The vibrational potential energy surfaces in electronic ground and excited states of several ring molecules were investigated using several different spectroscopic methods, including far-infrared (IR), Raman, ultraviolet (UV) absorption, fluorescence excitation (FES), and single vibronic level fluorescence (SVLF) spectroscopies. Based on new information obtained from SVLF and millimeter wave spectra, the far-IR spectra of coumaran were reassigned and the one-dimensional ring-puckering potential energy functions for several vibrational states in the S0 ground state were determined. The barrier was found to be 154 cm-1 and the puckering angles to be ± 25°, in good agreement with the millimeter wave barrier of 152 cm-1 and puckering angles of ± 23°. Moreover, the UV absorption and FES spectra of coumaran allowed the one-dimensional ring-puckering potential energy functions in the S1 excited state to be determined. The puckering barrier is 34 cm-1 for the excited state and the puckering angles are ± 14°. Several calculations with different basis sets have been carried out to better understand the unusual vibrational frequencies of cyclopropenone. It was shown that there is strong interaction between the C=O and symmetric C-C stretching vibrations. These results differ quantitatively from a previous normal coordinate calculation and interpretation. The vapor-phase Raman spectrum of 3,7-dioxabicyclo[3.3.0]oct-1,5-ene was analyzed and compared to the predicted spectrum from DFT calculations. The spectrum further shows it has D2h symmetry, in which the skeletons of both rings are planar. The infrared and Raman spectra of vapor-phase and liquid-phase 1,4-benzodioxan and 1,2,3,4-tetrahydronaphthalene were collected and the complete vibrational assignments for both molecules were made. Theoretical calculations predicted the barriers to planarity to be 4809 cm-1 for 1,2,3,4-tetrahydonaphthalene and 4095 cm-1 for 1,4-benzodioxan. The UV absorption, FES, and SVLF spectra of both molecules were recorded and assigned. Both one and two-dimensional potential energy functions of 1,4-benzodioxan for the ring-twisting and ring-bending vibrations were carried out for the S0 and S1(π,π*) states, and these were consistent with the high barriers calculated for both states. The low-frequency spectra of 1,2,3,4-tetrahydronaphthalene in both S0 and S1(π,π*) states were also analyzed.

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The X-ray absorption spectrum of silicon in of SiCl4 has been calculated for the LIII and LII edges. The resulting spectrum has been vibrationally resolved by considering the symmetric stretch vibrational mode and the results has been compared to experiment [4]. One peak from the experiment was found to be missing in the calculated vibrationally resolved spectrum. The other calculated peaks could be matched to the corresponding experimental peaks although significant basis set effects are present. An investigation of one peak beyond the Franck–Condon principle shows it to be a good approximation in the case of the studied system.

Synchrotron-based spectroscopic techniques enable investigations of the many important biological and environmental functions of the ubiquitous element sulfur. In this thesis the methods for interpreting sulfur K-edge X-ray absorption near edge structure (XANES) spectra are developed and applied for analyses of functional sulfur groups. The influence of coordination, pH, hydrogen bonding, etc., on the sulfur 1s electronic excitations is evaluated by transition potential density functional theory. Analyses have been performed of reduced sulfur compounds in marine-archaeological wood from historical shipwrecks, including the Vasa, Stockholm, Sweden and the Mary Rose, Portsmouth, U.K.. The accumulation of sulfur as thiols in lignin-rich parts of the wood on the seabed is also a probable pathway in the natural sulfur cycle for how reduced sulfur enters fossil fuels via humic matter in anaerobic marine sediments. Sulfur K-edge XANES spectra for several biochemical model compounds and for coexisting isomeric sulfur species in cysteine and sulfite(IV) aqueous solutions have been analyzed with the aid of theoretical calculations. Cysteine derivatives are important for biochemical detoxification, and mercury(II) cysteine complexes in solution have been structurally characterized by means of Extended X-ray Absorption Fine Structure (EXAFS), Raman and 199Hg NMR spectroscopy. Lanthanoid(III) ions were found to coordinate eight dimethyl sulfoxide oxygen atoms in a distorted square antiprism in the solid state and in solution, by combining crystallography, EXAFS, XANES and vibrational spectroscopy. The mean M-O bond distances for the disordered crystal structures are in good agreement with those from the lattice-independent EXAFS studies. The different sulfur K-edge XANES spectra for the dimethyl sulfoxide ligands in the hexasolvated complexes of the trivalent group 13 metal ions, Tl(III), In(III), Ga(III) and Al(III), were interpreted by theoretical calculations.

