Doctor of Philosophy / Department of Chemistry / Viktor Chikan / Colloidal semiconductor nanoparticles will be important and practical next generation materials that can be cheaply manufactured. The objective of this project is to gain more inside into chemistry is used to control the formation and assembly of semiconductor nanoparticles (NPs). As a model system CdSe and CdTe nanoparticles are used in this work. The growth kinetics, aggregation dynamics, and heterogeneous growth of NPs by using novel tools such as; in-situ monitored fluorescence and absorption techniques, time-resolved and static fluorescence spectroscopy, TEM (transmission electron microscopy), and numerical simulations are studied. This study can be divided into the following four parts. The first part presents experimental observation of the quantized growth of CdTe quantum dots (QD). The high-temperature absorption spectra indicate the evolution of multiple peaks corresponding to various sizes of QDs. The observed aggregation is driven by dipole-dipole interaction of NPs. The second part is an investigation of the aggregation dynamics of magic-sized CdTe quantum dots and how this process can be controlled. It is shown that the growth kinetics of the QDs is very sensitive to the Cd/Te ratio. Cd-rich conditions form very different aggregation pattern due to the lack of formation of magic-sized nanoparticles. Simulations also suggest that the formation mechanism is mainly coalescence of the particles rather than the ‘neck formation’ within the CdTe aggregates. The next part investigates the growth of NPs in the presence of two distinctly sized NPs in the bimodal growth regime via numerical simulations. The bimodal distribution (or quantized Ostwald ripening) technique is found to be a slower process than the repeated injection technique to focus the size distribution of NPs. Slower growth will reduce inhomogeneity in a scaled-up production of NPs. The last part focuses on the effect of addition of doping on vii heterogeneous growth and the growth kinetics. The low temperature synthesis lacks the heterogeneous growth regime. However, as the temperature is increased to 120 0C, two different sizes emerge. Addition of In dopants seems to accelerate the growth kinetics and the magic sized NPs in the solution possess a negative anisotropy that is most likely due to supperlatice formation of magic-sized NPs.

Master of Science / Department of Chemistry / Paul E. Smith / The increasing importance of ion-water interactions in the field of chemistry and biology is leading us to examine the structure and dynamic properties of molecules of interest, based on the application of computer-aided models using molecular dynamics simulations. To enable this type of MD study, a molecular mechanics force field was developed and implemented. Kirkwood-Buff theory has been proved to be a powerful tool to provide a link between molecular quantities and corresponding thermodynamic properties. Parameters are the vital basis of a force field. KB integrals and densities were used to guide the development of parameters which could describe the activity of aqueous solutions of interest accurately. In this work, a Kirkwood-Buff Force Field (KBFF) for MD simulation of ammonium sulfate, sodium sulfate, sodium perchlorate and sodium nitrate are presented. Comparison between the KBFF models and existing force fields for ammonium sulfate was also performed and proved that KBFF is very promising. Not only were the experimentally observed KB integrals and density reproduced by KBFF, but other properties like self diffusion constant and relative permittivity are also well produced.

