In this work we address two problems in computational chemistry relevant to biomolecular modeling. In the first project, we consider the conformer space of melatonin as a a representative example of “real-life” flexible biomolecules. Geometries for all 52 unique conformers are optimized using spin-component scaled MP2, and then relative energies are obtained at the CCSD (T) level near the complete basis set limit. These are then used to validate a variety of DFT methods with and without empirical dispersion corrections, as well as some lower-level ab initio methods. Basis set convergence is found to be relatively slow due to internal C-H…O and C-H…N contacts. Absent dispersion corrections, many DFT functionals will transpose the two lowest conformers. Dispersion corrections resolve the problem for most functionals. Double hybrids yield particularly good performance, as does MP2.5. In the second project, we propose a simple DFT-based diagnostic for nondynamical correlation effects. Aλ= (1-TAE [ΧλC]/TAE[XC])/λ where TAE is the total atomization energy, XC the “pure” DFT exchange-correlation functional, and ΧλC the corresponding hybrid with 100λ% HF-type exchange. The diagnostic is a good predictor for sensitivity of energetics to the level of theory, unlike most of the wavefunction-based diagnostics. For GGA functionals, Aλ values approaching unity …

Organic dyes are examined in photoelectrochemical systems wherein they engage in thermal (rather than photoexcited) electron donation into metal oxide semiconductors. These studies are intended to elucidate fundamental parameters of electron transfer in photoelectrochemical cells. Development of novel methods for the structure/property tuning of electroactive dyes and the preparation of nanostructured semiconductors have also been discovered in the course of the presented work. Acceptor sensitized polymer oxide solar cell devices were assembled and the impact of the acceptor dyes were studied. The optoelectronic tuning of boron-chelated azadipyrromethene dyes has been explored by the substitution of carbon substituents in place of fluoride atoms at boron. Stability of singlet exited state and level of reduction potential of these series of aza-BODIPY coumpounds were studied in order to employ them as electron-accepting sensitizers in solid state dye sensitized solar cells.

One of the central concerns of computational chemistry is that of efficiency (i.e. the development of methodologies which will yield increased accuracy of prediction without requiring additional computational resources – RAM, disk space, computing time). Though the equations of quantum mechanics are known, the solutions to these equations often require a great deal of computing power. This dissertation primarily concerns the theme of improved computational efficiency (i.e. the achievement of greater accuracy with reduced computational cost). Improvements in the efficiency of computational chemistry are explored first in terms of the correlation consistent composite approach (ccCA). The ccCA methodology was modified and this enhanced ccCA methodology was tested against the diverse G3/05 set of 454 energetic properties. As computational efficiency improves, molecules of increasing size may be studied and this dissertation explored the issues (differential correlation and size extensivity effects) associated with obtaining chemically accurate (within 1 kcal mol-1) enthalpies of formation for hydrocarbon molecules of escalating size. Two applied projects are also described; these projects concerned the theoretical prediction of a novel rare gas compound, FKrOH, and the mechanism of human glutathione synthetase’s (hGS) negative cooperativity. The final work examined the prospect for the parameterization of the modified embedded atom …

Computational chemistry has led to the greater understanding of the molecular world, from the interaction of molecules, to the composition of molecular species and materials. Of the families of computational chemistry approaches available, the main families of electronic structure methods that are capable of accurate and/or reliable predictions of energetic, structural, and spectroscopic properties are ab initio methods and density functional theory (DFT). The focus of this dissertation is to improve the accuracy of predictions and computational efficiency (with respect to memory, disk space, and computer processing time) of some computational chemistry methods, which, in turn, can extend the size of molecule that can be addressed, and, for other methods, DFT, in particular, gain greater insight into which DFT methods are more reliable than others. Much, though not all, of the focus of this dissertation is upon transition metal species – species for which much less method development has been targeted or insight about method performance has been well established. The ab initio approach that has been targeted in this work is the correlation consistent composite approach (ccCA), which has proven to be a robust, ab initio computational method for main group and first row transition metal-containing molecules yielding, on …

