The Abraham solvation model (ABSM) is an experimentally derived predictive model used to help predict various solute properties. This work covers various uses for the ABSM including predicting molar enthalpies of vaporization, predicting solvent coefficients for two new solvents (2,2,5,5-tetramethyloxolane and diethyl carbonate), predicting values for multiple new ionic liquids (ILs). This work also introduces a novel method for updating IL ABSM parameters by updating cation- and anion-specific values using linear algebra and binary matrices.

The first study project is based on modeling Earth abundant 3d transition-metal methoxide complexes with potentially redox-noninnocent ligands for methane C–H bond activation to form methanol (LnM-OMe + CH4 → LnM–Me + CH3OH). Three types of complex consisting of tridentate pincer terpyridine-like ligands, and different first-row transition metals (M = Ti, V, Cr, Mn, Fe, Co, Ni, and Cu) were modeled to elucidate the reaction mechanism as well as the effect of the metal identity on the thermodynamics and kinetics of a methane activation reaction. The calculations showed that the d electron count of the metal is a more significant factor than the metal's formal charge in controlling the thermodynamics and kinetics of C–H activation. These researches suggest that late 3d-metal methoxide complexes that favor σ-bond metathesis pathways for methane activation will yield lower barriers for C–H activation, and are more profitable catalyst for future studies. Second, subsequently, on the basis of the first project, density functional theory is used to analyze methane C−H activation by neutral and cationic nickel-methoxide complexes. This study identifies strategies to further lower the barriers for methane C−H activation through evaluation of supporting ligand modifications, solvent polarity, overall charge of complex, metal identity and counterion …

Semiconductor circuitry feature miniaturization continues in response to Moore 's Law pushing the limits of aluminum and forcing the transition to Cu due to its lower resistivity and electromigration. Copper diffuses into silicon dioxide under thermal and electrical stresses, requiring the use of barriers to inhibit diffusion, adding to the insulator thickness and delay time, or replacement of SiO2 with new insulator materials that can inhibit diffusion while enabling Cu wetting. This study proposes modified amorphous silicon carbon hydrogen (a-Si:C:H) films as possible diffusion barriers and replacements for SiO2 between metal levels, interlevel dielectric (ILD), or between metal lines (IMD), based upon the diffusion inhibition of previous a-Si:C:H species expected lower dielectric constants, acceptable thermal conductivity. Vinyltrimethylsilane (VTMS) precursor was condensed on a titanium substrate at 90 K and bombarded with electron beams to induce crosslinking and form polymerized a-Si:C:H films. Modifications of the films with hydroxyl and nitrogen was accomplished by dosing the condensed VTMS with water or ammonia before electron bombardment producing a-Si:C:H/OH and a-Si:C:H/N and a-Si:C:H/OH/N polymerized films in expectation of developing films that would inhibit copper diffusion and promote Cu adherence, wetting, on the film surface. X-ray Photoelectron Spectroscopy was used to characterize Cu metallization of …

The objective of this research problem was to synthesize aldohaloketenes and investigate the chemistry of this new class of ketenes.

This work includes two unrelated areas of research. The first portion of this work involved combusting densified refuse derived fuel (dRDF) with coal and studying the effect that Ca(0H)2 binder had on reducing polycyclic aromatic hydrocarbon (PAH) and polychlorinated biphenyl (PCB) emissions. The second area of work was directed at developing nondestructive infrared techniques in order to aid in the analysis of postage stamp adhesives. With Americans generating 150-200 million tons a year of Municipal Solid Waste (MSW) and disposing of nearly ninety percent of it in landfills, it is easy to understand why American landfills are approaching capacity. One alternative to landfilling is to process the MSW into RDF. There are technical and environmental problems associated with RDF. This work provides some answers concerning the amount of PAH and PCB emissions generated via the combustion of RDF with coal. It was found that the Ca(OH)2 binder greatly reduced both the PAH and the PCB emissions. In fact, PAH emissions at the ten-percent level were reduced more by using the binder than by the pollution control equipment. If the Ca(0H)2 binder can reduce not only PAH and PCB emissions, but also other noxious emissions, such as acid gases or dioxin, …

The determination of carbon monoxide is also possible by trapping CO on preconditioned molecular sieve and thermal desorption. Analysis in this case is performed by gas chromatography/mass spectroscopy, although the trapping technique is applicable to other suitable GC techniques.

