Chemistry & Biochemistry Theses and Dissertations
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Item SCANNING TUNNELING MICROSCOPY / SPECTROSCOPY STUDIES OF BINARY ORGANIC FILMS(2009) Jin, Wei; Reutt-Robey, Janice E; Chemical Physics; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)Multi-component organic molecular films have seen increasing applications in photovoltaic technologies and other organic electronic applications. These applications have been based upon assumptions regarding film structure and electronic properties. This thesis provides an increased understanding of factors that control structure in binary molecular films and begins to establish structure-electronic property relations. In this thesis, three technologically relevant "donor-acceptor" systems are studied with variable temperature STM/STS: pentacene (Pn):C60, zinc phthalocyanine (ZnPc): C60 and ZnPc: perfluorinated zinc phthalocyanine (F16ZnPc). These three model systems provide a systematic exploration of the impact of molecular shape and molecular band offset on morphology-electronic relations in thin film heterostructures. For Pn:C60, I show how domain size and architecture are controlled by composition and film processing conditions. Sequential deposition of pentacene, followed by C60, yields films that range from nanophase-separated, to co-crystalline phases, to a templated structure. These distinct structures are selectively produced from distinct pentacene phases which are controlled via pentacene coverage. For the ZnPc:C60 system, the shape of ZnPc and the lattice mismatch between ZnPc and C60 are quite different from the Pn:C60 films. Nonetheless, ZnPc:C60 films also yield chemical morphologies that can be similarly controlled from phase separated, to co-crystalline phases, to templated structures. In both of these binary films, I exploit relative differences in the component cohesive energies to control phase selection. In bilayer films of both systems, a common structural element of stress-induced defects is also observed. In ZnPc:F16ZnPc, I explore two components with similar shapes and cohesive energies while retaining molecular band offsets comparable to Pn:C60. In this shape-matched system, a checkerboard ZnPc:F16ZnPc arrangement stabilized by hydrogen bonds readily forms. This supramolecular structure introduces a new hybridization state close to the Fermi Level, yielding electronic properties distinct from the component phases. Through investigations of these three model systems, I have developed an understanding the control of chemical morphology along the donor-acceptor interface and the way this morphology influences electronic transport.Item Visible Light Photorelease of Carboxylate Anions by Mediated Photoinduced Electron Transfer to Pyridinium-based Protecting Groups(2009) Borak, John Brian; Falvey, Daniel E; Chemistry; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)The use of sensitized photoinduced electron transfer (PET) to trigger release of redox-active photoremovable protecting groups (PRPGs) allows a broad range of chromophores to be selected that absorb in difference wavelength ranges. Mediated electron transfer (MET) is particularly advantageous as sub-stoichiometric amounts of the often costly sensitizer (relative to the amount of protected substrate) can be combined with an excess amount of an inexpensive electron donor. Thus, the sensitizer acts as an electron shuttle between the donor and the protecting group to initiate release. The development of improved MET release systems using visible light as the trigger is the focus of the current work. The N-alkylpicolinium (NAP) group has demonstrated its utility as an aqueous-compatible PET-based PRPG, releasing protected substrates upon one electron reduction. Adaptation of MET PRPG release to visible light absorbing mediators began with employing ketocoumarin dyes that primarily form excited triplet states. These chromophores demonstrated high rates of release of NAP-protected carboxylates using sub-stoichiometric concentrations of mediator. Subsequently, nanomolar concentrations of gold nanoparticles were used to mediate electron transfer to NAP-protected compounds. This system exhibited rapid deprotection with very high release quantum efficiencies. In an effort to use highly stable visible-light-absorbing metal-centered dyes with modest redox properties, the NAP group has been synthetically modified to adjust its reduction potential to more positive values. Photolysis of solutions containing the protected substrate, a large excess of an electron donor, and substoichiometric amounts of the dye tris(bipyridyl)ruthenium(II) released the free carboxylates in high yields while photodegradation of the chromophore was minimal. To demonstrate the utility of the NAP group, a quasi-reversible photorheological fluid has been developed based on the formation and disruption of aqueous micelles. In solutions containing the surfactant cetyltrimethylammonium bromide, visible light photorelease of a carboxylate additive from the NAP-ester derivative induces a 105 increase in solution viscosity due to the