Atmospheric corrosion takes place on most metals as they interact with thesurrounding environment. A degradation of the metal is the common result,which often leads to a shortened lifespan of the material. Hence, knowledge onthe fundamental interaction between a gas containing corrosive constituentsand a metal surface, which is the starting point of atmospheric corrosion, isimportant in many contexts. As the nature of atmospheric corrosion is inherentlycomplex, it imposes demands on the analytical studies that are neededin order to understand the fundamentals on a molecular level. Consequently,in-situ vibrational techniques, providing molecular information, have beenutilized in this work to study atmospheric corrosion by targeting the initialstages of the interaction between corrosive air and a metal surface. The initialstages (from minutes until days of exposure) were studied as these havea large influence on the atmospheric corrosion for prolonged exposure times. More specifically, the interaction between humidified air to which organicacids were added, and zinc was targeted in order to address a situation inindoor atmospheric corrosion, where organic acids are of importance. Zinc isa constituent in e.g. brass, which is an alloy used in many indoor applications. A systematic investigation utilizing complementary acting vibrational techniquesthus enabled detailed information on the mechanisms of the onsetof atmospheric corrosion of zinc induced by acetic and formic acid. Corrosionproducts of both two dimensional and three dimensional character couldbe separately studied by combining VSFS (interface sensitive), IRAS (nearsurfacesensitive), and CRM (bulk sensitive). The Zn surface was found to be heterogeneous with different hydroxylgroups present on the surface. As this surface was exposed to formic or aceticacid, the OH groups on the surface were rapidly displaced in a ligand exchangewith formate or acetate. These ligands, organised in two dimensionalstructures, promoted corrosion by weakening the bonds of the Zn atoms totheir surrounding matrix. The subsequent growth of three dimensional corrosion products, Zn hydroxyacetate and formate, observed within short exposure times of Zn exposedto acetic and formic acid, was found to be electrochemical in nature.Cathodic areas consisting of more crystalline ZnO were observed. The potentialdifference between these more noble areas on the surface and those of lessnoble character created an electrochemical cell, initiating release of Zn ionsinto the aqueous adlayer in the anodic reactions. These Zn ions precipitatedas localised corrosion products. The cathodic areas increased the local pHon the surface, thereby promoting precipitation in their vicinity. The resultson initial stages of this type of corrosion were found to have similarities withprevious field studies of Zn exposed to real indoor environments. One way to decrease the corrosion rate of zinc is by adsorbing a corrosioninhibitor to the metal surface in order to protect it. As a model for sucha corrosion inhibitor, octadecanethiol (CH3(CH2)17SH) was seen to provideincreased corrosion protection of both reduced and oxidised Zn substrates byforming an adsorbed surface layer with an ordered structure. / QC 20100719

