UMD Theses and Dissertations

Permanent URI for this collectionhttp://hdl.handle.net/1903/3

New submissions to the thesis/dissertation collections are added automatically as they are received from the Graduate School. Currently, the Graduate School deposits all theses and dissertations from a given semester after the official graduation date. This means that there may be up to a 4 month delay in the appearance of a given thesis/dissertation in DRUM.

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STATE-RESOLVED QUENCHING DYNAMICS IN COLLISIONS OF VIBRATIONALLY EXCITED MOLECULES
(2010) Du, Juan; MULLIN, AMY S; Chemistry; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)
The collisional relaxation of highly excited molecules plays a very important role in many chemistry processes. The work presented in this thesis studies the collisional quenching dynamics of highly vibrationally excited molecules using high–resolution transient IR absorption spectroscopy. This work investigates “weak” (small energy transfer) and “strong” (large energy transfer) collisions between donor and bath molecules. The experimental results illustrate how the properties of donor molecules influence the collisional energy transfer. These properties include the molecular structure, internal energy, state density. In several weak collision studies, this thesis studies the vibration–rotation/translation pathway for pyrazine/DCl, pyrazine/CO₂ with different internal energies and for three excited alkylated pyridine molecules/CO₂ systems. A single–exponential rotational distribution and J–dependent translational energy distributions of scattered DCl molecules are observed. For CO₂ collisions, the scattered CO₂ has a biexponential rotational distribution and J–dependent translational energy distributions for all collision pairs. Recoil velocities scale with product angular momenta. The observed collision rates for these collision pairs match Lennard–Jones rates. The full energy transfer distribution for these pairs is determined by combining data for weak and strong collisions. Lowering the internal energy of donor molecules reduces the amount of rotational and translational energy transfer to CO₂. Reducing the internal energy of pyrazine decreases the probabilities of strong collision and increases the probabilities of weak collision. The average energy transfer reduces by ∼ 50% when the internal energy is decreased by only 15%. The collision rates are independent on the internal energy for these systems. Methylation of donor molecules decreases the magnitude of V—RT energy transfer. The collision results are affected by the number of methyl–groups, and not by the position of the group. Increasing the number of methyl groups increases the ratio of the measured collision rate to the Lennard–Jones collision rate. In the strong collision studies, the effects of alkylation and internal energy are studied. In collisions with alkylated pyridine donors with E ∼ 39000 cm−1, CO₂ molecules gain less energy from alkylpyridine than from pyridine. The alkylated donors undergo strong collisions with CO₂ via a less repulsive part of the intermolecular potential compared to pyridine. For azulene/CO₂ collisions with two different internal energies, scattered CO₂ molecules gain double the amount of rotational and translational energy when the azulene energy is doubled. The rate of strong collisions increases four times when the internal energy is doubled.
ARCHITECTURE-ELECTRONIC PROPERTY RELATIONS ACROSS MOLECULAR SEMICONDUCTOR INTERFACES
(2010) Wei, Yinying; Reutt-Robey, Janice E; Chemistry; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)