formation of an interpenetrating micelle network. Subsequent irradiation of the viscoelastic fluid with UV light induces a cis-trans isomerization within the released carboxylate thereby disrupting the micelle network and decreasing solution viscosity by 102.5.Item DENSITY FUNCTIONAL CALCULATIONS OF BACKBONE 15N CHEMICAL SHIELDINGS IN PEPTIDES AND PROTEINS(2009) Cai, Ling; Fushman, David; Kosov, Daniel S; Chemical Physics; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)In this dissertation, we describe computational and theoretical study of backbone 15N chemical shieldings in peptides and proteins. Comprehensive density functional calculations have been performed on systems of different complexity, ranging from model dipeptides to real proteins and protein complexes. We begin with examining the effects of solvation, hydrogen bonding, backbone conformation, and the side chain identity on 15N chemical shielding in proteins by density functional calculations. N-methylacetamide (NMA) and N-formyl-alanyl-X (with X being one of the 19 naturally occurring amino acids excluding proline) were used as model systems for this purpose. The conducting polarizable continuum model was employed to include the effect of solvent in the calculations. We show that the augmentation of the polarizable continuum model with the explicit water molecules in the first solvation shell has a significant influence on isotropic 15N chemical shift but not as much on the chemical shift anisotropy. The difference in the isotropic chemical shift between the standard &beta-sheet and standard &alpha-helical conformations ranges from 0.8 ppm to 6.2 ppm depending on the residue type, with the mean of 2.7 ppm. This is in good agreement with the experimental chemical shifts averaged over a database of 36 proteins containing >6100 amino acid residues. The orientation of the 15N chemical shielding tensor as well as its anisotropy and asymmetry are also in the range of values experimentally observed for peptides and proteins. Having applied density functional calculation successfully to model peptides, we develop a computationally efficient methodology to include most of the important effects in the calculation of chemical shieldings of backbone 15N in a protein. We present the application to selected &alpha-helical and &beta-sheet residues of protein G. The role of long-range intra-protein electrostatic interactions by comparing models with different complexity in vacuum and in charge field is analyzed. We show that the dipole moment of the &alpha-helix can cause significant deshielding of 15N; therefore, it needs to be considered when calculating 15N chemical shielding. We emphasize the importance of including interactions with the side chains that are close in space when the charged form for ionizable side chains is adopted in the calculation. We also illustrate how the ionization state of these side chains can affect the chemical shielding tensor elements. For &alpha-helical residues, chemical shielding calculations using a 8-residue fragment model in vacuum and adopting the charged form of ionizable side chains yield a generally good agreement with experimental data. We also performed computational modeling of the chemical shift perturbations occurring upon protein-protein or protein-ligand binding. We show that the chemical shift perturbations in ubiquitin upon dimer formation can be explained qualitatively through computation. This dissertation hence demonstrates that quantum chemical calculations can be successfully used to obtain a fundamental understanding of the relationship between chemical shielding and the surrounding protein environment for the elusive case of 15N and therefore enhance the role of 15N chemical shift measurements in the analysis of protein structure and dynamics.Item DEVELOPMENT OF ION-MOBILITY AND MASS SPECTROMETRY FOR PROBING THE REACTIVITY OF NANOPARTICLES AND NANOCOMPOSITES(2009) Zhou, Lei; Zachariah, Michael; Chemical Physics; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)Aerosols of diameter smaller than 100 nm, usually are referred as nanoparticles or ultrafines, have received considerable interests lately as a source of building blocks to novel materials. However, our capabilities for charactering these materials are greatly limited by lack of appropriate diagnostic tools. The objective of this work is to develop new aerosol-based techniques for the characterization of nanoparticles and nanocomposites. The scope of this dissertation can be categorized in two ways. First, to provide knowledge of just how reactive a material is, we develop particle ion-mobility spectrometry and Single Particle Mass Spectrometry methods to probe the intrinsic size-dependent reactivity of individual metal particles. And second, the development of a new Time-of-Flight mass spectrometer (TOFMS) combined with a temperature jump (T-Jump) technique to study particle-particle reaction, and probe the reactivity of nanocomposite materials under combustion-like condition.Item STRUCTURE TAILORED PROPERTIES AND FUNCTIONALITIES OF ZERO-DIMENSIONAL NANOSTRUCTURES(2009) Tang, Yun; Ouyang, Min; Chemical