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Computational Investigation of DNA Repair Enzymes: Determination and Characterization of Cancer Biomarkers and Structural Features

Description: Genomic integrity is important for living cells' correct functioning and propagation. Deoxyribonucleic acid as a molecule is a subject to chemical reactions with agents that can come from environment as well as from internal metabolism processes. These reactions can induce damage to DNA and thus compromise the genetic information, and result in disease and death of an organism. To mitigate the damage to DNA, cells have evolved to have multiple DNA repair pathways. Presented here is a computational study of DNA repair genes. The structure of the Homo sapiens direct DNA repair gene ALKBH1 is predicted utilizing homology modeling methods and using AlkB and DBL proteins as templates. Analysis of the obtained structure and molecular dynamics simulations give insights into potentially functionally important residues of the protein. In particular, zinc finger domains are predicted, and lysines that could perform catalytic activities are investigated. Subsequent mutagenesis experiments revealed the effect of the residues predicted to form zinc fingers on activity of ALKBH1. Structure and dynamics of AlkD, a Bascillus cereus base excision DNA repair protein is also studied. This protein has been shown to bind DNA with large alkyl adducts and perform excision catalysis without base flipping which is characteristic to other enzymes in the same family. MD simulations of AlkD revealed that B helix, which interacts with DNA, has higher fluctuations when AlkD is not bound to DNA, and thus could have a role in binding and recognition of DNA. For the purpose of finding biomarkers and to further our understanding of a mode of action of DNA repair genes, statistical methods were applied to identify mutations that are linked to cancer phenotypes. Analysis was based on case-control studies of patients with cancers of prostate, breast, pancreas, lung as well as chronic lymphocytic leukemia from NCBI dbGAP database. Those mutations ...
Date: May 2018
Creator: Silvestrov, Pavel

Computational Simulations of Cancer and Disease-Related Enzymatic Systems Using Molecular Dynamics and Combined Quantum Methods

Description: This work discusses applications of computational simulations to enzymatic systems with a particular focus on the effects of various small perturbations on cancer and disease-related systems. First, we cover the development of carbohydrate-based PET imaging ligands for Galectin-3, which is a protein overexpressed in pancreatic cancer tumors. We uncover several structural features for the ligands that can be used to improve their binding and efficacy. Second, we discuss the AlkB family of enzymes. AlkB is the E. coli DNA repair protein for alkylation damage, and has human homologues with slightly different functions and substrates. Each has a conserved active site with a catalytic iron and a coordinating His...His...Asp triad. We have applied molecular dynamics (MD) to investigate the effect of a novel single nucleotide polymorphism for AlkBH7, which is correlated with prostate cancer and has an unknown function. We show that the mutation leads to active site distortion, which has been confirmed by experiments. Thirdly, we investigate the unfolding of hen egg white lysozyme in 90% ethanol solution and low pH, to show the initial steps of unfolding from a native-like state to the disease-associated beta-sheet structure. We compare to mass spectrometry experiments and also show differing pathways based on protonation state. Finally, we discuss three different DNA polymerase systems. DNA polymerases are the primary proteins that replicate DNA during cell division, and have various extra or specific functions. We look at a proofreading-deficient DNA polymerase III mutant, the effects of solvent on DNA polymerase IV's ability to bypass bulky DNA adducts, and a variety of mutations on DNA polymerase kappa.
Date: May 2018
Creator: Walker, Alice Rachel

Electrodeposition of Molybdenum-Based Coatings from Aqueous Alkaline Solutions for Enhanced Corrosion Resistance

Description: Zn-Mo coatings are very promising environment friendly anticorrosive coatings as replacement materials for cadmium and chromium (VI) based conversion layers. Electrodeposition has become a favorable technique in fabricating coatings due to its low cost, ease of use, and overall experimental control of coating quality. Very little research so far has been done for the electrodeposition of Zn-Mo coatings under alkaline conditions. In this work, Zn and Zn-Mo coatings were electrochemically deposited on stainless steel from an aqueous alkaline citrate solution. An organic compound, vanillin, was added to the electrolyte as a leveling agent for improving interlayer adherence and corrosion resistance of Zn-Mo coatings. Ni-Mo alloys have been known to possess high tensile strength and excellent corrosion protection of steels, and MoTe2 layers have a potential for the application in anticorrosive coatings due to their hydrophobic properties. In this study, MoTe2-Ni-Mo coatings were deposited on stainless steel using both sputtering and electrodeposition methods. These coatings with high corrosion resistance and other desirable properties are in demand in the oil and gas industry since they can protect and thus extend the lifetime of the underlying materials when exposed to aggressive environments. The Zn-Mo and MoTe2-Ni-Mo coatings were evaluated for chemical composition and corrosion behavior using different types of instrumental and electrochemical techniques. The addition of vanillin to the electrolyte did not change the crystalline structure or composition of the Zn-Mo coating, however, the corrosion resistance of the coating was significantly improved by the leveling effect of vanillin during the electrodeposition. The corrosion resistance of the Ni-Mo coating was also enhanced by applying the hydrophobic MoTe2 monolayer on the top surface.
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Date: May 2018
Creator: Zhou, Ting

Using the Abraham Solvation Parameter Model to Predict Solute Transfer into Various Mono- and Multi-Functional Organic Solvents

