This thesis deals with the study of microbial pigment violacein in the real sample of lyophilized microorganisms. The sample was investigated by using methods of vibrational spectroscopy with focusing on the applicability of surface enhanced and resonance micro-Raman spectroscopy. For this purpose several different systems for enhancing Raman intensity together with the set of excitation lasers emitting in the visible light region were used. The conclusion of this thesis are the recommendations connected with the appropriateness of using each amplifying systems and excitation wavelengths for the successful identification of violacein pigment in the sample. Powered by TCPDF (www.tcpdf.org)

Title: Optical Responses of Biomolecules on Regular Metal Plasmonic Nanostructures Author: Martin Šubr Department: Institute of Physics of Charles University Supervisor of the doctoral thesis: prof. RNDr. Marek Procházka, Dr., Institute of Physics of Charles University Abstract: Adsorption of molecules on metal plasmonic nanostructures leads to significant enhancement of many optical processes, such as Raman scattering (surface-enhanced Raman scattering - SERS) or fluorescence (surface-enhanced fluorescence - SEF). Two groups of substrates were tested within this thesis: (i) Silver nanorods prepared by oblique angle vapor deposition, and (ii) silver and gold nanoislands growing on magnetron-sputtered polytetrafluoroethylene film. Step-by- step optimization process was performed on the nanoislands in order to obtain optimum SERS sensitivity and reproducibility. Detailed SERS intensity profiles were obtained using gradient nanostructures with the localized surface plasmon resonance (LSPR) condition varying across the sample and three different excitation wavelengths. It was also found that spectral position and height of the LSPR band can be controlled simultaneously using mixed gold/silver nanoislands. Detailed investigation of polarization- and angular- dependences of anisotropic silver nanorods was...

The first thermal cycling experiments of ionic self-assembled multilayer (ISAM) films have been reported examining their survivability through repeated thermal cycles from -20° C to 120° C in ambient atmospheric conditions. The films were constructed from alternating layers of Nile Blue A and gold nanoparticles which provided a strong absorbance in the optical wavelength range. No degradation of the optical characteristics of the ISAM films was observed [1]. Techniques for measuring the capacitance and resistivity of various ISAM films have also been developed allowing for a more complete electrical characterization of ISAM films. Capacitance measurements enabled a calculation of the dielectric function and breakdown field strength of the ISAM films. The capacitance measurement technique was verified by measuring the dielectric function of a spin-coated thin film PMMA, which has a well characterized dielectric function [2]. Surface-enhanced Raman spectroscopy (SERS) has been studied as a possible detection method for malignant melanoma revealing spectral differences in blood sera from healthy horses and horses with malignant melanoma. A SERS microscope system was constructed with the capability of resolving the Raman signal from biologically important molecules such as beta-carotene and blood sera. The resulting Raman signals from sera collected from horses with malignant melanoma were found to have additional peaks not found in the Raman signals obtained from sera collected from healthy horses. A systematic analysis of the combination of absorbance and fluorescence signals of blood sera collected from populations of healthy dogs and dogs with cancer has resulted in a rapid and cost-effective method for monitoring protein concentrations that could possibly be used as part of a cancer screening process. This method was developed using the absorbance and fluorescence signals from known serum proteins, the combinations of which were used to match the absorbance and fluorescence signals of blood sera allowing for an accurate determination of protein concentrations in blood sera [3]. Finally, a novel method for measuring the melting point of DNA in solution using capacitance measurements is presented. This method allows for the determination of the melting temperature as well as the melting entropy and melting enthalpy of DNA strands. Two different short strands of DNA, 5'-CAAAATAGACGCTTACGCAACGAAAAC-3' along with its complement and 5'-GGAAGAGACGGAGGA-3' along with its complement were used to validate the technique as the characteristics of these strands could be modeled using theoretical methods. This experimental technique allows for the precise determination of the melting characteristics of DNA strands and can be used to evaluate the usefulness of theoretical models in calculating the melting point for particular strands of DNA. Additionally, a micro-fluidic device has been proposed that will allow for a rapid and cost-effective determination of the melting characteristics of DNA [4]. / Ph. D.

