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Ch1 The X-ray structural determinations of the neutral 1',2',1'",2'"-tetranaphthylmethyl- and the 1', 3', 1', 3'-tetranaphthylmethyl- biferrocenium triiodide have been determined. Our Mossbauer measurement for 1.34 and 1.35 indicate that the intramolecular electron transfer rates are quite sensitive to the environmental perturbations caused by the grinding of the sample. An interesting finding is that the Mossbauer results indicate that the unground diffusing sample of 1.34 is valence delocalized on the Mossbauer time scale above 180K. However, the ground diffusing sample of 1.34 exhibits a Mossbauer spectrum characteristic of a valence-trapped cation which remains valence-trapped electronic state at 300K. The effects of grinding of samples are also observed in the EPR and XRD measurements. Ch2 A great deal of research has concentrated on long range electron and energy transport in transition metal- based system and conducting polymer. We have synthesis a new bis-terpyridine bridging ligand (2.40) which the spacer is biferrocene moiety. Incorporating of the Ruthenium (II) subunits via redox-active spacer group promote to construction polynuclear transition metal complexes (i.e. multicomponent system). Cyclic voltammetric analysis indicated that there are Fe-Fe electronic coupling in the bridging ligand, and the degree of Fe-Ru electronic coupling is weak. In addition to dominant UV absorption near 240 and 280 nm from terpyridinyl and MLCT absorption from Ru to terpyridine around 480 nm, the complexes containing ferrocene or biferrocene as endgroup exhibit an unusual absorption band around 560 nm which is due to a feccocene moiety to terpyridine MLCT transition.

Molecular recognition exploiting non-covalent interactions mediates the structure and function of many critical biological and synthetic molecules. There has thus been continuing and intense efforts in the design and synthesis of supramolecular systems with the capability of recognizing specific chemical species. Among various guest species, Prof. Sessler's group has been focused on the study of artificial anion receptors. Calix[4]pyrrole is a tetrapyrrolic macrocycle that is capable of binding anions via concerted and directional hydrogen bonding. Recently, a tetrathiafulvalene (TTF) functionalized calix[4]pyrrole (TTF-C4P) was synthesized and studied as a receptor for various guest species such as anions, electron deficient guest species, and C₆₀. This dissertation focuses on the recent discovery in supramolecular chemistry of TTF-calix[4]pyrrole derivatives. Chapter 1 provides a brief overview of the historical perspective, redox properties, and uses of TTF derivatives as functional building blocks for supramolecular assemblies, as well as previous findings involving the supramolecular chemistry of TTF-C4P. Chapter 2, as the major focus of this dissertation, describes ion mediated supramolecular and reversible electron transfer processes between TTF-C4P and bisimidazolium salts (BIQ²⁺2X⁻). We discovered that the electron transfer processes between these redox couples could be controlled reversibly by ion binding. Specifically, we found that anion binding to the TTF-C4P receptor promotes the forward ET processes. In contrast, cation complexation to the cavity of TTF-C4P causes the reverse ET processes. Such ion mediated ET processes play an essential role in biological ET systems including photosynthesis and respirations. These reversible ET processes were mapped out by spectroscopic (¹H-NMR, UV-Vis NIR titrations, and EPR analysis) and X-ray single crystallographic analyses of both the intermediate and products. Chapter 3 describes the synthesis of aromatic (thiophene and benzene) annulated TTF-calix[4]pyrroles as new and significantly improved receptors for poly-nitroexplosives. The resulting electronic modulations of the parent TTF-pyrrole structure result in significantly enhanced binding affinities for the corresponding TTF-C4Ps toward polynitro-explosives. This is reflected in a high level of positive homotropic allosterism. The degree of the cooperative effect was found to vary depending on the nature of both the receptors and guest species. The origin of the cooperative binding can be explained by conformational locking and an inductive effect of binding the first nitroaromatic guest. / text

Anion Binding has recently emerged as an important field of study due to the role these small inorganic species play in a plethora of biological processes. Chapter 1 of this thesis describes the biological relevance and scientific justifications for studying the ability of synthetic molecules to transport or extract anions under interfacial conditions. This chapter also serves to underscore the need to study both the thermodynamics and kinetics of anion binding as achieved using synthetic receptors. Methods for determining the thermodynamics of ion recognition are well-developed, and many equilibrium analyses of supramolecular binding events have been reported; however, the kinetics of such interactions are often neglected. Chapter 2 details the author's efforts to address this deficiency with respect to anion-binding and reports progress towards quantitative kinetic analyses of the interaction between cyclo[8]pyrrole (C8), an expanded porphyrin, and two test anions. It has been determined that stopped-flow analysis can provide on and off-rates, as well as activation parameters not accessible through thermodynamic means. Initial flash photolysis kinetic studies have also revealed that C8 has the potential to act as a photosensitizing agent through electron donation. This work is presented in Chapter 3, wherein the author discusses the construction of novel donor-acceptor dyads based on C8. As detailed in this chapter, time-resolved optical analyses have confirmed that photoinduced electron transfer occurs under conditions of photoexcitation and that the lifetime of the charge separated state is approximately 300 [mu]s. Finally, Chapter 4 describes a comprehensive set of spectroscopic work conducted by the author involving porphyrin and porphycenes that have a RuCp* (Cp*: pentamethylcyclopentadienyl) fragment either coordinated to the central porphyrinic core or directly attached to the "[pi]-face" of the macrocycle. These systems display unique intramolecular electron transfer properties that are ascribed to the metallated-porphyrin core acting as an electron acceptor, as opposed to a donor as is normally observed with porphyrins. / text

