Advances in computing capabilities have facilitated the application of quantum mechanical methods to increasingly larger and more complex chemical systems, including weakly interacting and biologically relevant species. One such ab initio-based composite methodology, the correlation consistent composite approach (ccCA), has been shown to be reliable for the prediction of enthalpies of formation and reaction energies of main group species in the gas phase to within 1 kcal mol-1, on average, of well-established experiment, without dependence on experimental parameterization or empirical corrections. In this collection of work, ccCA has been utilized to determine the proton affinities of deoxyribonucleosides within an ONIOM framework (ONIOM-ccCA) and to predict accurate enthalpies of formation for organophosphorus compounds. Despite the complexity of these systems, ccCA is shown to result in enthalpies of formation to within ~2 kcal mol-1 of experiment and predict reliable reaction energies for systems with little to no experimental data. New applications for the ccCA method have also been introduced, expanding the utility of ccCA to solvated systems and complexes with significant noncovalent interactions. By incorporating the SMD solvation model into the ccCA formulation, the Solv-ccCA method is able to predict the pKa values of nitrogen systems to within 0.7 pKa unit (less …

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.

Predictive methods have been employed to characterize chemical separation mediums including solvents and absorbents. These studies included creating Abraham solvation parameter models for room-temperature ionic liquids (RTILs) utilizing novel ion-specific and group contribution methodologies, polydimethyl siloxane (PDMS) utilizing standard methodology, and the micelles cetyltrimethylammonium bromide (CTAB) and sodium dodecylsulfate (SDS) utilizing a combined experimental setup methodology with indicator variables. These predictive models allows for the characterization of both standard and new chemicals for use in chemical separations including gas chromatography (GC), solid phase microextraction (SPME), and micellar electrokinetic chromatography (MEKC). Gas-to-RTIL and water-to-RTIL predictive models were created with a standard deviation of 0.112 and 0.139 log units, respectively, for the ion-specific model and with a standard deviation of 0.155 and 0.177 log units, respectively, for the group contribution fragment method. Enthalpy of solvation for solutes dissolved into ionic liquids predictive models were created with ion-specific coefficients to within standard deviations of 1.7 kJ/mol. These models allow for the characterization of studied ionic liquids as well as prediction of solute-solvent properties of previously unstudied ionic liquids. Predictive models were created for the logarithm of solute's gas-to-fiber sorption and water-to-fiber sorption coefficient for polydimethyl siloxane for wet and dry conditions. These models …

As the miniaturization of functional devices in integrated circuit (IC) continues to scale down to sub-nanometer size, the process complexity increases and makes materials characterization difficult. One of our research effort demonstrates the development and application of novel Multiple Internal Reflection Infrared Spectroscopy (MIR-IR) as a sensitive (sub-5 nm) metrology tool to provide precise chemical bonding information that can effectively guide through the development of more efficient process control. In this work, we investigated the chemical bonding structure of thin fluorocarbon polymer films deposited on low-k dielectric nanostructures, using Fourier transform infrared spectroscopy (FTIR), X-ray photoelectron spectroscopy (XPS) and scanning electron microscopy (SEM). Complemented by functional group specific chemical derivatization reactions, fluorocarbon film was established to contain fluorinated alkenes and carbonyl moieties embedded in a highly cross-linked, branched fluorocarbon structure and a model bonding structure was proposed for the first time. In addition, plasma induced damage to high aspect ratio trench low-k structures especially on the trench sidewalls was evaluated both qualitatively and quantitatively. Damage from different plasma processing was correlated with Si-OH formation and breakage of Si-CH3 bonds with increase in C=O functionality. In another endeavor, TiN hard mask defect formation after fluorocarbon plasma etch was characterized and investigated. …

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 …

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 …

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 …

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 …

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.

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. …

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 …

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.

The ability of gold(I) to activate many types of unsaturated bonds toward nucleophilic attack was not widely recognized until the early 2000s. One major challenge in gold catalysis is the control over regioselectivity when there are two or more possible products as a result of complicated mechanistic pathways. It is well know that the choice of ligand can have dramatic effects on which pathway is being followed but very rarely are the reasons for this selectivity understood. The synthesis of new acyclic diaminocarbenes was developed and a study of the ligand effects on the regioselectivity of a gold-catalyzed domino enyne cyclization hydroarylation reaction and a Nazarov cyclization was undertaken. New chiral acyclic diaminocarbenes were also developed and tested along side new C3-symmetric phosphite ligands in an asymmetric intramolecular hydroamination of allenes. Structure activity correlations were developed for the potential use in further rational ligand design. The synthesis of 6a,7-dihydro-5-amino-dibenzo[c,g]chromene derivatives via a gold-catalyzed domino reaction of alkynylbenzaldehydes in the presence of secondary amines was developed. These were sent to be screened for biological activity.

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 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 …

Within this educational endeavor instrumental development was explored through the investigation of microwave induce stable electromagnetic waves within a non-linear yttrium iron garnet ferromagnetic waveguide. The resulting magnetostatic surface waves were investigated as a possible method of rapid analytical evaluation of material composition. Initial analytical results indicate that the interaction seen between wave and material electric and magnetic fields will allow phase coherence recovery andanalysis leading to enhancement of analytical value. The ferromagnetic waveguide selected for this research was a high quality monocrystalline YIG (yttrium iron garnet) film. Magnetostatic spin waves (MSW) were produced within the YIG thin waveguide. Spin waves with desired character were used to analytically scan materials within the liquid and solid phase.

