Catalytic methods for C(sp3)--H amination are enabling technologies for both the synthesis and late-stage diversification of myriad organic molecules. Contemporary challenges that propel future development of such processes are presented by complex substrates approximating the architectures found in natural products along with polar, functional group-rich active pharmaceutical and agrochemical ingredients. In our efforts to address these limitations, we have established a catalytic system for C--H amination that markedly advances the ability of chemists to efficiently introduce nitrogen into molecules of different structural types. The discovery of pivalonitrile (t-BuCN) as a differential solvent for Rh-catalyzed intermolecular amination of C(sp3)--H bonds and phenyl sulfamate (PhsNH2) as a nitrene precursor has enabled efficient functionalization of a wide variety of complex molecule substrates including natural products and active pharmaceutical ingredients (APIs). Although limitations remain with oxidatively labile functional groups, including basic amines, our disclosure represents a definitive leap forward in the state-of-the-art for C--H bond oxidation. Mechanistic data strongly implicate a pathway for catalyst decomposition that initiates with solvent oxidation, thus providing rationale for the marked influence of pivalonitrile on this reaction process. The phenyl sulfamate nitrogen source can be unmasked under mild conditions using pyridine and water to unveil the corresponding primary amine products. Additionally, through amination of bromoalkane and mesyloxalkane substrates, SN2 cyclization can afford azetidines and other saturated azacycles in good to excellent yield. In pursuit of alternative, modular methods for the installation of sulfamate and sulfamide groups, we have developed pentafluorophenyl sulfamate (PfpsNH2) and trichlorphenyl sulfmatate (TcpsNH2) as bench-stable, versatile reagents for sulfamoylation of alcohol and amine nucleophiles to generate N-unsubstituted sulfamates and sulfamides. This type of 'click' reaction should find widespread use in academic and industrial labs.

Copper active sites catalyze a wide range of oxygen reactions in biology. While the majority of enzymes utilize Cu(I) to directly reduce O2, two families of enzymes instead use mononuclear Cu(II) sites to enhance the reactivity of organic molecules toward O2, which is a process known as Cu(II)-substrate activation. These are quercetin 2,4-dioxygenase (QD), which catalyzes the dioxygenation of flavones, and amine oxidase (AO), which utilizes Cu(II) to activate an active site tyrosine residue for a 6e- oxidation reaction to form its redox active cofactor, TPQ. Given the negligible reactivities of the free substrates and of Cu(II) toward O2, mechanistic proposals for these reactions invoke Cu(I)-substrate radical character as the basis for these sites reactivities. In order to evaluate these as well as alternate mechanisms, the electronic structures of these enzymes were first determined along with a number of closely related model complexes with combination of spectroscopic, computational, and kinetic techniques. These experimentally determined electronic structures were then used to calibrate DFT calculations to generate accurate electronic structure descriptions of the QD and AO enzyme-substrate complexes. Finally, these calculated active site models were used to evaluate possible mechanisms for their reactions with O2. Chapter 2 details the electronic structures of the QD enzyme-substrate complexes and a number of related model complexes. Unlike QD, these model complexes decrease the reactivity of bound flavones, and differ from QD primarily by their flavone binding mode. In the model complexes, the flavones bind to the metal in a bidentate fashion with the metal coordinated within the flavone molecular plane, while in QD the flavones bind monodentate with the metal out of the flavone molecular plane. This leads to considerably different electronic structures between the QD enzyme-substrate complexes and the model complexes. In the model complexes, flavone binding to Cu(II) primarily stabilizing the σ-bonding flavone orbitals, while in QD, flavone binding to Cu(II) stabilizes the flavone π-bonding molecular orbitals. Both types of binding geometries lead to moderate flavone-Cu(II) covalencies, but minimal ground state Cu(I)-flavone radical character and no thermally accessible charge transfer states. Calculations of the free flavone, model complex, and enzyme reaction mechanisms show that the models and enzyme increase the barrier for the reaction of O2 directly on the flavone by increasing the flavone ionization potentials. Given the low energy barrier for the O2 reaction performed by the enzyme, the active site Cu(II) must play a direct role in activating O2. In chapter 3, geometric and electronic structures are provided for the Cu(II)-loaded, pre-biogenesis AO active site (preAO). It was first shown that Cu(II) loading into the active site is slow, and that a second, non-catalytic, kinetically favored Cu(II) binding site affects the rate of Cu(II)-active site binding. Cu(II) stably binds to the active site, and prior to the biogenesis reaction is in a thermal equilibrium between two forms. The major form is entropically favored, and is a 4-coordinate site with 3-histidines and a hydroxide as the Cu(II) ligands. The minor form (which is present at 7% at room temperature) is a 5-coordinate site with three histidines, water, and the tyrosinate which processes to TPQ as its ligands. We showed that the minor form is active in biogenesis, and furthermore that this form has a low covalency interaction between the tyrosinate and Cu(II), no discernible Cu(I)-tyrosyl radical character, and no thermally accessible Cu(I)-tyrosyl radical states. Thus, the O2 activation step in biogenesis is performed by a fairly ionic Cu(II)-tyrosinate site. Chapter 4 provides spectroscopic and kinetic analyses of the AO biogenesis reaction. Four intermediates are observed during the biogenesis reaction. First, an intermediate with a 350nm absorbance band grows at the same rate that the minor, preprocessed form disappears. This band has an ε of 2800M-1cm-1, O2-dependent growth, and an O2-independent decay that allow its possible assignment as a dopaquinone intermediate. The 350nm species decays at a rate that is commensurate with the growth of a second intermediate, which has a set of 390nm/410nm bands in absorbance and an organic radical signal in EPR. The small amount of this intermediate that builds up during the biogenesis reaction places it as the minor species of an equilibrium with a Cu(II) form of the active site, and allows its likely assignment as the Cu(I)-organic radical form of trihydroxyphenylalanine, a species which undergoes a 2e- oxidation by reducing a molecule of O2 to H2O2 to become TPQ. Finally, a 330nm band forms at a rate that is commensurate with TPQ formation and then decays at a similar rate. Possible assignments for this species are discussed. A comprehensive kinetic model for the biogenesis reaction provides a lower limit of 1.5s-1 for the initial O2 activating step, giving its energy barrier an upper limit of ∆G^‡=11kcal/mol. This provides a key bench mark for evaluating possible mechanisms of tyrosinate activation for O2 reaction by a Cu(II) center.

