Analytical chemistry is a metrological science that develops, optimizes and applies analytical measurements in order to solve complex problems and to facilitate educated and effective decision-making processes. Throughout the history of science, analytical chemists have expanded the field beyond routine characterization of the compositions samples into a much broader discipline through the development of new analytical methods for scientific advances, improvement upon established methods, and extension of existing methods to completely new sample types. In addition, many aspects of analytical chemistry have evolved through time, such as analytical instruments, reagents, detection limits, dimensions of analytical information, and the more recent introduction of mathematical models, computer science, and big data into chemical analyses. Regardless of these evolutions, the fundamental principle of analytical chemistry, that is, to use analytical measurements as universal vehicles to obtain information, persists throughout the history of analytical chemistry. This dissertation introduces a three-step "analytical chemistry approach" to solve scientific problems based on the fundamental principle of analytical chemistry. The three steps include: (1) frame a research question; (2) identify analytical method(s) that can acquire data to answer the research question; (3) use the analytical method(s) to obtain data and answer the research question. This dissertation demonstrated the remarkable versatility of the analytical chemistry approach by applying it to solve a wide spectrum of scientific problems, ranging from bioorthogonal catalysis with therapeutics and diagnostics applications to soil organic carbon characterization with fundamental impacts on the global carbon cycle, highlighting the paramount importance of analytical chemistry in solving problems and advancing science. Chapter 1 is an introduction to analytical chemistry, the evolution of the field, and the three-step analytical chemistry approach used throughout this dissertation. Chapter 2 showed how the analytical chemistry approach was used to develop a general method to evaluate metal-catalyzed reactions in living systems. In this chapter, a Ru-based bioorthogonal pre-catalyst was used to activates a caged aminoluciferin probe in cellular environments. Upon catalytic cleavage, the activated aminoluciferin is turned over by its target enzyme, luciferase, in cells to produce a bioluminescence readout. With the ability to amplify and/or target imaging readouts, this system opens up many new opportunities in research, imaging, diagnostics, and therapy. By using the three-step analytical chemistry approach, key factors that affect product distribution for the catalytic reaction was found, and the location of that the catalytic reaction was identified to be extracellular. Chapter 3 and Chapter 4 of this dissertation demonstrated the versatilely of the analytical chemistry approach by shifting focus from bioorthogonal catalysis to soil organic carbon. In Chapter 3, the analytical chemistry approach was applied to develop the SOC-fga method, which combines Fourier-transform infrared spectroscopy (FT-IR) and bulk carbon X-ray absorption spectroscopy (XAS) to quantitatively characterize the compositions of soil organic carbon (SOC) across a subalpine watershed in East River, CO, without going through traditional alkaline extractions and chemical treatments that alter SOC compositions. A large degree of variability in SOC functional group abundances was observed between sites at different elevations. The ability to identify the composition of organic carbon in soils quantitatively across biological and environmental gradients will greatly enhance our ability to resolve the underlying controls on SOC turnover and stabilization. Chapter 4 built on the findings of Chapter 3 to further evaluate the SOC-fga method with density fractionation and cross polarization/magic angle spinning (CP/MAS) 13C NMR spectroscopy. This chapter summarized the strengths and weaknesses of the SOC-fga method and 13C NMR and set up a platform to launch future work on SOC turnover mechanisms. Finally, Chapter 5 concluded this dissertation with summaries of findings, future directions, and ending remarks on analytical chemistry.

The ability of organic chemists to design and synthesize functional molecules has revolutionized the ways in which we can probe biological systems. From catalysts capable of releasing bioactive molecules from bioinactive precursors to oligomers that enable or enhance the uptake of molecules across cell membrane and cell wall barriers, the work described herein emphasizes the power of designing for function. These new tools allow for control over the location of many biologically relevant molecules, including drugs, probes, imaging agents, metabolic modulators, and pesticides, with ramifications for a variety of biochemical, agricultural, and medicinal applications. Chapter 1 reviews the development of selective catalysts designed for use in biological systems. The catalysts have primarily been used for bioconjugations, expanding the classical repertoire of bioconjugation techniques to allow for selective chemistries at many more functional groups than was traditionally possible. Emerging strategies for imaging in biological systems using transition metal catalysis are also reviewed, as are transition metal-based catalytic therapeutics. The synthesis and evaluation of a novel bioorthogonal ruthenium catalyst designed for release of biologically active molecules from inactive precursors is the focus of Chapter 2. Although the challenges associated with using transition metals in biological systems are apparent, creative design ultimately led to the development of a useful bioorthogonal catalyst / substrate pair. This system allows for real-time visualization of transition metal catalysis to generate a biologically active compound that releases photons when it encounters its intracellular enzyme target. Chapters 3 and 4 detail the synthesis and application of molecular transporter scaffolds. Chapter 3 introduces a novel organocatalytic ring-opening oligomerization of guanidinylated cyclic carbonates to access molecular transporter scaffolds in 1 step. This strategy allows for rapid access to molecular transporters of varying lengths. In addition, the synthesis allows for concomitant probe or drug attachment and the carbonate-based backbones of the resulting transporters are biodegradable on a timescale allowing for cellular uptake and intracellular degradation. The ability of molecular transporters to cross not only cell membranes, but also cell walls, is discussed in Chapter 4. These studies focused on the delivery of small molecules and proteins across the algal cell wall and cell membrane barriers using D-octaarginine-based molecular transporters. With this method, it was shown that fluorescein-octaarginine conjugates were able to cross these barriers in a variety of algal species from the class Chlorophyceae, although several species showed no uptake or only cell surface staining. It was also shown in the algal model organism Chlamydomonas reinhardtii that octaarginine-protein conjugates could cross the cell wall and cell membrane barriers to deliver a functional protein to the intracellular algal space.

