Dynamics between organic molecules and surface enhanced Raman scattering (SERS) hot spots are extracted from far-field optical images by two experimental methods presented in this thesis: orientational imaging and super-resolution optical imaging. We introduce SERS orientational imaging as an all-optical technique able to determine the three-dimensional orientations of SERS-active Ag nanoparticle dimers. This is accomplished by observing lobe positions in SERS emission patterns formed by the directional polarization of SERS emission along the longitudinal axis of the dimer. We further extend this technique to discriminate nanoparticle dimers from higher order aggregates by observing the wavelength-dependence of SERS emission patterns, which are unchanged in nanoparticle dimers, but show differences in higher order aggregates involving two or more nanoparticle junctions. Dynamic fluctuations in the SERS emission pattern lobes are observed in aggregates labeled with low dye concentrations, as molecules diffuse into regions of higher electromagnetic enhancement in multiple nanoparticle junctions. In order to investigate these dynamic interactions between single organic molecules and nanoparticle hot spots we present the first super-resolution optical images of single-molecule SERS (SM-SERS), introducing super-resolution imaging as a powerful new tool for SM-SERS studies. Mapping the dynamic movement of SM-SERS centroid positions with +/- 5 nm resolution reveals the position-dependent SERS intensity as the centroid samples different positions in space. We have proposed that the diffusion of the SERS centroid is due to diffusion of a single molecule on the surface of the nanoparticle, which leads to changes in coupling between the scattering dipole and the optical near field of the nanoparticle. Finally, we combine an isotope-edited bi-analyte SERS spectral approach with super-resolution optical imaging and atomic force microscopy (AFM) structural analysis for a more complete picture of molecular dynamics in SERS hot spots. We demonstrate the ability to observe multiple molecule dynamics in a single hot spot and show that in addition to the single-molecule regime, a "few" molecule regime is able to report on position-dependent SERS intensities in a hot spot. Furthermore, we are able to identify multiple local hot spots in single nanoparticle aggregates. / text

Complementary electrochemical and spectroscopic techniques were used to characterize the behavior and composition of the passive layer formed at the gold-thiosulfate interface in the presence of copper. Raman studies of three different cationic (calcium, ammonium and sodium) thiosulfate leaching solutions showed that the concentrations of sulfate, thiosulfate, trithionate and tetrathionate remained constant. Initial leaching current densities for the three systems were identical, however, significant differences were noted in the open circuit potentials of these systems. Gold nanorod electrodes were employed as substrates for Surface Enhanced Raman Spectroscopy (SERS) studies of the gold-thiosulfate interface. The composition and behavior of the passive layer at the gold- thiosulfate interface greatly differed from that of the bulk solutions. Higher order polythionate species were not observed, and significant differences were noted in the behavior of species common between the three thiosulfate leaching solutions. Passivation levels determined from SERS indicate that in the presence of copper, the cation associated with thiosulfate may play a key role in the extent of passivation on the gold surface. / Barrick Gold Corp., NSERC

Patterned arrays of metallic nanostructures are commonly used in photonics, electronics, as well as functional materials and biotechnology because of their unique electronic and optical properties. Although great effort has been devoted to the development of nano-patterning techniques in the past decades, there are still existing challenges for nano-fabrication to achieve fine resolution and complex features over macroscopic areas in a reasonable time period. Herein, we devise two versatile patterning strategies, namely indentation colloidal lithography (ICL) and oblique colloidal lithography (OCL), for the stepwise patterning of planar substrates with numerous complex and unique designs. Those strategies combine colloidal self-assembly, imprint molding in conjunction with capillary force lithography and reactive ion etching, all of which are simple and straightforward. Hexagonal arrays of symmetric and nonconcentric gold features are fabricated on glass substrates with highly controllable geometric parameters. The width, size and asymmetry of each surface structure could be tuned down to the ~10 nm level while the scale of the patterned area could exceed 1 cm^(2). Moreover, our technique also leads to the ability to develop an enormous variety of patterns through stepwise amplification of feature types. In particular, some of the features are fabricated for the first time, including target-triangle, hexagram, hexagram-dot and triangle-dot. Distinctive surface plasmon resonance (SPR) properties, such as higher order surface plasmon modes and Fano resonances are both observed from our patterns, which would be highly desired forthe study of plasmonic coupling. In addition, we have demonstrated a surface orientation dependent Raman selectivity on two nano-structures for the first time. Molecular vibrations with opposite symmetries can be selectively enhanced on different substrates. As a demonstration, this property is applied to the odd-even effect of n-alkanethiol self-assembly monolayers (SAMs) on the gold surface. The alternative alternation of the intensity ratios of two vibration pairs have been shown by surface enhanced Raman spectroscopy (SERS) as a function of the number of carbon atoms. The results obtained exhibit high sensitivity and excellent agreement with previous publications.