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.

Carbon-carbon and carbon-nitrogen bonds are some of the most common motifs in organic molecules and as a result, the invention of new methods for selectively forming these bonds is highly important. The first half of this thesis describes the discovery of two novel and unexpected carbon-carbon bond forming reactions, and also includes a review on the unique chemistry of geminal and vicinal bis(sulfones). The second half of this work deals with enantioselective carbon-nitrogen bond formation, and describes the development of two transition metal-catalyzed asymmetric allylic alkylation reactions. It also contains a review on annulative allylic alkylation reactions between dual electrophiles and dual nucleophiles and their applications in complex molecule synthesis.

Polycyclic conjugated hydrocarbons (PCHs) containing four-membered cyclobutadienoids (CBDs) are of great fundamental and technical interest due to the antiaromaticity brought by CBD circuits. Synthetic accessibility of such molecules, however, has been challenging and limited in scope, thus hampering the exploration and understanding of such systems. In this thesis, a versatile and efficient synthetic strategy was developed to access a large variety of CBD-containing PCHs with variable carbon structures, electronics, and topologies via catalytic arene-(oxa)norbornene annulation (CANAL) from readily accessible aryl bromides and oxanorbornenes (oNBEs). This new synthetic capability opens a myriad of opportunities for systematic investigation into CBD antiaromaticity as well as the potential applications of CBD-PCHs. With this facile method, we proposed and synthesized a series of unprecedented [3]naphthylene regioisomers, and found the regioconnectivity of [3]naphthylenes strongly affects the degree of local antiaromaticity and aromaticity for the fused CBD and naphthalenoid, respectively. Further, the C-C bond activation of CBD units was demonstrated with unsubstituted V-shaped [3]naphthylene to yield helical structures. In addition, we designed and efficiently synthesized a novel CBD-containing acene analogues, dinaphthobenzo-[1,2:4,5]dicyclobutadiene (DNBDCs), with strong antiaromaticity of the CBD units. This design also features orthogonally tunable electronic properties and molecular packing, which resulted in good device performance in organic field effect transistors.

Anthropogenic climate change will cause irreparable damage to the environment if measures are not taken to abate the emissions of CO2. One way to drive emissions down is to valorize CO2 by using it as a carbon source for the synthesis of chemical feedstocks. The development of new technologies that produce chemicals from CO2 in a cost competitive and efficient way could put market pressure on existing fossil-derived petrochemicals and incentivize the capture of CO2 from concentrated point sources such as power plants. One attractive strategy for CO2 valorization is to use renewable energy to power the aqueous electrochemical reduction of CO2 and H2O to generate valuable C2+ chemical feedstocks such as ethylene, ethanol, propanol, and acetate. Unfortunately, the spontaneous reaction of CO2 and HO-- to form HCO3-- and CO32-- impedes the optimization of these systems. While the operation of CO2 reduction cells with alkaline electrolytes results in low total cell voltages, the super stoichiometric consumption of MOH in these systems represents a significant energy penalty. Furthermore, only low single-pass conversions have been achieved for CO2 electrolysis resulting in dilute product streams that are energy intensive to purify. Deconstructing CO2 reduction into two separate electrochemical steps may offer a path to overcome the challenges posed by direct electrochemical CO2 reduction. In this two-step process, CO2 is first converted to CO with a high temperature solid oxide electrolysis cell (SOEC), in which the reaction of CO2 and HO-- is avoided. The CO is subsequently reduced in a separate electrochemical cell to generate C2+ chemical feedstocks. While SOECs have recently been brought to market, relatively little is known about how to design an efficient CO electrolysis device that can achieve high single-pass conversions. For the first time, various cell configurations for CO electrolysis are evaluated and high single-pass conversions exceeding 80% are demonstrated corresponding to gas product streams which are greater than 24 vol% ethylene. Through device engineering liquid product streams that are greater than 1 M in sodium acetate are produced. Finally, an innovative deposition technique is developed to generate thick, highly active catalyst layers for CO reduction cathodes, resulting in improved device performance. The results obtained herein indicate the advantages of CO reduction over direct CO2 reduction. The exploration of various cell configurations informs future efforts to design and build larger scale CO electrolysis devices.

