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This dissertation describes a general synthetic platform for segmented polymers that have main-chain reversible linkages based on cyclopentadiene-maleimide Diels-Alder chemistry. Research in the area of thermally reversible (self-healing) polymers has been an ever-expanding area of interest in the current scientific literature. However most of the emphasis has been on systems containing furan-maleimide linkages. While inexpensive and synthetically accessible, furan chemistry is mostly limited to crosslinked and hyperbranched architectures due to its relatively weak binding with maleimides at suitable propagation temperatures. Following a general review of the literature in this area (Chapter 1) the first stage of our research (Chapter 2) entails the synthesis of 2-substituted hydroquinones, which are needed as monomers in the later stages. The novelty of our hydroquinone synthesis stems from the use of allylic and other alkenyl ethers as the source of the ring substituent, and from the utilization of catalytic hydroboration to improve atom-efficiency. We showed that hydroquinones with widely varying functionality can be prepared efficiently by our method; these findings were published in the journal Tetrahedron in 2018. The second stage (Chapter 3) involves the use of the new hydroquinones in step-growth syntheses of hydroquinone-terminated telechelic and chain-extension of these telomers via Diels-Alder chemistry to form segmented polymers having thermally reversible linkages. The novelty of our approach rests with the use of cyclopentadiene-maleimide chemistry for the linkages, while the overall physical properties such as the glass transition temperature were established by using well-defined aromatic polymers — poly(ether ether ketones) or PEEK and poly(aryl ether sulfones) or PAES — as segments. This approach represents an important departure from earlier work in our group in which reversible linkages were present in every repeat unit of a step-growth Diels-Alder polymer that showed thermal reversibility in solution but not in the bulk, owing to glass transition temperatures that were too high. Using scratch-healing and mechanical (tensile) tests, we show that our new segmented polymers exhibit self-healing characteristics that are competitive with or superior to previously reported systems based on different Diels-Alder chemistry. The third stage (Chapter 4) aims to explore new application areas for some of the more novel functionalized hydroquinones reported in Chapter 2. First we developed an efficient synthesis of a PAES derivative bearing 5-phenoxypentyl groups on the hydroquinone moiety. Then we showed that the 5-phenoxy group can be cleanly cleaved, post-polymerization, to afford a PAES having 5-bromopentyl substituents. The promise of our method rests with the potential of the pendant electrophiles to undergo reactions with nucleophilic reagents to post-modify these polymers further. As proof of concept, we showed that substitution of the pendant bromides with furfuryloxy groups enabled thermally reversible crosslinking with a bis-maleimide reagent to form a polymeric material that demonstrates partial scratch healing. Finally we are exploring the synthesis of new ion-containing polymers by substituting the pendant bromides with tertiary amines.

Renewable power generation is intermittent and non-dispatchable, but is steadily increasing in penetration due to lower costs associated with installation and demand for clean power generation. Without significant energy storage available to a grid with high renewable penetration, a mismatch between the load and the power available can. Furthermore, advanced high temperature nuclear reactors offer clean power generation, but only at a baseload operation scenario due to the significant thermal inertia associated with the reactor. Also, natural gas is expected to continue to play a major role during and after the transition from modest renewable use to a majority of renewable penetration, but will need to have a reduced carbon footprint. In this study, the storage of otherwise curtailed renewable power through hydrogen via high temperature electrolysis and the dispatch of shifted renewable power through hydrogen via reversible high temperature fuel cells is studied on a system level utilizing spatially resolved dynamic physical system models built upon fundamental principles. Reversible solid oxide fuel cell (RSOFC) systems are considered for the bulk of the analysis for standalone, thermally self-sufficient systems using a combustor and resistive heaters. RSOFC systems are also considered for integration with renewable power for storage and dispatch of renewable power at various scales including grid-scale energy storage. Additionally, a nuclear reactor is coupled with a solid oxide electrolyzer system in order to study the ability of dispatching a nuclear power plant by shifting the heat from the turbine generators to the electrolyzer during periods of high renewable generation. Molten carbonate electrolysis used in a reformer-electrolyzer-purifier (REP) concept is considered for the generation of hydrogen from steam and natural gas where the power input is renewable resulting in a portion of renewable hydrogen from natural gas feedstock. The results of the work provide valuable insights into the steady-state and dynamic operation of RSOFC systems under various loads and system configurations. Integration with renewables, nuclear, and grid energy storage were studied and the benefits and challenges discussed. The REP integration with renewable power and natural gas feedstock was verified with experimental data and dynamic simulations were conducted.