Using transition metal catalysis to rapidly increase complexity for the construction of small molecules has been one of the most important areas of research in the field of synthetic organic chemistry. In particular, cyclopentadienylruthenium (CpRu) catalysis has previously been shown by our research group and others to be a selective, cost-effective, and atom-economical means of achieving this goal. In an effort to extend CpRu catalysis to enantioselective variants of these reactions, our group had previously developed CpRu complexes containing tethered chiral sulfoxides for their successful application towards asymmetric allylic substitution reactions. This work describes our efforts to expand the chemistry of these CpRu-sulfoxide complexes and to synthesize novel chiral CpRu and indenylruthenium (IndRu) catalysts for the discovery of new catalytic asymmetric cyclization reactions. CpRu-sulfoxide complexes were used to perform an asymmetric redox bicycloisomerization reaction that constructed [3.1.0] and [4.1.0] bicycles from propargyl alcohols. Initial reaction optimization was performed on 1,7-enynes due to the products' similarity to known triple-reuptake inhibitor GSK1360707. CpRu complex containing a tethered para-methoxy sulfoxide ligand proved to be the optimal catalyst for this reaction. Variation of the 1,7-enyne substrate structure revealed that a bulky 2,4,6-triisopropylbenzenesulfonyl (Tris) protecting group on the nitrogen-containing backbone was essential for observing high enantioselectivities for [4.1.0] bicycles. While THF proved to be the optimal solvent for redox isomerization of [4.1.0] bicycles, acetone provided the best results for [3.1.0] bicycles. Enantiomeric ratios as high as 98.5:1.5 were observed with Tris-containing [3.1.0] bicycles. The chemistry could be extended to 1,6-enynes containing other substrate tethers, including tosyl, diphenyl phosphoramidate, and dibenzyl malonate tethers. Nitrogen protecting groups were shown to be removable under reducing conditions. Catalysis performed with enantiomerically enriched propargyl alcohols revealed a matched/mismatched effect that was strongly dependent on the nature of the solvent. To the best of our knowledge, this methodology was the first example of a ruthenium-catalyzed asymmetric cycloisomerization reaction. Unfortunately, CpRu-sulfoxide complexes were shown to be inefficient and poorly selective catalysts for the enyne cycloisomerization and redox isomerization/C-H insertion reactions. We hypothesized that either the bound sulfoxide ligand was too electron-rich or that the catalyst had an insufficient number of coordination sites available for catalysis. In order to test our hypothesis, we synthesized CpRu complexes that contained more electron-withdrawing S-chiral ligands. While chiral sulfimide- and sulfinamide-containing complexes could promote enyne cycloisomerization, these catalysts were poorly enantioselective. These results led us to believe that the ligands were too weakly ligated to the metal center and decomplexed under the reaction conditions. Novel coordinatively unsaturated chiral indenylruthenium complexes with a tethered chiral sulfoxide were designed and synthesized. Enantiomeric ratios of up to 75:25 for enyne cycloisomerization and 84:16 for enyne hydroxycyclization could be obtained using these catalysts. When applied to the asymmetric redox isomerization/C-H insertion reaction, chiral indenylruthenium complexes could promote this reaction in up to 90:10 e.r.. The main disadvantage of using these tethered complexes is that they are not commercially available and must be made through multistep syntheses. We discovered that commercially available catalyst CpRu(MeCN)3PF6, when used in conjunction with a chiral phosphoramidite ligand, can perform an asymmetric interrupted metallo-ene reaction of (E)-allylic chlorides in excellent enantioselectivity. To our knowledge, this represents the first example of using CpRu-phosphoramidite complexes for a catalytic asymmetric transformation. The C1-symmetry and 3,3'-substitution on the BINOL-based phosphoramidite were key to the high levels of enantioinduction observed. Carbocyclic and heterocyclic 5- and 6-membered rings could be constructed in > 20:1 d.r. and up to 99:1 e.r.. As a demonstration of the utility of this methodology, diastereoselective Friedel-Crafts reactions were performed on the chiral benzylic alcohol products that were observed to proceed with retention of configuration.