Chapter 1 shows that while nucleophilic substitution reactions are universally taught, they are often much more complicated than we think. A huge amount of work has been done to understand neighboring-group participation in SN1-type reactions both in a qualitative and quantitative sense. Studying the reactivity of dibromides and their surrogates led to important insights in physical organic chem-istry. However, the enantiospecificity and potential synthetic use of such processes are underexplored. Chapter 2 is a reprint of a review I coauthored entitled "Chiral Alkyl Halides: Un-derexplored Motifs in Medicine". While alkyl halides are valuable intermediates in synthetic organic chemistry, their use as bioactive motifs in drug discovery and me-dicinal chemistry is rare in comparison. This is likely attributable to the common misconception that these compounds are merely non-specific alkylators in biologi-cal systems. A number of chlorinated compounds in the pharmaceutical and food industries, as well as a growing number of halogenated marine natural products showing unique bioactivity, illustrate the role that chiral alkyl halides can play in drug discovery. Through a series of case studies, we demonstrate in this chapter that these motifs can indeed be stable under physiological conditions, and that halogenation can enhance bioactivity through both steric and electronic effects. Chapter 3 demonstrates that dihalides could be used to generate a configurational-ly stable bromonium ion either through Lewis acid activation or by using a strongly ionizing solvent. This bromonium ion can then be trapped by a host of nucleophiles inter- and intramolecularly. Using this strategy, a variety of natural products and natural product relevant motifs were synthesized in our laboratory. Chapter 4 describes the importance of studying archaeal lipids and the ongoing efforts toward their total syntheses. Archaeal lipids are structurally unique, their biosynthesis has several unanswered questions, and their biophysical properties have not been studied on pure compounds. Our work describes a highly convergent strat-egy toward GDGT-0, which exploits the molecule's C2 symmetry. We have shown the feasibility of a key enantioselective hydrogenation step, and alternative strategies have been described that may circumvent certain challenges.

Halide perovskites are an important, emerging family of electronic materials which have generated significant scientific interest due to their long carrier lifetimes, facile deposition procedures, and tolerance of large numbers of crystallographic defects. These properties have enabled the lead halide perovskites to be successfully used in a variety of optoelectronic devices including solar cells, light-emitting diodes, and photodetectors. Due to the toxicity of lead and the instability of the lead halide materials, it would be highly desirable to replace the lead halide perovskites with other materials which also demonstrate defect tolerance and long carrier lifetimes. One time-tested approach for identifying promising alternative materials is to synthesize structural analogs; materials with the same structure but different atomic compositions. This dissertation describes my efforts making one family of structural analogs, the halide double perovskites, and evaluating their optoelectronic properties. These materials also adopt the perovskite structure but divide the 2+ charge on the lead site unevenly over multiple sites allowing for a much wider variety of elements to be incorporated into the perovskite lattice. I report the synthesis of the first bismuth bromide double perovskite, Cs2AgBiBr6, and demonstrate that, due to its similar electronic configuration and structure, it possesses many of the same properties that the lead halide perovskites have including a similarly sized bandgap and long carrier lifetime as well as having higher stability. However, unlike the lead perovskites this bismuth double perovskite possesses an indirect bandgap. I next develop a model that describes the atomistic origins of double perovskite band structures. Using a qualitative Linear Combination of Atomic Orbitals method, I describe how band dispersion and band extrema in double perovskites arise naturally from the translational symmetry of the double perovskite structure and detailed bonding interactions. This treatment accurately predicts the band edge positions of almost every known double perovskite and allows for immediate prediction of the electronic structure of new double perovskites from the orbitals of the constituent elements. While the initial work on double perovskites proved promising, the bandgaps of most double perovskites known to date are too large to be useful for optoelectronic devices, particularly solar cells. I demonstrate that the doping or complete substitution of Tl3+ into Cs2AgBiBr6 reduces the bandgap of the material drastically. The completely substituted material, Cs2AgTlBr6, has the smallest bandgap of any known halide perovskite and is much smaller than is typical for bromide perovskites. I show that this small bandgap arises from the metal-to-metal charge transfer nature of double perovskite band edge transitions which allows significant control over the bandgap size through proper choice of metal pairs. Additionally, I demonstrate that Cs2AgTlBr6 undergoes a slow defect reaction, spontaneously evolving Br2 to the atmosphere and n-type doping itself. This defect reaction is analogous to the oxygen-exchange reaction in oxides and is likely general to all halide perovskites. Finally, I show that the halogen exchange reaction we found in Cs2AgTlBr6 occurs in other double perovskites as well. By carefully monitoring the electronic conductivity of the double perovskite Cs2SnI6 I demonstrate that it also undergoes reversible loss and incorporation of I2 with the atmosphere. The kinetics of this reaction follow a one-dimensional diffusion model which can be used to extract diffusion coefficients for halide vacancies and the standard enthalpy of the halogen exchange reaction. Combining these results with ionic conductivity and Hall measurements I am able to construct a detailed defect chemical model. This model predicts the concentrations of major defect species in Cs2SnI6 from experimentally measured thermodynamic parameters. I also demonstrate that deliberate Ba2+ doping of Cs2SnI6 is able to greatly reduce the extent of the halogen exchange reaction and fix the electronic doping to a specific level.