<p>DNA origami is a novel self-assembly technique that can be used to form various </p><p>2D and 3D objects, and to position matter with nanometer accuracy. It has been </p><p>used to coordinate the placement of nanoscale objects, both organic and inorganic, to make molecular motor and walkers; and to create optically active nanostructures. In this dissertation, DNA origami templates are used to assemble plasmonic structures. Specifically, engineered Surface Enhanced Raman Scattering (SERS) substrates were fabricated. Gold nanoparticles were selectively placed on the corners of rectangular origami and subsequently enlarged via solution-based metal deposition. The resulting assemblies exhibited "hot spots" of enhanced electromagnetic field between the nanoparticles. These hot spots significantly enhanced the Raman signal from Raman molecules covalently attached to the assemblies. Control samples with only one nanoparticle per DNA template, which therefore lacked inter-particle hot spots, did not exhibit strong enhancement. Furthermore, Raman molecules were used to map out the hot spots' distribution, as the molecules are photo-damaged when experiencing a threshold electric field. This method opens up the prospect of using DNA origami to rationally engineer and assemble plasmonic structures for molecular spectroscopy.</p> / Dissertation

Surface-enhanced Raman scattering (SERS) constitutes a spectroscopy of rapidly growing importance. To understand and control the enhancing surface is key for optimizing SERS. In this work, progressively more ordered substrates for SERS are investigated: gold clusters, scratched gold films, nanohole arrays in a copper film and nanoscale gratings in a gold film. Gold clusters constitute the most random SERS substrate: samples were prepared by alternating vapour deposition of gold and plasma-induced polymerization of styrene gas. The relationships between sample preparation parameters, gold-cluster morphology, and SERS intensity were elucidated. Using Wilson’s notation, vibrations were assigned to all bands between 250 and 1750 cm-1 in the ordinary Raman and SERS spectra of polystyrene. The orientation of polystyrene’s phenyl ring, relative to the gold surface, was determined. It has been suggested that reactions involving silver catalyze polystyrene degradation during SERS, but we found that silver is not necessary for the degradation to occur. Of intermediate order are scratched gold films. Polarization-dependent SERS was studied for scratched gold films placed in-situ and under electrochemical control. A quantitative method for evaluating the polarization dependence was developed. In addition, we established that polarization effects may be used to selectively remove solution-phase interference signals from the SERS spectrum of an adsorbed analyte. Nanohole arrays and nanoscale gratings, made by focused ion beam (FIB) milling, constitute the most ordered SERS substrates. SERS was observed for oxazine 720 molecules adsorbed on a copper film pierced by nanohole arrays. Each of the arrays had a different hole-periodicity, and the effect of this periodicity on SERS intensity was examined. Electric fieldstrength perpendicular to the surface of the metal was calculated for each array using the finite-difference time-domain (FDTD) method, and the array with the greatest calculated value matched the array that gave the greatest experimentally observed SERS intensity. Finally, SERS was observed for oxazine 720 molecules adsorbed on a gold film through which nanoscale gratings were milled. We varied the width of the grooves and the width of the metal lines between them, and we examined the resulting effect on SERS intensity.