Polyesters are a remarkable class of polymeric materials that have been featured as biodegradable textiles, implantable biomedical devices, and drug delivery vehicles for therapeutic applications. However, the synthesis of polyesters with rich functional group diversity, narrow molecular weight distributions and targeted molecular weighs remains a significant challenge. The selective aerobic oxidation of 1,5-diols with [(neocuproine)Pd(OAc)]2(OTf)2 (neocuproine = 1,9-dimethylphenanthroline), A, yields cyclic lactones. A selection of functionalized 1,5-diols was investigated to explore the substrate scope and to determine compatible functional groups for the oxidative lactonization reaction using A. These studies led a general strategy for the synthesis of functionalized lactones, specifically N-substituted morpholin-2-ones. The organocatalytic ring-opening polymerization of N-acyl morpholin-2-ones occurs readily to generate functionalized poly(aminoesters) with N-acylated amines in the polyester backbone. The thermodynamics of the ring-opening polymerization depends sensitively on the hybridization of the nitrogen of the heterocyclic lactone. N-Acyl morpholin-2-ones polymerize readily to generate polymorpholinones, but the N-aryl or N-alkyl substituted morpholin-2-ones do not polymerize. Experimental and theoretical studies reveal that the thermodynamics of ring opening correlates to the degree of pyramidalization of the endocyclic N-atom. A wide range of novel polyesters was synthesized. Deprotection of the N-Boc protected polyaminoesters yields water-soluble, cationic materials. Three novel cationic water-soluble polyaminoesters (PAEs) were synthesized. These materials were shown to be stable in neutral D2O for over two days, however, upon exposure to alkaline or buffered conditions, two of the PAEs degraded rapidly and quantitatively to single small molecule products. An immolative mechanism is proposed to account for the exquisite selectivity of the observed in the controlled degradation. The rate of degradation is sensitive to pH, providing a new class of water-soluble materials which can be induced to degrade under specific environmental conditions.

Hydrogen peroxide (H2O2) is a highly valuable chemical with wide range of applications in industry such as paper bleaching, textile manufacturing and environmental protection. Currently, the industrial synthesis of H2O2 is through an energy intensive anthraquinone process, which requires large-scale and complex infrastructure. Electrochemical synthesis of H2O2 from oxygen reduction offers an attractive alternative route for onsite applications, while the efficiency of this process greatly depends on identifying cost-effective catalysts with high activity and selectivity. As several classes of catalysts have been reported or proposed by theory to be good candidates of the targeted reaction, here we focus our attention upon a metal-organic framework (MOF) and high-performance carbon catalysts for the perspective of both fundamental understanding and the high cost-efficiency. Catalytic systems whose properties can be systematically tuned via changes in synthesis conditions are highly desirable for applications in catalyst design and optimization, namely, the 2D conductive metal--organic framework (MOF) with M-N4 units (M = Ni, Cu) and a hexaaminobenzene (HAB) linker as a catalyst for the oxygen reduction reaction (ORR). By varying synthetic conditions, we synthesized two Ni-HAB catalysts with different crystallinities, resulting in a catalytic system with variable electrical conductivity, electrochemical activity and stability. We show that crystallinity has a positive impact on conductivity and demonstrate that this improved crystallinity/conductivity improves the ORR performance of our model system.

