Thesis (Ph. D.)--Washington State University, December 2006. / Includes bibliographical references.

abstract: The origin of Life on Earth is the greatest unsolved mystery in the history of science. In spite of progress in almost every scientific endeavor, we still have no clear theory, model, or framework to understand the processes that led to the emergence of life on Earth. Understanding such a processes would provide key insights into astrobiology, planetary science, geochemistry, evolutionary biology, physics, and philosophy. To date, most research on the origin of life has focused on characterizing and synthesizing the molecular building blocks of living systems. This bottom-up approach assumes that living systems are characterized by their component parts, however many of the essential features of life are system level properties which only manifest in the collective behavior of many components. In order to make progress towards solving the origin of life new modeling techniques are needed. In this dissertation I review historical approaches to modeling the origin of life. I proceed to elaborate on new approaches to understanding biology that are derived from statistical physics and prioritize the collective properties of living systems rather than the component parts. In order to study these collective properties of living systems, I develop computational models of chemical systems. Using these computational models I characterize several system level processes which have important implications for understanding the origin of life on Earth. First, I investigate a model of molecular replicators and demonstrate the existence of a phase transition which occurs dynamically in replicating systems. I characterize the properties of the phase transition and argue that living systems can be understood as a non-equilibrium state of matter with unique dynamical properties. Then I develop a model of molecular assembly based on a ribonucleic acid (RNA) system, which has been characterized in laboratory experiments. Using this model I demonstrate how the energetic properties of hydrogen bonding dictate the population level dynamics of that RNA system. Finally I return to a model of replication in which replicators are strongly coupled to their environment. I demonstrate that this dynamic coupling results in qualitatively different evolutionary dynamics than those expected in static environments. A key difference is that when environmental coupling is included, evolutionary processes do not select a single replicating species but rather a dynamically stable community which consists of many species. Finally, I conclude with a discussion of how these computational models can inform future research on the origins of life. / Dissertation/Thesis / Doctoral Dissertation Physics 2018

Systems chemistry is an emerging field of chemistry that studies complex mixtures of molecules that give rise to emergent properties that are not always predictable when studying the components of the mixtures in isolation. A systems chemistry approach has been adopted in fields such as self-assembly and self-sorting, where the dynamic recognition of complementary binding motifs to organize molecules is the central focus. Supramolecular systems are assembled through reversible, non-covalent interactions. The reversibility of supramolecular systems makes them dynamic. Understanding the dynamic nature of complex systems will allow for a bottom-up approach to the rational design of complex mixtures, such as kinetically trapped self-sorting systems. The first objective of this work was to understand the effects the identity and concentration of biologically relevant metal cations have on a the mechanism of binding and rate of kinetics of a cucurbit[7]uril (CB[7])-guest complex. Metal cations are frequently added to cucurbit[n]uril (CB[n]) systems. While metal cations are known to decrease the overall equilibrium constant of a CB[n]-guest complex, there has not been much consideration about how different metal cations can affect the CB[n]-guest binding mechanism beyond introducing competitive equilibria. Kinetic studies of the interactions between CB[7] and 1-(2-naphthyl)-ethylammonium (NpH+) in the presence of Ca2+ and Na+ were investigated. It was found that the binding mechanism between NpH+ and CB[7] was the formation of an exclusion complex and an inclusion complex. An exclusion complex is the formation of a complex where the cationic ammonium group of the guest associates to the carbonyl lined portals of CB[7], while the aromatic group remains exposed to the surrounding; while an inclusion complex is formed when the aromatic group of the guest enters the hydrophobic cavity of CB[7]. By increasing the metal cation concentrations, the exclusion complex was seen to disappear from the overall kinetics. When Ca2+ cations were used instead of Na+ cations, a Ca2+ cation capped inclusion complex was formed. The Ca2+ cation capped inclusion complex was found to have a lower dissociation rate constant than the uncapped complex between NpH+ and CB[7]. The second objective of this work was to understand how the structure of guest molecules effected the kinetic time scale of reaction with CB[7]. The kinetics between CB[7] and three different aromatic dications were measured to understand the structural features that influence the change in kinetic time scales: methyl viologen (MV2+), benzidine (Bn2+) and 2,7’-dimethyl-diazapyrenium (MDAP2+). It was found that moving the cationic charges further apart slowed down the kinetics from the sub millisecond time scale (MV2+) to the millisecond time scale (Bn2+); further, it was found that adding rigidity and width to the molecule (MDAP2+) slowed down the kinetics onto the minute time scale. The final objective of this work was to use the understanding of complexity gained in the metal cation project and the guest design for kinetic time scales project to rationally design a kinetically-trapped self-sorting system. The equilibrium constants and time scale of kinetics between a ditopic guest molecule and three host molecules (CB[6], CB[7] and β-CD) were determined to investigate the feasibility of the kinetically-trapped self-sorting system. Due to the complexity introduced by metal cations discovered earlier, β-cyclodextrin (β-CD) was used to modulate the concentration of guest that could be bound by CB[n]s. As a concentration modulator the requirements of β-CD were that the kinetics must be faster than the millisecond time scale and the equilibrium constant with the guest must be much lower than the equilibrium constants between the guest and CB[n]s. CB[6] was proposed as a thermodynamic sink due to its slow kinetics for complex formation with benzyl ammonium. The requirements for the guest complexation with CB[6] were that the kinetics had to be on the minute to hour time scale and the equilibrium constant with the guest had to be the highest of the three host molecules. CB[7] was chosen as the kinetic trap of the self-sorting system. The requirements for the CB[7] complex were that the kinetics had to be on the millisecond to second time scale and the equilibrium constant needed to be lower than the equilibrium constant of the guest@CB[6] complex, but higher than the guest@β-CD complex. The kinetic and thermodynamic requirements between the guest molecule and CB[7], and between the guest molecule and β-CD were met. The kinetics between CB[6] and the guest molecule were on the hour time scale, meaning the kinetic requirement was met, however, the equilibrium constant was found to be lower than the equilibrium constant between the guest molecule and CB[7]. The results in this work showed that the rational design of kinetically-trapping self-sorting systems is possible, but some modifications to the structure of the guest molecule is required to make this self-sorting system work. / Graduate / 2021-06-05

