Mechanistic investigations of bipyrimidine-promoted palladium-catalyzed allylic acetoxylation of olefins

Several pyridine-like ligands were found to improve Pd(OAc)2-catalyzed allylic oxidation of allylbenzene to cinnamyl acetate by p-benzoquinone in acetic acid. The best ligand examined, bipyrimidine, was used to identify the catalyst precursor for this system, (bipyrimidine)Pd(OAc)2, which was fully characterized. Mechanistic studies suggest the reaction takes place through disproportionation of (bipyrimidine)Pd(OAc)2 to form a bipyrimidine-bridged dimer, which reacts with olefin to form a Pd^II-olefin adduct, followed by allylic C–H activation to produce (η^3-allyl)Pd^II species. The (η^3-allyl)Pd^II intermediate undergoes a reversible acetate attack to generate a Pd^0-(allyl acetate) adduct, which subsequently reacts with p-benzoquinone to release allyl acetate and regenerate (bipyrimidine)Pd(OAc)2. No KIE is observed for the competition experiment between allylbenzene-d0 and allylbenzene-d5 (CD2=CDCD2C6H5), suggesting that allylic C–H activation is not rate-determining. Catalytic allylic acetoxylations of other terminal olefins as well as cyclohexene were also effected by (bipyrimidine)Pd(OAc)2

Enzymes in Thymidylate Synthesis in Ureaplasma parvum as Medical Targets

The wall less bacterium Ureaplasma parvum (Up) is associated with ureathritis in adults and pneumonia in neonates. Up lack de novo nucleotide synthesis genes and has to import all DNA precursors. This thesis investigates known DNA biosynthesis pathways as targets for new antibiotics and concerns two enzymes in Up thymidylate synthesis; a thymidylate synthase (TS) and thymidine kinase (UpTK). TS activity was detected in Up-extracts and UU572 DNA could rescue a TS mutant E. coli. UU572 appeared to be proteolytic cleaved and cell cycle regulated in Up. Codon modified UU572 was cloned for expression in E. coli. However, no protein expression could be detected. A codon optimized synthesized UU572 homolog; MPN358 from Mycoplasma pneumonia was expressed in E. coli and showed TS activity. Low sequence homology to existing TSs suggests that UU572 and its homologs, belong to a new class of TS enzymes, which may contribute to future antibiotic development in human and veterinary medicine. Thirteen click chemistry-synthesized 3´-triazole thymidine analogs (1-13), using AZT as backbone, were evaluated with UpTK and hTK1. The bacterial TK exhibited a more open 3D structure than hTK1 explaining its substrate efficiency, while hTK1 seemed to have more closed structure as reflected by higher inhibition by the analogs. Docking models with 13 in TK1 structures revealed amino acid substitutions in the active site and most likely explain the different enzyme specificity. In addition, molecular docking could explain the 6-fold higher inhibition by the nucleoside analog 3´-azido-methyl-deoxythymidine (AZMT) with UpTK compared to hTK1. Nucleoside analogs have been used for fighting viruses with minimal side-effects. Why not use this strategy to control bacterial infections? The results presented in this thesis contribute towards attaining this goal

Zero bias conductance peak in Majorana wires made of semiconductor-superconductor hybrid structures

Motivated by a recent experimental report[1] claiming the likely observation of the Majorana mode in a semiconductor-superconductor hybrid structure[2,3,4,5], we study theoretically the dependence of the zero bias conductance peak associated with the zero-energy Majorana mode in the topological superconducting phase as a function of temperature, tunnel barrier potential, and a magnetic field tilted from the direction of the wire for realistic wires of finite lengths. We find that higher temperatures and tunnel barriers as well as a large magnetic field in the direction transverse to the wire length could very strongly suppress the zero-bias conductance peak as observed in Ref.[1]. We also show that a strong magnetic field along the wire could eventually lead to the splitting of the zero bias peak into a doublet with the doublet energy splitting oscillating as a function of increasing magnetic field. Our results based on the standard theory of topological superconductivity in a semiconductor hybrid structure in the presence of proximity-induced superconductivity, spin-orbit coupling, and Zeeman splitting show that the recently reported experimental data are generally consistent with the existing theory that led to the predictions for the existence of the Majorana modes in the semiconductor hybrid structures in spite of some apparent anomalies in the experimental observations at first sight. We also make several concrete new predictions for future observations regarding Majorana splitting in finite wires used in the experiments.Comment: 5 pages, 6 figures: revised submitted versio