Description: The Abraham Solvation Parameter Model (ASPM) is a linear, free-energy relationship that can be used to predict various solute properties based on solute-solvent interactions. The ASPM has been used to predict log (K or Cs,organic/Cs,gas) values, as well as log (P or Cs,organic/Cs,water) values for solute transfer into the following organic solvents: 2-methoxyethanol, 2-ethoxyethanol, 2-propoxyethanol, 2-isopropoxyethanol and 2-butoxyethanol. The derived log (K or Cs,organic/Cs,gas) correlations describe the experimental data to within 0.14 log units (or less). The derived log (P or Cs,organic/Cs,water) correlations describe the experimental data to within 0.16 log units (or less). The ASPM has also been used to predict the enthalpies of solvation of organic solutes dissolved in the following solvents: acetic acid, dimethyl carbonate, diethyl carbonate, 1-butanol, 1-pentanol, 1-hexanol. The derived enthalpy of solvation correlations, using the L solute descriptor, describe the experimental data to within 2.50 log units (or less). The derived enthalpy of solvation correlations, using the V solute descriptor, describe the experimental data to within 3.10 log units (or less). Validation analyses have been performed on several of the correlations; and, as long as the solute descriptors fall within the given ranges as reported, the original correlations show good predictive ability for determining 1) solute transfer into, and 2) enthalpy of solvation for the aforementioned solvents.
Date: May 2018
Creator: Hart, Erin F

Design, Synthesis and Optoelectronic Properties of Monovalent Coinage Metal-Based Functional Materials toward Potential Lighting, Display and Energy-Harvesting Devices

Description: Groundbreaking progress in molecule-based optoelectronic devices for lighting, display and energy-harvesting technologies demands highly efficient and easily processable functional materials with tunable properties governed by their molecular/supramolecular structure variations. To date, functional coordination compounds whose function is governed by non-covalent weak forces (e.g., metallophilic, dπ-acid/dπ-base stacking, halogen/halogen and/or d/π interactions) remain limited. This is unlike the situation for metal-free organic semiconductors, as most metal complexes incorporated in optoelectronic devices have their function determined by the properties of the monomeric molecular unit (e.g., Ir(III)-phenylpyridine complexes in organic light-emitting diodes (OLEDs) and Ru(II)-polypyridyl complexes in dye-sensitized solar cells (DSSCs)). This dissertation represents comprehensive results of both experimental and theoretical studies, descriptions of synthetic methods and possible application allied to monovalent coinage metal-based functional materials. The main emphasis is given to the design and synthesis of functional materials with preset material properties such as light-emitting materials, light-harvesting materials and conducting materials. In terms of advances in fundamental scientific phenomena, the major highlight of the work in this dissertation is the discovery of closed-shell polar-covalent metal-metal bonds manifested by ligand-unassisted d10-d10 covalent bonds between Cu(I) and Au(I) coinage metals in the ground electronic state (~2.87 Å; ~45 kcal/mol). Moreover, this dissertation also reports pairwise intermolecular aurophilic interactions of 3.066 Å for an Au(I) complex, representing the shortest ever reported pairwise intermolecular aurophilic distances among all coinage metal(I) cyclic trimetallic complexes to date; crystals of this complex also exhibit gigantic luminescence thermochromism of 10,200 cm-1 (violet to red). From applications prospective, the work herein presents monovalent coinage metal-based functional optoelectronic materials such as heterobimetallic complexes with near-unity photoluminescence quantum yield, metallic or semiconducting integrated donor-acceptor stacks and a new class of Au(III)-based black absorbers with cooperative intermolecular iodophilic (I…I) interactions that sensitize the harvesting of all UV, all visible, and a broad spectrum of near-IR ...
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Date: August 2017
Creator: Ghimire, Mukunda Mani

MBE Growth and Characterization of Graphene on Well-Defined Cobalt Oxide Surfaces: Graphene Spintronics without Spin Injection

Description: The direct growth of graphene by scalable methods on magnetic insulators is important for industrial development of graphene-based spintronic devices, and a route towards substrate-induced spin polarization in graphene without spin injection. X-ray photoelectron spectroscopy (XPS), low energy electron diffraction LEED, electron energy loss spectroscopy (EELS) and Auger electron spectroscopy (AES) demonstrate the growth of Co3O4(111) and CoO(111) to thicknesses greater than 100 Å on Ru(0001) surfaces, by molecular beam epitaxy (MBE). The results obtained show that the formation of the different cobalt oxide phases is O2 partial pressure dependent under same temperature and vacuum conditions and that the films are stoichiometric. Electrical I-V measurement of the Co3O4(111) show characteristic hysteresis indicative of resistive switching and thus suitable for advanced device applications. In addition, the growth of Co0.5Fe0.5O(111) was also achieved by MBE and these films were observed to be OH-stabilized. C MBE yielded azimuthally oriented few layer graphene on the OH-terminated CoO(111), Co0.5Fe0.5O(111) and Co3O4(111). AES confirms the growth of (111)-ordered sp2 C layers. EELS data demonstrate significant graphene-to-oxide charge transfer with Raman spectroscopy showing the formation of a graphene-oxide buffer layer, in excellent agreement with previous theoretical predictions. XPS data show the formation of C-O covalent bonding between the oxide layer and the first monolayer (ML) of C. LEED data reveal that the graphene overlayers on all substrates exhibit C3V. The reduction of graphene symmetry to C3V – correlated with C-O bond formation – enables spin-orbit coupling in graphene. Consequences may include a significant band gap and room temperature spin Hall effect – important for spintronic device applications. The results suggest a general pattern of graphene/graphene oxide growth and symmetry lowering for graphene formation on the (111) surfaces of rocksalt-structured oxides.
Date: August 2017
Creator: Olanipekun, Opeyemi B

