New enhancement strategies for plasmon-enhanced fluorescence biosensors

This thesis investigates metallic nanostructures exhibiting surface plasmon resonance for the amplification of fluorescence signal in sandwich immunoassays. In this approach, an analyte is captured by an antibody immobilized on a plasmonic structure and detected by a subsequently bound fluorophore labeled detection antibody. The highly confined field of surface plasmons originates from collective charge oscillations which are associated with high electromagnetic field enhancements at the metal surface and allow for greatly increased fluorescence signal from the attached fluorophores. This feature allows for improving the signal-to-noise ratio in fluorescence measurements and thus advancing the sensitivity of the sensor platform. In particular, the thesis presents two plasmonic nanostructures that amplify fluorescence signal in devices that rely on epifluorescence geometry, in which the fluorophore absorbs and emits light from the same direction perpendicular to the substrate surface.rnThe first is a crossed relief gold grating that supports propagating surface plasmon polaritons (SPPs) and second, gold nanoparticles embedded in refractive index symmetric environment exhibiting collective localized surface plasmons (cLSPs). Finite-difference time-domain simulations are performed in order to design structures for the optimum amplification of established Cy5 and Alexa Fluor 647 fluorophore labels with the absorption and emission wavelengths in the red region of spectrum. The design takes into account combined effect of surface plasmon-enhanced excitation rate, directional surface plasmon-driven emission and modified quantum yield for characteristic distances in immunoassays. Homebuilt optical instruments are developed for the experimental observation of the surface plasmon mode spectrum, measurements of the angular distribution of surface plasmon-coupled fluorescence light and a setup mimicking commercial fluorescence reading systems in epifluorescence geometry.rnCrossed relief grating structures are prepared by interference lithography and multiple copies are made by UV nanoimprint lithography. The fabricated crossed diffraction gratings were utilized for sandwich immunoassay-based detection of the clinically relevant inflammation marker interleukin 6 (IL-6). The enhancement factor of the crossed grating reached EF=100 when compared to a flat gold substrate. This result is comparable to the highest reported enhancements to date, for fluorophores with relatively high intrinsic quantum yield. The measured enhancement factor excellently agrees with the predictions of the simulations and the mechanisms of the enhancement are explained in detail. Main contributions were the high electric field intensity enhancement (30-fold increase) and the directional fluorescence emission at (4-fold increase) compared to a flat gold substrate.rnCollective localized surface plasmons (cLSPs) hold potential for even stronger fluorescence enhancement of EF=1000, due to higher electric field intensity confinement. cLSPs are established by diffractive coupling of the localized surface plasmon resonance (LSPR) of metallic nanoparticles and result in a narrow resonance. Due to the narrow resonance, it is hard to overlap the cLSPs mode with the absorption and emission bands of the used fluorophore, simultaneously. Therefore, a novel two resonance structure that supports SPP and cLSP modes was proposed. It consists of a 2D array of cylindrical gold nanoparticles above a low refractive index polymer and a silver film. A structure that supports the proposed SPP and cLSP modes was prepared by employing laser interference lithography and the measured mode spectrum was compared to simulation results.rn

Sulfur-containing polymers for surface attachment

Different concepts for the synthesis of sulfur-containing polymers as well as their adsorption onto gold surfaces were studied. The present work is divided into three parts. The main part focuses on the synthesis of poly(1,2-alkylene sulfides) (“polysulfides”) with complex architectures on the basis of polyether-based macroinitiators by the anionic ring-opening polymerization of ethylene sulfide and propylene sulfide. This synthetic tool kit allowed the synthesis of star-shaped, brush-like, comb-like and pom-pom-like polysulfides, the latter two with an additional poly(ethylene glycol) chain. Additionally, the number of polysulfide arms as well as the monomer composition could be varied over a wide range to obtain copolymers with multiple thioether functionalities.rnThe second section deals with the synthesis of a novel lipoic acid-based initiator for ring-opening polymerizations for lactones and epoxides. A straightforward approach was selected to accomplish the ability to obtain tailored polymers with a common used disulfide-anchoring group, without the drawbacks of post-polymerization functionalization. rnIn the third part, a new class of block-copolymers consisting of polysulfides and polyesters were investigated. For the first time this approach enabled the use of hydroxyl-terminated poly(propylene sulfide) as macroinitiator for the synthesis of a second block.rnThe adsorption efficiency of those different polymer classes onto gold nanoparticles as well as gold rnsupports was studied via different methods.rn

