This diploma thesis is focused on the combination of enantioselective organocatalysis and transition metal catalysis. In the experimental part of the work, the optimization of reaction conditions with respect to the reaction yields, enantioselectivity and diastereoselectivity was solved. The applicability of the reaction was verified on various substrates. The second part of the work is focused on the study of the mechanism of the reaction using the methods of quantum chemistry. The kinetics of the reaction were monitored by NMR spectroscopy and the mechanism of the reaction was investigated by quantum chemistry methods. Keywords: aminocatalysis, palladium, synergistic catalysis, reaction mechanism, DFT

The mechanism of RAPRENOx reactions - RAPid REduction of Nitrogen Oxides using Isocyanic acid - proposed by Robert A. Perry1 in an attempt to help control the emission of nitrogen oxides pollutant into the atmosphere, has been re-investigated theoretically. The study of reaction mechanisms was carried out using Chemist software2. All mathematically possible elementary steps have been evaluated and the chemically reasonable ones have been considered to propose new sets of reaction mechanisms. Density Functional Theory (B3LYP/6-31 G**) calculations using Gaussian 983 were made in order to study the relative energies of all species and to predict the energy barrier of each elementary step. As a consequence of our study, there are two more sets of reaction mechanisms (in addition to Perry’s mechanism), that could be possible for the propagation step of RAPRENOx process.

Use of biofuels, especially in automotive applications, is a growing trend due to their potential to lower greenhouse gas emissions from combustion. Ketones are a class of biofuel candidates which are produced from cellulose. However, ketones received rather scarce attention from the combustion community compared to other classes such as, alcohols, esters, and ethers. There is little knowledge on their combustion performance and pollutant generation. Hence their combustion chemistry needs to be investigated in detail. Diisopropyl ketone (DIPK) is a promising biofuel candidate, which is produced using endophytic fungal conversion. A detailed understanding of the combustion kinetics of the oxidation of DIPK in advanced engines such as, the homogeneous charge compression ignition (HCCI) engine is warranted. This dissertation concentrates on the combustion kinetics of DIPK over a wide range of temperature and pressure with a focus on HCCI engine application. An existing DIPK kinetic mechanism has been reviewed and a single zone HCCI engine model has been modeled and validated against recent experimental data from Sandia National Lab. Therefore different HCCI modeling assumptions were tested and the DIPK reaction mechanism was modified with missing reactions and the required thermochemical data. As a result, the HCCI pressure trace, heat release rate and reactivity have been improved. In order to improve the ignition delay time simulation results, the low temperature oxidation of DIPK was studied as the fuel chemistry effects on the autoignition behavior becomes important in low temperature. Therefore DIPK low temperature oxidation experimental data was obtained from the synchrotron photoionization experiments conducted at the Advanced Light Source (ALS) so that the primary products as well as the dominant oxidation pathways are identified. Furthermore, the aldehydes oxidation, as a result of partial or incomplete combustion and as the primary stable intermediate products in oxidation and pyrolysis of biofuel were studied at low temperature in ALS. A high temperature reaction mechanism was created using the reaction class approach. The reaction mechanism for DIPK was improved using the experimental data along with quantum chemical calculation of activation energies and barriers as well as vibrational modes for the important reactions identified in ALS experiment. The rate constants for important reactions were calculated based on modified Arrhenius equation. DIPK oxidation and pyrolysis were studied at high temperature and pressure using UCF shock tube. The ignition delay times as well as the product (methane) time histories were investigated and used as validation targets for the new model.

京都大学 / 新制・課程博士 / 博士(工学) / 甲第24634号 / 工博第5140号 / 新制||工||1982(附属図書館) / 京都大学大学院工学研究科分子工学専攻 / (主査)教授 佐藤 啓文, 教授 佐藤 徹, 教授 松田 建児 / 学位規則第4条第1項該当 / Doctor of Philosophy (Engineering) / Kyoto University / DGAM

In this work, the development of parameters for a series of imidazolium-based ionic liquids molecules, now included in the AMOEBA force field, is discussed. The quality of obtained parameters is tested in a variety of calculations to reproduce structural, thermodynamic, and transport properties. First, it is proposed a novel method to parameterize in a faster, and more efficient way parameters for the AMOEBA force field that can be applied to any imidazolim-based cation. Second, AMOEBA-IL polarizable force field is applied to study the N-tert-butyloxycarbonylation of aniline reaction mechanism in water/[EMIM][BF4] solvent via QM/MM approach and compared with the reaction carried out in gas-phase and implicit solvent media. Third, AMOEBA-IL force field is applied in alchemical calculations. Free energies of solvation for selected solutes solvated in [EMIm][OTf] are calculated via BAR method implemented in TINKER considering the effect of polarization as well as the methodology to perform the sampling of the alchemical process. Finally, QM/MM calculations using AMOEBA to get more insights into the catalytic reaction mechanism of horseradish peroxidase enzyme, particularly the structures involved in the transition from Cp I to Cp II.