This dissertation presents a detailed computational investigation into the vibrational properties of quinones involved in solar energy conversion processes in photosynthetic reaction centers. In particular, we focus on the vibrational properties of the ubiquinone molecule that occupies the QA binding site in purple bacterial photosynthetic reaction centers. To provide a foundation upon which to base computational studies of pigments in protein binding sites density functional theory based calculations of the vibrational properties of neutral ubiquinone in the gas phase and in solvent were undertaken. From single point energy calculations it was shown that at least eight ubiquinone conformers, each with slightly different FTIR spectra, could be present in solvent at room temperature. The calculated and experimental spectra for neutral ubiquinone in solution are very different from the spectra associated with ubiquinone in the QA binding in purple bacterial reaction centers. For this reason an ONIOM method was undertaken in which the pigment was treated using density functional theory based methods while the protein was treated using molecular mechanics. The ONIOM calculations not only modeled the experimental QA FTIR difference spectra but also resolved the long standing issue of whether a very strong hydrogen bond exists between the bound ubiquinone and the imidazole nitrogen of a histidine residue (HisM219). To further validate the usefulness of the ONIOM approach experimental isotope edited FTIR spectra obtained using purple bacterial reaction centers with a range of chainless symmetrical quinones incorporated were modeled. Again, the agreement between the calculated and experimental spectra is outstanding. We also modeled the vibrational properties of the ubisemiquinone anion radical both in solvent and in the QA binding site. Vibrational modes of ubisemiquinone display a greater degree of mixing of the various molecular groups of the molecule. Nonetheless the calculated FTIR spectra for ubisemiquinone in solution and in the QA site agree very well with that found experimentally. Vibrational frequencies of ubisemiquinone obtained from ONIOM calculated Raman spectra also agree very well with that found in experimental resonance Raman spectra associated with the ubisemiquinone anion radical in the QA binding site.

Close coupling scattering calculations have been conducted for the para spin modification of H₂-{He, Ne and Ar}. The XC(fit) potential energy surfaces for H₂-Ne and H₂-Ar have been used for calculations for these two systems, while a newly fitted version of the Schaefer and Kohler potential energy surface was used for the H₂-He system. The fitting procedure employs nine modified Lennard-Jones oscillator functions to describe accurately 90% of the original tabulated potential energy surface to better than 12% error. The scattering calculations for H₂-Arfailed at higher energies due to the presence of a previously undocumented potential energy surface turn-over at R less than 1. 0 Angstroms. Manifold-to-manifold v=1 vibrational relaxation calculations for each of these systems are compared with other experimental and theoretical calculations. These comparisons demonstrate a common discrepancy between previous calculations and the current calculations for each system. The current vibrational relaxation rate constants are generally too small when compared to low temperature values of Audibert et al. and Orlikowski, and the high temperature values obtained by Flower et al. and Dove andTeitelbaum. The current calculations indicate the presence of a dramatic up-turn in the low temperature H₂-He rate constants. Other experimental and theoretical treatments do not exhibit this same up-turn, which is puzzling. A set of follow-up calculations featuring a larger basis set (such as the {16,12,10,8} Flower et al. basis set) and a larger manifold of included relaxation pathways are needed to improve these calculations.

Oxide thin films and bimetallic model catalysts have been studied using metastable impact electron spectroscopy (MIES), ultraviolet photoelectron spectroscopy (UPS), low energy ion scattering spectroscopy (LEISS), X – ray photoelectron spectroscopy (XPS), low energy electron diffraction (LEED), infrared reflection absorption spectroscopy (IRAS) and temperature programmed desorption (TPD) under ultra high vacuum (UHV) conditions. Of particular interest in this investigation was the characterization of the surface morphology and electronic/geometric structure of the following catalysts: SiO2/Mo(112), Ag/SiO2/Mo(112), Au–Pd/Mo(110), Au–Pd/SiO2/Mo(110), and Pd– Sn/Rh(100). Specifically, different types of oxide surface defects were directly identified by MIES. The interaction of metal clusters (Ag) with defects was examined by work function measurements. On various Pd related bimetallic alloy surfaces, CO chemisorption behavior was addressed by IRAS and TPD. Observed changes in the surface chemical properties during the CO adsorption-desorption processes were explained in terms of ensemble and ligand effects. The prospects of translating this molecular-level information into fundamental understanding of ‘real world’ catalysts are discussed.