Doctor of Philosophy / Department of Chemistry / Takashi Ito / This dissertation describes the fabrication and characterization of nanoscale structures in commercially available polymers via multiphoton ablation and bottom-up self assembly techniques. High-resolution surface imaging techniques, such as atomic force microscopy (AFM) and chemical force microscopy (CFM) were used to characterize the physical features and chemical properties, respectively, of these nanoscale structures. Fabrication using both top-down and bottom-up methods affords flexibility in that top-down allows random, user-defined patterning whereas bottom-up self assembly produces truly nanoscale (1-100nm) uniform features. Multiphoton induced laser ablation, a top-down method, was used to produce random sub-micron scale features in films of poly(methylmethacrylate) (PMMA), polystyrene (PS), poly(butylmethacrylate) (PBMA) and poly[2-(3-thienyl)ethyloxy-4-butylsulfonate] (PTEBS). Features with 120-nm lateral resolution were obtained in a PMMA film which was concluded to be the best polymer for use with this method. It was also found that etching resolution was highest for polymers having high glass transition temperatures, low molecular weights and no visible absorption. Bottom-up self assembly of polystyrene-poly (methylmethacrylate) (PS-b-PMMA) diblock copolymer and UV/acetic acid treatment produced nanoscale cylindrical domains supported by a substrate. AFM imaging at the free surface showed metastable vertical PMMA domain orientation on gold substrates. In contrast, horizontal orientation was obtained on oxide-coated silicon regardless of surface roughness and annealing conditions. The horizontal domain orientation on silicon substrates was ideal to probe simultaneously the difference in surface charge and hydrophilicity of the two distinct nanoscale domains of UV/AcOH treated PS-b-PMMA films. CFM on UV/acetic acid etched PS-b-PMMA revealed the presence of –COO- groups which were found to be more abundant inside the etched trenches than on the unetched PS matrix as shown by ferritin adsorption onto etched PS-b-PMMA. Lastly, the PS-b-PMMA was cast as a free-standing monolith at the end of a quartz micropipette. AFM revealed circular PMMA dots at the free surface, indicating alignment parallel to the long axis of capillary. Ion conductance within nanochannels indicated surface –charge governed ion transport at low KCl concentrations and flux of negatively-charged sulphorhodamine dye demonstrated the permselective nature of nanochannels.

Master of Science / Department of Chemical Engineering / Larry E. Erickson / The reaction chemistry of uranium metal has been well documented for use in the development of nuclear fuels. The oxidation of uranium from the thermal stress of nearby combustion is different than that of a reactor environment due to the selectivity of the various competing reactions. This work extracts available information in literature and various experiments over the last 60 years to provide a critical look at the response of uranium metal to thermal stress. The oxide fume formed and the equilibrium phase shifts during the dispersal of the airborne particulate are of principal interest when determining potential consequences to the health and safety of the workers, members of the public, and the environment. The transport phenomena and reaction kinetics of the oxide fume are also discussed at various distances from the source material. Uranium is a versatile element that can form numerous compounds, of which the oxides are the forms that are most readily generated under thermal stress and also pose the largest health risk to human beings, primarily through inhalation. A general summary of uranium and the dry compounds (oxides and carbides) is provided discussing the different structures of each state. The reaction kinetics and selectivity as the oxidation progresses is discussed for typical uranium metal forms at temperatures above and below the ignition point. Characteristics of potential fires are qualified for determining thermal stress. The creation of the oxide fume is outlined followed by dispersal characteristics of the aerosol. These molecular processes are related to the release fractions of uranium under fire scenarios which are compared with available experimental data from the regulatory handbooks. A critical look at the conclusions of the handbook with recommendations for revising the existing guidelines and additional testing are made in the interest of ensuring that derived controls are appropriate to reduce the risk of accidents involving the oxidation of uranium metal.

Master of Science / Department of Physics / Christopher M. Sorensen / Gold Nanoparticles (AuNP) 5nm in diameter, ligated with n-dodecanethiol, were dissolved in various hydrocarbon solvents including normal alkanes from n-hexane to n-hexadecane as well as two aromatics, toluene and para-xylene. These solutions were centrifuged at room temperature under 12000g acceleration for one hour to separate larger clusters from AuNP monomers dissolved in the supernatants. UV-Vis absorbance data were taken on the supernatants and were then converted to concentrations in moles of Au atoms/L. These concentrations correspond to the saturated concentration of dissolved AuNP monomers in equilibrium with a precipitate at room temperature. For the alkanes, we discovered a non-monotonic functionality of saturated concentration vs. solvent chain length with a maximum corresponding to n-dodecane. This agreed with predictions made of the ligands’ interactions with the solvents based on comparisons of solubility parameters where the n-dodecanethiol ligands were approximated as n-dodecane. The concentrations of AuNPs when dissolved in the aromatics did not follow the trend predicted by solubility parameters.

