This dissertation contains the synthesis and characterization of squaraine based new functional materials. In the first part of this thesis work, a water soluble benzothiazolium squaraine dye was synthesized with pyridium pendents, and controlled aggregation properties were achieved. After formation of partially reversible J-aggregation on a polyelectrolyte (poly(acryl acid) sodium salt) template, the nonlinear, two-photon absorption cross section per repeat unit was found to be above 30-fold enhanced compared with nonaggregate and/or low aggregates. Using a similar strategy, sulfonate anions were introduced into the squaraine structure, and the resulting compounds exhibited good water solubilities. A ‘turn on’ fluorescence was discovered when these squaraine dyes interacted with bovine serum albumin (BSA), titration studies by BSA site selective reagents show these squaraine dyes can bind to both site I and II of BSA, with a preference of site II. Introduction of these squaraine dyes to BSA nanoparticles generated near-IR protein nano fabricates, and cell images were collected. Metal sensing properties were also studied using the sulfonates containing a benzoindolium squaraine dye, and the linear response of the absorption of the squaraine dye to the concentration of Hg2+ makes it a good heavy metal-selective sensing material that can be carried out in aqueous solution. Later, a squaraine scaffold was attached to deoxyribonucleosides by Sonogashira coupling reactions, in which the reaction conditions were modified. Iodo-deoxyuridine and bromo-deoxyadenosine were used as the deoxyribonucleosides building blocks, and the resulting squaraine dye-modified deoxyribonucleosides exhibited near-IR absorption and emission properties due to the squaraine chromophore. Interestingly, these non-natural deoxyribonucleosdies showed viscosity dependent photophysical properties, which make them nice candidates for fluorescence viscosity sensors at the cellular level. After incubation with cells, these iv viscosity sensors were readily uptaken by cell, and images were obtained showing regions of high viscosity in cells.

Molecular oxygen in its lowest electronically excited state plays an important roll in the field of chemistry. This excited state is often referred to as singlet oxygen and can be generated in a photosensitized process under one- or two-photon excitation of a photosensitizer. It is particularly useful in the field of photodynamic cancer therapy (PDT) where singlet oxygen formation can be used to destroy cancerous tumors. The use of two-photon activated photosensitizers possesses great potential in the field of PDT since near-IR light is used to activate the sensitizer, resulting in deeper penetration of light into biological tissue, less photobleaching of the sensitizer, and greatly improved resolution of excitation. The synthesis and photophysical characterization of new fluorene-based photosensitizers for efficient singlet oxygen production were investigated. The spectral properties for singlet oxygen production were measured at room temperature and 77 K. Two-photon absorption (2PA) cross-sections of the fluorene derivatives were measured by the open aperture Z-scan method. The quantum yields of singlet oxygen generation under one- and two-photon excitation (Φ∆ and 2PAΦ∆, respectively) were determined by the direct measurement of singlet oxygen luminescence at ≈ 1270 nm. The values of Φ∆ were independent of excitation wavelength, ranging from 0.6 - 0.9. The singlet oxygen quantum yields under two-photon excitation were 2PAΦ∆ ≈ ½Φ∆, indicating that the two processes exhibited the same mechanism of singlet oxygen production, independent of the mechanism of photon absorption.