Multicomponent organic films have increasing applications in photovoltaic technologies and other electronic devices. These applications depend strongly on the structural and electronic properties of the heterojunctions. This thesis reports a detailed investigation of these important aspects, such as structure control and structural-electronic correlation in molecular film heterojunctions, for two selected "donor-acceptor" model systems (TiOPc-C₆₀ and TiOPc-C₇₀) using STM/STS. The UHV-STM studies were started on a single component system, TiOPc deposited on Ag(111). Along with increasing deposition flux, TiOPc selectively forms three distinct ordered monolayer structures, namely honeycomb phase, hexagonal phase, and a misfit dislocation triangular network. Localized electrostatic intermolecular interactions can be utilized to stabilize kinetically accessible structures and cause different phase structures formed on surface. Molecular packing models for these phases are proposed based on STM measurements. By choosing different TiOPc monolayer phases as template for sequential C₆₀ deposition, low-dimensional monolayer TiOPc-C₆₀ interfaces have been prepared on Ag(111) and characterized with STM/STS. Thermally stable honeycomb and metastable hexagonal TiOPc templates rearrange upon C₆₀ deposition to yield several binary film structures in the monolayer regime. These structures include phase-segregated TiOPc and C₆₀ domains and co-crystalline TiOPc₍₂₎C₆₀₍₁₎ honeycomb network formed through a dynamic process balanced by intermolecular and molecular-substrate interactions. The least stable TiOPc phase, the dislocation network, turns out to be the most robust template for sequential C₆₀ growth by forming nanophase-segregated TiOPc-C₆₀ on the scale of 10 nm. The variations of C₆₀ energy gap across the heterointerface created by depositing C₆₀ on hexagonal TiOPc are evaluated with STS. Energy level shift on TiOPc-C₆₀ co-crystal domain boundary is identified. This energy shift is correlated to an electron transport barrier from donor material (TiOPc) to acceptor (C₆₀) in practical OPV cells. C₇₀-TiOPc heterostructures are characterized and compared with those of C₆₀. C₇₀ present a greater variety of molecular configurations and related properties than those of C₆₀because of the ellipsoid shape with lower symmetry and higher dipole polarizability. C₇₀deposited on TiOPc honeycomb phase shows completely different growth mode from that of C₆₀. The TiOPc honeycomb structure, functionalized as a dipole buffer layer, plays a substantial role on sequential C₇₀ growth up to the fourth layer. Simple geometric effect and dipole-induced dipole interactions are considered to rationalize the intriguing C₇₀a growth mode. The structural model for each layer is proposed. By employing fullerenes (C₆₀ or C₇₀) and TiOPc thin films as model system, I investigated the controlled formation of donor-acceptor molecular film architecture, measured the orientation and separation of donor-acceptor molecules along the domain boundaries, and correlated the structural information with the electronic structural information. These systematical works shed light on the optimization of molecular electronic devices from a fundamental microscopic perspective.
MOLECULAR DYNAMICS SIMULATION OF DICARBOXYLIC ACID COATED AQUEOUS AEROSOL: STRUCTURE AND PROCESSING OF WATER VAPOR
(2010) Ma, Xiaofei; Zachariah, Michael R; Applied Mathematics and Scientific Computation; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)
Low molecular weight dicarboxylic acids constitute a significant fraction of water-soluble organic aerosols in the atmosphere. They have a potential contribution to the formation of cloud condensation nuclei (CCN) and are involved in a series of chemical reactions occurring in atmosphere. In this work, molecular dynamics simulation method was used to probe the structure and the interfacial properties of the dicarboxylic acid coated aqueous aerosol. Low molecular weight dicarboxylic acids of various chain lengths and water solubility were chosen to coat a water droplet consisting of 2440 water molecules. For malonic acid coated aerosol, the surface acid molecules dissolved into the water core and form an ordered structure due to the hydrophobic interactions. For other nanoaerosols coated with low solubility acids, phase separation between water and acid molecules was observed. To study the water processing of the coated aerosols, the water vapor accommodation factors were calculated.
