Triptofano ir tirozino aminorūgščių funkcinės grupės – indolo ir fenolio žiedai, stabilizuoja baltymų tretinę struktūrą, sąveikauja su aktyviais centrais biomolekulėse, dalyvauja elektronų pernašos procesuose. Siekiant giliau suprasti kaip šios grupės sąveikauja, buvo sukonstruotos dirbtinės monosluoksninės struktūros, sudarytos iš susintetintų bifunkcinių junginių, turinčių galines tiolio ir indolo žiedo arba fenolio žiedo grupes ir gebančių formuoti savitvarkius monosluoksnius ant aukso, sidabro ir vario elektrodų. Jų savybės ištirtos Ramano, infraraudonosios ir suminio dažnio generacijos spektroskopijų metodais. Pagrindiniai darbo tikslai buvo nustatyti bifunkcinių alkantiolių struktūrą ir adsorbcijos ypatumus pradinėje monosluoksnio formavimosi stadijoje, elektrodo prigimties įtaką monosluoksnių struktūrai ir potencialo įtaką galinių funkcinių grupių savybėms. Paviršiaus sustiprintos Ramano spektroskopijos metodu pirmą kartą parodyta, kad pradinėse monosluoksnių formavimo stadijose metileno grupės sąveikauja su metalo paviršiumi. Darbe įrodyta, kad dėl sąveikos su metalu spektruose atsiranda žemesnio dažnio („minkšta“) CH juosta ties 2820 cm-1. Pirmą kartą parodyta, kad indolo žiedas sąveikauja su Ag paviršiumi, esant pakankamai neigiamiems potencialams ir tą sąveiką galima spektriškai atpažinti pagal W16 modos ties ~1010 cm-1 dažnio sumažėjimu iki ~ 1001 cm-1. Tiriant indolo žiedu terminuotus ir mišrius monosluoksnius su įterptomis oktadekantiolio molekulėmis nustatytas... [toliau žr. visą tekstą] / The indole and phenole rings comprise the main part of tryptophan and tyrosine side chains in proteins and play an important role in the stabilization of tertiary structure, interaction with active centers in biomolecules, and electron transfer phenomena. To get better insight into the interactions of these functional groups, the artificial monomolecular structures have been constructed from the synthesized bifuncional compounds with thiol and indole or phenole ring functional groups able to form self-assembled monolayers on gold, silver and copper electrodes. Properties of these monolayers were studied by Raman, infrared, and sum-frequency generation spectroscopies. The main tasks of this work were to assess the adsorption peculiarities of the bifunctional thiols at the initial stage of the monolayer formation, to determine the influence of the electrode nature on the monolayer structure, and to establish the potential influence on the properties of the terminal functional groups. It was demonstrated for the first time that at the initial stage of monolayer formation the methylene groups interact with the metal surface. Evidence for the metal-induced lowering of the C−H stretching mode frequency down to 2820 cm-1 was provided. It was demonstrated that indole ring interacts with the Ag electrode surface at sufficiently negative potentials and this interaction can be recognized from the downshift of the W16 mode from ~ 1010 cm-1 to ~ 1001 cm-1. Investigations of indole ring... [to full text]

Collagen fibrils are the main constituent of the extracellular matrix surrounding eukaryotic cells. Even though the assembly and structure of collagen fibrils is well characterized, very little is known about the physico-chemical properties of their surface which is one of the key determinants of their biological functions. One way to obtain surface sensitive structural and chemical data is to take advantage of the near field nature of surface and tip-enhanced Raman spectroscopy. Using Ag and Au nanoparticles bound to collagen type I fibrils, as well as tips coated with a Ag nanoparticles and a thin layer of Ag, we obtained Raman spectra characteristic of the first layer of collagen molecules at the surface of the fibrils. The most frequent Raman peaks were attributed to aromatic residues such as phenylalanine and tyrosine. We also observed in several instances Amide I bands with a full width at half maximum of 10-30 cm-1. The assignment of these Amide I bands positions suggests the presence of collagen-helices as well as alpha-helices and beta-sheets at the fibril’s surface. As a step towards in vivo characterization of collagen fibrils, fascicles removed from tendons were also examined with surface-enhanced Raman spectroscopy.

