Large scale chemical reaction networks are a ubiquitous phenomenon, from the metabolism of living cells to processes in planetary atmospheres and chemical technology. At least some of these networks exhibit distinctive global features such as the “small world” behavior. The systematic study of such properties, however, suffers from substantial sampling biases in the few networks that are known in detail. A computational model for generating them is therefore required. Here we present a Toy Model that provides a consistent framework in which generic properties of extensive chemical reaction networks can be explored in detail and that at the same time preserves the “look-and-feel” of chemistry:  Molecules are represented as labeled graphs, i.e., by their structural formulas; their basic properties are derived by a caricature version of the Extended Hückel MO theory that operates directly on the graphs; chemical reaction mechanisms are implemented as graph rewriting rules acting on the structural formulas; reactivities and selectivities are modeled by a variant of the Frontier Molecular Orbital Theory based on the Extended Hückel scheme. The approach is illustrated for two types of reaction networks:  Diels−Alder reactions and the formose reaction implicated in prebiotic sugar synthesis.

Patterns and controls of net primary production (NPP) remain a critical question in ecology especially as climate modeling efforts expand. Nutrients, particularly nitrogen (N), can regulate NPP, which couples the N and C cycles. Biological nitrogen fixation (BNF) is the primary natural pathway by which new N enters ecosystems. The magnitude of the natural BNF flux is still not well constrained and the effect of this new N on forest demography and C storage is not well understood. In chapter 1 we use tree census data and two approaches of estimating BNF to make an estimate of the total N fixed by trees across the U.S.: 0.30-0.88 Tg N yr-1 (1.4-3.4 kg N ha-1 yr-1), smaller than previously expected and on par with N inputs from understory or asymbiotic BNF and less than inputs from N deposition. The tree BNF input is dominated by two tree genera: Robinia and Alnus. In chapter 2 we use mixed effect models of forest census data to show that N-fixing trees have no net effect on forest biomass accumulate rate, indicating that though they can fertilize forests on long timescales, during the course of their lives the competitive influences they exert on neighbors balance any fertilization effect they may have. However, the net effect of N-fixing trees on forest development and carbon storage depends on local factors and can be significantly facilitative in contexts where N-fixers are less competitive or when neighbors occupy different forest niches. In chapter 3 we develop a theoretical model which shows lateral leaf litter is a plausible mechanism for observed N-fixer effects, wherein the percent of litter nutrients shared with neighbors can range from almost 0% for small trees to >90% for large isolated trees in low wind, fast decomposition environments. Litter nutrients spread more in windy environments or from trees whose leaf litter falls farther from trees and diffuses more quickly. In sum, N-fixing trees play an important role in temperate forests representing an important N input, however, the flux is smaller than previously expected and the fertilization effect of N-fixing trees is not observed during the census interval.

Abstract: Greener synthetic routes for producing organic molecules are desirable to reduce environmental pollution and lower manufacturing costs.2 In this context, Sharpless & co-workers reported that it is possible to achieve dramatic rate enhancements in a number of cycloaddition reactions, if they were conducted in vigorously mixed oil-water emulsions instead of bulk organic solvents.1 These interfacial reactions – which came to be known as “on-water” reactions – thus present a tantalizing prospect for green chemistry. However, despite many experimental and theoretical studies along this theme, a clear understanding of the governing factors and mechanisms remains unavailable. For instance, proposed mechanisms vary from dangling hydrogen bonds stabilizing transition states, to the specific adsorption of hydroxide ions at the water-organic interface, and the partial dissolution of reactants in water leading to products.3,4,5Additional effects include sharp variations in dielectric constants and hydration levels across the interface and hydrodynamic effects during vigorous stirring. In this thesis, we investigate a Diels-Alder reaction between two water-insoluble reactants – trans,trans-2,4-hexadienyl acetate and N-propylmaleimide– to disentangle the contributions of bulk reactions from interfacial reactions. We compare the conversion of reactants into products in the following scenarios: pure reactants (i) mixed into each other (neat condition), (ii) dissolved in hexane, (iii) dissolved in hexane and vigorously stirred with water (1:1 v/v), and (iv) dissolved in hexane and vigorously stirred in water-methanol mixtures. In addition to vigorously-stirred emulsions that produce polydisperse emulsions, we designed and developed microfluidic devices that allowed us to precisely controlled the water-organic interfacial area. With this6 device, we pin-point interfacial effects on the reaction rates.

No description available.

