NiSi is an attractive material in the production of CMOS devices. The problem with the utilization of NiSi, is that there is no proper method of cleaning the oxide on the surface. Sputtering is the most common method used for the cleaning, but it has its own complications. Dry cleaning methods include the reactions with radicals and these processes are not well understood and are the focus of the project. Dissociated NF3 and NH3 were used as an alternative and XPS is the technique to analyze the reactions of atomic fluorine and nitrogen with the oxide on the surface. A thermal cracker was used to dissociate the NF3 and NH3 into NFx+F and NHx+H. There was a formation of a NiF2 layer on top of the oxide and there was no evidence of nitrogen on the surface indicating that the fluorine and hydrogen are the reacting species. XPS spectra, however, indicate that the substrate SiO2 layer is not removed by the dissociated NF3 and NiF2 growth process. The NiF2 over layer can be reduced to metallic Ni by reacting with dissociated NH3 at room temperature. The atomic hydrogen from dissociated ammonia reduces the NiF2 but it was determined that the …

Computational methods were employed to investigate catalytic processes. First, DFT calculations predicted the important geometry metrics of a copper–nitrene complex. MCSCF calculations supported the open-shell singlet state as the ground state of a monomeric copper nitrene, which was consistent with the diamagnetic character deduced from experimental observations. The calculations predicted an elusive terminal copper nitrene intermediate. Second, DFT methods were carried out to investigate the mechanism of C–F bond activation by a low-coordinate cobalt(I) complex. The computational models suggested that oxidative addition, which is very rare for 3d metals, was preferred. A π–adduct of PhF was predicted to be a plausible intermediate via calculations. Third, DFT calculations were performed to study ancillary ligand effects on C(sp3)–N bond forming reductive elimination from alkylpalladium(II) amido complexes with different phosphine supporting ligands. The dimerization study of alkylpalladium(II) amido complexes indicated an unique arrangement of dative and covalent Pd-N bonds within the core four-membered ring of bimetallic complexes. In conclusion, computational methods enrich the arsenal of methods available to study catalytic processes in conjunction with experiments.

There is a consistent need in many industries, especially oil and gas, to develop coatings which have higher corrosion resistance and better hardness to extend the lifetime of equipment when it is exposed to hostile environments. Electrodeposition has been a favorable method in the synthesis of metal coatings because of its low cost, convenience, ability to work at low temperatures, and ability to control surface morphology and structure. The inclusion of ceramic nanoparticles in metal matrix composites has previously been investigated as a technique to not only increase the corrosion resistance of the native metal but also to improve the hardness and mechanical properties. Cerium oxide nanoparticles were modified through the grafting of organic groups with increasing hydrophobicity for use in nickel coatings on stainless steel to further improve the corrosion properties while maintaining the hardness of the nanocomposite coatings. The process of modifying the cerium oxide nanoparticles involved the use of aryl diazonium salts and resulted in multilayers forming on the surface of the nanoparticles. Praseodymium oxide nanoparticles were also investigated as additives to nickel coatings, since praseodymium oxide has not yet been studied as a possible corrosion protection enhancement in coatings. These coatings were evaluated for composition and …

Styrene production by a (FlDAB)PdII(TFA)(η2-C2H4) complex was modeled using density functional theory (DFT). Benzene C-H activation by this complex was studied via five mechanisms: oxidative addition/reductive elimination, sigma-bond metathesis, concerted metalation deprotonation (CMD), CMD activation of ethylene, and benzene substitution of ethylene followed by CMD of the ligated benzene. Calculations provided evidence that conversion of benzene and ethylene to styrene was initiated by the fifth pathway, arylation via CMD of coordinated benzene, followed by ethylene insertion into the Ru-Ph bond, and then β-hydrogen elimination. Also, monomer (active species)/dimer equilibrium concentrations were analyzed. The results obtained from present study were compared with that of a recently reported RhI complex to help identify more suitable catalysts for the direct production of styrene from ethylene and benzene. Second, theoretical studies of heterobimetallic {Ag–Fe(CO)5}+ fragments were performed in conjunction with experiments. The computational models suggested that for this first example of a heterodinuclear, metal-only FeAg Lewis pair (MOLP) that Fe(CO)5 acts as a Lewis base and AgI as a Lewis acid. The ῡCO bands of the studied molecules showed a blue shift relative to those measured for free Fe(CO)5, which indicated a reduction in Fe→CO backbonding upon coordination to silver(I). Electrostatic interaction is predicted …