Chapter 1 introduces anaerobic ammonium oxidizing (anammox) bacteria and the ladderane lipids, unusual membrane lipids consisting of linearly concatenated cyclobutane motifs. The distinctive biological features and global applications of anammox bacteria are covered, with a focus on anammox catabolism and the possible function of ladderane lipids. The isolation and structural determination of ladderane lipids are outlined, as well as previous and concurrent synthetic efforts. Chapter 2 details our extensive synthetic efforts toward the synthesis of ladderane lipids. Key features of our synthesis of a [5]-ladderane include a scalable synthesis of key building block bicyclo[2.2.0]hex-2-ene, copper(I)-mediated dimerization of this building block, and C--H functionalization of the ladderane core. We also present a synthesis of [3]-ladderane utilizing a [2+2] photocycloaddition with a chiral dihalide, stereospecific alkylzinc addition, and unusual bis-hydrazone oxidative decomposition. Our efforts to determine for the first time the absolute stereochemical configuration of ladderane lipids are also detailed. Finally, the synthesis of two natural and one unnatural ladderane phospholipid as well as biophysical interrogation of synthetic ladderane phospholipids is presented. Chapter 3 describes an ongoing synthetic campaign toward the phytotoxic sesquiterpene fomannosin. Our synthesis requires a challenging quaternary carbon-forming epoxide opening reaction, as well as a cascade cyclization-Ramberg--Bäcklund ring contraction sequence. Efforts toward the completion of the natural product are presented.

The delivery of small molecules, probes, and nucleic acids across impenetrable biological barriers represents a challenge for many current clinical strategies. Nucleic acids are of particular interest for delivery with potential clinical applications in cancer immunotherapy, gene editing and vaccines. Chapters 2-5 describe the development and use of charge-altering materials for the delivery of nucleic acids. The charge-altering materials described are dubbed Charge-Altering Releasable Transporters (CARTs), diblock or triblock oligomers consisting of a lipid-modified oligocarbonate block(s) followed by a charge-altering block. The charge-altering blocks, derived from either morpholinones or poly(serine esters), are initially cationic for complexation of the polyanionic nucleic acid cargo but degrade under basic conditions over time to neutral byproducts, providing a mechanism for nucleic acid release. These chapters describe the use of CARTs to deliver a range of nucleic acid cargos (plasmid DNA, messenger RNA, small interfering RNA) across a variety of cell types, including lymphocytes, as well as for in vivo gene delivery. Chapter 6 explores vault proteins as another scaffold for drug or probe delivery. Vaults are naturally occurring, large (13 MDa), hollow ribonucleic protein complexes. These proteins have the potential to be promising delivery agents based on their biocompatibility, size, and internal compartment that can encapsulate hundreds to thousands of molecules. In this chapter, we systematically study the chemical modification of vault proteins and used the developed strategies to prepare vaults modified with cell penetrating peptides for enhanced uptake into cells. Chapter 7 describes the synthesis and evaluation of prodrugs of PKC modulators. Prostratin, bryostatin 1, ingenol esters and their analogs, are potent PKC modulators and have been identified as latency reversing agents (LRAs) for HIV eradication. LRAs can be used to activate the HIV provirus in latent viral reservoir cells, which can then be subject clearance using a "kick and kill" approach. While promising agents, a major challenge associated with the clinical use of LRAs is sustaining therapeutically meaningful levels of the active agent while minimizing side effects. In this chapter, we describe the synthesis of PKC modulator prodrugs designed to slowly release the active drug over time. These PKC modulator prodrugs exhibit comparable but delayed in vitro activity relative to the parent compounds and avoid the problems associated with bolus administration in vivo.