Excited state properties of formamide in water solution: An ab initio study

We present ab initio quantum calculation of the optical properties of formamide in vapor phase and in water solution. We employ time dependent density functional theory for the isolated molecule and many-body perturbation theory methods for the system in solution. An average over several molecular dynamics snapshots is performed to take into account the disorder of the liquid. We find that the excited stateproperties of the gas-phase formamide are strongly modified by the presence of the water solvent: the geometry of the molecule is distorted and the electronic and optical properties are severely modified. The important interaction among the formamide and the water molecules forces us to use fully quantum methods for the calculation of the excited stateproperties of this system. The excitonic wave function is localized both on the solute and on part of the solvent.

Probing chiral interfaces by infrared spectroscopic methods

Biological homochirality on earth and its tremendous consequences for pharmaceutical science and technology has led to an ever increasing interest in the selective production, the resolution and the detection of enantiomers of a chiral compound. Chiral surfaces and interfaces that can distinguish between enantiomers play a key role in this respect as enantioselective catalysts as well as for separation purposes. Despite the impressive progress in these areas in the last decade, molecular-level understanding of the interactions that are at the origin of enantiodiscrimination are lagging behind due to the lack of powerful experimental techniques to spot these interactions selectively with high sensitivity. In this article, techniques based on infrared spectroscopy are highlighted that are able to selectively target the chiral properties of interfaces. In particular, these methods are the combination of Attenuated Total Reflection InfraRed (ATR-IR) with Modulation Excitation Spectroscopy (MES) to probe enantiodiscriminating interactions at chiral solid-liquid interfaces and Vibrational Circular Dichroism (VCD), which is used to probe the structure of chirally-modified metal nanoparticles. The former technique aims at suppressing signals arising from non-selective interactions, which may completely hide the signals of interest due to enantiodiscriminating interactions. Recently, this method was successfully applied to investigate enantiodiscrimination at self-assembled monolayers of chiral thiols on gold surfaces. The nanometer size analogues of the latter--gold nanoparticles protected by a monolayer of a chiral thiol--are amenable to VCD spectroscopy. It is shown that this technique yields detailed structural information on the adsorption mode and the conformation of the adsorbed thiol. This may also turn out to be useful to clarify how chirality can be bestowed onto the metal core itself and the nature of the chirality of the latter, which is manifested in the metal-based circular dichroism activity of these nanoparticles.

Translocation of particles and inflammatory responses after exposure to fine particles and nanoparticles in an epithelial airway model

ABSTRACT: BACKGROUND: Experimental studies provide evidence that inhaled nanoparticles may translocate over the airspace epithelium and cause increased cellular inflammation. Little is known, however, about the dependence of particle size or material on translocation characteristics, inflammatory response and intracellular localization. RESULTS: Using a triple cell co-culture model of the human airway wall composed of epithelial cells, macrophages and dendritic cells we quantified the entering of fine (1 mum) and nano-sized (0.078 mum) polystyrene particles by laser scanning microscopy. The number distribution of particles within the cell types was significantly different between fine and nano-sized particles suggesting different translocation characteristics. Analysis of the intracellular localization of gold (0.025 mum) and titanium dioxide (0.02-0.03 mum) nanoparticles by energy filtering transmission electron microscopy showed differences in intracellular localization depending on particle composition. Titanium dioxide nanoparticles were detected as single particles without membranes as well as in membrane-bound agglomerations. Gold nanoparticles were found inside the cells as free particles only. The potential of the different particle types (different sizes and different materials) to induce a cellular response was determined by measurements of the tumour necrosis factor-alpha in the supernatants. We measured a 2-3 fold increase of tumour necrosis factor-alpha in the supernatants after applying 1 mum polystyrene particles, gold nanoparticles, but not with polystyrene and titanium dioxide nanoparticles. CONCLUSION: Quantitative laser scanning microscopy provided evidence that the translocation and entering characteristics of particles are size-dependent. Energy filtering transmission electron microscopy showed that the intracellular localization of nanoparticles depends on the particle material. Both particle size and material affect the cellular responses to particle exposure as measured by the generation of tumour necrosis factor-alpha.