An opportunity exists to utilize both methane and wastewater as a source of chemical intermediates, monomers and polymers. This work describes methods that combine molecular synthesis and catalysis with synthetic biology to generate new sustainable materials. The aims of the work are twofold: 1. to develop strategies for poly(hydroxyalkanoate) (PHA) production by methanotrophic bacteria (Chapters 2-4), and 2. to use PHAs as an essentially renewable resource for the production of new chemicals and materials (Chapters 5-6). To meet these aims, studies in four key project areas will be described: (A) the use of new substrates for PHA production in methanotrophs, (B) a combined chemical--biological approach for medium to short chain-length PHA recycling, (C) 2-alkenoate dimerization chemistry, and (D) the synthesis of new materials from 2-alkenoates. PHAs are sustainable alternatives to non-biodegradable petroleum-based plastics, and can be microbially produced by certain types of either heterotrophic or methanotrophic bacteria. Prior to the commencement of this work, obligate methanotrophs capable of producing PHAs under nutrient-limited conditions were limited to the synthesis of poly(3-hydroxybutyrate) (P3HB). Diversifying the range of PHAs available from methanotrophs would greatly expand the range of PHA applications. Chapter 2 reports the first pure culture evidence of methanotrophic synthesis of poly(3-hydroxybutyrate-co-3-hydroxyvalerate) (P(3HB-co-3HV), often abbreviated to PHBV). When grown with methane as sole substrate, the Type II obligate methanotroph Methylocystis parvus OBBP produces P3HB, but not PHBV, under nutrient-limiting conditions. However, when strain OBBP was incubated with C1 substrates (methane, methanol, or formate) and a propionate or valerate co-substrate, synthesis of PHBV was observed. PHBV production was confirmed by gas chromatography, gel permeation chromatography, differential scanning calorimetry, and nuclear magnetic resonance with [13C1]-valerate. Chapter 3 describes further expansion of the range of PHAs available from obligate methanotrophs: by incorporating ω-hydroxyacid co-substrates under nutrient-limiting conditions, poly(3-hydroxybutyrate-co-4-hydroxybutyrate), poly(3-hydroxybutyrate-co-5-hydroxvalerate-co-3-hydroxyvalerate) and poly(3-hydroxybutyrate-co-6-hydroxcaproate-co-4-hydroxybutyrate) can be formed. For any polymer, end-of-life issues are important considerations. Medium chain-length PHAs are emerging products in the PHA market, and Chapter 4 demonstrates that these PHAs can be selectively depolymerized to their constituent monomers through base-catalyzed pyrolysis. The pyrolysis products can be fed back to the methanotrophic bacteria as a co-substrate with methane to recycle the products into short chain-length PHAs. Labeling studies have shed light on the mechanism of the incorporation of these pyrolysis products in methanotrophs. Chapter 5 considers synthetic chemistry that can be done with the products of PHA pyrolysis, namely 2-alkenoic acids. The simplest 3-alkyl-alk-2-enoic is crotonic acid, produced via P3HB depolymerization, but making chemical intermediates and materials using crotonates is a fundamental challenge in chemistry. Chapter 5 details a mild and rapid dimerization of 2-alkenoates to produce new monomers that can be used in novel step-growth polymerizations. Chapter 6 exploits this dimerization strategy to create novel organogels and polymers, and also details attempts at polymerizing crotonates.

The electricity derived from renewable energy sources (e.g. solar, wind) is intermittent and not perfectly matched with consumer demand. The widespread adoption of these renewable energy sources as a replacement for fossil fuels subsequently depends upon the development of energy storage systems. Homogeneous electrocatalysts are promising energy storage systems as they can mediate the efficient interconversion of electrical and chemical energy in a highly tuneable fashion. In this thesis, various electrochemical and spectroscopic studies have been conducted in order to improve homogeneous electrocatalysts along various metrics of activity (i.e. turnover frequency, overpotential), selectivity (i.e. Faradaic efficiency), and stability. Chapter 1 reviews the electrochemical and spectroscopic techniques used to assess homogeneous electrocatalysts; highlights the key metrics by which electrocatalysts are evaluated; and provides selected examples of homogeneous electroreduction and electrooxidation catalysts relevant to the work presented in this thesis. Chapter 2 examines the reactivity of a cyclopentadienyl Co complex bearing a protonated phenylazopyridine ligand towards proton, hydride, and hydrogen atom transfer. Chapter 3 uses Co K-edge X-ray absorption spectroscopy (XAS), extended X-ray absorption fine structure (EXAFS), density functional theory (DFT), and time-dependent DFT methods to investigate the effect that various bidentate ligands have on the electrochemical and protonation properties of cyclopentadienyl Co complexes. Chapter 4 uses Mn K-edge XAS, Mn-Kβ X-ray emission spectroscopy (XES), and DFT to understand the impact that redox active ligands have on the electrochemical properties and speciation of Mn tricarbonyl complexes. Chapter 5 examines the ability of an electrochemically regenerable hydrogen atom transfer reagent to lower the overpotential of electrocatalytic alcohol oxidation. Chapter 6 investigates the use of an Fe-based acceptorless alcohol dehydrogenation catalyst for the electrooxidation of alcohols. Chapter 7 examines the factors that mediate demographic performance gaps and the impact that various pedagogical changes have had on student performance in the introductory chemistry sequence.

N-Glycanase 1 (NGLY1) is the human cytosolic protein N-glycosidase. The relationship between NGLY1 and the transcription factor Nrf1 is examined, particularly observing cellular response to proteasomal stress in healthy, NGLY1 deficient, and cancer model systems using genetic and chemical tools. Additionally, the role of NGLY1 in innate immunological signaling and other stress-response pathways that are regulated by the ERAD pathway is explored. Finally, the further development of the Quadricyclane (QC) ligation, a bioorthogonal reaction between QC and nickel bis(dithiolene) is described.