This work presents the first alkaline redox flow battery (a-RFB) based on the coordination chemistry of cobalt(III/II) and iron(III/II) with amino-alcohol ligands in concentrated NaOH([subscript aq]). The a-RFB was developed by carrying out systematic structural and electrochemical characterizations of various redox-active coordination compounds to find the most suitable candidates for electrochemical energy storage. In the characterization studies, particular attention was given to the redox couple Fe(III/II)- TEA, where TEA = triethanolamine, because of its importance in the fields of supramolecular chemistry, magnetic memory films, and electrochemical energy storage. The structures of Fe(III)-TEA in the solid state and in alkaline solution are reported for the first time. Moreover, experimental evidence is presented for the existence of an EC reaction in the heterogeneous reduction of Fe(III/II)-TEA in concentrated base. Furthermore, experiments were carried out to study the reactivity of Fe(II)-TEA with O2. This is important because O2 reacts spontaneously with Fe(II)-TEA to produce hydrogen peroxide, decreasing the charging-discharging capacity of the a-RFB. The reduction of oxygen by Fe(II)-TEA in concentrated base was studied by UV-Vis spectroscopy and coulometric titrations. Additionally, a new method for the quick identification of redox couples with slow EC reactions, k[subscript f] < 0.1 s-1, is presented. The new method is based on scanning electrochemical microscopy (SECM) and consists of creating a thin-layer cell between the tip and substrate electrode. During analysis of a redox couple, the tip reports a current transient proportional to the decaying concentration of the product of the E reaction, from which an apparent forward rate constant for the C reaction can be determined. This method was designed for the field of RFB research, where the identification of redox couples with no EC reactions is necessary to ensure that a battery can run for thousands of cycles. Lastly, surface oxidation of polycrystalline Ir ultramicroelectrodes was studied by the surface interrogation mode of SECM (SI-SECM), using Fe(II)-TEA as the titrant. This was done to demonstrate the existence of hydrous oxides of Ir(IV) and Ir(V) prior to the onset of oxygen evolution in concentrated base. Numerical simulations were carried out using commercial software and were used to validate the experimental results reported in this work.

reversible reaction is a multimedia installation that employs audio, animation, sculpture, lights, and interactive motion tracking to create an immersive environment. The work is inspired by a molecular phenomenon of the same name, in which a chemical reaction’s products can rapidly revert into its reactants when the system’s surrounding environment changes. reversible reaction’s immersive environment operates on this principle, incorporating two alternating “states” that contrast significantly in their content and effect. The first state simulates a fluid, calm environment in which molecules join into large interconnected structures. The second state is chaotic and noisy, with audio and visual elements degrading into jagged particles. A Kinect infrared camera tracks participants’ movement in the space, triggering state changes as their physical presence disturbs the system’s equilibrium. For example, a participant moving into a designated area or a period of inactivity in the space may trigger a state change.reversible reaction’s visual elements abstractly depict molecular systems and their microscopic movements. Particle-based, procedurally generated animations are projected on numerous two-inch paper cubes, mounted on rectangular boards. Translucent lanterns printed with still images from the projected animations hang around the space. The light-emitting diodes inside these lanterns blink at different speeds in synchronization with audiovisual events to enhance the work's immersive environment.reversible reaction’s audio defines the piece’s temporal structure, consisting of two contrasting atmospheres that complement the visuals. An algorithmic system controls various musical parameters, employing gradual volume changes, alternation and phasing of sonic events, and harmonic changes to create “concentric” time scales that add variety over time. The installation’s undulating sound world is generated from synthesized soundfiles that are layered, filtered, and spatialized in real time using an algorithmic system.reversible reaction was first exhibited at the 2014 ArtsX event in the School of Art in December 2014.