Master of Science / Department of Biochemistry / Paul E. Smith / We are developing a force field (FF) for molecular dynamics (MD) simulations of peptides and small proteins that is grounded in the Kirkwood-Buff theory of solutions. Here we present the Kirkwood-Buff Force Field (KBFF) parameters for the aromatic amino acids, based upon simulations of binary mixtures of small molecules representative of these amino acids over their entire composition ranges (excluding Histidine). Many aromatics are not fully soluble in water, so they have instead been studied in solvents of methanol or toluene. The parameters were developed by studying the following binary solutions: Phenylalanine − benzene + methanol, toluene + methanol, and toluene + benzene; Tyrosine − toluene + phenol and toluene + p-Cresol; Tryptophan − pyrrole + methanol and indole + methanol; Histidine − pyrrole + methanol, pyridine + methanol, pyridine + water, histidine + water (at 0.25 molal), and histidine monohydrochloride + water (at 0.3 molal and 0.6 molal). Our simulations reproduce the Kirkwood-Buff integrals, which guarantees that the KBFF provides an adequate balance of solute-solvent, solute-solute, and solvent-solvent interactions. Additionally, we show that the KBFF does not sacrifice reproduction of other solution properties in order to achieve this improved description of intermolecular interactions. We present these results as validating evidence for the future use of the KBFF in simulations of peptides and small proteins.

Doctor of Philosophy / Department of Chemistry / Paul E. Smith / The force fields used in computer simulations play an important role in describing a particular system. In order to estimate the accuracy of a force field, physical or thermodynamic properties are usually compared with simulation results. Recently, we have been developing a force field which is called the Kirkwood-Buff Force Field (KBFF). This force field is established by transforming experimental data into Kirkwood-Buff (KB) integrals and then attempting to reproduce those KBIs with molecular dynamic (MD) simulations. Here we investigate a variety of intermolecular interactions in aqueous solutions through KB theory and molecular simulations. First, we describe a force field for the simulation of alkali halide aqueous solutions. These models are developed specifically to reproduce the experimentally determined Kirkwood-Buff integrals and solution activities as a function of molality. Additionally, other experimentally known properties including ion diffusion constants, relative permittivities, the densities and heats of mixing are reproduced by these models. Second, In an effort to understand the interactions which occur between amino acids in solution we have developed new force fields for simple amino acids and their analogs including glycine, betaine, β-alanine, dl-alanine, NH4Cl, NH4Br, N(CH3)4Cl, N(CH3)4Br, CH3NH3Cl, and CH3COONa. The new force fields reproduce the experimental Kirkwood-Buff integrals which describe the relative distribution of all the species in a solution mixture. Furthermore, it is shown that these simple amino acids can be understood in terms of the interactions of their functional groups and that, to a very good approximation, the transferability and additivity usually assumed in the development of biomolecular force fields appear to hold true. Third, an analysis of the effect of a cosolvent on the association of a solute in solution is presented by using the Kirkwood-Buff theory of solutions. The derived expressions provide a foundation for the investigation of cosolvent effects on molecular and biomolecular equilibria, including protein association, aggregation, and cellular crowding. Finally, in an effort to understand peptide aggregation at the atomic level we have performed simulations of polyglycine ((gly)n) using our recently developed force fields. Experimentally, the association of glycine polypeptides increases with n. Our force fields reproduce this behavior, and we investigated the reasons behind this trend. In addition to studying closed ensembles, we also simulate these systems in a semi-open ensemble that was designed to mimic cellular environments typically open to water, using a simple direct approach. The differences between the two ensembles are investigated and compared with our recent theoretical descriptions of aggregating systems using Kirkwood-Buff theory.