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 …

The direct epitaxial growth of multilayer BN by atomic layer deposition is of critical significance forfo two-dimensional device applications. X-ray photoelectron spectroscopy (XPS) and low energy electron diffraction (LEED) demonstrate layer-by-layer BN epitaxy on two different substrates. One substrate was a monolayer of RuO2(110) formed on a Ru(0001) substrate, the other was an atomically clean Ni(111) single crystal. Growth was accomplished atomic layer deposition (ALD) cycles of BCl3/NH3 at 600 K substrate temperature and subsequent annealing in ultrahigh vacuum (UHV). This yielded stoichiometric BN layers, and an average BN film thickness linearly proportional to the number of BCl3/NH3 cycles. The BN(0001)/RuO2(110) interface had negligible charge transfer or band bending as indicated by XPS and LEED data indicate a 30° rotation between the coincident BN and oxide lattices. The atomic layer epitaxy of BN on an oxide surface suggests new routes to the direct growth and integration of graphene and BN with industrially important substrates, including Si(100). XPS and LEED indicated epitaxial deposition of h-BN(0001) on the Ni(111) single crystal by ALD, and subsequent epitaxially aligned graphene was deposited by chemical vapor deposition (CVD) of ethylene at 1000 K. Direct multilayer, in situ growth of h-BN on magnetic substrates such as …

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. …

This dissertation focuses on the chemistry, detection, and control of metals and metal contaminants during manufacturing of integrated circuits (ICs) on silicon wafers. Chapter 1 begins with an overview of IC manufacturing, including discussion of the common aqueous cleaning solutions, metallization processes, and analytical techniques that will be investigated in subsequent chapters. Chapter 2 covers initial investigations into the chemistry of the SC2 clean - a mixture of HCl, H2O2, and DI water - especially on the behavior of H2O2 in this solution and the impact of HCl concentration on metal removal from particle addition to silicon oxide surfaces. Chapter 3 includes a more generalized investigation of the chemistry of metal ions in solution and how they react with the silicon oxide surfaces they are brought into contact with, concluding with illumination of the fundamental chemical principles that govern their behavior. Chapter 4 shows how metal contaminants behave on silicon wafers when subjected to the high temperature (≥ 800 °C) thermal cycles that are encountered in IC manufacturing. It demonstrates that knowledge of some fundamental thermodynamic properties of the metals allow accurate prediction of what will happen to a metal during these processes. Chapter 5 covers a very different but …

As countries pledge their commitment to a net-zero future, much of the previously forgotten climate change research were revitalized by efforts from both governmental and private sectors. In particular, the utilization of lignocellulosic materials saw a special spotlight in research interest for its abundance and its carbon removal capability during photosynthesis. The initial effort in mimicking enzymatic active sites of β-glucosidase will be explored. The crystalline covalent organic frameworks (COFs) allowed for the introduction of a variety of noncovalent interactions, which enhanced the adsorption and the catalytic activity against cellobiose and its glycosidic bonds. The physical processes associated with this reaction, such as the kinetics, equilibrium, and activation energies, will be closely examined and compared with existing standard materials and comparable advanced catalysts. In addition, several variants of COFs were synthesized to explore the effect of various noncovalent interactions with cellobiose. A radical-bearing COF was synthesized and characterized. The stability of this radical was examined by electron paramagnetic resonance spectroscopy (EPR) and its oxidative capability tested with model lignin and alcoholic compounds. The reaction products are monitored and identified using gas chromatography-mass spectroscopy (GC-MS). An oxidative coupling of phenol was explored, and its initial results are presented in chapter 5.

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 dissertation details the use of computational methods to understand the effect that cancer-related mutations have on proteins that complex with nucleic acids. Firstly, we perform molecular dynamics (MD) simulations of various mutations in DNA polymerase κ (pol κ). Through an experimental collaboration, we classify the mutations as more or less active than the wild type complex, depending upon the incoming nucleotide triphosphate. From these classifications we use quantum mechanics/molecular mechanics (QM/MM) to explore the reaction mechanism. Preliminary analysis points to a novel method for nucleotide addition in pol κ. Secondly, we study the ten-eleven translocation 2 (TET2) enzyme in various contexts. We find that the identities of both the substrate and complementary strands (or lack thereof) are crucial for maintaining the complex structure. Separately, we find that point mutations within the protein can affect structural features throughout the complex, only at distal sites, or only within the active site. The mutation's position within the complex alone is not indicative of its impact. Thirdly, we share a new method that combines direct coupling analysis and MD to predict potential rescue mutations using poly(ADP-ribose) polymerase 1 as a model enzyme. Fourthly, we perform MD simulations of mutations in the protection of …