The introductory chapter reviews the current state of mechanistic understanding of the hexadehydro-Diels-Alder (HDDA) reaction. With the rapid development of the HDDA reaction from its first discovery in 1997, the question of whether a concerted or stepwise mechanism better describes the thermally activated formation of ortho-benzyne from a diyne and a diynophile has been debated. Mechanistic and kinetic investigations were able to show that this is not a black or white situation, as minor changes can tip the balance. In chapter 2 of this thesis, the catalytic process leading from 1,11-bis(p-tolyl)undeca-1,3,8,10-tetrayne to fully-substituted naphthalene and azulene derivatives, by two different platinum-catalyzed dimerization pathways, was investigated. In chapter 3, the cannibalistic self-trapping reaction of an ortho-benzyne derivative generated from 1,11-bis(p-tolyl)undeca-1,3,8,10-tetrayne in an HDDA reaction was investigated. Without adding any specific trapping agent, the highly reactive benzyne is trapped by another bisdiyne molecule in at least three different modes. In chapter 4 direct UV/VIS spectroscopic evidence for the existence of an o-benzyne in solution is reported, and the dynamics of its formation in a photo-induced reaction are established. For this purpose, 1,11-bis(p-tolyl)undeca-1,3,8,10-tetrayne was investigated, using femtosecond transient absorption spectroscopy in the ultraviolet/visible region. In chapter 5, following the isolation and characterization of the reaction products discussed in chapter 3, further species resulting from reactions of the highly reactive ortho-benzyne derivative were identified. / Das einleitende Kapitel gibt einen Überblick über den aktuellen Stand des mechanistischen Verständnisses der Hexadehydro-Diels-Alder (HDDA)-Reaktion. Mit der rasanten Entwicklung der HDDA-Reaktion seit ihrer ersten Entdeckung im Jahr 1997 wurde die Frage diskutiert, ob ein konzertierter oder ein schrittweiser Mechanismus die thermisch aktivierte Bildung von ortho-Benzin aus einem Diin und einem Diinophil besser beschreibt. Mechanistische und kinetische Untersuchungen konnten zeigen, dass es sich hierbei nicht um eine Schwarz-Weiß-Situation handelt, da schon kleine Änderungen das Gleichgewicht verändern können. In Kapitel 2 dieser Arbeit wurde der katalytische Prozess, der von 1,11-Bis(p-tolyl)undeca-1,3,8,10-tetrain zu vollständig substituierten Naphthalin- und Azulen-Derivaten führt, über zwei verschiedene platinkatalysierte Dimerisierungspfade untersucht. In Kapitel 3 wurde die kannibalistische Selbsteinfangreaktion eines ortho-Benzin-Derivats untersucht, das aus 1,11-Bis(p-tolyl)undeca-1,3,8,10-tetrain in einer HDDA-Reaktion erzeugt wurde. Ohne Zugabe eines spezifischen Einfangmittels wird das hochreaktive Benzin von einem anderen Bisdiin-Molekül in mindestens drei verschiedenen Modi eingefangen. In Kapitel 4 wird der direkte UV/VIS-spektroskopische Nachweis für die Existenz eines o-Benzins in Lösung berichtet und die Dynamik seiner Bildung in einer photoinduzierten Reaktion aufgezeigt. Zu diesem Zweck wurde 1,11-Bis(p-tolyl)undeca-1,3,8,10-tetrayne mittels Femtosekunden-Transienter-Absorptionsspektroskopie im ultravioletten/sichtbaren Bereich untersucht. In Kapitel 5 wurden nach der Isolierung und Charakterisierung der in Kapitel 3 diskutierten Reaktionsprodukte weitere Spezies identifiziert, die aus Reaktionen des hochreaktiven ortho-Benzin-Derivats resultieren.

No description available.

No description available.

Diels-Alder polyphenylenes (DAPPs) are chemically and thermally stable polymers, used for dielectric resins, gas separation membranes, and fuel cell proton exchange membranes. Highly fluorinated DAPPs are expected to have better thermal stability and chemical resistance, higher glass transition temperatures, improved compatibility with other fluorinated polymers (like NafionTM), and better adhesion to certain surfaces such as some metals. This thesis proposes a synthesis of highly fluorinated DAPPs by reacting novel, fluorinated bis-cyclopentadienone (CPD) monomers with known aromatic dialkynes. This thesis starts with an introduction to DAPP synthesis, properties, and applications. The second chapter focuses on the synthesis of 4,4′-bis[1,2,4-tris(perfluoro-4-tolyl)cyclopentadien-5-one-3-yl]octafluorobiphenyl (CPD monomer). In the first step, disodiumbis(cyclopentadieny)octafluorobiphenyl was combined with 6 equivalents of octafluorotoluene in HMPA to give 4,4′-bis[1,2,4-tris(perfluoro-4-tolyl)cyclopentadiene-3-yl]octafluorobiphenyl. Oxidation to the corresponding diketone was effected using selenium dioxide. The synthesis of CPD monomer presented several unexpected challenges that were ultimately overcome. The third chapter describes a series of initial polymerization experiments as well as some model reactions that were carried out to understand monomer reactivity. Finally the future research plan of synthesizing different polymers by Diels-Alder reaction and nucleophilic substitution reaction has been discussed. / Master of Science