The chemoselective oxidation of vicinal diols to [Alpha]-hydroxyketones is a challenge in organic syntheses because not only does the diol need to be oxidized selectively to a monocarbonyl compound, but diols are also prone to overoxidation and oxidative cleavage. Employing a cationic palladium complex, [(neocuproine)Pd(OAc)]2(OTf)2, we were able to demonstrate the selective oxidation of glycerol to dihydroxyacetone mediated by either benzoquinone or O2 as the terminal oxidant, an accomplishment that has little precedent in homogeneous catalysis. Mechanistic studies were undertaken to uncover the nature of this remarkable chemoselectivity. Kinetic and deuterium-labeling studies implicate reversible [Beta]-hydride elimination from isomeric Pd alkoxides and turnover-limiting displacement of the dihydroxyacetone product by benzoquinone. We successfully extended this methodology to other terminal 1,2-diols and symmetric vicinal 1,2-diols and have carried out aerobic oxidation of these substrates catalyzed by 1. Examination of the reactivity of 1 with conformationally-restricted 1,2-cyclohexanediols suggests that the diol must chelate to the Pd center for effective oxidation to the hydroxyketone product. In a separate project, we have also investigated the electrocatalytic reduction of dioxygen by several dinuclear copper complexes, an important reaction for fuel cell applications.

Polymer organic solar cells (OSCs) possess many desirable properties include low temperature solution processibility of photoactive materials and the utilization of flexible substrates for conformal OSC design. However, challenges remain that may inhibit their adoption and implementation. Among these are thermochemical stability, optimized power conversion efficiency, and mechanical reliability. Indeed, for organic solar cells to be used on flexible substrates, mechanical reliability of the individual layers and interfaces is pertinent. In this dissertation, quantitative micromechanical testing techniques were employed to help characterize the mechanical reliability of the layers and interfaces for polymer OSCs. From testing, it was determined that the polymer:fullerene photoactive layer consistently failed cohesively. The cohesive strength of most photoactive layers generally ranged from 0.5 to 2.0 Joules per square meter. However, by using thermal annealing, manipulating the photoactive layer structure, and selecting polymer molecular weight, cohesion values as high as 17 Joules per square meter could be achieved. Indeed, polymer molecular weight affected cohesion the most due to significant plasticity within the photoactive layer. Conversely, improved cohesion did not always result in improved device electronic performance. By optimizing cohesion and efficiency, we are able to come closer to design guidelines for mechanically robust and efficient solar cells. Finally, because OSCs must operate in the environment at temperatures as high as 65 C, we analyzed OSCs under dry, inert environmental conditions and showed how temperature affects the decohesion kinetics within the device. It was demonstrated that the decohesion rate generally accelerated with increasing test temperature. We were able to develop a viscoelastic kinetic model that was able to describe and predict decohesion for these devices. This collective work and modeling will provide greater insight into the practical limitations of OSC design and will aid in future development of OSCs with greater mechanical reliability and in-service lifetimes.

Despite numerous advances in metal ion sensor design, it is still difficult, slow and laborious to rationally design, synthesize and optimize selective sensors for each individual metal ion for a wide variety of metal cations. In order to develop an approach to rapidly generate sensors for many different metal cations, a new molecular sensor design strategy based on DNA-like oligomers (oligodeoxyfluorosides or ODFs) was investigated. The ODF-based design incorporates fluorophores and metal ligands onto the DNA backbone, allowing the binding and reporting moieties to interact intimately by bringing them into direct contact by pi-pi stacking, analogous to the stacking of DNA bases. The highly modular molecular design allows for water solubility and enables rapid synthesis and discovery of sensors from combinatorial libraries. Using the ODF-based sensor design and a combinatorial library approach, a wide variety of metal ion sensors were discovered for many different metal cations. A selective ODF sensor for silver ions that functions similarly to the more classical type of metal ion sensors was discovered employing this approach. In addition, ODF sensors that have diverse responses (such as fluorescence enhancement, quenching, and blue- and red-shifts) for a number of different metal cations were also discovered utilizing this sensor design strategy. Five water-soluble ODF sensors were identified to exhibit responses beyond simple fluorescence quenching to eight typically quenching metal cations. The diversity of sensor responses enable as few as two ODF sensors to be utilized to successfully differentiate all eight metal cations based on the response pattern of the sensors. The modular nature of this sensor design strategy suggests a broadly applicable approach to finding sensors for many different cations, simply by varying the sequence and composition of ligands and fluorophores using a DNA synthesizer.

