Thesis advisor: Amir H. Hoveyda / Abstract Chapter 1: Development of Efficient and Kinetically E-Selective Cross-Metathesis to Generate Alkenyl Halides We have devised a broadly applicable strategy to achieve kinetically E-selective cross-metathesis to generate a valuable set of E-alkenyl chlorides and fluorides in high efficiency. The synthetic utility was demonstrated through several concise syntheses of E-alkenyl chloride and fluoride precursors to biologically active molecules. The design principles delineated in this study are expected to initiate a wider range of efficient and kinetically controlled E-selective olefin metathesis processes where there is a diminished preference for the E isomer such as macrocyclic ring-closing metathesis. Chapter 2: Development of Efficient and Kinetically E-Selective Macrocyclic Ring-Closing Metathesis We devised a strategy to achieve high E selectivity in ring-closing metathesis to afford E-macrocyclic alkenes of various ring sizes regardless of the associated thermodynamic preferences. The key findings revealed that E-alkenylB(pin), widely recognized for its broad use in catalytic cross-coupling chemistry, possesses the appropriate steric and electronic attributes to serve as a suitable cross-partner in ring-closing metathesis with Mo alkylidenes. Synthetic utility was demonstrated through ring-closing metathesis at a late stage of a multi-step route. The investigation described herein offers a practical solution to a compelling problem in olefin metathesis, further elevating the utility of this widely used transformation. Chapter 3: Stereoselective Synthesis of E- and Z-Trisubstituted Alkenes by Combining Stereoretentive Catalytic Cross-Metathesis and Catalytic Cross-Coupling We introduced a general solution to a longstanding and compelling problem in olefin metathesis: a broadly applicable strategy for the reliable and efficient synthesis of acyclic E- and Z-trisubstituted alkenyl halides. Complications resulted from the formation of an unstable methylidene species or less reactive disubstituted alkylidene complexes can be addressed by utilizing a stereo-defined E- or Z-trisubstituted alkene and a 1,2-disubstituted olefin as substrates. By merging two central catalytic transformations in organic synthesis, cross-coupling and CM, various E- or Z-trisubstituted alkenyl chloride and bromides were readily accessed by the same catalytic system without the need for directing groups. The synthetic utility of the present protocol was demonstrated through several concise and efficient synthesis of biologically active natural products/synthetic precursors. Notably, the E- or Z-trisubstituted alkenyl halides prepared by CM may be readily converted to other trisubstituted olefins with complete retention of stereochemical purity by means of a second cross-coupling reaction. Based on the new findings, we revisited previously unaddressed problems and establish that readily available isoprenoid alkenes can serve as a suitable surrogate for unhindered terminal alkenes in CM. Chapter 4: In situ Protection/Deprotection for Catalytic Olefin Metathesis in the Presence of Polar Protic Functional Groups We demonstrated that protic groups such as alcohols and carboxylic acids that are problematic with high-oxidation-state alkylidenes could be effectively masked in situ prior to CM reactions by an appropriate borane reagent. The commercial sample of alkenes that are usually contaminated with protic impurities could be ‘purified’ in situ by a sub-stoichiometric amount of pinacolborane. Deprotection of the in situ boron-based protecting group proceeded under mild conditions and could be performed in the same vessel. The one-pot protection/cross-metathesis/deprotection of alcohol and carboxylic acid-containing alkenes described herein is likely to have an impact on the diversity of organic molecules that can be prepared in a laboratory setting. / Thesis (PhD) — Boston College, 2018. / Submitted to: Boston College. Graduate School of Arts and Sciences. / Discipline: Chemistry.