Fluorescence Correlation Spectroscopy Studies of DNA Binding to Catanionic Surfactant Vesicles
(2010) Lioi, Sara Bethany; English, Douglas; DeShong, Philip; Chemistry; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)
Catanionic vesicles, made from mixtures of oppositely charged surfactants, have potential in drug delivery and gene therapy applications. Fluorescence correlation spectroscopy (FCS) was utilized to study the electrostatic binding of DNA molecules to vesicles made from cetyltrimethylammonium tosylate (CTAT) and sodium dodecylbenzenesulfonate (SDBS). FCS is employed to make sensitive measurements of bilayer adsorption and compare the adsorption of two single-stranded, dye-labeled DNA molecules of different lengths. Previous experimentation had shown that small organic fluorescent dyes bind to oppositely charged vesicles, thus positively charged CTAT-rich vesicles were used in the study of DNA binding. FCS was performed on samples with a constant DNA concentration and varying surfactant concentrations in order to construct binding isotherms for a 5mer ssDNA molecule and a 40mer ssDNA molecule. The binding constant determined for 40mer ssDNA (~ 106) was larger than the constant for 5mer ssDNA (~ 105), and binding constants for both lengths of DNA were larger than those previously determined for small organic molecule fluorescent dyes, which were on the order of 104. Additionally, 40mer ssDNA was found to probe the critical aggregation concentration, which is the lower limit at which vesicles can form in a surfactant mixture. Ordinarily it would be expected that very few vesicles would form at this surfactant concentration, however the autocorrelation curves indicate that the 40mer is bound only to vesicles. Salt studies were also done with the 40mer ssDNA to determine how the binding of cargo molecules to the exterior of the vesicle would be affected by physiological salt concentrations. Binding affinity of the 40mer ssDNA was reduced with increasing salt concentration; this was thought to be due to the tosylate ion, as it is hydrophobic and intercalates into the vesicle bilayer. Subsequent experiments using cetyltrimethylammonium bromide (CTAB) indicated that the counterion is not a factor in loss of binding affinity under normal saline conditions. Because these surfactant vesicles have been shown to have potential in both drug delivery and gene therapy, it is important that the binding of the cargo molecule be able to withstand normal saline conditions.
LINK BETWEEN DYNAMICS AND FUNCTION IN SINGLE AND MULTI-SUBUNIT ENZYMES
(2010) Chen, Jie; Thirumalai, Devarajan; Chemical Physics; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)
Biopolymers, such as proteins and DNA, are polymers whose three-dimensional conformations dene their biological functions. Current emphasis on structures has greatly advanced our understanding of the functions of biopolymers. However, there is a need to understand the deeper link between biopolymer dynamics and function, because in water and under cellular conditions, everything that biopolymers do can be understood in terms of "the jigglings and wigglings of atoms". These motions arise from thermal noise in the solvent and due to intrinsic motion of the enzymes. In biological systems, the motions are often highly regulated to ensure that cellular processes are executed over the required time scales. For enzymes, which are essentially proteins that catalyze chemical reactions or generate mechanical work, conformational fuctuations are coupled at various stages through interactions with ligands during the catalytic cycle. We have studied two dierent enzymes, dihydrofolate reductase (DHFR), which catalyzes reduction of dihydrofolate to tetrahydrofolate, and RNA polymerase (RNAP from bacteria and Pol II from yeast), which is responsible for RNA synthesis using DNA as a template. In order to study the link between dynamics and function we have developed new methods and extended a variety of computational techniques. For DHFR, we use both evolutionary imprints (SCA) and structure-based perturbation method (SPM) to extract a network of residues that facilitate the transitions between two distinct conformational states (closed and occluded states). The transition kinetics and pathways connecting the closed and occluded states are described using Brownian dynamics (BD) simulation. We found the sliding motion of Met20 loop across helix 2 is involved in the forward and reverse transitions between the closed and occluded states. We also found that cross-linking M16-G121 inhibits both the forward and the reverse transitions. In addition, we showed the transition states of these transitions are broad and resemble high energy states. For RNAP, we focus on the conformational changes of RNAP and DNA in promoter melting process. Using BD, we show that DNA conformation changes in promoter melting occur in three steps. We also show that internal dynamics of RNAP is relevant to facilitate the bending of DNA. For Pol II, the structural transitions between two initiation conformational states and between initiation state and elongation state are studied using SPM and BD. We determine the structural units that regulate structural transitions and describe the transition kinetics. The combination of three dierent methods, SCA, SPM and BD, provide results that are in accord with many experiments. Moreover, our description of the detailed structural transitions in these enzymes lead to new insights and testable predictions in these extraordinarily important enzyme functions.