Three-dimensional (3D) optical data storage based on two-photon processes provides highly confined excitation in a recording medium and a mechanism for writing and reading data with less cross talk between multiple memory layers, due to the quadratic dependence of two photon absorption (2PA) on the incident light intensity. The capacity for highly confined excitation and intrinsic 3D resolution affords immense information storage capacity (up to 1012 bits/cm3). Recently, the use of photochromic materials for 3D memory has received intense interest because of several major advantages over current optical systems, including their erasable/rewritable capability, high resolution, and high sensitivity. This work demonstrates a novel two-photon 3D optical storage system based on the modulation of the fluorescence emission of a highly efficient two-photon absorbing fluorescent dye (fluorene derivative) and a photochromic compound (diarylethene). The feasibility of using efficient intermolecular Förster Resonance Energy Transfer (RET) from the non-covalently linked two-photon absorbing fluorescent fluorene derivative to the photochromic diarylethene as a novel read-out method in a two-photon optical data storage system was explored. For the purpose of the development of this novel two-photon 3D optical storage system, linear and two-photon spectroscopic characterization of commercial diarylethenes in solution and in a polymer film and evidence of their cyclization (O→C) and cycloreversion (C→O) reactions induced by two-photon excitation were undertaken. For the development of a readout method, Resonance Energy Transfer (RET) from twophoton absorbing fluorene derivatives to photochromic compounds was investigated under one and two-photon excitation. The Förster's distances and critical acceptor concentrations were determined for non-bound donor-acceptor pairs in homogeneous molecular ensembles. To the best of my knowledge, modulation of the two-photon fluorescence emission of a dye by a photochromic diarylethene has not been reported as a mechanism to read the recorded information in a 3D optical data storage system. This system was demonstrated to be highly stable and suitable for recording data in thick storage media. The proposed RET-based readout method proved to be non-destructive (exhibiting a loss of the initial fluorescence emission less than 20% of the initial emission after 10,000 readout cycles). Potential application of this system in a rewritable-erasable optical data storage system was proved. As part of the strategy for the development of diarylethenes optimized for 3D optical data storage, derivatives containing Ï€-conjugated fluorene molecules were synthesized and characterized. The final part of this reasearch demonstrated the photostability of fluorine derivatives showing strong molecular polarizability and high fluorescence quantum yields. These compounds are quite promising for application in RET-based two-photon 3D optical data storage. Hence, the photostability of these fluorene derivatives is a key parameter to establish, and facilitates their full utility in critical applications.

Two-photon absorption (2PA) has been used for a number of scientific and technological applications, exploiting the fact that the 2PA probability is directly proportional to the square of the incident light intensity (while one-photon absorption bears a linear relation to the incident light intensity). This intrinsic property of 2PA leads to 3D spatial localization, important in fields such as optical data storage, fluorescence microscopy, and 3D microfabrication. The spatial confinement that 2PA enables has been used to induce photochemical and photophysical events in increasingly smaller volumes and allowed nonlinear, 2PA-based, technologies to reach sub-diffraction limit resolutions. The primary focus of this dissertation is the development of novel, efficient 2PA, fluorene-based molecules to be used either as photoacid generators (PAGs) or fluorophores. A second aim is to develop more effective methods of synthesizing these compounds. As a third and final objective, the new molecules were used to develop a write-once-read many (WORM) optical data storage system, and stimulated emission depletion probes for bioimaging. In Chapter I, the microwave-assisted synthesis of triarylsulfonium salt photoacid generators (PAGs) from their diphenyliodonium counterparts is reported. The microwave-assisted synthesis of these novel sulfonium salts afforded reaction times 90 to 420 times faster than conventional thermal conditions, with photoacid quantum yields of new sulfonium PAGs ranging from 0.01 to 0.4. These PAGs were used to develop a fluorescence readout-based, nonlinear three-dimensional (3D) optical data storage system (Chapter II). In this system, writing was achieved by acid generation upon two-photon absorption (2PA) of a PAG (at 710 or 730 nm). Readout was then performed by interrogating two-photon absorbing dyes, after protonation, at 860 nm. Two-photon recording and readout of voxels was demonstrated in five and eight consecutive, crosstalk-free layers within a polymer matrix, generating a data storage capacity of up to 1.8 x 1013 bits/cm3. The possibility of using these PAGs in microfabrication is described in Chapter III, where two-photon induced cationic ring-opening polymerization (CROP) crosslinking of an SU8 resin is employed to produce free-standing microstructures. Chapter IV describes the investigation of one- and two-photon stimulated emission transitions by the fluorescence quenching of a sulfonyl-containing fluorene compound in solution at room temperate using a picosecond pump-probe technique. The nature of stimulated transitions under various fluorescence excitation and quenching conditions were analyzed theoretically, and good agreement with experimental data was demonstrated. Two-photon stimulated transitions S1 to S0 were shown at 1064 nm. The two-photon stimulated emission cross section of the sulfonyl fluorophore was estimated as aproximately 240 - 280 GM, making this compound a good candidate for use in two-photon stimulated emission depletion (STED) microscopy.

