During the last decade, Raman microscopy is experiencing rapid development and increasingly applied in biological and medical systems. Especially, stimulated Raman scattering (SRS) microscopy, which significantly improves the sensitivity of Raman scattering through stimulated emission, has allowed direct visualization of many species that are previously challenging with conventional fluorescence imaging. Compared to fluorescence, SRS imaging requires no label or small label on the target molecule, thus with minimal perturbation to the molecule of interest. Moreover, Raman scattering is free from complicated photophysical and photochemical processes such as photobleaching, and has intrinsically narrower linewidth than fluorescence emission. This allows multiplexed Raman imaging with minimal spectral crosstalk and excellent photo-stability. To achieve the full potential of Raman microscopy, vibrational probes have been developed for Raman imaging. Multiple Raman probes with a few atoms in size are applied in Raman imaging with high sensitivity and specificity. An overview of both fluorescence and Raman microscopy and their imaging probes is given in Chapter 1 with a brief discussion on the SRS theory. Built on the current progress of Raman microscopy and vibrational probes, I write on my research in the development of carbon-deuterium, alkyne and nitrile probes for visualizing choline metabolism (Chapter 2), glucose uptake activity (Chapter 3), complex brain metabolism (Chapter 4) and polymeric nanoparticles (Chapter 5) in live cells and tissues, as well as the development of polyyne-based vibrational probes for super-multiplexed imaging, barcoding and analysis (Chapter 6).

Foram estudados através de espectroscopia vibracional, Raman e infravermelho, uma série de derivados do íon pentacianocobaltato(II), de fórmula geral [Co(CN)5-L-Co(CN)5]n-, onde L é H2C=CH2, H3COOC-C=C-COOCH3, C2H5COO-C=C-COOC2H5, SO2, O--2, O-2 ou NO2. Além desses Complexos, o íon dímero [Co2(CN)10]6- também foi objeto de estudo. No caso dos íons [Co(CN)5-L-Co(CN)5]n- os espectros vibracionais na região de estiramento CN são interpretados com base numa simetria C4v dos grupos Co(CN)5 isolados. A natureza das ligações C=N e das, ligações do ligante L para esses compostos é discutida com base nos resultados obtidos. / The vibrational spectra (Raman and infrared) of a series of compounds of general formula [Co(CN)5-L-Co(CN)5]n-, derived from the pentacianocobaltate(II) ion, where L is H2C=CH2, H3CCOO-C=C-COOCH3, C2H5COO-C=C-COOC2H5, NO2, SO2, O--2 or O-2, were studied. The dimer ion [Co2(CN)10]6- has also been subject of study. In the case of the [Co(CN)5-L-Co(CN)5]n- ions the vibrational spectra in the region of CN stretching vibrations were interpreted based on the C4v symmetry of the isolated Co(CN)5 groups. Characteristic frequencies of the ligand L and skeletal vibrations of Co(CN)5 group are tentatively assigned. The nature of C=N bonding and the structure of ligand L for these compounds are discussed on the basis of the obtained spectral results.

The stability of glass is linked to its composition and the atmosphere controls its alteration. The organic pollutants emitted by wooden showcases play a role in the alteration of historic glasses. This study examines the effects of acetic acid, formic acid and formaldehyde on objects from the National Museums of Scotland and on replica glasses aged artificially, all with a soda silicate composition. Composition was determined by electron microprobe and analytical decomposition of the Raman spectra was used to establish correlations between glass structure and composition. This allowed interpretation of the structural variations between bulk and altered glass. The structure of the glasses altered by pollutants is characteristic of an alteration by selective leaching, with transformation of the silicates linked to alkali into silanols, which subsequently underwent condensation reactions to form a more polymerised structure. The SIMS concentration profiles of glass aged in artificial and real atmospheres were used to follow the alteration evolution as a function of time, humidity and pollutant concentration. The water film formed by the humidity at the surface and its acidity control the alteration by leaching of alkali and hydration of the glass. Formaldehyde does not act on the leaching reaction while acids accelerate and amplify it. In mixed polluted atmosphere, formates compounds always predominate in the film even at low formic acid concentration. The humidity and temperature fluctuations in museums maintain the leaching reaction. Knowledge of the harmful effect of organic acid pollutants in the alteration of soda silicate glasses will help improve their conservation.