Since the enantiopurity of an organic molecule can have a profound impact on its unique biochemical and physical properties, the development of atom- and step-economical methods for constructing chiral chemical bonds is highly important and valuable. Besides asymmetric oxidation and reduction, recent advances have been made in reactions involving enantioselective carbon-carbon bond formation, enabling the synthesis of chiral complex molecules. This thesis describes the development of five novel and highly selective catalytic asymmetric transformations to construct chiral C-C bonds. Moreover, many of these methods have been applied to the total syntheses of alkaloids and other bioactive molecules. The first chapter of this thesis describes in detail the development and synthetic applications of dinuclear metal-ProPhenol catalysts. The ProPhenol ligand is a member of the chiral aza-crown family that forms bimetallic complexes upon treatment with alkyl metal reagents, such as Et2Zn and Bu2Mg. The resulting complexes can simultaneously activate both a nucleophile and an electrophile in the same chiral environment, enabling a broad range of asymmetric transformations, including aldol, Mannich, Henry reactions, alkynylations and conjugate additions. The second chapter details the development of the pseudo-C2-symmetric ProPhenol ligands, which enable a highly enantioselective vinylation of N-Boc aldimines using readily available vinylzirconocenes as nucleophiles. This asymmetric process led to the discovery of an unprecedented catalytic transmetallation between organozirconium reagents and Zn-ProPhenol, and also led to a short synthesis of (-)-dapoxetine. The next four chapters deal with asymmetric Mannich reactions catalyzed by the Zn-ProPhenol catalysts. The third chapter describes a Mannich reaction between alkynyl ketones and N-Boc imines. Alkynyl ketones are attractive yet challenging nucleophiles due to their intrinsic susceptibility to Michael additions and the difficulty of controlling the enolate geometry. Nonetheless, this method produces β-amino ynones with excellent chemo-, diastereo-, and enantioselectivity, and the products can be transformed into a broad range of structural scaffolds upon simple modifications. The fourth and fifth chapter describe the construction of quaternary stereocenters utilizing the Zn-ProPhenol Mannich reactions. Nonactivated enolate precursors that have either rarely or never been employed previously -- including α-branched aldehydes, enones, and ynones -- were successfully utilized to generate adducts featuring a quaternary stereocenter. The process involving α-branched aldehydes later led to the total syntheses of seven different isoqunioline alkaloids from the Genus Corydalis, discussed in the sixth chapter. The final chapter describes a unique way to utilize α-trifluoromethyl carbanions in palladium-catalyzed asymmetric cycloadditions. Although the electron-withdrawing nature of the CF3 group does increase the acidity of the neighboring protons, β-fluorocarbanions have rarely been utilized as nucleophiles due to their intrinsic propensity to undergo β-fluoro eliminations. Nonetheless, such elimination processes were successfully prevented by the presence of a neighboring cationic Pd-allyl motif. The resulting palladium-stabilized zwitterions can participate in asymmetric [3+2] cycloadditions with a broad range of acceptors, generating valuable di- and trifluoromethylated cyclopentanes, pyrrolidines, and tetrahaydrofurans.

The chloride channel (CLC) family is a class of membrane proteins that regulates the flux of chloride ions across cell membranes. These ion channels play critical roles in electrical excitation of muscles and neurons, as well as in maintaining proper water and salt balance in the body. CLCs are traditionally difficult drug targets, as demonstrated by the low potency and general lack of homolog selectivity among existing classes of CLC inhibitors. To address this challenge, we employed a rational-design approach to develop a novel, small-molecule scaffold that displays unprecedented selectivity for one CLC homolog. Specifically, this molecule inhibits one of the two homologs expressed in the kidney, CLC-Ka, with > 20-fold higher potency than the next most closely related CLC homolog, which is 90% identical in sequence. Following a similar approach, we identified and optimized a new class of potent and selective inhibitors for CLC-2, the most abundant voltage-gated chloride channel expressed in the brain. Data from genetic knockout studies in mice suggest a critical role for CLC-2 in ion homeostasis and electrical excitability in the central nervous system (CNS), but the mechanisms for these processes have been difficult to elucidate in the absence of specific and potent chemical modulators of CLC-2. Structure-activity relationship studies have allowed us to develop these inhibitors into a best-in-class molecule that represents the first and only nanomolar potency small-molecule inhibitor to target the CLC family. In addition to extraordinary selectivity among CLCs, we demonstrated that this molecule is highly selective for CLC-2 within the context of the brain, showing no off-target effects among a diverse panel of CNS receptors, channels, and transporters that we screened. Additionally, this inhibitor acutely and specifically blocks CLC-2 current in wild-type hippocampal CA1 neurons with no effect on CLC-2--/-- neurons. This exciting new molecular tool acts as a fast, reversible, and specific inhibitor of CLC-2 function in the brain and should enable study of CLC-2 in the CNS.

Protein kinase C (PKC) modulators are currently in clinical or preclinical development for a wide range of diseases that represent major causes of mortality and morbidity worldwide. For example, the marine natural product bryostatin 1, a lead PKC modulator, is in clinical trials for HIV/AIDS eradication and Alzheimer's treatment, with a trial for its use in small molecule-enhanced CAR-T cell therapy slated for the near future. Preclinically, bryostatin 1 has been evaluated for its use in treating fragile X syndrome, multiple sclerosis, ischemic stroke and Charcot-Marie-Tooth disease, among others. Other highly active PKC modulating natural products under clinical or preclinical evaluation include the tigliane natural product prostratin and several ingenane natural products. While nature has provided bioactive compounds that, conveniently, offer solutions to hugely important problems of global health and wellness, these compounds and methods of obtaining them are by no means optimal for clinical use. Many of these natural products are extremely scarce and require one to process staggering quantities of host organism to access even milligram quantities of the natural product. This is well illustrated in the case of bryostatin 1, where 14 tons of its host organism -- a coastal marine sponge -- were processed to access only 18 grams of the natural product. Additionally, while these natural products are excellent clinical leads, nature has not optimized them for use in human medicine. These compounds can have narrow therapeutic windows, undesired on- and off-target toxicities, poor metabolic stability and problematic solubility properties. The work presented herein focuses on solving both problems presented above through design, synthesis and evaluation of natural product leads and derivatives thereof. This document should provide a clear example of the influence that synthetic chemistry can have in supporting and driving forward clinical research on some of the most challenging problems in human healthcare to-date.

