The knowledge on the conformations of amino acids is essential to understand the biochemical behaviors and physical properties of proteins. Comprehensive computational study is focused to understand the conformational landscape of three aromatic amino acids (AAAs): tryptophan, tyrosine, and phenylalanine. Three different density functionals (B3LYP, M06-2X and wB97X-D) were used with two basis sets of 6-31G(d) and 6-31+G(d,p) for geometry optimizations of the conformers of AAAs followed by the vibrational frequencies. The goal was to identify the right choice of density functional theory (DFT) level for conformational analysis of amino acids by comparing the computational data against the available experimental results. Calculated infrared (IR) frequency values indicated that wB97X-D/6-31+G(d,p) level is less favorable than other DFT levels in case of O-H and N-H stretching frequencies for the conformers of AAAs. The C=O stretching frequencies at different computational levels were in good agreement with the experimental results. Interactions of AAAs (tryptophan, tyrosine, and phenylalanine) and two cyclic amino acids (histidine and proline) individually with two finite-sized graphene sheets (C62H20 and C186H36) were explored using M06-2X/6-31G(d) level. Computational investigations of the binding of amino acids with graphene provide knowledge for designing of new graphene-based biological/biocompatible materials. Selected conformers for each amino acid with different orientations on the surface of graphene were examined. The purpose of computational study on graphene-amino acids interactions was to identify the preferred conformer of amino acid to bind on graphene as well as to find the influence of amino acid binding on the band gap of graphene. Different conformers of AAAs generally prefer parallel orientation through π-π interactions to bind with graphene. However, bent orientation is more preferred over parallel to bind on the surface of graphene in case of conformer having relative energy approximately equal to 5 kcal/mol for all three AAAs. Histidine generally exhibits higher binding affinity than proline to form complex with graphene. The binding energies in the aqueous medium were slightly lower than those obtained in the gas phase with some exceptions. The adsorption of amino acids did not affect the band gap of graphene.

xvii, 147 p. : ill. (some col.) A print copy of this thesis is available through the UO Libraries. Search the library catalog for the location and call number. / Supramolecular chemistry is a relatively new and exciting field offering chemists simplistic approaches to generating complex assemblies through strategically designed ligands. Much like the many spectacular examples of supramolecular assemblies in nature, so too are chemists able to construct large, elegant assemblies with carefully designed ligands which bind preferentially to target metal ions of choice. An important concept of supramolecular chemistry, often subtle and overlooked, is secondary bonding interactions (SBIs) which in some cases, act as the glue to hold supramolecular assemblies together. This dissertation examines SBIs in a number of systems involving the pnictogen elements of arsenic and antimony as well as aromatic interactions in self-assembled monolayers. The first half of this dissertation is an introduction to the concepts of supramolecular chemistry and secondary bonding interactions and how they are used in the self-assembly process in the Darren Johnson laboratory. Chapter I describes how secondary bonding interactions between arsenic and aryl ring systems and antimony and aryl ring systems assist with the assembly process. Chapter II is a continuation of the discussion of SBIs but focuses on the interactions between arsenic and heteroatoms. The second half of this dissertation will describe work performed in collaboration with Pacific Northwest National Laboratory (PNNL) in Richland, WA. This work was performed under the guidance of Dr. R. Shane Addleman in conjunction with Professor Darren W. Johnson of the University of Oregon. This portion describes novel systems for use in heavy metal ion remediation from natural and unnatural water sources. Chapters III-V describe functionalized mesoporous silica for use in heavy metal uptake from contaminated water sources. Chapter V describes a new technology invented during this internship at PNNL which utilizes weak bonding interactions between aryl ring systems to produce regenerable green materials for toxic metal binding. This work is ongoing in the Darren Johnson lab. This dissertation includes my previously published and co-authored material. / Committee in charge: Michael Haley, Chairperson, Chemistry; Darren Johnson, Member, Chemistry; Shih-Yuan Liu, Member, Chemistry; James Hutchison, Member, Chemistry; Eric Johnson, Outside Member, Biology

It is widely accepted that the sharing of electrons constitutes a bond. Conversely, molecular interactions that do not involve electron transfer, such as van der Waals forces and electrostatics are defined as "non-bonding" or "non-covalent" interactions. More recently computational and experimental observations have shown situations where the division between "bonding" and "non-bonding" interactions is blurred. One such class of interactions are known as σ-hole interactions. Chapter 1 provides a literature review of investigations into the nature of σ-hole interactions, highlighting the individual contributing factors. Chapter 2 provides a detailed analysis into the nature of chalcogen-bonding interactions. Synthetic molecular balances are employed for experimental measurements of conformational free energies in different solvents, facilitating a detailed examination of the energetics and associated solvent and substituent effects on chalcogen-bonding interactions. The chalcogen-bonding interactions examined were found to have surprisingly little solvent dependence. The independence of the conformational free energies on solvent polarity, polarisability and H-bond characteristics showed that electrostatic, solvophobic or dispersion forces were not dominant factors in accounting for the experimentally observed trends. A molecular orbital analysis provided a quantitative relationship between the experimental free energies and the molecular orbital energies, which was consistent with chalcogen-bonding interactions being dominated by an n→σ* orbital delocalisation. Chapters 3 and 4 both use the molecular orbital modelling approach established in Chapter 2 to investigate the potential partial covalency in H-bonding and carbonyl···carbonyl interactions. H-bonding is generally considered to be an electrostatically dominated interaction. However, computational results have suggested a partial covalent character in H-bonding. The molecular orbital analysis revealed an n→σ* electron delocalisation in all H-bonding systems evaluated. However, no quantitative correlation could be found with experimental free energies. Similarly, the nature of carbonyl···carbonyl interactions has been subject to debate, with electrostatic or an n→π* electron delocalisation having been proposed as the dominant factors. The molecular orbital analysis employed here showed that n→π* delocalisation was exceptionally geometry dependent. Studies of literature systems reveal that n→π* delocalisation contributes to overall stability of a range of systems, with a quantitative link between molecular orbital energy and conformational free energies.