Multimetallic complexes based on phosphine- and phosphine oxide- appended p-hydroquinones

Presented here, is the work done with a series of binucleating ligands based on phosphine and phosphine oxide appended p-hydroquinones and their reactions towards various metals sources. The long term goal of the project was to produce coordination polymers that would have novel electronic, magnetic, and optical properties which would be of use in the field of molecular electronics. Binucleating ligands contained a p-hydroquinone motif in which various phosphine- and phosphine oxide substituents have been placed in the ortho position relative to each of the hydroxy position were synthesized. A previously published synthetic method for such lugands utilized n-BuLi to form a phenyl lithium intermediate which was quenched with chlorodiphenylphosphine. This technique was also used to produce a ligand with diisopropylphosphine groups. Phosphine ligands, containing the same structural motif, were also generated using LDA as the lithiating agent. This technique was found to be higher yielding. Phosphine chalcogenide ligands were accessed by further oxidizing the low valent phosphorous centers with either hydrogen peroxide or with elemental sulfur. These ligands were characterized using multinuclear NMR, low and high resolution mass spectroscopy, FTIR, and single crystal X-ray diffraction. Their electrochemical properties were explored with cyclic voltammetry. The phosphine appended ligands were used in the synthesis of a several bimetallic complexes. It was found that the ligands readily reacted with NiCp2 and NiCp*2, displacing one of the cyclopentadiene (Cp) or pentamethylcyclopentadiene (Cp*) rings. A cyclopentadiene complexes, containing diisopropylphine, was readily oxidized by[FeCp2]PF6 to give a NMR silent mixed valence complex. Cyclic voltammetry of these complexes showed a number of reversible waves with a large potential separation. The mixed valence compounds also showed a large absorbance band in the NIR region which was assigned to be an intervalence charge transfer. The cyclic voltammetry and NIR spectroscopy suggest that these systems are very capable of efficient metal-to-metal charge transfer. These complexes were characterized by multinuclear NMR, single crystal X-ray diffraction, UV/VIS-NIR spectroscopy and elemental analysis. The phosphine oxide ligands were reacted with a variety of different metal sources but limited success was gained in obtaining single crystals, allowing structural characterization of these compounds. Single crystals were obtained from products generated by reacting the diphenylphosphine oxide ligand with (Bipy)Cu(NO3)2 and Cu(NO3)2. In all cases the ligand had been further oxidized to a 2,5-dihydroxy-1,4-benzoquinone motif. In the reaction between the diphenylphosphine oxide ligand and (Bipy)Cu(NO3)2 it was found that the phosphine oxide moiety was involved with intermolecular coordination leading to the formation of a one-dimensional polymer composed of a series of bimetallic complexes tethered together. When NaSbF6 was present in the reaction with (Bipy)Cu(NO3)2 a unique tetrametallic complex was formed. Here the phospine oxide moiety was oriented so that two bimetallic complexes were bound together. If only Cu(NO3)2 was present, a two-dimensional polymeric sheet was formed where the ligand was present in two different coordination modes. The electronic properties of these complexes remained to be assessed.