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 …

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 …

The reaction of the chelating ligand 4-[4,6-bis(3,5-dimethyl-1H-pyrazol-1-yl)-1,3,5-triazin-2-yl]-N,N-diethyl-benzenamine, L, with pentacarbonylchlororhenium by conventional heating method produces the complexes fac-[ReL(CO)3Cl2] and fac-[Re2L(CO)6Cl2] in a period of 48 hours. The use of microwaves as the source of heat and the increase in the equivalents of one of the reactants leads to a more selective reaction and also decreases the reaction time to 1 hour. After proper purification, the photophysical properties of fac-[ReL(CO)3Cl] were analyzed. The solid-state photoluminescence analysis showed an emission band at 628 nm independent of temperature. However, in the solution studies, the emission band shifted from 550 nm in frozen media to 610 nm when the matrix became fluid. These results confirm that this complex possess a phenomenon known as rigidochromism.

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 …

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 …

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.

Porphyrins offer a very synthetically flexible template which can be modified in numerous ways to synthesize molecules with very useful properties applicable in areas such as non-linear optical properties, photodynamic therapy, dye-sensitized solar cells, chemical sensors and organic electronic devices. β-Substituted π-extended porphyrins offer unique capabilities in tuning the properties of the molecule towards practical applications. Increased π-conjugation allows the HOMO-LUMO gap to decrease and hence to redshift the absorption into the near-IR region. β-Fused benzoporphyrins offer additional benefits in which the benzene ring itself can be further modified using electron donating substituents and electron donating substituents to electronically tune these porphyrins for various uses. The goal of the research pursued in this dissertation was to develop new methods for the development of β-Substituted π-extended porphyrins and to study their optical and electronic properties. To accomplish this goal, we developed new method to synthesize A2B2 type tetrabenzoporphyrins and we studied the electron transfer in such systems. We also studied the effectiveness of such systems in dye sensitized solar cells. A new method to synthesize functionalized naphthalene fused porphyrins was also developed and we were also able to use this method to synthesize a push-pull naphthalene fused porphyrin.

This dissertation focuses on the development, characterization, and analysis of luminescent materials and coatings for sensing applications, including CO2, heavy metals, and silver. Chapter 2 involves the use of a gold(I) pyrazolate trimer that is able to detect silver ions with an AgNP medium. Detection of silver is vital, because there is an influx of silver into our environment caused by the increased use of AgNP. Therefore, having a sensor that is able to differentiate between and detect only Ag ions is an important first step to solving the toxicity mystery of AgNPs. Chapter 3 focuses on the development of sensor coatings containing a Eu(III) based luminescent system for sensing dissolved CO2 without the aid of an absorption-based dye. It is well-known that monitoring CO2 levels in our environment is important since even at low concentrations it can cause adverse health effects to the human body. This work demonstrates a pH-sensitive Eu complex being used directly as a CO2 sensor without the aid of any other absorption-based dye. Chapter 4 explores the idea of developing a heavy metal sensor for lead and its ability to detect lead in wide concentration range upon changing the pH of the medium and the …

This work discusses the C-H bond activation by transition metal complexes using various computational methods. First, we performed a DFT study of oxidative addition of methane to Ta(OC2H4)3A (where A may act as an ancillary ligand) to understand how A may affect the propensity of the complex to undergo oxidative addition. Among the A groups studied, they can be a Lewis acid (B or Al), a saturated, electron-precise moiety (CH or SiH), a σ-donor (N), or a σ-donor/π-acid (P). By varying A, we seek to understand how changing the electronic properties of A can affect the kinetics and thermodynamics of methane C–H activation by these complexes. For all A, the TS with H trans to A is favored kinetically over TS with CH3 trans to A. Upon moving from electron-deficient to electron-rich moieties (P and N), the computed C–H activation barrier for the kinetic product decreases significantly. Thus, changing A greatly influences the barrier for methane C–H oxidative addition by these complexes. Secondly, a computational study of oxidative addition (OA) of methane to M(OC2H4)3A (M = Ta, Re and A = ancillary ligand) was carried out using various computational methods. The purpose of this study was to understand how variation …

This work involves synthesis and characterization of isotropic and anisotropic noble metal nanoparticles for applications ranging from antimicrobial uses to anticancer applications. These nanomaterials are stabilized in genuinely benign biomaterials ranging from polymers to cross linked proteins for targeted cancer treatments. The nanoparticles are found to have tunable optical properties.