This dissertation describes a new platform for the synthesis of thermally reversible polymers, based on Diels-Alder reactions of bis-cyclopentadienes (bis-CPDs) and bis-maleimides (bis-MIs), that meets two main objectives. First, the bis-CPD must resist characteristic self-coupling. Second, the CPD-MI adducts should undergo the retro-Diels-Alder (rDA) reaction (i.e., thermal depolymerization) in a temperature regime that is comparable or slightly higher than that of the freely reversible bis-furan/bis-MI polymers (rDA between 80 °C and 130 °C) but much lower than that of bis-CPD homopolymers (rDA above 160 °C). Structure-reactivity relationships gleaned from the literature and from related but as yet unpublished work in our own laboratories led to our main hypothesis that a CPD moiety bearing one sterically encumbering substituent such as isopropyl (Pr) or tert-butyl (Bu) and one electronwithdrawing substituent such as perfluoroaryl would have the desired reactivity and adduct stability in combination with an -substituted maleimide. Synthetic considerations led to a bisCPD monomer design in which two alkylcyclopentadiene groups (alkyl = Pr or Bu) are connected by an octafluorobiphenylene linker. As an initial fundamental step (Chapter 3), 1-(nonafluorobiphenyl-4’-yl)-4-tertbutylcyclopentadiene (1) was synthesized to provide a monofunctional model for the proposed difunctional CPD monomer. Reactions of 1 and -(4-fluorophenyl)maleimide (FMI) afforded up to five regio- and stereo-isomeric adducts (of fourteen possible). Variable-temperature reactivity studies combined with NMR spectroscopic analysis, X-ray crystallography, and computational modeling enabled product distributions to be understood according to a conventional kinetic-vs- iii thermodynamic framework. These studies also predicted the microstructure of polymers derived from the proposed bis-CPD monomer, which is structurally analogous to 1, and bis-MIs. Moreover, 1 does not undergo DA self-coupling under ordinary conditions (T < 180 °C). Thermolysis studies of the major adducts revealed that the rDA becomes observable on a laboratory timescale (hours) at about 140 °C, which is at the upper end of the temperature range reported for furan+MI adducts but well below that of CPD+CPD adducts. In contrast, adducts formed from either of the analogous monosubstituted cyclopentadienes (BuC₅H₅ and C₆F₅C₅H₅) do not undergo rDA below 180 °C. These results strongly support the proposed bis-CPD monomer design. In a second fundamental step (Chapter 4), the hypothesis that an electron-withdrawing CPD substituent would destabilize a CPD-MI adduct was further tested by reacting -(4- fluorophenyl)maleimide with a series of triarylated cyclopentadienes (1,2,3-Ar₃C₅H₃ and 1,2,4- Ar₃C₅H₃, Ar = C₆F₅, C₆F₄CF₃, and Ar = C₅F₄N). The perfluorophenyl- and perfluorotolylsubstituted compounds were previously reported, but the perfluoropyridyl-substituted cyclopentadienes were prepared for this study using SNAr reactions of pentafluoropyridine and sodium cyclopentadienide. The least electron deficient cyclopentadiene in each series (Ar = C₆F₅) reacted the most quickly and with the highest ultimate equilibrium binding constant, confirming the electron-effects hypothesis as well as the underlying presumption that DA reactions of even relatively electron-poor CPDs with MI would behave according to normal-electron-demand principles. In the main section of this dissertation (Chapter 5) the proposed bis(cyclopentadiene)s reacted with a series of previously reported bis(maleimides) to form linear polymers having molecular weights (Mn) up to 40 kDa. Relationships among the length and flexibility of the bis-MI linker (C₆H₁₂, C₁₂H₂₄, C₆H₄OC₆H₄, and (C₂H₄O)₂), the identity of the CPD alkyl substitutent (CHMe₂, CMe₃ and CMe₂Ph) and the glass transition temperature (Tg) as measured by differential scanning calorimetry (DSC) were understood in terms of a general model of local segmental mobility and free volume. Solution thermolysis of a model polymer system (bis-MI linker = C₆H₁₂ (7), CPD alkyl substituent = Bu) showed a rapid decrease in molecular weight at 160 °C as determined by size exclusion chromatography (SEC). Solution thermolysis in the presence of excess FMI (as a trap for free CPD moieties) revealed that the onset temperature for rDA on a laboratory time scale (hours) was as low as 120 °C. In the bulk, thermolysis above 250 °C under vacuum led to recovery of a small portion of the bis-CPD monomer, but bulk thermolysis at 200 °C did not reveal a change in molecular weight as determined by SEC. The current interpretation of these observations is that limited mobility in these glassy polymers prohibits retro-DA decoupling. These findings largely validate the main hypothesis of this dissertation.