Greater understanding and accurate predictions of structural, thermochemical, and spectroscopic properties of chemical compounds is critical for the advancements of not only basic science, but also in applications needed for the growth and health of the U.S. economy. This dissertation includes new ab initio composite approaches to predict accurate energetics of lanthanide-containing compounds including relativistic effects, and optimization of parameters for semi-empirical methods for transition metals. Studies of properties and energetics of chemical compounds through various computational methods are also the focus of this research, including the C-O bond cleavage of dimethyl ether by transition metal ions, the study of thermochemical and structural properties of small silicon containing compounds with the Multi-Reference correlation consistent Composite Approach, the development of a composite method for heavy element systems, spectroscopic of compounds containing noble gases and metals (ArxZn and ArxAg+ where x = 1, 2), and the effects due to Basis Set Superposition Error (BSSE) on these van der Waals complexes.

The efforts of my research have led to the successful construction of several instruments that have helped expand the field of microwave spectroscopy. The classic Balle-Flygare spectrometer has been modified to include two different sets of antenna to operate in the frequency ranges 6-18 GHz and 18-26 GHz, allowing it to function for a large range without having to break vacuum. This modified FTMW instrument houses two low noise amplifiers in the vacuum chamber to allow for the LNAs to be as close to the antenna as physically possible, improving sensitivity. A new innovative Balle-Flygare type spectrometer, the efficient low frequency FTMW, was conceived and built to operate at frequencies as low as 500 MHz through the use of highly curved mirrors. This is new for FTMW techniques that normally operate at 4 GHz or higher with only a few exceptions around 2 GHz. The chirped pulse FTMW spectrometer uses horn antennas to observe spectra that span 2 GHz versus the standard 1 MHz of a cavity technique. This instrument decreases the amount of time to obtain a large spectral region of relative correct intensity molecular transitions. A Nd:YAG laser ablation apparatus was attached to the classic Balle-Flygare and chirped …

The purpose of this study is to find out what students in the first chemistry course at the undergraduate level (general chemistry for science majors) know about the affordances of instrumentation used in the general chemistry laboratory and how their knowledge develops over time. Overall, students see the PASCO™ system as a useful and accurate measuring tool for general chemistry labs. They see the probeware as easy to use, portable, and able to interact with computers. Students find that the PASCO™ probeware system is useful in their general chemistry labs, more advanced chemistry labs, and in other science classes, and can be used in a variety of labs done in general chemistry. Students learn the affordances of the probeware through the lab manual, the laboratory teaching assistant, by trial and error, and from each other. The use of probeware systems provides lab instructors the opportunity to focus on the concepts illustrated by experiments and the opportunity to spend time discussing the results. In order to teach effectively, the instructor must know the correct name of the components involved, how to assemble and disassemble it correctly, how to troubleshoot the software, and must be able to replace broken or missing components …

The purpose of this investigation (a quasi-experimental design called a non-equivalent design group (NEDG)) was to determine if allowing students in a science majors general Chemistry I course the choice in establishing the due dates that their homework was due to the instructor would improve course averages. This study covered two semesters with a total of 288 students participating with n = 158 in the fall and n = 130 in the spring. The students self-selected the homework group, VOICES, that best fit his/her needs which included (1) the instructor's homework schedule, (2) a student-customized schedule or a schedule that followed the exam schedule, or (3) all homework due by the last class day prior to the final exam. Online homework was assigned and graded with individual assignment and homework average grades collected and analyzed. No statistically significant differences were found among the VOICES groups with respect to final course average. Other results of this study replicated findings in the literature; namely, that there is a higher correlation between mathematics skills and course success. Course averages of students who had completed Calculus I or higher were statistically significantly higher than students with less completed mathematics coursework in all VOICES groups. …