The first optical detection of a single molecule (SM) at cryogenic temperatures 30 years ago laid the groundwork for the routine detection of SMs today at biologically relevant temperatures, thus uncovering hidden heterogeneity that might be obscured by ensemble techniques. In addition to enabling studies of the intricate photochemistry and photophysics of fluorescent labels at the SM level, SM fluorescence has also proven useful for the imaging and tracking of cellular structures and biomolecules in a non-invasive manner with high sensitivity. The ability to genetically express fluorescent protein fusions in live cells has allowed specific labeling, and thus imaging and tracking, of dynamic processes and structures in cells. This dissertation describes applications of SM-based single-particle tracking (SPT) and super-resolution (SR) microscopy for the study of spatial organization and dynamics of bacterial proteins in two and three spatial dimensions. In an SPT experiment, the position of a SM emitter at very low concentration is measured over time to generate a trajectory, allowing for observation and quantification of labeled biomolecule dynamics at the SM level. In a SR microscopy experiment, the diffraction-limited (DL) resolution of a conventional fluorescence microscope (~200 nm in xy) is circumvented by temporally separating the emission of many SM emitters decorating a structure through control of their emissive state. A "super-resolved" image, with a factor of ~5-10 resolution improvement over a conventional DL fluorescence image, is generated by estimating the positions of many non-moving SM emitters over many frames and building up an image reconstruction in a pointillist manner. Chapter 1 of this dissertation provides an introduction to fluorescence, SM imaging, SM-based SR microscopy, and SPT. Chapter 1 also gives a brief introduction to Caulobacter crescentus, the bacterium used as the model organism in the SM studies in Chapters 4 and 5. Chapter 2 describes the experimental methods used to perform quantitative SM imaging of bacterial cells. The combination of SM imaging with point spread function (PSF) engineering has enabled the accurate and precise localization of SMs in three dimensions (3D) by the intentional introduction of specifically chosen aberrations in the emission path of an SM microscope. Throughout this dissertation, the double-helix (DH) PSF, a rotating PSF composed of two lobes whose angle encodes axial position, was used to estimate 3D SM positions. Chapter 2 describes the implementation of the DH-PSF via optical Fourier processing, and Chapter 3 describes the robust and comprehensible two-color Easy-DHPSF v2 software for localizing molecules in 3D and for registering localizations from two spectral channels into the same coordinate system with nanoscale accuracy. The resolution improvement gained from SM-based techniques is particularly useful for bacteria, the sizes of which are on the order of the DL. 3D SM-based SR and SPT have enabled the observation of structures and dynamics at length scales below the DL. Caulobacter is a useful biological target where understanding of the mechanisms for asymmetric cell division need to be explored and quantified. Central to Caulobacter's asymmetric division is the dynamic spatiotemporal regulation of gene expression and protein localization. Chapters 4 and 5 describes research performed in collaboration with Prof. Lucy Shapiro's laboratory (Department of Developmental Biology, Stanford School of Medicine) to study gene expression and signaling proteins in Caulobacter. Chapter 4 describes work studying the spatial organization and dynamics of ribosomes and a RNA-degrading enzyme RNase E using 3D SR microscopy and SPT. Results showed that the organization and dynamics of RNase E and ribosomes are closely related to the transcriptional activity of the cell. Finally, Chapter 5 describes SPT studies of the membrane-bound histidine kinase and stalked cell fate determinant DivJ in an effort to probe the physical properties of the Caulobacter stalked pole. Preliminary SPT results suggest that disrupting the physical properties and interactions at the stalked pole has an influence on DivJ diffusion and signaling.

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.