Microwave-Assisted Synthesis and Photophysical Properties of Poly-Imine Ambipolar Ligands and Their Rhenium(I) Carbonyl Complexes

Description: The phenomenon luminescence rigidochromism has been reported since the 1970s in tricarbonyldiimine complexes with a general formula [R(CO)3LX] using conventional unipolar diimine ligands such as 2,2;-bipyridine or 1,10-phenanthroline as L, and halogens or simple solvents as X. As a major part of this dissertation, microwave-assisted synthesis, purification, characterization and detailed photoluminescence studies of the complex fac-[ReCl(CO)3L], 1, where L = 4-[4,6-bis(3,5-dimethyl-1H-pyrazol-1-yl]-N,N-diethylbenzenamine are reported. The employment of microwaves in the preparation of 1 decreased the reaction time from 48 to 2 hours compared to the conventional reflux method. Stoichiometry variations allows for selective preparation of either a mononuclear, 1, or binuclear, fac-[Re2Cl2(CO)6], 2, complex. The photophysical properties of 1 were analyzed finding that it possesses significant luminescence rigidochromism. The steady state photoluminescence emission spectra of 1 in solution shift from 550 nm in frozen media to 610 nm when the matrix becomes fluid. Moreover, a very sensitive emission spectral analysis of 0.1 K temperatures steps shows a smooth transition through the glass transition temperature of the solvent host. Furthermore, synthetic modifications to L have attained a family of ambipolar compounds that have tunable photophysical, thermophysical and other material properties that render them promising candidates for potential applications in organic electronics and/or sensors - either as is or for their future complexes with various transition metals and lanthanides.
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Date: August 2017
Creator: Salazar Garza, Gustavo Adolfo

Design Considerations and Implementation of Portable Mass Spectrometers for Environmental Applications

Description: Portable mass spectrometers provide a unique opportunity to obtain in situ measurements. This minimizes need for sample collection or in laboratory analysis. Membrane Inlet Mass Spectrometry (MIMS) utilizing a semi permeable membrane for selective rapid introduction for analysis. Polydimethylsiloxane membranes have been proven to be robust in selecting for aromatic chemistries. Advances in front end design have allowed for increased sensitivity, rapid sample analysis, and on line measurements. Applications of the membrane inlet technique have been applied to environmental detection of clandestine drug chemistries and pollutants. Emplacement of a mass spectrometer unit in a vehicle has allowed for large areas to be mapped, obtaining a rapid snapshot of the various concentrations and types of environmental pollutants present. Further refinements and miniaturization have allowed for a backpackable system for analysis in remote harsh environments. Inclusion of atmospheric dispersion modeling has yielded an analytical method of approximating upwind source locations, which has law enforcement, military, and environmental applications. The atmospheric dispersion theories have further been applied to an earth based separation, whereby chemical properties are used to approximate atmospheric mobility, and chemistries are further identified has a portable mass spectrometer is traversed closer to a point source.
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Date: May 2017
Creator: Mach, Phillip Michael

Disease Tissue Imaging and Single Cell Analysis with Mass Spectrometry

Description: Cells have been found to have an inherent heterogeneity that has led to an increase in the development of single-cell analysis methods to characterize the extent of heterogeneity that can be found in seemingly identical cells. With an understanding of normal cellular variability, the identification of disease induced cellular changes, known as biomarkers, may become more apparent and readily detectable. Biomarker discovery in single-cells is challenging and needs to focus on molecules that are abundant in cells. Lipids are widely abundant in cells and play active roles in cellular signaling, energy metabolism, and are the main component of cellular membranes. The regulation of lipid metabolism is often disrupted or lost during disease progression, especially in cancer, making them ideal candidates as biomarkers. Challenges exist in the analysis of lipids beyond those of single-cell analysis. Lipid extraction solvents must be compatible with the lipid or lipids of interest. Many lipids are isobaric making mass spectrometry analysis difficult without separations. Single-cell extractions using nanomanipulation coupled to mass spectrometry has shown to be an excellent method for lipid analysis of tissues and cell cultures. Extraction solvents are tunable for specific lipid classes, nanomanipulation prevents damage to neighboring cells, and lipid separations are possible through phase dispersion. The most important aspect of single-cell analysis is that it uncovers the extent of cellular heterogeneity that exists among cellular populations that remains undetected during averaged sampling.
Date: May 2017
Creator: Hamilton, Jason S

Elucidation of Photoinduced Energy and Electron Transfer Mechanisms in Multimodular Artificial Photosynthetic Systems