In recent years the microelectronics industry as found itself at an impasse. The tradition pathway towards smaller transistors at lower costs has hit a roadblock with the failure of 157 nm lithography and the continued delays in 13.5 nm extreme ultra violet light sources. While photolithography has been able to keep pace with Moore’s law over the past four decades, alternative patterning technologies are now required to keep up with market demand. The first section of this dissertation discusses the new resolution enhancement technique develop in the Willson lab termed pitchdivision. Through the incorporation of specifically tailored photobase generators (PBGs) into commercially available resists, the resolution of current 193 tools may be doubled. Special two-stage PBGs were designed and synthesized to increase the image fidelity of pitchdivision patterns. The next project deals with the design, synthesis, and evaluation of resists that find amplification through unzipping polymers. An aromatizing polyester polymer that acts as dissolution inhibitor in novolac and is inherently sensitive to 13.5 nm exposure is discussed. Initial results show excellent sensitivity and promise towards a new class of EUV resists. / text

京都大学 / 0048 / 新制・課程博士 / 博士(理学) / 甲第18783号 / 理博第4041号 / 新制||理||1582(附属図書館) / 31734 / 京都大学大学院理学研究科物理学・宇宙物理学専攻 / (主査)教授 佐々 真一, 准教授 篠本 滋, 准教授 武末 真二 / 学位規則第4条第1項該当 / Doctor of Science / Kyoto University / DFAM

Quand le mouvement de particules sous l'action d'un forçage extérieur est restreint par des mécanismes d'exclusion ou de blocage, des corrélations spatio-temporelles non triviales peuvent être observées, dans une dynamique caractérisé par des hétérogénéités spatiales et grandes fluctuations dans le temps.Dans cette thèse, nous étudions deux exemples d'un tel type de mouvement, en prenant en considération deux processus d'exclusion sur des réseaux discrètes en 2d et en 1d.Le premier modèle est inspiré par les mécanismes de relaxation lents observés dans le cisaillement ou le forçage de systèmes colloïdaux ou granulaires: pour des densités élevées, en augmentant le forçage la viscosité peut croitre énormément. Nous expliquons le mécanisme de blocage à grandes densités comme conséquence de l'existence simultanée de régions bloquées et mobiles dans le système, et nous déterminons la signature d'une telle dynamique par le moyen de la thermodynamique des histoires. Nous mesurons aussi l'extension spatiale des structures hétérogènes et fournissons un modèle phénoménologique reliant les propriétés microscopiques de la dynamique au comportement macroscopique de l'écoulement.Le deuxième modèle consiste en un processus d'exclusion en une dimension, incluant les effets dus à la présence structurelle d'un défaut dynamique localisé. Inspirés par la complexité et la richesse du processus de translation du ARN messager, nous proposons un nouveau modèle pour la dynamique de particules dont le mouvement est affecté par des modification stochastiques et structurelles de leur conditions de transport. Nous fournissons une description complète du modèle, avec la caractérisation de tous les régimes dynamiques possibles et une explication quantitative des profils macroscopiques du courant. / When the motion of particles driven by external forces is restricted by exclusion mechanisms or bottlenecks, non-trivial space-time correlations in their motion may be observed, giving rise to a dynamics which involves spatial heterogeneities and large fluctuations in time.Here we study two examples of such kind of motion, considering two exclusion processes on discrete lattices in 2d and 1d.The first model is inspired by the slow relaxation occurring when stirring or shearing colloidal or granular materials: at high densities (or packing fractions) increasing the external forcing may lead to a strong increase in the viscosity. We explain the blockage dynamics at high density as the coexistence of blocked and mobile regions and we determine the signature of such dynamics with the use of the thermodynamics of histories. We also quantify the spatial extension of such structures and provide a phenomenological model relating the microscopic properties of the dynamics to the macroscopic flow behavior.The second model consists in a one-dimensional exclusion process incorporating a structural, localized, dynamical defect. Inspired by the complexity and richness of mRNA translation, we propose a new model for the dynamics arising when the particles flow is regulated by structural or conformational changes in the transport medium. We provide a complete description of the model, characterizing all the possible dynamical regimes and addressing a quantitative explanation of the macroscopic current profiles.