The propagation of contaminants in the environment continues to threaten public health and safety. Conventional analytical techniques for environmental detection require centralized facilities and intensive resources for operation. An effective implementation of a wide network of field deployable point-of-use (POU) sensors can potentially enable real-time monitoring of water quality parameters and inform decision making on public health outbreaks. The use of nanotechnology and field-deployable analytical tools can potentially advance the development of POU sensors for future field application. In this dissertation, we developed environmental sensing techniques that utilize nanocomposites made of low-cost, biocompatible, and sustainable nanomaterials combined with Raman spectroscopy. First, a technology pre-assessment was performed that included a comprehensive evaluation of cellulose-derived nanocomposites and nanobiotechnology enabled techniques for their sustainable long-term environmental application. Furthermore, to contribute to the better understanding of the potential environmental implications of nanomaterial production and application, life cycle assessment (LCA) was used to evaluate the environmental impacts of six iron precursors and seven iron oxide nanoparticle synthesis methods. Secondly, in the technology development step, gold (Au) and iron oxide (Fe3O4) nanoparticles were incorporated onto bacterial cellulose nanocrystals and nanoscale magnetite were synthesized. As proof-of-concept environmental applications, the Au@Fe3O4@BCNCs were applied for the magnetic separation and surface-enhanced Raman scattering (SERS) detection of malachite green isothiocyanate (MGITC), and nanoscale magnetite were applied for phosphate (PO43-) removal and recovery from synthetic urine matrices. Finally, in the technological application step, three environmental sensing applications are presented that use nanomaterial-based sensor platforms and/or Raman spectroscopic techniques. The first application involved using Lectin-modified BCNCs coupled SERS and machine learning for discrimination of bacterial strains. The second application presents a simple Raman-stable isotope labeling approach for the study of viral infection of bacteria. The third application involved use of SERS pH nanoprobes for measuring pH in droplets of complex matrices (e.g., DMEM cell culture media, human saliva). / Doctor of Philosophy / The current generation of analytical tools for environmental detection rely upon centralized facilities and intensive resources for operation. The combination of nanotechnology and field deployable analytical tools can aid in the development of point-of-use (POU) sensors for field monitoring of environmental contaminants. In this dissertation, we combined low-cost, biocompatible, and sustainable nanomaterials with Raman spectroscopy-based techniques to develop potentially field-deployable environmental sensing techniques. First, a technology pre-assessment was performed which involved a comprehensive evaluation of cellulose-derived nanocomposites and nanobiotechnology enabled techniques for their sustainable long-term environmental application. Furthermore, life cycle assessment (LCA) was used to evaluate the environmental impacts of iron oxide nanoparticle synthesis methods to better understand environmental impacts of nanoparticle production. Secondly, in the technology development step, we developed the nanocomposites: Au and Fe3O4 nanoparticles incorporated bacterial cellulose nanocrystals and nanoscale magnetite. As proof-of-concept environmental applications, the Au@Fe3O4@BCNCs were used for the detection of malachite green isothiocyanate (MGITC), and the nanoscale magnetite were used for phosphate (PO43-) removal and recovery from synthetic urine. Finally, in the technological application step, (1) selective detection of bacteria was performed using lectin-modified BCNCs as SERS biosensors coupled with SERS and machine learning. (2) Viral infection of bacteria was evaluated using Raman spectroscopy and Deuterium isotope labeling, and (3) pH in micro-droplets of DMEM cell culture media and human saliva were observed using SERS pH nanoprobes.