Description: Multimodular designs of electron donor-acceptor systems are the ultimate strategy in fabricating antenna-reaction center mimics for artificial photosynthetic applications. The studied photosystems clearly demonstrated efficient energy transfer from the antenna system to the primary electron donor, and charge stabilization of the radical ion pair achieved with the utilization of secondary electron donors that permits either electron migration or hole transfer. Moreover, the molecular arrangement of the photoactive components also influences the route of energy and electron transfer as observed from the aluminum(III) porphyrin-based photosystems. Furthermore, modulation of the photophysical and electronic properties of these photoactive units were illustrated from the thio-aryl substitution of subphthalocyanines yielding red-shifted Q bands of the said chromophore; hence, regulating the rate of charge separation and recombination in the subphthalocyanine-fullerene conjugates. These multicomponent photosystems has the potential to absorb the entire UV-visible-NIR spectrum of the light energy allowing maximum light-harvesting capability. Furthermore, it permits charge stabilization of the radical ion pair enabling the utilization of the transferred electron/s to be used by water oxidizing and proton reducing catalysts in full-scale artificial photosynthetic apparatuses.
Date: May 2017
Creator: Lim, Gary Lloyd Nogra

Reductive Functionalization of 3D Metal-Methyl Complexes and Characterization of a Novel Dinitrogen Dicopper (I) Complex

Description: Reductive functionalization of methyl ligands by 3d metal catalysts and two possible side reactions has been studied. Selective oxidation of methane, which is the primary component of natural gas, to methanol (a more easily transportable liquid) using organometallic catalysis, has become more important due to the abundance of domestic natural gas. In this regard, reductive functionalization (RF) of methyl ligands in [M(diimine)2(CH3)(Cl)] (M: VII (d3) through CuII (d9)) complexes, has been studied computationally using density functional techniques. A SN2 mechanism for the nucleophilic attack of hydroxide on the metal-methyl bond, resulting in the formation of methanol, was studied. Similar highly exergonic pathways with very low energy SN2 barriers were observed for the proposed RF mechanism for all complexes studied. To modulate RF pathways closer to thermoneutral for catalytic purposes, a future challenge, paradoxically, requires finding a way to strengthen the metal-methyl bond. Furthermore, DFT calculations suggest that for 3d metals, ligand properties will be of greater importance than metal identity in isolating suitable catalysts for alkane hydroxylation in which reductive functionalization is used to form the C—O bond. Two possible competitive reactions for RF of metal-methyl complexes were studied to understand the factors that lower the selectivity of C—O bond forming reactions. One of them was deprotonation of the methyl group, which leads to formation of a methylene complex and water. The other side reaction was metal-methyl bond dissociation, which was assessed by calculating the bond dissociation free energies of M3d—CH3 bonds. Deprotonation was found to be competitive kinetically for most of the 1st row transition metal-methyl complexes (except for CrII, MnII and CuII), but less favorable thermodynamically as compared to reductive functionalization for all of the studied 1st row transition metal complexes. Metal-carbon bond dissociation was found to be less favorable than the RF reactions for most 3d transition ...
Date: May 2017
Creator: Fallah, Hengameh

Computational Studies of C–H/C–C Manipulation Utilizing Transition Metal Complexes

Description: Density Functional Theory (DFT) is an effective tool for studying diverse metal systems. Presented herein are studies of a variety of metal systems, which can be applied to accomplish transformations that are currently difficult/impossible to achieve. The specific topics studied utilizing DFT include: 1) C–H bond activation via an Earth-abundant transition metal complex, 2) C–H bond deprotonation via an alkali metal superbase, 3) and amination/aziridination reactions utilizing a CuI reagent. Using DFT, the transformation to methanol (CH3OH) from methane (CH4) was examined. The transition metal systems studied for this transformation included a model FeII complex. This first-row transition metal is an economical, Earth-abundant metal. The ligand set for this transformation includes a carbonyl ligand in one set of complexes as well as a phosphite ligand in another. The 3d Fe metal shows the ability to convert alkyls/aryls to their oxidized counterpart in an energetically favorable manner. Also, “superbasic” alkali metal amides were investigated to perform C—H bond cleavage. Toluene was the substrate of interest with Cs chosen to be the metal of interest because of the highly electropositive nature of this alkali metal. These highly electrophilic Cs metal systems allow for very favorable C—H bond scission with a toluene substrate. Finally, the amination and aziridination of C–H and C=C bonds, respectively, by a CuI reagent was studied. The mechanism was investigated using DFT calculations. Presently, these mechanisms involving the use of coinage metals are debated. Our DFT simulations shed some insight into how these transformations occur and ultimately how they can be manipulated.
Date: May 2015
Creator: Pardue, Daniel B.

