Thesis (Ph. D.)--Ohio State University, 2005. / Title from first page of PDF file. Document formatted into pages; contains xv, 323 p.; also includes graphics (some col.) Includes bibliographical references. Available online via OhioLINK's ETD Center

Thesis (Ph. D.)--Dept. of Chemistry and Dept. of Physics. University of Missouri--Kansas City, 2006. / "A dissertation in chemistry and physics." Advisor: James R. Durig. Typescript. Vita. Description based on contents viewed Jan. 29, 2007; title from "catalog record" of the print edition. Includes bibliographical references (leaves 447-460). Online version of the print edition.

Thesis (Ph. D.)--University of Idaho, 2005. / Also available online in PDF format Abstract. "October 2005." Includes bibliographical references.

In this dissertation,the membrane protein channelrhodopsin-1 from the green flagellate algae Chlamydomonas agustae (CaChR1) is studied using a variety of spectroscopic techniques developed in the Rothschild Molecular Biophysics Laboratory at Boston University. Over the last decade, channelrhodopsins have proven to be effective optogenetic tools due to their ability to function as light-gated ion channels when expressed in neurons. This ability allows neuroscientists to optically activate an inward directed photocurrent which depolarizes the neuronal membranes and triggers an action potential. Although a variety of channelrhodopsins with different properties have been used, the underlying mechanisms of channelrhodopsin functionality is not yet fully understood. The protein studied here has several advantageous properties compared to the more extensively studied channelrhodopsin-2 from Chlamydomonas reinhardtii including a red shifted visible absorption and slower light inactivation despite having a lower channel current. Elucidating the internal molecular mechanisms underlying the function of CaChR1 provides critical insight into the large class of channelrhodopsin proteins leading toward improved bioengineering for specific optogenetic applications. Here near-IR pre-resonance Raman spectroscopy of CaChR1 provides information on the structure of the unphotolyzed (P0) retinal chromophore, the Schiff base protonation state, and presence of carboxylic acid residues interacting with the Schiff base. Low-temperature FTIR difference spectroscopy combined with site-directed mutagenesis and isotope labeling provide information on changes occurring in the retinal chromophore and protein during the primary phototransition (P0 to P1). This includes information about changes involving protonation state of binding-pocket residues, protein backbone structure, and internal water molecules. Further experiments combining low-temperature and time-resolved FTIR-difference spectroscopy reveal additional information about structural changes during the transition from the unphotolyzed state to the active (open channel) state of the protein (P0 to P2). This work has resulted in an initial model that describes key proton transfer events which occur between the Schiff base and carboxylic acid residues inside the active site of CaChR1. The model raises the possibility that ion channel gating and ion specificity is regulated by the protonation changes of two key residues (Glu 169 and Asp299) located near the Schiff base.

xv, 108 p. : ill. (chiefly col.) / Aqueous aerosol surfaces are an important platform for chemical reactions through which gases are transported in the atmosphere. The chemical complexity of aqueous aerosols is well-established, but many questions remain about the molecular nature of their surfaces, particularly with respect to the uptake of gases. The pollutant sulfur dioxide, SO₂, has been implicated in environmental phenomena such as acid rain, climate change, and cloud formation. SO₂ is fundamentally interesting because it forms spectroscopically identifiable complexes with water at aqueous surfaces. This dissertation aims to understand how temperature and aqueous composition impact the formation of surface complexes between water and SO₂. Vibrational sum frequency spectroscopy (VSFS), a surface specific technique, is used to probe the vibrational modes of water and small organic molecules, investigating changes to the overall orientation, bonding environment, and structure of interfaces when aqueous surfaces are exposed to SO₂. SO₂ adsorption to water at tropospherically relevant temperatures (0--23 °C) is examined first. The results show enhanced SO₂ surface affinity at colder temperatures, with most of the topmost water molecules showing evidence of binding to SO₂ at 0 °C compared to a much lower fraction at room temperature. Surface adsorption results in significant changes in water orientation at the surface but is reversible at the temperatures examined. The surface and vibrational specificity of these studies can be used to distinguish between the effects of surface adsorption compared to bulk accommodation. This distinction is utilized to demonstrate that SO₂ complexation is independent of solution acidity, confirming that bulk absorption is unnecessary for surface adsorption to occur. Finally, the impact of the organic species succinic acid and formaldehyde on the formation of surface SO₂ complexes is examined. These experiments indicate that SO₂ surface complexation occurs primarily with water but that surface active organic species may interact with gases under certain circumstances, namely when the organic species are more chemically reactive towards the gas. These studies have important implications for atmospheric chemistry and the uptake of gases, particularly in the complex aqueous environments expected in the troposphere. / Committee in charge: Dr. Paul C. Engelking, Chair; Dr. Geraldine L. Richmond, Advisor Dr. Jeffrey A. Cina, Member; Dr. Thomas R. Dyke, Member; Dr. Alan D. Johnston, Outside Member