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. …

Computational chemistry employs mathematical algorithms, statistics, and large databases to integrate chemical theory with experimental observations. Computational modeling allows us to make predictions concerning molecular properties and reactivity that ultimately lead to accurate assessment of the most important fundamental properties of chemical systems. Advances in theoretical techniques and computer power have dramatically increased the usefulness and importance of computational chemistry as a complement to experimental studies. This is especially relevant to catalytic reactions of industrial importance as well as the analysis of structural properties and the resulting spectroscopic phenomena in what are often otherwise counterintuitive models. This dissertation is a representation of the research I performed during my years as a graduate student in the Chemistry Department at the University of North Texas. My research has examined novel carbenes as efficient organocatalysts, structure-based design and optimization of small molecule drugs, and surveying methods to accurately describe structure and bonding and catalytic abilities of inorganic and organometallic systems. The works presented herein have been published or are awaiting submission to peer-reviewed scientific journals. A variety of computational techniques were employed in studying metal-mediated catalysis and organocatalysis as well as the structural and photophysical properties of systems containing closed-shell transition metal ions.

A series of computational studies were carried out on Group 14 (C, Si and Ge) elements in organometallic and biological compounds. Theoretical studies on classical and H-bridged A3H3+ (A=C, Si and Ge) as p ligands with different organometallic fragments at B3LYP and B3P86 level reveal a reverse charge transfer from ligand to metal in Si and Ge complexes whereas in C complexes there is a small charge transfer from metal to ligand. The H-bridged complexes are more stable than the complexes based on Si3H3+ and Ge3H3+ ligands with terminal hydrogens. The stability of the bridged systems increases from Si to Ge. Corrective scale factors for computed harmonic CºO vibrational frequencies for 31 organometallic complexes have been determined at the HF and B3LYP levels. The scaled B3LYP frequencies exhibit a greater reliability than do HF frequencies. Experimental data have shown that Si/Ge-substituted decapeptides are advantageous over their C analog in vitro and in vivo studies in modern hormone therapy. A computational investigation was carried out on the synthesized decapeptides focusing on position 5 containing Si and Ge. The results have shown that there are some differences in C, Si and Ge-containing analogs. However, further investigations are needed to elucidate the observed …

This work discusses applications of computational simulations to a wide variety of chemical systems, to investigate intermolecular interactions to develop force field parameters and gain new insights into chemical reactivity and structure stability. First, we cover the characterization of hydrogen-bonding interactions in pyrazine tetracarboxamide complexes employing quantum topological analyses. Second we describe the use of quantum mechanical energy decomposition analysis (EDA) and non-covalent interactions (NCIs) analysis to investigate hydrogen-bonding and intermolecular interactions in a series of representative 1-butyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide ([bmim][Tf2N]) ion pairs extracted from classical equilibrium and non-equilibrium molecular dynamics simulations. Thirdly, we describe the use of multipolar/polarizable AMOEBA force field to study the extraction of benzene from a gasoline model employing 1,3-dimethylimidazolium tetrafluorobrorate, [DMIM][BF4], and ethylmethylimidazolium tetrafluorobrorate, [EMIM][BF4]. Fourthly, we cover the recent improvements and new capabilities of the QM/MM code "LICHEM". Finally, we describe the use of polarizable ab initio QM/MM calculations and study the reaction mechanism of N-tert-butyloxycarbonylation of aniline in [EMIm][BF4], and ground state destabilization in uracil DNA glycosylase (UDG).

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 …

With the reliability requirements of automobile microelectronics pushing towards near 0 ppb levels of failure control, halide induced corrosion issues in wire bonded devices have to be tightly controlled to achieve such a high reliability goal. With real-time corrosion monitoring, for the first time we demonstrated that the explosive H2 evolution coupled with the oxygen reduction reaction, occurring at the critical Al/Cu interfaces, is the key driving force for the observed aggressive corrosion. Several types of passivation coating on Cu wire surfaces to effectively block the cathodic H2 evolution were explored with an aim to disrupt this explosive corrosion cycle. The properties of the protective coating were evaluated using various analytical techniques. The surface coating exhibited high thermal stability up to 260 °C (evaluated using TGA analysis). A uniform, highly hydrophobic coating (surface contact angle of >130° with water), was achieved by carefully controlling CVD parameters such as time of deposition, surface control of Cu metal, amount of inhibitor compound loading, temperature of coating process etc. FTIR spectroscopy combined with corrosion screening was used to optimize the CVD passivated coating with strong chemisorption. SEM and EDX, XPS were carried out on various coated surfaces to understand the composition and selectivity …