of Doctor of Philosophy. / Spring Semester, 2007. / February 22, 2007. / Adeno-Associated Virus, Receptor, Antibody, X-ray Crystallography, Electron-Micrography, heparin hexsaccharide / Includes bibliographical references. / Michael S. Chapman, Professor Co-Directing Dissertation; Kenneth A. Taylor, Professor Co-Directing Dissertation; Robert H. Reeves, Outside Committee Member; Michael Blaber, Committee Member; Hong Li, Committee Member.