Kaskadinė fermentinė reakcija yra tokia cheminių reakcijų grandinė, kai vienos fermentinės reakcijos produktas yra panaudojamas kitose fermentinėse reakcijose tol, kol gaunamas galutinis rezultatas. Tokių reakcijų pavyzdžiai gamtoje yra kraujo krešėjimo reakcija, celiulozės skaidymas bei signalų perdavimas neuronuose. Norint, kad kaskadinė fermentinė reakcija vyktų efektyviai, fermentai, reikalingi reakcijai vykti, turi būti išsidėstę taip, kad po kiekvieno reakcijos etapo tarpinis produktas efektyviai pasiektų kitą reakcijai reikalingą fermentą. Tokių reakcijų efektyvumą galima bandyti pagerinti sutelkiant visus reikalingus reakcijai fermentus šalia vienas kito. Vienas iš variantų kaip būtų galima sukurti daugiafermentį kompleksą yra panaudojant segmentuotus metalinius nanostrypelius kaip koduojančią matricą bei genetiškai modifikuotas fermentų molekules. Prie fermentų molekulių būtų prijungiamos dideli giminiškumą reikalingam nanostrypelio metaliniam segmentui turinčios oligopeptidinės uodegėlės, kurios sukurtų sąlygas fermentams savaime organizuotis ant segmentuoto nanostrypelio paviršiaus. Magistrinio darbo užduotys buvo charakterizuoti susintetintus nanostrypelius, patikrinti ar modifikuotas giminiškomis sidabrui peptidinėmis uodegėlėmis streptavidinas sugeba prisijungti biotiną bei palyginti modifikuoto ir ir nemodifikuoto streptavidino giminiškumą sidabro paviršiui. Atlikus eksperimentus buvo nustatyta, kad naudojantis atominės jėgos mikroskopija nepavyko patikimai... [toliau žr. visą tekstą] / Biochemical enzyme cascade is a series of chemical reactions in which the products of one reaction are consumed in the next reaction. If one could organize all the necessary enzymes for the reaction in close quarters this could possibly lead to more effective cascade reactions. One way of organizing enzymes is by fusing them on barcoded nanowire matrices. This could be achieved by tayloring enzyme molecules with genetically engineered proteins for inorganics (GEPIs). My assignment was to characterise possible nanowire candidates for these biohybrid complexes using AFM and examine silver binding characteristics of GEPI taylored streptavidin using SERS. I could not realiably characterise nanowires because the interaction between AFM probe and nanowires was to interfering. Also the nanowires used to aggregate and it was difficult to separate them using ultrasound. 15nm diameter nanowires aggregated more thant 30nm diameter nanowires. Streptavidin taylored with Ag binding GEPIs showed stronger interaction with Ag electrode surface than ordinary streptavidin. Also this modified streptavidin was capable of binding with biotin. This proves that added oligopeptide chains did not negatively affect the chemical structure of streptavidin.

Title: Designing and testing of new metal nanosubstrates for biomolecular sensors based on surface-enhanced Raman scattering (SERS) spectroscopy Author: Vlastimil Peksa Department: Institute of Physics of Charles University Supervisor: doc. RNDr. Marek Procházka, Ph.D., Institute of Physics of Charles University Abstract: This experimental methodical work was aimed at the optimization of selected gold and silver substrates and their use in construction of SERS-based biosensors, including following practical application. Several types of substrates, fabricated via a combination of bottom-up techniques on solid surfaces, were tested. The properties of these substrates were examined with probe molecules, namely methylene blue, porphyrins and tryptophan, on a confocal Raman microspectrometer. Obtained findings about the influence of analyte application, objective focusing and internal intensity standard were exploited for optimization of measurement procedures with regard to sensitivity, accuracy and reproducibility. A method for quantitative detection of food dye azorubine (E 122) in commercially available drinks was developed, based on these findings. Its results have shown its potential as a pre-scan method for field application and preliminary testing. Keywords: Metal nanosubstrates, biomolecules,...