ARAÚJO, Bruno Sousa. Transições de fase induzidas por pressão e tamanho de partícula no ferroelástico Pb8O5(VO4)2. 2014. 79 f. Dissertação (Mestrado em Física) - Programa de Pós-Graduação em Física, Departamento de Física, Centro de Ciências, Universidade Federal do Ceará, Fortaleza, 2014. / Submitted by Edvander Pires (edvanderpires@gmail.com) on 2014-10-31T19:40:08Z No. of bitstreams: 1 2014_dis_bsaraujo.pdf: 4719840 bytes, checksum: 34b47793096a5251b04f1f4121ba3485 (MD5) / Approved for entry into archive by Edvander Pires(edvanderpires@gmail.com) on 2014-10-31T19:41:19Z (GMT) No. of bitstreams: 1 2014_dis_bsaraujo.pdf: 4719840 bytes, checksum: 34b47793096a5251b04f1f4121ba3485 (MD5) / Made available in DSpace on 2014-10-31T19:41:19Z (GMT). No. of bitstreams: 1 2014_dis_bsaraujo.pdf: 4719840 bytes, checksum: 34b47793096a5251b04f1f4121ba3485 (MD5) Previous issue date: 2014 / Ferroelastic compounds are characterized by the possibility to present two or more states of spontaneous strain which could be permuted by application of mechanical stress. Pb8O5(VO4)2 can be classified as belonging to this group. Its crystal structure is not well defined in the literature due to certain adversities found during the data analysis. However, making use of X-ray diffraction in several crystals of this compound we will discuss their probable point groups. It is also known that there is a direct relation between the states of strain and the domains pattern at ambient conditions of temperature and pressure. Several spectroscopic techniques were employed in order to analyze how the crystal structure of these compounds varies according to the dimensions of each crystal. Therefore, we observed the existence of three phases under ambient conditions as well as the possibility of a spontaneous phase transition in crystals of order to units of square micrometers. The structural behavior of Pb8O5(VO4)2 with increasing temperature has been studied in detail by different authors. They reported the existence of two phase transitions on heating, one second-order transition at about 440 K and another first-order around 520 K. The first-order phase transition leads the Pb8O5(VO4)2 crystals of ferroelastic phase to paraelastic phase. However, since ferroelastics crystals show changes of state of spontaneous strain through the application of mechanical stress, we made use of Raman scattering measures with increasing of hydrostatic pressure on samples of Pb8O5(VO4)2 to accompany the spectral behavior of the same during these pressure variations. This way we observed a phenomenon of amorphization of the sample around 11 GPa and obtained strong evidences from three phase transitions at approximately 1, 3.5 and 6 GPa. / Compostos ferroelásticos são caracterizados pela possibilidade de apresentarem dois ou mais estados de deformação ou strain espontâneos devendo haver a possibilidade de permutação entre estes estados através da aplicação de um stress mecânico. O Pb8O5(VO4)2 pode ser classificado como pertencente a este grupo. Sua estrutura cristalina ainda não é bem definida na literatura por conta de certas adversidades encontradas durante as análises das mesmas, no entanto, fazendo uso de difração de raios-X em diversos cristais deste composto discutiremos seus prováveis grupos pontuais. Sabe-se também que há uma relação direta entre os estados de strain e as estruturas de domínios sob condições ambientes de temperatura e pressão. Diversas técnicas espectroscópicas foram empregadas afim de analisar como a estrutura cristalina destes compostos pode variar de acordo com as dimensões de cada cristal. Dessa forma, verificamos a existência de três fases sob condições ambiente, bem como a possibilidade de uma transição de fase espontânea para cristais da ordem de unidades de micrometros quadrados. O comportamento estrutural do Pb8O5(VO4)2 com o aumento de temperatura foi estudado detalhadamente por diversos autores. Eles reportaram a existência de duas transições de fase durante o aquecimento, uma transição de segunda ordem por volta de 440 K e outra de primeira ordem por volta de 520 K. A transição de primeira ordem leva os cristais de Pb8O5(VO4)2 da fase ferroelástica para a fase paraelastica. Contudo, uma vez que cristais ferroelásticos apresentam mudanças de estados de strain espontâneos através da aplicação de stress mecânico, fizemos uso de medidas de espalhamento Raman com aumento de pressão hidrostática em amostras de Pb8O5(VO4)2 para acompanhar o comportamento espectral dos mesmos durante estas variações de pressão. Assim, observamos um fenômeno de amorfização da amostra por volta de 11 GPa e obtivemos fortes indícios de três transições de fase em aproximadamente 1, 3.5 e 6 GPa.