Devido à sua intensa absorção de luz na região visível do espectro, as porfirinas e seus derivados (clorinas e bacterioclorinas) são de grande importância na terapia fotodinâmica (TFD) para o tratamento de doenças neoplásicas. Neste trabalho foram sintetizadas as novas vinil-porfirinas estrategicamente funcionalizadas (47 e 48), seguida de uma sistemática de reações de Diels-Alder com dieófilos ativados, com o propósito de obter clorinas e/ou bacterioclorinas para potenciais aplicações em TFD. / Due to their strong absorption in the visible region, porphyrins and related derivatives (chlorins and bacteriochlorins) are very important in photodynamic therapy (PDT) for the treatment of neoplasic diseases. In this work were synthesized the novel and strategically functionalizated vinyl-porphyrins 47 and 48, followed by systematic Diels-Alder reactions with activated dienophiles to obtain chlorins and/or bacteriochlorins, potentially useful on PDT.

O objetivo deste trabalho foi iniciar o estudo de uma nova metodologia sintética para a obtenção do sistema 11-oxabiciclo[6.2.1]undecano, o esqueleto estrutural básico de uma classe de produtos naturais conhecidos como furanoeliangolidos. A abordagem sintética proposta envolveria a formação de um composto bicíclico através da reação de Diels-Alder com derivados de furano, seguida pela formação de um hexanel e, finalmente, ruptura de uma ligação central para formação do sistema macrocíclico. Além disso, a reação de Diels-Alder entre derivados de furano e acetileno dará origem a compostos que apresentam como esqueleto estrutural o sistema 7-oxabiciclo[2.2.1]heptano, que podem ser utilizados como material de partida para a síntese de diversos produtos naturais. Iniciamos este estudo com a reação de Diels-Alder entre o 3,4-dimetoxi-2-metil furano e o bromopropiolato de metila, onde foi obtido o produto 85, que após algumas modificações deu origem ao composto 92. Entretanto, após inúmeras tentativas não conseguimos transformar o composto 92 no triciclo desejado. Para evitar essas transformações que se mostraram problemáticas, resolvemos estudar a reação de Diels-Alder entre derivados de furano e benzoquinonas 2,5-dissubstituídas, que dará origem aos adutos devidamente funcionalizados para serem transformados no derivado do sistema 11-oxabiciclo [6.2.1]undecano. No entanto, após o estudo dessas reações de cicloadição, observamos que elas têm o equilíbrio fortemente deslocado no sentido dos materiais de partida. Por esse motivo, a continuidade desta metodologia sintética mostrou ser inviável. Iniciamos então, um estudo da reação de Diels-Alder entre os diverso derivados de furanos e acetilenos. Após o estudo dessas reações de Diels-Alder foi possível verificar que a maioria dos adutos derivados dos furanos é instável no meio reacional. Os melhores resultados obtidos nessas reações de Diels-Alder foram usando o acetilenodicarboxilato de dimetila como dienófilo. Os adutos obtidos são intermediários importantes e bem funcionalizados, que podem ser utilizados na continuidade do estudo de desenvolvimento de nova metodologia sintética para a obtenção do sistema 11-oxabiciclo[6.2.1]undecano / The aim of this work was to start the study of a new methodology to synthesize the 11-oxabicycle[6.2.1]undecane system, the main carbon skeleton of the furanoheliangolides. The proposed synthetic approach involves the preparation of a bicyclic compound through a Diels-Alder reaction with furan derivatives, followed by formation of a six membered ring and, finally, cleavage of the central bond to obtain of the macrocyclic system. The Diels-Alder reaction between furan and acetylene derivatives gives a compound with the 7-oxabicyclico[2.2.1]heptane system, that is a potential starting material for the synthesis of several natural products. We started this study with the Diels-Alder reaction between the 3,4-dimethoxy-2-methylfuran and methyl bromopropiolate, and obtained the product 85 that after some modifications furnished the compound 92. However, after various attempts we were unable to convert the compound 92 into the desired tricycle. We have then decided to study the Diels-Alder reaction between furan and 2,5-disubstituted benzoquinone derivatives, that could furnish the adducts properly functionalized to be transformed in the 11-oxabicyclico[6.2.1]undecane system. However, we observed that the equilibrium is strongly shifted towards the starting materials in these cycloaddition reactions. This methodology has thus showed to be impracticable. As a third alternative, we affected the study the Diels-Alder reaction between the furans derivatives and the acetylenes. The adducts obtained present 7-oxabicyclico[2.2.1]heptane system that could be used to synthesizes of structural skeleton of furanoheliangolide.