Micelle and Aggregate Formation in Amphiphilic Block Copolymer Solutions
(2010) Clover, Bryna Christine; Greer, Sandra C; Chemistry; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)
The amphiphilic nature of many block copolymers causes self-aggregation and micelle formation in solvents that are miscible with only one of the block polymers (selective solvents). Micelle and aggregate formation of amphiphilic block copolymers in selective solvents is a function of temperature and concentration. Such self-aggregation has been examined here in a variety of block copolymer systems. In dilute solutions of Pluronic P85 (PEO₂₆PPO₄₀PEO₂₆) (where PEO is poly(ethylene oxide) and PPO is poly(propylene oxide)) in D₂O, transitions between clustered unimers, spherical micelles, cylindrical micelles, and finally lamellar micelles were observed with increasing temperature. The effect of pressure on this system was examined through small angle neutron scattering (SANS) techniques. At temperatures above 95 oC, a new phase of “demixed lamellae” was observed. Pressure effects on the transition temperatures between the phases of this system were investigated. The self-aggregation of Reverse Pluronic 17R4 (PPO₁₄PEO₂₄PPO₁₄) in D₂O has also been examined. The phase diagram of this system was determined through visual cloud-point techniques. Three distinct regions have been observed in solutions of this system, as a function of temperature and concentration: a cloudy, one-phase region; a clear, one-phase system; and a region of phase separation. Copolymer structures were examined in the clear and cloudy one-phase regions through SANS and dynamic light scattering (DLS) techniques. A network, or clustering, of unimers was observed in the cloudy phase. Aggregates in the clear, one-phase region could not be identified definitively as micelles. Finally, micellization of PEO₁₃₂-PB₈₉ (where PB is polybutadiene) has been studied in solutions of deuterated methanol and deuterated cyclohexane. Spherical micelles were observed in solutions of deuterated methanol. These micelles change little in size or shape over a 50 oC temperature span. The difference in aggregates in protonated and deuterated solvents was also examined. In deuterated cyclohexane, the copolymer formed flexible, cylindrical micelles below 40 oC. These micelles became spherical in shape at higher temperatures.
INTERFACIAL SOLVATION AND EXCITED STATE PHOTOPHYSICAL PROPERTIES OF 7-AMINOCOUMARINS AT SILICA/LIQUID INTERFACES
(2010) Roy, Debjani; Walker, Robert A; Chemical Physics; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)
The properties of solutes adsorbed at interfaces can be very different compared to bulk solution limits. This thesis examines how polar, hydrophilic silica surfaces and different solvents systematically change a solute's equilibrium and dynamic solvation environment at solid/liquid interfaces. The primary tools used in these studies are steady state fluorescence spectroscopy and time correlated single photon counting (TCSPC) -a fluorescence method capable resolving fluorescence emission on the picosecond timescale. To sample adsorbed solutes, TCSPC experiments were carried out in total internal reflection (TIR) geometry. These studies used total of six different 7 aminocoumarin dyes to isolate the effects of molecular and electronic structure on solute photophysical behavior. Fluorescence lifetimes measured in the TIR geometry are compared to the lifetimes of coumarins in bulk solution using different solvents to infer interfacial polarity and excited state solute conformation and dynamics. Steady state emission experiments measuring the behavior of the coumarins adsorbed at silica surfaces from bulk methanol solutions show that all coumarins had a similar affinity &delta G _ads &sim &minus 25-30 kJ/mole. Despite these similar adsorption energetics solute structure had a very pronounced effect on the tendency of solutes to aggregate and form multilayers. Our finding suggests that hydrogen bonding donating properties of the silica surface plays a dominant role in determining the interfacial behavior of these solutes. The silica surface also had pronounced effects on the time dependent emission of some solutes. In particular, the strong hydrogen bond donating properties of the silica surface inhibit formation of a planar, charge transfer state through hydrogen bond donation to the solute's amine group. A consequence of this interaction is that the time dependent emission from solutes adsorbed at the surface appears to be more similar to emission from solutes in nonpolar solvation environments. To test the role of solvent identity on the photophysical properties of adsorbed solutes, additional experiments were carried out with a nonpolar solvent (decane), a moderately polar solvent (n decanol) and a polar aprotic solvent (acetonitrile). The results from these studies demonstrated that interfacial solvation depends sensitively on a balance of competing forces including those between the solute and substrate, the solute and solvent and the surface and adjacent solvent.
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.
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.
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.

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