No description available.

Poly(vinyl acetate) (PVAc) has a major application as an indoor wood adhesive. Low water stability is however, one of the greatest drawbacks of PVAc. By grafting PVAc from a chitosan (CS) backbone (CS-graft- PVAc) water stability of adhesive is increased while good mechanical and adhesive properties are retained. Simultaneously the percentage of bio-based content is increased. This work investigates the proposed re- action mechanisms between chitosan and cerium(IV) ammonium nitrate (CAN) which is used as an initiator for the grafting reaction. Litera- ture studies showed one dominating reaction mechanism and some not as common. The reaction mechanisms and their shortcomings are pre- sented and discussed in the report. / Poly(vinyl acetat)(PVAc) har ett stort användningsområde som ett trälim för möbler som ska användas inomhus. Den dåliga vatten stabiliteten är ett av de största problemen för användning av PVAc. Genom att ympa PVAc med chitosan(CS) (CS-graft-PVAc) kan vatten stabiliteten ökas samtidigt som en god limfunktion finns kvar och delen fossilbaserad monomer blir mindre och byts ut mot en biobaserad polymer. I detta arbete undersöks de föreslagna reaktionsmekanismerna mellan CS och cerium(IV) ammonium nitrat(CAN) som används som en katalysator för att grafta PVAc med CS. Litteraturstudier visade en dominerade reaktionsmekanism och några mindre förekommande. Reaktionsmekanis- merna och eventuella tillkortakommanden som finns gällande hur de fortlöper presenteras och diskuteras i detta arbete.

Cyclopropane derivatives are frequently utilized as "probes" for radical cation intermediates in a number of important chemical and biochemical oxidation. The implicit assumption in such studies is that if a radical cation is produced, it will undergo ring opening. Through a detailed examination of follow-up chemistry of electrochemically and chemically generated cyclopropylarene radical cations, we have shown that the assumption made in the use of these substrates as SET probes is not necessarily valid. While cyclopropylbenzene radical cation undergoes rapid methanol-induced ring opening (e.g., k = 8.9⁷ s⁻¹M⁻¹), the radical cations generated from 9-cyclopropylanthracenes do not undergo cyclopropane ring opening at all. The radical cations generated from cyclopropylnaphthalenes disproportionate or dimerize before undergoing ring opening. Utilizing cyclic, derivative cyclic, and linear sweep voltammetry, it was discovered that decay of radical cations generated from cyclopropylnaphthalenes in CH₃CN/CH₃OH is second order in radical cation and zero order in methanol. Anodic and Ce(IV) oxidation of all these naphthyl substrates in CH₃CN/CH₃OH led to cyclopropane ring-opened products. However, the rate constant for methanol-induced ring opening (Ar-c-C₃H₅⁺. + CH₃OH -> ArCH(·)CH₂CH₂O(H⁺)CH₃) is extremely small (<20 s⁻¹M⁻¹ for 1-cyclopropylnaphthalenes) despite the fact that ring opening is exothermic by nearly 30 kcal/mol. These results are explained on the basis of a product-like transition state for ring opening wherein the positive charge is localized on the cyclopropyl group, and thus unable to benefit from potential stabilization offered by the aromatic ring. Reactions of radical cations generated from 9-cyclopropylanthracenes in CH₃CN/CH₃CN have also been investigated electrochemically. The major products arising from oxidation of these anthryl substrates are attributable to CH₃OH attack at the aromatic ring rather than CH₃OH-induced cyclopropane ring opening. Ce(IV) oxidation of 9-cyclopropyl-10-methylanthracene and 9,10-dimethylanthracene further showed that radical cations generated from these anthryl substrates undergo neither cyclopropane ring opening nor deprotonation but nucleophilic addition. Side-chain oxidation products from Ce(IV) oxidation of methylated anthracenes arose from further reaction of nuclear oxidation products under acidic and higher temperature conditions. An analogous (more product-like) transition state picture can be applied for cyclopropane ring opening and deprotonation of these anthryl radical cations. Because of much higher intrinsic barrier to either nucleophile-induced cyclopropane ring opening or deprotonation of these anthryl radical cations, nucleophilic addition predominates. Stereoelectronic effects may be another additional factor contributing to this intrinsic barrier because the cyclopropyl group in these anthryl systems adopts a perpendicular conformation which may not meet the stereoelectronic requirements for cyclopropyl ring opening at either the radical cation or dication stage. / Ph. D.