Thesis (M.Sc.Eng.) / Sepsis is a serious medical condition in which a person becomes infected with bacteria in his or her bloodstream. The symptoms of sepsis are a result of the immune system’s interaction with the infecting agent. Currently, to diagnose a patient with sepsis, a blood sample must be collected and cultured for 24-48 hours before the infection can be confirmed. In the meantime, a broad-scope antibiotic is administered which may or may not be effective in treating the patient. If the antibiotic is ineffective, a different antibiotic must be chosen. When the results of the blood culture are available, a narrow scope antibiotic, appropriate to treat the infection is administered. However, sepsis has a mortality rate of 18-30% depending on the infecting agent and the treatment is highly time sensitive. Within 24 hours, the syndrome may progress to septic shock and mortality rates reach 50%. Therefore, it is important to quickly and correctly identify the infecting agent and provide immediate targeted treatment. Surface Enhanced Raman Spectroscopy (SERS) can be used to quickly identify and distinguish between different bacterial strains; however it requires higher bacterial concentrations than are present in the blood during the early stages of sepsis. A microfluidic evaporator chip has been developed to concentrate bacteria samples from 4μl to 100nl; the chip has been evaluated for concentration efficiency on Escherichia coli and methicillin-sensitive Staphylococcus aureus. Various blocking methods using bovine serum albumin (BSA) have been tested to reduce bacterial adhesion to the chip and have improved bacterial recovery to around 70% for both strains tested. Ongoing tests are being performed to improve bacterial recovery and sample purity for identification. / 2031-01-01

In this research, the use of gold nanostructures (AuNS) was explored to evaluate the interaction between molecules and the nanoparticle (NP) surface. In that way, three different projects were developed; one project using fluorescence and two projects using Raman spectroscopy as measuring technique. The fluorescence spectroscopy project used the fluorescence lifetime imaging microscope (FLIM) to evaluate the relative position of the molecules methylene blue (MB) and cucurbit[7]uril (CB) on the gold nanoparticle (AuNP) surface. Although the inclusion complex is favored in solution, it was found that MB forms an exclusion complex with CB, when CB is attached to the AuNP surface. The first project utilizing Raman spectroscopy, specifically surface enhanced Raman scattering (SERS), took advantage of a confined system (a reverse micelle) to evaluate the Raman signal of water molecules in close proximity to the AuNP surface. It was observed that the SERS water signal had a big shift to higher energies compared with the Raman signal of the bulk water; indicating the water molecules in the system are subjected to different bond-stretching energies. The second Raman project studied the modification of two different AuNS (specifically AuNP and gold nanorod -AuNR) with thiols. Different thiols were used to evaluate the kinetics of the modification of the AuNS surface, also the different AuNS presented different ligands on their surface. In general, and considering the difference in the bonding strength of the ligands present on the AuNS surface (by synthesis) and the size of the thiol, at least 2 h are required to modify the complete AuNS surface.

