A pulsed supersonic Laval nozzle flow reactor has been employed to investigate a variety of neutral-radical reaction processes at temperatures between 53 and 188 Kelvin. These supersonic flows simulate the conditions found in the Earth's upper atmosphere as well as certain environments in the interstellar medium and outer planetary atmospheres and thus provide direct information on the chemistry and physical processes occurring in those environments. Studies of this type, in the limit of 0 Kelvin, coupled with modern astronomical observations of planetary atmospheres and dense molecular clouds provide for a global understanding of chemistry in cold environments. With this in mind, the flow reactor was used to conduct fundamental studies involving the reactivity of hydroxyl (OH) and imidogen (NH) radical species with a variety of partners. More specifically, the reactions of OH+HBr and all of the H/D isotopic variants were explored between 53 and 135 K, with the goal of elucidating the kinetic isotope effects, both primary and secondary, for a reaction system occurring over a potential energy surface without an appreciable barrier, that demonstrates inverse temperature dependence. While not of direct astronomical importance, the reaction of OH+HBr does affect the partitioning of Br in the Earth's atmosphere, and knowledge of kinetic isotope effects helps one understand the chemistry leading to H/D fractionation observed in a variety of interstellar environments. The reactions of NH radical with NO, saturated, and unsaturated hydrocarbons were also studied between 53 and 188 Kelvin in the Laval nozzle flow reactor. These species were chosen as most are important constituents in the atmosphere of Titan, which is known to possess a rich organic chemistry. The reactions of NH with the unsaturated hydrocarbons are found to display negative temperature dependence over the window investigated, and are thought to proceed through an addition mechanism. Finally, the flow reactor was also coupled to a tunable vacuum and extreme ultraviolet frequency source based on four wave frequency mixing to allow for studies of radical species with their first electronic transitions in this frequency range. A discussion of the development, implementation, and future directions is included.

Nuclear magnetic resonance spectroscopy and molecular dynamics simulation have been used to study the structure and dynamics of biologically active peptide ligands for glucagon and melanocortin receptors, providing valuable insights into the receptor ligand interactions and useful information for the further design of more potent and selective ligands for these receptors. The NMR structure of the potent glucagon antagonist [desHis¹, desPhe⁶, Glu⁹]glucagon amide consists of an unstructured N-terminal segment (2-5), an irregular helix (7-14), a hinge region (15-18), and a well-defined α-helix (19-29). The two helices form an L-shaped structure with an angle of about 90° between the helix axes. There is an extended hydrophobic cluster, which runs along the inner surface of the L-structure and incorporates the side chains of the hydrophobic residues of each of the amphipathic helices. The outer surface contains the hydrophilic side chains. This result is the first clear indication of an overall tertiary fold for a glucagon analogue in the micelle-bound state. In addition to the structural difference, molecular dynamics simulations showed both N- and C-terminal residues in the glucagon antagonist are more highly ordered than those in glucagon. The single helix obtained for glucagon in the crystal state was found to unravel in the simulation around the region approximately corresponding to the hinge region in the antagonist. These results may have important implications for the biological activities of both peptides. The conformational study of cyclic alpha-melanocyte stimulating hormone analogues by NMR showed that their overall backbone structures are similar around the message sequence (His⁶-D-Phe⁷/D-Nal(2')⁷-Arg⁸-Trp⁹). beta-Turns spanning His⁶ and D-Phe⁷/D-Nal(2')⁷ were identified in all analogues. However, a stacking between the aromatic rings of His⁶ and D-Phe⁷/D-Nal⁷ was observed for the melanocortin agonists, but not for the antagonists. Based on the NMR structure of MTII, a library of new alpha-MSH analogues was designed and synthesized with a disulfide or lactam bridge used as a conformational constraint and the pharmacophore group in Arg⁸ mimicked by Nᵅ-alkylation via the Mitsunobu reaction. These new analogues exhibited high binding affinity and selectivity for the human melanocortin-4 receptor, thus suggesting the usefulness of the NMR structural model of α-MSH peptides.