No description available.

Les systèmes moléculaires sont constitués d'unités distinctes, qui se coordonnent pour permettre l'émergence d'une propriété, ou d'un comportement complexe. Les molécules entrelacées, et notamment les rotaxanes, sont des composés particulièrement adaptés à la réalisation de tels systèmes, en raison de la liaison mécanique qui les caractérise. Grâce au développement impressionnant des stratégies de synthèse permettant d'accéder de façon efficace à diverses architectures entrelacées, de nombreux systèmes fonctionnels ont été développés, et nous nous proposons d'enrichir ce panel à travers trois exemples.Nous avons élaboré le premier rotaxane enzymo-sensible capable de libérer sélectivement un agent anticancéreux, grâce aux actions successives de deux hydrolases. L'originalité de ce système réside dans l'ouverture contrôlée du macrocycle, qui conduit au désassemblage des constituants entrelacés. Notre rotaxane enzymo-sensible est stable dans le plasma et déclenche de façon autonome l'activité du paclitaxel au sein des cellules cancéreuses.Dans un deuxième temps, nous avons étudié la synthèse stéréosélective de rotaxanes présentant une chiralité mécanique et ses applications dans le cadre du contrôle du mouvement à l'échelle moléculaire.Enfin, le dernier projet concerne le développement d'un système moléculaire capable de mimer le fonctionnement d'une enzyme. Ce système doit être en mesure de fonctionner de façon catalytique au sein d'un mélange pour conduire à la formation sélective d'une molécule parmi une multitude de possibilités. / Molecular systems are composed of distinct units that coordinate to allow the emergence of a property, or a complex behavior. Within this framework, the design of functional interlocked molecules programmed to perform specific tasks in response to an external stimulus has received considerable attention. The main goal of this thesis is to enrich this field of research through the study of three novel such functional systems. First of all, we developed the first enzyme-sensitive [2]rotaxane designed to release a potent anticancer drug within tumor cells. The molecular device includes a protective ring that prevents the premature liberation of the drug in plasma. However, once located inside cancer cells the [2]rotaxane leads to the release of the drug through the controlled disassembly of the mechanically interlocked components, in response to a determined sequence of two distinct enzymatic activations.We also studied the stereoselective synthesis of chiral rotaxanes with the aim to control the direction of the motion at molecular level. These [2]rotaxanes include a thread with two identical triazole stations that can interact with an unsymmetrical fluorinated macrocycle in the presence of cupper (I). We demonstrated that the interaction of the macrocycle with one or the other of the stations lead to the synthesis of two mechanical diastereoisomers.Finally, we attempted to develop a molecular system able to mimic the operation of an enzyme in a complex mixture. This system was designed to allow the selective formation of one particular molecule among several other possibilities in a catalytic way.