This thesis work describes the fabrication and surface enhanced Raman spectroscopy (SERS) characterization of vertically aligned nitrogen (N) doped multi walled carbon nanotube (MWCNT) forests coated by silver (Ag) and gold (Au) nanoparticles. In the present work, the CNT forests were grown from a catalyst metal layer by the chemical vapor deposition (CVD) process at temperature of 800 oC and a physical vapor deposition (PVD) and annealing processes were applied subsequently for the evaporation and diffusion of noble metal nanoparticles on the forest. Transistor patterning of 20, 50 and 100 μm were made onto the silicon-oxide (SiO2) wafers through the photolithography process with and without depositing a thickness of 10 nm titanium (Ti) buffer layer on the Si-surfaces. Iron (Fe) and cobalt (Co) were used together to deposite a thickness of 5 nm catalyst layer onto the Single Side Polished (SSP) wafers. As carbon and nitrogen precursor for the CNT growth was used pyridine. Two different treatment times (20 and 60 minutes) in the CVD process determined the CNT forest height. Scanning Electron Microscopy (SEM) imaging was employed to characterize the CNT forest properties and Ag and Au nanoparticle distribution along the CNT walls. The existence of “hot spots” created by the Ag and Au nanoparticles through the surface roughness and plasmonic properties was demonstrated by the SERS measurements. Accordingly, the peak intensity at wave number of 1076 cm-1 was picked up from each SERS spectra to establish the Ag- and Au-trend curves with different concentrations of 4-ATP solution. The SERS mapping was also carried out to study the Ag- and Au-coated CNT surface homogeneity and “hot spots” distribution on the CNT surface. The SERS enhancement factors (EF) were calculated by applying an analyte solution of ethanolic 4-ATP on the CNT surface. The calculated values of EF from Ag- and Au-coated CNT forests were 9×106 and 2.7×105 respectively.

This thesis is focused on nanofabrication and its application in plasmonic chemical and bio- sensors. The contribution thus is the development of novel nanofabrication techniques and nano- structures for the sensors based on surface plasmon (SP). Part I (Chapter 1-3) is about novel nanofabrication techniques, especially nanoimprint lithography (NIL) and electron beam lithography (EBL). For NIL, the four major aspects of NIL were discussed, including the resist, mold, imprint process and equipment for NIL. Combined with NIL and soft lithography, hybrid nanoimprint-soft lithography was investigated. To overcome the difficulty of mold fabrication, a more robust solution of mold fabrication through a sacrificial poly(dimethyl glutarimide) (PMGI) master mold was designed in this work. Based on this method, the mold was fabricated without structure distortion, and pattern replication with sub-10 nm resolution was demonstrated. For EBL, several aspects were discussed to improve the performance of EBL, including the resist, development, and exposure condition. The charging effect to the pattern distortion was studied systemically for the electron beam exposure in large area with high current (>nA). Tilted periodic nanostructure was achieved by electron beam scanning on tilted sample with dynamic focus mode. EBL on irregular surface was realized by the exposure on evaporated polystyrene. Part II (Chapter 4-6) is the application in surface plasmonic chemical and bio-sensors. The first type of sensors is surface enhanced Raman scattering (SERS) sensor based on localized SP. Bowtie-shape nano-antenna structures of sub-10 nm gap were fabricated with the breakthrough of EBL resolution to 3 nm by exposing resist on Si3N4 membrane. By controlling the gap size during lithography, the surface plasmon enhancement was tuned accurately. High sensitivity of Au bowties antenna with sub-10 nm gap was achieved at low concentration of the target molecule (10^-7 mM, 1,2-di(4-pyridyl)ethylene in ethanol solution) and high enhancement of 10^7 resulting from the corresponding bowtie structure. The second type of sensors is extraordinary optical transmission (EOT) sensor based on propagating SP. The process of double liftoff was developed for the fabrication of nano-hole arrays on 100 nm-thick Au film utilizing EBL. This technique is versatile for the fabrication of many kinds of high-aspect-ratio noble metal structures. Additionally, annealing method was employed in this work to improve the smoothness of Au film. It was found that the RMS roughness of the deposited film was reduced by 72 % and the sensitivity was increased by 32 nm/RIU as a result of annealing. It was also found that the optical transmission intensity of the annealed NHA of similar hole diameter was increased more than twice which is due to the smaller absorption/scattering of the incident light and surface waves from the Au film surface. Besides the double liftoff process, several techniques were developed for EOT structures, including electroplating, imprint method, and deposition on membrane.

Gold nanoparticles were deposited onto a silicon substrate using electroless deposition. The process was optimized by adjusting the deposition time, the temperature of the plating solution, the amount of time that the silicon was exposed to hydrofluoric acid, and the concentration of the plating solution. The nanoparticles deposited on the silicon were characterized using scanning electron microscopy. The optimized electroless deposition process was then used to modify the surface of silicon solar cells with gold nanoparticles for enhanced power generation. Spectral response and I-V curve tests were performed on the modified solar cells to quantify the enhancements. The modified surfaces of the silicon solar cells were characterized by scanning electron microscopy and reflectance measurements. The electroless deposition process was also used to generate nanostructures for surface-enhanced Raman scattering (SERS). A template-nanohole array was fabricated on silicon by focused ion beam milling. Gold nanoparticles were deposited in the holes of the template, resulting in interesting gold-nanodoughnut structures. The gold nanodoughnuts were examined by scanning electron microscopy, and their potential as SERS substrates were tested using Rhodamine 6G as a molecular probe under 633 nm laser excitation. / Graduate / 0494 / 0485 / mmillard@uvic.ca