Ancient ships transported not only goods around the eastern Mediterranean, but the people and the diseases they carried. The diseases to which people adapted often lived long enough for their effects to appear in bone. The focus of this dissertation is to discern the comparative health from paleopathological analysis of the human skeletal remains dating to the Hellenistic and Roman periods from Paphos, Cyprus and Corinth, Greece. The samples are comprised of minimally 275 individuals from 31 tombs at Paphos and 94 individuals from 32 bone lots at Corinth. Analytical techniques include gross morphological and metrical examination and radiography of select samples while using the Skeletal Database Committee Recommendations (Rose et al. 1991) as a guide. Limited molecular analysis is also employed. In addition to the identification of paleopathologies, the minimum number of individuals, age, sex, reconstructed stature, and anomalies are determined. The results of both sites are compared and the evolutionary implications of the identified paleopathologies are discussed. Six chapters are presented in this dissertation, including: an introduction; materials and methods; results from Paphos; results from Corinth; comparative results between the two sites; and the conclusions of this research. Results indicate that there was a greater prevalence of infant mortality at Corinth when compared to Paphos. Of those adults that could be aged, however, adults at Corinth lived longer. Stress, as evidenced by enamel hypoplasias, was more prevalent at Corinth, but dental caries were more prevalent at Paphos. Although cribra orbitalia, indicative of anemia, was present at both sites, porotic hyperostosis was identified only at Paphos, perhaps suggesting a different type of anemia at Paphos. Malaria and the thalassemias have been identified in modern times at both locales, but based upon the paleopathological results herein, there is no gross evidence of congenital hemolytic anemias at ancient Corinth. Assuming that the city was repopulated by local Greeks during the Roman period, it is hypothesized that at least up to this time, thalassemia was not a serious problem at Corinth as it likely was at ancient Paphos. Further molecular analyses could test this hypothesis.

A dental study of the adult human skeletal series (N = 225) from Grasshopper Pueblo in east-central Arizona is undertaken to address archaeological inferences on diet and stress. An intra-site research design is implemented to evaluate hypotheses on (1) dietary differences over time, between sexes and across space, and (2) differences in physiological stress over time, between sexes and across space at the pueblo. The dentitions are analyzed to collect data on caries, antemortem tooth loss, tooth wear, wear plane angles, alveolar recession and enamel hypoplasia. The teeth are partitioned along biological variables of sex and age, and dimensional variables of time period (early and late) and room block (RB1, RB2 and RB3). The diet/tooth usage results suggest that the diet during the late period at Grasshopper Pueblo was different than the diet during the early period. This is consistent with the inferred intensification of maize agriculture in the late period. In addition, female diets were different than male diets when placed in a temporal context. This is possibly associated with the inferred overexploitation of wild game that may have forced males to hunt farther from home during the late period. The childhood stress data indicate three key findings. First, males exhibited greater enamel hypoplasia frequencies than females. This is possibly associated with an inferred matrilineal-matrilocal social organization at Grasshopper in which female children may have been given preferential treatment. Second, Room Block 2 inhabitants exhibited the lowest frequencies of enamel hypoplasia. This is consistent with the inference that residents of Room Block 2 represent the founding population. Finally, late period inhabitants of Grasshopper Pueblo exhibited significantly greater enamel hypoplasia frequencies than the early period inhabitants. These results are consistent with the inference that life during the late period at Grasshopper was more stressful. The changes in diet and increases in physiological stress that are suggested by this dental study are most likely associated with the dynamics that ultimately led to the abandonment of this 14th-century 500 room pueblo.