La thèse décrit les propriétés d’équilibre et hors d’équilibre de modèles mathématiques stochastiques de systèmes physiques. À l’aide de simulations numériques, on étudie les fluctuations des différentes quantités mais on s’interesse aussi aux grands déviations dans certains systèmes. La première partie de la thèse se concentre sur l’étude des interfaces rugueuses observées dans des processus de croissance. Ces interfaces sont simulées avec des nouvelles techniques de programmation en parallèle qui nous permettent d’accéder à des systèmes de très grande taille. D’une part, on discute le cas diffusif, représenté par l’équation d’Edward-Wilkinson dans des interfaces périodiques, pour lequel on obtient une solution exacte de l’équation discrète dans l’espace de Fourier. Avec cette solution on déduit le facteur de structure associé aux amplitudes des modes et l’expression exacte est comparée avec les valeurs numériques. De plus, on fait le lien entre les propriétés de premier passage des interfaces et le mouvement Brownien. On mesure la distribution des longueurs des intervalles et on compare les résultats avec une version modifiée du théorème de Sparre-Andersen. D’autre part, on étudie le cas général qui inclut les cas sous-diffusif et superdiffusif avec des conditions de bord périodiques. On étudie pour ces interfaces fractionnaires des propriétés de premier passage liées aux zéros des interfaces. Dans l’état stationnaire, on étudie également les premiers cumulants et propriétés d’échellement de la longueur des intervalles et de la densité de zéros. De plus, on mesure la largeur typique de l’interface et ses propriétés d’échellement. Finalement, on analyse le comportement de ces observables dans les interfaces hors d’équilibre et on discute leur dépendance en la taille du système. On discute également les conditions de stabilité des solutions del’équation discrète, importantes pour les simulations des interfaces. Dans une deuxième partie, on étude la transition de phase dynamique dans des modèles cinétiquement contraints afin d’étudier la transition vitreuse observée dans des verres structuraux. Pour un modèle en dimension un, on étudie la géométrie spatio-temporelle des bulles d’inactivité qui caractérisent les hétérogénéités dynamiques observées dans les verres. On trouve que les directions spatiales et temporelles des bulles ne sont pas liées par un comportement diffusif. En contraste, on confirme l’échellement de l’aire et d’autres quantités attendues pour un système, a priori diffusif. De plus, grâce à la théorie des grandes déviations et l’algorithme de clonage, on identifie la transition de phase dynamique dans des systèmes en deux dimensions spatiales. D’abord on mesure l’énergie libre dynamique pour différentes valeurs du paramètre λ. Après, on conjecture des valeurs critiques λ c = Σ/K, avec Σ la tension surface d’une ı̂le de sites actifs entourée par des sites inactifs dans un modèle effectif et K l’activité moyenne du système, pour laquelle la transition de phase a lieu dans la limite de taille infinie. En mesurant l’activité du système et le nombre d’occupation, on observe la dépendance de ces observables avec la taille des systèmes étudiés loin de la transition. Finalement, on mesure la propagation du front des sites actifs dans tout les systèmes. Pour l’un des systèmes étudiés, on identifie une vitesse balistique du front qui nous permet d’observer la transition de phase d’un point de vue dynamique. / This thesis investigates both equilibrium and nonequilibrium properties of mathematical stochastic models that as a representation of physical systems. By means of extensive numerical simulations we study mean quantities and their fluctuations. Nonetheless, in some systems we are interested also in large deviations. The first part of the thesis focuses on the study of rough interfaces observed in growth processes. These interfaces are simulated with state-of-the-art simulations based on parallel computing which allow us to study very large systems. On the one hand, we discuss the diffusive case given by the Edward-Wilkinson equation in periodic interfaces. For the discrete version of such an equation, we obtain an analytic solution in Fourier space. Fur-ther, we derive an exact expression of the structure factor related with the modes amplitudes describing the interface and compare it with the numerical values. Moreover, using a mapping between stationary interfaces and the Brownian motion, we relate the distribution of the intervals generated by the zeros of the interface with