Direct access to functionalized cyclic enones using Mannich, Morita-Baylis-Hillman and elimination reactions

A series of highly functionalized cyclic enones were obtained from Mannich, Morita-Baylis-Hiliman and elimination reaction with cyclic enones.

Comparative studies of hyperhomodesmotic reactions for the calculation of standard heats of formation of fullerenes

How can the accuracy of the calculated standard heats of formation Delta H-f(0) of fullerenes be improved? How reliable are the values of Delta H-f(0) calculated from hyperhomodesmotic reactions? This work is the first to address these questions. By comparing the results obtained from three hyperhomodesmotic reactions containing only fullerenes, it is illustrated that both the resonance contribution and the strain energy contribution should be considered in the construction of hyperhomodesmotic reactions. An attempt to construct such hyperhomodesmotic reactions for fullerenes has been carried out, and several new insights are indicated.

Accelerated leap methods for simulating discrete stochastic chemical kinetics

Biologists are increasingly conscious of the critical role that noise plays in cellular functions such as genetic regulation, often in connection with fluctuations in small numbers of key regulatory molecules. This has inspired the development of models that capture this fundamentally discrete and stochastic nature of cellular biology - most notably the Gillespie stochastic simulation algorithm (SSA). The SSA simulates a temporally homogeneous, discrete-state, continuous-time Markov process, and of course the corresponding probabilities and numbers of each molecular species must all remain positive. While accurately serving this purpose, the SSA can be computationally inefficient due to very small time stepping so faster approximations such as the Poisson and Binomial τ-leap methods have been suggested. This work places these leap methods in the context of numerical methods for the solution of stochastic differential equations (SDEs) driven by Poisson noise. This allows analogues of Euler-Maruyuma, Milstein and even higher order methods to be developed through the Itô-Taylor expansions as well as similar derivative-free Runge-Kutta approaches. Numerical results demonstrate that these novel methods compare favourably with existing techniques for simulating biochemical reactions by more accurately capturing crucial properties such as the mean and variance than existing methods.

Different routes to pure food allergens: extraction, recombinant techniques and total chemical synthesis for obtaining the plant-food pan-allergen LTP

La richiesta di allergeni puri è in continuo aumento per scopi diagnostici, come standard per metodi di rilevamento e di quantificazione, per l'immunoterapia e per lo studio a livello molecolare dei meccanismi delle reazioni allergiche, al fine di facilitare lo sviluppo di possibili cure. In questa tesi di dottorato sono descritte diverse strategie per l’ottenimento di forme pure di non-specific Lipid Transfer Proteins (nsLTPs), le quali sono state riconosciute essere rilevanti allergeni alimentari in molti frutti e verdure comunemente consumati e sono state definite come modello di veri allergeni alimentari. Una LTP potenzialmente allergenica, non nota in precedenza, è stata isolata dalle mandorle, mentre una LTP dall’allergenicità nota contenuta nelle noci è stata prodotta mediante tecniche di DNA ricombinante. Oltre a questi approcci classici, metodi per la sintesi chimica totale di proteine sono stati applicati per la prima volta alla produzione di un allergene, utilizzando Pru p 3, la LTP prototipica e principale allergene della pesca nell'area mediterranea, come modello. La sintesi chimica totale di proteinepermette di controllarne completamente la sequenza e di studiare la loro funzione a livello atomico. La sua applicazione alla produzione di allergeni costituisce perciò un importante passo avanti nel campo della ricerca sulle allergie alimentari. La proteina Pru p 3 è stata prodotta nella sua intera lunghezza e sono necessari solo due passaggi finali di deprotezione per ottenere il target nella sua forma nativa. Le condizioni sperimentali per tali deprotezioni sono state messe a punto durante la produzione dei peptidi sPru p 3 (1-37) e sPru p 3 (38-91), componenti insieme l'intera proteina. Tecniche avanzate di spettrometria di massa sono state usate per caratterizzare tutti i composti ottenuti, mentre la loro allergenicità è stata studiata attraverso test immunologici o approcci in silico.