Surface enhanced Raman spectroscopy (SERS) is highly promising analytical technique for trace detection of analytes. It is particularly well suited for environmental analyses due to its high sensitivity, specificity, ease of operation and rapidity. The detection and characterization of environmental contaminants, using SERS is highly related to the uniformity, activity and reproducibility of the SERS substrate. In this thesis, SERS substrates were produced by gold nanoparticle formation on wax patterned chromatography paper. In situ reduction of hydrogen tetrachloroaurate (gold precursor) by trisodium citrate dihydrate (reducing agent) was used to produce gold nanoparticles within a paper matrix. These gold nanoparticle based SERS substrates were analyzed by FE-SEM, UV-Vis and Raman spectroscopy. This work discusses the SERS signal enhancements for Raman active MGITC dye for a series of substrates prepared by in situ reduction of gold salt and pre-produced gold nanoparticles. UV-Vis analysis was performed to understand the effect of different molar ratio (reducing agent to gold precursor) and reaction time on the size and shape of the localized surface plasmon resonance (LSPR) band that dictates the SERS enhancements. It was concluded that lower molar ratio (1:1 and 2:1) of citrate-to gold produced better SERS signal enhancements and broader LSPR band. Therefore, use of lower molar ratio (MR) was recommended for paper-based substrates using in situ-based reduction approach. / Master of Science

Raman spectroscopy is a powerful tool in the field of biomedicine for disease diagnosis owing to its potential to provide the molecular fingerprint of biological samples. However due to the inherent weak nature of the Raman process, there is a constant quest for enhancing the sensitivity of this technique for enhanced diagnostic efficiency. This thesis focuses on achieving this goal by integrating advanced methods with Raman spectroscopy. Firstly this thesis explores the applicability of a laser based fluorescence suppression technique – Wavelength Modulated Raman Spectroscopy (WMRS) - for suppressing the broad luminescence background which often obscure the Raman peaks. The WMRS technique was optimized for its applications in single cell studies and tissue studies for enhanced sensing without compromising the throughput. It has been demonstrated that the optimized parameter would help to chemically profile single cell within 6 s. A two fold enhancement in SNR of Raman bands was demonstrated when WMRS was implemented in fiber Raman based systems for tissue analysis. The suitability of WMRS on highly sensitive single molecule detection techniques such as Surface Enhanced Raman Spectroscopy (SERS) and Surface Enhanced Resonance Raman Spectroscopy (SERRS) was also explored. Further this optimized technique was successfully used to address an important biological problem in the field of immunology. This involved label-free identification of major immune cell subsets from human blood. Later part of this thesis explores a multimodal approach where Raman spectroscopy was combined with Optical Coherence Tomography (OCT) for enhanced diagnostic sensitivity (>10%). This approach was used to successfully discriminate between ex-vivo adenocarcinoma tissues and normal colon tissues. Finally this thesis explores the design and implementation of a specialized fiber Raman probe that is compatible with surgical environments. This probe was originally developed to be compatible with Magnetic Resonance Imaging (MRI) environment. It has the potential to be used for performing minimally invasive optical biopsy during interventional MRI procedures.

Protein structures (cytochrome c) were visualized by TERS measurements on whole mitochondria referring to specific spectral features describing the electronic state of the heme moiety. / Dieser Beitrag ist mit Zustimmung des Rechteinhabers aufgrund einer (DFG-geförderten) Allianz- bzw. Nationallizenz frei zugänglich.

The adsorbate formed by adsorption of thiophenol on a polycrystalline gold electrode and brought into contact with aqueous solutions of 1 M HClO4 and 0.1 M KClO4 has been studied using cyclic voltammetry and surface-enhanced Raman spectroscopy. A strong adsorption is deduced from observations made using cyclic voltammetry. From the SER spectra, interactions of thiophenol with the gold surface via a gold–sulfur bond with the aromatic ring pointing away from the surface is concluded for both electrolyte solutions. / Dieser Beitrag ist aufgrund einer (DFG-geförderten) Allianz- bzw. Nationallizenz frei zugänglich.