This thesis is divided into six parts, all centered around the development of dynamic (i.e., reversibly interacting) systems of molecules and their applications in dynamic combinatorial chemistry (DCC) and organic synthesis. Part one offers a general introduction, as well as a more detailed description of DCC, being the central concept of this thesis. Part two explores the potential of the nitroaldol reaction as a tool for constructing dynamic systems, employing benzaldehyde derivatives and nitroalkanes. This reaction is then applied in part three where a dynamic nitroaldol system is resolved by lipase-catalyzed transacylation, selecting two out of 16 components. In part four, reaction and crystallization driven DCC protocols are developed and demonstrated. The discovery of unexpected crystalline properties of certain pyridine β-nitroalcohols is used to resolve a dynamic system and further expanded into asynthetic procedure. Furthermore, a previously unexplored tandem nitroaldol-iminolactone rearrangement reaction between 2-cyanobenzaldehyde and primarynitroalkanes is used for the resolution of dynamic systems. It is also coupled with diastereoselective crystallization to demonstrate the possibility to combine several selection processes. The mechanism of this reaction is investigated and a synthetic protocol is developed for asymmetric synthesis of 3-substituted isoindolinones. Part five continues the exploration of tandem reactions by combining dynamic hemithioacetal or cyanohydrin formation with intramolecular cyclization to synthesize a wide range of 3-functionalized phthalides. Finally, part six deals with the construction of a laboratory experiment to facilitate the introduction of DCC in undergraduate chemistry education. The experiment is based on previous work in our group and features an acetylcholinesterase-catalyzed resolution of a dynamic transthioacylation system. / QC 20100628

O Sistema Especialista SISTEMAT foi construído com o objetivo de auxiliar os pesquisadores da área de produtos naturais na tarefa de determinação estrutural, estendendo-se também ao químico orgânico sintético. Seus programas aplicativos fornecem propostas de esqueletos fazendo uso dos dados de diversas técnicas espectrométricas, sendo que a espectrometria de ressonância magnética nuclear de 13C tem um papel de destaque entre as demais. Este trabalho descreve a utilização do SISTEMAT como uma ferramenta auxiliar na determinação estrutural de substâncias pertencentes às subclasses dos alcalóides quinolínicos, quinolizidínicos, aporfínicos, benzilisoquinolínicos, isoquinolínicos, pirrolizidínicos, acridônicos e indólicos. Para a realização deste trabalho foi construído um banco de dados contendo 1182 alcalóides, sendo todos coletados da literatura. Nestes 1182 alcalóides, estão presentes 1156 espectros de RMN 13C, 354 espectros de RMN 1H, 320 espectros de massas e as substâncias de origem vegetal estão distribuídos em 49 Famílias, 164 Gêneros e 260 Espécies. Os testes realizados forneceram bons percentuais de acertos para o reconhecimento de esqueletos. Outro programa utilizado neste trabalho foi o de redes neurais artificiais. As redes foram treinadas para auxiliar na determinação estrutural dos alcalóides aporfínicos, fornecendo a probabilidade de uma determinada substância pertencer ao esqueleto pesquisado. Para utilização das redes neurais foi construída uma planilha com os deslocamentos químicos de RMN 13C, de 165 alcalóides aporfínicos, pertencentes a 12 esqueletos diferentes. A rede forneceu ótimos resultados, classificando os esqueletos com alto grau de confiabilidade. / The Expert System SISTEMAT was built with the objective of aiding the researchers of the area of natural products in the task of structural determination, also extending to the synthetic organic chemist. Their applications programs supply proposed of skeletons making use of the data of several techniques spectrometrics, and the 13C NMR has a main paper among the others. This work describes the use of SISTEMAT as an auxiliary tool in the structural determination of substances belonging to the underclass of the alkaloids quinoline, quinolizidine, aporphine, benzylisoquinoline, isoquinoline, pyrrolizidine, acridone and indoles. For the accomplishment of this work a database was built containing 1182 alkaloids, being all collected of the literature. In these 1182 alkaloids, are present 1156 spectra of 13C NMR, 354 spectra of RMN 1:00, 320 spectra of masses and the substances of botanical origin are distributed in 49 Families, 164 Genders and 260 Species. They were accomplished around 100 tests, of which 30 are presented in this thesis. These tests supplied good percentile of the successes for the recognition of skeletons. Another program used in this work the one of nets artificial neurais, in which the nets were trained to aid in the structural determination of the aporphine alkaloids was, supplying the probability of a certain substance to belong to the researched skeleton. For use of the nets neurais a spreadsheet was built with the chemical displacements of 13C NMR, of 165 aporphine alkaloids, belonging to 12 different skeletons. The net supplied great results, classifying the skeletons with high reliability degree.