Negative index metamaterials and metaspacers for optical frequencies

Metamaterials are artificial materials that exhibit properties, such as negative index of refraction, that are not possible through natural materials. Due to many potential applications of negative index metamaterials, significant progress in the field has been observed in the last decade. However, achieving negative index at visible frequencies is a challenging task. Generally, fishnet metamaterials are considered as a possible route to achieve negative index in the visible spectrum. However, so far no metamaterial has been demonstrated to exhibit simultaneously negative permittivity and permeability (double-negative) beyond the red region of the visible spectrum. This study is mainly focused on achieving higher operating frequency for low-loss, double-negative metamaterials. Two double-negative metamaterials have been proposed to operate at highest reported frequencies. The first proposed metamaterial is based on the interaction of surface plasmon polaritons of a thin metal film with localized surface plasmons of a metallic array placed close to the thin film. It is demonstrated that the metamaterial can easily be scaled to operate at any frequency in the visible spectrum as well as possibly to the ultraviolet spectrum. Furthermore, the underlying physical phenomena and possible future extensions of the metamaterial are also investigated. The second proposed metamaterial is a modification to the so-called fishnet metamaterial. It has been demonstrated that this ‘modified fishnet’ exhibits two double-negative bands in the visible spectrum with highest operating frequency in the green region with considerably high figure of merit. In contrast to most of the fishnet metamaterials proposed in the past, behavior of this modified fishnet is independent of polarization of the incident field. In addition to the two negative index metamaterials proposed in this study, the use of metamaterial as a spacer, named as metaspacer, is also investigated. In contrast to naturally available dielectric spacers used in microfabrication, metaspacers can be realized with any (positive or negative) permittivity and permeability. As an example, the use of a negative index metaspacer in place of the dielectric layer in a fishnet metamaterial is investigated. It is shown that fishnet based on negative index metaspacer gives many improved optical properties over the conventional fishnet such as wider negative index band, higher figure of merit, higher optical transmission and stronger magnetic response. In addition to the improved properties, following interesting features were observed in the metaspacer based fishnet metamaterial. At the resonance frequency, the shape of the permeability curve was ‘inverted’ as compared to that for conventional fishnet metamaterial. Furthermore, dependence of the resonance frequency on the fishnet geometry was also reversed. Moreover, simultaneously negative group and phase velocities were observed in the low-loss region of the metaspacer based fishnet metamaterial. Due to interesting features observed using metaspacer, this study will open a new horizon for the metamaterial research.

Fabrication of a Large, Ordered, Three-Dimensional Nanocup Array

Metallic nanocups provide a unique method for redirecting scattered light by creating magnetic plasmon responses at optical frequencies. Despite considerable development of nanocup fabrication processes, simultaneously achieving accurate control over the placement, orientation, and geometry of nanocups has remained a significant challenge. Here we present a technique for fabricating large, periodically ordered arrays of uniformly oriented three-dimensional gold nanocups for manipulating light at subwavelength scales. Nanoimprint lithography, soft lithography, and shadow evaporation were used to fabricate nanocups onto the tips of polydimethylsiloxane nanopillars with precise control over the shapes and optical properties of asymmetric nanocups.

Single-Molecule Conductance of Functionalized Oligoynes: Length Dependence and Junction Evolution

We report a combined experimental and theoretical investigation of the length dependence and anchor group dependence of the electrical conductance of a series of oligoyne molecular wires in single-molecule junctions with gold contacts. Experimentally, we focus on the synthesis and properties of diaryloligoynes with n = 1, 2, and 4 triple bonds and the anchor dihydrobenzo[b]thiophene (BT). For comparison, we also explored the aurophilic anchor group cyano (CN), amino (NH2), thiol (SH), and 4-pyridyl (PY). Scanning tunneling microscopy break junction (STM-BJ) and mechanically controllable break junction (MCBJ) techniques are employed to investigate single-molecule conductance characteristics. The BT moiety is superior as compared to traditional anchoring groups investigated so far. BT-terminated oligoynes display a 100% probability of junction formation and possess conductance values which are the highest of the oligoynes studied and, moreover, are higher than other conjugated molecular wires of similar length. Density functional theory (DFT)-based calculations are reported for oligoynes with n = 1−4 triple bonds. Complete conductance traces and conductance distributions are computed for each family of molecules. The sliding of the anchor groups leads to oscillations in both the electrical conductance and the binding energies of the studied molecular wires. In agreement with experimental results, BT-terminated oligoynes are predicted to have a high electrical conductance. The experimental attenuation constants βH range between 1.7 nm−1 (CN) and 3.2 nm−1 (SH) and show the following trend: βH(CN) < βH(NH2) < βH(BT) < βH(PY) ≈ βH(SH). DFT-based calculations yield lower values, which range between 0.4 nm−1 (CN) and 2.2 nm−1 (PY).