Because of their capability of assembling hierarchically into stable ordered conformations, polypeptides grafted to a surface can demonstrate strikingly high electromechanical and electrooptical efficiency as well as reversible response to an external trigger, and thus show promise for applications such as biosensors and optical storage and display devices. Because of the intrinsic advantages of SI-VDP and the significant progress on SI-VDP optimization, this method has become the most effective approach to synthesize grafted polypeptides. However, high vacuum has been required to achieve high surface-grafting efficiency. Moreover, little quantitative study has been done to understand the mechanistic details of an SI-VDP process, more specifically, of its five major sub-processes: monomer vaporization and reservoir polymerization in the monomer reservoir and NCA condensation and physisorbed and chemisorbed polymerization on the substrate surface. Moreover, the resulting thick surface-grafted PBLGs could contain a significant amount of secondary structures other than helices, making a conventional method like ER-FTIR improper for orientation study. In this work, we developed an SI-VDP system with improved pressure and temperature control to achieve comparable high grafting efficiency under rough vacuum. For example, we synthesized 167 nm chemisorbed PBLG film under 0.75 mbar at substrate temperature of 90 °C and monomer heating temperature of 110°C with nitrogen purge. Most importantly, we monitored the amount of vaporized NCAs and developed a VDP reaction profile (VDPRP) method to study the major monomer reservoir processes. Meanwhile, we also developed a quantitative FTIR analysis of both as-deposited PBLG and chemisorbed PBLG films in addition to ellipsometric data to evaluate the major substrate surface processes. We observed the monomer-heating-temperature-determined unstable and stable paths of the reservoir processes, which were characterized by unstable VDPRPs with random pulses and by stable VDPRPs with two peaks, respectively, and proposed possible mechanisms. We also found that two peaks of stable VDPRPs can selectively track both reservoir processes in real time. For surface processes, we proposed possible mechanisms to obtain the surface-grafted PBLGs that have either high packing density with mostly [alpha]-helix segments or low packing density with a significant amount of both random coil and [alpha]-helix segments. Wang and Chang developed a method that they termed "solvent quenching", in which surface-grafted PBLG films are treated by a good solvent to stretch out the molecular chains followed by a poor solvent to "freeze" the orientation. However, based on their external reflection-FTIR measurement, Wang and Chang reported that their solvent quenching method could decrease the average tilt angle of a thick surface-grafted film from 49° to 3°. In this study, we select Wang and Chang's solvent quenching process as our model system to demonstrate how to apply the extended variable angle linear polarized transmission FTIR (VALP-TFTIR) method to study the change of complex secondary structures and orientation of a thick chemisorbed PBLG film by monitoring their change during solvent quenching. After the quenching, the apparent PBLG film thickness increased from 151 [plus-minus] 5 to 308 [plus-minus] 16 nm, while the refractive index decreased from 1.59 [plus-minus] 0.01 to 1.17 [plus-minus] 0.02, as measured by ellipsometry. Based on the VALP-TFTIR measurements, we found that a significant amount of amine acid repeating units in random coils coexisted with those in [alpha]-helices in the film before solvent quenching. After solvent quenching, the amount of amino acid repeating units in random coils became undetectable, while those in [alpha]-helices decreased 11%. However, the average tilt angle ‹[theta]› of [alpha]-helices remained at 40° during solvent quenching. In contrast to Wang and Chang, we propose that the significant increase of the quenched film thickness is due to flexible random coils transforming to much less flexible structures, such as aggregated strands, instead of the PBLG [alpha]-helix orientation changing.

Access to novel forms of (+)-saxitoxin (STX), a potent and selective inhibitor of voltage-gated sodium ion channels (NaV), has been made possible through de novo synthesis. Saxitoxin is believed to lodge in the outer mouth of the sodium channel pore, thereby stoppering ion flux. Saxitoxin and derivatives thereof represent high-precision pharmacological tools that can be used to gain insight into the structure and integrated cellular function of sodium channel proteins. The preparation and biological evaluation of N21-carbamoyl-modified saxitoxins are described herein. The synthesis plan for assembling these molecules features a robust sequence that enables the preparation of gram quantities of a key nine-membered ring guanidine intermediate. Transformation of this advanced intermediate into a strained 5,6,5-fused tricycle through four-electron olefin oxidation affords an amine-reactive oxazolidinone from which all N21-modified saxitoxins are available. The potencies of STX and all analogous structures have been determined using heterologous gene expression and voltage clamp electrophysiology. These studies show that various N21 substituents are readily accommodated in the STX binding site of the protein with little loss of ligand-receptor binding affinity. This discovery has allowed for the design of photoaffinity and fluorescently labeled saxitoxins, which will serve to further our understanding of the architecture of the STX binding site, and represent a novel set of molecular probes that make possible real-time, live cell investigations of NaV function. Studies utilizing analogues of the pore blocker, saxitoxin, were complimented by an investigation of the aconine alkaloid, aconitine, a known Site II modifier of NaV function. A semi-synthetic pathway used to access derivatives of aconitine is detailed, along with an electrophysiological analysis of the ability of these derivatives to modify the conductive properties of the sodium channel.