Este trabalho de tese versa sobre o estudo espectroscópico da polianilina (PANI) formada em solução e nas cavidades de sólidos inorgânicos porosos e, também, sobre o monitoramento da interação entre a PANI e íons metálicos, através das técnicas espectroscópicas Raman ressonante, espectroscopia no infravermelho (IR), espectroscopia eletrônica no UV-VIS-NIR, ressonância paramagnética eletrônica (EPR) e absorção de raios X (XANES). Na síntese em solução, empregou-se o Cu(II) como agente oxidante em dois meios: (i) aquoso ácido e (ii) acetonitrila/água. As matrizes inorgânicas utilizadas foram a MCM-41, Cu(II)-MCM-41, Cu(II)-Montmorilonita e alfa-Zr(HOPO3)2.H2O. A espectroscopia Raman ressonante, utilizando diferentes radiações excitantes, demonstrou-se uma importante ferramenta no estudo dos diversos segmentos poliméricos nos diferentes ambientes químicos. Verificou-se a importância do meio reacional na natureza do polímero obtido. Usando Cu(II) em meio aquoso ácido, forma-se o de sal de esmeraldina enquanto em meio de acetonitrila/água, obteve-se um polímero contendo anéis fenazínicos e segmentos quinonadiimina e/ou fenilenodiamina. Os polímeros obtidos na sílica mesoporosa Cu(II)-MCM-41, na argila Cu(II)-MMT e no fosfato lamelar alfa-Zr(HPO4)2.H2O (alfa-ZrP) também apresentam novos segmentos provenientes de mecanismos de polimerização que diferem do usual acoplamento cabeça-cauda. Através da técnica \"layer-by-layer\" foi possível obter filmes de alfa-ZrP/PANI com a PANI na forma sal de esmeraldina e conformação estendida. Foi observado que complexação da esmeraldina base (EB) com Cu(II), Fe(III) e Zn(II) leva à formação de radicais cátions. O monitoramento do comportamento espectroscópico de soluções de EB e íons metálicos em solução de N-metil-pirrolidona demonstrou que as espécies presentes dependem da natureza dos íons metálicos, da proporção Metal/EB e das concentrações do polímero e do íon metálico. / This work presents the spectroscopic study of polyaniline (PANI) formed in solution and inside inorganic porous materials, and also the monitoring of the interaction of PANI and metallic ions through resonance Raman, infrared spectroscopy (IR), electronic UV-VIR-NIR spectroscopy, electronic paramagnetic resonance (EPR) and X-ray absorption near edge structure (XANES). In the polymerization of aniline in solution, Cu(II) ions were used as oxidizing in two different media: (i) acidic aqueous medium and (ii) acetonitrile/water. The inorganic hosts employed were MCM-41, Cu(II)-MCM-41, Cu(II)-Montmorillonite and alpha-Zr(HOPO3)2.H2O. Resonance Raman scattering by using exciting laser lines in a wide spectral range is an important technique for the structural investigation of the polymeric segments in different environments. It was verified the important role of the synthetic parameters in the structure of the polymeric material obtained. Using Cu(II) ions in acidic aqueous medium, emeraldine salt (ES) is formed while in acetonitrile/water medium it was observed a polymer having phenazine-like rings, quinonediimine and/or phenylenediamine segments. The obtained polymers into mesoporous silica Cu(II)-MCM-41, into Cu(II)-MMT clay and into the lamellar phosphate alpha-Zr(HPO4)2.H2O (alpha-ZrP) also present new segments resulted from distinct polymerization mechanisms from the usual head-to-tail coupling. Through the layer-by-layer technique it was possible to obtain alpha-ZrP/PANI films with PANI in the ES form and with extended conformation. It was observed that complexation of emeraldine base (EB) with Cu(II), Fe(III), and Zn(II) ions gives rise to radical cations formation. The monitoring of spectroscopic behavior of EB and metallic ions in NMP solution showed that the species present depend on the nature of metallic ion, on the Metal/EB ratio, and on the metallic ion and polymer concentrations.

Noninvasive glucose sensing has been studied widely. Near infrared (NIR) absorption spectroscopy and Raman scattering spectroscopy are proposed individually and combined as methods for glucose measurement in a three component sample matrix. In both techniques, the light transmits through human skin and a spectrum is collected. The research described in this thesis is like this. The use of individual NIR spectra data and individual Raman spectra data can give a good prediction ability of the partial least-squares (PLS) calibration model. Since the NIR and Raman spectroscopies have complementary nature of molecular vibrations, the research tried to prove the prediction ability of the PLS calibration model can be improved by combining NIR and Raman spectra data. Two approaches are investigated to ascertain the benefits of combining these spectral methods. First, NIR and Raman spectral data collected from a set of 60 samples concated and used to compute multivariate models based on PLS and net analyte signal (NAS) methods. The performance of models based on concated NIR-Raman spectra are compared to conventional models based on only NIR and only Raman spectra. The second strategy reported in this chapter is the simulated NIR and Raman spectra and computing PLS and NAS models by concating these simulated spectra. Spectral simulation permits systematic variations in noise levels. In both cases, various preprocessing methods are explored to find a suitable way to combine the different spectral types. The result from the real spectra data is that adding low signal-to-noise ratio (SNR) to high SNR spectra would make the calibration models worse. The result from the simulated spectra data is that with the same SNR and the same magnitude of the two spectra, the prediction ability of the calibration model can be improved.

The laser Raman spectra of tetrachlorocyclopropene in the liquid and solid phases have been recorded and vibrational assignments are presented. These results along with root mean squared vibrational amplitudes from electron diffraction data have been employed in a normal coordinate analysis in which a 19 parameter potential function is refined. This potential function, originally expressed in terms of compliance constants, is then used to derive the corresponding conventional and relaxed force constants.