This dissertation presents the results of several investigations into vibrational and rotational relaxation of neutral molecules at low temperatures. The use of the free jet flow reactor technique for production of very low local temperatures and the determination of relaxation data and derivation of rate coefficients are discussed. Four different molecules, HBr, CO, OH and OD, are examined in the free jet with various buffer gases to determine their vibrational and rotational relaxation properties. For HBr and CO, terminal rotational temperatures are measured in various buffer gases with the resonance enhanced multiphoton ionization (REMPI) technique, and results are analyzed and compared with translational temperatures. For OH and OD, discussion includes experimental production of radicals and relaxation within the X²Π and A²Σ states is made. With the use of laser induced fluorescence (LIF) and a novel method for production of radicals in the free jet, radical relaxation rates are determined for the first time at extremely low collision energies. We have measured the low temperature (T(trans) near 1 K) rate coefficients for: OH(A²Σ,vᵢ,Nᵢ)+Ar →(k) OH(A²Σv(f)N(f)) +Ar where v and N refer to the quantum numbers for vibration and pure rotational angular momentum, while the subscripts i and f refer to the initial and final states, respectively. The experiments reported in this dissertation help lead to a better understanding of collisions on a molecular level at very low collision energies.

The quantum mechanical investigation of molecular dimers, trimers and, to a greater extent, higher clusters, constitutes a legitimate attempt towards linking the gas and condensed phases of matter. The interaction of gas-phase clusters with ionizing media can result in anion formation, a special class of which, the dipole-bound anions is the main focus of this dissertation. By applying special techniques of ab initio calculations to model systems, we have addressed the question of the extent to which certain molecular species can form dipole-bound anions. We have shown the effects of attaching a dipole-bound electron on charge distribution, geometrical distortions, and mechanistic fates of certain reactive clusters. Our investigations include cases of homodimer anions where we reported the feasibility of formation of a dipole-bound anion for the dimer agglomerates to the exclusion of the single molecules (ethylene glycol and hydrogen fluoride). The hydrogen cyanide-water anion is a heterodimer system where our results demonstrate the effect of linkage isomerism on an isomer's ability to form dipole-bound states. Only the [H₂O...HCN]⁻ anion was experimentally detected and it corresponds to the higher EA we reported. In addition, the formation of meta-stable trimer and tetramer dipole-bound anions in the water cluster system is supported by our calculation. The water cluster study demonstrates the utility of ab initio calculation techniques for investigations of reaction mechanisms in the gas phase. For instance, both the mass spectrum intensity pattern and general mechanism of formation of the cluster anions can be inferred from the relative stabilities and geometries that we obtained for the anion and neutral systems. Finally, we point out the potential utility of an IR analysis in distinguishing neutral from anion systems, based on shifts of certain IR bands generated in our harmonic frequency analysis. We hope that our results for electron affinities, dipole moments, and vertical detachment energies will serve as a useful resource for the researchers in the field. In conjunction with the corresponding values measured by experimentalists, both results should provide a self-consistent system for identifying and overcoming shortcomings of both experimental and theoretical approaches of solving chemical and physical problems involving anion formation.

Termolecular association reactions were studied at the low temperatures produced within the core of a free jet expansion. A strong inverse temperature dependence was found in the termolecular association rate coefficients for the reactions of NO⁺ with NO and N₂ and the results are compared with existing literature and theories. The atmospheric ramifications of the reaction NO⁺ + 2 N₂ are discussed. The temperature dependence of the termolecular association reaction of H⁺ + 2 H₂ is reported for the range 1.6-3 Kelvin and a temperature dependent rate coefficient for the range 1.6-300 Kelvin is reported using the current results and the available high temperature literature. Measurement of the autoneutralization lifetime of SF₆⁻* formed by the attachment of low energy (1-100 meV) electrons to cold SF₆ molecules within the core of a free jet expansion were made. The excited anions were found to exhibit a single lifetime in accordance with the s-wave scattering law and with literature values for the temperature dependence of both the electron attachment rate coefficient and excited anion lifetime. These studies provide insight into the attachment/detachment dynamics of negative ion scattering states under single collision conditions. The effect of neutral temperature on termolecular association reactions is examined for several chemical systems and discussed within the context of models which include the formation of a long-lived collision complex.