To truly realize and exploit the extremely powerful information given from surface-enhanced Raman scattering (SERS) spectroscopy, it is critical to develop an understanding of how to design highly sensitive and selective substrates, produce specific and label-free spectra of target analytes, and fabricate long-lasting and in-the-field ready platforms for trace detection applications. The study presented in this dissertation investigated the application of two- and three-dimensional substrates composed of highly-ordered metal nanostructures. These systems were designed to specifically detect target analytes that would enable the trace, label-free, and real-time detection of chemicals and biomolecules. Specifically, this work provides new insight into the required properties for maximizing electromagnetic and chemical Raman enhancement in three-dimensional porous alumina substrates by designing metal nanostructure shape, density, aggregated state, and most importantly aligning the substrate pore size with the excitation wavelength used for plasmonic enhancement leading to the ppb detection of vapor phase hazardous chemicals. A new micropatterned silver nanoparticle substrate fabricated via soft lithography with specific functionalization was developed, which allows the simultaneous analyte and background detection for trace concentrations of the target biomolecule, immunoglobulin G. Also, a novel functionalized SERS hot spot fabrication technique, which utilizes highly specific aptamers as both the mediator for electrostatic assembly of gold nanoframe dimers as well as the biorecognition element for the target, riboflavin, to properly locate the tethered biomolecule within the enhanced region for trace detection, was demonstrated. We suggest that the understanding of SERS phenomena that occur at the interface of nanostructures and target molecules combined with the active functionalization and organization of metal nanostructures and trace detection of analytes discussed in this study can provide important insight for addressing some of the challenges facing the field of SERS sensor design such as high sensitivity and selectivity, reliable and repeatable label-free identification of spectral peaks, and the well-controlled assembly of functional metal nanostructures. This research will have a direct impact on the future application of SERS sensors for the trace detection of target species in chemical, environmental, and biomedical fields through the development of specific design criteria and fabrication processes.

<p>There is an urgent need to develop practical and effective systems to detect diseases, such as cancer, infectious diseases and cardiovascular diseases.</p><p>Nanotechnology is a new, maturing field that employs specialized techniques to detect and diagnose infectious diseases. To this end, there have been a wealth of techniques that have shown promising results, with fluorescence and surface-enhanced Raman scattering being two important optical modalities that are utilized extensively. The progress in this specialized niche is staggering and many research groups in academia, as well as governmental and corporate organizations, are avidly pursuing leads which have demonstrated optimistic results.</p><p>Although much fundamental science is still in the pipeline under the guise of both ex-vivo and in-vivo testing, it is ultimately necessary to develop diagnostic devices that are able to impact the greatest number of people possible, in a given population. Such systems make state-of-the-art technology platforms accessible to a large population pool. The development of such technologies provide opportunities for better screening of at-risk patients, more efficient monitoring of disease treatment and tighter surveillance of recurrence. These technologies are also intrinsically low cost, facilitating the large scale screening for disease prevention.</p><p>Fluorescence has long been established as the optical transduction method of choice, because of its wealth of available dyes, simple optical system, and long heritage from pathology. The intrinsic limitations of this technique, however, have given rise to a complementary, and more recent, modality: surface-enhanced Raman scattering (SERS). There has been an explosive interest in this technique for the wealth of information it provides without compromising its narrow spectral width.</p><p>A number of novel studies and advances are successively presented throughout this study, which culminate to an advanced SERS-based platform in the last chapter.</p><p>The finite element method algorithm is critically evaluated against analytical solutions as a potential tool for the numerical modeling of complex, three-dimensional nanostructured geometries. When compared to both the multipole expansion for plane wave excitation, and the Mie-theory with dipole excitation, this algorithm proves to provide more spatially and spectrally accurate results than its alternative, the finite-difference time domain algorithm.</p><p>Extensive studies, both experimental and numerical, on the gold nanostar and Nanowave substrate for determining their potential as SERS substrates, constituted the second part of this thesis. The tuning of the gold nanostar geometry and plasmon band to optimize its SERS properties were demonstrated, and significant 3-D modeling was performed on this exotic shape to correlate its geometry to the solution's exhibited plasmon band peak position and large FWHM. The Nanowave substrate was experimentally revived and its periodic array of E-field hotspots, which was until recently only inferred, was finally demonstrated via complex modeling.</p><p>Novel gold- and silver- coated magnetic nanoparticles were synthesized after extensive tinkering of the experimental conditions. These plasmonics-active magnetic nanoparticles were small and displayed high stability, were easy to synthesize, exhibited a homogeneous distribution, and were easily functionalizable with Raman dye or thiolated molecules.</p><p>Finally, bowtie-shaped cobalt micromagnets were designed, modeled and fabricated to allow the controllable and reproducible concentrating of plasmonics-active magnetic nanoparticles. The external application of an oscillating magnetic field was accompanied by a cycling of the detected SERS signal as the nanoparticles were concentrated and re-dispersed in the laser focal spot. This constituted the first demonstration of magnetic-field modulated SERS; its simplicity of design, fabrication and operation opens doors for its integration into diagnostic devices, such as a digital microfluidic platform, which is another novel concept that is touched upon as the final section of this thesis.</p> / Dissertation