Physics; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)The field of nanoscience and nanotechnology has achieved significant progress over last thirty years. Complex nanostructures with tunable properties for novel applications have been successfully fabricated and characterized. In this thesis, I will focus on our recent efforts on precise controlled synthesis of zero-dimensional nanostructures as well as fundamental understanding of the physical behavior of as-synthesized nanostructures. Particularly, three topics are presented: (1) Nanoscale crystallinity engineering: we have achieved nanoscale crystallinity control of noble metal nanoparticles with 100% yield by molecular engineering. We have used silver nanoparticles as example to demonstrate synthetic strategy and importance of such control in nanoscale chemical transformation, fundamental electron and phonon couplings and surface plasmon resonance based biological sensors. Such nanoscale crystallinity engineering provides a new pathway for design of complex nanostructures, tailoring nanoscale electronic and mechanical properties as well as controlling classical and quantum coupling interactions; (2) Precise control of core@shell nanostructures: we have developed a new universal strategy denoted as intermediated phase assisted phase exchange and reaction (iPAPER) to achieve layer-by-layer control of shell components in core@shell structures. Tunable plasmonic, optical and magnetic properties of core@shell structures enabled by our iPAPER strategy are further demonstrated. These characterizations are promising for understanding and manipulating nanoscale phenomena as well as assembling nanoscale devices with desirable functionality; and (3) Fundamental spin and structure manipulation of semiconductor quantum dots by hydrostatic pressure. Pressure provides a unique means of modifying materials properties. By measuring dependence of spin dynamics on pressure, we revealed that the spin states of semiconductor quantum dots are very robust. We further provided the first experimental evidence for the existence of a metastable intermediate state before the first-order phase transition of semiconductor quantum dots. Our results are crucial for the future development of quantum information processing based on spin qubits of quantum dots.Item Synthesis, Characterization and Catalytic Properties of Bimetallic Nanoparticles(2009) Dylla, Anthony Greg; Walker, Robert A; Eichhorn, Bryan W; Chemistry; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)Due to the ever-increasing desire for catalysts that possess high activities and selectivities for industrially relevant reactions, much effort is being spent on the synthesis of mono and bimetallic nanoparticles with tunable characteristics such as size, shape and bimetallic composition. Understanding how these characteristics influence catalytic performance is the key to rationally designing catalysts for a specific reaction. While significant breakthroughs have been made, particularly in the area of monometallic nanoparticles with regard to shape and size, relating the bimetallic structure, i.e., core@shell or alloy to a specific reactivity remains a difficult task. Work presented in this thesis describes the synthesis, characterization and catalytic properties of mono and bimetallic nanoparticles. Our efforts were motivated by the desire to understand the relationships that exist between metallic nanoparticle structure and their function as catalysts. This work also seeks to better understand the dynamic changes a nanoparticle's structure undergoes during typical catalytic operating conditions. Our approach is to use a wide array of analytical tools including optical methods, electron microscopy, XRD and mass spectrometry to provide an interlocking description of nanoparticle structure, function and durability. We show how the polymer coatings and degraded carbonaceous deposits affect propene hydrogenation catalytic activity of Pt nanoparticles. We also present a unique view of the interplay between thermodynamic and kinetic variables that control bimetallic nanoparticle alloy structures by looking at ordered and disordered PdCu alloy nanoparticles as a function of particle size. In another study we show that Ru@Pt and PtRu alloy nanoparticle catalysts have similar surface structures under oxidizing conditions but completely different surface structures under reducing conditions as probed by vibrational spectroscopy. These differences and similarities in surface composition correlate very well to their catalytic activity for CO oxidation under oxidizing and reducing environments, respectively. Finally, we present the synthesis and characterization of Cu@Pt nanoparticles with a particular focus on the core@shell formation mechanism. We also show how dramatic changes in the surface electronic structure of Cu versus Cu@Pt nanoparticles can affect their ability to transform light into heat by using Raman spectroscopy to observe graphite formation on the surface of these nanoparticles.Item MULTIPHOTON ABSORPTION: FABRICATION, FUNCTIONALIZATION AND APPLICATIONS(2009) Li, Linjie; Fourkas, John