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.

Reproduction de : Thèse de doctorat : Chimie organique et macromoléculaire : Lille 1 : 2005. / N° d'ordre (Lille 1) : 3641. Résumé en français et en anglais. Titre provenant de la page de titre du document numérisé. Bibliogr. f. 124-126.

Thèse de doctorat : Lasers, Molécules, Rayonnement atmosphérique : Lille 1 : 2003 ; 3358. / Articles en anglais en annexe. Résumé en français et en anglais. Bibliogr. p. 243-247.

Thesis (Ph. D.)--Lehigh University, 2002. / Includes vita. Includes bibliographical references (leaves 121-132).

Thesis (Ph. D.)--University of Washington, 2002. / Vita. Includes bibliographical references (leaves 65-82).

The utility of 193 nm ultraviolet photodissociation (UVPD) and negative electron transfer dissociation (NETD) for the characterization of peptide anions was systematically evaluated. UVPD outperformed NETD in nearly all metrics; however, both methods provided complementary information to traditional collision induced dissociation (CID) of peptide cations in high throughput analyses. In order to enhance the performance of NETD, activated ion negative electron transfer dissociation (AI-NETD) methods were developed and characterized. The use of low-level infrared photoactivation or collisional activation during the NETD reaction period significantly improved peptide anion sequencing capabilities compared to NETD alone. Tyrosine deprotonation was shown to yield preferential electron detachment upon NETD or UVPD, resulting in N - C[alpha] bond cleavage N-terminal to the tyrosine residue. LC-MS/MS analysis of a tryptic digest of BSA demonstrated that these cleavages were regularly observed under high pH conditions. Transmission mode desorption electrospray ionization (TM-DESI) was coupled with 193 nm UVPD and CID for the rapid analysis and identification of protein digests. Comparative results are presented for TM-DESI-MS/CID and TM-DESI-MS/UVPD analyses of five proteolyzed model proteins. In some cases TM-DESI/UVPD outperformed TM-DESI-MS/CID due to the production of an extensive array of sequence ions and the ability to detect low m/z product ions. 193 nm UVPD was implemented in an Orbitrap mass spectrometer for characterization of intact proteins. Near-complete fragmentation of proteins up to 29 kDa was achieved. The high-energy activation afforded by UVPD exhibited far less precursor ion charge state dependence than conventional methods, and the viability of 193 nm UVPD for high throughput top-down proteomics analyses was demonstrated for the less 30 kDa protein from a fractionated yeast cell lysate. The use of helium instead of nitrogen as the C-trap and HCD cell bath gas and trapping ions in the HCD cell prior to high resolution mass analysis significantly reduced the signal decay rate for large protein ions. As a result, monoclonal IgG1 antibody was isotopically resolved and mass accurately determined. A new high mass record for which accurate mass and isotopic resolution has been achieved (148,706.3391 Da ± 3.1 ppm) was established. / text

Visible-blind and solar-blind ultraviolet photodetectors based on GaN/AlGaN were designed, fabricated, and characterized for commercial and military applications. High performance back-illuminated solar-blind MSM achieved external quantum efficiency of ~48%. The dark current of 40x40μm MSM was less than the instrument measurement limitation of 20fA for a bias <100V. No photoconductive gain was observed. With an n-type doped high-Al ratio "window" Al₀.₆Ga₀.₄N layer, back-illuminated solar-blind p-i-n photodiode achieved a quantum efficiency of ~55% at zero-bias. Absorption edge study of both MSM and p-i-n photodetectors, based on device spectral responses, resulted in a performance comparison of MSMs and p-i-ns, as the solar-blind photodetection requires a sharp solar-blind rejection. Photoconductive detectors and avalanche photodetectors, with the internal gain advantage, have been discussed as well. A 30μm diameter GaN avalanche photodiode achieved a gain >23, with a dark current less than 100pA. The breakdown showed a positive temperature coefficient of 0.03 V/K that is characteristic of avalanche breakdown. SiC APDs, as candidates for visible-blind applications, have been designed, fabricated and characterized. An avalanche gain higher than 10⁵, with a dark current less than 1nA, showed the potential of SiC APD replacing PMTs for high sensitivity visible-blind UV detection. A silicon-based optical receiver has been presented in the Appendix. With the photodiode internal avalanche gain ~4, a sensitivity ~-6.9dBm at 10Gbps has been achieved. / text