Several new techniques were developed and applied to investigate various non-trivial aspects of vibrational motion. In particular, a novel strategy for accurate determination of vibrational energy levels in the presence of intramolecular hydrogen bonds was proposed. A small subset of convenient internal coordinates was chosen to represent a vibrational mode of interest, while the interdependence among all other coordinates was encoded in the g-matrix elements which appear in the kinetic energy operator. Individual g-matrix elements were modeled by series of shifted Gaussian functions, a newly proposed functional form that assured physically correct behavior for the entire domain of internal coordinates. The success in reproducing experimentally observed frequencies should be partly attributed to a new basis set of modified Hermite-type functions which has been introduced in this work and employed in all presented vibrational energy calculations. A novel functional representation for potential energy surfaces (PES) was also proposed in this work. The new representation, consisting of products of shifted Gaussians and shifted Morse functions, reproduces all local features near the bottom of the well and also possesses correct asympototic behavior. Determination of the functional parameters for the PES fits involved a simultaneous optimization of many linear and nonlinear parameters, and required a development of an efficient minimization routine. The new routine consisted of an iterative procedure, which treated sets of linear and nonlinear parameters separately and in successive order in each iteration. The above-mentioned set of developed tools was applied to study the intramolecular vibrational energy redistribution (IVR) in HDO molecule. The time-evolution of the O-H stretching local mode was studied by a time-propagation method based on matrix representation of the evolution operator. The energy transfer among the local modes was modeled by non-diagonal g-tensor terms in the kinetic energy operator and by three-dimensional potential energy operator. The results indicate that the O-H stretching local modes must be substantially long-lived within the chosen model. A new recursive programming technique combined with a very effective passing by reference methodology was developed and used in this study to implement the time-propagation routine. The introduced concept of a shared compound pointer in Fortran 90 automatically accounts for the changing sizes of all data structures, while working with only a single parameter, a pointer to a parent object.

This study examines several methodological issues pertaining to the application of isonymy techniques to a historical population located on the island of Guam in Micronesia. Since European contact the indigenous Chamorro population of Guam has undergone a series of precipitous population declines. The Spanish colonial administration imposed a dual surname system on the Chamorro. The surname information was compiled into a demographic database representing approximately 39,000 persons traced from late 19th century vital records. Analysis using the methods of isonymy was conducted on lineages established from the four parental surnames. Values were calculated from the progeny in the database, in effect focusing on the effective breeding population. Comparisons were made with inbreeding values obtained using other methods of surname analysis both for single and dual surname systems. In contrast to the paternal lineage, the values for the other lineages were influenced by their shallow temporal depth. The non-paternal lineages showed patterns of assortative mating reflecting choices of mate selection that have the potential to influence levels of inbreeding in the population.

To maintain its innovative and competitive edge the forestry sector is focused on conducting research into more efficient ways of manufacturing current products and generating new markets for by-products and technologies. It is the surface of pulp fibres which are of fundamental importance to the pulp and paper industry. A better understanding of the chemistry and morphology of Kraft pulp fibres is the primary motivation for this Master's thesis study. Through this work, we will show that simple and straight applications of newer technologies (X-ray photoelectron spectroscopy, Atomic Force microscopy, Optical Microscopy and Differential Scanning Calorimetry) could be employed by the pulp and paper industry to determine the surface chemistry of Kraft Pulp fibres (and therefore other lignocellulosic fibres). The effect that variability in the surface composition of such fibres has on industrial applications is commented on. / Pour maintenir son avantage innovateur et concurrentiel, le secteur de sylviculture est concentré sur la recherché dans des manières plus efficaces de produire des produits et des marchés courants pour des sous-produits et des technologies. C'est l'extérieure des fibres de pâte qui est d'importance fondamentale pour l'industrie de pâte et papier. Une meilleure compréhension de la chimie et de la morphologie des fibres de pâte Kraft est le raisonnement primaire pour cette thèse de maîtrise. Dons çe recherche nous démontrons que des applications simple et directes de nouvelles technologies (spectroscopie de photoélectron de rayon X, microscopie atomique de force, microscopie optique, analyse entalbique différentiel) peuvent être utilisés par l'industrie de pâte et papier pour déterminer la composition extérieure des fibres de pâte Kraft (et donc d'autre fibres lignocellulosique.) L'effect de la variabilité en composition extérieure sur des applications industrielles sera aussi étudié.