The regulations of many food products in the United States have been made and followed very well but unfortunately some products are not put under such rigorous standards as others. This leads to products being sold, that are thought to be healthy, but in reality contain unknown ingredients that may be hazardous to the consumers. With the use of several instrumentations and techniques the detection, characterization and identification of these unknown contaminates can be determined. Both the AZ-100 and the TE2000 inverted microscope were used for visual characterizations, image collection and to help guide the extraction. Direct analyte-probed nanoextraction (DAPNe) technique and nanospray ionization mass spectrometry (NSI-MS) was the technique used for examination and identification of all adulterants. A Raman imaging technique was than introduced and has proven to be a rapid, non-destructive and distinctive way to localize a specific adulterant. By compiling these techniques then applying them to the FDA supplied test samples three major adulterants were detected and identified.

Over the last 20 years, there has occurred an increase in the number, scope, and impact of nanomaterials projects. By leveraging the Surface Plasmon Resonance of metallic nanoparticles for labelling, sensing, and treatment, researchers have demonstrated the versatile utility of these nanomaterials in medicine. The literature provides evidence of use of simple, well-known chemistry for nanomaterials synthesis when the focus is new applications of nanomaterials. A case in point, is the synthesis of metallic nanoparticles, whereby HAuCl4, CuCl2, Cu(acac)2, and AgNO3 are typically employed as nanoparticle precursors. Unfortunately, the use of these precursors limits the number of applications available to these materials - particularly for AuNPs in medicine, where the byproducts of nanoparticle synthesis (most often surface-adsorbed reductants, toxic stabilizers, and growth directors) cause nanoparticles to fail clinical trials. Despite the several thousand publications detailing the advancements in nanoparticle therapeutics, as of 2017, there were only 50 FDA-approved nanoparticle formulations. Less than 10 were based on metallic nanoparticles. This is a problem because many of these nanoparticle therapeutics demonstrate potent cell killing ability and labeling of cells. A solution to this problem may be the use of weakly coordinated, monovalent metal complexes, which require only one electron to reduce them …

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 continuously increasing demand for innovation in the miniaturization of microelectronics has driven the need for ever more precise fabrication strategies for device packaging, especially for printed circuit boards (PCBs). Subtractive copper etching is a fundamental step in the fabrication process, requiring very precise control of etch rate and etch factor. Changes in the etching chemical equilibrium have significant effects on etching behavior, and CuCl2 / HCl etching baths are typically monitored with several parameters including oxidation-reduction potential, conductivity, and specific gravity. However, the etch rate and etch factor can be difficult to control even under strict engineering controls of those monitoring parameters. The mechanism of acidic cupric chloride etching, regeneration and recovery is complex, and the current monitoring strategies can have difficulty controlling the interlocking chemical equilibria. A complimentary tool, thin-film UV-Vis spectroscopy, can be utilized to improve the current monitoring strategies, as UV-Vis is capable of identifying and predicting etching behavior that the current standard methodologies have difficulty predicting. Furthermore, as a chemically-sensitive probe, UV-Vis can investigate the complex changes to the chemical equilibrium and speciation of the etch bath, and can contribute overall to significant improvements in the control of the copper etching system in order to …

Nanoparticles, simple yet groundbreaking objects have led to the discovery of invaluable information due to their physiological, chemical, and physical properties, have become a hot topic in various fields of study including but not limited to chemistry, biology, and physics. In the work presented here, demonstrations of various applications of chemical free nanoparticles are explored, from the determination of a non-invasive method for the study of the exposome via using soft-landing ion mobility (SLIM) deposited nanoparticles as a matrix-assisted laser desorption/ionization (MALDI-MS) matrix replacement, to the direct SLIM-exposure of nanoparticles onto living organisms. While there is plenty of published work in soft-landing at operating pressures of 1 Torr, the work presented here shows how this technology can be operated at the less common ambient pressure. The ease of construction of this instrument allows for various modifications to be performed for a wide array of applications, furthermore the flexibility in metallic sample, operating pressure, and deposition time only open doors to many other future applications. The work presented will also show that our ambient SLIM system is also able to be operated for toxicological studies, as the operation at ambient pressure opens the door to new applications where vacuum conditions are …

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.