PINHEIRO, S. O.; DIÓGENES, I. C. N. Sintese , caracterização e eletroatividade de sams formadas com compostos catiônicos de tetraaminas de rutênio. 2006. 116 f. Dissertação (Mestrado em Química Orgânica) - Centro de Ciências, Universidade Federal do Ceará, Fortaleza, 2006. / Submitted by José Jairo Viana de Sousa (jairo@ufc.br) on 2014-10-15T17:44:28Z No. of bitstreams: 1 2006_dis_sopinheiro.pdf: 2241358 bytes, checksum: 0dea1c8d56ba429bd77cc89b4b868d66 (MD5) / Approved for entry into archive by José Jairo Viana de Sousa(jairo@ufc.br) on 2015-10-22T22:42:52Z (GMT) No. of bitstreams: 1 2006_dis_sopinheiro.pdf: 2241358 bytes, checksum: 0dea1c8d56ba429bd77cc89b4b868d66 (MD5) / Made available in DSpace on 2015-10-22T22:42:52Z (GMT). No. of bitstreams: 1 2006_dis_sopinheiro.pdf: 2241358 bytes, checksum: 0dea1c8d56ba429bd77cc89b4b868d66 (MD5) Previous issue date: 2006 / Trans-[Ru(CNpy)(NH3)4(L)]2+ type complexes, where CNpy (4- Cyanopyridine), L= 1,4-dt (1,4-dithiane), pyS (4-mercaptopyridine), and Tio (thionicotinamide), were synthesized and characterized by HPLC, microanalysis, eletrochemistry and vibrational and eletronic spectroscopies. The eletrochemical and eletronic absorption results are indicative of a π back-bonding interaction, L(nπ*) ← RuII(dπ) for which L is the pyS, CNpy and Tio ligands. The half-wave formal potentials (E1/2) observed for the trans-[Ru(CNpy)(NH3)4(pyS)]2+, trans- [Ru(CNpy)(NH3)4(1,4-dt)]2+ and trans-[Ru(CNpy)(NH3)4(Tio)]2+ complexes: 1.00, 0.67 and 1.03 V vs NHE, respectively, are indicative of the stabilization of the metal in the reduced state comparatively to the start complex, trans-[Ru(CNpy)(NH3)4(OH2)]2+ (E1/2 = 0.35 V vs NHE). This result indicates, also, the strong π withdraw capability of the CNpy ligand. The shift observed for the νC≡N mode from 2239 cm-1 in the vibrational spectra of the CNpy free ligand to ∼2200 cm-1 upon coordination suggests that the coordination occurs through the nitrile fragment. For the pyS and Tio ligands, the observation of the signals assigned to the νC=S and νSH modes, respectively, in the vibrational spectra os the complexes indicates that the coordination occurs through the nitrogen atom os the pyridine ring. The SERS ex situ spectra of the gold surfaces modified with the isolated complexes allow the classification of these species as binfunctional molecules in which the sulfur atom of the pyS, 1,4-dt and Tio ligands is the adsorption site and the nitrogen atom of the CNpy pyridine ring is the functional terminal group. Also, the SERS results point for a trans conformation for the trans- [Ru(CNpy)(NH3)4(pyS)]2+ complex and for a gauche configuration for the trans- [Ru(CNpy)(NH3)4(1,4-dt)]2+ and trans-[Ru(CNpy)(NH3)4(Tio)]2+ complexes on gold. The intensity dependence of some signals in the SERS spectra with the applie potential reflects the π back-bonding effect on surface since this behavior is observed to be strongly related to the E1/2 values of the complexes. The reductive desorption potentials of the SAMs formed with the isolated compounds reflects the π withdraw capability of the CNpy ligand. This effect is much more intense for the trans-[Ru(CNpy)(NH3)4(1,4-dt)]2+ complex since the π back-bonding interaction of the 1,4-dt ligand is lower than the CNpy, pyS and Tio ligands. The heterogeneous electron transfer reaction of the cytochrome c metalloprotein was satisfactorily assessed with the SAMs formed by the isolated complexes (E1/2 = 0.05 V vs Ag⏐AgCl⏐Cl-). The Best voltammetric response was observed with the SAM of the trans- [Ru(CNpy)(NH3)4(pyS)]2+ complex due to the trans conformation on