Pour mieux comprendre leurs propriétés, diverses nanostructures individuelles ont été étudiées à l’aide d’une technique couplant microscopie à force atomique et spectroscopie Raman confocale. Sous excitation lumineuse polarisée, la composition chimique, la structure et la présence de défauts a pu être précisée dans des nanobâtonnets d’oxydes métalliques (ZnO et α-Fe2O3). Sous irradiation laser résonnante, les spectres de nanotubes de carbone monoparoi enrobés de polymères ont révélé notamment l’absence de transfert de charge polymère-nanotube et un effet de désolvatation. Finalement, des feuillets de graphène oxydé et des ADNs double-brin peignés ont pu être préparés et caractérisés par spectroscopie Raman exaltée par effet de pointe en atteignant une résolution spatiale latérale voisine du rayon de courbure de l’apex de la pointe utilisée (12 nm), bien plus faible que la limite de diffraction, ce qui ouvre la voie à de nouveaux travaux spectroscopiques à l’échelle nanométrique. / To better understand their properties, various nanostructures have been studied using a technique combining atomic force microscopy and confocal Raman spectroscopy. Under polarized light excitation, the chemical composition, the structure and the presence of defects has been described in metal oxides nanorods (ZnO et α-Fe2O3). Under resonant laser excitation, Raman spectra of polymer-wrapped single-walled carbon nanotubes have revealed the absence of polymer-nanotube charge transfer and an effect due to desolvation. Finally, graphene oxide sheets and combed double-stranded DNAs have been prepared and characterized using tip-enhanced Raman spectroscopy with a lateral spatial resolution down to the curvature radius of the apex of the used tip (12 nm), well below the diffraction limit, which opens new opportunities for spectroscopic works at the nanometer scale.