Doctor of Philosophy / Department of Chemistry / Peter M. Sherwood / This work is a detailed study of the interaction between two phosphorous-containing acids and the metals chromium and 316L stainless steel. The objective of this work is to investigate the formation of unique thin films on the two metals and to probe the surface chemistry of these films through the use of core level and valence band X-ray photoelectron spectroscopy (XPS). Chromium forms a wide array of oxides and can exist at several valencies. Valence band XPS is used in conjunction with band structure and multiple scattered wave X[alpha] calculations to distinguish which states are present in the resultant films. Both 99.99% chromium and 316L stainless steel foils were treated with orthophosphoric acid and 1-hydroxyethylidene-1,1-diphosphonic acid, otherwise known as etidronic acid. Two methods developed in the Sherwood research laboratory for forming oxide-free films on metal surfaces are utilized in this work. Core level XPS results did not provide sufficient information to draw conclusions regarding the products formed in the reactions. The valence band results showed clear evidence of multiple forms of phosphates forming on the metal surfaces as evidenced by the subtle differences in separation between the phosphorous 3p and 3s peaks as well as differences in separation between the O2s and phosphorous 3s peaks. The Valence Band XPS results were interpreted by X-[alpha] cluster and band structure calculations. Films formed on chromium foil from the orthophosphoric acid were found to be condensed phosphates that are stable in air. Etidronic acid formed very thin phosphate films on chromium with both treatment methods as well as on 316L stainless steel when the bench top method was applied. Treatment of etched 316L steel in the anaerobic cell generated an etidronate film. This sample was the only etidronate film formed, all other etidronate-based films were generated from disassembled portions of the etidronate ion to form phosphate films.

Doctor of Philosophy / Department of Chemistry / Paul E. Smith / In the study of biological systems, molecular dynamics (MD) simulations have played an important role in providing atomic details for phenomena of interest. The force field used in MD simulations is a critical factor determining the quality of the simulations. Recently, Kirkwood-Buff (KB) theory has been applied to study preferential interactions and to develop a new force field. KB theory provides a path from quantities determined from simulation data to the corresponding thermodynamic data. Here we combine KB theory and molecular simulations to study a variety of intermolecular interactions in solution. First, recent results concerning the formulation and evaluation of preferential interactions in biological systems in terms of KB integrals are presented. In particular, experimental and simulated preferential interactions of a cosolvent with a biomolecule in the presence of water are described. Second, a force field for the computer simulation of aqueous solutions of amides is presented. The force field is designed to reproduce the experimentally observed density and KB integrals for N-methylacetamide (NMA), allowing for an accurate description of the NMA activity. Other properties such as the translational diffusion constant and heat of mixing are also well reproduced. The force field is then extended to include N,N'-dimethylacetamide and acetamide with good success. The models presented here provide a basis for an accurate force field for peptides and proteins. Comparison between the developed KB force fields (KBFF) and existing force fields is performed for amide and glycine and proves that the KBFF approach is competitive. Also, explicit expressions are developed for the chemical potential derivatives, partial molar volumes, and isothermal compressibility of solution mixtures involving four components at finite concentrations using the KB theory of solutions. A general recursion relationship is also provided which can be used to generate the chemical potential derivatives for higher component solutions. Finally, a pairwise preferential interaction model (PPIM), described by KB integrals is developed to quantify and characterize the interactions between functional groups observed in peptides.

Doctor of Philosophy / Department of Chemistry / Paul E. Smith / In the past several decades, molecular dynamics (MD) simulations have played an important role in providing atomic details for phenomena of interest. The force field used in MD simulations is a critical factor determining the quality of the simulations. Kirkwood-Buff (KB) theory has been applied to study preferential interactions and to develop a new force field. KB theory provides a path from quantities determined from simulation data to the corresponding thermodynamic data. Here we combine KB theory and molecular simulations to study a variety of intermolecular interactions in solution. First, a force field for the computer simulation of aqueous solutions of alcohols is presented. The force field is designed to reproduce the experimentally observed density and KB integrals for a series of alcohols, allowing for an accurate description of alcohols’ activity. Other properties such as the translational diffusion constant and heat of mixing are also well reproduced. Second, the newly developed force field is then extended to more complicated systems, such as peptide or mini-proteins, to determine backbone dihedral potentials energetics. The models developed here provide a basis for an accurate force field for peptides and proteins. Third, we have then studied the surface tension of a variety water models. Results showed that different simulation conditions can affect the final values of surface tension. Finally, by using the Kirkwood-Buff theory of solution and surface probability distributions, we attempted to characterize the properties of the Gas/Liquid interface region. The same approach is then used to understand the relationship between changes in surface tension, the degree of surface adsorption or depletion, and the bulk solution properties.