Rational Design of Metal-organic Electronic Devices: a Computational Perspective

Description: Organic and organometallic electronic materials continue to attract considerable attention among researchers due to their cost effectiveness, high flexibility, low temperature processing conditions and the continuous emergence of new semiconducting materials with tailored electronic properties. In addition, organic semiconductors can be used in a variety of important technological devices such as solar cells, field-effect transistors (FETs), flash memory, radio frequency identification (RFID) tags, light emitting diodes (LEDs), etc. However, organic materials have thus far not achieved the reliability and carrier mobility obtainable with inorganic silicon-based devices. Hence, there is a need for finding alternative electronic materials other than organic semiconductors to overcome the problems of inferior stability and performance. In this dissertation, I research the development of new transition metal based electronic materials which due to the presence of metal-metal, metal-?, and ?-? interactions may give rise to superior electronic and chemical properties versus their organic counterparts. Specifically, I performed computational modeling studies on platinum based charge transfer complexes and d10 cyclo-[M(?-L)]3 trimers (M = Ag, Au and L = monoanionic bidentate bridging (C/N~C/N) ligand). The research done is aimed to guide experimental chemists to make rational choices of metals, ligands, substituents in synthesizing novel organometallic electronic materials. Furthermore, the calculations presented here propose novel ways to tune the geometric, electronic, spectroscopic, and conduction properties in semiconducting materials. In addition to novel material development, electronic device performance can be improved by making a judicious choice of device components. I have studied the interfaces of a p-type metal-organic semiconductor viz cyclo-[Au(µ-Pz)]3 trimer with metal electrodes at atomic and surface levels. This work was aimed to guide the device engineers to choose the appropriate metal electrodes considering the chemical interactions at the interface. Additionally, the calculations performed on the interfaces provided valuable insight into binding energies, charge redistribution, change in the energy ...
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Date: December 2012
Creator: Chilukuri, Bhaskar

Investigating Molecular Structures: Rapidly Examining Molecular Fingerprints Through Fast Passage Broadband Fourier Transform Microwave Spectroscopy

Description: Microwave spectroscopy is a gas phase technique typically geared toward measuring the rotational transitions of Molecules. The information contained in this type of spectroscopy pertains to a molecules structure, both geometric and electronic, which give insight into a molecule's chemistry. Typically this type of spectroscopy is high resolution, but narrowband ≤1 MHz in frequency. This is achieved by tuning a cavity, exciting a molecule with electromagnetic radiation in the microwave region, turning the electromagnetic radiation o, and measuring a signal from the molecular relaxation in the form of a free induction decay (FID). The FID is then Fourier transformed to give a frequency of the transition. "Fast passage" is defined as a sweeping of frequencies through a transition at a time much shorter (≤10 s) than the molecular relaxation (≈100 s). Recent advancements in technology have allowed for the creation of these fast frequency sweeps, known as "chirps", which allow for broadband capabilities. This work presents the design, construction, and implementation of one such novel, high-resolution microwave spectrometer with broadband capabilities. The manuscript also provides the theory, technique, and motivations behind building of such an instrument. In this manuscript it is demonstrated that, although a gas phase technique, solids, liquids, and transient species may be studied with the spectrometer with high sensitivity, making it a viable option for many molecules wanting to be rotationally studied. The spectrometer has a relative correct intensity feature that, when coupled with theory, may ease the difficulty in transition assignment and facilitate dynamic chemical studies of the experiment. Molecules studied on this spectrometer have, in turn, been analyzed and assigned using common rotational spectroscopic analysis. Detailed theory on the analysis of these molecules has been provided. Structural parameters such as rotational constants and centrifugal distortion constants have been determined and reported for most molecules in ...
Date: May 2011
Creator: Grubbs, Garry Smith, II

Computational Study of Small Molecule Activation via Low-Coordinate Late First-Row Transition Metal Complexes

Description: Methane and dinitrogen are abundant precursors to numerous valuable chemicals such as methanol and ammonia, respectively. However, given the robustness of these substrates, catalytically circumventing the high temperatures and pressures required for such transformations has been a challenging task for chemists. In this work, computational studies of various transition metal catalysts for methane C-H activation and N2 activation have been carried out. For methane C-H activation, catalysts of the form LnM=E are studied, where Ln is the supporting ligand (dihydrophosphinoethane or β-diketiminate), E the activating ligand (O, NCH3, NCF3) at which C-H activation takes place, and M the late transition metal (Fe,Co,Ni,Cu). A hydrogen atom abstraction (HAA) / radical rebound (RR) mechanism is assumed for methane functionalization (CH4 à CH3EH). Since the best energetics are found for (β-diket)Ni=O and (β-diket)Cu=O catalysts, with or without CF3 substituents around the supporting ligand periphery, complete methane-to-methanol cycles were studied for such systems, for which N2O was used as oxygen atom transfer (OAT) reagent. Both monometallic and bimetallic OAT pathways are addressed. Monometallic Fe-N2 complexes of various supporting ligands (LnFe-N2) are studied at the beginning of the N2 activation chapter, where the effect of ligand on N2 activation in end-on vs. side-on N2 isomers is discussed. For (β-diket)Fe-N2 complexes, the additional influence of diketiminate donor atom (N(H) vs. S) is briefly addressed. The remainder of the chapter expands upon the treatment of β-diketiminate complexes. First, the activation and relative stabilities of side-bound and end-bound N2 isomers in monometallic ((β-diket)M-N2) and bimetallic ((β-diket)M-N2-M(β-diket)) first row transition metal complexes are addressed. Second, the thermodynamics of H/H+/H- addition to (β-diket)Fe-bound N2, followed by subsequent H additions up to release of ammonia, is discussed, for which two mechanisms (distal and alternating) are considered. Finally, the chapter concludes with partial distal and alternating mechanisms for H addition to N2 ...
Date: May 2010
Creator: Pierpont, Aaron

Sensitization of Lanthanides and Organic-Based Phosphorescence via Energy Transfer and Heavy-Atom Effects