The increasing levels of CO2 in the atmosphere from the electricity and transportation sectors around the world is having adverse and irreversible effects on the fragile ecosystem of our planet. The problem will only get worse as the world's population continues to rise in the next few decades, straining our natural resources with increased demand for food, energy and water. The transition of the energy sector from being coal and natural gas-fired to renewable source of energy, such as wind and solar, will play a pivotal role in mitigating further climate change. Such a transition is already under way, as solar and wind energy technologies have become cheaper alternatives to coal. However, the total penetration of renewable sources in the global energy mix has yet to reach even double digit percentages. A potential game-changer in this arena is cheap and efficient renewable energy storage. Because of the intermittency of wind and solar energy, the excess energy produced by these sources must be reversibly stored. Pumped-hydro storage currently dominates this arena globally. This form of storage, however, suffers from low energy density and limited geographic deployment. Electrochemical energy storage is an attractive solution to this problem due to high theoretical efficiencies and high energy density of the products of electrochemical processes. Using excess electricity to convert readily available substrates such as CO2 into energy-dense fuels represents an attractive solution to grid-scale energy storage for extended times, while mitigating CO2 release into the atmosphere. Practical implementation of these ideas, however, faces four key limitations: (1) the high cost of materials used, (2) high overpotentials resulting in low energy efficiencies, (3) low selectivity for specific products, and (4) sluggish kinetics. Therefore, one of the grand challenges for chemists and chemical engineers is the development of active, earth-abundant catalysts for the reversible and selective electrocatalytic interconversion of small molecules such as H2, O2, CO2 and N2 into useful energy-dense products. My thesis has focused on developing earth-abundant molecular electrocatalysts for the two-electron, one-proton reduction of CO2 to formate. Formate can be subsequently protonated to formic acid, which is a high-value chemical and, effectively, a liquid H2 carrier. Transition metal complexes are attractive targets to catalyze this process, as the thermodynamics and kinetics of substrate binding, catalytic intermediates and electron transfer can be tuned with great control. Based on precedent from literature, the most promising pathway to formate from CO2 is a two-electron reduction of the metal complex followed by protonation at the metal center to form a transition metal hydride complex. CO2 insertion into the metal hydride bond produces a metal-bound formate. Dissociation of the formate ligand then regenerates the starting complex and completes the catalytic cycle. The metal hydride can also be protonated in a shunt pathway to H2, if the energetics permit. Additionally, the doubly reduced metal complex can bind CO2 directly, leading to de-oxygenation by another equivalent of CO2 and the subsequent production of CO. Chapters 2 through 5 describe comprehensive mechanistic studies of each of the catalytic steps described above, aimed at identifying key aspects of transition metal coordination environments that render each step towards the desired product ergoneutral. Chapter 2 describes the thermodynamics and kinetics of CO2 insertion into the Ru-H bond of a fast transfer hydrogenation catalyst that can reversibly hydrogenate ketones. In contrast to ketone insertion, CO2 insertion was too exergonic, producing a Ru-formate that traps the catalyst. Through in-silico ligand modifications using density functional theory (DFT), this work highlighted the importance of thermodynamic cis and trans influences in an octahedral coordination environment in leveling the free energy of the Ru-formate intermediate relative to the Ru-hydride intermediate. For transition metal complexes that catalyze H2 evolution from protons and electrons, it is often desirable to generate a metal hydride via an ECE pathway (E denotes a one-electron reduction, C denotes protonation) to reduce the overpotential associated with successive electrochemical reductions (EEC). Through my work with an air-stable Ni hydride complex, described in chapter 3, I showed that the ECE pathway is unsuitable for CO2 reduction because the intermediary open-shell hydride (generated after the EC step) will rapidly disproportionate to produce H2. Having established that EEC is the only viable mechanism for the production of the metal hydride intermediate, metal complexes must have a low electrostatic barrier for the second electrochemical reduction step. In chapter 4, I use DFT to show how a redox-active ligand, phenylazopyridine, in a cyclopentadienyl Co(III) complex makes the complex undergo a single-step two-electron reduction, akin to those known for Ir(III) and Rh(III) complexes, made possible by metal-ligand covalency in the singly-reduced state. Motivated by in-silico predictions of ergoneutral CO2 insertion in the metal hydride intermediate, I synthesized a cyclopentadienyl Ru-bipyridine complex. However, the complex binds CO2 at the Ru center after a single-electron bipyridine-based reduction leading, after subsequent reduction and deoxygenation, to a Ru-bound CO intermediate, which was found to be a thermodynamic trap under these conditions. Using simulations of the cyclic voltammograms and DFT, the rate constant of CO2 binding after one-electron reduction was found to be on the order of 10^5 M-1 s-1, and the Ru-CO intermediate was found to be downhill by ca. 24 kcal/mol relative to the parent solvato complex. The results of this work, described in chapter 5, highlight the importance of considering the relative energetics of both on-path as well as off-path catalytic intermediates during the design of optimal catalysts. Given the multiple pathways that are accessible under reducing conditions in the presence of CO2 and protons, it is impractical to systematically study the relative energetics of these pathways for a large set of transition metal complexes to arrive at general design principles. In chapter 6, I describe my in-silico work employing state-of-the-art DFT to model these pathways for a large number of metal and ligand combinations. I propose a design model based on two thermodynamic descriptors, viz. hydricity and carbonylicity, for optimal catalytic activity. Computing these descriptors for diverse sets of ligands and metals enables the rapid screening of promising catalyst candidates. Amongst different classes of ligands, a polypyridyl ligand environment around an Fe(II) center was predicted to confer optimal values of hydricity and carbonylicity. Based on the predictions of the descriptor based in-silico model, I synthesized an iron complex with a pentadentate ligand that mimicked the optimal ligand environment (two bipyridines and one pyridine). In agreement with the predictions, this complex was found to be active towards CO2 reduction as well as proton reduction near the thermodynamic potential for either process, with the latter becoming more prevalent as the proton strength of the medium was increased. This approach of catalyst design based on extensive theoretical predictions prior to experimental tests represents a paradigm shift in the design of molecular electrocatalysts. The strength of the prediction lies in the deep mechanistic understanding of the possible pathways as well as in the theoretical method itself. Given the ability of DFT to model the energetics of transition metal complexes to sufficient accuracy in non-aqueous environments, and the rapid strides being made in the development of efficient, superfast computing architectures, this work lays the foundations for the high-throughput discovery of novel catalysts for a whole suite of small molecule electrocatalytic transformations relevant to electrochemical energy storage and conversion to commodity chemicals, such as O2 reduction to water and N2 reduction to ammonia.