T; Chemistry; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)Despite the remarkable progress in micro/nano-scale fabrication that has occurred over the last decades, feature sizes are still restricted by the diffraction limit. The resolution in conventional photolithography is generally constrained to approximately one quarter of a wavelength (lamda) of the light used. Multiphoton absorption polymerization (MAP) offers another option for high-resolution fabrication. Using nonlinear optical and chemical effects, MAP can generate features with a transverse dimension as small as 80 nm using 800-nm laser excitation. MAP has the additional capability of fabricating arbitrary 3D structures, which is essential in many applications. Details of MAP fabrication setup and process are described in this thesis. Novel optical devices have been fabricated with MAP. One drawback of MAP is that the resolution in axial direction remains about three to five times poorer because of the shape of the laser focal point. A novel technique called Resolution Augmentation through Photo-Induced Deactivation (RAPID) lithography has been developed to overcome this issue. With RAPID, resolution of 40 nm in axial direction has been achieved. The aspect ratio of the volume element of MAP has been reduced from about 3 to 0.5. Selective functionalization of polymeric microstructure has been performed in two ways. In the first approach, microstructures are fabricated with hybrid resists that permits the chemical functionality only applies to one material. The second method is able to pattern both binary and gray-scale functionalities onto polymer surface. The density of the surface functional groups is determined by the intensity of the exposed light. The nonlinear novelty of multiphoton absorption has not only been realized in MAP, it also shows promise for multiphoton absorption based microscopy. Photoluminescence from noble metal nanostructures has been used for two-photon imaging of living cells. Multiphoton Absorption Induced Luminescence (MAIL) has been used to monitor the targeting and endocytosis of goldnanoparticles to human umbilical vein endothelial cells. Field-enhanced phenomena have been studied with MAIL and MAP.Item OPTICAL KERR EFFECT SPECTROSCOPY OF SIMPLE LIQUIDS(2009) Zhong, Qin; Fourkas, John T; Chemistry; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)Optical Kerr effect (OKE) spectroscopy has become a prominent nonlinear optical technique for studying liquids, which allows for the direct, time-resolved probing of collective orientational diffusion as well as Raman-active intermolecular and intramolecular modes. The temperature-dependent orientational dynamics of 1, n-dicyano n-alkane liquids ranging from dicyanomethane to 1,8-dicyanooctane has been investigated by ultrafast OKE spectroscopy. The dependence of the reorientational times on temperature and viscosity is consistent with the molecules adopting a largely extended structure in the liquid state, with a preference for gauche conformations at the methylenes bonded to the cyanide groups. The data are also suggestive of temperature-dependent, collective structural rearrangements in these liquids. Ultrafast OKE spectroscopy has also been used to study the intermolecular dynamics of aromatic liquids. A model that links the differences in the OKE spectra to corresponding differences in the local ordering of the liquids has been proposed previously based on the temperature-dependent OKE study of five aromatic liquids. The spectra of some other aromatic liquids such as pyridine, pyridine-d5, 2,4,6-trifluoropyridine and 1,3,5-tris(trifluoromethyl) benzene has been obtained to test this model, and the relative importance of molecular shape and electrostatic forces in determining the form of the OKE reduced spectral density for such liquids has been realized. It has recently been shown that liquid tetrahydrofuran (THF) has an unusual structure that features voids of significant dimension. Such voids should affect other observable properties of this liquid. Temperature-dependent, optical Kerr effect spectra for THF and a number of related liquids (furan, cyclopentane, tetrahydropyran, cyclohexane, diethyl ether, hexamethylphosphoramide and n-pentane) has been obtained to test whether the shape of the spectra can be used to reveal the presence of sizeable voids in liquids. Liquid under tension is another interesting system to study: A method based on Berthelot tube technique has been developed to hold benzene and acetonitrile under tension successfully. A new scheme for measuring different tensor elements of the OKE response is developed. A dual-ring, polarization dependent Sagnac interferometer is used to create two co-propagating probe pulses that arrive at the sample at different times but that reach the detector simultaneously and collinearly. The tensor element of the response that is measured is determined by the polarization of the pump pulse. By controlling the relative timing of the probe pulses it is also possible to perform optical subtraction of two different tensor elements of the response at