Starch is a water-insoluble glucose biopolymer used as an energy cache in plants and is synthesized and degraded in a diurnal cycle. Reversible phosphorylation of starch granules regulates the solubility and, consequentially, the bioavailability of starch glucans to degradative enzymes. Glucan phosphatases release phosphate from starch glucans and their activity is essential to the proper diurnal metabolism of starch. Previously, the structural basis of glucan phosphatase activity was entirely unknown. The work in this dissertation outlines the structural mechanism of activity of two plant glucan phosphatases called Starch EXcess4 (SEX4) and Like Sex Four2 (LSF2). The crystal structures of SEX4 and LSF2 were determined with and without phosphoglucan ligands bound, revealing the basis of their interaction with an endogenous substrate. The data show that SEX4 and LSF2 interact with starch glucans via distinctive mechanisms. SEX4 binds glucan chains via an aromatic-rich pocket spanning its Carbohydrate Binding Module (CBM) and catalytic Dual Specificity Phosphatase (DSP) domains. Conversely, LSF2 lacks a CBM and, instead, binds glucans at two non-catalytic surface-binding sites that are located distally from its active site. In addition, it was previously reported that SEX4 and LSF2 act upon distinct phospho-glucan substrates: SEX4 preferentially dephosphorylates the C6-position of starch glucans and LSF2 exclusively dephosphorylates the C3- position. The data herein reveal that SEX4 and LSF2 contain differences in their active site topology that serve to position the glucan chain in opposite orientations, therefore accounting for the differences in substrate specificity. Using these insights, SEX4 was engineered with reversed substrate specificity, i.e. preferential C3-specific activity. Previous work has established the interaction between phosphatases and protein, lipid, and nucleic acids; however, the current study represents the first insights into phosphatase interaction with carbohydrate substrates. In addition, the insights gained provide a model that will be used in future studies with the mammalian glucan phosphatase laforin, which is linked to neurodegeneration and the fatal epileptic disorder Laforaʼs Disease.

This dissertation describes the research that we have done concerning reversible Markov chains. We first present definitions for what it means for a Markov chain to be reversible. We then give applications of where reversible Markov chains are used and give a brief history of Markov chain inference. Finally, two journal articles are found in the paper, one that is already published and another which is currently being submitted. The first article examines estimation of the one-step-ahead transition probabilities in a reversible Markov chain on a countable state space. A symmetrized moment estimator is proposed that exploits the reversible structure. Examples are given where the symmetrized estimator has superior asymptotic properties to those of a naive estimator, implying that knowledge of reversibility can sometimes improve estimation. The asymptotic mean and variance of the estimators are quantified. The results are proven using only elementary results such as the law of large numbers and the central limit theorem. The second article introduces two statistics that assess whether (or not) a sequence sampled from a time-homogeneous Markov chain on a finite state space is reversible. The test statistics are based on observed deviations of transition sample counts between each pair of states in the chain. First, the joint asymptotic normality of these sample counts is established. This result is then used to construct two chi-squared-based tests for reversibility. Simulations assess the power and type one error of the proposed tests.