The technical feasibility of hypersonic flight (i.e., re-entry, hypersonic flight vehicles, cruise missiles, etc.) hinges on our ability to understand, predict, and control the transport of turbulence in the presence of non-equilibrium effects. A theoretical analysis of the governing equations suggests a mechanism by which fluctuations in internal energy are coupled to the transport of turbulence. Numerical studies of these flows have been conducted, but limited computational power results in reduced fidelity. Experimental studies are exceedingly rare and, consequently, experimental data available to build and evaluate turbulence models is nearly non-existent. The Decaying Mesh Turbulence (DMT) facility was designed and constructed to generate a fundamental decaying mesh turbulent flow field with passive grids. Vibrational non-equilibrium was achieved via a capacitively-coupled radio-frequency (RF) plasma discharge which required an operating pressure of 30 Torr. The flow velocity was 30 m/s. Data was recorded with each grid at multiple plasma powers (Off, 150 W, and 300 W). Over two terabytes of highly resolved (3,450 image pairs) two-dimensional particle image velocimetry (PIV) was acquired and archived. Temperature measurements were carried out using coherent anti-Stokes Raman spectroscopy (CARS). The primary objective of this study was to answer the fundamental scientific question: "Does thermal non-equilibrium alter the decay rate of turbulence?" The results of this study show that the answer is "Yes." The results demonstrate a clear coupling between thermal non-equilibrium and turbulence transport. The trends observed agree with those expected based on an analysis of the Reynolds stress transport equations, which provides confidence in transport equation-based modeling. A non-trivial reduction (~30%) in the decay rate downstream of the 300 W plasma discharge was observed. The data also show that the decay of TKE downstream of the plasma discharge was delayed (~20% downstream shift). In addition, the thermal non-equilbrium was observed to have no effect on the transverse stress. This suggests that, for this flow, the energy dilatation terms are small and unaffected by the plasma discharge, which simplifies modeling.

The vibrational potential energy surfaces in electronic ground and excited states of several ring molecules were investigated using several different spectroscopic methods, including far-infrared (IR), Raman, ultraviolet (UV) absorption, fluorescence excitation (FES), and single vibronic level fluorescence (SVLF) spectroscopies. Based on new information obtained from SVLF and millimeter wave spectra, the far-IR spectra of coumaran were reassigned and the one-dimensional ring-puckering potential energy functions for several vibrational states in the S0 ground state were determined. The barrier was found to be 154 cm-1 and the puckering angles to be ± 25°, in good agreement with the millimeter wave barrier of 152 cm-1 and puckering angles of ± 23°. Moreover, the UV absorption and FES spectra of coumaran allowed the one-dimensional ring-puckering potential energy functions in the S1 excited state to be determined. The puckering barrier is 34 cm-1 for the excited state and the puckering angles are ± 14°. Several calculations with different basis sets have been carried out to better understand the unusual vibrational frequencies of cyclopropenone. It was shown that there is strong interaction between the C=O and symmetric C-C stretching vibrations. These results differ quantitatively from a previous normal coordinate calculation and interpretation. The vapor-phase Raman spectrum of 3,7-dioxabicyclo[3.3.0]oct-1,5-ene was analyzed and compared to the predicted spectrum from DFT calculations. The spectrum further shows it has D2h symmetry, in which the skeletons of both rings are planar. The infrared and Raman spectra of vapor-phase and liquid-phase 1,4-benzodioxan and 1,2,3,4-tetrahydronaphthalene were collected and the complete vibrational assignments for both molecules were made. Theoretical calculations predicted the barriers to planarity to be 4809 cm-1 for 1,2,3,4-tetrahydonaphthalene and 4095 cm-1 for 1,4-benzodioxan. The UV absorption, FES, and SVLF spectra of both molecules were recorded and assigned. Both one and two-dimensional potential energy functions of 1,4-benzodioxan for the ring-twisting and ring-bending vibrations were carried out for the S0 and S1(π,π*) states, and these were consistent with the high barriers calculated for both states. The low-frequency spectra of 1,2,3,4-tetrahydronaphthalene in both S0 and S1(π,π*) states were also analyzed.