Reactions of strongly oxidizing pollutants with unsaturated hydrocarbon surfaces are important to many areas of scientific interest. For example, reactions of unsaturated hydrocarbons on the surface of tropospheric aerosols could have a great effect on the oxidizing capacity of the troposphere while the reaction products could be involved in the formation of clouds and smog. These reactions are also important in understanding the toxic effect inhalation of these pollutants have on the pulmonary surfactant of the lung, the only amicable air-water interface of the body. The fatty acids of this surfactant are as much as 30% unsaturated, and exposure to oxidizing pollutant is known to alter both the composition and function of the surfactant. Understanding the reaction mechanism will further the knowledge of how this toxicity occurs. While the reactions of strongly oxidizing pollutants, such as ozone and nitrogen dioxide, with alkenes in the gas and solution phases are well known, the interfacial reaction mechanisms of these species is not fully understood. The goal of this study is to determine the reaction mechanism when an unsaturated hydrocarbon monolayer at the gas-surface interface is exposed to gas phase nitrogen dioxide. An olefin-terminated thiol was synthesized and a self-assembled monolayer on Au(111) made and characterized using Reflection-Absorption Infrared Spectroscopy (RAIRS). This unsaturated surface was then exposed to NO2 at a pressure of 1x10-4 mbar in a UHV (Ultrahigh Vacuum) chamber. Time-resolved RAIRS was preformed in situ to monitor the reaction during exposure. X-ray Photoelectron Spectroscopy and RAIRS determined the surface reaction product as an aldehyde. While the mechanism can not be precisely determined, two mechanisms involving either the hydrogen abstraction or radical addition of the NO2 to yield an aldehyde are proposed. / Master of Science

Cellulase activity is due to the activity of multiple enzymes, including endoglucanases, cellobiohydrolases and glucosidases that work synergistically to solubilize crystalline cellulose efficiently. The dependence of hydrolysis reaction rate on temperature predicts that large increases in performance and decreased enzyme cost would be achieved if the enzymatic degradation could be operated at elevated temperatures. However there is always a tradeoff between the activity and stability of enzymes. So obtaining cellulases with high thermostability and simultaneously enhanced activity is a great challenge in the field of bioethanol production. In the studies presented in this dissertation, different computational techniques, such as Molecular Dynamics (MD), Molecular Docking, Quantum Mechanics (QM) and hybrid Quantum Mechanics and Molecular Mechanics (QM/MM), along with several site-directed mutagenesis and in vitro assays have been applied to the study and design of the activity and stability of cellulases. Using molecular dynamics to investigate the thermal unfolding of endoglucanases of family 5 of glycoside hydrolases (GH5), a good correlation between the optimum activity temperatures of cellulases and their structural fluctuations was revealed. These data led us to hypothesize that cellulase stability could be enhanced by redesign of enzyme dynamics through altering the amino acid composition in the highly flexible regions of an endoglucanase that would increase its local or global rigidity. Cellulase C, a GH5 member, was stabilized thermally and chemically by cross linking its highly flexible subdomain. Family 1 of glycoside hydrolases were investigated by QM and hybrid QM/MM methods to analyze the role of non-catalytic polar residues at the active site of GH1 glucosidases that make hydrogen bonds to the glucose moiety at subsite -1. A tyrosine residue in simultaneous interaction with O5 of the glucose ring and the carboxylate group of the nucleophilic glutamate was found to play a significant role in the energy profile along the hydrolysis reaction coordinates. It was shown to reduce the energy barrier of the deglycosylation step by ~12 Kcal/mol. Exclusion of this tyrosine from QM calculation substantially influenced the preactivated structure of the glucose moiety in the enzyme-substrate complex and affected the structural distortion and charge distribution in transition states. / Ph. D.