We conduct a comprehensive and systematic study of the temporal asymmetries of the fluctuations in properties of nonequilibrium, deterministic and reversible systems. Our motivation stems from the theories that predict asymmetry of fluctuation paths in stochastic dynamics. However, stochastic descriptions are an approximation in the sense that real systems obey deterministic reversible dynamics (at the classical level). In order to understand if the predicted asymmetry is an artifact of the stochastic model, we consider the results from studies of deterministic reversible systems composed of many particles. In order to examine these systems we used molecular dynamics simulations. We thoroughly investigate the presence of temporal asymmetry in the fluctuations of various properties in nonequilibrium, microscopic simulated systems, which are reversible and deterministic. We consider systems undergoing steady state Couette shear flow, and colour diffusion. For the first time we provide light on the particular path by which irreversibility emerges from microscopic reversible dynamics out of equilibrium. Asymmetry appears to be more accentuated in the larger the fluctuations. To assess the generality of temporal asymmetries in such deterministic systems, we consider identification of temporal asymmetries using differences of cross correlation functions: we establish from theoretical arguments and numerical evidence that a microscopic system undergoing colour diffusion exhibits asymmetry in a number of cross correlation functions. Furthermore we prove that some particular cross correlation functions have necessarily to be symmetric for a reversible and deterministic system to be regarded as “physical”. We then demonstrate how to mathematically express the fluctuation paths as a correlation function. We verify with strong numerical evidence that this equivalence holds for a simulated system. In light of this link between the asymmetry of correlation functions and that of fluctuation paths, we explain the presence of asymmetry in fluctuation paths via the transient time correlation formalism. We therefore give the first theoretical justification of the emergence of asymmetry in the fluctuations of microscopic deterministic and reversible systems. In this manner we are able to provide a sound theory to explain and characterize asymmetries in the fluctuations of mesoscopic systems. Finally we briefly outline possible future research directions.

Rabbit cytochromes P450 2E1 and P450 2E1 T303A were inactivated by tert-butyl acetylene (tBA) and tert-butyl 1-methyl-2-propynyl ether (tBMP) in a time-, concentration- and NADPH-dependent manner with KI values in the millimolar range. Losses in the enzymatic activity, the P450 CO spectrum and native P450 heme were accompanied by the formation of two different tBA- or tBMP-modified heme products as detected by ESI-LC-MS analysis (m/z of 661 or 705 Da, respectively). Only the tBA-inactivated P450 2E1 revealed a tBA adduct to the apoprotein. Surprisingly, losses in the activity, the CO spectrum and native heme of the tBA-inactivated T303A mutant were completely restored following dialysis, suggesting a reversible heme alkylation. Investigations into the mechanism for the novel reversible inactivation of P450 2E1 T303A by tBA demonstrated that the activity and CO spectral losses were restored following overnight incubation. The reversibility was time-dependent, required an intact P450 enzyme, and was independent of NADPH and tBA. ESI-LC-MS/MS analysis under non-denaturing conditions of a pre-acidified tBA-inactivated T303A sample yielded two tBA adducts (m/z 661 Da) that were absent in non-acidified samples. In contrast, both non- and pre-acidified tBA-inactivated wild-type 2E1 samples were able to form the two tBA adducts, suggesting that the T303A mutant was deficient in the delivery of protons to the enzyme active site. Substrate binding analysis of tBA and tBMP with the P450s 2E1 yielded KS values in the micromolar range. Spectral examination of the tBA-inactivated T303A mutant revealed the formation of a novel, reversible acetylene-iron intermediate with an absorption maximum at 485 nm. The artificial oxidants tert-butyl hydroperoxide (tBHP) and cumene hydroperoxide (CHP) supported the inactivation of P450 2E1 by tBA, but only tBHP supported the inactivation of 2E1 T303A, suggesting a disruption in proton delivery in this enzyme. The tBHP- and CHP-supported inactivations resulted in the formation of tBA-adducted heme products and were completely irreversible with dialysis. In support of these data, models of the P450s 2E1 with tBA bound in the active site suggest a role for the conserved T303 residue in proton delivery and in the inactivation of the 2E1 P450s by small acetylenic compounds.