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 …

In the development of covalent organic frameworks (COFs), often the scaffold linkers are assumed to be electro- and photoinactive, and this was also to be the case for 2,3,6,7,10,11-hexahydroxytriphenylene, a tritopic linker. However, as demonstrated in the present study, the reaction product of this linker, hexaoxatriphenylene, is electron rich and when connected to a suitable photosensitizer engages itself in an efficient excited-state charge separation process. In the present study, we have employed BF2-chelated dipyrromethenes (BODIPYs) as sensitizers, which are connected to hexaoxatriphenylene through the center boron, rendering paddle-wheel-type structures. Systematic photophysical, electrochemical, computational, and photochemical studies involving pump-probe femtosecond transient spectroscopy have been performed to establish efficient charge separation in these novel supramolecular structures.

Corrosion is one of the most expensive failures in industries that used metal components and other construction materials. In fact, corrosion is responsible for hundreds of billions-dollar loss in the US alone each year. In general, corrosion occurs when metal surfaces are exposed to water, oxygen, acids, bases, or salts. Therefore, metal substrates must be protected by using materials that act as barriers to avoid destructive corrosion attack. Aluminum is one of the most common metals used in the industry; and it is used in many places such as refining and petroleum production equipment, pipelines, and fossil fuel power plants. Aluminum is known to have corrosion resistance due to the forming of an oxide layer that can be reformed rapidly if the surface gets damaged. However, in the long-term the oxide layer cannot protect the aluminum surface from corrosion because it is stable only in neutral mediums and it is soluble in acidic and basic environments. Barrier protection is one of the most effective methods that prevent aluminum surfaces from being exposed to corrosive environments. These barriers can be organic or inorganic coatings that can limit the electron transport or the cathodic and the anodic reactions between aluminum alloys and …

Computational chemistry has gained interest as a characterization tool to predict photoluminescence, reactivity and structural properties of organic and transition metal complexes. With the rise of methods including relativity, these studies have been expanded to the accurate modeling of luminescence spectra of complexes with considerable spin-orbit splitting due to heavy metal centers as well as the reaction pathways for these complexes to produce natural products such as hydrogen gas. These advances have led to the synthesis and utility of more effective catalysis as well as the development of more effective organic light emitting diodes (OLEDs) through the incorporation of organometallic complexes as emitters instead of typical organic emitters. In terms of significant scientific advancement presented in this work is in relation to the discovery of significant spin-orbit splitting in a gold(I) alkylphosphine complex, where the splitting results in the states that emit in different colors of the visible region of the electromagnetic spectrum. This work also reveals the discovery both computationally and experimentally, of a genuine polar-covalent bond between two-closed shell metals. This work highlights a complex with an incredibly short gold(I) – copper(I) intermetallic distance leading to a vibrational frequency and dissociation energy that is on par with those …

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 …

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. …

Density functional theory is an efficient and useful method of solving single-reference computational chemistry problems, however it struggles with multi-reference systems. Modifications have been developed in order to improve the capabilities of density functional theory. In this work, density functional theory has been successfully applied to solve multi-reference systems with large amounts of non-dynamical correlation by use of modifications. It has also been successfully applied for geometry optimizations for lanthanide trifluorides.

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 …

The kinetics of the reaction of atomic sulfur and nitrogen dioxide have been investigated over the temperature range 298 to 650 K and pressures from 14 - 405 mbar using the laser flash photolysis - resonance fluorescence technique. The overall bimolecular rate expression k (T) = (1.88 ± 0.49) x10-11 exp-(4.14 ± 0.10 kJ mol-1)/RT cm3 molecule-1 s-1 is derived. Ab initio calculations were performed at the CCSD(T)/CBS level of theory and a potential energy surface has been derived. RRKM theory calculations were performed on the system. It is found that an initially formed SNO2 is vibrationally excited and the rate of collisional stabilization is slower than the rate of dissociation to SO + NO products by a factor of 100 - 1000, under the experimental conditions.

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, …