Description: The major topics discussed are the phosphorescence sensitization in the lanthanides via energy transfer and in the organics by heavy atom effects. The f-f transitions in lanthanides are parity forbidden and have weak molar extinction coefficients. Upon complexation with the ligand, ttrpy (4'-p-Tolyl-[2,2':6',2"]-terpyridine) the absorption takes place through the ligand and the excitation is transferred to the lanthanides, which in turn emit. This process is known as "sensitized luminescence." Bright red emission from europium and bright green emission from terbium complexes were observed. There is ongoing work on the making of OLEDs with neutral complexes of lanthanide hexafluoroacetyl acetonate/ttrpy, studied in this dissertation. Attempts to observe analogous energy transfer from the inorganic donor complexes of Au(I) thiocyanates were unsuccessful due to poor overlap of the emissions of these systems with the absorptions of Eu(III) and Tb(III). Photophysics of silver-aromatic complexes deals with the enhancement of phosphorescence in the aromatics. The heavy atom effect of the silver is responsible for this enhancement in phosphorescence. Aromatics such as naphthalene, perylene, anthracene and pyrene were involved in this study. Stern Volmer plots were studied by performing the quenching studies. The quenchers employed were both heavy metals such as silver and thallium and lighter metal like potassium. Dynamic quenching as the predominant phenomenon was noticed.
Date: May 2010
Creator: Arvapally, Ravi K.

Phosphorescent Emissions of Coinage Metal-Phosphine Complexes: Theory and Photophysics

Description: The major topics discussed are all relevant to the bright phosphorescent emissions of coinage metal complexes (Cu(I), Ag(I) and Au(I)) with an explanation of the theoretical background, computational results and ongoing work on the application in materials and optoelectronic devices. Density functional computations have been performed on the majority of the discussed complexes and determined that the most significant distortion that occurs in Au(I)-phosphine complexes is a near and beyond a T-shape within the P-Au-P angle when the complexes are photoexcited to the lowest phosphorescent excited state. The large distortion is experimentally qualified with the large Stokes' shift that occurs between the excitation and emission spectra and can be as large as 18 000 cm-1 for the neutral Au(I) complexes. The excited state distortion has been thoroughly investigated and it is determined that not only is it pertinent to the efficient luminescence but also for the tunability in the emission. The factors that affect tunability have been determined to be electronics, sterics, rigidity of solution and temperature. The luminescent shifts determined from varying these parameters have been described systematically and have revealed emission colors that span the entire visible spectrum. These astounding features that have been discovered within studies of coinage metal phosphorescent complexes are an asset to applications ranging from materials development to electronics.
Date: December 2009
Creator: Sinha, Pankaj

Interaction of learning approach with concept integration and achievement in a large guided inquiry organic class.

Description: A study was conducted to investigate the relationship of students' concept integration and achievement with time spent within a topic and across related topics in a large first semester guided inquiry organic chemistry class. Achievement was based on evidence of algorithmic problem solving; and concept integration was based on demonstrated performance explaining, applying, and relating concepts to each other. Twelve individual assessments were made of both variables over three related topics - acid/base, nucleophilic substitution and electrophilic addition reactions. Measurements included written, free response and ordered multiple answer questions using a classroom response system. Results demonstrated that students can solve problems without conceptual understanding. A second study was conducted to compare the students' learning approach at the beginning and end of the course. Students were scored on their preferences for a deep, strategic, or surface approach to learning based on their responses to a pre and post survey. Results suggest that students significantly decreased their preference for a surface approach during the semester. Analysis of the data collected was performed to determine the relationship between students' learning approach and their concept integration and achievement in this class. Results show a correlation between a deep approach and concept integration and a strong negative correlation between a surface approach and concept integration.
Date: August 2009
Creator: Mewhinney, Christina

Kinetic studies and computational modeling of atomic chlorine reactions in the gas phase.

Description: The gas phase reactions of atomic chlorine with hydrogen sulfide, ammonia, benzene, and ethylene are investigated using the laser flash photolysis / resonance fluorescence experimental technique. In addition, the kinetics of the reverse processes for the latter two elementary reactions are also studied experimentally. The absolute rate constants for these processes are measured over a wide range of conditions, and the results offer new accurate information about the reactivity and thermochemistry of these systems. The temperature dependences of these reactions are interpreted via the Arrhenius equation, which yields significantly negative activation energies for the reaction of the chlorine atom and hydrogen sulfide as well as for that between the phenyl radical and hydrogen chloride. Positive activation energies which are smaller than the overall endothermicity are measured for the reactions between atomic chlorine with ammonia and ethylene, which suggests that the reverse processes for these reactions also possess negative activation energies. The enthalpies of formation of the phenyl and β-chlorovinyl are assessed via the third-law method. The stability and reactivity of each reaction system is further rationalized based on potential energy surfaces, computed with high-level ab initio quantum mechanical methods and refined through the inclusion of effects which arise from the special theory of relativity. Large amounts of spin-contamination are found to result in inaccurate computed thermochemistry for the phenyl and ethyl radicals. A reformulation of the computational approach to incorporate spin-restricted reference wavefunctions yields computed thermochemistry in good accord with experiment. The computed potential energy surfaces rationalize the observed negative temperature dependences in terms of a chemical activation mechanism, and the possibility that an energized adduct may contribute to product formation is investigated via RRKM theory.
Date: August 2009
Creator: Alecu, Ionut M.