the first-passage distribution given by a the Sparre-Andersen theorem in the case of the Brownian motion. As a generalization of the results obtained in the diffusive case, we study a linear Langevin equation with a Riesz-Feller fractional Laplacian of order z used to simulate sub- and super-diffusive interfaces. In this general case, we identify three regimes based on the scaling behaviour of the cumulants of the intervallengths, the density of zeros and the width of the interface. Finally, we study the evolution in time of some of the observables introduced before. In the second part of the thesis, we study the dynamical phase transition in kinetically constrained models (KCMs) in order to get some insight on the glass transition observed in structural glasses. In a one-dimensional KCM we study the geometry of the bubbles of inactivity in space-time for systems at different temperatures. We find that the spatial length of the bubbles does not scale diffusively with its temporal duration. In contrast, we confirm a vidiffusive behaviour for other quantities studied. Further, by means of large deviation theory and cloning algorithms, we identify the dynamical phase transition in two-dimensional systems. To start with, we measure numerically the dynamical free energy both by measuring the largest eigenvalue of the evolution operator,for small systems, and via the cloning algorithm, for larger systems. We conjecture a value λ c = Σ/K, with Σ the surface tensionof a bubble of activity surrounded by a sea of inactive sites in an effective interfacial model and K the mean activity of the system, for each of the systems studied. For the activity of the system and the occupation number we discuss their scaling properties far from the phase transition. Starting from an empty system subject to different boundary conditions, we investigate the front propagation of active sites. We argue that the phase transition in this case can be identified by the abrupt slowing-down of the front. This is done by measuring the ballistic speed of the front in the simplest case studied. Finally, we propose an effective model following the Feynman-Kac formula for a moving front.-proprietés de premier passage, interface rugueuse, diffusion fractionnaire , système hors d'équilibre, transition de phase dynamique, modèle cinétiquement contraint, grandes déviations.-first-passage properties, rough interface, fractional diffusion, out-of-equilibrium system, dynamical phase transition, kinetically constrained model, large deviations

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The thesis entitled “Organic fluorine in crystal engineering: Consequences on molecular and supramolecular organization” consists of six chapters. The main theme of the thesis is to address the role of substituted fluorine atoms in altering the geometrical and electronic features in organic molecules and its subsequent consequences on crystal packing. The thesis is divided into three parts. Part I deals with compounds that are liquids under ambient conditions, crystal structures of which have been determined by the technique of in situ cryocrystallography. Part II demonstrates the utilization of in situ cryocrystallography to study kinetically trapped metastable crystalline phases that provide information about crystallization pathways. In part III, crystal structures of a series of conformationally flexible molecules are studied to evaluate the consequences of fluorine substitution on the overall molecular conformation. The genesis and stabilization of a particular molecular conformation has been rationalized in terms of variability in intermolecular interactions in the crystalline state. Part I. In situ cryocrystallography: Probing the solid state structures of ambient condition liquids. Chapter 1 discusses the crystal structures of benzoyl chloride and its fluorinated analogs. These compounds have been analysed for the propensity of adoption of Cl···O halogen bonded dimers and catemers. The influence of conformational and electronic effects of sequential fluorination on the periphery of the phenyl ring has been quantified in terms of the most positive electrostatic potential, VS,max (corresponding to σ-hole) on the Cl-atom. It is shown that fluorine also exhibits “amphoteric” nature like other heavier halogens, particularly in presence of electron withdrawing groups. Although almost all the derivatives pack through C–H···O, C–H···F, C–H···Cl, Cl···F, C–H···π and π···π interactions, the compound 2,3,5,6-tetrafluorobenzoyl chloride exhibited