Scheduling real-time, periodic jobs using imprecise results

A process is called a monotone process if the accuracy of its intermediate results is non-decreasing as more time is spent to obtain the result. The result produced by a monotone process upon its normal termination is the desired result; the error in this result is zero. External events such as timeouts or crashes may cause the process to terminate prematurely. If the intermediate result produced by the process upon its premature termination is saved and made available, the application may still find the result unusable and, hence, acceptable; such a result is said to be an imprecise one. The error in an imprecise result is nonzero. The problem of scheduling periodic jobs to meet deadlines on a system that provides the necessary programming language primitives and run-time support for processes to return imprecise results is discussed. This problem differs from the traditional scheduling problems since the scheduler may choose to terminate a task before it is completed, causing it to produce an acceptable but imprecise result. Consequently, the amounts of processor time assigned to tasks in a valid schedule can be less than the amounts of time required to complete the tasks. A meaningful formulation of this problem taking into account the quality of the overall result is discussed. Three algorithms for scheduling jobs for which the effects of errors in results produced in different periods are not cumulative are described, and their relative merits are evaluated

Imprecise results: Utilizing partial computations in real-time systems

In real-time systems, a computation may not have time to complete its execution because of deadline requirements. In such cases, no result except the approximate results produced by the computations up to that point will be available. It is desirable to utilize these imprecise results if possible. Two approaches are proposed to enable computations to return imprecise results when executions cannot be completed normally. The milestone approach records results periodically, and if a deadline is reached, returns the last recorded result. The sieve approach demarcates sections of code which can be skipped if the time available is insufficient. By using these approaches, the system is able to produce imprecise results when deadlines are reached. The design of the Concord project is described which supports imprecise computations using these techniques. Also presented is a general model of imprecise computations using these techniques, as well as one which takes into account the influence of the environment, showing where the latter approach fits into this model

Starch Structures and Physicochemical Properties of a Novel β-glucan enriched Oat Hydrocolloid Product with and without Supercritical Carbon Dioxide Extraction

Starch structures and physicochemical properties of C-trim30, a β-glucan-enriched oat product (32% β-glucan), with or without supercritical carbon dioxide extraction (SCD) were studied to evaluate suitability for commercial applications and potential to degrade starch to increase β-glucan concentration. Scanning electron micrographs showed C-trim30 was composed of 200-300 μm long, porous particles. HPSEC equipped with MALLS and RI detectors showed C-trim30 had three peaks, corresponding to amylopectin with weight-average molecular weight (Mw) of 1.0x108, breakdown amylopectin product (Mw 1.1x107) and amylose (Mw 1.7x106). β-glucans were not observed due to HPSEC column absorption. C-trim30 amylopectin Mw and gyration radii increased after SCD suggesting aggregation of molecules occurred. No thermal transitions were observed for C-trim30 heated 0-150°C. C-trim30 pasting properties, measured using Rapid ViscoAnalyser, showed high peak viscosity (291 RVU) at 30°C, high breakdown (200 RVU), final (273 RVU) and setback (183 RVU) viscosity after heated to 95°C while stirred. SCD increased peak (423 RVU) and breakdown (318 RVU) viscosity. C-trim30 heated from 15 to 110°C showed higher water-holding capacity occurred without SCD. SCD oil fatty acid composition of 82% unsaturated was apposite for health-food applications. Study suggests C-trim30 with and without SCD could function as fat substitutes

Scheduling periodic jobs using imprecise results

One approach to avoid timing faults in hard, real-time systems is to make available intermediate, imprecise results produced by real-time processes. When a result of the desired quality cannot be produced in time, an imprecise result of acceptable quality produced before the deadline can be used. The problem of scheduling periodic jobs to meet deadlines on a system that provides the necessary programming language primitives and run-time support for processes to return imprecise results is discussed. Since the scheduler may choose to terminate a task before it is completed, causing it to produce an acceptable but imprecise result, the amount of processor time assigned to any task in a valid schedule can be less than the amount of time required to complete the task. A meaningful formulation of the scheduling problem must take into account the overall quality of the results. Depending on the different types of undesirable effects caused by errors, jobs are classified as type N or type C. For type N jobs, the effects of errors in results produced in different periods are not cumulative. A reasonable performance measure is the average error over all jobs. Three heuristic algorithms that lead to feasible schedules with small average errors are described. For type C jobs, the undesirable effects of errors produced in different periods are cumulative. Schedulability criteria of type C jobs are discussed