Water is one of the most important substances in the world. It is used in a wide range of technologies and is an essential ingredient in all living cells we know today. The structure of water molecule is simple, yet it can form extended and versatile hydrogen bond (HB) network. This ability gives water extraordinary properties, such as high boiling and melting point. At the same time, the hydrogen bond network is not static. The constant breaking and re-forming of hydrogen bond occurs on the picosecond timescale. This dynamic network facilitates many functions of water, including ions solvation, protein folding and electricity conduction. Understanding the structure and dynamics of these processes is therefore of great importance. Ultrafast infrared (IR) spectroscopies offer a great method for accessing the sub-picosecond to picoseconds dynamics while a system in an electronic ground state. During the past two decades, hydrogen bond dynamics has been investigated extensively using ultrafast IR spectroscopies. But many questions still exist such as the effect of ions and confinement on the hydrogen bonding dynamics and the relation between the anomalous proton diffusion in dilute solution and hydrogen bonding. In Chapter 3, we examined the nature of molecular anion hydrogen bonding. The CN stretch of selenocyanate anions (SeCN-) was used as the vibrational probe in heavy water D2O. We observed the non-Condon effect on the CN stretch whose transition dipole changes with the strength of hydrogen bonding with water. In addition, HB rearrangement dynamics reported by SeCN- is almost the same as was that of the OH stretch of HOD molecules. This result shows that this anion does not perturb the surrounding HB network significantly in the low salt concentration solution. This ionic perspective is important and complements the results using OD or OH stretch of HOD molecules, which can only probe the effect of ions in a high salt concentration condition. In Chapter 4, we used SeCN- as the probe to examine water dynamics in confinement, and I focused on the nano waterpool formed in reverse micelles. The water pool is surrounded by surfactants which are further solvated by organic hydrophobic solvents. For large reverse micelle whose diameter is larger than 4 nm, the water pool is usually divided into two regions: the core region where water dynamics is like that in pure water and the interface region where water dynamics is slowed significant due to the confinement. Here we used ultrafast IR spectroscopies to measure the orientational relaxation of SeCN-, which reflects its interaction with water molecules and how "rigid" the HB network is. Based on the comparison between linear IR decomposition and ultrafast anisotropy dynamics, we proposed a three-component model of water in large reverse micelles. The interface component should be further separated into two layers. One layer corresponds to water in contact with the surfactant head group and has very slow reorientation. The other layer corresponds to water molecules whose coordinating structure still resembles that of bulk but the dynamics is slowed down due to the perturbation from confinement. In Chapter 5 and 6, hydrogen bonding dynamics in concentrated salt and acid solutions were investigated. Through electrochemical method, it was found decades ago that proton has extraordinary ion mobility, about 6 times larger than that of cations of similar sizse, such as sodium, ammonium or lithium. The great difference between them results from the cation transport mechanism. In dilute solution, the main transport mechanism of proton is through relay mechanism where the identity of proton transfers from one water molecule to another. This minimizes the physical diffusion of the atoms and greatly increases the proton mobility. The mechanism is generally called Grotthuss mechanism, which was came up with by Grotthuss in 1806 though not on the molecular level. However, the step time of a single proton transfer event between two water molecules is difficult to observe experimentally. Here we used the CN stretch of methyl thiocyanate (MeSCN) as the vibrational probe. In concentrated hydrochloric solutions, it has two frequency resolved states. One state refers to water hydrogen bonded to the nitrogen lone pair while the other state corresponds to hydronium ion hydrogen bonded to the CN. Chemical exchange phenomenon was observed between these two states. Ab initio simulation done by our collaborator shows that the proton hopping is the dominate mechanism for chemical exchange. The comparison experiment done in lithium chloride solution provides further contrast between hydronium and other metal ions. Therefore, we were able to track proton hopping in a time-resolved manner for the first time. Extrapolation to the dilute limit demonstrates that the HB rearrangement in pure water is the driving force of proton hopping in dilute solution.

The emergence of antibiotic-resistant bacteria, including methicillin-resistant Staphylococcus aureus (MRSA) and carbapenem-resistant Enterobacteriaceae (CRE), necessitates the development of new therapeutics. Antibiotic resistance can result in life-threatening infections, where resistant bacteria are able to proliferate in the presence of high concentrations of antibiotic due to mechanisms such as efflux and enzymatic deactivation. An additional phenomenon which can cause recalcitrant infection is antibiotic persistence. Persistent bacterial cells withstand antibiotic treatment by entering a dormant or slow-growing state in response to cellular stress and are often found within biofilms, which are communities of bacteria enmeshed in a self-produced extracellular matrix. Most clinically used antibiotics target metabolically active bacteria and are largely ineffective against biofilms and other persistent bacterial populations. Innovative therapeutic strategies are needed to treat both resistant and persistent bacteria, and this dissertation describes the development and characterization of new chemical approaches to target these pathogens. Our studies were inspired by the ability of uropathogenic E. coli (UPEC), the most common causative agent of urinary tract infection (UTI), to contribute to chronic infection via several mechanisms, including robust adhesion to bladder epithelial cells and formation of intracellular biofilms. We first investigated the molecular determinants of UPEC adhesion to bladder cells using a model mammalian cell culture system, enabling the identification and development of new strategies to prevent bacterial adhesion. We also investigated the ability of conventional antibiotics to treat intracellular UPEC, which motivated the use of cell-penetrating, guanidinium-rich molecular transporters (GR-MoTrs) to improve delivery of antibiotics to intracellular pathogens. We prepared and evaluated a series of antibiotic-GR-MoTr conjugates to treat UPEC, focusing on the glycopeptide class of antibiotics, which are unable to cross mammalian or bacterial cell membranes. While our antibiotic-transporter conjugates exhibited no activity against UPEC, we discovered a vancomycin-oligoarginine conjugate (V-r8) that exhibited extraordinary activity against MRSA biofilms and persister cells. We investigated its mechanism of action and observed rapid cell killing and enhanced cellular association as a result of covalent conjugation of vancomycin to octaarginine. Together with demonstrating its remarkable activity in eradicating biofilm-associated bacteria in a mouse wound infection model, we also generated testable hypotheses for the molecular-level mode of action of V-r8, consistent with all of our biochemical data. In parallel, we screened other glycopeptide conjugates in an effort to target UPEC, where we discovered a vancomycin-arginine conjugate (V-R) effective against UPEC and CRE. The V-R derivative appeared to access intracellular cell-wall targets and served to disrupt bacterial cell-wall synthesis. Our studies inform future antibiotic development efforts for difficult-to-treat bacterial populations and highlight the utility of conjugating antibiotics to GR-MoTrs to generate potent therapeutics with new activity and efficacy.