Quantification of gold nanoparticle cell uptake under controlled biological conditions and adequate resolution

Aim: We examined cellular uptake mechanisms of fluorescently labeled polymer-coated gold nanoparticles (NPs) under different biological conditions by two quantitative, microscopic approaches. Materials & methods: Uptake mechanisms were evaluated using endocytotic inhibitors that were tested for specificity and cytotoxicity. Cellular uptake of gold NPs was analyzed either by laser scanning microscopy or transmission electron microscopy, and quantified by means of stereology using cells from the same experiment. Results: Optimal inhibitor conditions were only achieved with chlorpromazine (clathrin-mediated endocytosis) and methyl-β-cyclodextrin (caveolin-mediated endocytosis). A significant methyl-β-cyclodextrin-mediated inhibition (63-69%) and chlorpromazine-mediated increase (43-98%) of intracellular NPs was demonstrated with both imaging techniques, suggesting a predominant uptake via caveolin-medicated endocytois. Transmission electron microscopy imaging revealed more than 95% of NPs localized in intracellular vesicles and approximately 150-times more NP events/cell were detected than by laser scanning microscopy. Conclusion: We emphasize the importance of studying NP-cell interactions under controlled experimental conditions and at adequate microscopic resolution in combination with stereology. Original submitted 10 July 2012; Revised submitted 23 January 2013.

Tidally Driven Exchange in an Archipelago Strait: Biological and Optical Responses

Measurements in San Bernardino Strait, one of two major connections between the Pacific Ocean and the interior waters of the Philippine Archipelago, captured 2-3 m s(-1) tidal currents that drove vertical mixing and net landward transport. A TRIAXUS towed profiling vehicle equipped with physical and optical sensors was used to repeatedly map subregions within the strait, employing survey patterns designed to resolve tidal variability of physical and optical properties. Strong flow over the sill between Luzon and Capul islands resulted in upward transport and mixing of deeper high-salinity, low-oxygen, high-particle-and-nutrient-concentration water into the upper water column, landward of the sill. During the high-velocity ebb flow, topography influences the vertical distribution of water, but without the diapycnal mixing observed during flood tide. The surveys captured a net landward flux of water through the narrowest part of the strait. The tidally varying velocities contribute to strong vertical transport and diapycnal mixing of the deeper water into the upper layer, contributing to the observed higher phytoplankton biomass within the interior of the strait.

Significant Contribution of Large Particles to Optical Backscattering in the Open Ocean

The light scattering properties of oceanic particles have been suggested as an alternative index of phytoplankton biomass than chlorophyll-a concentration (chl-a), with the benefit of being less sensitive to physiological forcings (e.g., light and nutrients) that alter the intracellular pigment concentrations. The drawback of particulate scattering is that it is not unique to phytoplankton. Nevertheless, field studies have demonstrated that, to first order, the particulate beam-attenuation coefficient (c(p)) can track phytoplankton biomass. The relationship between c(p) and the particulate backscattering coefficient (b(bp)), a property retrievable from space, has not been fully evaluated, largely due to a lack of open-ocean field observations. Here, we present extensive data on inherent optical properties from the Equatorial Pacific surface waters and demonstrate a remarkable coherence in b(bp) and c(p). Coincident measurements of particle size distributions (PSDs) and optical properties of size-fractionated samples indicate that this covariance is due to both the conserved nature of the PSD and a greater contribution of phytoplankton-sized particles to b(bp) than theoretically predicted. These findings suggest that satellite-derived b(bp)could provide similar information on phytoplankton biomass in the open ocean as c(p).

Hierarchical self-assembly of the DNA-grafted supramolecular polymers

Conjugation of functional entities with a specific set of optical, mechanical or biological properties to DNA strands allows engineering of sophisticated DNA-containing architectures. Among various hybrid systems, DNA-grafted polymers occupy an important place in modern materials science. In this contribution we present the non-covalent synthesis and properties of DNA-grafted linear supramolecular polymers (SPs), which are assembled in a controllable manner from short chimeric DNA-pyrene oligomers. The synthetic oligomers consist of two parts: a 10 nucleotides long DNA chain and a covalently attached segment of variable number of phosphodiester-linked pyrenes. The temperature-dependent formation of DNA-grafted SPs is described by a nucleation-elongation mechanism. The high tendency of pyrenes to aggregate in water, leads to the rapid formation of SPs. The core of the assemblies consists of stacked pyrenes. They form a 1D platform, to which the DNA chains are attached. Combined spectroscopic and microscopic studies reveal that the major driving forces of the polymerization are π-stacking of pyrenes and hydrophobic interactions, and DNA pairing contributes to a lesser extent. AFM and TEM experiments demonstrate that the 1D SPs appear as elongated ribbons with a length of several hundred nanometers. They exhibit an apparent helical structure with a pitch-to-pitch distance of 50±15 nm. Since DNA pairing is a highly selective process, the ongoing studies are aimed to utilize DNA-grafted SPs for the programmable arrangement of functional entities. For example, the addition of non-modified complementary DNA strands to the DNA-grafted SPs leads to the cooperative formation of higher-order assemblies. Also, our experiments suggest that the fluorescent pyrene core of 1D ribbons serves as an efficient donor platform for energy transfer applications.