ARAÚJO, Bruno Sousa. Transições de fase induzidas por pressão e tamanho de partícula no ferroelástico Pb8O5(VO4)2. 2014. 79 f. Dissertação (Mestrado em Física) - Programa de Pós-Graduação em Física, Departamento de Física, Centro de Ciências, Universidade Federal do Ceará, Fortaleza, 2014. / Submitted by Edvander Pires (edvanderpires@gmail.com) on 2015-04-09T19:07:17Z No. of bitstreams: 1 2014_dis_bsaraujo.pdf: 4719840 bytes, checksum: 34b47793096a5251b04f1f4121ba3485 (MD5) / Approved for entry into archive by Edvander Pires(edvanderpires@gmail.com) on 2015-04-10T20:49:59Z (GMT) No. of bitstreams: 1 2014_dis_bsaraujo.pdf: 4719840 bytes, checksum: 34b47793096a5251b04f1f4121ba3485 (MD5) / Made available in DSpace on 2015-04-10T20:49:59Z (GMT). No. of bitstreams: 1 2014_dis_bsaraujo.pdf: 4719840 bytes, checksum: 34b47793096a5251b04f1f4121ba3485 (MD5) Previous issue date: 2014 / Ferroelastic compounds are characterized by the possibility to present two or more states of spontaneous strain which could be permuted by application of mechanical stress. Pb8O5(VO4)2 can be classified as belonging to this group. Its crystal structure is not well defined in the literature due to certain adversities found during the data analysis. However, making use of X-ray diffraction in several crystals of this compound we will discuss their probable point groups. It is also known that there is a direct relation between the states of strain and the domains pattern at ambient conditions of temperature and pressure. Several spectroscopic techniques were employed in order to analyze how the crystal structure of these compounds varies according to the dimensions of each crystal. Therefore, we observed the existence of three phases under ambient conditions as well as the possibility of a spontaneous phase transition in crystals of order to units of square micrometers. The structural behavior of Pb8O5(VO4)2 with increasing temperature has been studied in detail by different authors. They reported the existence of two phase transitions on heating, one second-order transition at about 440 K and another first-order around 520 K. The first-order phase transition leads the Pb8O5(VO4)2 crystals of ferroelastic phase to paraelastic phase. However, since ferroelastics crystals show changes of state of spontaneous strain through the application of mechanical stress, we made use of Raman scattering measures with increasing of hydrostatic pressure on samples of Pb8O5(VO4)2 to accompany the spectral behavior of the same during these pressure variations. This way we observed a phenomenon of amorphization of the sample around 11 GPa and obtained strong evidences from three phase transitions at approximately 1, 3.5 and 6 GPa. / Compostos ferroelásticos são caracterizados pela possibilidade de apresentarem dois ou mais estados de deformação ou strain espontâneos devendo haver a possibilidade de permutação entre estes estados através da aplicação de um stress mecânico. O Pb8O5(VO4)2 pode ser classificado como pertencente a este grupo. Sua estrutura cristalina ainda não é bem definida na literatura por conta de certas adversidades encontradas durante as análises das mesmas, no entanto, fazendo uso de difração de raios-X em diversos cristais deste composto discutiremos seus prováveis grupos pontuais. Sabe-se também que há uma relação direta entre os estados de strain e as estruturas de domínios sob condições ambientes de temperatura e pressão. Diversas técnicas espectroscópicas foram empregadas afim de analisar como a estrutura cristalina destes compostos pode variar de acordo com as dimensões de cada cristal. Dessa forma, verificamos a existência de três fases sob condições ambiente, bem como a possibilidade de uma transição de fase espontânea para cristais da ordem de unidades de micrometros quadrados. O comportamento estrutural do Pb8O5(VO4)2 com o aumento de temperatura foi estudado detalhadamente por diversos autores. Eles reportaram a existência de duas transições de fase durante o aquecimento, uma transição de segunda ordem por volta de 440 K e outra de primeira ordem por volta de 520 K. A transição de primeira ordem leva os cristais de Pb8O5(VO4)2 da fase ferroelástica para a fase paraelastica. Contudo, uma vez que cristais ferroelásticos apresentam mudanças de estados de strain espontâneos através da aplicação de stress mecânico, fizemos uso de medidas de espalhamento Raman com aumento de pressão hidrostática em amostras de Pb8O5(VO4)2 para acompanhar o comportamento espectral dos mesmos durante estas variações de pressão. Assim, observamos um fenômeno de amorfização da amostra por volta de 11 GPa e obtivemos fortes indícios de três transições de fase em aproximadamente 1, 3.5 e 6 GPa.