a not so commonly observed Cl···O halogen bonded catemer. On the other hand, the proposed Cl···O mediated dimer is not observed in any of the structures due to geometrical constraints in the crystal lattice. Chapter 2 presents the preferences of fluorine to form hydrogen bond (C–H···F) and halogen bonds (X···F; X= Cl, Br, I). Crystal structures of all three isomers of chloro-, bromo-and iodo-fluorobenzene have been probed in order to gain insights into packing interactions preferred by fluorine and other heavier halogens. It has been observed that homo halogen…halogen (Cl···Cl, Br···Br and I···I) contacts prevail in most of the structures with fluorine being associated with the hydrogen atom forming C–H···F hydrogen bond. The competition between homo and hetero halogen bonds (I···I vs I···F) is evident from the packing polymorphism exhibited by 4-iodo fluorobenzene observed under different cooling protocols. The crystal structures of pentafluoro halo (Cl, Br, I) benzenes were also determined in order to explore the propensity of formation of homo halogen bonds over hetero halogen bonds. Different dimeric and catemeric motifs based on X···F and F···F interactions were observed in these structures. Chapter 3 focuses on the effect of different cooling protocols in generating newer polymorphs of a given liquid. The third polymorph (C2/c, Z'=6) of phenylacetylene was obtained by sudden quenching of the liquid filled in capillary from a hot water bath (363 K) to the nitrogen bath (< 77 K). Also, different polymorphs were obtained for both 2¬fluoro phenylacetylene (Pna21, Z'=1) and 3-fluoro phenylacetylene (P21/c, Z'=3) when crystallized by sudden quenching in contrast to the generally followed method of slow cooling which results in isostructural forms (P21, Z'=1). The rationale for these kinetically stable “arrested” crystalline configurations is provided in part II of the thesis. Part II. Tracing crystallization pathways via kinetically captured metastable forms. Chapter 4 explains the utilization of the new approach of sudden quenching of liquids (detailed in chapter 3) to obtain kinetically stable (metastable) crystalline phases that appear to be closer to the unstructured liquids. Six different examples namely, phenylacetylene, 2-fluorophenylacetylene, 3-fluorophenylacetylene, 4-fluorobenzoyl chloride, 3-chloro fluorobenzene and ethyl chloroformate are discussed in this context. In each case, different polymorphs were obtained when the liquid was cooled slowly (100 K/h) and when quenched sharply in liquid nitrogen. The relationship between these metastable forms and the stable forms (obtained by slow cooling) combined with the mechanistic details of growth of stable forms from metastable forms provides clues about the crystallization pathways. Part III. Conformational analysis in the solid state: Counterbalance of intermolecular interactions with molecular and crystallographic symmetries. Chapter 5 describes the crystal structures of a series of conformationally flexible molecules namely, acetylene and diacetylene spaced aryl biscarbonates and biscarbamates. While most of the molecules adopt commonly anticipated anti (transoid) conformation, some adopt unusual cisoid and gauche conformations. It is shown that the unusually twisted conformation of one of the compounds [but-2-yne-bis(2,3,4,5,6¬pentafluorocarbonate)] is stabilized mainly by the extraordinarily short C–H···F intermolecular hydrogen bond. The strength of this rather short C–H···F hydrogen bond has been authenticated by combined single crystal neutron diffraction and X-ray charge density analysis. It has also been shown that the equi-volume relationship of H-and F-atoms (H/F isosterism) can be explored to access various possible conformers of a diacetylene spaced aryl biscarbonate. While biscarbonates show variety of molecular conformations due to absence of robust intermolecular interactions, all the biscarbamates adopt anti conformation where the molecules are linked with antiparallel chains formed with N–H···O=C hydrogen bonds. Chapter 6 presents a unique example where the commonly encountered crystallographic terms namely, high Z' structure, polymorphism, phase transformation, disorder, isosterism and isostructuralism are witnessed in a single molecular species (parent compound benzoylcarvacryl thiourea and its fluorine substituted analogs). The origin of all these phenomenon has been attributed to the propensity of formation of a planar molecular dimeric chain mediated via N–H···O [R2 (12)] and N–H···S [R2 (8)] dimers.