Predicting Chemical and Biochemical Properties Using the Abraham General Solvation Model

Description: Several studies were done to illustrate the versatillity of the Abraham model in mathematically describing the various solute-solvent interactions found in a wide range of different chemical and biological systems. The first study focused on using the solvation model to construct mathematical correlations describing the minimum inhibitory concentration of organic compounds for growth inhibition towards the three bacterial strains Porphyromonas gingivalis, Selenomonas artemidis, and Streptococcus sobrinus. The next several studies expand the practicallity of the Abraham model by predicting free energies of partition in chemical systems. The free energy studies expand the use of the Abraham model to other temperatures and properties by developing correlations for the enthalpies of solvation of gaseous solutes of various compounds dissolved in water, 1-octanol, hexane, heptane, hexadecane, cyclohexane, benzene, toluene, carbon tetrachloride, chloroform, methanol, ethanol, 1-butanol, propylene carbonate, dimethyl sulfoxide, 1,2-dichloroethane, N,N-dimethylformamide, tert-butanol, dibutyl ether, ethyl acetate, acetonitrile, and acetone. Also, a generic equation for linear alkanes is created for use when individual datasets are small. The prediction of enthalpies of solvation is furthered by modifying the Abraham model so that experimental data measured at different temperatures can be included into a single correlation expression. The temperature dependence is directly included in the model by separating each coefficient into an enthalpic and entropic component. Specifically, the final study describes the effects of temperature on the sorption coefficients of organic gases onto humic acid. The derived predicted values for each research study show a good correlation with experimental values.
Date: May 2009
Creator: Mintz, Christina

Metallization and Modification of Low-k Dielectric Materials

Description: Aluminum was deposited onto both Teflon AF and Parylene AF surfaces by chemical vapor deposition of trimethylaluminum. This work shows that similar thin film (100 Angstroms) aluminum oxide adlayers form on both polymers at the low temperature dosing conditions used in the studies. Upon anneal to room temperature and above, defluorination of the polymer surfaces increased and resulted in fluorinated aluminum oxide adlayers; the adlayers were thermally stable to the highest temperatures tested (600 K). Angle-resolved spectra showed higher levels of fluorination toward the polymer/adlayer interface region. Copper films were also deposited at low temperature onto Teflon AF using a copper hexafluoroacetylacetonate-cyclooctadiene precursor. Annealing up to 600 K resulted in the loss of precursor ligands and a shift to metallic copper. As with aluminum adlayers, some polymer defluorination and resulting metal (copper) fluoride was detected. Parylene AF and polystyrene films surfaces were modified by directly dosing with water vapor passed across a hot tungsten filament. Oxygen incorporation into polystyrene occurred exclusively at aromatic carbon sites, whereas oxygen incorporation into parylene occurred in both aromatic and aliphatic sites. Oxygen x-ray photoelectron spectra of the modified polymers were comparable, indicating that similar reactions occurred. The surface oxygenation of parylene allowed enhanced reactivity toward aluminum chemical vapor deposition. Silicon-carbon (Si-Cx) films were formed by electron beam bombardment of trimethylvinylsilane films which were adsorbed onto metal substrates at low temperatures in ultra-high vacuum. Oxygen was also added to the films by coadsorbing water before electron beam bombardment; the films were stable to more than 700 K, with increasing silicon-oxygen bond formation at elevated temperatures. Copper metal was sputter deposited in small increments onto non-oxygenated films. X-ray photoelectric spectra show three-dimensional copper growth (rather than layer-by-layer growth), indicating only weak interaction between the copper and underlying films. Annealing at elevated temperatures caused coalescence or growth ...
Date: December 2008
Creator: Martini, David M.

Preparation of flat dendrimers and polycyclic aromatic hydrocarbons connected via 1,3,5-triethynylbenzene core.

Description: Flat dendrimers, consisting of a hexavalent aromatic core and rigid ethynyl units locked in place by ether connections were developed based upon the divergent synthetic method. Alternating functional groups were adopted on each site of the hexa-substituted benzene, in order to avoid undesired cyclization pathways. The flat structures of conjugated dendrimers would allow investigation on the discotic liquid crystal properties. In addition, these ethylnyl dendrimers are expected to show directed energy and electron transfer with a highly conjugated system, and thus are effective in the preparation of photoreactive materials such as electronic sensors or light harvesting materials. Conjugated polycyclic aromatic hydrocarbons, consisting of naphthalene, anthracene, pyrene, and phenanthrene groups connected via 1,3,5-triethynylbenzene cores, were synthesized. These molecules exhibited luminescence properties and the π-complexation with a mercury trifunctional lewis acid are expected to enhance the phosphorescence in the presence of the heavy metal due to the spin-orbit coupling. Besides, owing to the presence of heavy metal atom in the Au (I) complexes linked by s-bonded triethynyltriphenylene luminophore, the phosphorescence occurs from a metal-centered emission. The conjugated organic luminophores have been developed to produce excellent quantum efficiencies, brightness, and long lifetimes.
Date: December 2008
Creator: Jung, Jiyoung