Orientador: Peter Alexander Bleinroth Schulz / Dissertação (mestrado) - Universidade Estadual de Campinas, Instituto de Fisica Gleb Wataghin / Made available in DSpace on 2018-08-13T03:40:09Z (GMT). No. of bitstreams: 1 PaezGonzalez_CarlosJose_M.pdf: 17726649 bytes, checksum: 92453a3b81784c5899922a7943ef209f (MD5) Previous issue date: 2009 / Resumo: Neste trabalho estudamos a localização dos modos vibracionais de três modelos simples do DNA: cadeia unidimensional,dupla cadeia e o modelo de quatro cadeias; nestes modelos substituímos os grupos atômicos por massas efetivas ligadas entre si com molas. Para cada modelo calculamos e diagonalizamos a matriz dinâmica obtendo os modos vibracionais e suas freqüências. Cada componente de um modo vibracional representa a amplitude da oscilação nesse sitio, permitindo calcular a razão de participação e a fiutuação relativa desse modo. A partir destas grandezas se mostrou que nos sistemas quasi-unidimensionais (dupla cadeia e quatro cadeias) existe um intervalo a baixas freqüências onde todos os modos vibracionais são estendidos independentemente da seqüencia e as possíveis constantes de mola. / Abstract: ln this work we studied the localization of vibrational modes of three simple models of DNA: unidimensional chain, double chain and the model of falir chains. ln these models, atomic groups were replaced by effective fiasses linked to each other by springs. For each model, the dynamic matrix was calculated and diagonalized obtaining the vibrational modes with their frequencies. Each component of a vibrational mode represents the amplitude of the oscillation in that site, allowing the calculation of the participation fatia and the relative fluctuation of that mode. From these quantities we showed that there is a range at low frequencies in quasi-one-dimensional systems (double chain and falir chains) where alI vibrational modes are extended regardless the sequence and spring constants. / Mestrado / Física da Matéria Condensada / Mestre em Física

No description available.