The number and types of diagnostic ions obtained by infrared multiphoton dissociation (IRMPD) and collision induced dissociation (CID) were evaluated for supercharged peptide ions created by electrospray ionization of solutions spiked with mnitrobenzyl alcohol. IRMPD of supercharged peptide ions increased the sequence coverage compared to that obtained by CID for all charge states investigated. Multiply charged, N-terminally derivatized peptides were subjected to electron transfer reactions to produce singly charged, radical species. Upon subsequent “soft” CID, highly abundant z-type ions were formed nearly exclusively, which yielded simplified fragmentation patterns amenable to de novo sequencing methods. Furthermore, the simplified series of z ions were shown to retain labile phosphoric acid moieties. Infrared multiphoton dissociation (IRMPD) was implemented in a novel dual pressure linear ion trap for rapid “top-down” proteomics. Due to secondary dissociation, IRMPD yielded product ions in significantly lower charge states as compared to CID, thus facilitating more accurate mass identification and streamlining product ion assignment. This outcome was especially useful for database searching of larger proteins (~29 kDa) as IRMPD substantially improved protein identification and scoring confidence. Also, IRMPD showed an increased selectivity towards backbone cleavages N-terminal to proline and C-terminal to acidic residues (especially for the lowest precursor charge states). Ultraviolet photodissociation (UVPD) at 193 nm was implemented on a linear ion trap mass spectrometer for high-throughput proteomic workflows. Upon irradiation by a single 5 ns laser pulse, efficient photodissociation of tryptic peptides was achieved with production of a, b, c, x, y, and z sequence ions, in addition to immonium ions and v and w side-chain loss ions. The factors that influence the UVPD mass spectra and subsequent in silico database searching via SEQUEST were evaluated. 193 nm ultraviolet photodissociation (UVPD) was employed to sequence singly and multiply charged peptide anions. Upon dissociation by this method, a-/x-type, followed by d and w side-chain loss ions, were the most prolific and abundant sequence ions, often yielding 100% sequence coverage. LC-MS/UVPD analysis using high pH mobile phases yielded efficient characterization of acidic peptides from mitogen-activated protein kinases. / text

The overall efficiency of organic photovoltaics cells (OPVs) is influenced by the nature of the charge injection barrier at the transparent conducting oxide (TCO) bottom contact. Modification of the transparent conducting oxide (TCO)/organic interface with an electroactive molecular monolayer will potentially create a robust ohmic contact that will influence the efficiency of hole injection into the TCO. Asymmetric zinc Phthalocyanines (ZnPc) with a flexible phosphonic acid (PA) linker have been synthesized and used to modify indium tin oxide (ITO) surfaces. The adsorption of PA functionalized asymmetric ZnPcs on an ITO/waveguide was monitored using attenuated total reflectance (ATR) spectroscopy. Polarized dependent ATR spectroscopy was used to determine the orientation of these absorbed subpopulations species on ITO modified surfaces as a function of wavelength using transverse electric (TE) or transverse magnetic (TM) polarized light. The first oxidation potential on absorbed monolayers was found by cyclic voltammetry to be resolved into two peaks indicative of two electrochemically distinct subpopulations of molecules, atributed to aggregates and monomerics forms of PA functionalized ZnPcs. Potential modulated ATR (PM-ATR) spectroelechtrochemistry was employed to measure the charge transfer rates constants (k(s,app)) at ITO modified surfaces using TE and TM polarized light. Faster charge transfer rate constants were found for molecules with a smaller tunneling distance. A k(s,app) of 3.9 x 10⁴ s⁻¹ represents the fastest rate measured for PA functionalized ZnPc chromophore tethered to an ITO waveguide electrode by PM-ATR. We synthesized and characterized the first examples of PA functionalized RuPcs to investigate the effect of molecular orientation on charge transfer properties at an ITO/organic interface. PA functionalized RuPcs have the ability to coordinate axial ligand to suppress aggregation, providing the flexibility of connecting the anchoring group through the axial position of the metal and allowing chemisorption of the molecule in plane with ITO. Cyclic voltammetry and ATR UV/vis spectroscopy on the modified ITO surface demonstrated a surface composition of a closed-packed monolayer of monomeric species. Measurement of the charge transfer rates constants demonstrated that RuPc anchored to ITO exhibited slow rates compared to corresponding surface bound ZnPcs. Finally, we describe the synthesis and characterization of a new PA functionalized N-pyridinyl perylenediimide (PDI)-RuPc donor-acceptor dyad capable of chemisorption to ITO surfaces as a molecular-level heterojunction system to study photo induced charge separated states. The developed ensemble was proven to be stable on ITO for further study of charge injection events from the dyad to the oxide surface.

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