two different times, a strategy that can be used to enhance or suppress particular contributions to the OKE response.Item Collisional Quenching Dynamics and Reactivity of Highly Vibrationally Excited Molecules(2008-11-13) Liu, Qingnan; Mullin, Amy S.; Chemistry; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)Highly excited molecules are of great importance in many areas of chemistry including photochemistry. The dynamics of highly excited molecules are affected by the intermolecular and intramolecular energy flow between many different kinds of motions. This thesis reports investigations of the collisional quenching and reactivity of highly excited molecules aimed at understanding the dynamics of highly excited molecules. How do molecules behave in collisions with a bath gas? How do the energy distributions evolve in time? How is the energy partitioned for both the donor and bath molecules after collisions? How do molecule structure, molecule state density and intermolecular potential play the role during collisional energy transfer? To answer these questions, collisional quenching dynamics and reactivity of highly vibrationally excited azabenzene molecules have been studied using high-resolution transient IR absorption spectroscopy. The first study shows that the highly vibrationally excited alkylated pyridine molecules impart less rotational and translational energy to CO2 than pyridine does. The strong collisions are reduced for donors with longer alkyl chains by lowering the average energy per mode but longer alkyl chain have increased flexibility and higher state densities that enhance energy loss via strong collisions. In the second study, the role of hydrogen bonding interactions is explored in collision of vibrationally excited pyridines with H2O. A torque-inducing mechanism is proposed that involves directed movement of H2O between sigma- and pi-hydrogen bonding interactions with the pyridine donors. In the third study the dynamics of strong and weak collisions for highly vibrationally excited methylated pyridine molecules with HOD are reported. Lower limits to the overall collision rate are directly determined from experimental measurements and compared to Lennard-Jones models which underestimate the collision rate. The fourth study explores reactive collisions of highly vibrationally excited pyridine molecules. D-atom abstraction reactions of pyridine-d5 and Cl show a rate enhancement of ~90 with vibrational energy. A single quantum of C-D stretching vibration is observed to be used for the vibrational driven reaction. Reactions of 2-picoline-d3 with Cl do not show a similar enhancement. For this case, the fast rotation of -CD3 group in highly vibrationally excited 2-picoline-d3 inhibits the D-atom abstraction.Item Protein folding and amyloid formation in various environments(2008-11-21) O'Brien, Edward Patrick; Thirumalai, Devarajan; Brooks, Bernard; Chemical Physics; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)Understanding and predicting the effect of various environments that differ in terms of pH and the presence of cosolutes and macromolecules on protein properties is a formidable challenge. Yet this knowledge is crucial in understanding the effect of cellular environments on a protein. By combining thermodynamic theories of solution condition effects with statistical mechanics and computer simulations we develop a molecular perspective of protein folding and amyloid formation that was previously unobtainable. The resulting Molecular Transfer Model offers, in some instances, quantitatively accurate predictions of cosolute and pH effects on various protein properties. We show that protein denatured state properties can change significantly with osmolyte concentration, and that residual structure can persist at high denaturant concentrations. We study the single molecule mechanical unfolding of proteins at various pH values and varying osmolyte and denaturant concentrations. We find that the the effect of varying solution conditions on a protein under tension can be understood and qualitatively predicted based on knowledge of that protein's behavior in the absence of force. We test the accuracy of FRET inferred denatured state properties and find that currently, only qualitative estimates of denatured state properties can be obtained with these experimental methods. We also explore the factors governing helix formation in peptides confined to carbon nanotubes. We find that the interplay of the peptide's sequence and dimensions, the nanotube's diameter, hydrophobicity and chemical heterogeneity, lead to a rich diversity of behavior in helix formation. We determine the structural and thermodynamic basis for the dock-lock mechanism of peptide deposition to a mature amyloid fibril. We find multiple basins of attraction on the free energy surface associated with structural transitions of the adding monomer. The models we introduce offer a better understanding of protein folding and amyloid formation in various environments and take us closer to understanding and predicting how the complex environment of the cell can effect protein properties.