Phosphorescent transition metal complexes make up an important group of compounds that continues to attract intense research owing to their intrinsic bioimaging applications that arise from bright emissions, relatively long excited state lifetimes, and large stokes shifts. Now for biomaging assay a model organism is required which must meet certain criteria for practical applications. The organism needs to be small, with a high turn-over of progeny (high fecundity), a short lifecycle, and low maintenance and assay costs. Our model organism C. elegans met all the criteria. The ideal phosphor has low toxicity in the model organism. In this work the strongly phosphorescent platinum (II) pyrophosphito-complex was tested for biological applications as a potential in vivo hypoxia sensor. The suitability of the phosphor was derived from its water solubility, bright phosphorescence at room temperature, and long excited state lifetime (~ 10 µs). The applications branched off to include testing of C. elegans survival when treated with the phosphor, which included lifespan and fecundity assays, toxicity assays including the determination of the LC50, and recovery after paraquat poisoning. Quenching experiments were performed using some well knows oxygen derivatives, and the quenching mechanisms were derived from Stern-Volmer plots. Reaction stoichiometries were derived from …

The growth of single and multilayer BN films on several substrates was investigated. A typical atomic layer deposition (ALD) process was demonstrated on Si(111) substrate with a growth rate of 1.1 Å/cycle which showed good agreement with the literature value and a near stoichiometric B/N ratio. Boron nitride films were also deposited by ALD on Cu poly crystal and Cu(111) single crystal substrates for the first time, and a growth rate of ~1ML/ALD cycle was obtained with a B/N ratio of ~2. The realization of a h-BN/Cu heterojunction was the first step towards a graphene/h-BN/Cu structure which has potential application in gateable interconnects.

Carbon nanostructure based functional hybrid molecules hold promise in solarenergy harvesting. Research presented in this dissertation systematically investigates building of various donor-acceptor nanohybrid systems utilizing enriched single walled carbon nanotube and graphene with redox and photoactive molecules such as fullerene, porphyrin, and phthalocyanine. Design, synthesis, and characterization of the donor-acceptor hybrid systems have been carefully performed via supramolecular binding strategies. Various spectroscopic studies have provided ample information in terms of establishment of the formation of donor-acceptor hybrids and their extent of interaction in solution and eventual rate of photoinduced electron and/or energy transfer. Electrochemical studies enabled construction of energy level diagram revealing energetic details of the possible different photochemical events supported by computational studies carried out to establish the HOMO-LUMO levels in the donor acceptor systems. Transient absorption studies confirmed formation of charge separated species in the donor-acceptor systems which have been supported by electron mediation experiments. Based on the photoelectrochemical studies, IPCE of 8% was reported for enriched SWCNT(7,6)-ZnP donor-acceptor systems. In summary, the present investigation on the various nanocarbon sensitized donor-acceptor hybrids substantiates tremendous prospect, that could very well become the next generation of materials in building efficient solar energy harvesting devices andphotocatalyst.

Experimental data were obtained for the computation of mole fraction solubilities of three dichloronitrobenzenes in organic solvents at 25oC, and solubility ratios were obtained from this data. Abraham model equations were developed for solutes in tributyl phosphate that describe experimental values to within 0.15 log units, and correlations were made to describe solute partitioning in systems that contain either "wet" or "dry" tributyl phosphate. Abraham model correlations have also been developed for solute transfer into anhydrous diisopropyl ether, and these correlations fit in well with those for other ethers. Abraham correlations for the solvation of enthalpy have been derived from experimental and literature data for mesitylene, p-xylene, chlorobenzene, and 1,2-dichlorobenzene at 298.15 K. In addition, the enthalpy contribution of hydrogen bonding between these solutes and acidic solvents were predicted by these correlations and were in agreement with an established method. Residual plots corresponding to Abraham models developed in all of these studies were analyzed for trends in error between experimental and calculated values.