<p>In diploid yeast cells, mitotic recombination is very important for repairing double-strand breaks (DSB). When repair of a DSB results in crossovers, it may cause loss of heterozygosity (LOH) of markers centromere-distal to the DSB in both daughter cells. Gene conversion events unassociated with crossovers cause LOH for an interstitial section of a chromosome. Alternatively, DSBs can initiate break-induced replication (BIR), causing LOH in only one of the daughter cells. Mapping mitotic LOH contributes to understanding of mechanisms for repairing DSBs and distribution of these recombinogenic lesions. Methods for selecting mitotic crossovers and mapping the positions of crossovers have recently been developed in our lab. Our current approach uses a diploid yeast strain that is heterozygous for about 55,000 SNPs, and employs SNP-Microarrays to map LOH events throughout the genome. These methods allow us to examine selected crossovers on chromosome V and unselected mitotic recombination events (crossovers, gene conversion events unassociated with crossovers, and BIR events) at about 1 kb resolution across the genome.</p><p>Mitotic recombination can be greatly induced by UV radiation. However, prior to my research, the nature of the recombinogenic lesions and the distribution of UV-induced recombination events were relatively uncharacterized. Using SNP microarrays, we constructed maps of UV-induced LOH events in G1-synchronized cells. Mitotic crossovers were stimulated 1500-fold and 8500-fold by UV doses of 1 J/m2 and 15 J/m2, respectively, compared to spontaneous events. Additionally, cells treated with 15 J/m2 have about eight unselected LOH events per pair of sectors, including gene conversions associated and unassociated with crossovers as well as BIR events. These unselected LOH events are distributed randomly throughout the genome with no particular hotspots; however, the rDNA cluster was under-represented for the initiation of crossover and BIR events. Interestingly, we found that a high fraction of recombination events in cells treated with 15 J/m2 reflected repair of two sister chromatids broken at roughly the same position. In cells treated with 1 J/m2, most events reflect repair of a single broken sister chromatid (Chapter 2). </p><p>The primary pathway to remove pyrimidine dimers introduced by UV is the nucleotide excision repair (NER) pathway. In NER, the dimer is excised to generate a 30-nucleotide gap that can be replicated to form DSBs if not filled in before DNA replication. The NER gap can also be expanded by Exo1p to form single stranded gaps greater than one kilobase. Alternatively, in the absence of NER, unexcised dimers could result in blocks of DNA replication forks. Resolving the stalled replication fork could lead to recombinogenic breaks. In Chapter 3 and Chapter 4, we analyzed recombination events in strains defective in various steps of processing of UV-induced DNA damage, including exo1 and rad14 mutants. </p><p>In Chapter 3, I show that Exo1p-expanded NER gaps contribute to UV-induced recombination events. Interestingly, I also found that Exo1p is also required for the hotspot activity of a spontaneous crossover hotspot involving a pair of inverted Ty repeats. In addition to its role of expanding a nick to a long single-stranded gap, Exo1p is also a major player in DSB end resection. Therefore, I examined the gene conversion tract lengths in strains deleted for EXO1. I found that, although crossover-associated gene conversion tracts become shorter in the exo1 mutant as expected, noncrossover tract lengths remained unaffected. As a result, noncrossover tracts are longer than crossover tracts in the exo1 mutant while the opposite result was observed in the wild-type strains. I proposed models to rationalize this observation.</p><p>In Chapter 4, to investigate whether the substantial recombinogenic effect in UV in G1-synchronized cells requires NER, we mapped UV-induced LOH events in NER-deficient rad14 diploids treated with 1 J/m2. Mitotic recombination between homologs was greatly stimulated, which suggests that dimers themselves can also cause recombination without processing by NER. We further show that UV-induced inter-homolog recombination events (noncrossover, crossover and BIR) depend on the resolvase Mus81p, and are suppressed by Mms2p-mediated error-free post-replication repair pathway. </p><p>The research described in Chapters, 2, 3, and 4 are in the publications Yin and Petes (2013), Yin and Petes (2014), and Yin and Petes (2015), respectively.</p> / Dissertation

The interaction of intense laser pulses with nanometer scale atomic clusters has been an active area of study since the advent of amplified femtosecond lasers. In the case of infrared irradiation of noble gas clusters, direct field-driven ionization results in the ejection of energetic electrons, high ion charge states, and Coulomb explosion of the ion core of the clusters. These processes result from electron motion driven by the cluster potential and the large ponderomotive potential of the laser field. When extreme ultraviolet (XUV) pulses interact with clusters, the mechanisms responsible for the infrared response are 'turned off' because the ponderomotive potential is very small. We have conducted cluster experiments at 38nm using focused XUV pulses produced by high harmonic generation with a 15TW Ti:Sapphire laser. We measured the charge states and kinetic energy spectra of ions produced in the interaction, and observe substantial ion population up to Xe⁵⁺, with a small number of Xe⁶⁺-Xe⁸⁺ ions produced by collisional ionization by hot plasma electrons. The ion kinetic energy spectrum indicates a hydrodynamic expansion at an ion temperature of 8eV. This is in stark contrast to intense infrared/cluster interactions, where clusters are stripped of electrons to a large degree and expand by Coulomb forces, resulting in far higher ion kinetic energy for similar degrees of ionization. / text

Molecules are traditionally treated quantum mechanically using the Born-Oppenheimer formalism. In this formalism, different electronic states of the molecule are treated independently. However, most photo-initiated phenomena occurring in nature are driven by the couplings between different electronic states in both isolated molecules and molecular aggregates, and therefore occur beyond the Born-Oppenheimer formalism. These couplings are relevant in reactions relating to the perception of vision in the human eye, the oxidative damage and repair of DNA, the harvesting of light in photosynthesis, and the transfer of charge across large chains of molecules. While these reaction dynamics have traditionally been studied with visible and ultraviolet spectroscopy, attosecond XUV pulses formed through the process of high harmonic generation form a perfect tool for probing coupled electronic dynamics in molecules. In this thesis, I will present our work in using ultrafast, XUV spectroscopy to study these dynamics in molecules of increasing complexity. We begin by probing the relaxation dynamics of superexcited states in diatomic O₂. These states can relax via two types of electronic couplings, either through autoionization or neutral dissociation. We find that our pump-probe scheme can disentangle the two relaxation mechanisms and independently measure their contributing lifetimes. Next, we present our work in observing a coherent electron hole wavepacket initiated by the ionization of polyatomic CO₂ near a conical intersection. The electron-nuclear couplings near the conical intersection drive the electron hole between different orbital configurations. We find that we can not only measure the lifetime of quantum coherence in the electron hole wavepacket, but also control its evolution with a strong, infrared probing field. Finally, we propose an experiment to observe the migration of an electron hole across iodobenzene on the few-femtosecond timescale. We present experimental modifications made to the high harmonic generation set-up in order to probe this ultrafast and elusive charge migration. These results demonstrate the potential of ultrafast, XUV spectroscopy in probing the inner-workings of electronic couplings occurring in nature.