Reducing the Computational Cost of Ab Initio Methods

Description: In recent years, advances in computer technology combined with new ab initio computational methods have allowed for dramatic improvement in the prediction of energetic properties. Unfortunately, even with these advances, the extensive computational cost, in terms of computer time, memory, and disk space of the sophisticated methods required to achieve chemical accuracy - defined as 1 kcal/mol from reliable experimental data effectively - limits the size of molecules [i.e. less than 10-15 non-hydrogen atoms] that can be studied. Several schemes were explored to help reduce the computational cost while still maintaining chemical accuracy. Specifically, a study was performed to assess the accuracy of ccCA to compute atomization energies, ionization potentials, electron affinities, proton affinities, and enthalpies of formation for third-row (Ga-Kr) containing molecules. Next, truncation of the correlation consistent basis sets for the hydrogen atom was examined as a possible means to reduce the computational cost of ab initio methods. It was determined that energetic properties could be extrapolated to the complete basis set (CBS) limit utilizing a series of truncated hydrogen basis sets that was within 1 kcal/mol of the extrapolation of the full correlation consistent basis sets. Basis set truncation for the hydrogen atom was then applied to ccCA in the development of two reduced basis set composite methods, ccCA(aug) and ccCA(TB). The effects that the ccCA(aug) and ccCA(TB) methods had upon enthalpies of formation and the overall percent disk space saved as compared to ccCA was examined for the hydrogen containing molecules of the G2/97 test suite. Additionally, the Weizmann-n (Wn) methods were utilized to compute the several properties for the alkali metal hydroxides as well as the ground and excited states of the alkali monoxides anion and radicals. Finally, a multi-reference variation to the correlation consistent Composite Approach [MR-ccCA] was presented and utilized in the computation ...
Date: August 2008
Creator: Mintz, Benjamin

Synthesis, characterization, and kinetics of isomerization, C-H and P-C bond activation for unsaturated diphosphine-coordinated triosmium carbonyl clusters.

Description: Substitution of MeCN ligands in the activated cluster Os3(CO)10(MeCN)2 by the unsaturated diphosphine ligands (Z)-Ph2PCH=CHPPh2 (cDPPEn) or 4,5-bis(diphenylphosphino)-4-cyclopenten-1,3-dione (bpcd) proceeds rapidly at room temperature to furnish the ligand-bridged cluster 1,2-Os3(CO)10(P-P) (P-P represents cDPPEn or bpcd). Heating 1,2-Os3(CO)10(P-P) leads to the formation of the thermodynamically more stable chelating isomer 1,1-Os3(CO)10(P-P). Each compound of Os3(CO)10(P-P) has been characterized by x-ray diffraction, IR, 31P NMR and 1H NMR. Ligand isomerization kinetics have been investigated by UV-VIS and 31P NMR (for cDPPEn) or 1H NMR (for bpcd) spectroscopies. The isomerization mechanism is discussed based on the activation parameters and CO inhibition (for cDPPEn) or ligand trapping experiments (for bpcd). Thermolysis of 1,1-Os3(CO)10(bpcd) in refluxing toluene gives the hydrido cluster HOs3(CO)9[μ-(PPh2)C=C{PPh(C6H4)}C(O)CH2C(O)] and the benzyne cluster HOs3(CO)8(μ3-C6H4)[μ2,η1-PPhC=C(PPh2)C(O)CH2C(O)]. Photolysis of 1,1-Os3(CO)10(bpcd) using near UV light affords HOs3(CO)9[μ-(PPh2)C=C{PPh(C6H4)}C(O)CH2C(O)] as the sole product. HOs3(CO)8(μ3-C6H4)[μ2,η1-PPhC=C(PPh2)C(O)CH2C(O)] has been characterized in solution by IR and NMR spectroscopies. Furthermore its molecular structure has been determined by X-ray crystallography. Reversible C-H bond formation in HOs3(CO)9[μ-(PPh2)C=C{PPh(C6H4)}C(O)CH2C(O)] is demonstrated by ligand trapping studies to give 1,1-Os3(CO)9L(bpcd) (where L = CO, phosphine) via the unsaturated intermediate 1,1-Os3(CO)9(bpcd). The kinetics for reductive coupling in HOs3(CO)9[γ-(PPh2)C=C{PPh(C6H4)}C(O)CH2C(O)] and DOs3(CO)9[μ-(PPh2-d10)C=C{P(Ph-d5)(C6D4)}C(O)CH2C(O)] in the presence of PPh3 give rise to a kH/kD value of 0.88, whose magnitude supports the existence of a preequilibrium involving the hydride(deuteride) cluster and a transient arene-bound Os3 species that precedes the rate-limiting formation of 1,1-Os3(CO)9(bpcd). Strong proof for the proposed hydride(deuteride)/arene preequilibrium has been obtained from photochemical studies employing the isotopically labeled cluster 1,1-Os3(CO)10(bpcd-d4ortho), whose bpcd phenyl groups each contain one ortho hydrogen and deuterium atom. Equilibrium and kinetic isotope effects in the orthometallation step has been determined by 1H NMR in photochemical studies. Kinetics for the transformation from HOs3(CO)9[μ-(PPh2)C=C{PPh(C6H4)}C(O)CH2C(O)] to HOs3(CO)8(μ3-C6H4)[μ2,η1-PPhC=C(PPh2)C(O)CH2C(O)] has been studied by UV-VIS spectroscopy for which the mechanism is discussed.
Date: May 2008
Creator: Wu, Guanmin