A novel application of ionic liquid as a charge carrier for the analysis and detection of neutral organometallic complexes using a mass spectrometer has been presented. The mass spectrometer detects only charged compounds which raise a difficulty in analyzing a neutral molecule that lacks a basic site to associate with charge. Therefore, an effective way of providing charge has always been an area of keen interest in the field of mass spectrometry. Ionic liquids have a very fascinating property of forming a cation-? interaction with other molecules to give a charged complex. In order to take advantage of this, it is important to know the geometric structure of the complex. Advanced methodologies like hydrogen-deuterium exchange and computational calculations have been used assisting in better understanding of the structure of the ionic liquid complexes.

Experimental data for the logarithm of the gas-to-ionic liquid partition coefficient (log K) have been compiled from the published literature for over 40 ionic liquids over a wide temperature range. Temperature independent correlations based on the Gibbs free energy equation utilizing known Abraham solvation model parameters have been derived for the prediction of log K for 12 ionic liquids to within a standard deviation of 0.114 log units over a temperature range of over 60 K. Temperature independent log K correlations have also been derived from correlations of molar enthalpies of solvation and molar entropies of solvation, each within standard deviations of 4.044 kJ mol-1 and 5.338 J mol-1 K-1, respectively. In addition, molar enthalpies of solvation and molar entropies of solvation can be predicted from the Abraham coefficients in the temperature independent log K correlations to within similar standard deviations. Temperature independent, ion specific coefficients have been determined for 26 cations and 15 anions for the prediction of log K over a temperature range of at least 60 K to within a standard deviation of 0.159 log units.

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. …

Boron carbide-aromatic composites, formed by plasma-enhanced co-deposition of carboranes and aromatic precursors, present enhanced electron-hole separation as neutron detector. This is achieved by aromatic coordination to the carborane icosahedra and results in improved neutron detection efficiency. Photoemission (XPS) and FTIR suggest that chemical bonding between B atoms in icosahedra and aromatic contents with preservation of π system during plasma process. XPS, UPS, density functional theory (DFT) calculations, and variable angle spectroscopic ellipsometery (VASE) demonstrate that for orthocarborane/pyridine and orthocarborane/aniline films, states near the valence band maximum are aromatic in character, while states near the conduction band minimum include those of either carborane or aromatic character. Thus, excitation across the band gap results in electrons and holes on carboranes and aromatics, respectively. Further such aromatic-carborane interaction dramatically shrinks the indirect band gap from 3 eV (PECVD orthocarborane) to ~ 1.6 eV (PECVD orthocarborane/pyridine) to ~1.0 eV (PECVD orthocarborane/aniline), with little variation in such properties with aromatic/orthocarborane stoichiometry. The narrowed band gap indicate the potential for greatly enhanced charge generation relative to PECVD orthocarborane films, as confirmed by zero-bias neutron voltaic studies. The results indicate that the enhanced electron-hole separation and band gap narrowing observed for aromatic/orthocarborane films relative to PECVD orthocarborane, …

This work focuses on finding the complete iodine and nitrogen nuclear electric quadrupole coupling tensors for fluoroiodoacetonitrile using chirped-pulse Fourier transform microwave spectroscopy. Fluoroiodoacetonitrile contains two hyperfine nuclei, iodine (I=5/2) and nitrogen (I=1) and the spectra were observed with great resolution. A total of 499 transitions were observed for this molecule. The a, b and c rotational constants were obtained. A study of chloropentafluoroacetone was also done using chirped-pulse Fourier transform microwave spectroscopy. The two chlorine isotopes for this molecule, Cl-35 and Cl-37 were observed and 326 and 170 transitions were recorded, respectively.