Electrochemical and spectroelectrochemical data was obtained for a silver electrode modified with oxazine 720. A quasi-reversible redox behaviour was observed for the modified electrode. Surface adsorption density, calculated from the measured electrochemical charge transfer, is higher than would be expected for a monolayer of flat-adsorbed ox¬azine 720. Surface-enhanced Raman scattering (SERS) data, in conjunction with results of a density functional theory (DFT) calculation, suggest that the molecule is adsorbed with its rings perpendicular to the electrode surface, consistent with the electrochemically estimated adsorption density. SERS was recorded in situ at different applied potentials. The SERS intensity remains relatively stable between -200 and -500 mV (versus AglAgCl Cl-sat), but decreases dramatically as the applied potential is made more negative than -500 mV. Ths is consistent with the onset of oxazine 720 reduction observed during cyclic voltammetry. The spectroelectrochemical data indicates that oxazine 720 remains adsorbed at the SERS-active sites even in its reduced form. Similar in situ SERS data was collected for rhodamine 6G and pyridine. Spectra in the Stokes and anti-Stokes regions were obtained at several applied potentials using two different laser excitation energies. Normalized ratios of the anti-Stokes to Stokes intensities were calculated for various vibrational bands of the three molecules. The measured ratios vary with changes in the excitation energy, the applied voltage and the energy of the vibrational mode being investigated. The ratios for oxazine 720 show a preferential enhancement of the Stokes scattering while the ratios for rhodamine 6G indicate an enhancement of the anti-Stokes scattering. For pyridine, the preferential enhancement changes between Stokes and anti-Stokes depending on the excitation wavelength used, the applied voltage and the vibrational band being examined. The main trends of the anti-Stokes to Stokes ratios can be satisfactorily explained using resonance models based on standard SERS theories. No evidence of a SERS-induced non-thermal population distribution among the vibrational states of the adsorbed molecules (vibrational optical pumping) was observed.

Gold nanoparticles were deposited onto a silicon substrate using electroless deposition. The process was optimized by adjusting the deposition time, the temperature of the plating solution, the amount of time that the silicon was exposed to hydrofluoric acid, and the concentration of the plating solution. The nanoparticles deposited on the silicon were characterized using scanning electron microscopy. The optimized electroless deposition process was then used to modify the surface of silicon solar cells with gold nanoparticles for enhanced power generation. Spectral response and I-V curve tests were performed on the modified solar cells to quantify the enhancements. The modified surfaces of the silicon solar cells were characterized by scanning electron microscopy and reflectance measurements. The electroless deposition process was also used to generate nanostructures for surface-enhanced Raman scattering (SERS). A template-nanohole array was fabricated on silicon by focused ion beam milling. Gold nanoparticles were deposited in the holes of the template, resulting in interesting gold-nanodoughnut structures. The gold nanodoughnuts were examined by scanning electron microscopy, and their potential as SERS substrates were tested using Rhodamine 6G as a molecular probe under 633 nm laser excitation. / Graduate / 0494 / 0485 / mmillard@uvic.ca

The clinical evaluation of people with possible myocardial infarction (MI) is often limited by atypical symptoms and inconclusive initial electrocardiograms. A recent consensus from the American College of Cardiology has redefined acute MI to include cardiac markers as central to diagnosis. To address this clinical need, a sensitive microfluidic surface-enhanced Raman spectroscopy (SERS) nanochannel-based optical device is being developed for ultimate use as a point-of-care device for the simultaneous measurement of MI blood biomarkers. The device can provide enhancements of the Raman signal of the analyte measured of up to 1013 using a mechanical aggregation technique at the interface of nanofluidic structures enabling repeatable SERS measurements. Specifically in this research iterations of a sensitive, low volume SERS platform technology were designed that provided quantitative information across a specific range. With the SERS platforms studied, not only were SERS enhancements of up to 1013 achieved but also imprecision values of less than 10% across the 10-50 pM range using a ratiometric approach and qualitative detection down to 100 aM was achieved. Beyond assessment of SERS substrates, assay designs were investigated and characterized including, label-free techniques and competitive immunoassay formats. Lastly, detecting the SERS signal of multiplexed reporter molecules was investigated. By identifying the analyte and assay constraints the design and optimization of future assays will be aided using this SERS platform technology.