The delivery of cell-impenetrable therapeutic agents across biological barriers represents a challenging problem in the field of life science research and medicine. Many bacterial pathogens are inherently resistant to glycopeptide antibiotics such as vancomycin due to the antibiotic's relatively large size and mode of action, which requires actively growing cells. Recently, genetically-resistant vancomycin strains have emerged, adding to vancomycin's inefficaciousness against certain bacterial populations. The emergence and understanding of phenotypically and genetically resistant bacteria coupled to a declining pipeline of antibiotic development necessitates new strategies to combat bacterial infections. As part of a collaboration between the Wender and Cegelski labs, we have designed, synthesized and evaluated a novel vancomycin cell-penetrating peptide conjugate. We have shown that this new conjugate exhibits a unique mode of action compared to vancomycin, allowing it to be extremely effective against vancomycin-insensitive bacterial populations.

My graduate studies have focused on the development of novel drug delivery technologies of research, clinical, and industrial significance. More specifically, my research has focused on the design, synthesis, and application of guanidinium-rich molecular transporters for the delivery of siRNA into cells. My studies have also focused on using molecular transporters to develop the first molecular method to deliver cargo into algae, and on the development of new strategies to control the timing and amount of drug or probe release in cells. Though all of this research is fundamentally based on organic chemistry, these projects have broad applications in research, industrial and clinical settings. Chapter 1 reviews the strategies that have been developed for the delivery of siRNA in both cells and animals. Rather than divide the field by chemical type (e.g. peptide vs. protein) or disease indication, this review categorizes siRNA deliver agents by the identity of their cationic moiety for siRNA complexation. Guanidinium-containing delivery vectors are presented, as are vectors containing ammonium and phosphonium groups. Highlighting this field by cationic moiety reveals how little research has been done to compare the effects of the cation's identity on deliver efficacy, toxicity, and pharmacokinetics. Chapter 2 describes the design, synthesis, and evaluation of guanidinium-rich amphipathic oligocarbonate molecular transporters for the complexation, delivery, and release of siRNA in cells. The synthetic ease of the metal-free carbonate oligomerization to synthesize these transporters afforded fast access to a series of transporters that systematically probed the functionality required for effective complexation, delivery, and release of siRNA. Transporters were characterized and evaluated for biological activity in immortalized human keratinocytes. The transporters discovered in this study were highly effective, with target gene silencing of up to 90% observed. Chapter 3 focuses on efforts towards expanding the scope of both the chemical space and cell types tested in the delivery of siRNA with amphipathic oligocarbonate molecular transporters. These second generation delivery systems have improved physical properties, including smaller and more stable particle sizes, relative to their first generation counterparts described in Chapter 2. These transporters delivered siRNA to primary keratinocytes, melanoma cells, and ovarian cancer cells. Chapter 4 details the development of the first molecular method for the delivery of small molecule probes and large protein cargos into algal cells. It was shown that oligoarginine could facilitate the uptake of fluorescein, or the larger, FAM-streptavidin protein, into cells. A catalytically active protein was delivered into cells and was shown to maintain catalytic activity even after delivery. Chapter 5 describes the design of new strategies to control the timing and amount of cargo released inside cells. Efforts towards a novel linker carrying two copies of drug or probe are described, as well as the combination of microneedles and luciferin-transporter conjugates for transdermal delivery in vivo.