Vibrational imaging approaches including Raman microscopy and IR-absorption micro-spectroscopy can provide rich chemical information about biological samples. This dissertation contributes to improve the capabilities of vibrational microscopy in three aspects each with corresponding biological applications. First, along the line of combining electronic resonant effect with stimulated Raman scattering (SRS), we studied the spectroscopic characteristics for on-resonant SRS case and demonstrated the utility of electronic pre-resonant SRS on super-multiplexed imaging for live cells and tissue sections. Second, we provided a new light-matter interaction as a hybrid technique of Raman and fluorescence, called stimulated Raman excited fluorescence (SREF), bringing the long-sought-after goal of detecting single-molecule Raman scattering without plasmonic enhancement into view. Coupling SREF with vibrational sensing, local electric field and hydrogen-bonding environment can thus be visualized in situ. Third, we brought small vibrational probes into mid-infrared imaging for the goal of rich-information-content, high-throughput metabolic imaging. Chapter 1 introduces some basis of Raman scattering, and provides an overview of state-of-art SRS microscopy. Chapter 2 explores on the rigorous electronic resonant region with SRS (er-SRS) through suppression of electronic background and subsequent retrieval of vibrational peaks. In agreement with theoretical prediction, changing of vibrational band shapes from normal Lorentzian, through dispersive shapes, to inverted Lorentzian is observed when approaching electronic resonance. As large as 10-23 cm2 of resonance Raman cross section is estimated in er-SRS. In Chapter 3, a new light-matter interaction called stimulated Raman excited fluorescence (SREF) is studied. Through stimulated Raman pumping to an intermediate vibrational eigenstate followed by an upconversion to an electronic fluorescent state, SREF encodes vibrational resonance into the excitation spectrum of fluorescence emission. By leveraging superb sensitivity of SREF, we achieved all-far-field single-molecule Raman spectroscopy and imaging without plasmonic enhancement. Chapter 4 details the development of SREF into a novel water-sensing tool, by coupling with vibrational solvatochromism of environment-sensitive Raman mode. This new technique allows direct visualization on spatially-resolved distribution of water states inside single mammalian cells. Interesting intracellular heterogeneity of water states between nucleus and cytoplasm has been revealed. Chapter 5 demonstrates the utility of epr-SRS in super-multiplexed imaging with either commercial fluorophores in lives cells or our MARS probes on tissue sections. Multiplex protein-based tissue imaging is completed with newly-designed functional MARS dye with up to 12 channels simultaneously. Chapter 6 focus on metabolic imaging by mid-infrared (MIR) microscopy with vibrational probes. Raman scattering microscopy has made a major advance in metabolic imaging utilizing vibrational probes, yet is limited to relatively low throughput. As an alternative solution, MIR microscopy provides significantly higher cross section and exhibits as a rich-information-content, high-throughput technique with recent rapid technical advances. We introduced three types of small vibrational probes as azide, 13C and carbon-deuterium for studying dynamic metabolic activities of protein, lipids and carbohydrates in cells, small organisms and mice for the first time. Two MIR microscopy platforms as Fourier transform infrared (FTIR) absorption microscopy and discrete frequency mid-infrared (DFIR) microscopy were utilized to validate the generality of our vibrational probes and applicability for single-cell metabolic profiling and metabolism study on large-scale tissues.