O Sistema Especialista SISTEMAT foi construído com o objetivo de auxiliar os pesquisadores da área de produtos naturais na tarefa de determinação estrutural, estendendo-se também ao químico orgânico sintético. Seus programas aplicativos fornecem propostas de esqueletos fazendo uso dos dados de diversas técnicas espectrométricas, sendo que a espectrometria de ressonância magnética nuclear de 13C tem um papel de destaque entre as demais. Este trabalho descreve a utilização do SISTEMAT como uma ferramenta auxiliar na determinação estrutural de substâncias pertencentes às subclasses dos alcalóides quinolínicos, quinolizidínicos, aporfínicos, benzilisoquinolínicos, isoquinolínicos, pirrolizidínicos, acridônicos e indólicos. Para a realização deste trabalho foi construído um banco de dados contendo 1182 alcalóides, sendo todos coletados da literatura. Nestes 1182 alcalóides, estão presentes 1156 espectros de RMN 13C, 354 espectros de RMN 1H, 320 espectros de massas e as substâncias de origem vegetal estão distribuídos em 49 Famílias, 164 Gêneros e 260 Espécies. Os testes realizados forneceram bons percentuais de acertos para o reconhecimento de esqueletos. Outro programa utilizado neste trabalho foi o de redes neurais artificiais. As redes foram treinadas para auxiliar na determinação estrutural dos alcalóides aporfínicos, fornecendo a probabilidade de uma determinada substância pertencer ao esqueleto pesquisado. Para utilização das redes neurais foi construída uma planilha com os deslocamentos químicos de RMN 13C, de 165 alcalóides aporfínicos, pertencentes a 12 esqueletos diferentes. A rede forneceu ótimos resultados, classificando os esqueletos com alto grau de confiabilidade. / The Expert System SISTEMAT was built with the objective of aiding the researchers of the area of natural products in the task of structural determination, also extending to the synthetic organic chemist. Their applications programs supply proposed of skeletons making use of the data of several techniques spectrometrics, and the 13C NMR has a main paper among the others. This work describes the use of SISTEMAT as an auxiliary tool in the structural determination of substances belonging to the underclass of the alkaloids quinoline, quinolizidine, aporphine, benzylisoquinoline, isoquinoline, pyrrolizidine, acridone and indoles. For the accomplishment of this work a database was built containing 1182 alkaloids, being all collected of the literature. In these 1182 alkaloids, are present 1156 spectra of 13C NMR, 354 spectra of RMN 1:00, 320 spectra of masses and the substances of botanical origin are distributed in 49 Families, 164 Genders and 260 Species. They were accomplished around 100 tests, of which 30 are presented in this thesis. These tests supplied good percentile of the successes for the recognition of skeletons. Another program used in this work the one of nets artificial neurais, in which the nets were trained to aid in the structural determination of the aporphine alkaloids was, supplying the probability of a certain substance to belong to the researched skeleton. For use of the nets neurais a spreadsheet was built with the chemical displacements of 13C NMR, of 165 aporphine alkaloids, belonging to 12 different skeletons. The net supplied great results, classifying the skeletons with high reliability degree.