Hierarchical self-assembly of the DNA-grafted supramolecular polymers

Conjugation of functional entities with a specific set of optical, mechanical or biological properties to DNA strands allows engineering of sophisticated DNA-containing architectures. Among various hybrid systems, DNA-grafted polymers occupy an important place in modern materials science. In this contribution we present the non-covalent synthesis and properties of DNA-grafted linear supramolecular polymers (SPs), which are assembled in a controllable manner from short chimeric DNA-pyrene oligomers. The synthetic oligomers consist of two parts: a 10 nucleotides long DNA chain and a covalently attached segment of variable number of phosphodiester-linked pyrenes. The temperature-dependent formation of DNA-grafted SPs is described by a nucleation-elongation mechanism. The high tendency of pyrenes to aggregate in water, leads to the rapid formation of SPs. The core of the assemblies consists of stacked pyrenes. They form a 1D platform, to which the DNA chains are attached. Combined spectroscopic and microscopic studies reveal that the major driving forces of the polymerization are π-stacking of pyrenes and hydrophobic interactions, and DNA pairing contributes to a lesser extent. AFM and TEM experiments demonstrate that the 1D SPs appear as elongated ribbons with a length of several hundred nanometers. They exhibit an apparent helical structure with a pitch-to-pitch distance of 50±15 nm. Since DNA pairing is a highly selective process, the ongoing studies are aimed to utilize DNA-grafted SPs for the programmable arrangement of functional entities. For example, the addition of non-modified complementary DNA strands to the DNA-grafted SPs leads to the cooperative formation of higher-order assemblies. Also, our experiments suggest that the fluorescent pyrene core of 1D ribbons serves as an efficient donor platform for energy transfer applications.

High-Frequency in Situ Optical Measurements During a Storm Event: Assessing Relationships Between Dissolved Organic Matter, Sediment Concentrations, and Hydrologic Processes

Dissolved organic matter (DOM) dynamics during storm events has received considerable attention in forested watersheds, but the extent to which storms impart rapid changes in DOM concentration and composition in highly disturbed agricultural watersheds remains poorly understood. In this study, we used identical in situ optical sensors for DOM fluorescence (FDOM) with and without filtration to continuously evaluate surface water DOM dynamics in a 415 km(2) agricultural watershed over a 4 week period containing a short-duration rainfall event. Peak turbidity preceded peak discharge by 4 h and increased by over 2 orders of magnitude, while the peak filtered FDOM lagged behind peak turbidity by 15 h. FDOM values reported using the filtered in situ fluorometer increased nearly fourfold and were highly correlated with dissolved organic carbon (DOC) concentrations (r(2) = 0.97), providing a highly resolved proxy for DOC throughout the study period. Discrete optical properties including specific UV absorbance (SUVA(254)), spectral slope (S(290-350)), and fluorescence index (FI) were also strongly correlated with in situ FDOM and indicate a shift toward aromatic, high molecular weight DOM from terrestrially derived sources during the storm. The lag of the peak in FDOM behind peak discharge presumably reflects the draining of watershed soils from natural and agricultural landscapes. Field and experimental evidence showed that unfiltered FDOM measurements underestimated filtered FDOM concentrations by up to similar to 60% at particle concentrations typical of many riverine systems during hydrologic events. Together, laboratory and in situ data provide insights into the timing and magnitude of changes in DOM quantity and quality during storm events in an agricultural watershed, and indicate the need for sample filtration in systems with moderate to high suspended sediment loads.