The field of direct inject mass spectrometry includes a massive host of ambient ionization techniques that are especially useful for forensic analysts. Whether the sample is trace amounts of drugs or explosives or bulk amounts of synthetic drugs from a clandestine laboratory, the analysis of forensic evidence requires minimal sample preparation, evidence preservation, and high sensitivity. Direct inject mass spectrometry techniques can rarely provide all of these. Direct analyte-probed nanoextraction coupled to nanospray ionization mass spectrometry, however, is certainly capable of achieving these goals. As a multifaceted tool developed in the Verbeck laboratory, many forensic applications have since been investigated (trace drug and explosives analysis). Direct inject mass spectrometry can also be easily coupled to assays to obtain additional information about the analytes in question. By performing a parallel artificial membrane assay or a cell membrane stationary phase extraction prior to direct infusion of the sample, membrane permeability data and receptor activity data can be obtained in addition to the mass spectral data that was already being collected. This is particularly useful for characterizing illicit drugs and their analogues for a biologically relevant way to schedule new psychoactive substances.

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 …

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 …

A study was conducted to investigate the relationships between cybergaming treatment groups and the control group (N = 99: ncontrol = 8; nlogic = 29; nspatial = 30; ncombination = 32) with success in the organic chemistry I course as measured by achievement over a 10-week period. The treatment groups included logic training, spatial training, and combination logic-spatial training. Students' ability was measured by pre/post exams using the Group Assessment of Logical Thinking (GALT) to measure logic ability, Purdue Visualizations of Rotations (ROT) test to measure spatial skills, and the General-Organic-Biochemistry (GOB) Exam to measure content attainment. Finally, students' responses about participation in this experience were evaluated using open- and closed-ended questions on a self-developed survey. A second study was conducted to evaluate the relationship between the cybergaming treatment and control groups (N = 88: nexperimental = 27; ncontrol = 61) with success in the general chemistry I course as measured by achievement and final course averages and grades. The cybergaming treatment group underwent intensive combination logic-spatial training for 10 weeks. Students' progress was measured using three pre/post instruments: Group Assessment of Logical Thinking (GALT) measured logic ability, Purdue Visualizations of Rotations (ROT) Test measured spatial skills, and the California …

Cyclic voltammetry experiments were performed to compare the electrodeposition characteristics of bismuth on ruthenium. Two types of electrodes were used for comparison: a Ru shot electrode (polycrystalline) and a thin film of radio-frequency sputtered Ru on a Ti/Si(100) support. Experiments were performed in 1mM Bi(NO3)3/0.5M H2SO4 with switching potentials between -0.25 and 0.55V (vs. KCl sat. Ag/AgCl) and a 20mV/s scan rate. Grazing incidence x-ray diffraction (GIXRD) determined the freshly prepared thin film electrode was hexagonally close-packed. After thermally oxidizing at 600°C for 20 minutes, the thin film adopts the tetragonal structure consistent with RuO2. a hydrated oxide film (RuOx?(H2O)y) was made by holding 1.3V on the surface of the film in H2SO4 for 60 seconds and was determined to be amorphous. Underpotential deposition of Bi was observed on the metallic surfaces and the electrochemically oxidized surface; it was not observed on the thermal oxide.

Zinc-nickel ?-phase silicate and copper-nickel silicate corrosion resistant coatings have been prepared via electrochemical methods to improve currently available corrosion resistant materials in the oil and gas industry. A layered silicate, montmorillonite, has been incorporated into the coatings for increased corrosion protection. For the zinc nickel silicate coatings, optimal plating conditions were determined to be a working pH range of 9.3 -9.5 with a borate based electrolyte solution, resulting in more uniform deposits and better corrosion protection of the basis metal as compared to acidic conditions. Quality, strongly adhering deposits were obtained quickly with strong, even overall coverage of the metal substrate. The corrosion current of the zinc-nickel-silicate coating is Icorr = 3.33E-6 for a borate based bath as compared to a zinc-nickel bath without silicate incorporation (Icorr = 3.52E-5). Step potential and direct potential methods were examined, showing a morphological advantage to step potential deposition. The effect of borate addition was examined in relation to zinc, nickel and zinc-nickel alloy deposition. Borate was found to affect the onset of hydrogen evolution and was examined for absorption onto the electrode surface. For copper-nickel silicate coatings, optimal conditions were determined to be a citrate based electrolytic bath, with pH = 6. …

In the oil and gas industry, high corrosion resistance and hardness are needed to extend the lifetime of the coatings due to exposure to high stress and salt environments. Electrodeposition has become a favorable technique in synthesizing coatings because of low cost, convenience, and the ability to work at low temperatures. Electrodeposition of metal matrix composites has become popular for enhanced corrosion resistance and hardness in the oil and gas industry because of the major problems that persist with corrosion. Two major alloys of copper-nickel, 90-10 and 70-30, were evaluated for microbial corrosion protection in marine environments on a stainless steel substrate. Copper and copper alloys are commonly used in marine environments to resist biofouling of materials by inhibiting microbial growth. Literature surveying the electrodeposition of Cu-Ni incorporated with nano- to micro- particles to produce metal matrix composites has been reviewed. Also, a novel flow cell design for the enhanced deposition of metal matrix composites was examined to obtain the optimal oriented structure of the layered silicates in the metal matrix. With the addition of montmorillonite into the Ni and Cu-Ni matrix, an increase in strength, adhesion, wear and fracture toughness of the coating occurs, which leads to an increase …

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 …