Microbial biofilms are significant in a variety of settings including the human microbiome, infectious disease, industrial processes, and environmental remediation. Due to the ubiquitous nature of biofilms, there is a great interest in understanding cellular activities within the biofilm matrix. Biofilm cells are able to better withstand environmental stress, experience increased horizontal gene transfer, and live longer. The purpose of this research is to grow Pseudomonas sp. strain ADP as a biofilm and examine the chemical and physical characteristics the microbe undertakes in a sticky extracellular matrix. ADP is the organism of choice because of its ability to metabolize atrazine. Cells are grown in a drip biofilm reactor and flow cells under varying time lapse to gain insight to biofilm formation. Some cells are grown with atrazine as the sole nitrogen source, while others are grown in a nutrient-rich medium to compare cells response under nutrient-limited conditions with atrazine particles in the matrix. As a positive control, Escherichia coli are grown in a similar manner. Raman spectroscopy was the main analytical technique used to evaluate the chemical and molecular characteristics of this system. Scanning electron microscopy is used to examine cellular distribution, and several assays are performed for molecular composition analysis. Raman analysis in the fingerprint region revealed distinct differences between free cells and cells in biofilm. Soluble extracellular polymeric substances (EPS) were found to be more prevalent than tightly bound EPS and lightly bound EPS in the biofilm matrix. Comparison of relative peak intensity ratios suggests that it is possible to track atrazine degradation by means of intermediates using Raman spectroscopy. SEM micrographs revealed EPS role as an immobilizing agent when in contact with compounds, such as atrazine. Further research is needed to determine if atrazine can bind to EPS fractions outside the presence of cells and whether its affinity to EPS is mostly attributed to physical conditions, due to the architecture of biofilm, or chemical, based on functional groups presents. The results obtained from this research will contribute to the development of a less invasive microscale approach to address the acquisition and induction of biotransformation activity occurring in xenobiotic degrading systems. The extracellular interactions observed can be used to further characterize biofilm-mediated bioremediation. Results have contributed to the Raman spectra library for microorganisms and organic compounds. .

Thesis (Ph. D.)--University of Hong Kong, 200 . / Title proper from title frame. Also available in printed format.

Thesis (Ph. D.)--University of Chicago, Dept. of Chemistry, December 1997. / Includes bibliographical references. Also available on the Internet.

The fate and mobility of boric acid in the environment is largely controlled by adsorption reactions with soil organic matter and soil minerals to form surface complexes (Marzadori et al., 1991; Su and Suarez, 1995; Yermiyahu et al., 1995; Peak et al., 2002). The effects of humic acid (HA) and dissolved CO2 on boric acid adsorption on amorphous (am)-Al(OH)3 were investigated as their influence on sorption is potentially important. Although a model system was used in the studies, the findings should be generally useful to better understand the mobility and bioavailability of boric acid in the soil ecosystems.<p>In this dissertation, boric acid adsorption on pure am-Al(OH)3 and 5% w/w HA coated am-Al(OH)3 were investigated both as a function of pH (4.5 11) and initial boric acid concentration (0 4.5 mmol L-1). Batch adsorption isotherm experiments were also conducted with samples exposed to atmospheric CO2 and anaerobic (N2) conditions to examine the effects of dissolved CO2 on boric acid adsorption. Both the pH envelope and the adsorption isotherm experiments showed that the HA coating on am-Al(OH)3 and the presence of dissolved CO2 decreased boric acid adsorption. <p>Raman spectroscopy and boron (B) K-edge X-ray Absorption Near Edge Structure (XANES) spectroscopy were used to investigate the coordination of boric acid adsorbed at mineral/water interfaces. The Raman spectroscopy was less successful than expected as there were difficulties in identifying B bands in the 5% w/w HA coated am-Al(OH)3 samples.<p>The B K-edge XANES spectroscopy yielded better results. The XANES spectra of boric acid adsorption samples showed that both trigonal BO3 and tetrahedral BO4 coordinated complexes are present on the pure and HA coated mineral surfaces. At pH 7.0 and 9.2, the adsorption of boric acid on am-Al(OH)3 is predominantly inner-sphere trigonal complexes; with minor amounts of inner-sphere tetrahedral complexes. Both macroscopic and spectroscopic experiments revealed that the combination of HA coating on am-Al(OH)3 and dissolved CO2 decreased boric acid adsorption compared to adsorption on pure am-Al(OH)3.<p>The discoveries in this dissertation contribute significantly in understanding the effects of HA and dissolved CO2 has on boric acid adsorption in the environment. Since B speciation and the stability of am-Al(OH)3 mineral and HA changes with pH, the bioavailability of B is expected to change as well with pH. The adsorption on boric acid on am-Al(OH)3 and/or HA coated am-Al(OH)3 is expected to decrease the amount of boric acid available to plants. Therefore the nutrient management regimen will have to be modified for soils that are high in natural organic matter, carbonate and/or aluminum hydroxyl species.