Dynamic simulation of chemical plant

A CSSL- type modular FORTRAN package, called ACES, has been developed to assist in the simulation of the dynamic behaviour of chemical plant. ACES can be harnessed, for instance, to simulate the transients in startups or after a throughput change. ACES has benefited from two existing simulators. The structure was adapted from ICL SLAM and most plant models originate in DYFLO. The latter employs sequential modularisation which is not always applicable to chemical engineering problems. A novel device of twice- round execution enables ACES to achieve general simultaneous modularisation. During the FIRST ROUND, STATE-VARIABLES are retrieved from the integrator and local calculations performed. During the SECOND ROUND, fresh derivatives are estimated and stored for simultaneous integration. ACES further includes a version of DIFSUB, a variable-step integrator capable of handling stiff differential systems. ACES is highly formalised . It does not use pseudo steady- state approximations and excludes inconsistent and arbitrary features of DYFLO. Built- in debug traps make ACES robust. ACES shows generality, flexibility, versatility and portability, and is very convenient to use. It undertakes substantial housekeeping behind the scenes and thus minimises the detailed involvement of the user. ACES provides a working set of defaults for simulation to proceed as far as possible. Built- in interfaces allow for reactions and user supplied algorithms to be incorporated . New plant models can be easily appended. Boundary- value problems and optimisation may be tackled using the RERUN feature. ACES is file oriented; a STATE can be saved in a readable form and reactivated later. Thus piecewise simulation is possible. ACES has been illustrated and verified to a large extent using some literature-based examples. Actual plant tests are desirable however to complete the verification of the library. Interaction and graphics are recommended for future work.

Simultaneous chemical reaction and distillation of formaldehyde

The thesis is concerned with the development and testing of a mathematical model of a distillation process in which the components react chemically. The formaldehyde-methanol-water system was selected and only the reversible reactions between formaldehyde and water giving methylene glycol and between formaldehyde and methanol producing hemiformal were assumed to occur under the distillation conditions. Accordingly the system has been treated as a five component system. The vapour-liquid equilibrium calculations were performed by solving iteratively the thermodynamic relationships expressing the phase equilibria with the stoichiometric equations expressing the chemical equilibria. Using optimisation techniques, the Wilson single parameters and Henry's constants were calculated for binary systems containing formaldehyde which was assumed to be a supercritical component whilst Wilson binary parameters were calculated for the remaining binary systems. Thus the phase equilibria for the formaldehyde system could be calculated using these parameters and good accuracy was obtained when calculated values were compared with experimental values. The distillation process was modelled using the mass and energy balance equations together with the phase equilibria calculations. The plate efficiencies were obtained from a modified A.I.Ch.E. Bubble Tray method. The resulting equations were solved by an iterative plate to plate calculation based on the Newton Raphson method. Experiments were carried out in a 76mm I.D., eight sieve plate distillation column and the results were compared with the mathematical model calculations. Overall, good agreement was obtained but some discrepancies were observed in the concentration profiles and these may have been caused by the effect of limited physical property data and a limited understanding of the reactions mechanism. The model equations were solved in the form of modular computer programs. Although they were written to describe the steady state distillation with simultaneous chemical reaction of the formaldehyde system, the approach used may be of wider application.

Organic reactions in ionic liquids: ionic liquid-accelerated facile synthesis of 3-alkyl-2,4-thiazolidinediones

The room temperature ionic liquid [bmim]PF6 is a new green solvent for the N-alkylation of 2,4-thiazolidinones. Significant rate enhancement and improved yields have been observed.

Organic reactions in ionic liquids: Ionic liquid-promoted three-component condensation of benzotriazole with aldehyde and alcohol

1-(alpha-Alkoxyalkyl)benzotriazoles are readily synthesized from three-component condensation of benzotriazole with aldehyde and alcohol in ionic liquid [Bmim]PF6.