This thesis presents the first use of a novel direct-write, non-line-of-sight, two-photon photoelectrochemical etching technique for etching of single crystal silicon carbide substrates. The use of this technique has resulted in structuring of 3-dimensional structures in high quality single crystal silicon carbide wafers. The 3-dimensional structures demonstrated cannot be formed by any single or combination of traditional silicon carbide machining techniques. This thesis outlines the development of the optical, electrical, and diagnostic components required to achieve two-photon photoelectrochemical etching in silicon carbide. The diagnostic sub-assemblies --a single pixel confocal detector assembly and an in-situ optical microscope assembly-- and their design is also discussed. Several etched structures using the two-photon photoelectrochemical etching technique are presented.

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In this thesis, advanced spectroscopy methods are discussed and applied to gain understanding of the physical properties of organic conjugated molecules, II-VI thin film semiconductors, and vertical cavity surface emitting lasers (VCSEL). Experiments include single photon and two-photon excitation with lasers, with subsequent measurements of the absorption and photoluminescence, as well as photocurrent measurements using tungsten and xenon lamps, measuring the direct current and the alternating current of the devices. The materials are investigated in dissolved form (conjugated polymers), thin films (polymers, II-VI semiconductors), and complex layer structures (hybrid device, VCSEL). The experiments are analyzed and interpreted by newly developed or applied theories for two-photon saturation processes in semiconductors, bandgap shrinkage due to optically induced electron hole pairs, and the principle of detailed balance to describe the photoluminescence in thin film cadmium sulfide. / Ph. D.

As the boundaries of Moore's Law rapidly approach, research is increasingly turning to exotic materials and metamaterials to advance the capabilities of electronic and micromechanical systems. This thesis presents systems, models, and simulation techniques for novel microfabrication in the realms of silicon carbide (SiC) and metal mesh filters. Through the unification of femtosecond laser pulses, high numerical aperture (NA) objective lenses, and system power and motion control, a system capable of achieving arbitrary 3D features without line-of-sight with aspect ratios up to 109:1 in SiC is developed. Additionally, a model of a direct-write femtosecond-laser-ablation fabricated metal mesh filter (MMF) is simulated in ANSYS High Frequency Structure Simulator (HFSS) and validates the novel fabrication technique. Finally, a transmission-line-theory based MMF model is presented as an alternative to modelling multilayer filters in HFSS. This model produces comparable results to an HFSS simulation with dramatically reduced computational intensity.

Les groupes protecteurs photolabile (GPP) ont été largement utilisés en synthèse organique et pour des applications biologiques. Parmi la grande diversité de ces groupes, les groupement o-nitrobenzyl sont les plus utilisés. En particulier, ils ont été abondamment employés dans la préparation de nombreux précurseurs photolabiles d’effecteurs biologiques. Ce qui permet d’utiliser une réaction photochimique afin de transformer un composé biologiquement inerte en composé actif avec formation d’un sous-produit de photolyse. Afin de pouvoir quantifier le saut de concentration de l’effecteur biologique en particulier sur des cellules, nous avons développé des nouveaux GPP dérivés d’o-nitrobenzyle, qui libère un sous-produit de photolyse présentant des propriétés de fluorescence. Ainsi en nous basant sur le mécanisme de photolyse de dérivés o-nitrobenzyl sensible à l’excitation bi-photonique, nous avons pu concevoir un GPP non-fluorescent qui libère un fluorophore après photoclivage. Les propriétés de fluorescence du sous-produit de photolyse ont également été optimisées. Enfin à l’aide de ces PPG pro-fluorescent nous avons pu valider que la réaction photolytique peut être suivie par microscopie de fluorescence sur des cellules en culture. / Photoremovable Protecting Groups (PPG) have been widely used in organic synthesis and in various biological applications. Among the wide diversity of these groups, o-nitrobenzyl groups are the mostly used chromophores. In particular, they have been extensively used for the design of caged compounds. Those latter type of compounds are able to release a biological effector together with an uncaging side-product leading to the spatiotemporal control of various biological processes. In order to acutely monitor the uncaging event for example in cells, we developed new PPGs, based on o-nitrobenzylderivatives, able to release a fluorescent side product. Based on the photolytical mechanism of two-photon sensitive o-nitrobenzyl PPGs, we were able to design new non-fluorescent PPGs able to release fluorophores as side products. We were also able to tune the fluorescent properties of the photo-released by product using molecular engineering. Finally, those pro-fluorescent PPGs have been used in order to follow the uncaging events by fluorescent microscopy on cell cultures.