Nesta tese de doutorado foram desenvolvidas metodologias para obter espectros Raman intensificados pela superficie de adsorbatos orgânicos em eletrodos de Fe, Co e Ni, que são metais que apresentam baixo fator de intensificação SERS. Foram desenvolvidos procedimentos de ativação eletroquímica para eletrodos puros dos três metais. Os protocolos de ativação eletroquímica foram utilizados para obter espectros SERS de piridina, 1,10-fenantrolina e 2- e 4-aminopiridina. O fator de intensificação determinado para o três metais, da ordem de 102-103 vezes, depende fortemente do modo vibracional do adsorbato. Os espectros SERS da piridina nos metais de transição, quando comparados com os cálculos de espectros vibracionais de cluster da piridina com átomos metálicos por DFT mostram que a formação do radical α-piridil com a adsorção nos metais de transição, proposta na literatura, não ocorre. Os perfis de excitação SERS calculados pelo modelo de transferência de carga da piridina apresentaram boa correlação com os dados experimentais. Os resultados SERS para a 1,10-fenantrolina mostraram que a espécie que adsorve é a molécula livre, com a espécie adsorvida semelhante ao complexo sintetizado. A dependência das intensidades relativas com o potencial nos espectros SERS é diferente da observada para os espectros Raman ressonante dos complexos da phen com metais de transição, mostrando que o estado excitado monitorado pelas duas técnicas é diferente. O monitoramento da adsorção das 2-aminopiridinas nos metais de transição permitiu sugerir a adsorção pelo anel piridínico para potenciais menos negativos e através dos nitrogênios piridínico e amínico para potenciais mais negativos em eletrodos de Co e Ni, e para o Fe adsorve apenas pelo nitrogênio piridínico. Em solução eletrolítica 0,1 mol.L-1 KCl, a 4-aminopiridina passa de fracamente ligada para um complexo de superficie semelhante ao complexo sintetizado para potenciais mais negativos. Utilizando a solução eletrolítica 0,1 mol.L-1 KI, as duas espécies são observadas para um intervalo maior de potenciais. No eletrodo de Ni, observa-se 4-aminopiridina protonada para E = -0,7 V; para potenciais mais negativos um complexo de superficie semelhante ao complexo sintetizado é observado. Os filmes eletrodepositados de Co e Ni em eletrodos de Ag ativado eletroquimicamente permitiram a obtenção de espectros SERS da py com alto fator de intensificação. Os filmes com espessuras maiores que 2 monocamadas de Co ou Ni apresentaram bandas intensas da piridina adsorvida nestes metais, sem bandas da piridina adsorvida em Ag, indicando que os filmes não apresentam pinholes, com intensidade SERS 100 vezes maior do que os metais puros. As intensidades relativas dos espectros SERS são similares à obtidas nos espectros SERS da piridina nos metais puros para filmes finos mais espessos do que 7 monocamadas. Foram construídos substratos de Au SERS-ativos com alto desempenho e reprodutibilidade por eletrodeposição sobre uma máscara de microesferas de poliestireno. Os espectros SERS da 4-mercaptopiridina adsorvida nos substratos otimizados apresentaram intensidade 2 vezes maior do que o eletrodo de Au ativado eletroquimicamente. A reprodutibilidade do sinal SERS para estes substratos foi de ± 15 %, indicando que estes substratos podem ser utilizados como sensores para sistemas de interesse analítico. / Surface-enhanced Raman spectra of organic adsorbates on Fe, Co and Ni electrodes were acquired after the development of specific methodologies described in this PhD thesis. Electrochemical activation procedures were developed for the three bare metaIs electrodes. The electrochemical activation protocols were applied for the acquisition of SERS spectra of pyridine, 1,10-phenanthroline and 2- and 4-aminopyridine on Fe, Co e Ni electrodes. The total and relative intensities changes of SERS bands with the applied potentials were explained by the charge transfer mechanism, which had a large contribution in the SERS enhancement for these metaIs. The enhancement factor determined for the three metaIs, on the 102-103 times range, strongly depends on the adsorbate\' s vibrational modes. The SERS spectra of pyridine on the transition metals and vibrational spectra calculations of pyridine with metallic atoms showed that the formation of α-pyridil in the adsorption on transition metaIs, suggested in the literature, didn\'t occur. The calculated pyridine SERS excitation profiles present reasonable correlaton with the experimental data. The SERS results for 1,10-phenanthroline showed that the free molecule was the adsorbing species. The potential dependence of the SERS relative intensities was different from those of the resonance Raman spectra of 1,10-phenanthroline complexes with transition metal ions, indicating that different excited states were probed by the two techniques. 2-aminopyridine adsorbed through the pyridinic ring at less negative potentials and through both pyridinic and aminic nitrogens at more negative potentials on Co and Ni electrodes, but for Fe electrode it adsorbed exclusively through the pyridinic nitrogen. 4-aminopyridine adsorbed perpendicularly to the electrode. In 0,1 mol.L-1 KCl electrolytic solution, 4-aminopyridine changed from weak1y bound to a surface complex similar to the synthesized complex at more negative potentials. In 0,1 mol.L-1 KI electrolytic solution, both species were observed in a larger potential interval. On the Ni electrode, protonated 4aminopyridine was observed for V = -0.7 V, and for more negative potentials a surface complex, similar to the synthesized one, was observed. The electrodeposition of ultrathin film of Co and Ni on electrochemically-activated Ag electrodes allowed obtaining SERS spectra of pyridine with high enhancement factors. The SERS spectra of py for films thickness higher than 2 monolayers of Co or Ni presented intense bands of pyridine adsorbed on these metals, and no bands of pyridine adsorbed on Ag were observed, indicanting the absence of pinholes in the films. The relative intensities of SERS spectra on the thin films were similar to those obtained for the SERS of pyridine on the bare metaIs electrodes for films thicker than 7 monolayers, but with SERS intensity 100 times higher. The SERS activity and signal strength reproducibility of Au nanostructured substrates obtained by electrodeposition on a polystyrene masking were evaluated. The SERS spectra of 4-mercaptopyridine adsorbed on optimized electrodes presented intensities 2 times greater than those of the electrochemically activated Au electrode. The SERS intensity reproducibility for these substrates was ± 15%, indicating the potential use of such substrates as sensors.