Atomistic simulations provide detailed information about a molecular system's dynamics at finer time and length scales than experiments can access. However, the modeling and interpretation of simulation datasets in an unbiased and statistically sound way require dedicated algorithms. One analysis method is the so-called variational approach to conformational dynamics, which introduces an objective framework for the ranking of models. One such class of models are Markov state models (MSMs), which separate the configuration space explored by a simulated molecule, such as a protein, into discrete, disjoint states between which the transitions can be modeled as Markovian. In Chapter 1, I summarize the essentials of MSM construction and the variational approach. In Chapters 2 and 3, I describe systematic studies in varying MSM parameters, in pursuit of general trends for variationally optimal models of proteins, with a focus on clustering into states. In Chapters 4 and 5, I present algorithmic advances in comparing multiple related models and in coarse-graining MSMs, also using clustering. In Chapter 6, I summarize the current state of the art in MSM methods and identify frontiers in their application and methods development. Finally, in Chapters 7 and 8, I apply clustering to different problems, such as in fluid dynamics. I discuss the possibility of extending the methods motivated here to a broader class of dynamical systems in Chapter 9. Overall, the methods presented in this work focus on interpretability and statistical robustness.

Molecular polymer confinement can be achieved in hybrid nanocomposites where individual polymer molecules are confined by a nanoporous matrix to dimensions comparable to or less than the molecular size of the polymer. Such molecular confinement can induce changes in a wide variety of properties of the confined polymer and the nanocomposite. In this dissertation, I focus on the mobility of the molecularly confined polymers as well as the thermal and fracture properties of the nanocomposite. In my first project, I show that the polymer mobility and the nanocomposite thermal and mechanical properties can be significantly influenced by the interaction of the molecularly confined polymer with the pore surface, which can be manipulated by surface chemical functionalization of the pores. Polyimide nanocomposites hold great promise for applications demanding fracture resistance at high temperature. In my second project, I discuss the strategy of improving fracture resistance of polyimide nanocomposites by increasing polymer fill level and polymer-surface interaction.

Direct methanol fuel cells are a promising means of generating electricity from methanol and dioxygen. However, state of the art catalysts for the oxidation of methanol and reduction of dioxygen must operate at significant overpotentials to obtain reasonable reaction rates. Finding alternative catalysts operative at lesser overpotentials would make direct methanol fuel cells more attractive. Among the many alternative catalyst designs that have been explored, the use of discrete molecular complexes is particularly appealing as molecular structure may be methodically modified to provide mechanistic insight. Such surface immobilized metal complexes have shown activity towards alcohol and water oxidation as well as dioxygen reduction. Described herein, are advances made in the development of discrete molecular complexes for methanol oxidation and dioxygen reduction. A ruthenium polypyridyl complex covalently attached to a carbon electrode shows methanol oxidation. Benzyl alcohol oxidation is used as a benchmark to compare with related complexes. This complex shows a 240 mV decrease in overpotential for benzyl alcohol oxidation compared to the best surface immobilized ruthenium polypyridyl complexes, an order of magnitude larger turnover frequency, and a 15% improvement in faradaic efficiency. Pourbaix and mechanistic analysis suggests that the active oxidant is a RuIV=O complex. Formation of this active catalyst is strongly dependent on surface immobilization under dry, inert atmosphere conditions. Methanol oxidation is not observed from carbon electrodes under aqueous surface immobilization conditions. Nor is methanol oxidation observed from metal oxide electrodes under nonaqueous immobilization treatment. Thus, the surface, the tether bonding the discrete molecule to the surface, and the solution, contribute to forming this active electrocatalyst. The organized distribution of binuclear copper complexes on a carbon electrode significantly enhances dioxygen reduction compared to a random distribution of mononuclear copper complexes. Nafion coatings enhance the stability of the surface immobilized molecular complex. Surface immobilized discrete metal complexes are significantly more robust than complexes prepared from metalation of surface immobilized ligands. These results highlight the value of surface immobilized discrete metal complexes as electrocatalysts.