surface. / Os complexos trans-[Ru(CNpy)(NH3)4(1,4-dt)]2+ (CNpy = 4-Cianopiridina, 1,4- dt = 1,4-ditiano), trans-[Ru(CNpy)(NH3)4(pyS)]2+ (pyS = 4-mercaptopiridina) e trans- [Ru(CNpy)(NH3)4(Tio)]2+ (Tio = tionicotinamida) foram sintetizados e caracterizados por Cromatografia Líquida de Alta Eficiência, análise elementar, eletroquímica e espectroscopias eletrônica e vibracional. Os espectros de absorção eletrônica e os resultados de eletroquímica evidenciaram uma interação do tipo π back-bonding do centro metálico RuII para os ligantes piridínicos. Os valores dos potenciais formais de meia onda (E1/2) observados para os complexos trans-[Ru(CNpy)(NH3)4(1,4-dt)]2+, trans-[Ru(CNpy)(NH3)4(pyS)]2+ e trans-[Ru(CNpy)(NH3)4(Tio)]2+: 1,00, 0,67 e 1,03 V vs ENH, respectivamente, indicam a estabilização do estado reduzido do centro metálico em relação ao complexo de partida trans-[Ru(CNpy)(NH3)4(OH2)]2+ (E1/2 = 0,35 V vs ENH). Esse resultado indica, também, a forte capacidade π retiradora do ligante CNpy que, no caso do complexo trans-[Ru(CNpy)(NH3)4(1,4-dt)]2+, é tão intensa que facilita comparativamente o processo de oxidação do centro metálico. Podese concluir, portanto, que a capacidade π retiradora dos ligantes CNpy, pyS e Tio é similar. O deslocamento na freqüência de estiramento da ligação C≡N do ligante Cnpy livre de 2239 para ∼2200 cm-1 após coordenação ao centro metálico [Ru(NH3)4]2+ nos espectros vibracionais indica que a coordenação do ligante CNpy ocorre pelo grupamento nitrila. Para os ligantes pyS e Tio, a observação das bandas atribuídas aos νC=S e νSH, respectivamente, indica que a coordenação ocorre pelo átomo de nitrogênio do anel piridínico. Os espectros SERS ex situ das superfícies modificadas com os compostos isolados permitem a classificação destes como moléculas modificadoras bifuncionais, onde o átomo de enxofre dos ligantes pyS, 1,4-dt e Tio atuam como sítio de adsorção e o átomo de nitrogênio piridínico do ligante CNpy atua como grupo funcional terminal. Além disso, os resultados SERS sugerem uma conformação trans para o complexo trans-[Ru(CNpy)(NH3)4(pyS)]2+ e gauche para os complexos trans-[Ru(CNpy)(NH3)4(1,4-dt)]2+ e trans-[Ru(CNpy)(NH3)4(Tio)]2+ sobre ouro. A dependência nas intensidades das bandas com o potencial aplicado aos eletrodos modificados ilustra o efeito π back-bonding dos íons metálicos dos adsorbatos inorgânicos, uma vez que observa-se uma relação direta com os valores dos potenciais formais de meia onda dos complexos estudados. Os valores dos potenciais de dessorção redutiva observados para as SAMs dos complexos isolados refletem a capacidade π retiradora do ligante CNpy que se encontra na posição para em relação ao sítio de adsorção. Esse efeito é bem mais intenso no complexo trans- [Ru(CNpy)(NH3)4(1,4-dt)]2+, uma vez que a capacidade de interação π back-bonding do ligante 1,4-dt é significativamente menor que as dos ligantes pyS e Tio. Sugere-se, para esse complexo, uma oxidação parcial do centro metálico o que implica em uma intensificação da interação σ com o ligante 1,4-dt (RuII-S) e, conseqüentemente, um enfraquecimento da ligação Au-S. A reação hTE da metaloproteína cyt c foi observada em valor consistente com seu estado in natura indicando que as SAMs estudadas acessam satisfatoriamente o processo hTE do cyt c além de evitar a desnaturação desta proteína. A forma das curvas voltamétricas, entretanto, apresentou uma dependência com a configuração dos complexos sobre a superfície. Curvas de melhor definição foram obtidas com a SAM do complexo trans-[Ru(CNpy)(NH3)4(pyS)]2+ que apresenta uma configuração trans em relação à superfície.